merenlab/SAAV-structural-mapping

Map single amino acid variants onto protein structures. Modus operandi: explore relationships between genetic variation and structural biology.

Don't use this!

The premise of this repositoriy has been superseded by an extension of anvi'o, and this repo still exists only for archival purposes / reproducibility. Please visit https://merenlab.org/software/anvio-structure/ if you want to map SAAVs onto structures, and do much more as well.

Requirements

1. PyMOL

   • All molecular visualizations are done using PyMOL (https://pymol.org). If you do not have a licensed version, not all features will be available to you. With the educational version everything will work except that the output images will be low quality (https://pymol.org/edu/?q=educational). With the open source version (https://sourceforge.net/projects/pymol/) SAAV coloring, transparency, and radius size will not work as expected :(

2. Python 2

   • All python programs with the line import pymol are written for Python 2. This is because it makes use of the program PyMOL (https://pymol.org/) for molecular visualization which is only developed for Python 2. If you want to go down the rabbit hole, you should be able to run the open source PyMOL version on Python 3 (https://sourceforge.net/projects/pymol/), but any of the programs with import pymol will need to be converted. Also, unfortunately some features we utilize are not available in the open source code :(