[Chimera-users] Gap between C=O mainchain bond and supersmooth ribbon

[Elaine Meng]

Hi JD,
The path of the ribbon is a smoothed interpolation over the backbone  
atom locations, so regardless of style (smooth, supersmooth, edged,  
flat, etc.) the "real" backbone atom positions do not necessarily fall  
on the ribbon.

Showing both the ribbon and backbone atoms can be enabled with the  
command "ribbackbone".  However, even if the atoms are shown you will  
still have the same gap as when you displayed just the bond.

Currently there is no way to get rid of gaps between ribbon and any  
displayed backbone atoms.  We would like to allow constraining the  
ribbon to go closer to the actual atom positions, but this has not  
been done yet.  It is problem report #6661:
<http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/6661>

This common problem is discussed in previous posts:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002385.html>
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003295.html 
 >

I will attempt to put you on the notification list for changes to the  
problem report #6661.
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Mar 6, 2009, at 2:41 AM, Dr. Jean-Didier Maréchal wrote:

> Dear all,
>
> I want to represent the C=O bond that chelates an ion in my  
> structure and
> the rest of the prot in ribbon (supersmooth). I don't want the carbon
> explicitly represented but yes the bond and the oxygen with a ball  
> and stick
> representation. Following a previous post, I have two copies of my  
> model.
> One is represented in ribbon. In the other one, I have the oxygen in  
> bs and
> for the bond I did "bonddisplay always #1:22 at C,O". It does pretty  
> much what
> I want but I see that in many cases I have a empty gap between the  
> end of
> the bond and the ribbon. Something I don't want. Is there a way to  
> remove
> this gap? Or should I always represent the carbon also (something I  
> find
> less esthetic that the other option).
>
> All the best,
> JD
>