It's also possible to add your own fragments to the substituents SEQCROW can use. Here's my solution to the thread that Elaine linked using SEQCROW: http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2021-February/001913.html. I know it can be a bit of a nuisance to build/acquire a structure for all the sidechains you might want to use - especially when SEQCROW is lacking some of the more biologically relevant pieces.

From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Madeline Grace Rollins <m-rollins@northwestern.edu>
Sent: Wednesday, March 24, 2021 2:22 PM
To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] SwissSidechain equivalent for ChimeraX

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hi all,

I would like to mutate a serine residue to phosphoserine for one of the proteins I am working with. I have used SwissSidechain in Chimera to do this in the past, but I was wondering if there is an equivalent module like SwissSidechain but for ChimeraX? I tried downloading the SEQCROW bundle for structure editing, but I couldn't find the same range of sidechain derivatives. If not, can you use SwissSidechain in ChimeraX? I apologize in advance if this question has been asked already.

Thank you,

Madeline