[Chimera-users] Secondary structure recognition issue in homology model

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 13 11:02:25 PST 2018

Hi Monika,
It took me a while to realize that the two places where the ribbon looks weird (approx. residues 496-500,513-519) are left-handed helices.  It is a known problem that Chimera does a terrible job of drawing ribbons for left-handed helices, sorry.  However, they are correctly identified as “helix” … you can tell by selecting them with the command:

select helix

However, I can see a big hairpin in the homology model that you might want assigned as strand.  If you re-run secondary structure identification with a slightly less stringent cutoff than the default, that hairpin will be shown as strands, e.g. command:

ksdssp -c -0.25 #0

< http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>

You don’t want to go much less stringent than that, however, or else some parts will be assigned as both helix and strand at the same time and then the ribbon will look really weird.

(You can also assign secondary structure  manually with the “setattr” command as mentioned in this tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> )

As for the left-handed helices, one possibility is to show the secondary structure with pipes and planks ( Tools… Depiction… PipesAndPlanks) instead of as ribbons.  It will use the current secondary structure assignments.  If you do show pipes and planks, after that hide ribbons so you’re not showing them both at the same time:


I’m not sure how your homology model got left-handed helices, since your template does not have them.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 12, 2018, at 8:24 PM, Monika Tokmina-Lukaszewska <tokminalukas at gmail.com> wrote:
> Dear Chimera Team,
> In my homology model (see attachment) it looks like there has been some issue with secondary structure recognition in one of the domains (highlighted in cyan). In .py file I added one of the protein templates (yellow) based on which the C-terminal domain was constructed. I am not sure what has happened to a final model, since template for that domain looks good. I was wondering if there is an option in Chimera which could fix that issue?
> Thank you for your time,
> Sincerely,
> Monika Lukaszewska

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