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...
Thanks for the information, Elaine ----- Elaine C. Meng, Ph.D. meng@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@d.umn.edu
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