Swapaa only works for standard amino acids, I'm afraid. There *is *a command in ISOLDE you can use for this, but keep in mind it's a little unpolished and requires some common-sense in the types of situations you should apply it to. Specifically, it doesn't take chirality into account (although it *will* highlight chiral centres for you to double-check), and isn't always great about choosing the placement of new atoms (I should really rewrite it using the newer ChimeraX structure-building tools). That being said, it works well enough for this case (it does place one of the oxygens in the terminal thiophosphate on top of another, but that settles out easily with energy minimisation). Also incorrectly labels the two phosphodiester phosphorus atoms as chiral (probably because the CCD template has them protonated, in which case they *would* be), but that's a minor thing. Anyway, once you have the GSP parameters loaded in ISOLDE, select the GTP and do: isolde replace ligand sel GSP Best, Tristan On Wed, Nov 15, 2023 at 10:42 AM Dmitry Semchonok via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Dear colleagues,

I have a short question -

how to substitute nonstandard residue with other ChimeraX. My task is to substitute GTP for GSP.

The one may use swapaa, right? Could anyone drop the usage for nonstandard residue?

Many thanks.

Sincerely, Dmitry

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