Hi Madeline, As far as I know, the SwissSidechain developers have not yet made a plugin for ChimeraX, only Chimera. Although I haven't tried, it might be possible with the ISOLDE plugin to ChimeraX, see this previous post: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-February/001915.html> ...from Ligand Expo, looks like the residue name for phosphoserine is SEP <http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&targe...> If you get the extra protons as shown there, you could just select and delete them. A second possibility in ChimeraX is to use the Build Structure tool, Modify Structure section to build outward from the serine sidechain: starting by modifying the hydroxyl H to P, then changing the atoms sprouting from P to oxygens. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#modify> You may need to get a newer version of ChimeraX (e.g. daily build) to have the latest features of Build Structure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Mar 24, 2021, at 11:22 AM, Madeline Grace Rollins <m-rollins@northwestern.edu> wrote:

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

Madeline, 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. Best, Tony ________________________________ 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