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Pymol ScrIpt COllection (PSICO)
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README

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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