PyMOL pyKVFinder Tools

The pyKVFinder package is integrated into PyMOL through a plugin, called PyMOL pyKVFinder Tools. This plugin allows the user to run pyKVFinder in PyMOL and visualize the results directly on the PyMOL viewer.

Installation

First, it is required to install Anaconda or Miniconda (Python 3.10 or later). If you do not have it installed, please refer to Anaconda or Miniconda websites.

In the Anaconda Prompt, create a new environment and activate it:

conda create -n pymol python=3.10
conda activate pymol

Then, install one of the following versions of PyMOL:

  • PyMOL v3.0 (Schrodinger):

    conda install -c conda-forge -c schrodinger pymol-bundle

  • PyMOL v2.6 (Schrodinger):

    conda install -c conda-forge -c schrodinger pymol-bundle=2.6

  • PyMOL Open-Source:

    conda install -c conda-forge pymol-open-source

After installing one of the PyMOL versions (v3.0, v2.6 or Open-Source), you need to install the pyKVFinder package, if you have not done it yet:

pip install pyKVFinder

Then, to install the PyMOL pyKVFinder Tools on PyMOL, download the latest PyMOL-pyKVFinder-Tools.zip from here and follow these steps:

  1. Open PyMOL.

  2. Go to Plugin menu, click on Plugin Manager.

  3. The Plugin Manager window will open, go to the Install New Plugin tab.

  4. Under Install from local file panel, click on Choose file….

  5. The Install Plugin window will open, select the PyMOL-pyKVFinder-Tools.zip that you downloaded earliar.

  6. The Select plugin directory window will open, select /home/<user>/.pymol/startup and click OK.

  7. The Confirm window will open, click OK.

  8. The Sucess window will appear, confirming that the plug-in has been installed.

  9. Restart PyMOL.

  10. PyMOL pyKVFinder Tools is ready to use.

Or, instead of selecting PyMOL-pyKVFinder-Tools.zip (Step 5), you can select __init__.py file on pyKVFinder/plugins/PyMOL-pyKVFinder-Tools directory tree.

Summary

  1. Download and install Anaconda or Miniconda.

  2. Open the Anaconda Prompt and execute the following commands:

conda create -n pymol python=3.10
conda activate pymol
conda install -c conda-forge -c schrodinger pymol-bundle
pip install pyKVFinder
pymol

  1. Download the latest PyMOL-pyKVFinder-Tools.zip and install it on PyMOL: Plugin > Plugin Manager > Install New Plugin > Choose file… > PyMOL-pyKVFinder-Tools.zip > OK > OK.

Tutorial

This section offers step-by-step tutorials on how to use the PyMOL pyKVFinder Tools to detect and analyze cavities in biomolecular and supramolecular cage structures. The tutorials are organized into two categories: