[chimerax-users] SwissSidechain equivalent for ChimeraX

[Madeline Grace Rollins]

Hi Elaine,
Thank you very much - I will try out these options.
All the best,

Madeline
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, March 24, 2021 1:51 PM
To: Madeline Grace Rollins <m-rollins at northwestern.edu>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at 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-users/2021-February/001915.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!HfjAp6nGpoH4ZezS1wutwzWDZHWkvGU2_OKHzHcbEGNaP10KYKMmDVaTr_SnRPf0vEMnBQ8$ >

...from Ligand Expo, looks like the residue name for phosphoserine is SEP
<https://urldefense.com/v3/__http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=SEP&operation=ccid__;!!Dq0X2DkFhyF93HkjWTBQKhk!HfjAp6nGpoH4ZezS1wutwzWDZHWkvGU2_OKHzHcbEGNaP10KYKMmDVaTr_SnRPf0yLI8ov0$ >

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/buildstructure.html*modify__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!HfjAp6nGpoH4ZezS1wutwzWDZHWkvGU2_OKHzHcbEGNaP10KYKMmDVaTr_SnRPf0nAAiobs$ >

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

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