Macs in Chemistry

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PyMOL 2.3 released

 

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We are happy to announce the release of PyMOL 2.3. Download ready-to-use bundles from https://pymol.org/2/ or update your installation with "conda install -c schrodinger pymol". New features include: - Atom-level cartoon transparency - Fast MMTF export - Sequence viewer gaps display

This is the first time there are PyMOL bundles with Python 3. If you use custom or third-party Python 2 scripts, they might stop working until you convert them.

Full release notes are here https://pymol.org/dokuwiki/?id=media:new23 and


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New release of MayaChemTools

 

A new release of MayaChemTools is now available, these comprise a fantastic collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.

The core set of command line Perl scripts available in the current release of MayaChemTools has no external dependencies and provide functionality for the following tasks:

  • Manipulation and analysis of data in SD, CSV/TSV, sequence/alignments, and PDB files
  • Listing information about data in SD, CSV/TSV, Sequence/Alignments, PDB, and fingerprints files
  • Calculation of a key set of physicochemical properties, such as molecular weight, hydrogen bond donors and acceptors, logP, and topological polar surface area
  • Generation of 2D fingerprints corresponding to atom neighborhoods, atom types, E-state indices, extended connectivity, MACCS keys, path lengths, topological atom pairs, topological atom triplets, topological atom torsions, topological pharmacophore atom pairs, and topological pharmacophore atom triplets
  • Generation of 2D fingerprints with atom types corresponding to atomic invariants, DREIDING, E-state, functional class, MMFF94, SLogP, SYBYL, TPSA and UFF
  • Similarity searching and calculation of similarity matrices using available 2D fingerprints
  • Listing properties of elements in the periodic table, amino acids, and nucleic acids
  • Exporting data from relational database tables into text files

The command line Python scripts based on RDKit provide functionality for the following tasks:

  • Calculation of molecular descriptors and partial charges
  • Comparison of 3D molecules based on RMSD and shape
  • Conversion between different molecular file formats
  • Enumeration of compound libraries and stereoisomers
  • Filtering molecules using SMARTS, PAINS, and names of functional groups
  • Generation of graph and atomic molecular frameworks
  • Generation of images for molecules
  • Performing structure minimization and conformation generation based on distance geometry and forcefields
  • Performing R group decomposition
  • Picking and clustering molecules based on 2D fingerprints and various clustering methodologies
  • Removal of duplicate molecules and salts from molecules

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
  • Mutating amino acids and nucleic acids
  • Generating Ramachandran plots
  • Visualizing X-ray electron density and cryo-EM density
  • Visualizing macromolecules in terms of chains, ligands, and ligand binding pockets
  • Visualizing cavities and pockets in macromolecules
  • Visualizing macromolecular interfaces
  • Visualizing surface and buried residues in macromolecules

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New functionality in PyMOL command line scripts

 

MayaChemTools is a growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.

The PyMOL command line scripts now have additional functionality:

  • Volume objects to visualize X-ray and cryo-EM density for complex, chains, ligands, binding pockets, pocket solvents, pocket inorganics, etc.
  • Alignment of macromolecules and densities during visualization of X-ray and cryo-EM densities
  • Surface colored by vacuum electrostatics at residue level for chains and pockets
  • Surface colored by hydrophobicity along with charge at atom level for chains and pockets
  • Aromatic, polar, positively charged, negatively charged, and other residue group objects for chains and pockets

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MayaChemtools

 

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.


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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.

900px-Cluster_mols_py_pymol

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.


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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.


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PyMOLProbity

 

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.

1600px-pymolprobity_gui.png

Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21 DOI.

Full installation instructions are here

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.


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Pymol and very large PDB files. The Zika Cryo-EM structure as a case study

 

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.


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jupyter-docker-pymol

 

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

This project uses PyMol 1.8.2.0 and Python 3

png0


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Pymol under El Capitan

 

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 1.7.6.0.
 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/1.7.6.0/libexec/lib/python2.7/site-packages/pymol/__init__.py" "$@&ldquo;

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.

pymol

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