[chimerax-users] SwissSidechain equivalent for ChimeraX

[Elaine Meng]

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&target=SEP&operation=ccid>

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 at 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