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

Monika Tokmina-Lukaszewska tokminalukas at gmail.com
Tue Nov 13 20:54:00 PST 2018


thank you very much for your email. I was stuck with this model since I am
familiar only with basic structure editing. Now when I know what the
problem is I can explore Chimera and learn more functionalities. Thank you
for the link to tutorial, this is very informative.

Best regards,


On Tue, Nov 13, 2018 at 12:02 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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:
> ~ribbon
> I’m not sure how your homology model got left-handed helices, since your
> template does not have them.
> I hope this helps,
> Elaine
> -----
> 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

Monika Lukaszewska, Ph.D.

Senior Research Scientist
Chemistry & Biochemistry Department
Montana State University
Bozeman MT, 59717
lab: (406) 994 5418
tokminalukas at montana.edu <tokminalukas at chemistry.montana.edu>
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