[Chimera-users] secondary structure assignment

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 10 09:43:11 PST 2007

Hi Nurul,
If the input protein PDB file has HELIX and SHEET information, that  
information is used.  If the input file does not have secondary  
structure information, the "ksdssp" function is automatically used to  
assign it.  This is an implementation of the DSSP method.  More  

Again, you do not have to run it because it will be run automatically  
if the input file does not have secondary structure information.   
However, you can re-run the algorithm if you want to use different  
parameters.  Here are a couple of ways:
(1) use the "ksdssp" command (as described in the link above)
(2) in the Model Panel (Favorites... Model Panel), choose the models  
of interest on the left, change from "frequently used" functions to  
"infrequently used," and then click "compute SS" on the right.

I hope this helps,
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 Jan 10, 2007, at 12:12 AM, nurul wrote:

> hello
> i'm a student from malaysia and i'm using chimera in my studies,
> i have one question regarding this software, how does it assign the
> secondary structure? is it using dssp or stride or any other secondary
> structure assignment program? thank you
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

More information about the Chimera-users mailing list