[Chimera-users] proposed "backbone" change

Eric Dawson eric.dawson at vanderbilt.edu
Fri May 12 13:23:44 PDT 2006

On Thu, 11 May 2006, Eric Pettersen wrote:

> Hi all,
> 	RIght now, if you do "Actions->Atom/Bonds->backbone only" Chimera
> shows the minimum number of atoms to produce a connected peptide/
> nucleic acid backbone, which therefore does not include peptide
> carbonyl oxygens nor nucleic sugar rings/charged phosphate oxygens.
> We are thinking of changing the behavior so that "backbone only"
> includes everything that isn't in the side chain/base.  The question
> is: does anyone need/want the current behavior?  If not, I'd not only
> change "backbone only" but would also change Select->Structure-
>  >backbone from a menu (has "full" and "minimal" in it) to just a
> menu item that selects the full backbone.  If there are some people
> who do use the current behavior, then instead I'd change "backbone
> only" to be a menu too.
> --Eric
>                          Eric Pettersen
>                          UCSF Computer Graphics Lab
>                          pett at cgl.ucsf.edu
>                          http://www.cgl.ucsf.edu

It is a nice feature to have a quick button to grab just C,CA,N atoms.
Although, one could make the argument that a short Chimera script would
work just as well or better for customization.

I am thinking of teaching new students about molecular graphics and not
sure if I'd like to lose the backbone minus CO oxygen option.


Eric S. Dawson, Ph.D.
CSB Computation, Education & Outreach
Research Instructor, Biochemistry
Center for Structural Biology (CSB)
Vanderbilt University
Nashville, TN 37232-8755
Tel: (615)-936-5579 (MRB III)
Tel: (615)-322-3303 (5119 SC)
Fax: (615)-936-2211

"All that is gold does not glitter, not all those who wander
  are lost." J.R.R. Tolkien - Fellowship of the Ring

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