[Chimera-users] Helix represented as sheet, dispite best efforts

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 13 10:10:18 PDT 2017


Hi Matthias,
The problem is not helix vs. sheet (it is definitely assigned as helix, for example try command “select helix”), but instead how the ribbon is calculated for that helix.  I don’t know the precise problem nor have I been able to identify a workaround, so I’ll submit it as bug report.  If I come up with anything, will let you know.

In the meanwhile, I note that our newer program ChimeraX uses different methods to calculate the ribbon and does not have a problem with this structure - image attached.  You can get ChimeraX prerelease daily builds; it has some features Chimera does not, but it’s not a replacement (overall functionality-wise) for Chimera yet, so it all depends on what you want to do.  You could certainly use both programs.
<http://www.rbvi.ucsf.edu/chimerax/index.html>

Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 13, 2017, at 4:21 AM, Matthias Vorländer <matthias.vorlaender at embl.de> wrote:
> 
> Hi everyone,
> for some reason, chimera displays one helix in a structure as a messed up beta sheet. I am attaching the PDB file and an image (same structure as backbone and ribbon representation). I have tried adding HELIX records manually, ksdssp or the setattr command, but the result is always the same. I would be very grateful for suggestions what could be causing this problem, as I will have to remake all my figures in pymol otherwise (which displays the helix correctly). 
> Many thanks
> Matthias Vorländer

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