[Chimera-users] SwissSidechain plugin for Chimera

[Elaine Meng]

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