[Chimera-users] Manual placement of ligand into the receptor binding site

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 20 08:39:26 PDT 2011

Hi George,
You can move one structure interactively with the mouse while the other is frozen in place ("deactivated for motion"). 

Model activation/deactivation can be controlled with the "A" or "Active" checkboxes in the Model Panel (this tool is under Favorites), or the checkboxes under the Command Line, or with the select command.


Or, if you are using motion commands (move, turn, etc.) instead of the mouse, there are command options to move only certain models instead of everything.  However, that would require knowing the desired rotation or translation quantity and direction.  It is more likely you will be using the mouse.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 20, 2011, at 8:03 AM, George Tzotzos wrote:

> Hi everybody,
> I'm trying to simulated ligand binding by molecular dynamics. I'd like to place a ligand into the binding site of a receptor molecule downloaded from the Protein Data Bank.
> The ligand has not been co-crystalised with the protein and its coordinates do not match those of the protein. Is there a way that I can achieve a coordinate "translation" manually by using Chimera?
> Thanks in advance for any suggestions
> Regards
> George

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