PyVOL Documentation

PyVOL Pocket Identification

Overview

PyVOL is a python library packaged into a PyMOL GUI for identifying protein binding pockets, partitioning them into sub-pockets, and calculating their volumes. PyVOL can be run as a PyMOL plugin through its GUI or the PyMOL prompt, as an imported python library, or as a command-line program. Visualization of results is exclusively supported through PyMOL though exported surfaces are compatible with standard 3D geometry visualization programs. The project is hosted on github by the Schlessinger Lab. Please access the repository to view code or submit bugs. The package has been most extensively tested with PyMOL 2.3+ running Python 3.7. Support for all python versions 2.7+ is intended but not as thoroughly tested. Support for PyMOL 1.7.4+ without the GUI is as yet incomplete. Unfortunately, PyVOL can not currently run on MacOS Catalina due to its restrictions on running 32-bit executables. The Mac-compatible MSMS executable is not yet available in a 64-bit form.

Quick Installation into PyMOL 2.0+

PyVOL can be installed into any python environment, but installing directly into PyMOL 2.0+ is easiest. Download the basic GUI installer and then use the PyMOL plugin manager to install that file: Plugins ‣ Plugin Manager ‣ Install New Plugin ‣ Install from local file ‣ Choose file…

This installs the PyVOL GUI. Select Plugins ‣ PyVOL ‣ Settings ‣ Install PyVOL from PyPI to fetch PyVOL and any missing dependencies. Once PyVOL has been installed, the location of MSMS must be added to the path. In the MSMS Settings panel, common locations for the executable can be searched. Once an executable has been identified and is displayed, Change MSMS Path can be clicked to make that executable visible to the back-end. The GUI should then display that it can find MSMS. For academic users and non-academic users with the Schrodinger incentive PyMOL distribution, installation is now complete. For all others MSMS Installation.

Example Basic Run

A simple calculation using the PyMOL prompt is to load a protein of interest and then run the pocket command. This is an example for the Sorafenib-bound structure of BRAF:

fetch '1uwh'
pocket protein="1uwh and chain B"

• Introduction
  • Overview
  • Quick Installation into PyMOL 2.0+
  • Example Basic Run
• Installation
  • GUI Installation into PyMOL from PyPI
  • GUI Installation into PyMOL from a Packaged Installer
  • PyMOL Prompt Installation into PyMOL
  • Manual Installation
  • MSMS Installation
  • Updating
  • Uninstalling
• Basic Usage
  • Protein Selection
  • Minimum and Maximum Probe Radii
  • Input Constraint
• Pocket Specification
  • All Mode
  • Largest Mode
  • Specific Mode
    • Ligand Specification
    • Residue Specification
    • Coordinate Specification
• Partitioning Options
  • Enabling Subpocket Partitioning
  • Controlling the Number of Subpockets
  • Other Partitioning Parameters
• Output and Display Options
  • File Output Options
  • Logger Options
  • Display Options
• Shell Interface
  • Running from the Shell
  • Template Configuration File Generation
  • Rerunning Previous Calculations
• Loading Previous Results
• Development
  • Package Design
  • Algorithm Design
  • GUI Design
  • Version Incrementation
  • Distribution
  • Documentation
  • Testing
• PyVOL Package
  • Submodules
  • PyVOL Cluster Module
  • PyVOL Identify Module
  • PyVOL Pymol Interface Module
  • PyVOL Pymol Utilities Module
  • PyVOL Spheres Module
  • PyVOL Utilities Module

Indices and tables

• Index

• Module Index