Hi Alexis and Oli, I have a workaround for these kinds of cases, getting modified residues that are part of a chain to run in Isolde. Step 1: Fetch P1L from the CCD in chimera (don’t use the Isolde add ligand command) Step 2: After adding hydrogens, use the Isolde interface to parametrize P1L but DO NOT use the available MD template. Instead, parametrize the selected residue, having ‘Override existing’ enabled. Maybe copy and save the .xml file that’s created in the working directory for next time. Step 3: Go to your cysteine that needs the palmitoylation and manually rebuild the residue to add the lipid. For that, use the ChimeraX structure modification tools. It takes a few minutes to manually rebuild the cysteine atom by atom into the P1L residue. Don’t forget hydrogens. Step 4: Now you can run Isolde directly on the model – if Isolde complains about the residue, you should be able to supply and rebuild the residue with the custom .xml file it created in step 2. I got it to run on my end, and I have attached the .xml file for P1L and a little movie that shows that within a random ACG tripeptide the palmitoylation seems to run well in Isolde (though I don’t have a map, but fingers crossed that doesn’t change much). I got this method to work with modified protein and also modified nucleic acid. Sometimes, this method rebuilds residues to have an atom or two too many where the modified residues connect with the rest of the chain (for example an extra oxygen in a phosphate diester link in an RNA chain). In that case, just manually delete the extra atoms before real space refinement and let phenix take care of the exact geometry and bond lengths. Would be curious if this works for other people as well and if Tristan approves, Cheers Paul From: Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Wednesday, June 11, 2025 at 09:15 To: Alexis Rohou <http://a.rohou@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: cysteine palmitoylation with ISOLDE? Hi Alexis, I have not tried this in ISOLDE, but in Coot I would replace the residue with P1L (Palmitoylated cysteine) - might run into the same error though, not sure... Cheers Oli On Jun 11, 2025, at 11:20 AM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hi ISOLDE users & Tristan, Has anyone got experience building a palmitoylated cysteine residue? I'd appreciate any pointers you may have. Based on how glycosylations can be built (see thread<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>) I was thinking to start with isolde add ligand PLM but that fails with "ValueError: No template for residue type PLM" Are we in covalent ligand (unsupported) territory here? Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/