<p>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.</p>

CC BY-SA 4.0
2020-05-22T15:18:25.323Z
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.
Devon Ryan
CC BY-SA 4.0
2020-05-22T14:09:40.850Z
2020-05-22T14:09:40.850Z
LauraCZD
<p>X-posted from the Main Stack Overflow because folks here are possibly more familiar with PyMol(?)</p>

<p>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.</p>

<p>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 <a href="http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/" rel="nofollow noreferrer">http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/</a></p>

<p>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?</p>

<p>I am using Pymol 2.3.1 and Python 3.7.1</p>

CC BY-SA 4.0
2020-05-15T22:21:47.160Z
Use Biopython pdb, cross check manually in Pymol a subset of the output
M__
CC BY-SA 4.0
2020-05-18T15:33:08.313Z
@Michael it's not clear to me that Biopython.PDB would be better here than PyMOL.
marcin
CC BY-SA 4.0
2020-05-18T15:35:46.267Z
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.
marcin
CC BY-SA 4.0
2020-05-19T21:33:39.723Z
Covered here: https://bioinformatics.stackexchange.com/questions/12862/extract-autodocked-protein-ligand-connections-programatically/12888#12888
Matteo Ferla
CC BY-SA 4.0
2020-05-22T14:08:37.833Z
@marcin I need to get the list of contacts and their distances for further analysis, not just visualise them.
LauraCZD
<python><protein-structure><protein-protein-interaction><structural-biology><pymol>
Outputting crunchable list of HBonds from Pymol
# Outputting crunchable list of HBonds from Pymol

(Asked by: username_0 on 2020-05-15)

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

**Tags:** python, protein-structure, protein-protein-interaction, structural-biology, pymol
> **Comments:**
> **username_1**: Use Biopython pdb, cross check manually in Pymol a subset of the output  
> **username_2**: @Michael it's not clear to me that Biopython.PDB would be better here than PyMOL.  
> **username_2**: 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.  
> **username_3**: Covered here: https://bioinformatics.stackexchange.com/questions/12862/extract-autodocked-protein-ligand-connections-programatically/12888#12888  
> **username_0**: @marcin I need to get the list of contacts and their distances for further analysis, not just visualise them.  

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## 1 answers

### Answer by username_0 on 2020-05-22. Score: 1

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.

> **Comments:**
> **username_4**: 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.  

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