[Chimera-users] Problems detecting a left-handed helix

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 10 16:46:50 PDT 2015


Hi,
Chimera simply reads the HELIX records from the input PDB file and uses those for determining which residues are defined as “helix” (for example, you can select all such residues with command “select helix).  So if you are just opening a structure from the RCSB PDB and the helix is described in a HELIX line in that PDB file, Chimera does not have to detect anything.

However, I have noticed that Chimera ribbons are poorly rendered for left-handed helices, for example 1HXX residues 142-147. It just looks wrong, but the 

But if you are opening your own PDB file without HELIX lines in it, you could:

(A) manually add them according to the standard PDB format before opening it in Chimera, as per
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>
-OR-
(B) open the file without HELIX/SHEET info, which will automatically run some automatic detection, as described here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>
… however, I do not know if that will detect any left-handed helices.  I suspect it does not. Thus, a third alternative...
-OR-
(C) manually define those residues as helix in Chimera.  For example if the desired residues were selected, you could use commands:
setattr r isStrand false sel
setattr r isHelix true sel

(A) and (C) require you to know or figure out yourself which residues should be in the helix, but as I mentioned at the start, it may be that the correct residues are already defined as helix, they just don’t look good when drawn as ribbons in Chimera.  They do look OK when shown as cylinders with either Axes/Planes/Centroids or the PipesAndPlanks tool.

I hope this clarifies,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 10, 2015, at 9:24 AM, Felipe Vasquez <anfelvas at gmail.com> wrote:

> Hi,
> I am trying to visualize several of the secondary structure details on a protein of interest, and I recently had notice (by several research papers) about the existence of a left-handed helix on it. However, I could not detect the helix using UCSF Chimera (it is simply considered as a loop). Why could this happen and how could be resolved? I have tried to modify the ksdssp cut-off parameter, but it was unsuccessful, so I think now that maybe the specific nature of the helix (left-handed polyproline-like type II) could be a bit tricky for the program. What would you suggest?
> Thanks in advance for your help an patience.
> Best regards,



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