<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>

CC BY-SA 4.0
2024-07-14T17:26:25.720Z
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/
pippo1980
CC BY-SA 4.0
2024-07-19T14:40:24.793Z
Thank you @pippo1980
aspergillus
<python><protein-structure><pymol><protein-protein-interaction><interactions>
LigPlot (LigPlus) Giving Different Interactions on Command Line and GUI
# 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:
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.

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

**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 @pippo1980  

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## 0 answers

