Hi Elaine, Thank you very much - I will try out these options. All the best, Madeline ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, March 24, 2021 1:51 PM To: Madeline Grace Rollins <m-rollins@northwestern.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] SwissSidechain equivalent for ChimeraX 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://urldefense.com/v3/__https://www.rbvi.ucsf.edu/pipermail/chimerax-use... > ...from Ligand Expo, looks like the residue name for phosphoserine is SEP <https://urldefense.com/v3/__http://ligand-expo.rcsb.org/pyapps/ldHandler.py?... > 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://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/b... > 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