Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-22T15:18:25.323Z
Answers.Text: 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.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-22T14:09:40.850Z
Answers.LastActivityDate: 2020-05-22T14:09:40.850Z
Answers.UserDisplayName: LauraCZD
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-15T22:21:47.160Z
Comments.Text: Use Biopython pdb, cross check manually in Pymol a subset of the output
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-18T15:33:08.313Z
Comments.Text: @Michael it's not clear to me that Biopython.PDB would be better here than PyMOL.
Comments.UserDisplayName: marcin
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-18T15:35:46.267Z
Comments.Text: 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.
Comments.UserDisplayName: marcin
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-19T21:33:39.723Z
Comments.Text: Covered here: https://bioinformatics.stackexchange.com/questions/12862/extract-autodocked-protein-ligand-connections-programatically/12888#12888
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-22T14:08:37.833Z
Comments.Text: @marcin I need to get the list of contacts and their distances for further analysis, not just visualise them.
Comments.UserDisplayName: LauraCZD
Tags: <python><protein-structure><protein-protein-interaction><structural-biology><pymol>
Title: Outputting crunchable list of HBonds from Pymol
ThreadText: # 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**: @username_2 I need to get the list of contacts and their distances for further analysis, not just visualise them.  
  
  ---
  
  ## 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.  
  
  ---
  
  