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

[Elaine Meng]

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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