[chimerax-users] Modeling post-translational modifications

[Tristan Croll]

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 at 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 at 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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>
>
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