[Chimera-users] docking sphere visualization

Trent E. Balius tbalius at aol.com
Wed Nov 2 10:40:30 PDT 2011

Hi Elaine,

I believe this program will be helpful to us and we will try it out and let you know.  

However, In the future, it might be useful to have a .sph reader and witter in chimera to eliminate the intermediate steps.

Chimera is a very useful program especially for DOCKing preparation and this might add to this functionality.




-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Trent E. Balius <tbalius at aol.com>
Cc: chimera-users <chimera-users at cgl.ucsf.edu>; sudipto.mukherjee <sudipto.mukherjee at gmail.com>; brianfochtman <brianfochtman at gmail.com>; rizzorc <rizzorc at gmail.com>; jianglilian68 <jianglilian68 at gmail.com>
Sent: Wed, Nov 2, 2011 1:09 pm
Subject: Re: [Chimera-users] docking sphere visualization

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 

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 
> 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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