[Chimera-users] Chimera and secondary structure annotations

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 28 12:51:23 PDT 2005

I agree with all Tom said; just a couple of additions:

(1) for  nucleic acids, the ribbon stays a constant width and does not 
use any secondary structure annotations

(2) the Kabsch and Sander calculation in Chimera can also be accessed 
through a GUI (if you would rather not use the command line) but is 
slightly buried.  It is one of the "infrequently used" operations in 
the Model Panel.  First, you open the Model Panel (Favorites... Model 
Panel), then in that, switch from the "frequently used" to the 
"infrequently used" list, then click "compute SS."  The GUI with the 
Kabsch and Sander parameters will then appear.  If you have favorite 
parameter settings you can save them for subsequent use.

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

On Oct 28, 2005, at 12:35 PM, Thomas Goddard wrote:

>   The "ksdssp" command in Chimera will compute secondary structure for
> proteins.  This uses the Kabsch and Sander algorithm.  As far as I know
> you do not need any secondary structure info for the ribosomal RNA to 
> make
> a nice ribbon.
>   To use this command use Chimera menu entry Favorites / Command Line
> and then type ksdssp in the command entry at the bottom of the Chimera
> window.
>   More details are in the Chimera manual:
> 	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
>   Here are some ribosome pictures I made with Chimera a few months ago.
> 	http://www.cgl.ucsf.edu/chimera/complexes05/bakeoff-talk.html
>     Tom

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