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PyRAMA

Python3 implementation of the Ramachandran plot

Package does work with Python2.7 but it is recommended to use Python3

For easy installation use pip:

pip3 install pyrama

Usage:

pyrama my_pdb_file.pdb -o output_folder --no-show

Note: The script is able to read in multiple PDB files, and can also process multiple chain automatically now. The outliers would be annotated with labels.

Example output:

Example output

Dependencies:

Running PyRAMA requires matplotlib, numpy and biopython

To install these on a standard Linux system:

apt install python3-matplotlib
apt install python3-biopython
apt install python3-numpy

For the standard PSI and PHI preferences see:

Lovell et al. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. 2003; DOI: 10.1002/prot.10286