[Chimera-users] SwissSidechain plugin for Chimera

[Madeline Rollins]

Thank you, I hadn't even noticed that. But I have tried swapnaa as well,
only with a different error message reading "Unrecognized command:
'swapnaa'." I think my main problem is that the plugin hasn't installed,
given that swapnaa doesn't work at the command line and there is no option
for SwissSidechain in the Tools > Structure Editing drop down menu. I'm not
sure where to direct this question, but I was wondering if this problem is
common or if there were any known solutions (I couldn't find any in the
archived answers).

Madeline

On Tue, Apr 17, 2018 at 12:40 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Madeline,
> One tiny “a” makes a big difference!
>
> The command should be “swapnaa,”  as described on the SwissSidechain
> website:
> <https://swisssidechain.ch/visualization/chimera.php>
>
> e.g.
> swapnaa SEP #0:95.A
>
> The “swapna” command is for nucleic acids. Easy mistake to make, of
> course, with the commands being so similar.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Apr 17, 2018, at 9:45 AM, Madeline Rollins <madelinerollins2015 at u.
> northwestern.edu> wrote:
> >
> > To whom it may concern,
> > I am trying to mutate a residue of my protein of interest to one of the
> non-natural sidechains (phosphoserine) in the SwissSidechain database. I
> downloaded the SwissSidechain plugin onto my computer a few months ago and
> it worked fine, but it recently disappeared and I have been trying to
> re-download it. I have downloaded the zip file from the SwissSidechain
> website, extracted all of the files inside (both the dependent and
> independent Rotamer folders) and have added the directory containing the
> location in the tools category. However, the SwissSidechain module still
> doesn't appear under the Tools > Structure Editing menu. When I try to use
> the command "swapna SEP #0:95.A" (for example), I get an error message that
> reads "No connectivity template for residue 'SEP'." Do you have any advice
> on how to solve this issue?
> > Thank you,
> >
> > Madeline Rollins
>
>
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