[Chimera-users] SwissSidechain plugin for Chimera

[Madeline Rollins]

That is exactly what I was doing. I tried again and added the directory
above the SwissSidechain directory and it's working fine.
Thank you so much,

Madeline

On Tue, Apr 17, 2018 at 1:26 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Madeline,
> I tried the whole installation process myself this morning to verify that
> it worked.  One confusing thing is that you should not add the
> “SwissSidechain” directory itself, but the directory above it.  E.g. I put
> it inside ~/Desktop/plugins/ and added the plugins directory to my
> locations and everything worked : it was in the menu and the command
> worked.  I did not change the name of the SwissSidechain folder produced by
> unzipping the downloaded file from the SwissSidechain website, I just moved
> it inside my plugins folder, Other than that, I have no idea what to tell
> you.
> I hope this helps,
> Elaine
>
>
> > On Apr 17, 2018, at 11:18 AM, Madeline Rollins <madelinerollins2015 at u.
> northwestern.edu> wrote:
> >
> > 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
> >
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180417/5adfc780/attachment.html>