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PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
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README.md

PyMod 3

PyMod 3 is an open source PyMOL plugin, designed to act as an interface between PyMOL and several bioinformatics tools (for example: BLAST+, HMMER, Clustal Omega, MUSCLE, PSIPRED and MODELLER). The current PyMod release, PyMod 3, is compatible with the most recent PyMOL versions (2.3 or higher) and has been extended with new functionalities with respect to its predecessor (PyMod 2). Starting from the amino acid sequence of a target protein, users may take advantage of PyMod 3 to carry out the three steps of the homology modeling process (that is, template searching, target-template sequence alignment and model building) in order to build a 3D atomic model of a target protein (or protein complex). Additionally, PyMod 3 may also be used outside the homology modeling context, in order to extend PyMOL with numerous types of functionalities. Sequence similarity searches, multiple sequence/structure alignment building, evolutionary conservation analyses, domain parsing and loop modeling can be performed in the PyMod 3/PyMOL environment.

Requirements

PyMod 3 runs on Windows, macOS and Linux versions of PyMOL. It is compatible with PyMOL version >= 2.3 and is supported by both incentive PyMOL builds (distributed by Schrodinger) and open source builds.

Download

PyMod 3 plugin file (current version 3.0.0): download from here

Installation

Please refer to the PyMod 3 User's Guide to learn how to install PyMod 3 on your system. Long story short: PyMod 3 can be installed as any other PyMOL plugin. Download the PyMod 3 plugin file (a ZIP file named pymod3.zip, see the link above) and use the PyMOL plugin manager (Plugin -> Plugin Manager from the menu of its main window) to install it. The external tools of PyMod 3 can be obtained and configured through an easy-to-use installer dialog which can be launched by the plugin (Help -> Install PyMod Components from the main menu of the plugin). The way to configure MODELLER in PyMod may vary according to your PyMOL version (in the User's Guide we cover different scenarios).

How to use PyMod

A series of introductory tutorials and in-depth information about all the PyMod 3 functionalities can be found in its User's Guide.

User's Guide: download from here

Home page (to be updated soon): http://schubert.bio.uniroma1.it/pymod/index.html

Old PyMod 2 packages (obsolete, they only work on PyMOL 1.X): if necessary available from here

Contact: giacomo.janson@uniroma1.it

Licence

PyMod 3 is licensed under the LGPL.

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