[Chimera-users] selecting zone, minimizing, docking

[Elaine Meng]

On Dec 21, 2009, at 11:30 PM, gytjyb wrote:

> hello,Mr meng !
> I have 3 questions.
> <1>
> I select one residues or animo acid
> But how can I made a radius around this residues or animo acid,
> I aslo can select neighbor residues or animo acid within some radius.
> <2>
> If I should add water for model minization and refine,
> how can I refine for a new model.
> I want to do a mutation,wether I must fix other residues when I do  
> minization.
> <3>
> how can I prepare for a docking, dose this software do docking?
> thank you for your answer!

Hello,
It is better to send Chimera questions to chimera-users at cgl.ucsf.edu  
(instead of to me directly) and include something meaningful in the  
"Subject" line.  Also, you can use "Help... Search Documentation" in  
the Chimera menu to look up information by keyword.

(1) menu "Select... Zone."  You can also specify zones in commands.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones 
 >

(2) That is up to your own scientific judgement. As mentioned in an  
earlier reply, the minimization capabilities in Chimera are rather  
limited.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html 
 >

(3) Chimera does not do docking calculations.  You can move two  
structures together by hand... of course that is only approximate.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html>

However, Chimera does have tools that are related to docking:
"Dock Prep" for preparing structures for docking or other calculations  
(with other programs outside of Chimera) and "ViewDock" for looking at  
docking results output by other programs, mainly DOCK.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html 
 >
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html 
 >
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html>

Here is the Web site for DOCK.
<http://dock.compbio.ucsf.edu/index.html>
They also have tutorials:
<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm>

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