Answers.Body: <p><em>Answer from @maximilian-press, converted from comment. Please improve where possible:</em></p>
  <p>It seems that many of the files are not being found, including both run executables and your pdb files. That's what all the <code>No such file or directory</code> stuff is about.</p>
  <p>I would suggest confirming that you have completely installed PyMol and any of the relevant dependencies such as <code>Process_ligand</code> that are not being found. <a href="http://biophys.umontreal.ca/nrg/ewExternalFiles/NRGsuite_Guide.pdf" rel="nofollow noreferrer">Here is one resource</a> that might be relevant for that tool. Is <code>run_flexaid.sh</code> a script that you have written or a third-party tool? I can't find it by google. Can you show us how you ran it?</p>
  <p>I am guessing that <code>sh ./run_flexaid.sh</code> is the terminal command that you are using to run the script, but I still don't know where the script comes from. It's possible that running within the script is not using your environment properly somehow. What happens if you try to run <code>Process_ligand</code> on its own (if that's possible?). Have you confirmed that your input pdb files are in the right directory? Basically, it's hard to know what's going on without seeing the script and knowing where your input files live on your computer.</p>
  <p><em>Note: Comments are <strong>temporary</strong> &quot;Post-It&quot; notes left on a question or answer. They should be used for clarification or constructive criticism of questions or answers, not for answering (no matter how minor). More details on this StackExchange policy <a href="https://bioinformatics.stackexchange.com/help/privileges/comment">here</a>.</em></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-04-11T00:31:13.503Z
Answers.LastActivityDate: 2022-04-11T00:31:13.503Z
Answers.UserDisplayName: gringer
Body: <p>I have attached a screenshot from terminal, which is the result of me attempting to run Flexaid on my Mac.</p>
  <p>I was wondering if anyone knows why this isn't running?</p>
  <p>Thanks
  <a href="https://i.sstatic.net/TsBrM.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/TsBrM.jpg" alt="enter image description here" /></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-03T11:01:08.127Z
Comments.Text: Could you kindly check whether the answer below suffices @microbeprincess?  If so please do mark as "accepted", it helps with site stats
Comments.UserDisplayName: M__
Tags: <proteins><docking><pymol>
Title: Running into an error when loading Flexaid on PyMol 3.7
ThreadText: # Running into an error when loading Flexaid on PyMol 3.7
  
  (Asked by: username_0 on 2022-04-09)
  
  I have attached a screenshot from terminal, which is the result of me attempting to run Flexaid on my Mac.
  
  I was wondering if anyone knows why this isn't running?
  
  Thanks
  [![enter image description here](https://i.sstatic.net/TsBrM.jpg)](https://i.sstatic.net/TsBrM.jpg)
  
  **Tags:** proteins, docking, pymol
  
  > **Comments:**
  > **username_1**: Could you kindly check whether the answer below suffices @username_0?  If so please do mark as "accepted", it helps with site stats  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2022-04-11. Score: 1
  
  *Answer from @maximilian-press, converted from comment. Please improve where possible:*
  
  It seems that many of the files are not being found, including both run executables and your pdb files. That's what all the `No such file or directory` stuff is about.
  
  I would suggest confirming that you have completely installed PyMol and any of the relevant dependencies such as `Process_ligand` that are not being found. [Here is one resource](http://biophys.umontreal.ca/nrg/ewExternalFiles/NRGsuite_Guide.pdf) that might be relevant for that tool. Is `run_flexaid.sh` a script that you have written or a third-party tool? I can't find it by google. Can you show us how you ran it?
  
  I am guessing that `sh ./run_flexaid.sh` is the terminal command that you are using to run the script, but I still don't know where the script comes from. It's possible that running within the script is not using your environment properly somehow. What happens if you try to run `Process_ligand` on its own (if that's possible?). Have you confirmed that your input pdb files are in the right directory? Basically, it's hard to know what's going on without seeing the script and knowing where your input files live on your computer.
  
  *Note: Comments are **temporary** "Post-It" notes left on a question or answer. They should be used for clarification or constructive criticism of questions or answers, not for answering (no matter how minor). More details on this StackExchange policy [here](https://bioinformatics.stackexchange.com/help/privileges/comment).*
  
  
  ---
  
  