[chimerax-users] problem with displaying secondary structures

[Elaine Meng]

Hi Ela,
Structures from the PDB database already have helix and strand assignments, so ChimeraX does not change anything.  It just displays the assignments that are already in the file.

If you have some other file that does not already contain the assignments, then ChimeraX will automatically run dssp for you, and the Log will say so.  

When you use "setattr" to change "ss_type" you probably also need to change "ss_id" ... for example, there may be helix residues 1-5 with ss_id = 1 and helix residues 6-10 with ss_id = 2.  Since they are two different helices they would be shown with a small loop between, even though all the residues 1-10 are helix.

ss_id is explained here:
<https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>

... and was discussed in some previous posts, for example:
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-August/000629.html>
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-February/000902.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 Oct 23, 2021, at 2:51 PM, Elżbieta Wątor via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi, 
> I am trying to prepare figures for my publications and I have a problem with ss assignment. When I open structure in pymol, everything is assigned correctly. However, when I open the same structure in ChimeraX (1.2.5) I have gaps in helices and also not all of B strands are assigned correctly. 
> 
> <image.png>
> 
> I tried "dssp" command, but I probably type something wrong, because everytime I got "expected keyword" reply.
> Also I tried to do that manually using such commands 
> 
> setattr /B:5-7 res ss_type 1 
> 
> and for some regions it works and for some not e.g  I can change the whole helices with gaps to loop but in other way around it again gives me back helices with gaps. 
> 
> I've just started learning ChimeraX so probably there is some easy explanation, but I would be really grateful for your help. 
> 
> Best regards, 
> Ela Wator