[Chimera-users] how to select spheres for docking?

[Elaine Meng]

Hi Vinay,
See the DOCK 6 tutorials
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm

especially the one about spheres
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/ 
generating_spheres.htm

In that tutorial, the surface is calculated for the whole receptor,  
but then programs that come with DOCK are used to select only some of  
the spheres.  Those sphere-selection accessories are not visually  
interactive, and you could use any visualization program (not  
necessarily Chimera) to see the results.

Some possibilities for how you could use Chimera in the process, not  
described in the tutorials.  However, these both involve some manual  
editing of text files:

(1) Only calculating the surface for part of the receptor.  DMS has a  
"-i file" option to only calculate the surface for the specified  
residues.  The format is described in this online manual page for dms:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/dms1.html

In Chimera, you could select those residues and write out the  
selection to a text file (for example, with Actions... Write List)  
but then you would have to edit it to get the format required by DMS.

(2) Interactively choosing spheres.  The sphere tutorial mentioned  
above describes the DOCK showsphere program and the sphere file  
format.  After using showsphere to make the spheres into PDB format,  
you can display them in Chimera.   You could label the spheres,  
decide which ones to delete, and then delete them from the sphere  
file.  Or, you could select all the spheres you want and write that  
information into a text file as described in (1), then edit the  
sphere file to include only these spheres.   Either way you would  
have to manually edit the sphere file using information from Chimera.

Best,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Aug 6, 2007, at 9:20 AM, Vinay Kumar wrote:

> Hello all,
> I have a few queries to ask. hoping you all will reply.
>
>  i use DOCK6.0, the dms program under DOCK, can create and execute  
> a total of 9999 spheres. I would want to know, how do i selectively  
> select spheres using chimera? Is it possible to select certain  
> residues and generate the molecular surface for it? and use it for  
> docking??
>
> My previous problem with chimera got resolved. Thank you Greg. I  
> had to change the OS from RHL9.0 to fedora core.
> with regards,
> Vinay
> ps- please ignore if off-topic. i have posted the same query on  
> dock mailing list. still awaiting a reply there.
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