[Chimera-users] missing ribbon loop

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 2 14:45:39 PST 2009

Hi Tomas,
I don't see any missing ribbon loop when I look at the structure.  I  
see one continuous protein ribbon for residues 56-195 of chain A.   
There is also a short peptide, residues 10-14 of chain Q.   However,  
chains A and Q are separate molecules so they should not be connected,  
if that is what you meant.

The only weird things I can see in the display are
- Glu 89 in chain A is broken into two parts because it does not have  
a CG atom
- Asn 185 in chain A is broken into two parts because it does not have  
a CB atom

However, neither of these things affects the ribbon because all of the  
backbone atoms are there.  Maybe you are seeing the sidechain pieces  
of these two residues?

I looked at the structure in both the current 1.4 release candidate  
and the current 1.5 daily builds of Chimera.
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 2, 2009, at 3:38 AM, klumpler at sci.muni.cz wrote:

> Dear Elaine,
> I think PDB is alright, I send it as a attachment. Could you help me  
> with
> the editing?
> Thank you very much
> Tomas

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