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
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
Dear Elaine， Thank you for your prompt and detailed answer, it very helpful！ Best Regards, Lingyi On 3/25/2022 23:12，Elaine Meng<meng@cgl.ucsf.edu> wrote： 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
participants (2)
-
Elaine Meng -
令怡