[Chimera-users] Movie - Display Spheres

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 20 09:12:36 PDT 2006

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,

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.
> 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 at vanderbilt.edu
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