The essential iOS search tool Wolfram Alpha has been updated.

Building on 25 years of development led by Stephen Wolfram, Wolfram|Alpha has rapidly become the world's definitive source for instant expert knowledge and computation. Across thousands of domains--with more continually added--Wolfram|Alpha uses its vast collection of algorithms and data to compute answers and generate reports for you. Parts of Wolfram|Alpha are used in the Apple Siri Assistant; this app gives you access to the full power of the Wolfram|Alpha computational knowledge engine.

 

Apple have published some of their artificial intelligence research, arXiv:1612.07828

With recent progress in graphics, it has become more tractable to train models on synthetic images, potentially avoiding the need for expensive annotations. However, learning from synthetic images may not achieve the desired performance due to a gap between synthetic and real image distributions. To reduce this gap, we propose Simulated+Unsupervised (S+U) learning, where the task is to learn a model to improve the realism of a simulator's output using unlabeled real data, while preserving the annotation information from the simulator. We develop a method for S+U learning that uses an adversarial network similar to Generative Adversarial Networks (GANs), but with synthetic images as inputs instead of random vectors. We make several key modifications to the standard GAN algorithm to preserve annotations, avoid artifacts and stabilize training: (i) a 'self-regularization' term, (ii) a local adversarial loss, and (iii) updating the discriminator using a history of refined images. We show that this enables generation of highly realistic images, which we demonstrate both qualitatively and with a user study. We quantitatively evaluate the generated images by training models for gaze estimation and hand pose estimation. We show a significant improvement over using synthetic images, and achieve state-of-the-art results on the MPIIGaze dataset without any labeled real data.

 

I've just been sent details of an app to aid generating regular expressions, Expressions. I use BBEdit for most of my regular expression searching but this looks a brilliant way to build the query.

 

The Medicinal Chemistry Toolkit has been updated.

What's New in Version 2.1. Along with bug fixes, the drug -drug interaction app is updated so fraction metabolised by CYP, fmCYP, and fraction extracted by gut, fgut, can be input if these values are known.

The Medicinal Chemistry Toolkit app is a suite of resources to support the day to day work of a medicinal chemist. Based on the experiences of medicinal chemistry experts, these otherwise difficult-to-access tools were developed in a portable format for use in meetings, on the move and in the lab.

There is a review of the the Medicinal Chemistry Toolkit here.

 

The latest version Mnova 11.0.2 is a minor release with improved  automatic phase correction algorithm as main feature as well as some minor bug fixes.

Mnova is a multipage, multivendor, multitechnique and multiplatform analytical chemistry software suite designed as a container for plugins to address different aspects of spectroscopy.

There is also a page dedicated to spectroscopy

 

Everytime I mention Fortran there is an uptick in the site views so I know there are plenty of readers with an interest in Fortran on a Mac.

There is an interesting post on the NextMove Software blog, Just what you wanted for Christmas – a compiler for Gaussian.

This package provides a “pgf77” script that emulates the Portland Group’s PGI fortran 77 compiler, instead using the Free Software Foundation’s GNU gfortran compiler instead. This emulation is sufficient to allow packages such as Gaussian03, that would otherwise require a commercial compiler, to be built using open source tools. In addition, this package also allows Gaussian03 to be built on a case-insensitive file system (such as when using Mac OS X, cygwin or a FAT32 drive) by overriding the behaviour of “cp” and “gau-cpp” such that they don’t cause problems when used by Gaussian’s build scripts on non case-sensitive file systems.

gXXforrtran is available on GitHub In theory, it should work for a standard Linux or Mac system.

However, as they don’t have access to the Gaussian source code they can't check it. Anyone out there care to try it?

See also Fortran on a Mac page

 

This looks very cool, Mathpix is a great utility for creating mathematical documents from hand written text.

Mathpix is the world's first technology that can read pictures of your handwritten math. Simply take a photo, crop your equation of interest, and you instantly get solutions and plots.

Scanned equations can be exported to PDF, LaTeX, and Overleaf to be used in publications. It also includes a maths solver and interactive 2D, 3D plotting.

The website Mathpix.com has videos of it in action.

 

Just noticed this paper.

MayaChemTools: An Open Source Package for Computational Drug Discovery 10.1021/acs.jcim.6b00505">DOI.

MayaChemTools is a growing collection of Perl scripts, modules, and classes to support a variety of computational drug discovery needs, such as manipulation and analysis of data, generation of two-dimensional (2D) fingerprints, similarity searching, and calculation of physicochemical properties.

MayaChemTools is freely available online at www.MayaChemTools.org, under the terms of the GNU LGPL, as published by the Free Software Foundation.

It is possible to access them using a Vortex script.

 

My favourite text editor BBEdit has just been updated. BBEdit 11.6.3 requires Mac OS X 10.9.5 or later, and is compatible with macOS 10.12 "Sierra". This update contains no new features but includes a number of bug fixes.

BBEdit is my Swiss army knife for opening and editing all sorts of text based file formats, other text editors are available.

 

Virtual reality apps for the iPhone are becoming more common and the latest is Learning Carbons VR. This is an educational virtual reality (VR) app where students can learn about the various forms of carbon.

For many of these types of apps you will need a VR Google Cardboard headset with head straps and a Bluetooth gamepad (MFi certified - made for iPhone).

 

Increasing numbers of electronic alternatives to the traditional paper lab book are available, offering advanced opportunities for managing your research. Hear from researchers and PIs across the disciplines who are using Electronic Lab Notebooks (ELNs) and those considering a trial, and from current providers.

The Office of Scholarly Communication provides a range of transferable skills and more specific research skills training. This training is tailored for researchers, however the courses are also open to:

All Graduate students in the University of Cambridge Librarians who are employees of the University and any of the Colleges Administrative staff who provide research support in the University

This event is sponsored by Dotmatics

 

As a happy owner of a new MacBook Pro I am aware of the limitations of only having USB-C connectors. It is clear that this is the future since Apple are not the only company to make this transition. However a number of the scientific application I use regularly were supplied on DVD and I suspect others may be in a similar situation so I thought I'd mention this tip. Instead of investing in an adaptor if you have an older Mac you can use DVD or CD sharing. Open up system preferences and select "Sharing", click the checkbox for "DVD or CD Sharing".

If you now open a "Finder" window on the MacBook Pro you should find "Remote Disc in the side bar. You may need to change your preferences to display CCs, DVDs etc. (Finder:Preferences)

You can then use it as normal.

 

Royal Society of Chemistry members will be getting their annual subscription details around now. Can I remind people that your membership entitles you to membership of up to THREE Interest Groups. I'd urge you to make use of them, in particular:-

33 Biological and Medicinal Chemistry Sector
86 Chemical Information and Computer Applications Group.

Reduced subscription rates are also available to:

Full time postgraduate students (including PGCE students) – £19 Low income members with an income below £26,000 per annum – Fellow £74, Member £65, Associate £39, Affiliate £41 Retired members – Fellow £74, Member £65, Associate £39, Affiliate £41

 

Swift Playgrounds is a revolutionary new app for iPad that makes learning Swift interactive and fun. Solve puzzles to master the basics using Swift, ideal for keeping occupied over the Christmas break.

Learning to code with Swift Playgrounds is incredibly engaging. The app comes with a complete set of Apple-designed lessons. Play your way through the basics in “Fundamentals of Swift” using real code to guide a character through a 3D world. Then move on to more advanced concepts.

There is a video here

I also notice that there have been a few updates to the Swift Algorithm Club there are now 79 contributors and an ever increasing list of algorithms.

All content is licensed under the terms of the MIT open source license.

 

I've only just noticed that UnityMol has been updated.

UnityMol is a molecular viewer and prototyping platform for the Unity3D game engine developed by Marc Baaden's team in Paris. It includes HyperBalls designed to visualize molecular structures using GPU graphics card capabilities based on shaders (GLSL or Cg). It can read Protein Data Bank (PDB) files, Cytoscape networks, OpenDX maps and Wavefront OBJ meshes.

There is a UnityMol WebGl demo available http://www.baaden.ibpc.fr/umol/webgl/ which gives you a great way to explore the display options now available.

 

It is sometimes difficult to remember that the heart of Mac OSX is the open-source Darwin source code.

Apple have recently released the latest update OS X 10.12 Source.

In addition Apple have made Swift open-source which supports a wider variety of platforms.

 

A while back I mentioned a JMOL script for creating files for 3Dpriting the paper desiring the work has now been published in Journal of Cheminformatics DOI.

Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files.

The Jmol 3D Print website allows the creation of STL and VRML files for 3D printing for any structure in the Open Crystallography Database. You can search either the full COD and then design your own model for printing, or search the more than 30,000 predefined sample files in the figshare collection and download the STL or WRL files that have already been created for those structures.

There is more information on the 3D printing page

 

The electronic LabNotebook Findings has been updated to version 1.4.2. There is a review of Findings here

Two new features:

• Today' button in the experiment header to scroll to today, applicable to both the text view and the calendar view.
• Special window for mailing list signup

Plus a host of bug fixes and improvements.

 

iScienceSearch is an internet search portal for scientists that allows you to perform a search across multiple data sources with a single query. I wrote a review a while back but it has undergone several updates since then and has been significantly expanded.

iScienceSearch allows both text and structure based searches, but the really interesting thing is that when you do a search using a single query item it automatically searchs in the background for other synonyms, structure, CAS Registry Number, InChI etc.

The screenshot below (click to enlarge) was generated using a structure-based query, as you can see the search results also include the results from text-based queries using synonyms. The filters on the left-hand side allow you to sort and filter the results to allow you to focus on the most relevant information.

The searching is free and requires no registration.

 

Sent some time updating the software reviews, many thanks for the readers who reported broken links.

 

Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. I’ll update the list regularly and feel free to send in information.

When I compiled a similar lists for Yosemite and El Capitan they proved very popular with 13,000 page views, I hope this page is similarly useful.

4Peaks no reported issues

Avogadro all seems OK

BBEdit version 11.6.2 and newer are compatible, recommend against using earlier versions

Brainsight requires version 2.3.3 for full compatibility with 10.12 Sierra. You could note too that 2.0 through 2.2.x will never work because 10.12 removed support for garbage collected applications. 2.3.x uses ARC

ChemDraw the official line is that it is not supported, even under El Capitan there were reports of copy/paste issues. One user reports “ChemDraw 15 is working fine for me. copy/paste, everything without issues”.

ChemDoodle no reported issues

CrystalMaker “We are pleased to confirm that all our latest software runs fine on macOS “Sierra”, as well as OS X 10.11 “El Capitan”, 10.10 “Yosemite”, and earlier.”

CYLview app launcher (icon on the desktop or the dock) does not work need to start using “Terminal”

DataDesk Data Desk 8 for Mac runs on OS X 10.7 up to 10.12

DataWarrior requires Java installation

DEVONagent has been updated to version 3.9.5 to support Sierra, in addition this update brings support for Qwant. DEVONthink has also been updated for Sierra.

EndNote From Endnote (Thomson Reuters) version 7: Message for Mac user planning to update to Sierra: In preparation for Apple's release of macOS Sierra on September 20, we have been testing various versions of EndNote. Through our testing, we discovered some issues with the EndNote PDF viewer. These issues have been reported to Apple, but in the meantime, we recommend that you DO NOT upgrade to macOS Sierra.

EnzymeX no reported issues

Evernote a bug in some versions of Evernote for Mac that can cause images and other attachments to be deleted from a note under specific conditions. We've released an updated version of Evernote for Mac, version 6.9.1, to resolve this.

Findings no reported issues

Fortran users will be happy to hear there are no reported issues with FTranProjectBuilder

GAMESS no reported issues.

Homebrew, after every update it is worth checking your homebrew installation.

Username$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: /usr/local is not writable.

You should probably change the ownership and permissions of /usr/local
back to your user account.
  sudo chown -R $(whoami) /usr/local

Warning: /usr/local is not writable.
Even if this directory was writable when you installed Homebrew, other
software may change permissions on this directory. For example, upgrading
to OS X El Capitan has been known to do this. Some versions of the
"InstantOn" component of Airfoil or running Cocktail cleanup/optimizations
are known to do this as well.

You should probably change the ownership and permissions of /usr/local
back to your user account.
sudo chown -R $(whoami) /usr/local

Once corrected you can then type

brew update
brew upgrade

You may get this error

$brew update
/usr/local/Library/brew.sh: line 32: /usr/local/Library/ENV/scm/git: No such file or directory

simply retyping brew update seems to resolve the issue

If you have previously installed Openbabel using

brew install mcs07/cheminformatics/open-babel --HEAD

The "--HEAD" part means install the latest development version from GitHub. The latest version of OpenBabel is now available so type

brew uninstall mcs07/cheminformatics/open-babel
Uninstalling /usr/local/Cellar/open-babel/HEAD... (309 files, 14.6M)
brew install mcs07/cheminformatics/open-babel

You can check you have the latest version installed by type this in a Terminal window

obabel -V
Open Babel 2.4.0 -- Sep 24 2016 -- 14:01:18

iBabel seems to work fine with the latest version of OpenBabel under Sierra. One advantage to updating to OpenBabel 2.4.0 is that previews now work with Quicklook.

IDL does run under Sierra but does require some tuning. Detailed instructions here

iPython Notebook all working fine

Lego Mindstorms At the moment everything seems to be running really great on Sierra. However, please let you readers know they are welcome to contact us via the website way you did if they run into any errors. We'd be happy to solve them!

Manuscripts no reported issues

MarvinSketch I had to reinstall Java for Mac OSX this is the last version of Java Apple created to support legacy applications, similarly MarvinSpace and MarvinView.

Matlab in general appears to be fine except for certain language localisations these languages a patch is available for download. A patch is also available for MATLAB Runtime R2016b.

Mathematica 11.0.1 has been compatibility tested with macOS Sierra and you should not run into any OS-specific compatibility issues. The font-panel is disabled, but we are actively working to address this as soon as possible.

Mendeley no issues reported

MOE working fine, XQuartz did not need reinstalling. However the MOE app launcher (icon on the desktop or the dock) does not work because Apple changed some fundamental system components which affects lots of programs not specifically compiled for the newest MacOSXs. Also you cannot double click on a file to open it in MOE. You can still start MOE from the command line

Applications/moe2015/bin/MOE

It then works perfectly. Update, just had an email from CCG support, The problem with the MOE app launcher on MacOSX Sierra has been fixed in the MOE 2016 release.

MOPAC all seems to be working fine.

osra crashed with error abort trap: 6. I uninstalled using brew then reinstalled

brew uninstall osra
Uninstalling /usr/local/Cellar/osra/2.0.1... (7 files, 1.6M)
brew install osra

Then worked fine

Pandoc depends on llvm-3.5, not supported on Sierra. Llvm-3.9 is supported, installation using Homebrew seems to be OK.

Papers Mac 3.4.7 (527) is now available! Fixes a couple of problems under Sierra. A crash that can occur when switching PDFs, The search in PDF functionality is restored

R latest version (3.3.1) all seems fine

rdkit installed using home-brew works fine.

Readcube Version 2.22.13732 is Mac OS Sierra (v10.12) compatibility update.

Scansnap Note for using ScanSnap or ScanSnap Applications on macOS Sierra In order to avoid the ScanSnap compatibility problems, please do not use ScanSnap or ScanSnap applications on macOS Sierra in the following manner as doing so may cause some pages to be deleted or to become blank. Do not use [ScanSnap Organizer], [ScanSnap Merge Pages], or [CardMinder] Do not use Excellent mode when scanning A3 (11.7 in. x 16.5 in.) documents No image data will be lost nor any blank pages produced when content that has been scanned in the A4 (8.3 in. x 11.7 in.), Letter (8.5 in. x 11 in.), Legal (8.5 in. x 14 in.), or smaller sizes is saved.

Schrodinger a reader sent in this response. We received your query regarding MacOS Sierra. Unfortunately our current, 2016-3 release, do not yet support MacOS Sierra but we have plans to include support for this OS for the upcoming 2016-4 release of our software.

SeeSAR version 5.3 now, 5.4 will come out shortly. No compatibility issues observed/reported.

Studies no reported issues

UCSF Chimera version 1.11.1 seems to be working fine

Wizard worked great with the developer pre-releases, no reported issues

Vortex no problems so far, the embedded chemical drawing app Elemental appears to have no issues.

XQuartz did not require reinstallation :-) however there are reports of an intermittent display not found error when launching apps from a Linux box.

Allow applications downloaded from anywhere in macOS Sierra, if you open the security panel in the Settings the default options in Sierra are as shown below. There is no longer the option to open applications from Anywhere.

Apple have removed this function on macOS Sierra, but you can re-enable it running this in terminal

sudo spctl --master-disable

You can restore it back to the default setting using

sudo spctl --master-enable

I’ll add more updates later.

 

I just had a look at the new LG UltraFine 4K monitor for Mac, looking at the box (image below) with the Mac logo, it seems likely that Apple were heavily involved in the design

A single USB-C cable (included) provides up to 60W of charging power to the MacBook Pro. And three downstream USB-C ports (480 Mbps) offer additional connectivity and power to compatible devices and accessories. There are no other ports.

 

With Safari 5 one of the most interesting new features is the support for Extensions and there are now many different [extensions availabl(https://safari-extensions.apple.com).

There are a section of extensions that might be of interest to scientists and I've started listing the here.

I've just created a new extension that might be of interest.

Ever come across an interesting paper that is behind a paywall? Many of these publications may also be available via green open access.

Self-archiving, also known as green open access, refers to the practice of depositing articles in an institutional repository or a subject repository such as arXiv.

However locating the open version can be a bit hit and miss given there are so many potential repositories. Fortunately oaDOI provides a simple way to search for open access versions

You can simply paste the DOI into the search engine at oadoi.org, however this web service is ideal for linking to a Safari Extension.

Read more…

 

I've just heard about three new science apps for iOS.

PROtein VR allows you to explore 3D structures of molecules including proteins, DNA and ligands in Virtual Reality. To use it you will need a VR Google Cardboard headset with head straps and a Bluetooth gamepad (MFi certified - made for iPhone).

MoleculE VR is a virtual reality tour introducing some of the basic concepts about cell communication and signalling: how cells receive and respond to messages from their environment, interact with other cells and coordinate their biological processes.

The app includes 5 chapters:

• An introduction to cell communication
• The adenosine A2A receptor
• The corticotropin-releasing hormone receptor 1 (CRF1)
• The glucagon receptor
• The metabotropic glutamate 5 (mGlu5) receptor

MoleculE VR is a Virtual Reality app for phones requiring gyroscope and a VR headset like Google Cardboard.

Chemistry Docking is a game app that allows you to match a small molecule ligand with a large protein to maximize the number of possible interactions.

Chemistry Docking is an ad-supported app. The advertisements are served through iAd

 

There is a review of ChemDraw 16 over on Chemistry and Computers.

A key feature is found-trip editing, wherein a user could make a drawing in one application, copy and paste the drawing into another application, and then later copy and paste back into the original application, and still be able to edit the drawing. Generations of Mac users relied on this feature to go from applications like ChemDraw into PowerPoint and back again. This has been has been regularly broken as we had various updates to Mac oSX, Microsoft Office, iWork and ChemDraw. It sounds like some interoperability has returned but it may depend on which versions of the various components you are running.

Now updated to include Mac OSX Sierra, ChemDraw 16 works and round-trip editing using Word 2011 still works! Unfortunately round-trip editing appears to be broken in Pages, Keynote and Numbers.

 

I just heard that David Weininger had died last Wednesday, for me his invention of SMILES was one of those ideas that you instantly knew was going to change the way we did science. So much of what we do in storing, searching and analysing chemical information is based on his pioneering work. I only met him once at a Daylight UGM but it was clear from our first conversation that he was a scientist with a special insight.

SMILES as a simple yet comprehensive chemical language in which molecules and reactions can be specified using ASCII characters representing atom and bond symbols

Anthony Nicholls of OpenEye has written a lovely tribute that is well worth reading

 

This was a joint meeting Organised by SCI's Fine Chemicals Group and RSC's Chemical Information and Computer Applications Group. Held at Imperial War Museum, Duxford, UK, on Wednesday 12 October 2016. This was an excellent meeting and the conference centre at Duxford was superb, many participants arrived early to have a wander around the historic collection of aeroplanes.

Read full report.

 

Chirality is a new iOS app to help with teaching chemistry.

Learning Chemistry can be challenging. Chirality is a short iOS based game that aims to teach some fundamental concepts in 1 st year University level organic chemistry in a fun and innovative way, using drag and drop and touch based interfaces to solve puzzles and answer questions. There are many more iOS apps for science available here.

 

I see a new version of ChemDraw has been released. The flyer suggests improved Mac support

ChemDraw 16 for Mac is 6x faster than previous versions and includes features such as: auto-save and versioning, an improved UI, Unicode support, Improved text rendering including for subscript characters and atom labels. What’s more, ChemDraw 16 for Mac offers improved multi-monitor and Retina (high DPI) display support.

Requirements are shown below, no mention of Mac OS X 10.12 (Sierra)

Following are the system requirements for the latest version of ChemDraw.

OS

• Mac OS X 10.10 (Yosemite)
• Mac OS X 10.11 (El Capitan)

RAM

• 32 bit OS: 1 GB
• 64 bit OS: 2 GB

Microsoft Office

• Microsoft Office 2011
• Microsoft Office 2016
• including Office 365 support

Initial comments suggest round-trip editing is now supported. No mention of Pages, Keynote, Open Office.

 

I was at the Dotmatics UGM recently and they gave an insight into some of the future directions. One of the areas under consideration is the use of Vortex support for Biological data analysis.

Vortex is a very high performance data analysis and plotting tool, capable of handling many millions of rows of data. It also has chemical intelligence built in, allowing structure-based searching, physicochemical properties calculation, clustering and match pair analysis.

The support for biology is a new addition and I've written a brief review here.

Added to the growing list of software reviews.

 

PUPIL,Program for User Package Interface and Linking, is a software environment - the program - that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation. More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use most of the functionalities that may have those external programs interfaced without the necessity to be implemented again on independent interfaces. In fact, this simulation interface concentrates all the common code involved in the coupling terms of the QM/MM approach.

 

XQuartz 2.7.11 is available for download.

Changes in 2.7.11

All changes in 2.7.10 plus:

lib:

• fontconfig
• Fix font caching (#97546)

libpng 1.6.26

libX11

• Plug a memory leak

libXi 1.7.8

• Plus fixes for a memory leak and improved error handling

mesa 12.0.1

 

Scriptarian allows you to easily automate macOS using the Swift programming language, providing an alternative to AppleScript.

Scriptarian is built using Swift the new open-source programming language developed by Apple. Scriptarian analyzes all of your installed applications for AppleScript support and dynamically generates native Swift interfaces for them.

In addition to full support for the Swift Standard Library, Scriptarian includes ScriptingKit, a scripting framework we built from the ground up with Swift in mind. It lets you communicate with any AppleScript-enabled app and even provides various utility functions for speech synthesis, sound playback, file management, process management, and more.

 

I just go this message

"We're giving away Halloween promo code treats for PhySyCalc for iOS. If you want to share with your readers feel free to post this link."

http://redeemco.com/g/physycalc-scientific-and-engineering-calculator_fpjc/

PhySyCalc reinvents the calculator. More intuitive than conventional calculator apps, PhySyCalc lets you do full calculations with units. For example, you drive 250 miles on a full 12 gallon tank of gas and want to calculate your mileage. In PhySyCalc you can skip all the unit conversions and just enter 250 mi/12 gal. PhySyCalc gives you the answer in mi/gal. Or, if you like, km/L or L/100 km, all in a few touches of your finger.

 

The new Apple laptops come equipped with only Thunderbolt 3 (USB-C) ports, I suspect the whole industry will standardise on USB-C pretty soon but at the moment there is obviously the need to support legacy peripherals. Fortunately Apple have put together a page describing most of the adaptors that might be needed. This includes standard USB, HDMI, VGA and Lightening cables. Remember up to six devices can be daisy-chained to each Thunderbolt 3 port of the MacBook Pro; and the Thunderbolt 3 (USB-C) to Thunderbolt 2 adapter doesn't count as a device against that limit.

Also note.

MacBook Pro (15-inch, Late 2016) delivers full Thunderbolt 3 performance on all four ports.

MacBook Pro (13-inch, Late 2016, Four Thunderbolt 3 Ports) supports Thunderbolt 3 at full performance using the two left-hand ports. The two right-hand ports deliver Thunderbolt 3 functionality, but have reduced PCI Express bandwidth.

MacBook Pro (13-inch, Late 2016, Two Thunderbolt 3 Ports) delivers full Thunderbolt 3 performance on both ports.

 

MolSoft have announced the release of ICM version 3.8-5.

• Generate a 2D Interaction Diagram of a ligand with the binding pocket. The image is annotated with hydrogen bonds and interacting residues.
• 3D ligand editor is a powerful tool for the interactive design of new lead compounds in 3D
• ICMJS is a JavaScript/HTML5 viewer for 3D Molecular Graphics which does not require any plugin or installation.
• Support for MMTF format. The Macromolecular Transmission Format (MMTF)
• Support for Mac retina display
• Add docking restraints by selecting atoms in the receptor
• Updates to protein modelling, bioinformatics and cheminformatics

Full release notes are here

 

Hats off to Apple for putting disabled access to technology front and centre in the Apple event last night. I’m sure most of the reports will focus on the MacBook Pro but I’d like to give a mention to the accessibility help available.

The AppleStore has a page dedicated to accessibility, and the system preferences pane also has a section on Accessibility.

 

A Jmol Script for Programmatic Conversion of Crystal Structures into 3D Printable Files can be downloaded here created by Vincent F. Scalfani, Antony Williams and Valery Tkachenko.

 

There has been a new update to SeeSAR, this latest update brings.

2D molecule browsing - time to look at things from a different angle

While the molecule table offers great functionality for prioritizing compounds based on the data, it does not provide an overview of the molecules themselves. This release, however, sees the introduction of 2D molecule browsing. The table now offers two views - the one you already know and a 2D browser - flick between them using the switch below the table. Both views are always kept in sync so if you add a filter or sort etc. the 2D browser will show you the same result in the same order as the table. Also try expanding the table area to see how more molecules fit into the view.

Fantastic new 3D graphics features

This release also brings with it some great new 3D graphics improvements. As much as we all like visualising the binding site surface, it lay often times in the way… The binding site surface can now be switched to transparent allowing you to see through it and therefore making the analysis of the binding site and molecules within much more comfortable. Also, the feeling of depth in the 3D view has been improved to help orientation - a so-called "fog effect" fades out the protein and molecules that are further away to bring the foreground more into focus.

Persistent amino acid labels and better view of reference

So far, labels on binding site components unfortunately disappeared when browsing through different molecules in the table. Now amino acid, co-factor and water labels remain present if you change to a different molecule in the 3D view and even if you enter the molecule editor. The view of the reference compound has also been improved. For better visibility, the thickness of the bonds has been increased and instead of coloring the whole molecule in a uniform blue color, only the carbon atoms are colored blue so that hetero atoms can be distinguished more easily.

There is a review of an early version of SeeSAR here.

 

Chemical Computing Group are running a free hands-on workshops on Structure-Based Drug Design

CAMBRIDGE – December 1, 2016 St John's Innovation Centre Cowley Road, Cambridge, Cambridgeshire, CB4 0WS, UK

09:00-12:30 Structure-Based Drug Design and Ligand Modification Molecular Surfaces and Maps / Ligand Interactions / Conformational Searching / Ligand Optimization / Ligand Selectivity / Protein Alignements and Superposition

12:30-13:30 Lunch break*

13:30-17:00 Advanced Structure-Based Drug Design Pharmacophore Modeling / Docking / Fragment-based Design / Scaffold Replacement / R-Group Screening / Project Search / Protein-Ligand Interaction

REGISTER @ http://www.chemcomp.com/Workshops-Europe-2016.htm

Note: Computers will be provided. No prior software experience required.
*Lunch and refreshments will be provided.

 

The Mobile Science site is a resource for finding scientific applications for iOS devices. The is an option for people to vote for apps and while this is needs to be taken with a pinch of salt I thought it might be interesting to highlight the current top 10.

1. ChemDoodle Mobile
2. Medicinal Chemistry Toolkit
3. WolframAlpha
4. Elemental
5. Papers 3 for iOS
6. Findings - LabNotebook
7. Stanford iOS course
8. Asteris
9. Approved drugs App
10. Open Drug Discovery Teams

 

I needed to buy a new monitor and since Apple don’t supply one at the moment I spent a week searching through online reviews and then looking at a selection at various stores. Eventually decided to get the Dell P2715Q 27-Inch Ultra HD 4K LCD Monitor. Very happy with the selection I just hope Apple don’t announce a new monitor next week!

I should have noted that you have to buy a separate AmazonBasics High-Speed HDMI 2.0 Cable - 0.9m / 3 Feet (Latest Standard) Supports Ethernet, 3D, Audio Return . Also if you need a Mac compatible web cam, this one is highly regarded.

 

XQuartz 2.7.10 has been released. OS X 10.6.3 or later is required to install this package.

I did some very limited (MOE and PYMOL) testing under Mac OSX 10.12 (Sierra) and didn’t find any issues. Changes in 2.7.10 All changes in 2.7.9 plus

app

• mkfontdir
• Fix a buffer underrun crash (#96905) quartz-wm
• Properly handle updates to WM_PROTOCOLS property changes (#92652)
• xinit
• Fixed support for enabling TCP server connections (#95379)
• Added support for enabling IGLX (#96260)
• defaults write org.macosforge.xquartz.X11 enable_iglx -bool true
• xterm 326

proto:

• xcb-proto 1.12
• xproto 7.0.31

lib:

• fontconfig 2.12.1
• CVE-2016-5384
• freetype 2.7
• libpng 1.5.27
• libpng 1.6.25
• libxcb 1.12
• libX11 1.6.4
• libXfixes 5.0.3
• libXfont 1.5.2
• Fix a buffer overrun (#83224)
• libXfont2
• Fix a buffer overrun (#83224)
• libXi 1.7.7
• libXrandr 1.5.1
• libXrender 0.9.10
• libXt
• libXt.6.dylib is now a two-level-namespace dylib
• libXt.7.dylib is now a stub dylib that re-exports libXt.6.dylib (for binary compatibility with anything built against XQuartz 2.7.9)
• A flatnamespace version of libXt is available in /opt/X11/lib/flatnamespace to help ease the transition (#96292)
• Set DYLDLIBRARYPATH=/opt/X11/lib/flat_namespace when executing older non-compliant software (eg: Motif-based applications)
• Motif users are encouraged to file bugs against Motif to encourage them to fix that library.
• libXtst 1.2.3
• libXv 1.0.11
• CVE-2016-5407
• libXvMC 1.0.10
• mesa 11.2.2
• xcb-util-cursor 0.1.3

server:

• xorg-server 1.18.4 plus other patches
• Fix the issue where the h key could be come “stuck” after hiding XQuartz with cmd-h (#92648)

 

The latest update on the Swift Blog describes one of the important changes in Swift 3.

In Swift 3, the id type in Objective-C now maps to the Any type in Swift, which describes a value of any type, whether a class, enum, struct, or any other Swift type.

 

Chemical Computing Group have just announced an update to MOE. This release has fixed a couple of Mac OSX 10.12 (Sierra) issues but also brings a host of new features.

• MOEsaic: Web-Application for Ligand Analytics
• Spectral Analysis for Structure Determination
• Enhanced Protein Patch Analyzer
• Integrated Antibody Project Database and Antibody Homology Modeler
• Small Footprint MOE to Facilitate Large Scale Deployments
• Physical and Virtual Rendering of Structures

A more detailed description of the new and enhanced features in MOE 2016.08 can be found at http://www.chemcomp.com/print/moe2016.08.pdf.

 

 

The Swift Algorithm Club is a new site that described implementations of popular algorithms and data structures in Swift. However there is also an added bonus in that there are also detailed explanations of how they work. The list below gives an idea of what is available or under construction, and I’m sure they would be delighted to receive contributions.

The algorithms

Searching

• Linear Search. Find an element in an array.
• Binary Search. Quickly find elements in a sorted array.
• Count Occurrences. Count how often a value appears in an array.
• Select Minimum / Maximum. Find the minimum/maximum value in an array.
• k-th Largest Element. Find the k-th largest element in an array, such as the median.
• Selection Sampling. Randomly choose a bunch of items from a collection.
• Union-Find. Keeps track of disjoint sets and lets you quickly merge them.

String Search

• Brute-Force String Search. A naive method.
• Boyer-Moore. A fast method to search for substrings. It skips ahead based on a look-up table, to avoid looking at every character in the text.
• Knuth-Morris-Pratt
• Rabin-Karp
• Longest Common Subsequence. Find the longest sequence of characters that appear in the same order in both strings.

Sorting

It's fun to see how sorting algorithms work, but in practice you'll almost never have to provide your own sorting routines. Swift's own sort() is more than up to the job. But if you're curious, read on...

Basic sorts:

• Insertion Sort
• Selection Sort
• Shell Sort

Fast sorts:

• Quicksort
• Merge Sort
• Heap Sort

Special-purpose sorts:

• Counting Sort
• Radix Sort
• Topological Sort

Bad sorting algorithms (don't use these!):

• Bubble Sort

Compression

• Run-Length Encoding (RLE). Store repeated values as a single byte and a count.
• Huffman Coding. Store more common elements using a smaller number of bits.

Miscellaneous

• Shuffle. Randomly rearranges the contents of an array.
• Comb Sort. An improve upon the Bubble Sort algorithm.

Mathematics

• Greatest Common Divisor (GCD). Special bonus: the least common multiple.
• Permutations and Combinations. Get your combinatorics on!
• Shunting Yard Algorithm. Convert infix expressions to postfix.
• Statistics

Machine learning

• k-Means Clustering. Unsupervised classifier that partitions data into k clusters.
• k-Nearest Neighbors
• Linear Regression
• Logistic Regression
• Neural Networks
• PageRank

 

IBM’s Fletcher Previn delivered an update on the company’s rollout of Macs at the Jamf Nation User Conference this week. IBM plans to reach over 100,000 Macs by the end of the year and is now deploying 1300 a week on average.

“I can confidently say every Mac that we buy is making and saving IBM money” said Previn. IBM is saving a minimum of $265 (up to $535 depending on model) per Mac compared to a Lenovo PC, over a 4-year lifespan.

More details on Computerworld and 9To5Mac

 

The latest version of APBS includes several notable features and bug fixes. This release includes the addition of Poisson-Boltzmann Analytical-Method (PB-AM), Poisson-Boltzmann Semi-Analytical Method (PB-SAM) and the Treecode-Accelerated Boundary Integral Poisson-Boltzmann method (TABI). Additionally, we have made improvements to the build system and the system tests, as well as miscellaneous bug fixes.

APBS & PDB2PQR: Electrostatic and solvation properties from complex molecules. Solve the Poisson-Boltzmann and related equations to calculate solvation energies and electrostatic properties for analysis and visualization

APBS 1.5 changes

Binary releases may be found on GitHub and on SourceForge. New Features

• Poisson-Boltzmann Analytical Method (PBAM, see Lotan & Head-Gordon) and Semi-Analytical Method (PBSAM, see Yap & Head-Gordon) integrated with APBS.
• PBSAM is currently only available in the Linux and OS X distributions.
• Examples are located with the APBS examples in the pbam/ and pbsam/ directories.
• More information and documentation may be found in the PBAM and PBSAM sections of the APBS-PDB2PQR website.
• Tree-Code Accelerated Boundary Integral Poisson-Boltzmann Method (TABI-PB) integrated with APBS.(See Geng & Krasny)
• Examples are located with the APBS examples in the bem/, bem-pKa/, and bem-binding-energies/ folders
• Included NanoShaper alternative to MSMS.
• More information and documentation may be found in the Contributions section of the APBS-PDB2PQR website
• Added binary DX format support to the appropriate APBS tools.
• Test suite amended and expanded.
• Removed hard-coded limitation to number of grid points used to determine surface accessibility.

Known Bugs / Limitations

• PBSAM not building in windows due to C standard restrictions in the Microsoft compiler implementation.

Full details here

 

The increased use of robotics and automation in experiments is rapidly developing field but coding the experiments can be a tedious and require expert programming knowledge. A recent publication “BioBlocks: Programming protocols in biology made easier” DOI describes a simple drag and drop web interface.

Here, we present a web-based visual development environment called BioBlocks for describing experimental protocols in biology. It is based on Google's Blockly and Scratch, and requires little or no experience in computer programming to automate the execution of experiments.

The Software, Tutorials and Code available on the webpage http://www.lia.upm.es/index.php/software/Bioblocks.

 

I just noticed that the latest version of iBabel has been downloaded over 1000 times, this is fantastic news and it certainly allows me to justify the effort put into creating the application.

iBabel started out as an AppleScript Studio application designed as a front-end to OpenBabel DOI, this was updated several times and is now an ApplescriptObjC application built with Xcode. As well as acting as a front-end to OpenBabel it also provided a front-end to tools built on OpenBabel and a molecule viewer using a selection of javascript viewers via an embedded web view.

I’m occasionally asked about the best way to install OpenBabel and I usually refer people to the page I wrote on installing cheminformatics tools on a Mac, this gives instructions on how to install a wide variety of cheminformatics toolkits and applications.

If you only want to install Openbabel then the best way is to use Homebrew.

Homebrew is a package manager for Mac OSX that installs packages in it’s own directory then symlinks the files to /usr/local. To install Homebrew you first need to have access to the command line tools for Xcode, the easiest way to do this is to download Xcode from the Mac Appstore

1. Start Xcode on the Mac.
2. Choose Preferences from the Xcode menu.
3. In the General panel, click Downloads.
4. On the Downloads window, choose the Components tab.
5. Click the Install button next to Command Line Tools. You are asked for your Apple Developer login during the install process.

Or You can download the Xcode command line tools directly from the developer portal as a .dmg file. https://developer.apple.com/downloads/index.action. On the "Downloads for Apple Developers" list, select the Command Line Tools entry that you want.

To install Homebrew type this command in the Terminal

ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"

Then type

brew doctor

The 'brew doctor' command checks everything is fine. e.g. it will warn if the developer tools are missing, and if there are unexpected items in /usr/local/bin and /usr/local/lib that may clash and might need to be deleted.

It is a good idea to first update the package list

brew update

To install a range of cheminformatics packages we can use a custom “tap” created by Matt

brew tap mcs07/cheminformatics

Then to specifically install Openbabel use

brew install mcs07/cheminformatics/open-babel

To check OpenBabel is working type this in a Terminal window:

obabel -:'C1=CC=CC=C1F' -ocan 
Fc1ccccc1   
1 molecule converted

 

A reader just alerted me to a serious bug in Evernote effecting Mac users.

We have identified a bug in some versions of Evernote for Mac that can cause images and other attachments to be deleted from a note under specific conditions. We've released an updated version of Evernote for Mac, version 6.9.1, to resolve this. Please open Evernote and navigate to Evernote > Check for updates… to get this latest version. If you are using the Mac App Store version of Evernote, this new release has been submitted for approval with Apple, and is estimated at being available for download from the App Store next week.

More comments in the Evernote forum

 

I’ve updated the 3D printing page to include Chemtube3D which has a number of chemical reaction transition states in both the .stl and .x3d format which work with most printers.

A list of available transition state classes is shown below:

• (C=O) Nucleophilic Substition and Addition
• Pericyclic and Diels-Alder Reactions
• Heterocycles
• Rearrangements
• Radical and Stereospecific Reactions
• Organometallic Reactions  

 

Brian Christmas has compiled an absolutely invaluable list of tips and samples of code for those using AppleScript or AppleScriptObjC. He has kindly allowed me to host a page containing all these tips

Applescript & ASObjC ’Things to watch out for’ list.

This list is a great resource for those just starting out but will also be invaluable for more experienced scripters.

If you would like to contribute probably the best way is to subscribe to one of the Apple mailing lists

https://lists.apple.com/mailman/listinfo/applescriptobjc-dev

https://lists.apple.com/mailman/listinfo/applescript-users

There is a page of other AppleScript Resources here.

 

Even the best charge models are useless if protonation states are wrong. QUACPAC attempts to offer everything necessary to do charges correctly. It includes pKa and tautomer enumeration in order to get correct protonation states, partial charges using multiple models that cover a range of speed and accuracy, and electrostatic potential map construction and storage.

This update contains amount other things

• Significant improvements have been made to the reasonable tautomer algorithm that affect its aliphatic and non-aromatic resonance portions.
• Inclusion of AM1BCC ELF10, a new method for applying partial charges to a molecule
• TIP3P water charges are now assigned when using Amber charge sets on molecules containing waters.

Support for Mac OS X 10.10 and 10.11 has been added.
Mac OS X 10.7 and 10.8 are no longer supported.

Full release notes are here

 

This blog post looks very interesting, a notebook environment for coding, data visualisation based on Juypter (aka iPython) notebooks

With nteract, you can create documents, that contain executable code, textual content, and images, and convey a computational narrative. Unlike Jupyter, your documents are stand-alone, cross-platform desktop applications, providing a seamless desktop experience and offline usage.

nteract can run your existing Jupyter notebooks without any modification, and supports multiple Jupyter kernels: Python, R, Julia, and JavaScript. Being a native Jupyter notebook, nteract applications can be easily saved to Domino, versioned, shared, and if needed, run on high-performance machines in the cloud, in your VPC, or on-premise.

More details are on GitHub.

 

ASObjC Explorer has just been updated to version 4.1.17, with fixes relating to Sierra. Choose 'Check for Updates...' to update.

Note also that ASObjC Explorer is no longer available for general sale. Barring bug-fixes, this is the last release -- there will be no further development. You can read more here:

http://www.macosxautomation.com/applescript/apps/explorer.html

Registered users are eligible for a 50% discount on Script Debugger 6 until mid-November as compensation, and should email Shane Stanley for details.

Development of Script Debugger 6

Its AppleScriptObjC code completion will be familiar to users of ASObjC Explorer, but goes further. And Script Debugger 6 ability to step through scripts and explore Cocoa results, to the point of being able to explore the contents of collection classes.

 

I often need to tag individual molecules within a dataset with a specific property, perhaps the results of clustering algorithms, the results of PAINS filtering, or Liver toxicity filters. Alternatively if you have a drug discovery project with multiple chemotypes you might want to tag particular groups of compounds as belonging to a named series to aid analysis.

A question that might then arise is “How many molecules belong to each category?”. Whilst you can see the numbers in the sidebar there is not an easy way to export the results.

Hopefully this script can help.

 

A major new update to OpenBabel has been released, version 2.4.0 is a significant change and is highly recommended.

New file formats

• DALTON output files (read only) and DALTON input files (read/write) (Casper Steinmann)
• JSON format used by ChemDoodle (read/write) (Matt Swain)
• JSON format used by PubChem (read/write) (Matt Swain)
• LPMD's atomic configuration file (read/write) (Joaquin Peralta)
• The format used by the CONTFF and POSFF files in MDFF (read/write) (Kirill Okhotnikov)
• ORCA output files (read only) and ORCA input files (write only) (Dagmar Lenk)
• ORCA-AICCM's extended XYZ format (read/write) (Dagmar Lenk)
• Painter format for custom 2D depictions (write only) (Noel O'Boyle)
• Siesta output files (read only) (Patrick Avery)
• Smiley parser for parsing SMILES according to the OpenSMILES specification (read only) (Tim Vandermeersch)
• STL 3D-printing format (write only) (Matt Harvey)
• Turbomole AOFORCE output (read only) (Mathias Laurin)
• A representation of the VDW surface as a point cloud (write only) (Matt Harvey)

New file format capabilities and options

• AutoDock PDBQT: Options to preserve hydrogens and/or atom names (Matt Harvey)
• CAR: Improved space group support in .car files (kartlee)
• CDXML: Read/write isotopes (Roger Sayle)
• CIF: Extract charges (Kirill Okhotnikov)
• CIF: Improved support for space-groups and symmetries (Alexandr Fonari)
• DL_Poly: Cell information is now read (Kirill Okhotnikov)
• Gaussian FCHK: Parse alpha and beta orbitals (Geoff Hutchison)
• Gaussian out: Extract true enthalpy of formation, quadrupole, polarizability tensor, electrostatic potential fitting points and potential values, and more (David van der Spoel)
• MDL Mol: Read in atom class information by default and optionally write it out (Roger Sayle)
• MDL Mol: Support added for ZBO, ZCH and HYD extensions (Matt Swain)
• MDL Mol: Implement the MDL valence model on reading (Roger Sayle)
• MDL SDF: Option to write out an ASCII depiction as a property (Noel O'Boyle)
• mmCIF: Improved mmCIF reading (Patrick Fuller)
• mmCIF: Support for atom occupancy and atom_type (Kirill Okhotnikov)
• Mol2: Option to read UCSF Dock scores (Maciej Wójcikowski)
• MOPAC: Read z-matrix data and parse (and prefer) ESP charges (Geoff Hutchison)
• NWChem: Support sequential calculations by optionally overwriting earlier ones (Dmitriy Fomichev)
• NWChem: Extract info on MEP(IRC), NEB and quadrupole moments (Dmitriy Fomichev)
• PDB: Read/write PDB insertion codes (Steffen Möller)
• PNG: Options to crop the margin, and control the background and bond colors (Fredrik Wallner)
• PQR: Use a stored atom radius (if present) in preference to the generic element radius (Zhixiong Zhao)
• PWSCF: Extend parsing of lattice vectors (David Lonie)
• PWSCF: Support newer versions, and the 'alat' term (Patrick Avery)
• SVG: Option to avoid addition of hydrogens to fill valence (Lee-Ping)
• SVG: Option to draw as ball-and-stick (Jean-Noël Avila)
• VASP: Vibration intensities are calculated (Christian Neiss, Mathias Laurin)
• VASP: Custom atom element sorting on writing (Kirill Okhotnikov)

Other new features and improvements

• 2D layout: Improved the choice of which bonds to designate as hash/wedge bonds around a stereo center (Craig James)
• 3D builder: Use bond length corrections based on bond order from Pyykko and Atsumi (http://dx.doi.org/10.1002/chem.200901472) (Geoff Hutchison)
• 3D generation: "--gen3d", allow user to specify the desired speed/quality (Geoff Hutchison)
• Aromaticity: Improved detection (Geoff Hutchison)
• Canonicalisation: Changed behaviour for multi-molecule SMILES. Now each molecule is canonicalized individually and then sorted. (Geoff Hutchison/Tim Vandermeersch)
• Charge models: "--print" writes the partial charges to standard output after calculation (Geoff Hutchison)
• Conformations: Confab, the systematic conformation generator, has been incorporated into Open Babel (David Hall/Noel O'Boyle)
• Conformations: Initial support for ring rotamer sampling (Geoff Hutchison)
• Conformer searching: Performance improvement by avoiding gradient calculation and optimising the default parameters (Geoff Hutchison)
• EEM charge model: Extend to use additional params from http://dx.doi.org/10.1186/s13321-015-0107-1 (Tomáš Raček)
• FillUnitCell operation: Improved behavior (Patrick Fuller)
• Find duplicates: The "--duplicate" option can now return duplicates instead of just removing them (Chris Morley)
• GAFF forcefield: Atom types updated to match Wang et al. J. Comp. Chem. 2004, 25, 1157 (Mohammad Ghahremanpour)
• New charge model: EQeq crystal charge equilibration method (a speed-optimized crystal-focused charge estimator, http://pubs.acs.org/doi/abs/10.1021/jz3008485) (David Lonie)
• New charge model: "fromfile" reads partial charges from a named file (Matt Harvey)
• New conversion operation: "changecell", for changing cell dimensions (Kirill Okhotnikov)
• New command-line utility: "obthermo", for extracting thermochemistry data from QM calculations (David van der Spoel)
• New fingerprint: ECFP (Geoff Hutchison/Noel O'Boyle/Roger Sayle)
• OBConversion: Improvements and API changes to deal with a long-standing memory leak (David Koes)
• OBAtom::IsHBondAcceptor(): Definition updated to take into account the atom environment (Stefano Forli)
• Performance: Faster ring-finding algorithm (Roger Sayle)
• Performance: Faster fingerprint similarity calculations if compiled with -DOPTIMIZE_NATIVE=ON (Noel O'Boyle/Jeff Janes)
• SMARTS matching: The "-s" option now accepts an integer specifying the number of matches required (Chris Morley)
• UFF: Update to use traditional Rappe angle potential (Geoff Hutchison)

Language bindings

• Bindings: Support compiling only the bindings against system libopenbabel (Reinis Danne)
• Java bindings: Add example Scala program using the Java bindings (Reinis Danne)
• New bindings: PHP (Maciej Wójcikowski)
• PHP bindings: BaPHPel, a simplified interface (Maciej Wójcikowski)
• Python bindings: Add 3D depiction support for Jupyter notebook (Patrick Fuller)
• Python bindings, Pybel: calccharges() and convertdbonds() added (Patrick Fuller, Björn Grüning)
• Python bindings, Pybel: compress output if filename ends with .gz (Maciej Wójcikowski)
• Python bindings, Pybel: Residue support (Maciej Wójcikowski)

Development/Build/Install Improvements

• Version control: move to git and GitHub from subversion and SourceForge
• Continuous integration: Travis for Linux builds and Appveyor for Windows builds (David Lonie and Noel O'Boyle)
• Python installer: Improvements to the Python setup.py installer and "pip install openbabel" (David Hall, Matt Swain, Joshua Swamidass)
• Compilation speedup: Speed up compilation by combining the tests (Noel O'Boyle)
• MacOSX: Support compiling with libc++ on MacOSX (Matt Swain)

 

The Green Solvents app has been updated.

You can read the full story behind the app in this blog post.

There are now over 400 apps in the MobileScience database.

 

The Chemistry Keyboard is a specialised Keyboard Extension for anyone who needs to enter chemical formulae. The latest update brings compatibility with iOS10 and a tidied up UI.

There is also a Math keyboard and a Science keyboard

 

The latest version of swift has been released.

Swift 3 is a source-breaking release, largely due to the changes in SE-0005 and SE-0006. These changes not only impact the names of the Standard Library APIs, but also completely change how Objective-C APIs (particularly from Cocoa) import into Swift. Many of the changes are largely mechanical, but they can be numerous in a typical Swift project. To help with moving to Swift 3, Xcode 8.0 contains a code migrator that can automatically handle many of the need source changes. There is also a migration guide available to guide you through many of the changes — especially through the ones that are less mechanical and require more direct scrutiny.

Thus there is better translation of Objective-C APIs into Swift, meaning that code imported from Objective-C and translated into Swift will be more readable and Swift-like. The bad news is any code previously imported from Objective-C into Swift will not work in Swift 3; it will need to be re-imported.

There was also a blog post describing how to work with JSON in swift, this is particularly important if your app communicates with a web application, information returned from the server is more often than not formatted as JSON.

import Foundation

let data: Data // received from a network request, for example
let json = try? JSONSerialization.jsonObject(with: data, options: [])

 

Thomas Sander from openmolecules.org has provided a version of DataWarrior that can directly import the Open Source Malaria Data.

The new version can be downloaded here http://www.openmolecules.org/datawarrior, once downloaded and you will need to temporarily adjust your security settings to open it the first time. This is because DataWarrior is not from the Mac App Store or an identified developer. Once open make sure you reset your security settings.

Once installed and opened select the macro as shown below to retrieve the Open Source Malaria Data.

The import only takes a few seconds and pulls the data directly from the Open Source Malaria spreadsheet so it will contains the latest information.

There are now a variety of different options for accessing the Open Source Malaria data you can use the Cheminfo spreadsheet, or use a Vortex script or even an iPython notebook.

 

This is a joint meeting Organised by SCI's Fine Chemicals Group and RSC's Chemical Information and Computer Applications Group. To be held at Imperial War Museum, Duxford, UK, on Wednesday 12 October 2016.

There is an interesting line up of speakers and exhibitors and a chance to have a look around the aerospace museum. More details and the booking form are here https://www.soci.org/Events/Display-Event?EventCode=FCHEM481.

 

m/z EPA CompTox is a new app on the Appstore. It allows you to search chemical structure by exact mass (m/z) in EPA CompTox structures. Instant search in a database of more than 700,000 structures. This joins the increasing number of chemistry apps for mobile devices

For more information about chemistry on mobile devices here is the meeting report for the Chemistry on Mobile Devices: Create, Compute, Collaborate conference that was held 7 September 2016 in Cambridge UK. Organized by RSC CICAG.

 

With the release of iOS 10 comes an update to Xcode. Xcode 8.0 is a free download for OS X 10.11 or later. (An Apple ID is required for iOS development, and App Store submissions require registration in the Apple Developer Program.) The latest version brings Swift 3 and SDKs for iOS 10, watchOS 3, tvOS 10, macOS Sierra, Siri extensions, iMessage apps, and sticker packs for Messages, along with many other changes.

Xcode 8 includes everything you need to create amazing apps for iPhone, iPad, Mac, Apple Watch, and Apple TV. This radically faster version of the IDE features new editor extensions that you can use to completely customize your coding experience. New runtime issues alert you to hidden bugs by pointing out memory leaks, and a new Memory Debugger dives deep into your object graph. Swift 3 includes more natural and consistent API naming, which you can experiment with in the new Swift Playgrounds app for iPad.

Swift 3 is the first major release of the innovative programming language built completely in the open with the community of developers at Swift.org. This release unifies core API naming rules under a new public API Naming Guidelines document that makes writing Swift code feel even more natural. Popular system APIs such as Core Graphics and Grand Central Dispatch are more expressive and harmonize well with Swift.

 

Molmil is a new platform-independent web-based molecular viewer using JavaScript and WebGL. DOI

Molmil has been designed as a light-weight and full-featured viewer for the PDB. As such, Molmil can load legacy PDB flat files, PDBx/mmCIF and PDBML formatted files. Molmil can also load a custom format which we call PDBx/mmJSON, which is a JSON version of the PDBx/mmCIF data. Other formats which Molmil supports are GRO, MOL2, MDL, CCP4 (for electron density maps and EM data), MyPresto’s trajectory format, Gromacs’ TRR and XTC trajectory formats and our own developed MPBF polygon format which we are using for our eF-site service for large structures. Users can also load these files from their local hard drive.

The source code is available at http://github.com/gjbekker/molmil under the LGPLv3 licence.

 

Here is the meeting report for the Chemistry on Mobile Devices: Create, Compute, Collaborate conference that was held yesterday. Organized by RSC CICAG.

Mobile devices are now ubiquitous, there are now estimated to be over two billion SMART phones and tablets in use globally. Each with the computing power to handle most of a chemists needs. The aim of the meeting was to look at the many ways that mobile devices could become the chemist’s essential companion. From searching and consuming content, to performing computational calculations and providing interactive visualizations. From electronic notebooks to devices accessing Cloud based resources.

Nice of Apple to chose to release the iPhone 7 after the meeting :-)

 

A new update to SeeSAR has been released. The most exciting new feature it the new 2D/3D-sync. Atoms in the 3D and the 2D representation will now simultaneously be highlighted, giving you full flexibility. In the editor you may choose to select atoms and bonds now also in 2D. Particularly handy here is the lasso-style selection.

SeeSAR is a software tool for interactive, visual compound prioritization as well as compound evolution. Structure-based design work ideally supports a multi-parameter optimization to maximize the likelihood of success, rather than affinity alone. Having the relevant parameters at hand in combination with real-time visual computer assistance in 3D is one of the strengths of SeeSAR.

Other cool features are:

• manually adjust conformations after editing
• key information of a PDB file at hand in the protein table
• text labels that automatically change color according to your choice of background
• and last but not least a floating licensing option

There is a review of an earlier version here.

 

mathStatica 2.72 is fully compatible with Mathematica 11

mathStatica 2.7 unleashes the power of your computer — automatically — featuring phenomenal speed and power for users with multi-processor machines.

mathStatica 2.7 Parallel Processing Engine — on Mathematica 11

Timings in seconds using Mathematica 11 running on an R2-D2 Mac Pro computer

There is a listing of data analysis tools for MacOSX here

 

This looks very cool

First integration of @UnityMol in the @HoloLens !
Future of scientific visualization ! @LimsiLab VENISE team ! pic.twitter.com/65XHAyyRBP

— Xavier (@N3zix) September 1, 2016

 

There has been an interesting discussion about installing rdkit-postgresql95 on Mac OS X on the rdkit mailing list and I thought it might be of wider interest.

Here's the resolution of the difficulties I was having installing rdkit-postgresql95 on Mac OS X. The problem turned out to be that the package originally posted used Py3.5, and I'm still using 2.7. I may change to 3.5 at some point, but Greg was kind enough to add a 2.7 version of the package.

So, the following invocations work to set up rdkit with the cartridge in a new env on Mac OS X. I'm on El Capitan, by the way, and for clarity, I've not tested the installation, but only checked that it completed successfully.

conda create -n rdk1 -c rdkit rdkit
. activate rdk1
conda install -c greglandrum rdkit-postgresql95

(The last command also installs postgresql 9.5.4-0.)

 

Findings 1.4 has been released. This sounds an important update to this popular electronic Lab notebook.

Better editor, better tables, better sharing, better protocols, better performance.

The full release notes are here

 

Jonas Boström from EduChemVR will be speaking at the Chemistry on Mobile Devices Meeting organised by RSC Chemical Information and Computer Applications Group, 7 September 2016 10:00-16:30, Cambridge, United Kingdom

Our vision is to educate and make chemistry the coolest and most fun subject to learn, and introduce a new way to learn chemistry (and biology) using virtual reality on smartphones…We aim to take a lead in digitalizing life science education by gamification. With EduChemVR apps, teachers can take students on virtual tours to explore small and large molecules.

He has also agreed to give demos at the “poster” session which should be fun.

 

The latest update to the CRAN R archive brings the total number of packages to 9004.

Milestones:

2016-08-22: 9000 packages
2016-02-29: 8000 packages
2015-08-12: 7000 packages
2014-10-29: 6000 packages
2013-11-08: 5000 packages
2012-08-23: 4000 packages
2011-05-12: 3000 packages
2009-10-04: 2000 packages
2007-04-12: 1000 packages
2004-10-01: 500 packages
2003-04-01: 250 packages

There is a listing of data analysis tools for Mac OSX here.

 

Mathematica 11 has been released.

We are pleased to announce that Mathematica 11 has arrived, with over 500 new functions! Continuing on the path of aggressive innovation that Stephen Wolfram first embarked on 30 years ago, Version 11 embraces new areas of modern technology and introduces cutting-edge functionality to match. With Mathematica, you can now print 3D models and plots directly through either local or cloud-based 3D printers. Or instead, identify over 10,000 objects, and classify and extract features in your data with the customizable suite of enhanced machine learning tools. You can also construct, train and evaluate high-performance neural networks with both CPU and GPU support, enabling powerful deep learning in just a few lines of code. Integrated support for audio, from trimming and filters to synthesizing sounds and measuring audio, makes Mathematica 11 a flexible platform for digital audio processing and analysis.

You can read more about it in Stephen Wolfram’s blog post.

 

I just noticed that iScienceSearch has been updated.

Search by structure, text, name and identifiers in 100 chemical and biological databases. A single front-end allows you to get links with answers for your query searching the scientific web! NEW! iScienceSearchlite is a new iScienceSearch version with a simplified UI, which is optimized for smaller screens and slow Internet connections.

There is an review of an earlier version here

 

The CICAG newsletter is now available here

CICAG aims to keep its members abreast of the latest activities, services, and developments in all aspects of chemical information, from generation through to archiving, and in the computer applications used in this rapidly changing area through meetings, newsletters and professional networking

 

This looks interesting, Perfect

Perfect is an application server for Linux or OS X which provides a framework for developing web and other REST services in the Swift programming language. Its primary focus is on facilitating mobile apps which require backend server software, enabling you to use one language for both front and back ends.

Perfect relies on Home Brew for installing dependencies on OS X, once done you are up and running and can follow the Perfect tutorials

I’ve just heard that the poster deadline for the Cheminformatics for Drug Design: Data, Models & Tools meeting organised by SCI's Fine Chemicals Group and RSC's Chemical Information and Computer Applications Group has been extended.

Imperial War Museum, Duxford, UK Wednesday 12 October 2016

Full details are available here https://www.soci.org/Events/Display-Event?EventCode=FCHEM481

Sounds an excellent meeting and you will have a chance to look around the aircraft at the Duxford Imperial War Museum.

 

Orange NMR has been updated.

Orange NMR is an App to predict 13C and 1H NMR spectra: draw a structure to see its spectrum. The accuracy of the algorithm is about 1.9 ppm for 13C and 0.21 ppm for 1H (RMSD=3.4 and 0.31 ppm correspondingly). The number of heavy atoms in structure to predict for free is restricted to 12 atoms. This restriction can be removed by purchasing additional licenses.

• Instantly re-calculate spectrum while changing structure;
• Predicted spectra stored in iCloud and synchronised among all iOS devices and Mac version (itunes.apple.com/app/orange-nmr/id680184249);
• Email PDF report;
• Zoom in spectrum;
• Zoom in structure (important for iPhone users);
• Option to display chemical shift values on structure;
• Simple clean interface.

The prediction algorithm is derived by: K. A. Blinov, E. D. Smurnyy, T. S. Churanova, M. E. Elyashberg, A. J. Williams, Chemom. Intell. Lab. Syst. 2009, 97, 91

What's New in Version 2.4 More accurate 3J H-H couplings prediction.

There are many more science apps for mobile devices here.

Chemistry on Mobile Devices Meeting

 

A couple of updates.

Molecule World.

What's New in Version 3.0

• Download individual structures and entire collections of molecules to support teaching activities
• Lock a chain to prevent changes in appearance
• Performance improvements make rendering faster and improve behavior with larger structures

WebMO: Molecular Editor, Viewer, and Computational Chemistry Interface

What's New in Version 1.6.2

• WebMO 17 compatibility
• Bugfixes to molecular mechanics cleanup
• Improved rendering of atom labels
• Resolved issues when connecting to WebMO via Safari hotlink

Chemistry on Mobile Devices Meeting

 

A publication currently in press, SwissSimilarity: A Web Tool for Low to Ultra High Throughput Ligand-Based Virtual Screening DOI describes a new web tool for virtual screening of vast virtual libraries.

SwissSimilarity is a new web tool for rapid ligand-based virtual screening of small to unprecedented ultralarge libraries of small molecules. Screenable compounds include drugs, bioactive and commercial molecules, as well as 205 million of virtual compounds readily synthesizable from commercially available synthetic reagents. Predictions can be carried out on-the-fly using six different screening approaches, including 2D molecular fingerprints as well as superpositional and fast nonsuperpositional 3D similarity methodologies. SwissSimilarity is part of a large initiative of the SIB Swiss Institute of Bioinformatics to provide online tools for computer-aided drug design, such as SwissDock, SwissBioisostere or SwissTargetPrediction with which it can interoperate, and is linked to other well-established online tools and databases. User interface and backend have been designed for simplicity and ease of use, to provide proficient virtual screening capabilities to specialists and nonexperts in the field.

The website is at http://www.swisssimilarity.ch.

One thing to bear in mind is that any potential hits from screening virtual libraries will require synthetic chemistry resources to make the molecules for confirmation!

 

A great publication on Open Source Molecular Modeling.

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io.

From toolkits to desktop applications a fantastic and comprehensive listing.

 

A few more details on the Chemistry on Mobile Devices Meeting organised by RSC Chemical Information and Computer Applications Group,

7 September 2016 10:00-16:30, Cambridge, United Kingdom

The presentation agenda is now complete but there will be time set aside for poster/demonstrations of apps. If you want to demo your app simply sign up as a delegate and let us know you would like to demo.

Looks like it should be an interesting meeting with couple of “first disclosures” already in place.

 

An overview of the BioExcel Project.

BioExcel is based on improving three aspects of biomolecular research. Firstly, improving the performance and scalability of the most commonly used software, such as GROMACS (www.gromacs.org), HADDOCK (www.haddocking.org) and CPMD (www.cpmd.org), to take advantage of next-gen HPC systems and the expected increase in the amount of data produced. It’s also important to improve how easy it is for users to access and use these types of software. Not all researchers have experience in efficiently handling data and software. BioExcel aims to provide customisable workflow environments, which will allow relatively novice HPC/HTC users take advantage of the analysis software provided in ways that suit their specific research. In addition to this, hands-on training and public webinars are already underway, aiming to teach researchers best practices and how to best utilise the software and resources available.

 

The SCINDR project aims to develop a way to connect, in real time, globally disparate researchers who are doing similar science so that they can work better and faster towards the development of new medicines

Once a researcher has their data stored on the ELN, or on any similar open database, for that matter, SCINDR would be able to detect if similar molecules, chemical reactions, biological assays or other features of importance in health research have been entered by someone else. If the robot identifies another scientist looking into similar features, it will suggest introducing the two to each other, so that they could start working together and combine their efforts and knowledge for the good of both science and the public.

 

A new update to the popular spectroscopy application Mnova has been announced.

This is a major release that incorporates many new features in NMR, MS, Molecule Editor, Database, Verify and NMRPredict plugins. We have integrated a new PhysChem properties module as well as important enhancements in our Scripting Engine. This version has fixed several bugs.

There is also a page of spectroscopy applications here

 

SeeSAR has been updated to 5.2, with loads of features that many people had on their wish list

1. ReCore-improvements: auto-avoid clashes and duplicates; load and install the index from within SeeSAR
2. Simplify binding mode visualization, e.g. by hiding all amino acids not interacting with your compound
3. Color coded protein surface: by either element, depth of the pocket, hydrophilicity
4. For more details and all improvements see: http://www.biosolveit.de/SeeSAR/changes.html

SeeSAR is a software tool for interactive, visual compound prioritization as well as compound evolution. Structure-based design work ideally supports a multi-parameter optimization to maximize the likelihood of success, rather than affinity alone. Having the relevant parameters at hand in combination with real-time visual computer assistance in 3D is one of the strengths of SeeSAR.

 

An interesting development on the Jupyter Blog

It's been a long time in the making, but today we want to start engaging our community with an early (pre-alpha) release of the next generation of the Jupyter Notebook application, which we are calling JupyterLab.

Full presentation is here

 

I see the iOS version of the very popular writing software package Scrivener is now available.

It looks like you need to updated version (2.8) of the desktop version for synching.

Tailor-made for creating long manuscripts, Scrivener banishes page fright by allowing you to compose your text in any order, in sections as large or small as you like. Got a great idea but don’t know where it fits? Write when inspiration strikes and find its place later. Grow your manuscript organically, idea by idea. Whether you plan or plunge, Scrivener works your way: meticulously outline every last detail first, or hammer out a complete draft and restructure later. Or do a bit of both. All text sections in Scrivener are fully integrated with its outlining tools, so working with an overview of your manuscript is only ever a click away, and turning Chapter Four into Chapter One is as simple as drag and drop.

 

An update to UCSF Chimera (version 1.11) is available for download.

General Changes:

• model-display checkboxes can be shown below the command line, and the model-active checkboxes can be hidden (see Preferences, Command Line)
• new input format: IMAGIC density map
• mouse focus (so that Chimera accepts typed input) can be restored by clicking into the Side View as well as the main window
• command-line “atomspec” expanded to handle surface piece names (such as from Multiscale Models)
• new flat ribbon publication preset
• “wall-eye stereo pair” option added to Save Image dialog
• revamped Getting Started tutorials, new Ribbon Styles image tutorial
• molecule descriptions (shown in the status line on mouseover) now read from mmCIF, not just PDB
• PubChem fetch changed to get structures from PubChem3D (NCBI) instead of Pub3D (Indiana University)
• command history navigation skips completely identical lines, and additionally pressing Shift (along with Ctrl-p, Ctrl-n, ↑, or ↓) goes to the previous/next occurrence of the same command (same initial string) instead of the * immediately adjacent command
• atom specification tolerates spaces after commas
• implemented standard keyboard shortcuts Ctrl-o,s,S,q (on Mac, Command instead of Ctrl) for File menu entries Open, Save Session, Save Session As, and Quit, respectively

Full release note are here

This is the last release for 32-bit operating systems, both the 32-bit and 64-bit versions run on Mac OS X 10.8 or later (including OS X 10.11 "El Capitan")

Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).

 

WolframAlpha has been updated to version 1.7.2.

Wolfram|Alpha. Building on 25 years of development led by Stephen Wolfram, Wolfram|Alpha has rapidly become the world's definitive source for instant expert knowledge and computation. Across thousands of domains--with more continually added--Wolfram|Alpha uses its vast collection of algorithms and data to compute answers and generate reports for you. Parts of Wolfram|Alpha are used in the Apple Siri Assistant; this app gives you access to the full power of the Wolfram|Alpha computational knowledge engine.

 

A new update for the very popular chemical drawing application ChemDoodle has been released. Version 8.1 looks to be a significant update with several useful new features and a few bug fixes.

Additions

• New bitmap colorspace output options: Color, Greyscale, Monochrome. The images are not just in the colorspace, but the image data is correctly defined, so that monochrome images are much smaller than grayscale, which will be smaller than color.
• Added Functions setting to use either the Bondi or current literature value for the van der Waals radius in the VABC calculator.
• Added support for implicit hydrogen overrides to all capable formats.
• Added some more recent elemental data.
• Updated and expanded vdW values.
• Added the latest new element names from IUPAC, completing the last row.
• Alpha colors are now stored in ChemDoodle Documents.
• Chain tool now merges with previous drawn structures in the same manner as rings and templates. Red rings will be shown for auto-connect overlaps and this behvior can be controlled in General Preferences. All issues involving drawing chains on top of previous structures have been resolved.
• Auto-connect range when drawing rings, chains and templates is now controllable in General Preferences.
• Added option to suppress implicit hydrogens from groups 1-12.
• Functional hydrogen settings have been moved from Atom Visuals Preferences to Functions Preferences.
• Added more refined options for controlling double bond symmetry. Now terminal double bonds connected to a ring can be made symetrical as a case.
• Updated to OPSIN 2.1.
• OPSIN warnings now still produce a result and display an appropriate warning instead of failing.
• Added templates for tetroses.
• Keyboard shortcuts have been added for the atom label tool, so you can bold, italicize and underline text via the keyboard.

Fixes

• Added HTTPS support for NIH Cactus, returning functionality to the 3D clean tool.
• Corrected Elemental Analysis and Mass Parent Peak simulation results for structures with multiple charges.
• Addressed a number of issues for implicit hydrogen calculations in resonance systems.
• Fixed issue where arbitrary rings and and crown ethers drawn to a bond of length that was different from the standard length didn’t work properly.
• Fixed bug where Preferences boolean button sets were flagging visuals changes for non-visual settings.
• Fixed incorrect behavior where General or Advanced Preferences settings were falsely notifying the user of style sheet changes.
• Fixed issue where output ChemDoodle 3D Scene (ic3) files from ChemDoodle were flipped on the y-axis.
• Corrected a number of minor graphical glitches with vertical connections and wedge/bold bonds.
• Closing the color select window no longer conforms colors, but does update the color button.
• Using the color scrubber of the Quick Colors button now also sets the selection to that color after choosing.
• Quick Colors button now correctly adjusts an entire label, even if chemical interpretation is off.
• Minor updates to the Periodic Table.
• The Center>Selection menu items are now correctly context sensitive.
• iChemLabs extensions to JCAMP DX files have been removed and are no longer necessary. Note that older JCAMP spectra written from ChemDoodle that used these extensions (typically simulation output) will not be able to be read anymore.
• Fixed rare crash that occured when Preferences bounds somehow ended up out of the defined bounds.
• Fixed some minor IUPAC naming issues.
• Isotopes from ChemDraw files are now displayed correctly.
• Isotope labels are now correctly accounted for in bond retraction.
• Ring, chain and template actions that don’t actually change the document are now ignored in history.
• Minor text sizing considerations and corrections.
• Kekulizer now ignores zero order bonds.
• Improved text layout in tabs not to overlap with close buttons.
• Restoring the document now correctly updates the History widget.
• Restoring the document now correctly clears the selection if there is one defined.
• Fixed issue where loading an autosave didn’t correctly enable the Restore menu item.
• Fixed issue where dialogs were not reappearing after being deiconified.
• Carbon labels will now be displayed in the implicit hydrogen count is overridden to 0.
• Fixed the Login window cutoff.
• Completely uppercase element symbols are now correctly handled when reading in MDL CT files.

 

ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 100 million purchasable compounds in ready-to-dock, 3D formats. Sterling and Irwin, J. Chem. Inf. Model, 2015. This is an invaluable resource for any type of virtual screening or for anyone looking to create a physical screening or fragment collection.

Once you have done the virtual screening you will rapidly realise that the really time-consuming a tedious part now lies ahead. Finding out which vendors stock a particular molecule and then ordering them. Looking up the vendor details for individual compounds is extremely tedious and so this Vortex script may be very useful.

Many more scripts, iPython notebooks and tutorials can be found here.

 

BBEdit is my favourite text editor and I’ve been a user since way before Mac OSX. The latest update BBEdit 11.6 brings a number of bug fixes and updates but also introduces a new demo mode. For 30 days the full feature set is available for free after which time BBEdit will remain permanently functional with a revised feature set that includes its powerful text editing capabilities but not its web authoring tools or other exclusive features. These features may be re-enabled at any time with a purchased license.

BBEdit 11.6 requires Mac OS X 10.9.5 or later, and is compatible with OS X 10.11 "El Capitan".

BBEdit can be obtained from the online store.

There is also a listing of markdown editors here

 

An interesting article from ChemAxon on the history and demise of Java Applets.

 

Findings the electronic lab notebook for both MacOS and iOS has been updated.

Release Notes
Compatibility with the upcoming Findings for Mac 1.4.

Looks like there are more good things on the way!

 

The latest update to iNMR version 6.0.0 is available for testing.

Version 6.0.0 requires Mac OS X El Capitan. Today only 60% of Mac users have it. This doesn’t seem the right moment for replacing version 5. In conclusion, version 6 is currently available for a few selected testers only. Anybody can apply. Testers will receive a key that is going to expire in December. The keys for version 5 are not valid for version 6.

iNMR is a high performance NMR analysis program.

See also the spectroscopy page.

Optibrium have just announced the release of StarDrop 6.3, perhaps the highlight of this release is the introduction of the new SeeSAR module.

The SeeSAR module developed in collaboration with BioSolve ITprovides seamless access in StarDrop to 3D structures based on X-ray crystallography or predicted with any docking software. The intuitive link between this 3D information and StarDrop’s cheminformatics analyses and visualisations, based on 2-dimensional compound structure, gives new insights into structure-activity relationships (SAR) within your project chemistry and aids the design of improved compounds. It also supports collaboration between computational and synthetic chemists, helping to share the results of 3D modelling with all decision makers.

You can watch a video tutorial here

 

Dotmatics User Group Meeting – Cambridge, UK
Churchill College, Cambridge, UK
Tuesday, 13 September 2016 at 09:00 - Wednesday, 14 September 2016 at 16:00 (BST)

Full details and agenda here

 

I just noticed that the latest version of iBabel has now been downloaded over 700 times since it was released at the start of the year.

iBabel started out as an AppleScript Studio application designed as a front-end to OpenBabel DOI, this was updated several times and is now an ApplescriptObjC application built with Xcode. As well as acting as a front-end to OpenBabel it also provided a front-end to tools built on OpenBabel and a molecule viewer.

 

Just looking at the speakers at the Mobile Chemistry conference organised by RSC Chemical Information and Computer Applications Group 7 September 2016 10:00-16:30, Cambridge, United Kingdom.

Andy Davies is talking about the RSC Medicinal Chemistry Toolkit app a suite of resources (Chemical Formula, MWt, GCLogP, Ligand Efficiency, Ligand Lipophilic Efficiency and AZFilters calculations) to support the day to day work of a medicinal chemist. Based on the experiences of medicinal chemistry experts, it was developed otherwise difficult-to-access tools in a portable format for use in meetings, on the move and in the lab. The app was developed in collaboration with Molecular Materials Informatics.

The latest version includes computational structural filters developed by AstraZeneca drug design teams. This looks like an excellent opportunity to hear more about this swiss army knife for medicinal chemists and feedback what new features you might want.

 

Freeform –calc conf estimates the free energy of transforming a single molecular conformer from an ensemble of solution phase conformers to a single bioactive conformation. Several new features have been added, including:

• Multiple input conformers can now be tracked. For example, input conformers could be top scoring poses of docked molecules, alternative x-ray conformations (from the PDB), or alternative ligand refinements (e.g. from AFITT).
• In addition to the standard Sheffield solvation model, Freeform energy calculations can now be run using a Poisson-Boltzmann corrected solvation model.
• Conformational search has been improved by including solvation throughout the conformational sampling.

• An extension of the AM1BCC charging model that considers Electrostatically Least-interacting Functional groups (ELF), AM1BCC ELF10, is now the default method for applying partial charges to a ligand. This mitigates electrostatics problems that frequently arise for charged ligands.

• Support for Mac OS X 10.10 and 10.11 has been added.

• Mac OS X 10.7 and 10.8 are no longer supported.

 

Molsoft have just announced and interesting new product ICM-Scarab, a one-stop shop for capturing and analysing bioinformatics and chemoinformatics data. It provides and electronic notebook for storing experimental information integrated with query tools that allow the user to effortlessly search both internal and external SQL databases.

There is a webinar Wed, Jun 29, 2016 5:00 PM - 6:00 PM BST if you want to find out more.

 

Swift Blog Update

Swift 3 beta was just released as part of Xcode 8 beta and includes numerous enhancements, many contributed by the open source community. The primary goal of Swift 3 is to implement the last major source changes necessary to allow Swift to coalesce as a consistent language throughout, resulting in a much more stable syntax for future releases.

 

An interesting post on chemistry and computers, Pymol and very large PDB files. The Zika Cryo-EM structure as a case study. Always good to see people stress testing computational tools.

 

An interesting conference organised by RSC Chemical Information and Computer Applications Group 7 September 2016 10:00-16:30, Cambridge, United Kingdom

Mobile devices are now ubiquitous: there are estimated to be over two billion smart phones and tablets in use globally, each with the computing power to handle most of a chemist's needs. The meeting will explore the many ways that mobile devices could become the chemist's essential companion, from consuming content to performing computational calculations, from electronic notebooks to devices accessing cloud-based resources, and much more.

More details

http://www.rsc.org/events/detail/22602/chemistry-on-mobile-devices-create-compute-collaborate

 

Just noticed this message.

ChemDoodle 8.0.1 is now available. However, automatic update is not allowed for Mac OS X. You must manually update ChemDoodle by downloading the latest version of ChemDoodle from www.chemdoodle.com, and re-installing it. NOTE: You must close ChemDoodle before re-installing the new version.
Changes in ChemDoodle 8.0.1
Executive Summary
This is a minor update fixing issues brought to our attention since the ChemDoodle 8 launch. For changes to version 8, scroll down.
Fixes

1. Periodic table should now open again from the View menu.
2. Fixed the interpretation of deuterium and tritium in complex condensed labels.
3. Charges in left oriented labels are now located in better positions.
4. Default cyclopentadiene and cycloheptatriene tools now place saturation on the sprout point unless not chemically feasible.
5. Adding rings and templates will no longer merge multiple atoms into a single point if multiple adding atoms are within the merging distance of a present atom.
6. Fixed rendering of Bold and Thin double bonds when in perspective merges.
7. Improved the vitamin templates.
8. Added feature to lock polyline drawing to the horizontal and vertical positions if the shift key is held down.
9. Flipping while retaining stereochemistry now accounts for meso centers.
10. Torsion bond function now preserves stereochemistry if set to do so by the option under the Functions tab in Preferences.
11. Search widget will no longer execute a search when the drop panel is empty.
12. Fixed issue where single atom results were not rendered in the Search widget.
13. Search widget results are now sorted with hits appearing first.
14. Search widget searches with stereochemistry defined in query structures now work properly.
15. Fixed bug where the Search widget could not be manually stopped.
16. Fixed bug where query labels would disappear in the document after being dropped in the Search widget.
17. Fixed minor SKC import issues with text labels.

ChemDoodle 8 is a massive update to ChemDoodle. Included are hundreds of new features and improvements, recommended to us by users like you. Enjoy and please spread the word!
New Features

1. The graphics system has been improved even beyond current industry standards for graphics. Every bond merge and pixel was scrutinized. Chemical structures have never looked better. ChemDoodle provides the best graphics in chemistry, everything else is a waste of money.
2. Major IUPAC naming improvements, including very advanced ring systems.
3. Full support for Retina display Macs and support for high-DPI Windows hardware.
4. A new query structure system for defining sets of molecules and for searching partner services.
5. New powerful tools for drawing arbitrary rings and crown ethers to atoms and bonds.
6. Superscript and subscript merging to easily create atomic notations and other chemical text.
7. More specific cleaning tool for adjusting only a selection of a structure.
8. Text output options and improvements for EPS and SVG files in addition to PDF.
9. A dramatically improved Templates widget with new and more aesthetic templates.
10. Read in NTUPLES (multiple spectra) from JCAMP files.
11. Added support for both the SketchEl (el) and Crystallographic Information Format (cif) filetypes.
12. More support for working with the ChemDoodle Web Components.
13. Dozens of new BioArt graphics.
14. Performance improvements for faster work.
15. Dozens more new features: two new bond types, implicit hydrogen control, automatic IUPAC locant labelling, vastly improved condensed labels, search files based on query structures, recursive SMARTS, metric support for document aids and rulers, a new precise form for scaling a specific bond, many interface improvements and so much more.

 

The results of the annual data analysis poll are in and show some interesting trends, in particular the dramatic increase in Python use.

R remains the leading tool, with 49% share (up from 46.9% in 2015), but Python usage grew faster and it almost caught up to R with 45.8% share (up from 30.3%).

Actually looking down the list I notice there is also an entry for scikit-learn, which is Python based, and if you add that in Python is now the most commonly used data analysis tool.

There was a 10% drop in the use of KNIME, and a 36% drop in the use of TIBCO Spotfire two products used in cheminformatics.

In terms of programming languages Python is by far the most extensively used.

Python	45.8% share (was 30.3%)	51% increase
Java	16.8% share (was 14.1%)	19% increase
Unix shell/awk/gawk	10.4% share (was 8.0%)	30% increase
C/C++	7.3% share (was 9.4%)	23% decrease
Other programming languages	6.8% share (was 5.1%)	34.1% increase

In the Big Data area Hadoop (22.1%) and Spark (21.6%) dominate.

There is a listing of data analysis tools for MacOSX here.

 

I’m not a Fortran user but overtime I mention it there is a sharp uptick in page views so there are obviously a significant number of users who might be interested in this workshop.

Fortran modernisation workshop at Culham Centre for fusion energy

Date: 24 - 25 August 2016. Time: 09:30 - 17:30. Location: Learning Resource and Development Centre (Library), E building, Culham Centre for Fusion Energy, Culham Science Centre, Abingdon, OX14 3DB

TOPICS WILL INCLUDE:

• Software engineering for computational science;
• Modern Fortran standards and how to write optimized and efficient Fortran;
• NetCDF and HDF5 scientific file formats for data sharing in Fortran;
• GNU Automake to automate the build process;
• pFUnit unit testing framework for testing Fortran codes;
• Doxygen for Fortran code documentation;
• Git version control for collaborative code development;
• In-memory visualisation using PLplot in Fortran;
• IEEE Floating Point Exception Handling
• Software verification and portability using the NAG Fortran compiler
• Fortran interoperability with C, Python and R;
• Introduction to parallelism for Fortran.

There is a page of Fortran Resources here.

 

With the Apple WWDC just around the corner it is fun to look at the current hardware rumours. The latest MacPro was first disclosed at the WWDC in 2013 and so it perhaps is due for an update. That said I’m currently using a MacPro as the desktop workhorse for my work and I’m really impressed, to be honest I can’t see a compelling need for extra performance.

Intel's Xeon E3-1200 V4 (Broadwell) and the equivalent E3-1200 V5 (Skylake) Xeon processors have been launched, and so an upgrade to the CPU would seem to be an obvious step. GPU provides a more interesting discussion, the existing MacPro has either Dual AMD FirePro D500 graphics processors with 3GB of GDDR5 VRAM each or dual AMD FirePro D700, each with 6GB of GDDR5 VRAM. However Nvidia introduced a new GPU the Tesla P100, based on its new Pascal architecture and targeted at high-performance computing.

Currently there are 4 USB ports and 6 Thunderbolt 2 ports on the Mac Pro, I’m finding the Thunderbolt 2 ports are unused so the rumours suggesting 10 USB 3.0 ports seem plausible, but Thunderbolt 3 must be included surely?

One thing I’d like to see is the RAM increased, currently the MacPro can accommodate a maximum of 64GB (four slots of 16GB), I’ve managed to max that out on numerous occasions.

 

The news section on the University of Liverpool site highlights two apps that provide a guide to interactions that may occur between different hepatitis or HIV drugs and over 600 co-medications that a patient may be prescribed, as well as recreational drugs and herbals.

Liverpool HIV iChart and Liverpool HEP iChart are available for free download.

 

I just noticed that the popular electronic laboratory notebook Findings has been updated.

Release Notes Version 1.3.4

• Reduced CPU activity at app launch, in particular for large libraries.
• Better responsiveness when typing in large documents.
• Faster loading of large experiments or protocols, avoiding operations that could even lead to the dreaded spinning beach ball.
• Automatic scrolling to the insertion point when pasting or when inserting various elements in experiments or protocols, like attachments, section titles, etc.
• Superflous confusing newline after tables in experiments or protocols.
• Automatic scrolling to the insertion point when typing was not always working.
• Problems with some keyboard input methods (in particular Chinese: Pinyin) when used on a new empty line.
• Document library path wrongly reset when Dropbox folder is in /Users/Shared.

 

With the Apple WWDC just around the corner it is fun to look at the current hardware rumours. The MacBook Pro currently looks well overdue for an update and so there are plenty of rumours about an imminent update.

One of the more intriguing suggestions is that an OLED display touch bar will replace the physical function keys, this would presumably allow developers to create and display custom application specific function keys. The other rumours suggest a thinner and lighter form factor resulting in elimination of all but USB-C ports. Connectivity could be enhanced by incorporation of 4G.

The current MacBook Pro processor is now rather out-dated, and a move to Intel Skylake processors seems certain, this might be expected to improve both performance and battery life.

Upgrades to both GPU and display have all been suggested in various rumours with some suggesting the introduction of a touchscreen. Personally I’d keep touchscreen with tablets, but with more scientific applications using the GPU to improve performance this could be an important upgrade.

There have also been rumours of introducing touchID into the laptops as an extra security measure.

 

I’ve just been made aware of an issue with one of the Calculated properties iPython Notebook.

The latest update to Pandas

the respective piece of the pandas API got restructured for 0.18.1 and that the “format" module got moved from pandas.core to pandas.formats:

The consequence is that PandasTools now raises an error on attempting to import molecules into a data frame.

from rdkit.Chem import PandasTools
df = PandasTools.LoadSDF("demo.sdf")

AttributeError                          Traceback (most recent call last)
/Users/philopon/mysrc/python/mordred/.direnv/python-3.5.1/lib/python3.5/site-packages/IPython/core/formatters.py in __call__(self, obj)
    341             method = _safe_get_formatter_method(obj, self.print_method)
    342             if method is not None:
--> 343                 return method()
    344             return None
    345         else:

/Users/philopon/mysrc/python/mordred/.direnv/python-3.5.1/lib/python3.5/site-packages/pandas/core/frame.py in _repr_html_(self)
    566 
    567             return self.to_html(max_rows=max_rows, max_cols=max_cols,
--> 568                                 show_dimensions=show_dimensions, notebook=True)
    569         else:
    570             return None

/usr/local/Cellar/rdkit-python/2016.03.1/lib/python3.5/site-packages/rdkit/Chem/PandasTools.py in patchPandasHTMLrepr(self, **kwargs)
    129   Patched default escaping of HTML control characters to allow molecule image rendering dataframes
    130   '''
--> 131   formatter = pd.core.format.DataFrameFormatter(self,buf=None,columns=None,col_space=None,colSpace=None,header=True,index=True,
   132                                                na_rep='NaN',formatters=None,float_format=None,sparsify=None,index_names=True,
    133                                                justify = None, force_unicode=None,bold_rows=True,classes=None,escape=False)

AttributeError: module 'pandas.core' has no attribute 'format'

At the moment the only solution is to make sure you are using Pandas version 0.18.0

pip uninstall pandas    
pip install pandas==0.18.0

 

With the Apple WWDC just around the corner it is fun to look at the current hardware rumours. Just reported on Slashdot

MojoKid quotes a report from HotHardware: If you head over to Apple's website, the Cupertino outfit will happily sell you a 27-inch Thunderbolt display for $999, at least until its inventory runs out. Word on the web is that it's nearly out of stock and Apple doesn't plan to replenish them. Instead, Apple will launch a new version of its Thunderbolt monitor, one that's been upgraded to a 5K resolution and has a discrete GPU stuffed inside. It's an interesting product actually, if you think about it. Depending on the task, it can take some serious graphics muscle to drive a 5K resolution display. It amounts to over 14.7 million pixels (5120x2880), compared to Apple's current generation Thunderbolt display which runs at 2560x1440, or less than 3.7 million pixels. Apple's thinking is likely that if it integrates a GPU capable of driving a 5K resolution into the display itself, it won't have to worry about trying to balance graphics performance with thin and light designs for its future Mac systems.

 

Facio is a free GUI for computational chemistry softwares (TINKER, MSMS, Firefly, Gamess, MOPAC and Gaussian).

 

The major release version SeeSAR 5.0 just came out. It brings along a number of terrific new features:

• The user is now in charge to define a common binding site, which makes comparing different poses much simpler and enhances the speed of display;
• Editing and the Hyde visual affinities have so far been completely separate. Now you can easily switch back and forth between these two essential tasks;
• Editing covalently bound molecules is also possible with this new version:

 

A couple of people have asked me about the software I use to edit images on the website. I have two tools that I use regularly.

Pixelmator is an easy to use image editing app that comes with an impressive selection of features.

Graphic Converter is a tool that I’ve used for a long, long time. In fact I seem to remember the first copy I got was bundled with my first Mac.

 

An update from X11.org

On Thu, 2016-05-26 at 16:34 +0000, Cook, Rich wrote:

Hello, I recently heard on the Apple x11-users mailing list that remote OpenGL rendering (IGLX) is being phased out of XOrg and not being replaced. Is this really the case or am I misunderstanding?

You have heard incorrectly. It is disabled by default for security reasons, as it's been a repeated source of exploitable bugs, but the feature itself isn't going away.

One caveat is there's no easy way to enable it other than the command line, and not all display managers give you a mechanism to pass arbitrary options in (which is reasonable enough). I've added an xorg.conf option to enable IGLX in master, and I'll be backporting that to the various stable branches as well.

 

The GPView program is a C++ package for wave function analysis and visualization.

It is developed and maintained by Tian Shi and Ping Wang Ref](http://arxiv.org/abs/1602.07302)

In this manuscript, we will introduce a recently developed program GPView, which can be used for wave function analysis and visualization. The wave function analysis module can calculate and generate 3D cubes for various types of molecular orbitals and electron density related with electronic excited states, such as natural orbitals, natural transition orbitals, natural difference orbitals, hole-particle density, detachment-attachment density and transition density. The visualization module of GPView can display molecular and electronic (iso-surfaces) structures. It is also able to animate single trajectories of molecular dynamics and non-adiabatic excited state molecular dynamics using the data stored in existing files. There are also other utilities help to extract and process the output of quantum chemistry calculations. The GPView provides full graphic user interface (GUI) which makes it very easy to use.

 

A joint meeting Organised by SCI's Fine Chemicals Group and RSC's Chemical Information and Computer Applications Group

More Details and booking form

 

There is an important discussion taking place on the X11 users list regarding the support of indirect GLX (iGLX) in XQuartz.

Indirect GLX is an extension offered by X11 that enables the transmission of OpenGL commands from an X11 client on a remote machine to an X11 server on your desktop over the network. For example, when your OpenGL science application running on a remote host tries to draw images using OpenGL and display on your local XOrg (XQuartz) desktop, IGLX (red line below) is used to send the commands to your local X server, which then uses OpenGL locally to draw the commands.

In seems in the latest version of XQuartz (2.7.9) this is turned off by default and there appears to be a move to deprecate this protocol. This seems to have been prompted by security concerns but I know nothing of the details.

However many scientific applications use this capability and it seems there is no alternative. If this is likely to be an issue for you I suggest you subscribe to the X11 list and make your views known.

 

Interesting post on structure based searching via a web interface.

The MolSync website and the technology behind it have been moving forward rapidly. The public-facing deployment now shows a proof of concept page for performing molecule searches: http://molsync.com/search/molecule.php.

 

Cytoscape has been updated to version 3.4.0

Note, This update requires Java 8 is installed and Mac OS X 10.9 and later.

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

 

The very popular reference management application Papers has been updated. to version 3.4.5 (512).

Release Notes

• Match with Selection now works in the Reader mode.
• Papers no longer crashes if an incorrect EZProxy address is entered in the Access preferences.
• General stability improvements.

There are more reference management applications here.

 

Orange NMR has been updated, with more accurate 4J HH couplings prediction and improvements to the peaks table.

Orange NMR is an App to predict 13C and 1H NMR spectra: draw a structure to see its spectrum. The accuracy of the algorithm is about 1.9 ppm for 13C and 0.21 ppm for 1H (RMSD=3.4 and 0.31 ppm correspondingly).

There are an increasing number of spectroscopy application available for mobile devices.

 

I came across the jupyter-docker-pymol recently and thought I'd give it a mention. It is a Container-based installation of PyMol, with interaction through the browser via ipymol and Jupyter notebook (based on jupyter/notebook).

This project uses PyMol 1.8.2.0 and Python 3

 

I just noticed that iBabel has now been downloaded over 500 times since the start of the year. I'm surprised and delighted that it has proved so popular.

iBabel is a GUI (graphical user interface) for the open source cheminformatics toolkit OpenBabel. It also provides an interface to a variety of tools built using OpenBabel and a variety of molecule viewers.

 

Data Extractor has been updated to version 1.4.2

Data Extractor allows to extract data in a sparse format contained inside various files and collect the data you need in an internal structured table. Data extractor can parse thousands and thousands of file in few seconds and collect the data inside

More details here…

There more tools for data analysis here

 

I've added Topspin to the Spectroscopy page, this is an NMR processing package from Bruker. Looks to be free for academics.

In order to provide students, researchers and teachers with unlimited access to the best tools for off-line NMR processing, Bruker is making their market leading NMR processing software TopSpin available free of charge for all academic users.

There are also an increasing number of spectroscopy application available for mobile devices.

 

I've added USPEX Universal Structure Predictor: Evolutionary Xtallography to the alphabetical listing of applications

A.R. Oganov, J.C. Schon, M. Jansen, S.M. Woodley, W.W. Tipton, and R.G. Hennig. Appendix: First Blind Test of Inorganic Crystal Structure Prediction Methods, pages 223–231. Wiley-VCH Verlag GmbH & Co. KGaA, 2010.

 

The latest market share data is available from NetMarketShare.com, Mac market share has been rising over the last few years and in April hit a peak of 9.20%, largely at the expense of Windows.

 

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL). A few components are included that are in the public domain or which have other, open-source, licenses. The sander program now has the LGPL license. AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers

The Amber16 package builds on AmberTools16 by adding the pmemd program, which resembles the sander (molecular dynamics) code in AmberTools, but provides (much) better performance on multiple CPUs, and dramatic speed improvements on GPUs. Major new features include:

Semi-Isotropic Pressure Scaling (GPU)
Charmm VDW Force Switch (CPU, GPU)
Enhanced NMR Restraint support + R^6 averaging support (GPU)
Gaussian Accelerated Molecular Dynamics (CPU, GPU)
Support for external electric fields (CPU)
Expanded umbrella sampling support (GPU)
Constant pH supported with replica exchange along pH coordinate (GPU)
Support for gas phase MD (igb=6) (CPU, GPU)
Support and significant performance improvements for the latest Kepler, Maxwell and Pascal GPUs from NVIDIA.

 

One of the issues for machine learning models in helping understand structure activity relationships (SAR) is providing a nice chemist friendly visualisation. This excellent blog post provides a description of how to colour code the parts of molecules that are predicted to contribute to an activity.

 

I've been sent details of a couple of jobs and I thought I'd pass them on.

BIO – Cheminformatics Data Scientist (Stratified Medical)

We are looking for an experienced and innovative cheminformatician to make a significant contribution in influencing the drug discovery process by applying your expertise in chemical methods development and use of intelligent algorithms to chemical data. Working within the Biomedical Data R&D team, you will be required to bring your experience and ideas across a broad range of drug design areas.

More details here…

Technical Expert Cheminformatics, (Syngenta, Jealotts Hill)

In this role, you will provide cheminformatics and mathematical modeling support to the computational chemistry platform in Chemical Research.

More details here…

 

Cresset have just announced the release of Spark V10.4.

Spark finds biologically equivalent replacements for key moieties in your molecule. Whether your goal is R-group exploration, patent busting or scaffold hopping, your results will include structures you have thought of yourself, plus new structures that make chemical sense and are totally unexpected.

The new features include:-

• New Cresset reagent databases derived from eMolecules’ building blocks, replacing previous reagents based on ZINC, include availability information for every result
• New analysis of the conformation of every result using the Torsion Library method of Guba et al. that is based on an analysis of the Cambridge Structural Database (CSD)
• New configurable connection to external REST service for properties that enables you to add your own data and properties to the Spark experiment
• Improved Radial Plots to support enhanced multi-parameter optimization.

 

RDkit has been updated .

If you used home-brew to install RDkit as described here updating is very simple

brew update
brew upgrade rdkit

You can check which version you have installed using

MacPro> python
Python 2.7.11 (default, Dec 23 2015, 16:11:50) 
[GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import rdBase
>>> print rdBase.rdkitVersion
2016.03.1
>>>

 

I will be moving the website to a new server over the next few days, apologies in advance for any interruptions.

 

If you regularly have to manually edit files containing data in delimited text format then this application maybe of interest.

DB-Text is a general purpose tool for editing delimited text files. It can automatically recognise the used format analysing the content inside. It can accept data with mixed use of quotas and provides tools to copy in CSV (comma separated),TSV (tab separated) or HTML format of selected rows in the clipboard, with a simple click.

I've added it to the Data Analysis Tools page

 

This is just a very quick tip when dealing with Greek characters in Vortex column names when creating a script. It may be obvious to many but I struggled for several hours before finding the problem and a solution

Read more…

 

Apple today announced that it will hold its 27th annual Worldwide Developers Conference (WWDC) from June 13 through 17 in San Francisco.

Developers can apply for tickets via the WWDC website (developer.apple.com/wwdc/register/) now through Friday, April 22 at 10:00 a.m. PDT. Tickets will be issued to attendees through a random selection process, and developers will be notified on the status of their application by Monday, April 25 at 5:00 p.m. PDT. For the second consecutive year, there will be up to 350 WWDC Scholarships available, giving students and STEM organization members from around the world an opportunity to earn a ticket to meet and collaborate with some of the most talented developers of Apple’s ever-growing app ecosystem (developer.apple.com/wwdc/scholarships/). Additionally, this year, we will provide travel assistance to up to 125 scholarship recipients to ensure aspiring developers with financial limitations have an opportunity to participate.

 

I'm making increasing use of iPython notebooks and this package looks like it will be very useful.

nglview is a Python package that makes it easy to visualize molecular systems, including trajectories, directly in the Jupyter Notebook. The recent 0.4.0 release of nglview brings a convenient interface for visualizing MDAnalysis Universe and AtomGroup objects directly:

More details here…

The notebook widget allows you to rotate and zoom the molecule and lets you select atoms by clicking on the molecule.

Easily installed using PIP

pip install nglview

Update

There have been a number of comments and responses via twitter highlighting this superb demo.

http://arose.github.io/ngl/

The project is on Github, feel free to contribute!

 

MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach.

Pengfei Li and Kenneth M. Merz, Jr., "MCPB.py: A Python Based Metal Center Parameter Builder." J. Chem. Inf. Model., 2016, Accepted, DOI.

There is an excellent and very detailed online page describing the use of MCPB.py http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm.

 

I just came across an interesting paper on cross-platform OpenCL programming. The Hitchhiker’s Guide to Cross-Platform OpenCL Application Development. In particular it highlights a number of issues and offers workarounds. These include Framework bugs, Specification limitations and Program bugs.

There are an increasing number of scientific applications taking advantage of GPU acceleration.

 

Version 1.7.0 of Wolfram|Alpha has been released.

No real details on update other than "bug fixes".

Wolfram|Alpha. Building on 25 years of development led by Stephen Wolfram, Wolfram|Alpha has rapidly become the world's definitive source for instant expert knowledge and computation. Across thousands of domains--with more continually added--Wolfram|Alpha uses its vast collection of algorithms and data to compute answers and generate reports for you.

 

I was just sent a link to PAST free software for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy.

Current version (February 2016): 3.11 runs under Mac OSX 10.8 and later.

Hammer, Ø., Harper, D.A.T., Ryan, P.D. 2001. PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4(1): 9pp. http://palaeo-electronica.org/20011/past/issue101.htm

I've added it to the page of data analysis packages for Mac OSX.

 

The latest version of iBabel has now been downloaded over 400 times since it was released in January.

iBabel is a GUI (graphical user interface) for the open source cheminformatics toolkit OpenBabel. It also provides an interface to a variety of tools built using OpenBabel and molecule viewers

 

With the release of ChEMBL 21 has come a set of updated target predicted models.

The good news is that, besides the increase in terms of training data (compounds and targets), the new models were built using the latest stable versions of RDKit (2015.09.2) and scikit-learn (0.17). The latter was upgraded from the much older 0.14 version, which was causing incompatibility issues while trying to use the models.

I've been using the models and I thought I'd share an iPython Notebook I have created. This is based on the ChEMBL notebook with code tidbits taken from the absolutely invaluable Stack Overflow. I'm often in the situation where I actually want to know the predicted activity at specific targets, and specifically want to confirm lack of predicted activity at potential off-targets. I could have a notebook for each target but actually the speed of calculation means that I can calculate all the models and then just cherry pick those of interest.

Read on…

 

Now in its fourth year, the International Workshop on OpenCL will be held during April at the C3 Convention Center in Vienna, Austria. The majority of sessions will run April 20–21 and will consist of a mix of keynotes, academic papers, technical presentations, tutorials and poster sessions. The workshop kicks-off on April 19 with an Advanced Hands On OpenCL tutorial.

There is a page of scientific applications taking advantage of GPU here.

 

The top 10 upvoted apps on the Mobile Science website are:-

ChemDoodle Mobile

Draw chemical structures. View 3D. Generate IUPAC names. Calculate properties. Simulate NMR. ChemDoodle Mobile! NOTE: ChemDoodle® Mobile is accessed with your ChemDoodle account that is provided to you for free when you purchase ChemDoodle desktop. You can use the Guest account to access this app without purchasing ChemDoodle, but you will not be able to save your chemistry drawings and some features may be restricted.

Medicinal Chemistry Toolkit

The Medicinal Chemistry Toolkit app is a suite of resources to support the day to day work of a medicinal chemist. Based on the experiences of medicinal chemistry experts, we developed otherwise difficult-to-access tools in a portable format for use in meetings, on the move and in the lab. The app is optimised for iPad and contains calculator functions designed to ease the process of calculating values of: Cheng-Prusoff; Dose to man; Gibbs free energy to binding constant; Maximum absorbable dose calculator; Potency shift due to plasma protein binding.

Elemental

Elemental from Dotmatics the FREE Chemistry Sketch Utility Elemental is now a Universal App that support iPad, iPhone and iPod Touch. Elemental is the Dotmatics chemistry sketch utility provided at no charge within many Dotmatics products. We are happy to provide this as a FREE app on the iTunes store.

WolframAlpha

Wolfram|Alpha. Building on 25 years of development led by Stephen Wolfram, Wolfram|Alpha has rapidly become the world's definitive source for instant expert knowledge and computation.

Papers 3 for iOS

Papers is your personal library of research. Find, read, organize, sync your research papers -- anytime, anywhere!

ElementalDB

Use ElementalDB to sketch and search within the 1.2M compound ChEMBL dataset. Searching, property calculation and depiction is done from the stored 2D co-ordinates from ChEMBL within the app on your device not via a web service

Developing iOS 7 Apps for iPhone and iPad

Download Free Content from Stanford on iTunes Updated for iOS 7. Tools and APIs required to build applications for the iPhone and iPad platform using the iOS SDK. User interface designs for mobile devices and unique user interactions using multi-touch technologies.

Findings - Lab Notebook

Findings is your lab notebook, reinvented. When running experiments, it is crucial to keep track of what one is doing, to be able to later reproduce the results, assemble and publish them. This is what lab notebooks are for. With Findings, your lab notebook is always with you and always up to date, be it on the field, at the bench, or at a conference. Findings for iOS is even more powerful when used in combination with Findings for Mac.

Open Drug Discovery Teams

Open Drug Discovery Teams (ODDT) provides a magazine-style interface to collated information on a range of topics, primarily regarding research into cures for rare and neglected diseases.

Approved Drugs App

The Approved Drugs app contains over a thousand chemical structures and names of small molecule drugs approved by the US Food & Drug Administration (FDA). Structures and names can be browsed in a list, searched by name, filtered by structural features, and ranked by similarity to a user-drawn structure.

 

ResearchKit is an open-source framework that allows researchers and developers to create powerful apps for medical research.

The Parkinson app is one of the first five apps built using ResearchKit.

mPower is a unique iPhone application that uses a mix of surveys and tasks that activate phone sensors to collect and track health and symptoms of Parkinson Disease (PD) progression - like dexterity, balance or gait. The goal of this app is to learn more about the variations of PD, and to improve the way we describe these variations and to learn how mobile devices and sensors can help us to measure PD and its progression to ultimately improve the quality of life for people with PD.

The initial results have now been published Scientific Data 3, Article number: 160011 (2016) ​DOI, with around 15,000 people contributed data to the study.

 

BALL (Biochemical ALgorithms Library) is an application framework implemented in C++ that has been specifically designed to reduce development times in the field of Computational Molecular Biology and Molecular Modeling. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.

BALLView is BALL’s standalone molecular modelling and visualization application. Furthermore, it is also a framework for developing molecular visualization functionality.

It can be downloaded from here and requires

• CMake >= 2.8.12
• git
• Python 2.7
• Qt 5.4

Installation instructions for Mac OSX are here

 

There is an interesting bundle offer running at the moment.

"A collection of seven fantastic Mac apps to help you be more productive. Focused around writing, editing, researching and organising, these apps are the perfect companion to all researchers and scientists. The best part? This selection of Mac apps normally cost $305, but during this promotion (which won't last for long), the whole bundle is just $49.99!”

The apps are:-

Papers $80 Your personal library of research designed for your Mac. Papers ​is a multiple a​ward winning​ application developed for researchers. It turns your messy heap of PDFs into your personal library. It helps you collect, curate and stay up to date with your field.

Manuscripts $40 A writing tool like nothing you have seen before. Manuscripts is a writing tool for complex documents unlike any you have seen: it helps you with a complex writing project from outline to editing, proof reading and publishing stages, all within a beautiful Mac app.

Records $30 Records is a delightful and easy to use personal database. The perfect companion for everything you want to collect and organize in life, from your favorite movies to your customer invoices, offering a great balance between easy of use and powerful features.

Soulver $11 Soulver helps you work things out. It's more than a spreadsheet, and smarter than a calculator. Soulver helps you do quick calculations and work things out. Use Soulver to play around with numbers, do "back of the envelope" calculations, and solve day-to-day problems.

DEVONagent Pro $50 Your smart Internet (re)search assistant. DEVONagent Pro helps you search more efficiently on the web. It searches multiple sources, frees you from hunting for the really relevant results, and gives you power tools for your research.

TextSoap $45 Automate tedious text document cleaning. Automatically remove unwanted characters, fix messed up carriage returns, and pretty much anything else you can think. Stop manually fixing text documents and emails. TextSoap can automate away that tediousness.

Findings $49 Your research notebook, reinvented.

All 7 applications for $49.99

 

A new version of PDB2PQR has been released.

APBS (Adaptive Poisson-Boltzmann Solver) and PDB2PQR are software packages designed to help you analyze the solvation properties of small and macro-molecules such as proteins, nucleic acids, and other complex systems

• Added alternate method to do visualization using 3dmol.
• Replaced the Monte Carlo method for generating titration curves with graph cut. See http://arxiv.org/abs/1507.07021 (If you prefer the Monte Carlo method, please use http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/)
• Added compile options to allow for arbitrary flags to be added. Helps work around some platforms where scons does not detect the needed settings correctly.
• Added a check before calculating pKa's for large interactions energies.

OSX binaries require OSX 10.6 or newer. The OSX binary is 64-bit.

Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007. DOI

Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res, 32, W665-W667, 2004. DOI

 

Opsin (Open Parser for Systematic IUPAC Nomenclature) has been updated. If you used Homebrew to install it you can get the latest version by simply typing

brew update
brew upgrade opsin

Opsin is a freely available, algorithm that interprets the majority of organic chemical nomenclature DOI. You can try it out using this website http://opsin.ch.cam.ac.uk.

 

The suite of software to support crystallography has been updated

CrystalDiffract brings the world of x-ray & neutron powder diffraction to your computer.

CrystalMaker is the easiest way to build, visualize and understand structures of crystals and molecules

CrystalViewer a free viewer offers high-quality graphics, plus distance and measurement tools, multi-touch control (Mac) and the ability to view crystal lattices along specific lattice vectors or plane normals. 3D Printing Support - save any displayed structure as an STL file, as supported by most 3D printers.

 

I just stumbled across this page recently

In which journals should I publish my software?

Looks like a very comprehensive listing of journals that accept submissions about software.

 

Stack Overflow is a community of nearly 5 million developers who ask and answer programming questions, if I ever have questions about programming or scripting it is the first site I look to for answers.

They also run an annual survey looking at current trends within the developer community, the results probably represent the most comprehensive survey of it's type. The results make interesting reading and I'd certainly suggest that you go an look at the results in details, but I've pulled out a couple of interesting points.

JavaScript is the most commonly used programming language, but that is probably because the web is now the most popular front-end to applications and services. If you look at the developers involved in Math and Data the profile is rather different with Python now the dominant language.

The most loved programming languages are Rust and Swift, and the most dreaded Visual Basic, interestingly none of which appear in the most used technologies.

Among the desktop operating systems MacOSX is increasingly popular rising from 18% in 2013, largely at the expense of Windows.

 

ReadCube, best known for their innovative software serving researchers, publishers, academic and commercial organizations, today acquired Papers from global academic publisher Springer Nature.

Papers is a very popular multi-platform reference management tool.

There is a listing of reference management tools here.

 

SeeSAR Version 4.2 just came out! The main new features are

• You now control when the compute-intense Hyde-calculation runs, this means large sets of molecules can now be loaded, analyzed and processed (e.g. filtering, calculating properties) before the intensive affinity calculations are run.
• Much improved version of grouping all poses of the same molecule

Version 4.2 comes with a load of minor improvements, particularly for the command line use. The full release notes are here.

I've been following this software since it was first released and there is a review here, every update brings useful features. It is well worth downloading the free 1 week trial to have a look at.

 

The ADF modelling suite has been a popular modelling package used in many areas of chemistry and materials science. SCM have recently announced an important update to ADF

Software for Chemistry & Materials (SCM) is an Amsterdam-based computational chemistry software company. Originally spinning out from the Vrije Universiteit as Scientific Computing & Modelling NV in 1995, the SCM team supports and develops the ADF Modeling Suite, centered around the flagship program Amsterdam Density Functional (ADF), which was originally developed in the 1970s in the theoretical chemistry department.

Key new features::

• New XC functionals: range-separated hybrid HSE06, long-range corrected hybrids and new meta-GGAs
• SM12 solvation model and Constrained DFT in ADF
• Spectroscopy: excitations from CV(n)-DFT, fast TDDFT+TB and sTDDFT, X-ray emission, surface-enhanced ROA, new kernel for periodic TDDFT, vibrationally resolved spectra from TDDFTB, hole states in BAND
• Improved robustness for SCC-DFTB, COSMO, periodic optimizations, new HF exchange scheme
• Analysis: unrestricted and periodic energy decomposition (pEDA), Fukui functions, Natural Transition Orbitals
• Reactivity, PES: Automated reaction pathways for ReaxFF trajectories, new Transition State search options, MECP, analytic lattice gradients
• GUI: job chaining, multiple spectra, orbital interaction visualization
• Scripting: ASE interface for all codes, scripting support for COSMO-RS, job chaining, extensions to FlexMD multi-scale dynamics
• Parameters, databases: Quasinano15 including repulsive potentials for light elements, latest 3OB parameters, new parameter sets for ReaxFF, ionic liquids database COSMO-RS

Full release notes are here

 

I've just finished updating the Mobile Science site there are now over 400 entries covering all areas of science. The latest entry is Notelus an electronic lab notebook (ELN). ELNs seem to be increasingly popular, and having access to your notebook on a mobile device that you can carry into the lab/library etc. is very attractive.

There are a selection of ELNs for iOS, some also have desktop versions, whilst there are other systems that are web-based and can be accessed from most devices.

 

Occasionally developers contact to ask about platforms/operating systems/versions/web browsers that are used by readers.

Recently I was asked about web browsers and so I contacted a number of scientific databases, scientific app developers, web sites. They were kind enough to provide information but asked that the details were not made public. The 12 sites range from 10's of thousands of hits per month to many millions hits of hits per month. The data shown below is from Jan 1st this year. It appears that Internet Explorer has almost disappeared as a mainstream browser.

Some people reported that they felt the drop in IE use was due to poor javascript performance.

Update

I've just been sent this image which also serves to underline the dramatic fall in the use of Internet Explorer (at least among chemists).

Optibrium have announced the latest update to the StarDrop application. The highlight for version 6.3 is perhaps the integration of SeeSAR an intuitive structure-based design tool.

The new SeeSAR module for StarDrop provides a state-of-the-art and scientifically rigorous approach to understanding the binding of compounds in their protein targets in 3D. Users can import ligand and protein structures, derived from crystal structures or predicted with any docking software, and visualise the key interactions driving potency. This is seamlessly linked to StarDrop’s chemoinformatics methods based on 2-dimensional (2D) compound structure and its unique Card View approach to interpreting the resulting structure-activity relationships.

A preview of StarDrop 6.3 will be on show at the American Chemical Society National Meeting, 13th-17th March 2016.

There are reviews of SeeSAR and StarDrop in the reviews section.

 

The applications for the Open Science Prize are now in, 92 proposals, all look brilliant. They include apps for mobile devices, machine learning from public datasets, linking science and scientists, tracking disease and much, much more. Well worth popping over and having a look.

 

With the release of ChEMBL21 we also get updates to the web services.

ChEMBL 21 introduced a few new tables, which are now available via the API. Keyword searching has been improved.

Compound images have transparent background by default

The official Python client library has been updated as well in order to reflect recent changes. This can be installed using PIP

pip install -U chembl_webresource_client

 

A reader flagged this issue for me.

Word 2016 for Mac: I can't cut-and-paste an image from a vector drawing program I am a scientist and I routinely create images in a vector drawing program called ChemBioDraw. In past versions of Word, I was always able to copy these images to the clipboard and paste directly into the text of a document. With Word 2016 for Mac, all I get is many lines of gibberish code and no image. Am I missing something, or has the ability to handle vector graphics been eliminated from the program? FYI- a friend of mine who does design is having the same problem with a CAD program.

A quick search of the ChemBioDraw support forum highlights several threads that appear to be about the same issue.

I'm a new user of ChemDraw, and I have tried to copy/paste my structure into word and just end up with heaps of text like this:

0 0 0 0 0 0 0 0 0 0 0E 3.9121 2.7155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0E 3.9385 1.8909 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1 2 4 0  1 3 4 0  3 4 4 0  4 5 4 0  6 7 1 0  7 8 2 0  8 9 1 0  9 10 2 0  10 11 1 0  6 11 2 0  12 13 1 0  13 14 2 0  14 15 1 0  15 16 2 0  16 17 1 0  12 17 2 0  2 18 1 0  18 5 1 1  19 20 4 0  19

With the rather unhelpful response

Currently our products are not supported with MS Office 2016. We plan to support MS Office 2016 for the future release/update.

The only thing I can suggest in the meantime is use the "Paste as PDF" functionality, this should allow display and round-trip editing.

I did a quick test with ChemDoodle and there don't seem to be any issues with this chemical drawing programme.

 

I've been making increasing use of iPython notebooks, both as a way to perform calculations but also as a way of cataloging the work that I've been doing. One thing I seem to be doing quite regularly is calculating physicochemical properties for libraries of compounds and then creating a trellis of plots to show each of the calculated properties. In the past I've done this with a series of applescripts using several applications. This seemed an ideal task to try out using an iPython notebook.

Read more ….

 

If you want to stay on top of the proposed changes to the Swift programming language then this repository is worth a browse https://github.com/apple/swift-evolution

This repository tracks the ongoing evolution of Swift. It contains:

Goals for upcoming Swift releases (this document). The Swift evolution review schedule tracking proposals to change Swift. The Swift evolution process that governs the evolution of Swift. Commonly Rejected Changes, proposals which have been denied in the past. This document describes goals for the Swift language on a per-release basis, usually listing minor releases adding to the currently shipping version and one major release out. Each release will have many smaller features or changes independent of these larger goals, and not all goals are reached for each release.

 

The release of ChEMBL_21 has been announced. This version of the database was prepared on 1st February 2016 and contains:

• 1,929,473 compound records
• 1,592,191 compounds (of which 1,583,897 have mol files)
• 13,968,617 activities
• 1,212,831 assays
• 11,019 targets
• 62,502 source documents

Data can be downloaded from the ChEMBL ftpsite or viewed via the ChEMBL interface. 

Please see ChEMBL_21 release notes for full details of all changes in this release.

 

I was just sent details of this

Interested in doing some chemistry programming this summer? Have students that might be interested?

Open Chemistry has been accepted into the Google Summer of Code for 2016 - including Open Babel, Avogadro, cclib and 3DMol.js.

If you are a student and interested in doing open chemistry software development this summer (or know of someone who is), we're definitely up for good proposal ideas. Take a look at our suggestions or come up with one on your own:

https://summerofcode.withgoogle.com/organizations/6290185763422208/ http://wiki.openchemistry.org/GSoCIdeas2016

Student proposals can be submitted between March 14th and March 25th. Instructions are at the Summer of Code website.

 

Data analysis tools are becoming ever more important as the volume of data increases and I thought I'd flag a new resource Feature viewer

A new visual approach by UniProt, the universal protein resource, presents protein sequence features in one compact view using a highly interactive BioJS component. This is the first visualisation feature in a public resource that lets users see different types of protein sequence features such as domains, sites, PTMs and natural variants from multiple sources in a single view.

 

iSpartan has been updated.

What's New in Version 1.4.6 Improved stability for iOS9 for Spartan'14 Parallel Suite (Serve)r users Enhanced charge labels in Sketch mode Increased electrostatic potential surfaces integrity

iSpartan is a versatile app for molecular modeling on the iPad, iPhone, and iPod Touch. The app allows any chemist fast and easy access to computational methods that have proven reliable for a large range of molecules.

 

OpenEye have announced the release of OpenEye Toolkits v2016.Feb. These libraries include the usual support for C++, Python, C# and Java.

The update address several key features.

Security

OpenEye toolkits are used in web services that require protection from malicious users. The most obvious attack vector against the OpenEye toolkits is file format parsing since scientific file formats are complex and often underdefined and there is the potential for embedded malicious code. This update closes a number of potential vulnerabilities.

FastROCS TK: Database Loading Performance

An interesting development is that physical memory limits on GPU's mean that for loading larger libraries the loading of the dataset actually takes longer than the actual search. This release addresses that issue.

OEMedChem TK

This also contains first official release of OEMedChem TK, in particular access to matched molecular pairs.

This 2016.Feb release no longer support OSX 10.8 , but support has been added for OSX 10.11. This 2016.Feb release supports Python 3.5 for the following platforms: OSX 10.10, OSX 10.11, Ubuntu 12, Ubuntu 14, RedHat 6, and RedHat 7

Full release notes are here ….

 

I thought I'd have a look at the number of downloads of iBabel there have been since I announced the latest release last month. So far there have been over 250 downloads and there seems to be a steady stream of downloads as shown in the plot below.

iBabel is a GUI (graphical user interface) for the open source cheminformatics toolkit OpenBabel. It also provides an interface to a variety of tools built using OpenBabel and a selection of molecule viewers

 

For those interested in learning more about Swift there are a couple of blogs that are worth keeping an eye on. Swift is a modern open-source programming language for iOS, OS X, tvOS, watchOS and Linux.

There is the official Swift blog from Apple which has updates and code snippets, however more recently there has been a lot of activity of the Swift@ IBM blog.

In particular Bring Swift to the Cloud and the IBM Swift Sandbox that allows you to write Swift code in a browser and then execute it. You can try it out here https://swiftlang.ng.bluemix.net/#/repl.

Introduced in 2014, Swift is one of the fastest growing and most widely used programming languages. In just over two months since Apple open sourced the Swift language and IBM released its Swift Sandbox for early exploration of server-side programming in Swift, more than 100,000 developers from around the world have used the IBM Swift Sandbox and more than half a million code runs have been executed in the Sandbox to date

Press release

 

Calculating solvent accessible surface area is an important calculation in the study of protein structure and whilst there are many tools to undertake this sort of calculation FreeSASA represents the first open-source free standing tool for this sort of calculation. FreeSASA is an open source C library for SASA calculations that provides both command-line and Python interfaces.

Source code is available for download here and building the FreeSASA library and command-line interface only requires standard C and GNU libraries and a C99-compliant compiler, and should be straightforward on any UNIX system (has been tested in Mac OS X 10.8 and Debian 8).

Mitternacht S. FreeSASA: An open source C library for solvent accessible surface area calculations [version 1; referees: awaiting peer review]. F1000Research 2016, 5:189 DOI

 

When Apple introduced iOS8 one of the features that perhaps didn't grab the headlines was that it allowed you to install third-party keyboard apps from other developers. Whilst the early examples seemed to do little more than change keyboard colour more recent ones have introduced novel features and discipline specific keys. There are three keyboards in the mobile science database.

Chemistry Keyboard The Chemistry Keyboard is a specialized Keyboard Extension for anyone who needs to enter chemical formulae. Allows you to add those nice superscript or subscript 2s. Or a proper arrow glyph, or a triple bond?

The Math Keyboard The Math Keyboard is the ideal keyboard for typing Math and Scientific characters.

SciKey - Scientific Keyboard SciKey is a Scientific Keyboard that brings you the essential scientific characters for your iPad, iPhone, and iPod touch. Now fully customizable, with more than 3,000 characters to choose from, to build your perfect keyboard (requires in-app purchase). It includes Greek and Latin letters, mathematical symbols, emoji and much more missing from the standard iOS keyboard. It also works for text snippets

 

SeeSAR has been updated. SeeSAR is a software tool for interactive, visual compound design and prioritization. There is a review of an earlier version here

Release Notes

User-defined visualization settings

Up until now, the 3D view settings were optimized for the current scenario, i.e. when you loaded a protein from file or project it was shown in overview, while after selecting a molecule, the view was focused in more detail on the binding site, ... This was quite comfortable - particularly for first-time users - but at the same time limited your freedom to choose your own viewing preferences. As of version 4.1, the user is back in charge. The optimized settings are still shown to start with but now you can choose to show or hide the following:

• logP
• Hyde coloring for the selected molecule
• torsion coloring for the selected molecule
• whole protein
• surface for the binding site of the selected molecule
• unoccupied space in the binding site of the selected molecule
• all waters in the binding site of the selected molecule

The controls can be found in a panel above the 3D view on the main tool bar. There were previously some switches scattered about in different places in SeeSAR to control some of the these view settings - these have now disappeared having been replaced by the cleaner, less cluttered interface in the new panel.

Annotating molecules

Many users have requested the option to add comments to specific molecules. We have now implemented this as a new feature that can be accessed via the notepad icon for the currently selected molecule in the table. A sticky note is opened where you can enter your comments for this molecule as free-form text. The annotations are saved along with the user name of the author. Molecules with annotations are indicated in the table by a yellow marker at the top left of the row in the molecule table. If you move the mouse over the marker, the annotation appears as a tool tip making it easy to quickly scan through all the notes in the table. These notes are saved to the project allowing you to keep your ideas and thoughts for later, or also to share them with others.

Enhanced project handling

As of version 4.1, SeeSAR will now remind you to save your project if you have unsaved changes before you close SeeSAR or start a new project (either by choosing "New" or "Load" from the Project menu). You now also have the option to "Export" the raw data from your current project to a folder or directory of your choice. This will include the PDB file for the protein, all loaded molecules and any molecules you created using the editor.

 

New in version 1.3 of Findings

• Support for iPad.
• Support for landscape orientation on all iOS devices, & improved layout for all screen sizes.
• Support for iOS 9 multitasking enhancements for iPad (Split Screen and Slide Over).
• Export Findings archive via the Share button.
• Import of Findings archive from other applications (Mail, iCloud Drive, Dropbox, etc.). Like on Mac, you can select which document to add or merge.
• Significant improvements to the protocol browser (p<0.001): relevant science fields and separation of your protocols, protocols from others and Findings example.
• Create a new experiment directly from a protocol
• Support for 3D Touch on application icon, with shortcut items to show your experiments, the protocol browser, or a new experiment.

We also improved a lot of things in version 1.3:

• Clearer requests to enable notifications (for timers).
• Nicer-looking superscript & subscript.
• Easier selection of subfield in protocol metadata editor.
• Message to the user when an attachment does not support Quicklook & cannot be previewed on iOS.
• More options for troubleshooting sync under the 'Advanced' section in the settings, including manual sync trigger, Dropbox cache reset, Dropbox file removal, and sync diagnostic logs.
• Completed experiments are automatically marked as ongoing when adding new content for current or future days.
• Example protocols that come with the app are now read-only.
• Tweaks to the app icons, in particular adding missing assets for 3x resolution on iPhone 6S+.
• Allows navigation back to last day of an experiment after moving to today, by having the 'Today' button become 'Last Edit'.
• Creating a new experiment uses a clearer 'Create' button instead of the potentially confusing 'Save'.
• Experiment and protocol deletion now possible in the metadata editor ('i' button).
• Protocol creation possible from any screen of the protocol browser (previously, it was only possible from within a subfield).
• Sharing via AirDrop.
• Full-fledge protocol browser to select a protocol to add to an experiment.
• Watch: start countdown timer immediately when adding via the Watch app.
• Watch: dismissing iPhone alert when timer is stopped on Watch app.
• Watch: clearer accessibility labels on Watch app.

We also fixed a lot of small annoyances and bugs:

• Hiding the irrelevant calendar icon when editing protocols.
• Table display bugs and truncation in document view.
• List numbering wrongly interrupted by table.
• Update completed state of paragraphs after reordering.
• Actually query start date when duplicating an experiment.
• Correctly displaying experiments pending completion under the 'Ongoing' tab when selecting an experiment to duplicate.
• Missing information in diagnostic section of pre-filled feedback emails.
• Using the correct tint color in the various protocol-related views.
• Insertion of picture below selected paragraph when using the paragraph toolbar.
• Keyboard hiding modal menu for changing note type.
• Extraneous space in support button.
• Removing unused options wrongly displayed for Findings in the Settings app.
• Icon missing or incorrect icon when using swipe-to-right to toggle the completion state of a paragraph in the experiment editor.
• Displaying multi-line text in the metadata editor screen.
• For a paragraph added on Mac, a timer could only be added after "deleting" a (non-existing) timer.
• Attachments not duplicated when duplicating an experiment.
• Correctly displaying styled text (bold, italics, etc.) in bullet-list paragraphs.
• Watch: unreliable notification when starting timer from Watch app.
• Watch: glance update after updating experiment progress or timer in the Watch app.

 

UniChem is a web resource provided by the EBI, it is a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between multiple databases. Currently the UniChem contains data from 27 different data sources. Currently UniChem provides links to 108,941,995 structures.

Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S. and Overington, J.P. UniChem: A Unified Chemical Structure Cross-Referencing and Identifier Tracking System. Journal of Cheminformatics 2013, 5:3 (January 2013). DOI: http://dx.doi.org/10.1186/1758-2946-5-3

The previous script showed how to search using ChEMBLID, however one of the attractions of UniChem is that you can search with any molecule identifier if you know the corresponding datasource. This script allows the user to use any molecule identifiers and then search a specified datasource using a common web service.

Read more …

 

UniChem is a web resource provided by the EBI, it is a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between multiple databases. Currently the UniChem contains data from 27 different data sources. Currently UniChem provides links to 108,941,995 structures.

Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S. and Overington, J.P. UniChem: A Unified Chemical Structure Cross-Referencing and Identifier Tracking System. Journal of Cheminformatics 2013, 5:3 (January 2013). DOI: http://dx.doi.org/10.1186/1758-2946-5-3

ChEMBL also provide a RESTful Web service that users can use to retrieve data from the UniChem database in a programmatic fashion.

Read more…

 

PolyPharma has been updated, it uses structure activity relationships to view predicted activities against biological targets, physical properties, and off-targets to avoid. Calculations are done using Bayesian models and other kinds of calculations that are performed on the device. There is more detailed information here. The latest update includes toxicity models from EPA Tox21 dataset measurements.

There are many more iOS apps for science on the mobile science site.

 

I've just been sent a link to an advanced charting kit for mobile devices Shinobicontrols if you are developing an iOS app that requires plots or charts this may be a useful addition.

If you are looking for a graphing toolkit for both iOS and MacOS then it might be worth looking at the tools from VVI

 

If you want to convert your Objective_Code to Swift this could be very useful ObjCConverter.

There is also an online converter if you want to try before you buy

The latest post on the Swift blog highlights interactive playgrounds.

Xcode 7.3 beta 3 adds interactive iOS and OS X playgrounds that allow you to click, drag, type, and otherwise interact with the user interfaces you code into your playground. These interfaces react just as they would within a full application. Interactive playgrounds help you to quickly prototype and build your applications, and simply provide another great way to interact with your code.

 

Added NCIPLOT to the alphabetical listing of applications. NCI (Non-Covalent Interactions) is a visualization index based on the density and its derivatives. It enables identification of non-covalent interactions. NCIPLOT is available for download.

Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.

Erin R. Johnson, Shahar Keinan, Paula Mori-Sanchez, Julia Contreras-Garcia, Aron J. Cohen, and Weitao Yang, J. Am. Chem. Soc. 2010, 132, pp 6498-6506.
J. Contreras-Garcia, E. R. Johnson, S. Keinan, R. Chaudret, J-P. Piquemal, D. N. Beratan, and W. Yang. J. Chem. Theory Comput. 2011, 7, pp 625-632.

 

OpenEye have announced the release of OEDocking v3.2. This is an upgrade that adds new features and fixes several bugs.

NEW FEATURES

• POSIT is now integrated with the OEDocking suite. A POSIT license is still required to run POSIT.
• POSIT‘s clash detection algorithm has been enhanced. It now ignores clashes with the protein on a per atom basis if the crystallographic ligand makes these same clashes.
• OpenMPI version 1.6 is now supported on all platforms. The -mpinp and -mpihostfile flags are now used to run FRED, HYBRID and POSIT in MPI mode. These new flags replace the oempirun script.
• PDB2RECEPTOR now incorporates all of MAKEPOSERECEPTOR functionality. MAKEPOSERECEPTOR is no longer supported.
• PDB2RECEPTOR now supports the identification and selection of a desired ligand in a protein-ligand complex.

• MAKERECEPTOR, PDB2RECEPTOR, APOPDB2RECEPTOR, DOCKINGREPORT, RECEPTORSETUP and RECEPTORTOOLBOX now all accept either a POSIT or FRED2 license.

• Support for Mac OS X 10.9 and 10.10 was added.

• Mac OS X 10.6 and 10.7 are no longer supported.

 

I recently needed to download the supplementary information provided with a publication, my heart sank when I saw it was provided as a PDF file. My worst fears were justified when I tried to simply copy and paste SMILES strings together with 5 columns of data into a spreadsheet, no chance of it copying across in an ordered manner!

Then I tried Tabula a tool for "liberating data tables locked inside PDF files". It worked perfectly, nearly 2000 rows of data spread over 11 pages converted to a csv file in a couple of mouse clicks. This is wonderful and should be part of any data scientists toolkit.

It is included on the Data Analysis Tools page but really deserves a special mention.

 

I've just added Unicon and Mona to the alphabetical listing of applications.

UNICON is a command-line tool to cope with common cheminformatics tasks. The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, and PDB via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states and conformer ensemble.

Mona is an interactive tool that can be used to prepare and visualize large small-molecule datasets. A set centric workflow allows to intuitively handle hundred thousands of molecules.

 

WebMO version 16

WebMO version 16 has been officially released and is available for FREE download at http://www.webmo.net/download

New features in WebMO version 16 include:

• Support for both iOS and Android WebMO free apps
• Support for the newest versions of ORCA, PSI, and Q-Chem
• Support for hydrogen bonds in the WebMO editor
• Improved support for building/cleanup of fused aromatic rings
• Incorporation of modern HTML5 user interface elements including: drag-and-drop of jobs between folders, fewer pop-up windows, live updating of output files while jobs run, and expandable results page
• Support for unlimited number of user folders and sub-folders (Pro)
• Enhanced support for resource specification with external batch queues (Enterprise)
• Various bug fixes

Important changes in the previous version include:

• Java security warnings are reduced/eliminated with new signed applet
• Support for the newest versions of GAMESS, MOPAC
• Lookup feature to build structures by name (type "aspirin" or "vancomycin")
• Links to external databases to lookup molecular properties, spectra, and data
• Huckel molecular orbital calculations from within Build Molecule page (Pro)

WebMO is the most popular interface to computational chemistry programs, with over 22,000 unique WebMO licenses issued to date!

WEBMO iOS AND ANDROID APPS

WebMO has released a new Android app and updated its popular Apple iOS app!

The WebMO apps for portable devices are FREE.  

The Android and iOS WebMO apps provide equivalent features including:

• Standalone molecular editing, optimization, symmetry, and orbital calculations
• Integrated web lookup of molecular properties, spectra, and data
• Access to WebMO servers (Free, Pro, and Enterprise versions of WebMO 16 and higher)

The WebMO apps supports all chemistry courses by calculating and displaying:

• VSEPR structures for General Chemistry
• 3-D structures to replace model kits for Organic Chemistry
• Data and properties for Analytical Chemistry
• Point group and symmetry elements for Inorganic Chemistry
• Small proteins and bimolecules for Biochemistry
• Molecular orbitals and vibrations for Physical Chemistry
• WebMO calculations for undergraduate and graduate level Research

Thousands of students and scientists use the WebMO apps on their smartphones and tablets each month.  You can join them today for free!

WEBMO SUPPORTS CLOUD COMPUTING

More computational services are moving away from local hardware and into the "cloud".  Cloud computing requires zero upfront capital outlay, eliminates hardware maintenance, and can dramatically lower the cost of computing.

WebMO now supports installation on cloud computing platforms.  In less than 10 minutes, you can use your web browser to create a virtual machine, run the WebMO SITC ("Server in the Cloud") script, and have a functioning WebMO 16 server.

The cost of a WebMO cloud server can be amazingly low: <$1 per day for a WebMO server capable of running jobs on standard ab initio chemistry engines, and just $0.12 per day for a WebMO server running MOPAC!  And when you don't need it, you just turn it off.

Complete documentation is available at http://www.webmo.net/cloud/sitc.html

Since Google Compute Engines are free for the first 60 days, so there is no cost or risk to try cloud computing today.

 

BBEdit 11.5 has been released.

BBEdit 11.5 adds a variety of new features, and includes changes to existing features and behaviors as well as fixes for reported issues.

Of particular note are

BBEdit now supports the use of iCloud Drive for sharing application support and setup items. This works similarly to the existing Dropbox support: in your "iCloud Drive" folder, create a folder named "Application Support", and then within that create a folder named "BBEdit". You can populate that folder with the contents of your /Users/USERNAME/Library/Application Support/BBEdit/ folder.

BBEdit now supports the use of iCloud Drive for a shared backup folder: in your "iCloud Drive" folder, create a folder named "BBEdit Backups", and if you have turned on Use Historical Backups, BBEdit will use this folder.

 

The iOS app PolyPharma has been updated. PolyPharma uses structure activity relationships to view predicted activities against biological targets, physical properties, and off-targets to avoid. Calculations are done using Bayesian models and other kinds of calculations that are performed on the device.

More details are available in this presentation.

 

The RSC's Undergraduate Research Bursaries are now open for 2016 entries, seeking talented chemical sciences students to undertake a research placement this summer.

These research bursaries are to fund short (6-8 weeks) summer research projects for undergraduate chemistry students in the middle years of their course. The purpose of the awards is to give experience of research to undergraduates with research potential and to encourage them to consider a career in scientific research.

The bursary is worth £200 per week (£210 in London) for up to 8 weeks to cover a defined research placement.

The deadline for applications is 21 February 2016.

Please note that, for the first time, in 2016 CICAG will be funding one student bursary for research work which falls into one or more of the following areas: cheminformatics, chemical information, chemical data management, chemistry data analytics, applications of computational chemistry.

For more information about guidelines, eligibility criteria, award conditions, and the application form please see the Undergraduate Research Bursaries web page http://www.rsc.org/Education/HEstudents/undergraduate-bursary.asp

Any questions should be directed to the Under Graduate Bursaries team (see link on the Undergraduate Research Bursaries web page linked to above).

Here is an interview with Matias Piipari CEO and Co-founder of Manuscriptsapp. Manuscriptsapp is a new tool for writing scientific publications it is a writing tool for scientists designed and built by scientists.

There is more information on Manuscripts on the website.

You can start writing using a manuscript template.
We supply at the time of writing 1,100 of them and are building literally thousands of them for varied uses like journals across all sciences, university specific PhD theses, grant applications).
You can outline and plan your writing project using a powerful manuscript outline that updates live as you write.
The outline helps you navigate a complex document.
It allows you to focus on a particular subsection of it when needed.
Editing has been tuned to needs of scholarly writing: clean, simple and built for purpose.
We want you to focus on your story and not twiddling how the document looks. You will not find half a dozen ribbons of nonsense like in MS Word from Manuscripts.
Top of the range citing workflow and automated bibliography formatting, either using Citations from Papers, or a built-in citation tool for which you can import references from pretty much any common format: EndNote XML, RIS, BibTeX, Citeproc JSON, MODS, and several more.
Manuscripts is not a reference manager itself, but it works with a reference manager better than other word processors or text editors.
The interface to reference management tools is built in a generic way using AppleScript, so other reference managers in addition to Papers can add support too.
On exporting a document, references are formatted for Word and exported to LaTeX.
Cross-referencable multi-panel figures, tables and equations.
Manuscripts exports figures based on the needed format, and keeps original files intact.
We export mathematical equations to both LaTeX and Word.
Import and export the key formats used for scholarly writing: MS Word, LaTeX, Markdown.
We have spent lot of effort into getting our Word export into a good shape. All content is exported, including figures, tables, equations, citations and cross-references.
Manuscripts works with Markdown and LaTeX too — it's something more powerful than a markup text editor though: you can drag in or paste markup in either these formats to produce beautiful rich text, and then export it back out as Markdown or LaTeX (or indeed HTML).
You can also drag out or or otherwise export into these markup formats as well as Word (docx) and more.
The manuscript file format is versioned.
You can revert back to older versions as needed.
We are working on the ability to merge and synchronise different versions of the document.
For those writing peer reviewed literature, we are going to allow you to directly submit your work to thousands of different journals.

 

Checkmol is a command-line utility program which reads molecular structure files in different formats and analyzes the input molecule for the presence of various functional groups and structural elements. At present, approx. 200 different functional groups are recognized. Output can be either clear text (English or German), a bitstring or its ASCII representation, or a set of special 8-character codes. This output can be easily placed into a database table, permitting the creation of chemical databases with a functional group search option. It was written by Norbert Haider, Department of Pharmaceutical Chemistry (now: Department of Drug and Natural Product Synthesis), University of Vienna, Austria.

The software is available both as source code and as a binary compiled for Linux (x86 architecture). It is entirely written in Pascal and it was compiled with Free Pascal 1.0.11 or Free Pascal 2.4.0 (starting from v0.4c). So to install we first need to get a Pascal compiler, this can be downloaded from Sourceforge.

Full details are here.

 

ChemDoodle 3D has been updated and in addition for a limited period any customer that upgrades to or purchases ChemDoodle 8 will receive a free license for ChemDoodle 3D v2.

New features in ChemDoodle 3D v2:

• Full Retina display support on Mac OS X.
• Support for high DPI Windows hardware.
• The visual specifications of the scene can now be applied to selected content, or individual objects, as opposed to the entire scene. Right-click on objects and select the Format… menu item to show visual options for that object. New representation quick buttons are now available for modifying residue atoms and bonds, ribbon models and nucleic acid models in addition to non-residue atoms and bonds.
• Protein and nucleic acid information can now be loaded from PDB files. Ribbon, trace and tube models can be generated for proteins. Ladder models can be generated for nucleic acids. The models are fully customizable. Control dimensions, alpha helix widths, coloring and more. Both B-spline and Catmull-Rom splines can be used to generate models. Water can be displayed as stars. Residue atoms can be controlled separately from hetatoms. Load PDB files by PDB id.
• Periodic data can now be loaded from CIF files. Unit cells of any geometry are resolved. Functions for periodic systems will be provided in the Periodic menu. Build supercells.
• An advanced selection system has been implemented. Select, deselect and reselect content. Select all, next molecule, inverse and by SMARTS. Use the new selection mode to select content or use the selection window to list the contents of the scene and select the content you wish to work with. The selection window is very advanced and will show you what you are currently hovering.
• Fogging can now be defined in scenes using linear, exp1 or exp2 algorithms. Fog color can be defined as well as fog ranges.
• A compass can be added on the bottom left of the scene or through the camera’s origin.
• 3D scenes can now be printed.
• Added quick quality options in the View menu to quickly switch between a range of higher and lower quality rendering settings to allow you to improve graphics or performance.
• Image export now allows for transparent backgrounds in capable image types. This allows you to easily use ChemDoodle 3D generated graphics in various media with custom backgrounds.
• Many new smaller features: added an option to remove shadows from text, added projection menu items, certified the correct 3D stereochemistry is generated from 2D drawings, picking can now handle any number of objects, and more.
• Updated to support ChemDoodle Web Components v7. Shapes can now be read/written using ChemDoodle JSON.
• Your iChemLabs account can now be accessed from ChemDoodle 3D. ChemDoodle 3D customers receive a free account for accessing ChemDoodle Mobile. If you also have ChemDoodle desktop, this is the same account.
• Dozens more improvements and additions.

 

The increasingly popular chemical drawing package ChemDoodle has been updated, this is a major update to an already excellent application. There also looks to be offers at the moment so this is a great time to purchase.

What is new in ChemDoodle 8

• The graphics system has been improved even beyond current industry standards for graphics. Every bond merge and pixel was scrutinized. Chemical structures have never looked better. ChemDoodle provides the best graphics in chemistry, everything else is a waste of money.
• Major IUPAC naming improvements, including very advanced ring systems.
• Full support for Retina display Macs and support for high-DPI Windows hardware.
• A new query structure system for defining sets of molecules and for searching partner services.
• New powerful tools for drawing arbitrary rings and crown ethers to atoms and bonds.
• Superscript and subscript merging to easily create atomic notations and other chemical text.
• More specific cleaning tool for adjusting only a selection of a structure.
• Text output options and improvements for EPS and SVG files in addition to PDF.
• A dramatically improved Templates widget with new and more aesthetic templates.
• Read in NTUPLES (multiple spectra) from JCAMP files.
• Added support for both the SketchEl (el) and Crystallographic Information Format (cif) filetypes.
• More support for working with the ChemDoodle Web Components.
• Dozens of new BioArt graphics.
• Performance improvements for faster work.
• Dozens more new features: two new bond types, implicit hydrogen control, automatic IUPAC locant labelling, vastly improved condensed labels, search files based on query structures, recursive SMARTS, metric support for document aids and rulers, a new precise form for scaling a specific bond, many interface improvements and so much more.

 

The popular electronic notebook Findings has been updated.

Release notes are here

 

Sampling conformational space is a key requirement for several areas of ligand design in small molecule drug discovery. A recent paper BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library DOI describes a new conformational search method.

The project homepage provides a download, supports Mac OSX 10.4 or higher.

 

A couple of readers have asked if they need to install OpenBabel in order to use iBabel. The answer is YES, iBabel is a graphical user interface that means you don't have to remember all the command line instructions in order to use OpenBabel.

More details here…

 

The current version is CCP4 7.0 (07 January 2016). The new packages include:
SHELX suite: co distribution for academic users
CCP4I2: new ccp4 interface
DIALS: data processing and integration
ARCIMBOLDO-LITE: molecular replacement pipeline
The updated packages include PHASER, XIA2, REFMAC, MONOMER LIBRARY, AMPLE, COOT, AIMLESS POINTLESS, CTRUNCATE, DIMPLE, BLEND and many more

CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques.

The latest version supports Mac OSX and Linux and requires X11. Source code is also available.

 

If you are renewing your Royal Society of Chemistry subscription remember your membership covers up to three interest groups. If you are interested in cheminformatics you might be interested in the Chemical Informations and Computer Applications group.

I'm on the committee and we have a couple of interesting meeting in the planning stage.

 

XQuartz 2.7.9_rc1 is available for download. This update contains a workaround for an issue that users have been reporting on El Capitan. If you're on El Capitan and have been seeing OpenGL surfaces remain onscreen after they should have been dismissed, please give this update a try and report back to the developers.

http://www.xquartz.org/releases/XQuartz-2.7.9_rc1.html

 

iBabel started out as an AppleScript Studio application designed as a front-end to OpenBabel DOI, this was updated several times and is now an ApplescriptObjC application built with Xcode. As well as acting as a front-end to OpenBabel it also provided a front-end to tools built on OpenBabel and a molecule viewer using a selection of java applets and plugins via an embedded web view.

This all worked perfectly for a while but various security issues mean that java applets and plugins via an embedded web view no longer function, in addition calls to remote web servers to provide javascript viewers also cause security issues. In addition OpenBabel has been substantially rewritten so that many of the small programs built on OpenBabel are no longer supported. This functionality has not been lost however, they have now been incorporated into the main OpenBabel program. Security updates, Sandboxing and changes within El Capitan also meant I had to update a number of features.

Now things have settled down a bit I've restarted work on iBabel and an update is now available.

I've transitioned most of the calls to babel over to obabel the differences are highlighted here and replaced the calls to the tools based built on OpenBabel with the new corresponding calls to obabel.

Updating the viewers however has taken more time than I expected with new security features in Mac OSX updates causing unexpected issues. Whilst not yet complete, I have removed all the java or plugin-based molecular viewers and replaced them with javascript versions.

Full details are here.

 

Happy New Year everyone!

As in previous years I take the opportunity at the end of the year to review the website.

Overall there were just under 200,000 page views with about 70% of the visitors being new to the site. The visitors came from 189 countries with US, UK and Germany topping the list. On average the visitors spent 1 min 30 secs browsing the site.

85% of the visitors use a desktop/laptop (Mac 61%, Windows 20%, Linux 4%), of the mobile users iOS predominates (iOS 9%, Android 2%, Nokia 1%).

The most viewed blog pages were

• Scientific Applications under Yosemite
• Installing Molden
• Scientific Applications under El Capitan
• 3D stereo viewing on a Mac
• Tools for Mac Fortran Programmers

The most popular web pages were (other than the main page)

• Clipboard Managers
• Data Analysis Tools
• Fortran on a Mac
• Mobile Science
• Spectroscopy
• Chemoinformatics on a Mac
• Reference Management