[Chimera-users] Changes after 1.3

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 8 09:21:45 PST 2009

Dear Dr. Rumbley,
We were waiting on feedback before actually deleting anything on this  


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.

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.

Thanks for the information,
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

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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