[Chimera-users] how to select spheres for docking?
meng at cgl.ucsf.edu
Mon Aug 6 09:55:30 PDT 2007
See the DOCK 6 tutorials
especially the one about spheres
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:
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.
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 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
> My previous problem with chimera got resolved. Thank you Greg. I
> had to change the OS from RHL9.0 to fedora core.
> with regards,
> ps- please ignore if off-topic. i have posted the same query on
> dock mailing list. still awaiting a reply there.
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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