[Chimera-users] helices display in latest snapshots

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 30 11:21:35 PDT 2005

Hi Boaz,
As far as we know, and in our testing, the ribbons are behaving  
normally in these
newer versions.  Some possibilities as to what is happening:

(A) a different scaling scheme is being used than the default.  Open  
Depiction... Ribbon Style Editor, then under Ribbon Scaling, make  
sure it
is set to "Chimera default" and then click OK or Apply (without  
anything selected)
If someone had made different scalings before and saved them, one of  
those might
have been in use rather than the default.  Those are saved in the  
preferences file.

(B) secondary structure assignments:  are the helices known to be  
One way to check is to use the command
    select helix
and see if the areas you believe to be helices are selected.
(I'm assuming you are viewing a protein, not nucleic acids)
You can change assignments
      (a) manually (by selecting the desired parts, then clicking the  
reporting what is selected on the bottom right corner of the Chimera  
to open the Selection Inspector, Inspect "Residue" instead of "Atom,"  
"in helix" to "true" and "in strand" to "false")
      (b) by running ksdssp with different parameters
(open Model Panel, which is under Favorites, then make sure the line
for your protein is chosen, change from "frequently used" to the
"infrequently used" list, click "compute SS" and set parameters as  

A final possibility if these methods (a,b) do not make what you want
into a helix is that there are some atom-naming or PDB format  
problems that
prevent the coordinates from being recognized correctly as peptide/ 

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 30, 2005, at 2:21 AM, Boaz Shaanan wrote:

> Hello,
>  I the latest snapshots (Windows 2143 and linux 2154) helices show  
> up as thin worms when I ask for 'ribbons' under action (they used  
> to look like nice ribbons in previous releases). I found the tools/ 
> depiction/ribbons display and managed somehow to change the look of  
> the ribbons (still, they looked nicer before) but failed to change  
> the look of the helices. Where can I do this now ?
>    Thanks,
>          Boaz
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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