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Hi Elaine,</div>
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Thank you very much - I will try out these options.</div>
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All the best,</div>
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Madeline</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Wednesday, March 24, 2021 1:51 PM<br>
<b>To:</b> Madeline Grace Rollins <m-rollins@northwestern.edu><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] SwissSidechain equivalent for ChimeraX</font>
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<div class="PlainText">Hi Madeline,<br>
As far as I know, the SwissSidechain developers have not yet made a plugin for ChimeraX, only Chimera.<br>
<br>
Although I haven't tried, it might be possible with the ISOLDE plugin to ChimeraX, see this previous post:<br>
<<a href=""></a>https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-February/001915.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!HfjAp6nGpoH4ZezS1wutwzWDZHWkvGU2_OKHzHcbEGNaP10KYKMmDVaTr_SnRPf0vEMnBQ8$ ><br>
<br>
...from Ligand Expo, looks like the residue name for phosphoserine is SEP<br>
<<a href=""></a>https://urldefense.com/v3/__http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=SEP&operation=ccid__;!!Dq0X2DkFhyF93HkjWTBQKhk!HfjAp6nGpoH4ZezS1wutwzWDZHWkvGU2_OKHzHcbEGNaP10KYKMmDVaTr_SnRPf0yLI8ov0$ ><br>
<br>
If you get the extra protons as shown there, you could just select and delete them.<br>
<br>
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.<br>
<<a href=""></a>https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html*modify__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!HfjAp6nGpoH4ZezS1wutwzWDZHWkvGU2_OKHzHcbEGNaP10KYKMmDVaTr_SnRPf0nAAiobs$ ><br>
<br>
You may need to get a newer version of ChimeraX (e.g. daily build) to have the latest features of Build Structure.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Mar 24, 2021, at 11:22 AM, Madeline Grace Rollins <m-rollins@northwestern.edu> wrote:<br>
> <br>
> Hi all,<br>
> 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.<br>
> Thank you,<br>
> Madeline<br>
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