[Chimera-users] Chimera and secondary structure annotations

Thomas Goddard goddard at cgl.ucsf.edu
Fri Oct 28 12:35:19 PDT 2005

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

  More details are in the Chimera manual:


  Here are some ribosome pictures I made with Chimera a few months ago.



> Date: Fri, 28 Oct 2005 21:21:44 +0200
> From: "Dr .Julio Ortiz" <ortiz at biochem.mpg.de>
> To: Thomas Goddard <goddard at 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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