[chimerax-users] dssp works on whole chain

[Elaine Meng]

Dear Haofeng Wang,
There is an additional value that needs to be set (ss_id), to tell the program that it is really one long helix and not two helices (some structures have two different helices that are adjacent).

How to do this is described in previous posts, for example,part #2 of this message:
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-February/000902.html>

... here are additional messages on the same topic, but they say basically the same thing as the above:
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-August/000629.html>
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-March/002006.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 25, 2021, at 9:14 PM, 王镐锋 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear Elaine C. Meng, 
>      Thanks for your advice. It helps me a lot with redefining secondary structure of  amino acid residues. But one problem described by my picture, the red helix showed in the picture in chimeraX break into two helixes. But from the corresponding sequence, it show a constant helix in the sequence viewer. Also, when I use PyMOL or chimera to open this pdb file, this part is presented as a constant helix. It confused me a lot and I don't how to solve this, although I have tried the setattr command on this zone, but the cartoon doesn't change. Could you please help me combine this two seperate helixes to form constant one? Thanks so much.
> Best,
> Haofeng Wang
> Ph.D student 
> Tianjin University, China