Skip to main content
Help improve PyPI by participating in a 5-minute user interface survey!

Shows protein backbone structures in compact graphical form using Ramachandran numbers

Project Description

  ____             _    __  __          _____  
 |  _ \           | |  |  \/  |   /\   |  __ \ 
 | |_) | __ _  ___| | _| \  / |  /  \  | |__) |
 |  _ < / _` |/ __| |/ / |\/| | / /\ \ |  ___/ 
 | |_) | (_| | (__|   <| |  | |/ ____ \| |     
 |____/ \__,_|\___|_|\_\_|  |_/_/    \_\_|     
                       (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

Release history Release notifications

History Node

0.2.4.post0.dev3

History Node

0.2.4.post0.dev2

History Node

0.2.3.post0.dev3

History Node

0.2.2

History Node

0.2.1

History Node

0.2.0

History Node

0.1.0.post0.dev1

History Node

0.0.3.post0.dev4

History Node

0.0.3.post0.dev3

History Node

0.0.3.post0.dev1

History Node

0.0.2.post0.dev1

History Node

0.0.1.post0.dev13

This version
History Node

0.0.1.post0.dev12

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
backmap-0.0.1.post0.dev12.tar.gz (24.3 MB) Copy SHA256 hash SHA256 Source None Apr 6, 2018

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page