PYMOL: Output Polar Contacts Between Chains to Text File
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9 weeks ago

I am new to PyMOL but have a very specific task that I need to do.

I have a PDB structure file of protein homo-oligomer, and I want to use PyMol to determine polar contacts between chain A and all other chains.

However, I not only want to visualize these polar contacts (which is easy to do via PyMOL GUI), but I also want to be able to store/save pairs of interacting residues in a dictionary or whatever may be the most convenient data structure to do this. The end goal to create a sort of "interaction map" in a csv or text file where each interacting pair of residues has its own line.

I would ideally like to do this via a Python script where I call the PyMOL API or through a PYMOL script - whichever is easier.

I have reviewed a similar question on Stack Overflow (https://stackoverflow.com/questions/49633809/pymol-select-residues-for-which-i-have-found-hydrogen-bonds) but found it unhelpful because I not only want to select and visualize these polar contacts but also want to save/record them in a list or dictionary (and then to a text or csv file), which the above question does not address.

PyMol Python • 268 views
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Cross-posted and answered on bioinfo SE: https://bioinformatics.stackexchange.com/questions/17548/pymol-output-polar-contacts-between-chains-to-text-file

Berk,

Please do not create the same post on multiple forums - it is bad etiquette and is frowned upon. See this discussion: https://bioinformatics.meta.stackexchange.com/questions/265/about-posting-queries-in-stack-bioinformatics

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