Dear Lingyi, The issue is that even when all the residues are "helix" they might be in different helices from each other, and ChimeraX will still draw a short loop between different helices. You can fix this by making sure all of those helix residues are in the same helix as each other, using the "ss_id" residue attribute ("SS ID" meaning secondary structure identifier). Residue attributes: <http://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue> You can control the attribute values of residues using the "setattr" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html> For example, to make sure that residues 130-144 of chain B are all helix (ss_type = 1) and in the same helix as each other (ss_id 999): settatr /B:130-144 res ss_type 1 setattr /B:130-144 res ss_id 999 See these previous posts for more explanation and examples: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-August/000632.html> <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-March/002008.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 Mar 25, 2022, at 7:04 AM, 令怡 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear developers,
Hello! I recently encountered some problems when using ChimeraX.
When displaying the structure with cartoon, some helix is displayed as loop (Fig A). How to force it to be displayed as helix? I checked the User Guide and used the command "setattr sel residues is_helix true" for the selected amino acids, but only some amino acids can be displayed as helix (Fig B). Is that need to change ss_ id? I have tried, but it didn't work. I will appreciate it if you could answer my question. Looking forward to your reply!
Best Regards
Lingyi
<1DBF6A0C-D523-4CDB-ACB1-D7B975A7836D.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users