Pymol ScrIpt COllection (PSICO)

psico is a python module which extends PyMOL, a molecular visualization tool (https://pymol.org).

Documentation

https://pymolwiki.org/index.php/psico

A reference document with all commands can be generated with:

psico.helping.write_html_ref('psico-commands.html')

Installation

Option 1: Install from source. In your activated (conda or venv) environment, run:

pip install .

Option 2: Use a conda-compatible package manager. In your activated conda environment, run:

micromamba install speleo3::pymol-psico

To activate all psico commands in PyMOL, add this to your ~/.pymolrc.py file (or just enter into the PyMOL command line):

import psico.fullinit

Dependencies

• PyMOL 2.3+ (https://pymol.org/)
• Python 3.7+

Some functions in psico require the following python modules:

• numpy
• Bio (biopython)
• csb (https://github.com/csb-toolbox/CSB)
• modeller
• prody
• rdkit (http://www.rdkit.org/)
• indigo (https://github.com/epam/Indigo)

psico has several wrappers for external tools. For full support, you need these binaries:

• dssp (https://swift.cmbi.umcn.nl/gv/dssp/)
• stride (http://webclu.bio.wzw.tum.de/stride/)
• TMalign (https://zhanggroup.org/TM-align/)
• TMscore
• MMalign
• theseus (http://www.theseus3d.org)
• needle (http://emboss.sourceforge.net)
• DynDom (http://dyndom.cmp.uea.ac.uk/dyndom/)
• qdelaunay (http://www.qhull.org)
• mencoder (http://www.mplayerhq.hu)
• pdbmat (http://ecole.modelisation.free.fr/modes.html)
• diagrtb
• apbs (http://www.poissonboltzmann.org/)
• pdb2pqr
• prosmart (http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/)
• p_sstruc3
• msms (https://ccsb.scripps.edu/msms/)