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

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -- The church says the earth is flat, but I know that it is round, for I have seen the shadow on the moon, and I have more faith in a shadow than in the church. --Ferdinand Magellan

Hi Gabor, If we eliminated keyboard shortcuts there would be new commands or buttons that do the things that only shortcuts can currently do. But I more and more think we need to keep the shortcuts because I frequently give demonstrations and use them very heavily. It doesn't seem right to give demonstrations using shortcuts that are not available to users. You can still extract a subregion of a volume by outlining it with a box using the volume dialog subregion panel, or by using the "vop" command resample option. The subregion panel has improved in Chimera 1.3 and 1.4 so it allows rotating the subregion box to an arbitrary orientation. Tom Gabor Papai wrote:

Hi,

I wonder if you discontinue keyboard shortcuts, the features - like "erase outside" - will be discontinued also? I use some of these features. An other question: is it possible to cut out a subregion from a density map in old style, I mean to set the position, size and resolution of the cube, which defines the new volume?

Gabor