Pymol ScrIpt COllection (PSICO)
DESCRIPTION
"psico" is a python module which extends PyMOL, a molecular visualization
tool (http://pymol.org).
DOCUMENTATION
http://pymolwiki.org/index.php/psico
https://github.com/speleo3/pymol-psico
A reference document with all commands can be generated with:
PyMOL> psico.helping.write_html_ref('psico-commands.html')
INSTALLATION
(1) Any of:
(1.1) Use the conda package manager:
conda install -c schrodinger pymol-psico
(1.2) Use the setup.py script:
python setup.py install
(1.3) Or just copy the "psico" directory to
PYTHONPATH (for example /path/to/pymol-xxx/modules/).
(2) Add to your ~/.pymolrc.py file (or just enter into the PyMOL command
line):
import psico.fullinit
EXTERNAL PROGRAMS AND LIBRARIES
Some functions in psico require the following python modules:
* numpy
* Bio (biopython)
* MMTK
* 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 (http://www.cmbi.ru.nl/dssp.html)
* stride (http://webclu.bio.wzw.tum.de/stride/)
* TMalign (http://zhanglab.ccmb.med.umich.edu/TM-align/)
* TMscore
* MMalign
* theseus (http://www.theseus3d.org)
* needle (http://emboss.sourceforge.net)
* DynDom (http://fizz.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 (http://mgltools.scripps.edu/packages/MSMS)
AUTHORS
Thomas Holder (1,2,3) <thomas.holder@schrodinger.com>
Steffen Schmidt (1) <steffen.schmidt@tuebingen.mpg.de>
(1) Max Planck Institute for Developmental Biology, Germany
(2) Warren L. DeLano Memorial PyMOL Open-Source Fellowship 2011-2012
(3) Schrodinger, Inc.
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