[chimerax-users] Modeling post-translational modifications

[Guillaume Gaullier]

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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