[chimerax-users] dssp works on whole chain

[Elaine Meng]

Dear Haofeng Wang,
The "dssp" secondary structure calculation works by identifing hydrogen-bonding patterns throughout the whole protein, so even if you specify few atoms, it will still apply to the whole chain:

>From the help page, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/dssp.html>:

"The calculation applies to all protein/peptide chains in models containing the specified atoms."

If you want to manually change the secondary structure of any amino acid residues, you could use the "setattr" command instead.  See for example this previous post:
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-February/000362.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 24, 2021, at 9:48 PM, 王镐锋 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear guys, 
>     Sorry to disturb you guys. When I use the UCSF ChimeraX, I try to define the second structure for part of model. I type the command like "dssp (#1 & sel) energy cutoff 0.5 minheliexlen 3", it works for the whole model instead of what I choose specially. Could you please help me? Thanks so much!
> Best,
> Haofeng Wang
> Ph.D student 
> Tianjin University, China