[Chimera-users] secondary structure assignment

[Elaine Meng]

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  
information:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html

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)
or
(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
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html




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
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