[Chimera-users] representing 70s ribosome in ribbon

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 12 10:56:51 PDT 2008

Dear BG,

Currently it is not possible to draw ribbons given only one point per  
residue.  The additional atoms determine the plane of the ribbon.   
Although it would make sense to allow drawing just a circular  
"tube" (spaghetti or licorice), that has not been done.  We have filed  
a request in our bug/request database for Chimera to be changed to  
allow this in the future.

In the meanwhile, you could try showing the backbone trace as sticks,  
but it will have sharp bends instead of being smooth like a ribbon.   
You can control stick thickness, for example with a command like
   setattr m stickScale 2.5

There are some Web servers (e.g. Maxsprout) to build coordinates for  
proteins from the alpha-carbons, but that would be too impractical in  
this situation and also would not help for the RNA part.  Sorry for  
the inconvenience,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 11, 2008, at 6:22 PM, Bong-Gyoon Han wrote:
> Hi,
> I am tring to show the full 70S ribosome structure (PDB id: 1GIX and  
> 1GIY) in ribbon representation with EM experimental density together.
> These PDB data consist of backbone atoms only (single alpha carbon  
> for each a.a and single phosphate for each nucleotide).
> Ribbon option does not generate any ribbon (due to the incomplete  
> information in the PDB?).
> Is there any way to show this molecule in ribbon format?   I assume  
> that backbone atoms must be enough to generate ribbons.
> BGHan

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