[Chimera-users] Question about connectivity

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 22 14:50:32 PST 2005

Hello Dr. Gimble,
Is this a publicly available PDB file?  We may be better able to answer
the question if we can take a look at what causes the break.  Without
that knowledge, however, the most relevant tool is probably the Ribbon
Style Editor.  With that tool you can define different "ribbon residue
classes" - these are defined by which atom is used to guide the  
ribbon path,
which is used to set the ribbon orientation, and which atoms are  
part of the mainchain or backbone.  There is no distance parameter,  
By default, the built-in "nucleic acid" class will be used for your DNA.
You could experiment with defining a new class and using that.  It is
possible to select part of the structure and apply the new class to only
that part; however, that might introduce discontinuities where the  
classes are used.  It is hard to tell without some experimentation.

Man page for Ribbon Style Editor
(the bottom section deals with residue classes)

This approach is via the user interface.  Others may have suggestions
that involve Python or other code.

On Nov 18, 2005, at 7:23 AM, Frederick Gimble wrote:

> I have just begun using Chimera on my Mac, and find that it will be
> able to produce the graphics that I need for publication and display
> purposes.  I recently opened a pdb file of a protein that we study
> bound to DNA and used the depiction, nucleotides tool to render the
> DNA backbone as ribbons with the bases shown as slabs.  I noticed a
> discontinuity in one of the DNA strands, which may be caused by the
> severe distortion of the DNA.  I think that this also happened with a
> previous program that I used called SPOCK that I used to draw the DNA
> strands as worms.   In that case I could repair the break by changing
> the settings for the connectivity distances.  How would I repair the
> break in Chimera?
> Thanks for your help.
> Sincerely,
> Fred Gimble
> Frederick S. Gimble, Ph. D.
> Associate Professor
> Department of Biochemistry
> BCHM 315
> 175 S. University St.
> Purdue University
> West Lafayette, IN  47906
> Telephone: (765) 494-1653
> Fax: (765) 494-7897
> Email: fgimble at purdue.edu
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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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

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