psico is a python module which extends PyMOL, a molecular visualization tool (https://pymol.org).
https://pymolwiki.org/index.php/psico
A reference document with all commands can be generated with:
psico.helping.write_html_ref('psico-commands.html')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-psicoTo activate all psico commands in PyMOL, add this to your ~/.pymolrc.py
file (or just enter into the PyMOL command line):
import psico.fullinit- 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/)