I was *going* to say there's a (slightly hacky) way to do this with ISOLDE, but it currently only works for residues for which ISOLDE has an MD parameterisation (and it doesn't for KCX - will try to remedy that). If it did, though: setattr #1/a:9 res name KCX del #1/a:9@HZ1,HZ2,HZ3 # (to ensure that it's not recognised as a normal lysine residue) ... then open ISOLDE's unparameterised residues widget and let it fill in the missing atoms. On Tue, Apr 11, 2023 at 3:35 PM Guillaume Gaullier via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello chimerax-users,
I am trying to model a PTM, and the most sensible way to me seems to use the swapaa command and specify the sensible monomer from the PDB Chemical Component Dictionary as the target residue.
Here is what I tried (residue #1/a:9 is a Lys):
open 1kx5 swapaa #1/a:9 KCX
And the error I got: Dynameomics rotamer library does not support KCX
I tried all the rotamer libraries listed in the swapaa help page ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/swapaa.html#rotLib ), but none of them can provide stereochemical info for KCX.
I can open the monomer I want (carbamylated Lys) with: open ccd:KCX But of course in this case it’s floating by itself as a new model, not incorporated in the protein sequence and structure I am interested in.
Is this the correct way to model a PTM? If it is, where can I find a rotamer library that will contain the stereochemical info for KCX, and how do I tell ChimeraX to use it? If it is not how modelling a PTM is done, then how else should I do this?
Thank you in advance,
Guillaume
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