[Chimera-users] discontinuous ribbon for nuc. structure

Eric Pettersen pett at cgl.ucsf.edu
Wed Jun 20 14:02:54 PDT 2007

On Jun 18, 2007, at 3:49 AM, bala wrote:
> Hello,
> While i make the ribbon representation for an RNA duplex, sometimes  
> ribbon is discontinuous in between, what could be the reason for it ?
> I hve two conformation sof the same duplex taken at 1ns interval  
> from MD trajectory.  For one conformation, ribbon is continuous but  
> for the other there is a discontinuity at the middle.. I analysed  
> the structure, it seems ok.
Okay, with the files you sent I see that the problem is that Chimera  
isn't forming all of the inter-residue bonds.  When the inter-residue  
bond is missing (i.e. the two residues don't connect) then the ribbon  
breaks there.  I'm going to open a bug report for this, with you on  
the recipient list so that you will be notified when it's fixed.

What you can do in the interim to fix the breaks is to put in the  
inter-residue bonds yourself.  Where you see a ribbon break, look at  
the two residues (probably turning off ribbons so you can see the  
backbone atoms too) and find where the bond should be.  Select the  
two atoms and type "bond sel" in the command line (Favorites->Command  
Line) to form the bond.  If you've got a lot of models open you might  
want to use the Model Panel's "show only" button to show one model at  
a time.

You could save a session afterward which would preserve the bond info.


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