select by atom number
Hello: Is any trick to select by atom number? Having NAMD files with CHARMM FF, i.e., SEGID and no chain ID, I find now difficult to use CHIMERA the way I used it. Thanks francesco pietra
Hi Francesco, Well, it's not really a trick, you can just use the "serialNumber" attribute like other attributes in the command line, for example: select @/serialNumber=19 sel @/serialNumber>12 and serialNumber<16 see "atom specification" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> especially the section on attributes <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descrip...> and atom attributes list <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#atprops> Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 9, 2011, at 12:21 PM, Francesco Pietra wrote:
On Mar 9, 2011, at 12:31 PM, Elaine Meng wrote:
If you will be doing many commands with serial numbers, you can reduce the strain on your fingers with the "alias" command, e.g.: alias sn @/serialNumber then the two commands Elaine gave would be: select sn = 19 sel sn > 12 & sn < 16 Note that alias is a simple textual substitution and that therefore there have to be spaces around the "sn" (e.g. "sn > 12" rather than "sn>12"). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (3)
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Elaine Meng -
Eric Pettersen -
Francesco Pietra