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@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. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users