tekpinar/correlationplus

A Python package to calculate, visualize and analyze correlation maps of proteins.

correlationplus's Issues

correlationplus paths

Hi,

When using correlationplus paths, how can I just extract just the residues in the path. I get a tcl and pml file as the output at the end but the residues in those two files are different. Also, if I am running correlationplus paths analysis with wild type and a mutant, how can I interpret the data if I see that the path differs between them?
Also, does the frequency/stride of trajectory affect the nLMI calculations?

module 'pyparsing' has no attribute 'operatorPrecedence'

correlationplus visualize -p nvt_run_1_solute.pdb -i nLMI.dat -o nLMI.png

outputs this error

AttributeError: module 'pyparsing' has no attribute 'operatorPrecedence'

color scale for pml

What is the color scale for the pymol (pml) files? and what are red/orange spheres?

using correlationplus for DNA-protein systems

I was wondering if their is anyway to use corrplus for direct dna-protein trajectory analysis ? I noticed that the way its currently coded it assumes that the system is composed strictly of a protein but it seems like a very minor modification to allow it to directly compute dna-protein correlations. Is such a feature intended? If not, could you perhaps advise how I should proceed to modify it to this purpose ?

Thanks in advance,

Rotations and translations

Hello. Thank you very much for this helpful tool. I would like to ask in the case of an MD trajectory input, if the program removes rotations and translations or if I should take care of them beforehand.

Thank you very much.
Alexis

About the LMI equation (6) in your correlation_plus paper

Hi, I read the paper titled with "Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Conmmunication in Proteins by correlationplus", I wonder where does the equation (6) comes from. It looks different from the general mutual information equation I learned before. Could you give me some explanations about it?

change axes (residue indices)

Hello!
I am currently using correlationplus to analyze residue based ndcc matrices on a dimer.
I want to change the residue indices spacing to like 0 10 20 30 40 50...all the way to 550
However I am not sure how I can achieve that
correlationplus visualize -h does not give me any options to play with the scale of the residue axis.

Thanks in advance