I've docked a large inorganic compound (receptor) with an organic molecule that isn't a protein (ligand). I wanted to see the interaction between them in a 2D diagram, but BIOVIA Discovery Studio (DS) doesn't work well with pdb files converted from pdbqt. And since the receptor isn't a protein or a fragment of DNA/RNA, DS also won't show the diagrams (the same with PLIP and Proteins Plus). I've also tried LigPlot, LeView and PoseView, but none of them worked as well. Does anyone know another software that draws 2D diagrams, and, if not, is there any way to do this in R???

  • $\begingroup$ Hi @ginn are you sure R is the right platform for this job? Generally, this is where Python excels. $\endgroup$
    – M__
    Commented Jun 2, 2023 at 14:36
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    $\begingroup$ Oh... I hadn't thought of that yet 😳🙈 but thank you so much for your input. Would you know, perhaps, of any package that does this job...? 👉🏻👈🏻 $\endgroup$
    – ginn
    Commented Jun 3, 2023 at 15:13
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    $\begingroup$ Beyond Bio.pdb biopython.org/docs/1.75/api/Bio.PDB.html and of course pymol - I dunno - I'm not a specialist in this area. There are members here who are experts, so maybe they'll respond. $\endgroup$
    – M__
    Commented Jun 3, 2023 at 17:02
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    $\begingroup$ I've tried PyMOL, but apparently you have to install the pose view plugin, which you need to be licensed to use... But thank you so much once again!!! I'll try bio.pdb in the meantime ☺️ $\endgroup$
    – ginn
    Commented Jun 3, 2023 at 17:10


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