HI Rayees, I don't understand your question because the residues can only have one ss_id. So your commands will already work to display those residues as a continuous helix, and they will have ss_id = 999 not 1. However, for display it doesn't matter what the actual ss_id value is as long as the residues all have the same value and it's not the same as some other residues elsewhere in the model. Maybe you mean if you save a PDB file after that, it does not keep your ss_id value of 999? A PDB file does not have ss_id; that is just a concept within ChimeraX. The PDB will keep the helix assignments that you made, however, and it will sequentially number the helices without paying any attention to what you value you had assigned for ss_id. Yes you can text-edit (not using ChimeraX, just any text editor) the start and end numbers of each helix in the PDB file (and I believe mmCIF although I'm not so familiar with editing that format). Just look at the PDB file format description and the requirements for what the HELIX records should contain. <https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.html> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.html#secondary> <https://www.wwpdb.org/documentation/file-format> 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 Jul 25, 2025, at 3:29 PM, Rayees Mattoo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I have a region in my structure (res 208-229) which is displayed as a discontinuous helix when I am certain it is a continuous helix. I want to modify the pdb file to consider it as a continuous helix using chimeraX. I used the following commanlines:
settatr #1/K:208-229 res ss_type 1 setattr #1/K:208-229 res ss_id 999
It works. However, I believe the command assigns the same region with a new unique ss_id (999), leaving the original ss_id intact. If I want to replace the the original ss_id with a new sequence range (res 208-229) how would I do that? Also, is there a way to directly text edit pdb file secondary structure list in ChimeraX?
Best Rayees