Hi George, I'm pretty sure there is no need to select both. For example, you would select the ligand only and then use "Select... Zone" to get the residues around it. Or, if you are using Find Clashes/Contacts you would select the ligand only and designate checking it against all other atoms. Or if you have a bunch of models (not just ligand and receptor) and you want the other ones to be ignored, you would select and designate the ligand as first set, then select and designate the receptor as the second set. They would not be selected at the same time. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...
If you are using commands it is not necessary to do any selection beforehand, as in my example commands in the previous message. The findclash example performed the selection itself when finding the contacting residues, you did not have to select anything before that. Also, the zone specifier can be used to find atoms in a different model than the ligand. For example, if the ligand is all of model #1.1 and receptor is model #0, ~disp disp #1.1 disp #0 & #1.1 z<4.5 Of course, you can select atoms from multiple models at once, and there are several ways. For example, command select #0,1 or select #0:1-25#1:his or you could open the Model Panel (from Favorites menu), choose both models on the left side, and then click the "select" button on the right side. With commands you can specify only certain atoms from the multiple models. However, I very rarely make such selections and am not sure why you would need them; I just use the specification directly in the command (for coloring, displaying or whatever). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 6, 2011, at 5:06 AM, George Tzotzos wrote:
Hi Elaine, One additional question.
I'm dealing with docking simulations. I have to open the ligand and receptor as separate models. Somehow I need to select both ligand and receptor before I use distance cutoff or Find Clashes/Contacts. Is there a way of doing this?
Of course I could concatenate the receptor and ligand pdb files but this would be rather laborious. Many thanks in advance for your help George