[chimera-dev] Help

[Eric Pettersen]

On Monday, November 25, 2002, at 01:00 PM, Srinivasan, Mythily wrote:

> I am using Chimera (Windows 2000) operating system. I have a protein 
> complex with two distinct chains. I would like to find the 
> intersections of groups of atoms between the two chains. As I 
> understand from the tutorials for Midas, the & operator should help 
> me. However, I get a syntax error message. Can you please tell me the 
> correct command?

Hi Mythily,
	Are you really using Midas tutorials?  If so, you should stop and use 
Chimera tutorials instead.  They are in the user's guide (from the 
Chimera menus, go to "Help", then "User's Guide").

	To more directly answer your question, if the chain's IDs are "A" and 
"B", then:

	color red :.a & :.b z<3

will color red all residues of chain A that have any part within 3 
angstroms of chain B.  Conversely:

	color green :.b & :.a z<3

will color green all residues of chain B within 3 angstroms of chain A. 
  There is a lengthy discussion of how to construct command-line "atom 
specifications" in the Chimera user's guide under "Built-in Functions" 
and then "Atom Specs" under that.  The last part of the "Atom Specs" 
page talks about "&" (intersections), though I should note the the very 
last example is slightly wrong; instead of

	#1:/type=asp and type=glu & #0 z<10

it should be:

	#1:/type=asp or type=glu & #0 z<10

	Please let me know if you have any further questions.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu