[Chimera-users] Protein secondary structure

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 8 10:40:02 PDT 2009

Hi John,
There is "helix" and "strand" but no breakdown of the different  
subtypes of helix.

To see the assignments on the sequence, use the Sequence tool  
(Favorites... Sequence).  The light yellow boxes show helices, the  
light green boxes the strands.  You can click on the boxes to select  
all residues in helices or all residues in strands.

Also, you can use these terms as specifiers in the command line, for  

color yellow helix
select strand

or from the menu, for example

Select... Structure... secondary structure... helix

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 8, 2009, at 6:35 AM, Beale, John wrote:

> I realize that this is probably simple, but I haven’t been able to  
> work this problem out.
> Is there a way to read a single pdb file into Chimera and then have  
> the program show me what amino acid sequences of the protein are  
> alpha helices, what are beta sheets, and what are 3,10 helices, etc?
> Thanks!
> John

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