Dear Meinan, It would be useful if you would say what structure you are displaying, so I could check your commands exactly and make sure the residue numbers etc. are right. However, I can see that there are two issues:
(1) your “setattr” command actually changes all of chain A into helix. Instead of :467-469/A it should be /A:467-469. The first one means all residues 467-469 (in all chains) plus all of chain A, whereas I’m guessing you mean 467-469 in chain A only. This is explained here: http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#implicit
(2) even though you set the entire chain to type helix, there are still thin pieces because it is trying to show that the residues don’t belong to the same helix as each other. In other words, there will be a thin piece between 10 and 11 if residues 1-10 are one helix and residues 11-20 are a different helix.
If you want the residues to be in the *same* helix as each other, you’d need to give them all the same ss_id attribute, e.g.:
setattr /A:1-20 res ss_id 999
http://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue http://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.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 Feb 24, 2020, at 12:12 PM, Meinan Lyu mxl1032@case.edu wrote:
Dear cgl.ucsf.edu, In chimerax, Helix is disrupted for some reason, could I change the intermediate residues into helix? There are two ways I tried, 1: use 'dssp' command, 2: use 'setattr :467-469/A res ss_type 1'. But both didn't not work. Could you tell me how to change this? Best regards, Meinan