[Chimera-users] Stick and Ribbon Connection

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 17 10:41:18 PDT 2012

Hi Ardian,
I'm not sure if the gap in this situation is due to the ribbon path, or simply that the two ends don't quite meet even though their paths are coincident.

As for path, the solution is to use a different ribbon spline, such that the ribbon more closely matches the true backbone atom positions.   The default B-spline path is nice and smooth but can deviate from those positions.

Here's a summary and small image:

You can control ribbon spline with the command "ribspline" or in the molecule model attributes panel.  For example, to use the cardinal spline without smoothing (follow exact c-alpha positions):

ribspline card

... however, then beta-strands look very ripply.  You might want to try using the cardinal spline with some compromise smoothing, and see if the junction still looks good enough, for example:

ribspline card smooth strand

If it is mainly a gap rather than path mismatch, you can show both ribbon and stick for a given residue, and do that for the first and last stick residues.  You can enable showing both for a given residue using the command "ribbackbone."

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 17, 2012, at 8:02 AM, Ardian Soca Wibowo wrote:

> Hello, 
> I have modeled a structure where a portion is model as sticks while an adjacent portion is a ribbon. The space between the two representation is disconnected. In the overall view of the figure, this broken space is an eyesore, thus I would like to know a way/command that will connect the disconnected portion between the stick and ribbon representations. Thanks in advanced for the help. 
> Ardian 

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