Re: [Chimera-users] Chimera and secondary structure annotations
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
-- Max-Planck Institut für Biochemie Abteilung Molekulare Strukturbiologie Am Klopferspitz 18 D-82152 Martinsried Germany Tel: +49 (89) 8578 2032 fax: +49 (89) 8578 2641
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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
participants (2)
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Elaine Meng -
Thomas Goddard