Hi Jared, First question: It is not necessary to use a single command. You can use > rep sphere [stuff] > rep sphere [more stuff] and then both sets of things will be shown as spheres. Most commands only affect what you specify. (main exceptions are "show" and "chain" ... more on this below) If you did want to use a single command, the proper separator for the specifications is a vertical bar "|" (logical OR, union) and not the ampersand "&" (logical AND, intersection). For example: > rep sphere #0:426,431,432 | :atp although I'm thinking this would also work (I don't know which PDB you're using, or I'd verify this myself): > rep sphere #0:426,431,432:atp Second question: As alluded to above, "show" displays what you specify, undisplays the rest. If you don't want to undisplay the rest, use "display" instead of "show" - the rest of what you had looks correct, though. If you want to undisplay all atoms except those residues and ATP, first "~display" everything and then specify what you want to show with "display" either in a single command or multiple commands. I hope this helps, Elaine On Oct 20, 2006, at 8:57 AM, Jared Godar wrote:
Hello,
I am trying to use the 'represent spheres' command to draw attention to specific residues in a model that is displayed as a ribbon.
I would like to first show the ATP binding site of the molecule with magenta spheres, then show the three residuse which get phosphorolated.
Currently, I am able to display one of these elements or the other as spheres, but not both at the same time. I've tried to use a single represent sphere command to specify all of the desired atoms, but can't seem to get the context right,
represent sphere #0:426,431,432,ATP and represent sphere #0:426,431,432 & #0::ATP weren't working.
Help on the syntax to simultaneously display the two commands listed below which are currently mutually exclusive would be appreciated.
#SHOW ATP:
color magenta #0::ATP; color magenta #0::mg; represent sphere #0::ATP
#SHOW PO4 Residues
show #0:426,431,432; color yellow #0:426; color orange red #0:431; color red #0:432; represent sphere #0:426,431,432
Thanks,
Jared
-- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Department of Molecular Physiology & Biophysics 708 Light Hall 2215 Garland Ave. Nashville, TN 37232-0615 Work: 615.322.7898 Fax: 615.322.7236
jared.godar@vanderbilt.edu _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users