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Shows protein backbone structures in compact graphical form using Ramachandran numbers

Project description

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                       (Multi-angle Picture)                                             

This tool provides easily readable "pictures" of protein conformations, ensembles, and trajectories saved as either a combined protein databank (PDB) structure file, or a directory of such files, and produces graphs.

Installation

pip install backmap

RE-installation

pip install -I backmap

Usage

Module Usage

import backmap
print backmap.R(phi=0,psi=0)

See the manuscript for more information regarding uses.

Stand-alone Usage

python -m backmap.__init__ -pdb ./pdbs/ProteinDatabankStructureFilename.pdb
python -m backmap.__init__ -pdb /directory/containing/pdbs/

The .__init__ is needed because the main file we are referencing is backmap/__init__.py.

Expected output to the stand alone mode

Three graphs (in both png/raster and pdf/vector format)

./pdbs/reports/filename.rcode.pdf/png      (y-axis: residue #; color: R number based on "-signed" and <rcode_cmap>)
./pdbs/reports/filename.rcode.his.pdf/png  (y-axis: Ramachandran number (R); color: frequency of R in model)
./pdbs/reports/filename.rcode.rmsf.pdf/png (y-axis: residue #; color: RMSF in R from the previous model)
./pdbs/reports/filename.rcode.rmsd.pdf/png (y-axis: residue #; color: RMSD in R from the previous model)

(the last two files may not be created if only one model exists in the PDB file.)

Additional tags

-h       -     Prints a help file
-ss      -     Color the ramachandran number codes (R-codes) by 
               secondary structure (default: color by chirality and sign)
-signed  -     Use the signed version of the ramachandran number

Publications

The Ramachandran number concept is discussed in the following manuscripts (this tool is discussed in the first reference):

  1. Mannige (2018) "The Backmap Python Module: How a Simpler Ramachandran Number Can Simplify the Life of a Protein Simulator" Manuscript Prepared. Preprint available the manuscript/manuscript subdirectory of this repo.
  2. Mannige, Kundu, Whitelam (2016) "The Ramachandran Number: An Order Parameter for Protein Geometry" PLoS ONE 11(8): e0160023. Full Text: https://doi.org/10.1371/journal.pone.0160023

Project details


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