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@cgl.ucsf.edu http://www.cgl.ucsf.edu