Shows protein backbone structures in compact graphical form using Ramachandran numbers
____ _ __ __ _____ | _ \ | | | \/ | /\ | __ \ | |_) | __ _ ___| | _| \ / | / \ | |__) | | _ < / _` |/ __| |/ / |\/| | / /\ \ | ___/ | |_) | (_| | (__| <| | | |/ ____ \| | |____/ \__,_|\___|_|\_\_| |_/_/ \_\_| (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.
pip install backmap
pip install -I backmap
import backmap print backmap.R(phi=0,psi=0)
See the manuscript for more information regarding uses.
python -m backmap.__init__ -pdb ./pdbs/ProteinDatabankStructureFilename.pdb python -m backmap.__init__ -pdb /directory/containing/pdbs/
.__init__ is needed because the main file we are referencing is
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.)
-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
The Ramachandran number concept is discussed in the following manuscripts (this tool is discussed in the first reference):
- 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.
- 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