Thanks Elaine !! I was trying to use dssp command. "Dssp report true" gives helices and beta strands Thanks !! Regards Ruchika ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, March 18, 2025 10:27 AM To: Bajaj, Ruchika <http://Ruchika.Bajaj@ucsf.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] secondary structures !-------------------------------------------------------------------| This Message Is From an External Sender This message came from outside your organization. |-------------------------------------------------------------------! Hi Ruchika, If you are opening a PDB file that already has the helix and strand assigned, then you do not need to use ChimeraX. You can just look in the HELIX and SHEET lines of the PDB file (using your favorite text-editor) for this information. We have some brief description of PDB file format here: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.html> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.html#secondary> However, if you need to do it for a protein structure inside of ChimeraX for some reason, you could just use the "info residues" command to list all the protein residues and whether they are in a helix or strand. Example command: info residues protein attribute ss_type saveFile ~/Desktop/info.txt see the help, the ss_type attribute value is 0 for coil (neither helix nor strand), 1 for helix, 2 for strand: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue> ... which would save it in a file named info.txt in my Desktop on a mac. If you don't have the "saveFile filename" part, it will put the information in the Log instead: info residues protein attribute ss_type 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 18, 2025, at 10:01 AM, Bajaj, Ruchika via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi I want to determine helices and betasheet and their ranges in a structure. Could you please let me know which command and its usage I can use to get it. Please let me know. Thanks !! Regards Ruchika