Non contiguous residues selection from command line
Hello there! I wondered if there is a way to quickly select noncontiguous residues from the command line (useful, for example, when selecting a set of residues defining an active site, a template for docking, etc.). In standard chimera, I would use the command SELECT with numbers, commas, and hyphens (e.g., SELECT: 172,192,193,208:214). Thanks, Leonardo Polytechnic University of Marche, Ancona, Italy
Hi Leonardo, Selecting a bunch of residue using their numbers is basically the same as in Chimera, e.g. in ChimeraX you could use command: select :172,192-198,208,214 Command-line specification in ChimeraX: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> Differences in command-line specification vs. Chimera: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec-diffsum.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 Jan 22, 2023, at 8:54 AM, LEONARDO SORCI via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello there! I wondered if there is a way to quickly select noncontiguous residues from the command line (useful, for example, when selecting a set of residues defining an active site, a template for docking, etc.). In standard chimera, I would use the command SELECT with numbers, commas, and hyphens (e.g., SELECT: 172,192,193,208:214). Thanks, Leonardo Polytechnic University of Marche, Ancona, Italy
Thank you, Elaine, It works now, and I noticed that the issue was in the syntax as I did not include a space after "select". As per your example: select :172,192-198,208,214 (OK) select: 172,192-198,208,214 (error in ChimeraX, unknown command) Standard Chimera looks more permissive in this regard, as both options work. L -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, January 22, 2023 6:32 PM To: LEONARDO SORCI <l.sorci@staff.univpm.it> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Non contiguous residues selection from command line Hi Leonardo, Selecting a bunch of residue using their numbers is basically the same as in Chimera, e.g. in ChimeraX you could use command: select :172,192-198,208,214 Command-line specification in ChimeraX: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> Differences in command-line specification vs. Chimera: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec-diffsum.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 Jan 22, 2023, at 8:54 AM, LEONARDO SORCI via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello there! I wondered if there is a way to quickly select noncontiguous residues from the command line (useful, for example, when selecting a set of residues defining an active site, a template for docking, etc.). In standard chimera, I would use the command SELECT with numbers, commas, and hyphens (e.g., SELECT: 172,192,193,208:214). Thanks, Leonardo Polytechnic University of Marche, Ancona, Italy
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LEONARDO SORCI