Hi Julio, 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
Date: Fri, 28 Oct 2005 21:21:44 +0200 From: "Dr .Julio Ortiz" <ortiz@biochem.mpg.de> To: Thomas Goddard <goddard@cgl.ucsf.edu> Subject: Chimera and secondary structure annotations
Hi Thomas: It is time for a couple of new questions about Chimera. I am trying to generate some nice representations of the 70S ribosome showing its proteins as ribbons, but the PDBs do not have annotations of secondary structure. In many papers that I have seen the people use the program "Ribbons" and a collegue suggested me also "DSSP" to generate the annotations and visualize the results in "PyMOL". I am still fighting with some installation problems, so I have not succeed yet in my original goal.
The question for you is if Chimera, or some assotiated tool can generate the annotations for secondary structure from a PDB file. In particular, do you have some suggestions for the ribosome structures (large file with also RNA?).
Thanks, Julio
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