This readme is out of date. Currently the scripts are in development. This readme will be updated once a stable version is achieved.

The aim is to roll out TMSOC like function into 3D protein structures. This allows us to study the role of anchors, as well as TMHs with function beyond anchorage, in 3D space. The higher the complexity, the more likely the transmembrane helix is to have function beyond anchorage.

Currently, the software is available for Linux distributions only since it is dependent on the decodeanhmm file underlying Phobius.

The script uses Phobius to estimate TMH boundaries. TMSOC is then used to assess complexity and the results are viewable in Pymol. The TMH regions are coloured accordingly:

Figure. Cartoon of a GPCR structure coloured according to Complexity of the TMHs.

This software requires Linux, python3, biopython, TMSOC (included), Phobius (included), and Pymol.

Move the pdb file into the complexity_in_pymol/pymol/ directory and then run bash runme.sh in a terminal from the complexity_in_pymol/pymol/ folder. In Pymol, navigate to the complexity_in_pymol/pymol/ and after loading the structure enter run bfactors.py and then complexb YOURSTRUCTURENAME, start position of strcutre, bfactors_YOURSTRUCTURENAME_SUBCHAIN.txt.

These scripts are in development and are provided as is. Use at your own risk.

Complexity In Pymol Copyright (C) 2017 James Alexander Baker

This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions.

An unmodified copy of Phobius (provided on 3rd April 2017) is included along with these scripts. Phobius was licensed for private study, education or non-profit research only, granted to James Baker, who agreed to these conditions on http://software.sbc.su.se/cgi-bin/request.cgi?project=phobius

To cite Phobius:

Lukas Käll, Anders Krogh and Erik L. L. Sonnhammer. A Combined Transmembrane Topology and Signal Peptide Prediction Method. Journal of Molecular Biology, 338(5):1027-1036, May 2004.