[Chimera-users] docking sphere visualization

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 2 10:09:12 PDT 2011

Dear Trent,
If I remember correctly there was a utility program included with DOCK, "showsphere" to convert sphere format to PDB.  It was pretty decent for display in Midas, but not so great in Chimera, so in 2008 I wrote a fortran program (yeah, yeah stop laughing) to convert sphere format for better display in Chimera.

This is not to say your suggestion isn't valid (or has been taken care of), but in the meanwhile this program I wrote might be helpful.

I will dig up that 2008 email with the program attached and more detailed information and forward it momentarily.  Best,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 2, 2011, at 9:09 AM, Trent E. Balius wrote:

> Dear Chimera-user list,
> I believe, currently, Chimera can not visualize docking spheres (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OrientingtheLigand) files directly, in order to do so, we need to create a pdb file of the spheres and then visualize them.  
> It would be vary helpful for DOCK users if we could visualizes spheres directly from the .sph files produced by sphgen (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Sphgen) or sphgen_cpp.  Radius and color information could then also be displayed. 
> This might be a helpful new feature to be included in a future release of Chimera.  
> Thank you,
> Trent E. Balius
> Graduate Student, Rizzo Group,
> Department of Applied Mathematics and Statistics,
> Stony Brook University.
> Office: Math Tower 3-129, Phone: (631) 632-8519
> URL: http://www.ams.sunysb.edu/~tbalius/

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