[Chimera-users] longer bonds in image

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 3 09:26:53 PST 2008

Hi Bala,
This is an expected behavior of Chimera:  the ribbon is a smoothed  
path that does not go exactly through the atom positions.  When  
ribbon is shown, the default is to simply draw the longer or shorter  
bonds where the ribbon is farther from or closer to the displayed  
atoms (ribose/base or amino acid side chain) than are the backbone  
atoms that the ribbon represents.

However, there are ways to change the behavior:

(A) use the command "ribbackbone" to allow display of both backbone  
atoms and ribbon.  This will not make any bonds look longer or  
shorter, but it is usually ugly because the ribbon is not in the same  
place as the backbone atoms.

(B) with Ribbon Style Editor, "Residue Class" section, you can set  
which atoms control the ribbon path and which are hidden  
automatically (by default, without using "ribbackbone") when ribbon  
is shown:

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

P.S. you can send attachments such as images to chimera-users, but  
the message will not appear until the moderator has a chance to  
approve it... just be patient and it will be sent!

On Mar 2, 2008, at 9:00 PM, bala wrote:
> -----Original Message-----
> From: bala
> Sent: Fri 2/29/2008 12:13 PM
> To: chimera-users at cgl.ucsf.edu
> Subject: longer bonds in image
> Hi all,
> Thank you for the suggestions for my previous query.
> When the ribbons are displayed for the backbone of a RNA molecule.  
> Some of the bonds look longer than usual. Herewith i have attached  
> the image of a RNA molecule in which residues colored in cyan have  
> some bonds longer in appearance. Kindly help me to get this of this.
> Thanks,
> Bala
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