[Chimera-users] (no subject)

Eric Pettersen pett at cgl.ucsf.edu
Wed Mar 8 16:06:37 PST 2006

On Mar 8, 2006, at 2:22 PM, Todd T Talley wrote:
> Hay,
>             Sorry to bother you, but you were so helpful last week  
> I thought that I would try again.  Is there a way to show the  
> carbonyl of the backbone of a specific residue?  I would like to  
> show the H bond between my ligand and a specific Trp.
Well, the vanilla answer is (if we're talking about residue 12.A for  
example) "disp :12.a at c,o".  However, I'm guessing that the reason  
you've undisplayed the carbonyl in the first place is because you're  
showing a ribbon -- in which case there are a few more useful things  
to know.  By default the ribbon depiction replaces the backbone atoms  
(including the carbonyl oxygen) so even if you turn the display of  
specific backbone atoms back on (e.g. with the above "disp" command),  
no atoms will be shown.  However, Chimera will know that these atoms  
are now "displayed" and will begin to show things such as H-bonds  
that involve those atoms (drawing the end of the H-bond to the  
interpolated ribbon position of the backbone atom).  You can force  
backbone atoms to be explicitly depicted even in the presence of a  
ribbon with the "ribbackbone" command (e.g. "ribbackbone :12.a") --  
they will be shown at their normal non-interpolated positions.


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