Dear Nan,
Different programs use slightly different rules to automatically detect "helix" and "strand" in structures when the files do not already include these assignments.

So probably ChimeraX default assignment did not assign that part as helix.  However, you can assign it manually, for example, if that part is already selected like in your ChimeraX image,

(1) choose menu: Actions... Inspect
(2) in the resulting Selection Inspector, Inspect "Residues" and then change the Secondary structure type to "helix"

Selection Inspector help:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html>

Or, you could do it with a command:

setattr sel r ss_type 1

"setattr" help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html>

names and values of residue attributes (ss_type: 0 for coil, 1 for helix, 2 for strand):
<https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>

If you didn't have the residues selected, you could specify them directly in the command, for example, residues 61-69 in chain A:

setattr /A:61-69 r ss_type 1

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

On Mar 4, 2024, at 6:09 AM, 张楠 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear developers,
I have a question I'd like to ask. The structure after refinement appears as helices when opened in PyMOL, but in ChimeraX, it doesn't display as helices, as shown in the figures. What could be the reason for this? Is there a way to make it display as helices in ChimeraX?

Looking forward to your answer, thank you！
Best regards,
Nan

张楠
zhangnan@nankai.edu.cn

_______________________________________________
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/