Hello, 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 ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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