Body: <p>I am trying to determine the interaction of the targeted amino acid with other amino acids, but I am having trouble. When I pass a PDB file of a protein that has ligands, I can see the interactions. However, when I pass a PDB file of a protein without ligands, I don't see any interactions. Interestingly, when I run this ligand-free PDB file through LigPlot GUI, it shows the interactions.</p>
  <p>PDB ID example: 1BBT</p>
  <p>Here is the code I wrote:</p>
  <pre class="lang-py prettyprint-override"><code>filename = &quot;1BBT.pdb&quot;
  ligPlotLoc = &quot;LigPlus&quot;
  programLoc = f&quot;{ligPlotLoc}/lib/exe_linux64/&quot;
  ligplot_prm = f&quot;{ligPlotLoc}/lib/params/ligplot.prm&quot;
  atom_number = 82
  chain_ID = 1
  
  os.system(f&quot;{programLoc}hbadd {filename} {ligPlotLoc}/components.cif -wkdir ./&quot;)
  os.system(f&quot;{programLoc}hbplus -L -f hbplus.rc -h 2.90 -d 3.90 -N {filename} -wkdir ./&quot;)
  os.system(f&quot;{programLoc}hbplus -L -f hbplus.rc -h 2.70 -d 3.35 {filename} -wkdir ./&quot;)
  os.system(f&quot;{programLoc}ligplot {filename} {atom_number} {atom_number} {chain_ID} -wkdir ./ -prm {ligplot_prm} -ctype 1&quot;)
  </code></pre>
  <p>Below is the image of the interaction I obtained from running the LigPlot command line.
  <a href="https://i.sstatic.net/tCHoO6hy.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/tCHoO6hy.png" alt="enter image description here" /></a></p>
  <p>Below is the interaction that I am trying to get using the LigPlot command line but haven't been able to. However, I successfully obtained it using the LigPlot GUI. But wanted to get it done through ligplot command
  <a href="https://i.sstatic.net/Lhi7kjJd.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Lhi7kjJd.png" alt="enter image description here" /></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-14T17:26:25.720Z
Comments.Text: its not free, so you better ask to the user community or here https://www.ebi.ac.uk/thornton-srv/software/LigPlus/contactus.html In case of any problems or questions relating to LigPlot+, please contact (preferably by e-mail):
  
  Roman Laskowski
  European Bioinformatics Institute,
  Wellcome Trust Genome Campus,
  Hinxton,
  Cambridge, CB10 1SD,
  United Kingdom
  
  Phone Number: +44 (0)1223 492 542
  Fax Number: +44 (0)1223 494 468
  Email: roman@ebi.ac.uk
  Personal Page: http://www.ebi.ac.uk/~roman/
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-19T14:40:24.793Z
Comments.Text: Thank you @pippo1980
Comments.UserDisplayName: aspergillus
Tags: <python><protein-structure><pymol><protein-protein-interaction><interactions>
Title: LigPlot (LigPlus) Giving Different Interactions on Command Line and GUI
ThreadText: # LigPlot (LigPlus) Giving Different Interactions on Command Line and GUI
  
  (Asked by: username_0 on 2024-07-02)
  
  I am trying to determine the interaction of the targeted amino acid with other amino acids, but I am having trouble. When I pass a PDB file of a protein that has ligands, I can see the interactions. However, when I pass a PDB file of a protein without ligands, I don't see any interactions. Interestingly, when I run this ligand-free PDB file through LigPlot GUI, it shows the interactions.
  
  PDB ID example: 1BBT
  
  Here is the code I wrote:
  
  ```py
  filename = "1BBT.pdb"
  ligPlotLoc = "LigPlus"
  programLoc = f"{ligPlotLoc}/lib/exe_linux64/"
  ligplot_prm = f"{ligPlotLoc}/lib/params/ligplot.prm"
  atom_number = 82
  chain_ID = 1
  
  os.system(f"{programLoc}hbadd {filename} {ligPlotLoc}/components.cif -wkdir ./")
  os.system(f"{programLoc}hbplus -L -f hbplus.rc -h 2.90 -d 3.90 -N {filename} -wkdir ./")
  os.system(f"{programLoc}hbplus -L -f hbplus.rc -h 2.70 -d 3.35 {filename} -wkdir ./")
  os.system(f"{programLoc}ligplot {filename} {atom_number} {atom_number} {chain_ID} -wkdir ./ -prm {ligplot_prm} -ctype 1")
  
  ```
  
  Below is the image of the interaction I obtained from running the LigPlot command line.
  [![enter image description here](https://i.sstatic.net/tCHoO6hy.png)](https://i.sstatic.net/tCHoO6hy.png)
  
  Below is the interaction that I am trying to get using the LigPlot command line but haven't been able to. However, I successfully obtained it using the LigPlot GUI. But wanted to get it done through ligplot command
  [![enter image description here](https://i.sstatic.net/Lhi7kjJd.png)](https://i.sstatic.net/Lhi7kjJd.png)
  
  **Tags:** python, protein-structure, pymol, protein-protein-interaction, interactions
  
  > **Comments:**
  > **username_1**: its not free, so you better ask to the user community or here https://www.ebi.ac.uk/thornton-srv/software/LigPlus/contactus.html In case of any problems or questions relating to LigPlot+, please contact (preferably by e-mail):  Roman Laskowski European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom  Phone Number: +44 (0)1223 492 542 Fax Number: +44 (0)1223 494 468 Email: roman@ebi.ac.uk Personal Page: http://www.ebi.ac.uk/~roman/  
  > **username_0**: Thank you @username_1  
  
  ---
  
  ## 0 answers
  
  