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View Code? Open in Web Editor NEWA Python package to calculate, visualize and analyze correlation maps of proteins.
License: GNU Lesser General Public License v3.0
A Python package to calculate, visualize and analyze correlation maps of proteins.
License: GNU Lesser General Public License v3.0
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
correlationplus visualize -p nvt_run_1_solute.pdb -i nLMI.dat -o nLMI.png
outputs this error
AttributeError: module 'pyparsing' has no attribute 'operatorPrecedence'
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?
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?
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.
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,
What is the color scale for the pymol (pml) files? and what are red/orange spheres?
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