Hi Kenward, There *is* a command-line way to specify atoms/residues in a zone defined by other atoms. It might have been hard to find since it's not a separate command, but instead an atom specification that can be used with many commands. The general form is command atom-spec za<N for example select ligand za<3.5 to select all atoms within 3.5 angstroms of any ligand atoms. Analogously, "za>N" could be used for all atoms farther away than N angstroms. Using "z" or "zr" instead of "za" gives a residue-based cutoff - you would always get whole residues even if only parts of them fall in the zone. The "command" can be "select" or many other things (color, display, etc.). Here are a couple more examples: rlabel ions z<4 (label residues within 4 angstroms of any ions) disp #0 & #2 z<5 (display residues in model 0 that are within 5 angstroms of any atoms in model 2). The description in the manual (click the "zones" link): http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html It can be confusing, so feel free to write back if you have problems generating the command needed in your particular situation! Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 30, 2006, at 8:16 AM, Kenward Vaughan wrote:
I'm putting together a demo for my students this next semester, and was hoping to be able to do a zone selection about the ligand. Is this possible with the command line? I haven't been able to pull out a reference for such, yet.
Certainly I could pull together the list of residues myself, but thought it'd be nice to have the command available. Some students might like to create a demo file for their reports, and this would become a pivotal tool for a subset of those.
If not directly available, then a wishlist addition, perhaps? Something like:
zonesel [within|beyond] [+/- angstroms] [atom-spec]
where the sign of the angstrom value denotes whether to include (+) or exclude (-) the atoms in atom-spec.
Cheers,
Kenward Vaughan -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$???
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