elelab / angle_histograms Goto Github PK

Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark


The chi_histo_plot.py is a simple python script that contains a function that can be used to generate histogram plots of protein dihedral angles (backbone or sidechain) from a molecular dynamics simulations.
The script uses in input files generated by the gmx chi tool of GROMACS and provides a histogram plot with a color scale over the simulation time.
It is a convenient tool to perform a dihedral scan along the entire protein structure during the simulation.

It contains two main functions:
1. a function to handle the plotting:
def hisColum(filelists, bins=36.0, figsize=(11.96, 6), njumps=11, shift=0):
    """Takes ((file1_1,file1_2,..),(file2_1,file2_2,..),..) and plots 
    histograms of file1* over file2* over ...
    njumps: coarse-grainedness of the time-coloring
    bins: number of bins in histogram
    shift: shift of residue number in the label"""

2. a helper function that plots for dir-names and the angles specified 
(Only good for up to ~10-15 residues)
def combined_plot(dir_names, angles=["phi", "psi", "chi1"], **kwargs):


You can use this script for different sequences, providing a sequence alignment file as input.
In the alignmen file the gap is '-'. If one of your sequence is shorter then the other than you should use ' ' where is no residue in the sequence. The labels must be the same in the alignment file as it is in the config file. This implies that you should separate the labels and the sequence with 'tab'.
Examples of the formats of config and alignment file are provide in the example_input_align format.

REQUIREMENTS:

The user needs first to have a working installation of GROMACS5 or higher and use the gmx chi tool to generate the input-files. Example of command line:
gmx_mpi chi -s $conf -f $traj -phi -psi -omega -all -maxchi 6

In cases in which you have more than one chain in the system, it is necessary to split the trajectory and the conf file into separated files and then run gmx chi.

If the user runs the analyses in remote, the graphical interface support should be used.

HOW TO RUN:

python chi_histo_plot.py -f config.cfg -align align.aln

When using the chi_histo_plot.py for publication please cite:

Matteo Lambrughi, Matteo Tiberti, Maria Francesca Allega, Valentina Sora, Mads Nygaard, Agota Toth, Juan Salamanca Viloria, Emmanuelle Bignon, Elena Papaleo*, Analyzing biomolecular ensembles, in preparation. 
Methods Mol Biol. 2019;2022:415-451. doi: 10.1007/978-1-4939-9608-7_18.