Macs in Chemistry

Insanely Great Science

Status of Lisa 7/7 source release


I just came across this post on the Lisa operating system group.

Just wanted to let everyone know the sources to the OS and applications were recovered, I converted them to Unix end of line conventions and spaces for Pascal tabs after recovering the files using Disk Image Chef, and they are with Apple for review. After that's done, CHM will do an @CHM blog post about the historical significance of the software and the code that is cleared for release by Apple will be made available in 2018. The only thing I saw that probably won't be able to be released is the American Heritage dictionary for the spell checker in LisaWrite

It sounds like the Lisa operating system will be available for download from the Computer History Museum, details should be on their blog in due course.

Lisa was a desktop computer released by Apple in 1983, although technically ahead of it's time it was too expensive and was a commercial failure, however it is regarded as a pivotal element in personal computing.


Full details on the Lisa are on the wikipedia page.


RSC CICAG Membership


If you are a Royal Society of Chemistry member renewing your annual mebership, can I remind you that your membership entitles you to membership of up to THREE Interest Groups. Apparently only around 25% take advantage of this option so I'd urge you to have a look at the groups available.

In particular

86 Chemical Information and Computer Applications Group

The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Groups, which exist to benefit RSC members and the wider chemical science community, and to meet the requirements of the RSC’s strategy and charter.

If you have already submitted your form you can make a request to join a group via email ( or telephone (01223 432141).

The first announcement of a CICAG/BMCS meeting to be held next year.

RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry Friday, 15th June 2018 Royal Society of Chemistry at Burlington House, London, UK.
Twitter hashtag - #RSC_AIChem


iOS 11 hits 76% adoption


Looking at the adoption of iOS11 on Mixpanel it is now over 76% with older versions of iOS disappearing.


It will be interesting to see if there are a flurry of Christmas iPhone upgrades.


Open Drug Discovery Toolkit


Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and make extensive use of Numpy/Scipy.

Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field DOI.

The Open Drug Discovery Toolkit was developed as a free and open source tool for both computer aided drug discovery (CADD) developers and researchers. ODDT reimplements many state-of-the-art methods, such as machine learning scoring functions (RF-Score and NNScore) and wraps other external software to ease the process of developing CADD pipelines. ODDT is an out-of-the-box solution designed to be easily customizable and extensible.

To install

Install a clean Miniconda environment, if you already don't have one.

Install ODDT:

conda install -c oddt oddt

Or you can use PIP

pip install oddt


Python 2.7+ or 3.4+
OpenBabel (2.3.2+) or/and RDKit (2016.03)
Numpy (1.8+)
Scipy (0.13+)
Sklearn (0.18+)
joblib (0.8+)
pandas (0.17)
Skimage (0.10+) (optional, only for surface generation)


WolframAlpha updated


WolframAlpha has been updated to version 1.8 to bring in support for iPhone X and some bug fixes.

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. The Wolfram|Alpha App plugs directly into the Wolfram|Alpha supercomputing cloud, computing answers to your questions quickly, efficiently, and without draining your battery.


Take note of this customer review

I recommend that people ignore the one star reviews, those people have no idea how to use the app. They think this is some search engine like google but it’s more suited for running calculations. If you’ve heard of Mathematica and know what the wolfram alpha website is then you are basically getting full support with this app for peanuts compared to what the website charges. It’s not as mathematically powerful as Mathematica but for running quick calculations on the fly, this is indispensable.


Manuscriptsapp is now open source


Manuscriptsapp is a great writing tool designed from the ground up for creating scientific publications. This week we heard an interesting development, it's now free, it will be open source.

There is a detailed blog post here giving the background.


I integrates nicely with a variety of reference managers (Mendeley, Zotero, Papers 3, Bookends and EndNote) with a couple of clicks and you can cite directly with specially supported reference managers, F1000Workspace New, Papers (Magic Citations) or Bookends. It has a Simple table editor with header, body and footer styles built-in and customizable. Tables can be imported from and exported to Word, Markdown, even LaTeX. You can create equations in LaTeX markup, or paste from MathType. Chemistry support is limited but is certainly on their todo list and they would love to have interested chemists to work with.

If you have not used it before now would be a good time to download and try it out.


RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry


The first announcement of a meeting to be held next year.

RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry Friday, 15th June 2018 Royal Society of Chemistry at Burlington House, London, UK.
Twitter hashtag - #RSC_AIChem


Artificial Intelligence is presently experiencing a renaissance in development of new methods and practical applications to ongoing challenges in Chemistry. We are pleased to announce that the Biological & Medicinal Chemistry Sector (BMCS) and Chemical Information & Computer Applications Group (CICAG) of the Royal Society of Chemistry are organising a one-day conference entitled Artificial Intelligence in Chemistry to present the current efforts in applying these new methods. We will combine aspects of artificial intelligence and deep machine learning methods to applications in chemistry.

Applications for oral and poster presentations are welcomed. Posters will be displayed throughout the day and applicants will be asked if they would like to provide a two-minute flash oral presentation when submitting their abstract. Closing dates are 31st January for oral and 13th April for poster submissions.

More details here


RSC CICAG Membership


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:-

86 Chemical Information and Computer Applications Group


Currently it seems Members who wish to change/join interest groups and divisions currently need to request this via email ( or telephone (01223 432141).

The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Groups, which exist to benefit RSC members and the wider chemical science community, and to meet the requirements of the RSC’s strategy and charter.

Scope and Aims

The storage, retrieval, analysis and preservation of chemical information and data are of critical importance for research, development and education in the chemical sciences. All chemists, and everybody else who works with chemical substances, need tools and techniques for handling chemical information.

CICAG works to:

  • Support users of chemical information, data and computer applications and advance excellence in the chemical sciences
  • Inform RSC members and others of the latest developments in these rapidly evolving areas
  • Promote the wider recognition of excellence in chemical information and computer applications at this level.

CICAG also organises a number of meetings each year at which members get reduced rates. Details of previous meetings are here.

You can also follow CICAG on Twitter or LinkedIn



Python and compchem


Python seems to becoming the lingua franca for scientific scripting/progamming and it is perhaps not surprising that we now see increasing support for computational chemistry.

Chemtools is a set of modules that is intended to help with more advanced computations using common electronic structure methods/ programs. Currently the is some limited support for Gamess-US and MolPro program packages but other codes can be easily interfaced. It requires:

  • Python works with Python 2.7.x and 3.x
  • numba
  • numpy
  • mendeleev
  • scipy
  • setuptools

Chemtools is NOT hosted on pypi yet but in can be installed by pip from the bibbucket repository with:

pip install

Pygamess is a GAMESS wrapper for Python, it requires:

  • Python 2.6 or later (not support 3.x)
  • RDKit

It can be installed using pip

pip install pygamess


single point calculation with RDKit

from pygamess import Gamess
from rdkit import Chem
from rdkit.Chem import AllChem
m = Chem.MolFromSmiles("CC")
m = Chem.AddHs(m)
g = Gamess()
nm =

PyQuante: Python Quantum Chemistry, an open-source suite of programs for developing quantum chemistry methods, it currently supports

  • Hartree-Fock: Restricted closed-shell HF and unrestricted open-shell HF;
  • DFT: LDA (SVWN, Xalpha) and GGA (BLYP) functionals;
  • Optimized-effective potential DFT;
  • Two electron integrals computed using Huzinaga, Rys, or Head-Gordon/Pople techniques; C and Python interfaces to all of these programs;
  • MINDO/3 semiempirical energies and forces;
  • CI-Singles excited states;
  • DIIS convergence acceleration;
  • Second-order Moller-Plesset (MP2) perturbation theory.

cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. The goals of cclib are centered around the reuse of data obtained from these programs and contained in output files, specifically

  • ADF (versions 2007 and 2013)
  • DALTON (versions 2013 and 2015)
  • Firefly, formerly known as PC GAMESS (version 8.0)
  • GAMESS (US) (version 2012)
  • GAMESS-UK (version 7.0)
  • Gaussian (versions 03 and 09)
  • Jaguar (versions 7.0 and 8.3)
  • Molpro (versions 2006 and 2012)
  • NWChem (versions 6.0 and 6.5)
  • ORCA (versions 2.9 and 3.0)
  • Psi (versions 3.4 and 4.0)
  • Q-Chem (version 4.2)

FragBuilder a tool to create, setup and analyse QM calculations on peptides. DOI.


And of course there is OpenBabel that can be used create input files for a variety of computational chemistry packages.

If I've missed anything please feel free to let me know.




The LiteMol suite consists of three components, data delivery services (CoordinateServer and DensityServer), the BinaryCIF compression format, and a new lightweight 3D molecular viewer (LiteMol Viewer)

You can try it out at


The LiteMol suite works on all modern web browsers and mobile devices.

LiteMol Viewer is an HTML5 web application for 3D visualization of molecules and other related data. LiteMol is written in TypeScript, a typed extension of JavaScript and uses WebGL for 3D visualization.

Among other things, LiteMol provides:

  • Standard visualizations: cartoons, surface, balls and sticks, etc.
  • Assemblies and symmetry mates.
  • Electron Density and CryoEM maps.
  • Integration with PDBe API: view and explore validation and annotation data.
  • Integration with the Coordinate Server: download only parts of structures you are interested in.
  • Support for the BinaryCIF format that reduces the amount of data that needs to be sent to the client several times.


Collaborative Computational Project No. 4 for Macromolecular X-Ray Crystallography


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.

update 047 is out and contains updates to:

Component Description Mac OS 64-bit Linux 32-bit Linux 64-bit Windows 32-bit Windows 64-bit
panddas update to 2.11 yes yes yes - -
Molrep PFMOD correction yes yes yes yes yes
pointless 1.11.6 yes yes yes yes yes
pointless1.11.5 bug fix for multi lattice data yes yes yes yes yes
ccp4i2 fixes in molrep interface yes yes yes yes yes
edstats new version yes yes yes yes yes
ccp4i lorestr: fix for interface yes yes yes yes yes
monomers add 0WD,2Q5,6G6,6ZL,79F,7K9,8LL, 9Q8,FJI,OMZ,QUJ,QVE,RU2,YY9 yes yes yes yes yes
monomers Format fix: CPN,CPO,DEF,GCR,IMF,QPT yes yes yes yes yes
monomers Replace: UAP yes yes yes yes yes
ccp4mg fixes bug which causes MG/MrBUMP to not work for many sequences yes yes yes yes yes
ccp4mg update for https access to PDBe yes yes yes yes yes
mmdb2 False "duplicate sequence number" error in case of short residue names yes yes yes yes yes
numpy update to 1.12.1 yes yes yes - -
scipy update to 1.16.1 yes yes yes - -


“Found in Translation”: Predicting Outcomes of Complex Organic Chemistry Reactions


An interesting paper uses 1,808,938 reactions from the patent literature as a training set to build a model to predict reactions.

There is an intuitive analogy of an organic chemist's understanding of a compound and a language speaker's understanding of a word. Consequently, it is possible to introduce the basic concepts and analyze potential impacts of linguistic analysis to the world of organic chemistry. In this work, we cast the reaction prediction task as a translation problem by introducing a template-free sequence-to-sequence model, trained end-to-end and fully data-driven. We propose a novel way of tokenization, which is arbitrarily extensible with reaction information. With this approach, we demonstrate results superior to the state-of-the-art solution by a significant margin on the top-1 accuracy. Specifically, our approach achieves an accuracy of 80.1% without relying on auxiliary knowledge such as reaction templates. Also, 66.4% accuracy is reached on a larger and noisier dataset.

There is also a brief video describing the work.


Cluster mols


cluster_mols is a PyMOL plugin that allows the user to quickly select compounds from a virtual screen to be purchased or synthesized.


The most up to date version (recommended) of clustermols is available through BitBucket at:

This plugin has a number of dependencies that are required. And it is currently only supported on Linux and OSX.

Baumgartner, Matthew (2016) IMPROVING RATIONAL DRUG DESIGN BY INCORPORATING NOVEL BIOPHYSICAL INSIGHT. Doctoral Dissertation, University of Pittsburgh.




Just noticed this on Bioconda

r-maldiquant a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

To install

conda install -c bioconda r-maldiquant

More details here

There are more spectroscopy applications here




LigParGen is a web-based service that provides force field (FF) parameters for organic molecules or ligands, offered by the Jorgensen group.

It is available here.

LigParGen provides bond, angle, dihedral, and Lennard-Jones OPLS-AA parameters with 1.14CM1A or 1.14CM1A-LBCC partial atomic charges. Server provides parameter and topology files for commonly used molecular dynamics and Monte Carlo packages OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO. Also, the PQR file is generated. Supported input formats: SMILES, MOL and PDB.Maximum ligand size allowed is 200 atoms.

It is also possible to install LigParGen locally on Mac or Linux machines using Anaconda as described here

More details here

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands, DOI


A short ‘how-to’ on making macromolecular structures viewable in the ‘Augment’ augmented reality app


Allister Crow recently posted a brilliant twitter post of a movie showing a crystal structure in augmented reality: and he posted a simple HowTo. I've taken the original instructions and expanded them to include a few extra options including how to add colours based on a comment by @tomkazimiers.

You can read the detailed instructions here.


Wizard Pro updated


Wizard Pro is a data analysis with ease of use a key design feature. It is designed to encourage the user to click and explore data.


There is a listing of Data Analysis tools for MacOSX here.


Creating a Bioconda recipe


A little while back I mentioned BioConda. You can read more details in this publication "Bioconda: A sustainable and comprehensive software distribution for the life sciences", DOI. Conda is a platform- and language-independent package manager that sports easy distribution, installation and version management of software.

The conda package manager has recently made installing software a vastly more streamlined process. Conda is a combination of other package managers you may have encountered, such as pip, CPAN, CRAN, Bioconductor, apt-get, and homebrew. Conda is both language- and OS-agnostic, and can be used to install C/C++, Fortran, Go, R, Python, Java etc

The bioconda channel is a Conda channel providing bioinformatics related packages for Linux and Mac OS. Looking through the packages it is clear there it already contains a number of chemistry packages. These include: Updated 24 November 2017

  • OpenBabel
  • Rdkit
  • Opsin
  • chemfp
  • gromacs
  • osra
  • Autodock Vina
  • openmg
  • align-it
  • strip-it
  • shape-it
  • np-likeness-scorer
  • Smina

Bioconda offers a collection of over 3100 software tools, which are continuously maintained, updated, and extended by a growing global community of more than 330 contributors. Rather than try to duplicate this effort for a "Chemconda" it seems more efficient to encourage chemists to contribute to Bioconda. If you do package a chemistry application for Bioconda please let me know and I'll publicise it on my blog and add it to the list above. To start things rolling I've added to Bioconda and I've written a page describing how to create a bioconda recipe.

Link to page Creating a Bioconda recipe


The OS X Molecular DataSheet (XMDS)


The OS X Molecular DataSheet (XMDS) is an interactive cheminformatics tool for viewing and editing molecular structures, chemical reactions and data. It is designed to be instantly intuitive to anyone who has used a Mac, a spreadsheet and any chemical structure sketcher.

Its primary functionality is to provide a chemically aware spreadsheet editor: it operates on a grid of editable cells, made up of typed columns, that can be molecules, numbers or plain text, it also includes a chemical drawing app.


This is a significant foray into the desktop space for Molecular Materials Informatics who are best known for their excellent suite of tools for iOS, which includes the mobile SAR Table app and the Mobile Molecular Datasheet.


2017 The State of Data Science & Machine Learning


A new review looking at data science and machine learning.

This year, for the first time, we conducted an industry-wide survey to establish a comprehensive view of the state of data science and machine learning. We received over 16,000 responses and learned a ton about who is working with data, what’s happening at the cutting edge of machine learning across industries, and how new data scientists can best break into the field.


The full dataset is there for you to explore, and the interactive web page allows you to slice and dice on the fly. The above plot looks at the tools being used by scientists, Python dominates and interesting to see the number using Jupyter notebooks. The methods used are shown in the plot below.



iOS 11 adoption approaches 70%


There have been a flurry of updates to iOS apps recently, presumably linked to the iOS11 update. Looking at the adoption of iOS11 on Mixpanel it looks like it is approaching 70% with older versions of iOS disappearing. From a developers point of view this is good news since they only have to concentrate on supporting a single version.



Nature Style guide for chemical structures


Nature have provided a style guide for drawing chemical structures

Although there are a number of ways that chemical structures can be drawn based on individual preferences, our journals aim to use consistent styling wherever possible.



Atomic Simulation Environment


The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations. The code is freely available under the GNU LGPL license.

It requires

  • Python 2.7, 3.4-3.6
  • NumPy


  • SciPy
  • For ase.gui: Matplotlib (2D Plotting)

It can be installed using PIP

pip install --upgrade --user ase

Full details of the MacOSX installation are here.




FreeSASA is a command line tool, C-library and Python module for calculating solvent accessible surface areas (SASA).

The Read Me gives download, build and installation instructions, in addition it details how to build the Python interface.

Simon Mitternacht (2016) FreeSASA: An open source C library for solvent accessible surface area calculations. F1000Research 5:189. DOI


Scripting PubMed searches


PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. They also provide a number of programming tools that allow access to the information, E-utilities are a set of server-side programs that provide a stable interface into the Entrez query and database system.

To access these data, a piece of software first posts an E-utility URL to NCBI, then retrieves the results of this posting, after which it processes the data as required. The software can thus use any computer language that can send a URL to the E-utilities server and interpret the XML response; examples of such languages are Perl, Python, Java, and C++.

A while back I wrote a vortex script that helps with these sort of searches if you have multiple terms you want to search. I've updated this script to incorporate the changes requiring api keys to allow multiple requests to the E-utilities api, and I've highlighted where you need to add your own api key in the script. I've also tried to ensure that any query string should be encoded to make it URL safe.

The update is detailed more fully here….



Downloading from the RCSB Protein Data Bank using Python


The RCSB Protein Data Bank is an absolutely invaluable resource that provides archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps scientists understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. Currently the PDB contains over 134,000 data files containing structural information on 42547 distinct protein sequences of which 37600 are human sequences. They also provide a series of tools to search, view and analyse the data.

Downloading an individual pdf file is pretty trivial and can be done from the web page as shown in the image below. They also provide a Download Tool launched as stand-alone application using the Java Web Start protocol. The tool is downloaded locally and must be then opened. I've found this a little temperamental and had issues with Java versions and security settings.

Since I've been making extensive use of the web services to interact with RCSB I decided to explore the use of Python to download multiple files. I started off creating a Jupyter notebook using the web services provided by RCSB.

I've also used variations on this code to create a python script and a Vortex script.

Full details are here …


It’s not just a game, it’s a quest to help scientists fight dementia!


Sea Hero Quest was created by GLITCHERS, presented by Deutsche Telekom and supported by scientists from University College London and University of East Anglia and the lovely people at Alzheimer’s Research, SEA HERO QUEST is an epic culmination of science and gameplay that will change the way dementia research is done forever.

One of the first symptoms of dementia is loss of navigational skills. Doctors cannot differentiate between getting lost caused by disease and getting lost caused by natural ageing because a benchmark of “normal” does not exist.

Until now … because as you play, your navigational data is tracked anonymously, stored securely and combined with every other player from around the globe, to create the world’s largest crowd sourced data set benchmarking human spatial navigation. This incredible resource will eventually lead to the development of new diagnosis tools and treatments for dementia.

In fact playing SEA HERO QUEST for just 2 minutes will generate the equivalent of 5 hours of lab-based research data.

Sea Hero Quest uses ResearchKit to ask optional scientific questions for further helping the research.

There are more scientific iOS apps here


New API Keys for the E-utilities


If you regularly use the E-utilities API you might want to read this.

After May 1, 2018, NCBI will limit your access to the E-utilities unless you have one of these keys. Obtaining an API key is quick, and simple, and will allow you to access NCBI data faster. If you don’t have an API key, E-utilities will still work, but you may be limited to fewer requests than allowed with an API key.

After May 1, 2018, any computer (IP address) that submits more than 3 E-utility requests per second will receive an error message. This limit applies to any combination of requests to EInfo, ESearch, ESummary, EFetch, ELink, EPost, ESpell, and EGquery.

If you write software of scripts that access the E-utilities API then the users will need to get their own api key. Calls will have this format


2017 Wolfram Technology Conference


An interesting blog entry on the recent 2017 Wolfram Technology Conference. This is a unique experience where researchers and professionals interacted directly with those who build each component of the Wolfram technology

I particularly like this comment.

It was not uncommon for software engineers or physicists to glean new tricks and tools from a social scientist or English teacher—or vice versa—a testament to the diversity and wide range of cutting-edge uses Wolfram technologies provide.

The blog entry is well worth a read.

Delighted to see the ubiquitous presence of MacBook Pros!




An interesting patent has just been granted.

OCEANSIDE, CA, USA, October 31, 2017 ̶ US Patent No. 9,754,085 has been granted to Integrated Chemistry Design, Inc. (ICD) headquartered in Oceanside, CA. The patent covers the technology used in Chirys Draw™ and Asteris™ products designed to replace cumbersome and outdated template tables with a natural circle gesture to rapidly draw chemical rings including complex fused structures. Chirys Draw and Asteris are available worldwide for Apple iPad®.

“We mapped how chemists draw with pen and paper to touch-screen gestures that enable the chemist to focus on capturing their ideas instead of operating the software,” said ICD co-founder and president, Dr. M. Catherine Johnson. “ICD’s comprehensive set of patented touch gestures empowers chemists to draw complex chemical structures and reactions quickly and easily. The newly issued patent represents a foundational piece to the ICD patent portfolio.”


Integrated Chemistry Design products include Chirys Draw, Asteris, Chirys View™, and Chromys™


LigandScout 4.2 released


LigandScout has been updated.

Even more efficient and intuitive​​​​​​:

  • New buttons for ligand-based modeling
  • New features for MD trajectory analysis
  • New data management capabilities
  • New interactive charts


The LigandScout software suite comprises the most user friendly molecular design tools available to chemists and modelers worldwide. The platform seamlessly integrates computational technology for designing, filtering, searching and prioritizing molecules for synthesis and biological assessment.

There is a review of LigandScout here


Interacting with the RCSB Protein Data Bank


The RCSB Protein Data Bank is an absolutely invaluable resource that provides archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps scientists understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. Currently the PDB contains over 134,000 data files containing structural information on 42547 distinct protein sequences of which 37600 are human sequences. They also provide a series of tools to search, view and analyse the data.

The latest addition to the Hints and Tutorials page is a couple of Vortex scripts for interacting with the RCSB Protein Data Bank, specifically they search for PDB structures associated with a list of Uniprot codes, and then search for associated information. Read more here…


Scientific Applications under High Sierra (Update 3)


Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. Based on the number of page views on the lists for Sierra, El Capitan and Yosemite it is apparently a useful resource. The major change with High Sierra is the update to the file system so hopefully this will be a benign update, but a Time Machine backup is always a good idea.

I’ll update the list regularly and feel free to send in information.

High Sierra is a major download 5GB and a couple of people have asked if it is possible to keep the installer and then use it on multiple machines.

The initial installer is small (15 MB) but after the main installer has successfully downloaded (5GB+), when you are prompted to start the installation process, click Cancel, and the installer will be in the /Applications folder. You must make a copy of this to another location; otherwise if you launch the installer and it completes the High Sierra update, it'll be deleted.

When you upgrade to macOS High Sierra, systems with all flash storage configurations are converted automatically. Systems with hard disk drives (HDD) and Fusion drives won't be converted to APFS. You can't opt-out of the transition to APFS.

AppleScriptObjC there are a couple of bugs, because the issues stem from the .bridgesupport file, they will potentially pose problems in other languages that use the scripting bridge.

Avogadro no issues

BBEdit have a comprehensive list of compatibility notes for each application and versions BBEdit 12 has just been released which bring full High Sierra compatibility.

ChemDoodle all seems fine no issues reported

ChemDoodle3D all seems fine no issues reported

ChemDraw as a policy they do not test until after new operating systems have been released, will check back later

ChirysView no issues to date

Cresset No issues to date, more detailed testing underway.

CrystalMaker no problems

DataWarrior no issues to date

Findings no issues

iBabel no issues to date

MarvinSketch latest version no issues, earlier versions may require the old Apple supplied JDK to be reinstalled

MarvinView no issues

Microsoft have already announced the results of preliminary testing of the Office suite.

Office version 15.35 and later, Word, Excel, PowerPoint, Outlook, and OneNote will install and run on 10.13, but there maybe some issues

Office 15.34 and earlier. These versions are not supported on 10.13. In some cases, you may not be able to launch the Office apps.

Office for Mac 2011. Word, Excel, PowerPoint, Outlook and Lync have not been tested on macOS 10.13 High Sierra, and no formal support for this configuration will be provided.

Mnova lite no issues reported

MOE There seem to be no problems running MOE 2016.0804 or higher on MacOS 10.13.

Please note that all of our Mac users should upgrade to MOE 2016.0804 due to bugs identified in earlier versions. You can download the patch to 2016.0804

The default python is

 ~ /usr/bin/python
Python 2.7.10 (default, Jul 15 2017, 17:16:57) 
[GCC 4.2.1 Compatible Apple LLVM 9.0.0 (clang-900.0.31)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

PyCharm no issues

StarDrop Our initial tests suggest that everything is working as expected.

Vortex no issues reported.

xQuartz "I would like to report that xquartz now works in the latest macOS 10.13". Download here

Updated 14 October 2017


Science Journal app


Science Journal by Google is an electronic notebook for recording experiments.

Whether you're a science educator or a hobbyist doing science at home, you can keep your notes, photos, and observations all in one convenient place. Use the sensors in your iPhone or iPad to measure and graph phenomena such as light, sound, and motion, or connect to external sensors via bluetooth to conduct experiments on the world around you.

With the Science Journal app, you can:

  • Measure light, sound, acceleration, air pressure, and more using your device’s built-in sensors.
  • Take notes and photos to document your science experiments.
  • Connect to external sensors using select Bluetooth-enabled Arduino devices.
  • Create automated triggers for recording data and taking notes.
  • Use sonification to hear the movement of your graphs.

Permissions notice:

  • Bluetooth: needed to scan for bluetooth sensor devices.
  • Camera: needed to take pictures to document experiments and for the brightness sensor.
  • Photo Library: needed to store pictures taken to document experiments and for adding existing photos from your library to experiments.
  • Microphone: needed for sound intensity sensor.
  • Push notifications: needed to inform you of recording status when backgrounding the app.


SAMPL6 comp chem challenge update


Version 1.3: Add pKa prediction challenge instructions, input files, submission template files, update on the future plans of logD challenge.

SAMPL6 pKa Challenge Instructions

Challenge timeframe: Oct 25, 2017 to Jan 10, 2018

This challenge consists of predicting microscopic and macroscopic acid dissociation constants(pKa)s of 24 small organic molecules. These fragment-like small molecules are selected for their similarity to kinase inhibitors and for experimental tractability. Our aim is to evaluate how well current pKa prediction methods perform with drug fragment-like molecules through blind predictions.

Three formats of pKa prediction results will be evaluated:

  • microscopic pKa values and related microstates
  • microstate populations as a function of pH
  • macroscopic pKa values


UCSF Chimera 1.12 released


A new production release of UCSF Chimera (version 1.12) is available:

Download is free for noncommercial use. Platforms: Windows, Mac OS X, Linux.

New since version 1.11 see release notes for the full list:

General I/O, Display:

  • Updated URLs for fetching PDB, mmCIF, EDS
  • improved initial display of EDS difference map (shows both positive and negative isosurfaces)
  • "click-to-center" mouse mode (default Ctrl-right button) uses surface vertex instead of entire surface
  • "clip" and "thickness" commands prevent placing the back plane in front of the front plane

Structure Analysis and Modeling:

  • AmberTools updated to version 17
  • Add Charge uses precalculated charges for NAD and NDP
  • Morph Conformations "core fraction" exposed for more control over hinge detection
  • "hbonds" command option to show as dashed or dotted lines


  • Mol2 output includes metal-coordination bonds
  • Dock Prep consistent handling of alternate locations in adjacent residues


Bioconda: A sustainable and comprehensive software distribution for the life sciences


Bioconda is a channel for the conda package manager specializing in bioinformatics software.

Bioconda supports only 64-bit Linux and Mac OSX.

Bioconda offers a collection of over 2900 software tools, which are continuously maintained, updated, and extended by a growing global community of more than 250 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.

The conda package manager has recently made installing software a vastly more streamlined process. Conda is a combination of other package managers you may have encountered, such as pip, CPAN, CRAN, Bioconductor, apt-get, and homebrew. Conda is both language- and OS-agnostic, and can be used to install C/C++, Fortran, Go, R, Python, Java etc

You can read more details in this publication "Bioconda: A sustainable and comprehensive software distribution for the life sciences", doi.

Whilst there are a number of compilaions of Bioinformatics software, Bioconda looks to be by far the most comprehensive.

After installing Conda, the first step is to set up the Bioconda channel

conda config --add channels conda-forge
conda config --add channels bioconda

Packages can then be installed using

conda install cnvkit

This installs CNVkit plus the appropriate Python and R dependencies.


The SAMPL6 Blind Prediction Challenge for Computational Chemistry


SAMPL6 includes challenges based on aqueous host-guest binding data (binding free energies and, optionally, binding enthalpies) for three different host molecules; and on physical properties (distribution coefficients and possibly solubilities), for a set of fragment-like molecules. The host-guest systems are useful to test simulation methods, force fields, and solvent models, in the context of binding, without posing the setup issues and computational burden of protein simulations. The physical properties offer efficient tests of force field accuracy when detailed simulations are used, and can also test pKa prediction methods, continuum solvation models, and knowledge-based prediction methods. SAMPL6 will also introduce a new challenge component, the “SAMPLing challenge”, in which computational methods will be evaluated on how efficiently their calculations approach well-converged reference results generated by the organizers. Participants will be provided with machine readable setup files for the molecular systems, including force field setups, along with recommended cutoffs and treatments of long-ranged interactions. The SAMPLing challenge is expected to include one or more cases from each challenge component (host-guest binding on each system; log D calculation).

If you would like to participate in the challenge join up here.


SAMSON, Software for Adaptive Modeling and Simulation Of Nanosystems


SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON's generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means "Software for Adaptive Modeling and Simulation Of Nanosystems.


SAMSON has an open architecture which allows anyone to extend it - and adapt it to their needs - by downloading SAMSON Elements (modules). SAMSON Elements come in many flavors: apps, editors, controllers, models, parsers, etc., and are adapted to different application domains. SAMSON Elements help users build new models, perform calculations, run interactive or offline simulations, visualize and interpret results, and more. Add new SAMSON Elements to SAMSON straight from SAMSON Connect.

In the latest news Python scripting is coming to SAMSON 0.7.0. Most of the SAMSON API is now exposed in Python, and this will allow you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from scripts. Python will make it even easier to integrate and pipeline SAMSON and SAMSON Elements with well-known packages from diverse fields, e.g. TensorFlow, PyRosetta, RDKit, ASE, etc., to name a few


SeeSAR Updated


SeeSAR 7.1 has just been released.

  • 3D-pharmacophores to identify compounds of interest By now, you can run so many bulk actions, your solution list will grow by the minute. This made it just the right time to implement another filter option to help you keep track! Pharmacophore filters can now be defined using so-called sphere constraints. You can apply these pharmacophores at lightning speed to the molecule table and drill down solutions sets quickly and effectively with queries such as: Which molecules have an acceptor at this position? Filter out molecules that occupy this position! Give me all molecules with an aromatic moiety here!
  • Linking and merging fragments with the integrated ReCore It is now possible to enter the 3D molecule editor with more than just one molecule. Among other things, this facilitates linking and merging operations with ReCore. Simply select the atoms you seek to replace (eg the terminal atoms of two fragment binders that should be linked). A click on the ReCore button retrieves for you in seconds fragments that link the two binders, leaving them as closely as possible in place.
  • Better measure and label-options (with adjustable font size) Partially hidden labels in 3D won't bother you anymore! Instead, the simple labels for showing distances, angles, and so on have been upgraded to the more advanced labels which we have always used for Hyde and more recently for displaying torsion information. These labels are movable (simply click and drag) and are always at the front. Plus, as a bonus feature, you may now also adjust the font size on the labels in the appearance settings menu in the toolbar.
  • Parallel high-throughput docking A lot of users have been waiting for this feature! Now bulk docking can be carried out with just one click. Plus we have parallelized the docking calculation so that it now uses all processors on your computer, providing you with solutions swiftly — just as your hardware permits.
  • Multiple selections for bulk actions Frankly speaking we previously "abused" the favorite icon for making selections to initiate bulk actions. This itself undermined the point of being able to mark molecules as favorites. Now you may conveniently select multiple molecules using the new check box feature, and initiate bulk actions on the basis of this selection. For your convenience we also added a few functions to make working with these selections even more effective (un/check all, invert, ...). Just as for the favorites, shift + left mouse click works on the check boxes as a multiple un/check feature.


BBEdit 12 released


BBEdit everyone's favourite text editor has been updated. This looks to be a substantial update with over 100 new features and refinements, the full release notes are available here.

A couple of features look very useful

There's a new submenu on the Edit menu, "Columns". This submenu contains commands to help you work more easily with column-delimited text files. The three basic commands, "Cut Columns", "Copy Columns", and "Clear Columns" work similarly to their top-level analogues. The columns to be cut/copy/cleared are determined by the selection range: to cut a single column, for example, click in the middle of it. You can cut/copy/clear multiple columns by selecting text across them. The "Rearrange Columns" command gives you an easy way to, well, rearrange the columns in a column-delimited text document. Choose the menu command, and then drag the items into the list to order them as you would like, then press the "Apply" button.

There's a new command on the Text menu: "Canonize". This command is useful for doing batch search-and-replace operations in a file, using another file as a list of search-and-replace transformations.

BBEdit 12.0 requires macOS 10.11.6 ("El Capitan") or later, and is compatible with macOS 10.13 "High Sierra". I've added it to the list of Scientific Applications under High Sierra


iOS 11 overtakes iOS 10


According to the data captured by mixpanel three weeks after launch iOS 11 has overtaken iOS 10. This is important information for developers who can start to focus on the latest version of the mobile operating system.


In contrast for Android there is a much larger spread of operating systems in use.


MobileScience updates


A couple of apps have been updated recently.

Wolfram|Alpha 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. Always one of the top apps on the MobileSciencesite.

ChemistryKeyboard is a specialized Keyboard Extension for anyone who needs to enter chemical formulae. This update brings:

  • Improved layout for wider iPads including tab button and less intrusive labels
  • Added arrow types
  • More elements keys on wide displays
  • Keyboard in the Chemistry Keyboard app was not showing localization

Elemental from Dotmatics the FREE Chemistry Sketch Utility now supports iOS 11 (64-bit support).

R Instructor now version 2.1.4 with core code rewritten.

NEB Tools brings New England Biolabs’ most popular web tools to your iPhone. Use Enzyme Finder to select a restriction enzyme by category or recognition sequence, or search by name to find information on any NEB enzyme.

iSpartan includes viewing NMR data from iSpartan 16.

Findings electronic lab notebook.




I just came across a new Electronic LabNotebook (ELN), eLabFTW is an open source solution powered by PHP/MySQL in Docker containers. One install can be for a team, or the whole institution. You can also install it on your computer for a personal notebook.

All the user needs is a web browser to access the notebook.

Upload any type of files, embed images in the text, Draw doodles directly with your mouse, Use templates for your experiments, Draw molecules with Chemdoodle, REST API for accessing programmatically your experiments, SAML2 authentication if you have an identity provider, Growing community of users and contributors scrutinizing the code and improving it, Highly customizable: you can change the colors, the status list, the items types list, etc. Can fit any kind of lab (chemistry, biology, physics, astronomy, etc.)

Full details are available here and there is a presentation here

There is also a demo account available


A review of ChemDraw 17

ChemDraw is a very established chemical drawing package that probably set the standard for publication quality chemical drawing. However, on the Mac platform in particular I think it is true to say Cambridgesoft have taken their eye off the ball and released versions that were not up to their usual standard.

ChemDraw 17 is in someways a fresh beginning you can read the full review here.


The 3rd Tony Kent Strix Annual Lecture - FREE Event



Booking Reminder! The 3rd Tony Kent Strix Annual Lecture - FREE Event - Friday October 20th 2017

In 2016 the UK eInformation Group (UKeiG), in partnership with the International Society for Knowledge Organisation UK (ISKO UK), the Royal Society of Chemistry Chemical Information and Computer Applications Group (RSC CICAG) and the British Computer Society Information Retrieval Specialist Group (BCS IRSG) was delighted to announce that the winner of the prestigious Tony Kent Strix Award was Maristella Agosti, Professor in Computer Science, Department of Information Engineering at the University of Padua, Italy. The Award is given in recognition of an outstanding practical innovation or achievement in the field of information retrieval.

Professor Agosti has built a world-wide reputation for her work in many aspects of information retrieval and digital libraries. She was one of the first people to work in information retrieval in Italy where she acted as a catalyst for creating a vibrant and internationally recognised IR research community.

Her 2017 Strix Lecture will be given at The Geological Society, Burlington House, Piccadilly, London during the afternoon of Friday 20th October.

The 2017 Tony Kent Strix Award winner will also be announced during the afternoon.

* This is a FREE event, open to everyone, BUT advance bookings ARE required. Please book your place by emailing Gary Horrocks at: * Full programme details:
1.30 Registration
2.00 Doug Veal - Chairman's welcome
2.10 - A presentation from Alan Gilchrist
Title: 'Reflections: Some thoughts on the past, present and future of Information Retrieval'
(Doug and Alan are founding members of the Working Group that initiated the Award, first presented in 1998.)
2.45 - Questions & Discussion
3.00 - Tea & coffee
3.45 Maristella Agosti - The Tony Kent Strix Annual Memorial Lecture
Title: Behind the Scenes of Research and Innovation

Abstract: We often excel in producing scientific achievements, but at times turning those achievements into innovation and technology transfer can be a tall order. Furthermore, even though we may document our findings well in scientific publications and reports, we are far less accomplished and proficient in documenting and explaining how the complex process of transforming scientific results into innovation has been performed and proven successful. In general, most of the knowledge of this transfer process remains only with those taking part in it, while certain aspects such as the time and context when the transfer took place may be rich in lessons to be learnt and provide opportunities for future teaching in diverse fields. This talk addresses the complex process of transforming research outcomes into innovation using some relevant examples in the fields of information retrieval and digital libraries.

4.30 Questions & discussion

5.00 Meeting closes

The Annual Lecture series is sponsored by Google.

For more information about UKeiG and the Tony Kent Strix Award visit:


ChemTube3D now for iOS


ChemTube3D is a web based Open Educational Resource containing interactive 3D animations and structures, with supporting information for some of the most important topics covered during an undergraduate chemistry degree. It was developed by the ChemTube3D team including students at the University of Liverpool.

This is an absolutely fantastic resource that offers invaluable insight into the 3D structure of molecules and reactions.

e.g. Diels-Alder


I'm delighted to hear that it is now accessible from a mobile device

There are many more science apps listed on the Mobile Science site.


RDKit conformer generation script


Pharmacelera we have written a python script to generate conformations with RDKit and made it available here .

Conformer generation is one of the first and most important steps in most ligand based experiments, particularly when the ligand’s 3D structure is unknown. For example, the quality of the conformers could affect the results of virtual screening experiments.


Rdkit warning


I just saw this message on the rdkit mailing list and I thought I'd flag it.

I've noticed a problem with anaconda python on the Mac. This may also be a problem on linux, but I haven't tested that yet.

Due to some changes in the way the anaconda team is doing python builds, the most recent conda python builds seem to no longer work with the RDKit. The symptom is an error message like "Fatal Python error: PyThreadState_Get: no current thread" when you try to import the rdkit.

I've observed this for the newest 3.5 (3.5.4-hf91e95415) and 3.6 (3.6.2-hd0bf7f115) builds. A workaround is to downgrade to 3.5.3 (conda install python=3.5.3) or 3.6.1 (conda install python=3.6.1).


Chemotion ELN: an Open Source electronic lab notebook for chemists in academia


A web-based chemistry ELN using the OpenBabel toolkit published recently

The web based application is available as an Open Source software that offers modern solutions for chemical researchers. The Chemotion ELN is equipped with the basic functionalities necessary for the acquisition and processing of chemical data, in particular the work with molecular structures and calculations based on molecular properties. The ELN supports planning, description, storage, and management for the routine work of organic chemists. It also provides tools for communicating and sharing the recorded research data among colleagues. Meeting the requirements of a state of the art research infrastructure, the ELN allows the search for molecules and reactions not only within the user’s data but also in conventional external sources as provided by SciFinder and PubChem.

Project home page:

Developed/tested on Linux and Mac, deployed on Linux.

Other requirements: Modern internet browser supporting HTML5 and JavaScript. Recommended browsers: Chrome, Firefox (IE not supported).


Scoria: a Python module for manipulating 3D molecular data


Just catching up on reading the literature and came across this interesting python paper in Journal of Cheminformatics. DOI.

Scoria is useful for both analyzing molecular dynamics (MD) trajectories and molecular modeling. For example, we have used beta-version Scoria functions to create large-scale lipid-bilayer models, to construct small-molecules models with improved predicted binding affinities, to measure MD-sampled binding-pocket shapes and volumes , and to develop neural-network docking scoring functions, among other applications. As an additional example, in this manuscript we describe a trajectory-analysis Scoria script that colors the atoms of one protein chain by the frequency of their contacts with a second chain.



Pymol 2.0 released


The popular molecular visualisation application Pymol has been updated to version 2.0. This is a major update and the changes are detailed below.

You can either download a disk image (117 MB) or instal using Anaconda (Python 2.7)

conda install -c schrodinger pymol


Major Changes

  • Unified modern interface
  • PyQt interface replaces Tcl/Tk and MacPyMOL on all platforms
  • Anaconda Python distribution
  • Better third-party plugin and custom scripting support
  • Open access incentive executables with new licensing mechanism

New Features

  • Native retina resolution / 4k display support
  • Dock/undock and rearrange certain panels (Builder, Feedback Browser, Volume Editor)
  • Support for trackpad gestures (pinch for zoom in/out, z-rotate)
  • Dedicated dialogs for opening MAE files, MTZ files, maps and trajectory files
  • New APBS Plugin panel
  • .pymolrc script editor with syntax highlighting
  • Properties editor
  • Improved Draw / RayTrace dialog
  • MPEG-4 and GIF movie export panel
  • Excel exporter plugin (Windows and Mac)
  • Open files by dragging from file browser to PyMOL window
  • wire and licorice representation aliases for combined lines/nonbonded and sticks/nb_spheres
  • New commands: “copy_to” and “uniquify”
  • Single-letter code labels (“label oneletter”)
  • Label Wizard menus for colors and transparency
  • Improved file types registration on Windows (Setting > Register File Extensions)

Settings changes

  • Changed default values for several settings:
  • opaque_background=off
  • cartoongapcutoff=10
  • autoshowclassified=1 (=3 for > 500k atoms)
  • valence=on
  • stickhscale=0.4
  • smoothsurfaceedges=on

Menu changes

  • “Open Recent” file menu
  • File > New Window opens new PyMOL window
  • Setting > Register File Extensions
  • Plugin > Legacy Plugins
  • New > Pseudoatom > Callout
  • A > Copy to object
  • A > State > Split

Bug fixes

  • Fixed slow performance of “extract” command
  • Better unicode/UTF-8 handling
  • Fixed inconsistent look of labels and connectors on Retina and non-Retina displays
  • Fixed labelrelativemode=2 raytracing
  • Improved Maestro and MOE format compatibility
  • Fixed internal GUI clipping on certain Windows systems with integrated Intel graphics

The new user interface and all core improvements will be pushed to the open source SVN repository early next year.


Predicting sites of metabolism Vortex script


It is really useful to have two sites of metabolism tools available that use contrasting methodologies, FAME 2 using curated dataset of experimentally determined metabolism data to build a machine learning model using simple descriptors. In contrast SMARTCyp uses precomputed activation energies from density functional theory (DFT) calculations of model compounds.

I previously wrote a script displaying the [results of a SMARTCyp calculation in a webview. The first part of the script imports the smartcyp.jar, however with each update I was finding issues so I thought it might be better to simply treat SMARTCyp as a command line application and use subprocess to access it.

Using a similar script we can also access FAME2

More details here.



Xcode 9.0 is available for download


The new version of Xcode is available for download. Xcode 9.0 includes Swift 4 and SDKs for iOS 11, watchOS 4, tvOS 11 and macOS High Sierra 10.13.

  • The source code editor has been completely rebuilt for amazing speed. It scrolls at a constantly smooth rate, no matter the files size, also supports Markdown.
  • Refactoring to easily select and modify structure of code
  • Swift 4 compiler can also compile Swift 3 to aid transition
  • Xcode 9 makes working with source control – and with GitHub – easier and more tightly integrated.
  • Simulator app updated.


chemfp 1.3 released


Chemfp is a set of command-line tools and a Python library for working with cheminformatics fingerprints. It can use OEChem/OEGraphSim, RDKit, or Open Babel to create fingerprints in the FPS format, and it implements a high-speed Tanimoto search.

The software is available under the MIT license. For more information see Documentation is available from .

There are many changes over chemfp 1.1, which was the last release of the public/no-cost version of chemfp. The biggest ones are:

  • Tested against the current version of all of the toolkits

  • Added support for the Avalon and pattern fingerprints in RDKit

  • In-memory Tanimoto searches for 166-bit MACCS keys on computers with the POPCNT instruction is about 30% faster.

  • FPS loading is about 40% faster. As a result, file-based searches are about 25% faster.

  • The in-memory search algorithms in version 1.1 were parallelized with OpenMP, but the NxM k-nearest search was left out. That case is now also parallelized.

  • Some of the APIs from the commercial version were backported to 1.3, including the fingerprint writer API and functions for substructure fingerprint screening.

  • Added and improved docstrings

This release support Python 2.7 but it no longer supports Python 2.5 or Python 2.6. The commercial version supports Python 2.7 and Python 3.5+, handles more than 4GB of fingerprint data, and has a binary fingerprint format for fast loading.

It is available from


GROMACS 2016.4 has been released


Molecular dynamics simulation in general, and GROMACS in particular, has made it possible to study large and complex biomolecular systems such as membranes and membrane proteins and probe atomic detail that is not accessible to any experimental methods. GROMACS can already use thousands of cores and hundreds of accelerators efficiently in parallel, even for a single quite small system. When adding ensemble-level parallelization with Copernicus the total problem scaling extends another two orders of magnitude.

These release notes document the changes that have taken place in GROMACS since version 2016.3 to fix known issues. It also incorporates all fixes made in version 5.1.4 and several since.

  • Fixes where mdrun could behave incorrectly
  • Disabled PME tuning with the group scheme
  • Fixed value of Ewald shift
  • Fixed orientation restraint reference
  • Fixed bugs with setup for orientation restraints
  • Worked around missing OpenMP implementation in orientation restraints
  • Enable group-scheme SIMD kernels on recent AVX extensions
  • Fix FEP state with rerun
  • Fixed COM pull force with SD
  • Fix PBC bugs in the swap code
  • Fixed flat-bottomed position restraints with multiple ranks
  • Fixed null pointer print in DD
  • Improved the “files not present” error message
  • Fixed LJ-PME + switch grompp error
  • Fixed unused SIMD PME table kernel
  • Fixed bugs in most double-precision Simd4 implementations
  • Avoid inf in SIMD double sqrt()
  • Fix NVML error messages
  • Fixed IMD interface malfunctions
  • Fixed initial temperature reporting
  • Fix exception in SIMD LJ PME solve
  • Fixes for gmx tools
  • Fixed memory access issues in gmx solvate
  • Fixed a consistency check in gmx make_edi for flooding
  • Supported quiet trajectory-handling I/O
  • Improved documentation
  • Migrated much content from the wiki to the user guide
  • Corrected the PDF manual to reflect that all tools are called gmx
  • Clarified gmx editconf help text
  • Added missing .mdp file documentation for the enforced rotation module
  • Fixed parameter description for dihedral_restraints
  • Replaced instance of “group” by “coord” in pull .mdp documentation
  • Portability enhancements
  • Supported CUDA 9/Volta for nonbonded kernels
  • Really enabled AVX512 in the GROMACS-managed build of FFTW
  • Fixed aspects for compiling and running on Solaris
  • Fixed AVX512F compiler flags
  • Fixed compiler flags for using MKL
  • Fixes compilation issues with ARM SIMD


SeeSAR Updated


SeeSAR has been updated to version 7. There is a review of an older version of SeeSAR here. However SeeSAR is a constantly evolving and improving piece of software.

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.


This update includes

  • Full integration of ReCore functionality. Now - besides fragment-replacement, joining and merging of fragments is also possible. In addition, you can fine-tune results delivered by ReCore using pharmacophore filters.
  • Editing turns into full-blown designing. Besides atom by atom changes you may now add the most common rings with just one klick. So large changes can quickly be made to molecules and this in itself necessitates another new feature — namely that multiple poses are generated based on a superposition of the maximum common substructure.
  • Display of torsion distribution. On the one hand, we have now integrated the latest update of the database of torsion angle distributions from the CSD, while on the other, it is now possible to view the torsion angle distribution for a particular rotatable bond.
  • Miscellaneous enhancements. The SDF export covers your particular selection of favourites and any comments attached to a molecule. For a numerical filter it is now possible to define both a lower and upper bound. Last but not least, besides distances, you may now measure angles and torsions.


A tutorial on KNIME Deeplearning4J Integration


An interesting blog post

The aim of this blog post is to highlight some of the key features of the KNIME Deeplearning4J (DL4J) integration, and help newcomers to either Deep Learning or KNIME to be able to take their first steps with Deep Learning in KNIME Analytics Platform.


Accessing Jupyter Notebook model from Vortex

Chemical Drawing Programs – The Comparison of Accelrys (Symyx) Draw, ChemDraw, DrawIt, ACD/ChemSketch, ChemDoodle and Chemistry 4-D Draw

There is also a comparison of six chemical drawing packages here