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I have the PDB 6LU7.

  • I extracted the ligand using extract lig, org and then the protein using extract prot, poly. The ligand has three parts: 02J, PJE, and 010.

  • I want to select the 02J and 010 IN A SCRIPT and delete them.

I know how to do it by simply clicking, but want to incluse this in a script.

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  • $\begingroup$ Hi @user8338 and welcome. I think what you are asking is PyMol scripting, I suspect Modeller will do something similar. Do you use PyMol/Modeller? If so could you please update and clarify your post accordingly. Thanks! $\endgroup$
    – M__
    Jul 8, 2020 at 15:58

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I know that structure way too well —SARS-COV-2 MPro.

In PyMOL command line

 remove resn 02J or 010

or

 cmd.remove('resn 02J or 010')

In python

 import pymol2
 with pymol2.PyMOL() as pymol:
      pymol.cmd.fetch('6LU7')
      pymol.cmd.remove('resn 02J or 010')
      pymol.cmd.save('6LU7.mod.pdb') 
      #or pdbblock = pymol.cmd.get_pdbstr()

From the sounds of it you'd like to make the peptidomimetic a peptide. If you wanted to do the horrid thing of making PJE, the capped side chain glutamine ketamide, into glutamine, the command to rename atoms is a multitude of cmd.alter('resn PJE and name <atomname>', 'name="<newname>") followed by a cmd.alter('resn PJE', 'resn="GLN"') and lastly cmd.sort() to commit the changes. Not pretty, but is all in PyMOL.

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  • $\begingroup$ Wow, impressive response - thanks $\endgroup$
    – M__
    Jul 8, 2020 at 16:07
  • $\begingroup$ And, related, for the structure 6M2N, there are four 3WL ligands, one in each of the four protein chains. I'd like to remove 3WL in chains B, C, and D, retain chain A ligand, also scripted (not select and remove). Thanks! $\endgroup$
    – user8338
    Jul 11, 2020 at 13:58
  • $\begingroup$ The selection algebra is listed in pymolwiki.org/index.php/Selection_Algebra But basically you want to select based on meeting two criteria so it's an and. Namely, cmd.remove('3WL and not chain A') $\endgroup$ Jul 11, 2020 at 16:01
  • $\begingroup$ Typo: cmd.remove('resn 3WL and not chain A') $\endgroup$ Jul 11, 2020 at 21:07

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