Macs in Chemistry

Insanely Great Science

Molecule viewer

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

screenshot4

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.


Comments

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.

ajmpoeimeppbbkmo

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.

Comments

Review of ChemDoodle3D ver3

I've just written a review of the latest version of ChemDoodle3D

ChemDoodle 3D is a scientific visualization platform with a focus on user customizability and universal support. Just like its 2D counterpart, all of the graphics are fully customizable and controllable. The large feature set is well organized for intuitive access and we develop ChemDoodle 3D to work with the vast majority of graphics cards in use.

chemdoodle3Dver3_proteins

ChemDoodle3D really excels at the creation of high quality publication ready graphics, the ability to specifically select every atom or bond enables the user to precisely create the desired image. It performs well using modest hardware that would be accessible to any student. Perhaps one of the real attractions however is the ability to use the ChemDoodle Web Components to easily share structures via the web.

Read more…

Comments

SeeSAR update 6.0

 

The all new SeeSAR 6 provides you with a completely redesigned and now fully customizable GUI. You can choose between different bright and dark themes and GUI layouts so that you can optimally adapt SeeSAR for different use cases.

gmgomgmkfkmkhmch

GUI design
The new design is more streamlined and customizable. Instead of having 8 different kinds of buttons in different regions of the application, we now have just a main menu top left and a toolbar top right. The main menu changes depending on the mode of use (editing, site definition, ...), while the toolbar stays the same throughout. This way you are never overwhelmed with choices, but are only presented with options that you may need. Depending on you current use case, you may also want to change the overall layout (many molecules tables to the left; many properties tables below to make use of the whole width; 2 monitors tables docked out) and/or the overall appearance (bright theme for presentations; dark theme for desktop work; we have also integrated a color blindness mode just in case).
Help
In order to give you a jump start when you begin working with SeeSAR (both as a newcomer, as well as a seasoned user of the old GUI design), we have introduced an in-application help facility in this new version. First of all, upon starting the tool for the first time or after a long break in use, SeeSAR offers you a short introductory slide show, reminding you of a few basics that can make life a lot easier. But you can also now request help from within the application with a click on the lifesaver button. The help window then shows you – context dependent – explanations on the mode in which you are currently working or on the functions that you are trying to use so you can leave the help window open, consulting it when you need it. Of course you may also navigate between help pages in the help window and from there access online resources such as tutorial videos.

There is also a free webinar: introduction to SeeSAR 6.0

The design of SeeSAR has changed a lot and many new features – like multi-protein handling – have been added. So this webinar is of interest for both, seasoned users and newcomers to SeeSAR. It shall give you an update of the recent changes and guide you through the most important features based on medicinal chemistry use cases. Webinar attendees are entitled to a free 4-week trial license. date/time:    Tuesday, June 27th, 7:00 am PDT, 10:00 am EDT, 16:00 CEST

https://www.biosolveit.de/webinars/


Comments

ChemDoodle 3D v3 is available

 

It has been a little while but ChemDoodle 3D is out, and looking at the new features it was certainly worth the wait, this is a major upgrade!

slider3dMainv3

New features in ChemDoodle 3D v3:

  • Faster and more advanced shaders for the most realistic graphics or captivating cartoon rendering. There are now 6 shaders to choose from.
  • Fully customizable and dynamic real-time shadow rendering.
  • Molecules can now be built using intuitive tools and a continuous running optimization (using the new Minimizer widget) to allow you to build accurate models and the specific conformations you desire. It is a lot of fun to physically interact with the structures you build!
  • New bond types, more aromatic ring representations, more cheminformatics functions.
  • Distances can now be measured between any combination of bond centers and atoms; previously only atoms were allowed. Visual specifications for all shapes can now be independently edited.
  • Fully customizable surfaces can now be built for selections of atoms.
  • Selector tools have been added, and you can now select objects by lasso and rectangular marquee.
  • Our interface engine is now fully implemented including drawing toolbars, widgets, autosaving, workspace control and more.
  • Style sheets (and scene settings files) can now be created, saved and loaded.
  • Quaternions can now be used for all rotations, instead of just X-Y axis rotation.
  • Full support for the new RCSB MacroZZmolecular Transmission Format.
  • A more advanced copy and paste system.
  • After effects are new multipass shader options that provide additional graphical effects. Blurring and outlining are currently available.
  • Outlines are now rendered for highlighted and selected objects.
  • Model settings in the Visuals panel in Preferences are now organized by model type.
  • A new Custom Element Color Set. Color choosers have been upgraded and now affect graphics in real time. Improved MacOS look and feel.
  • Added the last of the new element names recommended by IUPAC. Added more published van der Waals values.
  • Polishing, new icons, and performance improvements affecting just about every asproect of the product, from picking to animations to rendering and saving images.

Comments

Chirys View

 

Chirys View is a simple molecular spreadsheet for Mac OSX. It has been designed as a fast viewer for collections of molecules represented as an SDF file (Structured Data Format). On import molecular weight, exact mass, molecular formula, hydrogen bond acceptor and donor counts are automatically calculated. You can combine multiple SDF files by multiple file imports or by coping and pasting from one document into another. You can then save selected compounds as new SDF file.

I imported 1 million structures from ChEMBL and whilst it took a few minutes to load and used 27GB RAM it did so without complaints, scrolling down a list of a million compounds is a little impractical but list sorting is pretty responsive. I had a look at some of the more complex structures and they molecular layout seems excellent and clearly legible.

chirys

As a simple molecular selection tool Chirys View works very well. My only complaint is that when you import 3D structures (e.g. from a docking run) the structures can be difficult to discern (see below), it would be nice to have a convert to 2D option.

docked


Comments

Molecule Viewers and sketchers for iOS

 

With withdrawal of ChemDraw and Chem3D from iOS I thought it might be of interest to highlight some of the alternatives.

Put together two pages.

Molecule Viewers for iOS

and

Chemical Sketchers for iOS


Comments

UnityMol Updated

 

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.


Comments

Programmatic conversion of crystal structures into 3D printable files using Jmol

 

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.

13321_2016_181_Fig3_HTML

There is more information on the 3D printing page


Comments

Script for 3D printing from Jmol

 

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.


Comments

Over 1000 downloads of iBabel

 

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.

3dviewers

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

Comments

Molmil: a molecular viewer for the PDB and beyond

 

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

molmil

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.


Comments

First integration of @UnityMol in the @HoloLens !

 

This looks very cool


Comments

UCSF Chimera (version 1.11) is available

 

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).


Comments

Molecular visualization in the Jupyter Notebook with nglview

 

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/

nglviewer

The project is on Github, feel free to contribute!


Comments

Over 400 iBabel downloads

 

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

3dviewers

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


Comments

BALL Project

 

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.

BALLView_01

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


Comments

Unicon and Mona

 

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.


Comments

ChemDoodle 3D updated

 

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.

chemdoodle3D

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.
Comments

iBabel 3.6 is released

 

Bable

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.

Comments

Browser plugin-free CIF visualization

 

A nice comparison of the options for displaying crystal structures within a browser without the need for plugins/applets.

Full blog post is here

Here we compare four open-source browser engines for plugin-free rendering of the crystalline structures in CIF format.

Comments

Lucas, Molecule viewer and editor

 

Lucas is a novel program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus is able to visualise dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to reveal a geometrical feature or a physical quantity. The program is developed as a graphical interface for the MOLCAS program package, however its adaptive nature makes possible to use luscus with other computational program packages and chemical formats. All data files are opened via simple plug-ins which makes easy to implement a new file format in luscus. The easiness of editing molecular geometries makes luscus suitable for teaching students chemical concepts and molecular modelling.

lucas

Journal of Cheminformatics 2015, 7:16 [DOI](http://dx.doi.org/10.1186/s13321-015-0060-z}

The source code is available on Sourceforge

Comments

PYMOL under Yosemite

 

Reading through the discussion on Scientific Applications under Yosemite it seems some people are having problems with PYMOL, I thought I'd mention that installation of PYMOL using Homebrew is included on the page describing how to set up a Mac for Cheminformatics. The page also describes how to install a wide range of other useful tools.

Comments

BioBlender is now opensource

 

BioBlender, the molecular visualization and animation tool based on Blender, is now an Open Program on GitHub. You can find it here: https://github.com/MonZop/BioBlender.

BioBlender is an addon for Blender, aimed at providing tools for the import and elaboration of biological molecules. It consists of several functions, some executed by Blender and/or its Game Engine, and some others performed by external programs, such as PyMOL, APBS etc.

It was developed by the Scientific Visualization Unit of the Institute of Cliniclal Physiology of the CNR of Italy in Pisa, with the contribution of several colleagues.

Comments