[Chimera-users] Restrict View

Elaine Meng meng at cgl.ucsf.edu
Sun Mar 6 09:52:34 PST 2011

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  

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 #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


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 C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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

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