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

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 13 10:22:46 PDT 2017


Oh, I see it is a left-handed helix, and (apparently) the Chimera ribbon calculation does not handle such helices well.  Before my previous reply I’d checked the chirality of the amino acids but had forgotten to examine the handedness of the helix.

I do not know if this is something that will be fixed in Chimera since we are concentrating more on ChimeraX now, but I will still report the bug.
Best,
Elaine

> On Jun 13, 2017, at 10:10 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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
> 
> <grab.png>
> 
>> 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
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




More information about the Chimera-users mailing list