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X-posted from the Main Stack Overflow because folks here are possibly more familiar with PyMol(?)

I have been trying to assess the strength of an interface I want to mutate using Pymol. What I am interested in is a list of contacts withing a specified interface (which I have calculated using the InterfaceResidues.py script from the PyMol wiki script library). My aim is to produce a bunch of mutants using the mutagenesis wizard and assess how the HBond network changes.

Actions>Find>Polar Contacts does the trick in visualising them, but doesn't output a file with numbers which I can then crunch to assess which mutations weaken my interface most. I have been trying the scripts list_contacts.py and list_hb.py from Prof. Robert Campbell of Queen's University at Kingston, but with limited success (nothing gets printed or written to the file). The scripts can be found here http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

I am going to contact Prof. Campbell directly re: scripts but, in the meantime, and in case he's too busy to deal with a Pymol noob, does anyone have any ideas of what else I could try?

I am using Pymol 2.3.1 and Python 3.7.1

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  • $\begingroup$ Use Biopython pdb, cross check manually in Pymol a subset of the output $\endgroup$
    – M__
    May 15 '20 at 22:21
  • $\begingroup$ @Michael it's not clear to me that Biopython.PDB would be better here than PyMOL. $\endgroup$
    – marcin
    May 18 '20 at 15:33
  • $\begingroup$ How do you use these script? I had only a quick look at them: running these scripts defines a new command in PyMOL. Then you need to run that command. $\endgroup$
    – marcin
    May 18 '20 at 15:35
  • $\begingroup$ Covered here: bioinformatics.stackexchange.com/questions/12862/… $\endgroup$
    – Matteo Ferla
    May 19 '20 at 21:33
  • $\begingroup$ @marcin I need to get the list of contacts and their distances for further analysis, not just visualise them. $\endgroup$
    – LauraCZD
    May 22 '20 at 14:08
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Thanks a lot to all who commented/replied, the author of the scripts provided a response. It was down to a syntax change in PyMol of which I wasn't aware that caused my selection to come up empty.

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  • $\begingroup$ Can you expound upon the syntax change, ideally giving the exact line or two of code in question? That may help others running into the same problem. $\endgroup$
    – Devon Ryan ♦
    May 22 '20 at 15:18

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