Secondary structure recognition issue in homology model
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@montana.edu <tokminalukas@chemistry.montana.edu>
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@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
On Nov 13, 2018, at 11:02 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
(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> )
Oops THIS tutorial <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html> Elaine
Elaine, 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, Monika On Tue, Nov 13, 2018 at 12:02 PM Elaine Meng <meng@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@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@montana.edu <tokminalukas@chemistry.montana.edu>
participants (2)
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Elaine Meng -
Monika Tokmina-Lukaszewska