Selecting part of an extracted ligand

Question

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.

Matteo Ferla · Answer

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.

Selecting part of an extracted ligand

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