MayaChemTools now includes a collection of python scripts for PyMol
The command line Python scripts based on PyMOL provide functionality for the following tasks:
Aligning macromolecules Splitting macromolecules into chains and ligands Listing information about macromolecules Calculation of physicochemical properties Comparison of marcromolecules based on RMSD Conversion between different ligand file formats Visualizing X-ray electron density and cryo-EM density Visualizing macromolecules in terms of chains, ligands, and ligand binding pockets
MayaChemTools is a growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.
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: https://bitbucket.org/mpb21/clustermols_py/overview
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.
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
- 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
- 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)
- Changed default values for several settings:
- autoshowclassified=1 (=3 for > 500k atoms)
- “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
- 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.
Just heard of a new PYMOL plugin, created by Jared Sampson, called PyMOLProbity which allows a PyMOL user to visualize MolProbity-style structural validation data directly in a PyMOL session. PyMOLProbity is a plugin allows the user to produce MolProbity-style visualization of atomic interactions within a structure (e.g. H-bonds, van der Waals interactions and clashes) directly within a PyMOL session.
The plugin runs local copies of several executable programs from the Richardson Lab at Duke University, authors of the MolProbity software, parses the output, and displays the results in the PyMOL viewport. There are both a graphical user interface (GUI) for general point-and-click use, and a command-line interface (CLI) suitable for scripting.
Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21 DOI.
The Reduce, Probe, and Prekin executables are only available for Linux and MacOS, PYMOL is available from Schrödinger and also available via Homebrew, you will need to install XQuartz first.
There are detailed instructions on how to install a variety of chemistry/cheminfomatics/biology packages on a Mac here.
An interesting post on chemistry and computers, Pymol and very large PDB files. The Zika Cryo-EM structure as a case study. Always good to see people stress testing computational tools.
When El Capitan first came out I upgraded a machine with an existing installation of a variety of cheminformatics tools installed using Homebrew and PIP as described here. Under this situation Pymol worked without problem. However I have had a few readers email me saying they are having problems so I took a new machine running El Capitan and tried to instal the same cheminformatics tools including Pymol using Homebrew and PIP. All worked fine except Pymol which opened but crashed with the following error.
Username:~ prompt$ pymol PyMOL(TM) Molecular Graphics System, Version 18.104.22.168. Copyright (c) Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at "http://www.pymol.org". Enter "help" for a list of commands. Enter "help <command-name>" for information on a specific command. Hit ESC anytime to toggle between text and graphics. Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: NVIDIA GeForce 8600M GT OpenGL Engine GL_VERSION: 2.1 NVIDIA-10.0.40 310.90.10.05b12 Detected 2 CPU cores. Enabled multithreaded rendering. libpng warning: Application built with libpng-1.6.19 but running with 1.5.23 /usr/local/bin/pymol: line 4: 3628 Segmentation fault: 11 "/usr/local/opt/python/bin/python2.7" "/usr/local/Cellar/pymol/22.214.171.124/libexec/lib/python2.7/site-packages/pymol/__init__.py" "$@“
The helpful on the Pymol user list pointed me to this message on the Homebrew-Science issues
First uninstall pymol and libpng
brew uninstall pymol brew uninstall libpng
then install pymol first.
brew install pymol brew install libpng
Now when you type pymol in a Terminal window you should see.