[Chimera-users] docking sphere visualization

Eric Pettersen pett at cgl.ucsf.edu
Wed Nov 2 10:32:46 PDT 2011

Hi Trent,
	Elaine's tool seems like a good start since it helps you visualize  
the various sphere clusters.  You are right that it would be nice to  
have a tool more closely integrated with Chimera that would also allow  
you to delete spheres and rewrite your sphere file.  I will open an  
enhancement-request ticket in our bug-tracking database with you and  
the other cc recipients on it so that you all will be notified when it  
gets implemented.
	I hope Elaine's program will be helpful enough until I have time to  
get to it.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Nov 2, 2011, at 10:09 AM, Elaine Meng wrote:

> 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
> -----
> 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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