[Chimera-users] Changes after 1.3

[Kenward Vaughan]

On Thu, 2009-01-08 at 09:21 -0800, Elaine Meng wrote:
> Dear Dr. Rumbley,
> We were waiting on feedback before actually deleting anything on this  
> list,
> 
> <http://www.cgl.ucsf.edu/chimera/removepost1-3.html>
> 
> so it is good you said something!  I would also encourage anybody else  
> who relies on any of those features to let us know.  The idea is to  
> remove features that are less useful so that Chimera doesn't just get  
> bigger and bigger, making it harder to access the features that are  
> the most useful.
> 

I definitely use the Delphi controller, so it would be a loss for me as
well.  :-(

As I am not a theoretician deeply imbedded within the field, nor well
trained in all the intricacies of each of the apps. I use, having such
an interface is a tremendous boon for me.  I'd guess that us "merely
mortal" teachers teaching themselves this stuff always welcome such
things (though I don't know how many of us are out here... ???)

My $0.02   ;-)

Cheers,


Kenward


> We haven't made a final decision yet, but perhaps considering your  
> input, DelPhiController will be retained.  There is not anything to  
> directly replace it, that is, no graphical interface for running  
> finite-difference Poisson-Boltzmann (FDPB) calculations with DelPhi or  
> any other FDPB program.  In the version 1.4 builds, we just added a  
> tool to color surfaces by Coulombic electrostatic potential calculated  
> within Chimera, which could partly compensate for a lack of FDPB  
> calculations, but that is a more approximate approach.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html 
>  >
> 
> Thanks for the information,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 
> 
> 
> On Jan 6, 2009, at 1:11 PM, Jon Rumbley wrote:
> 
> > I noticed you were going to remove the DelPhi interface after  
> > Chimera ver
> > 1.3. I have used this interface to generate electrostatic surfaces in
> > Chimera for both teaching and research, will there be something  
> > replacing
> > it?
> >
> > Thank you,
> > Jon Rumbley
> >
> >
> > Dr. Jon N. Rumbley
> > Assistant Professor
> > Dept. of Chemistry and Biochemistry/
> > Dept. of Pharmaceutical Sciences
> > University of Minnesota-Duluth
> > 253C SSB
> > 1035 Kirby Dr.
> > Duluth, MN 55812
> >
> > Phone: 218-726-7423
> > email: jrumbley at d.umn.edu
> 
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