[Chimera-users] Delphi Controller

Eric Pettersen pett at cgl.ucsf.edu
Mon Dec 11 11:51:09 PST 2006

On Dec 11, 2006, at 10:00 AM, Thomas Goddard wrote:

>   We have been thinking recently about how to make electrostatics
> calculations in Chimera easier.  Ideas include a simple Coulomb
> calculation, or using APBS which would be included in Chimera.

I am evaluating the speed of a simple Coulombic calculation vs.  
Poisson-Boltzmann for interactive use.  If the PB calculation always  
takes many minutes for reasonable results then I would probably make  
the Coulombic calculation available "directly" (i.e. the results made  
available in that same session as a volume data set or a surface  
coloring) but allow the PB input (i.e. a PQR file for APBS) to be  
easily created.  Adding these features has become feasible now that  
Chimera includes charge-assignment capabilities.   I'm open to  
opinions/suggestions about what people would like to see in this regard.

>   It may be simple to make DelphiController work on Windows since the
> only obvious problem I saw was in the command used to invoke Delphi.
> That seems like a simple step to try before we include some other
> electrostatics calculation.  Eric Pettersen is the one who is looking
> at electrostatics and maybe he can comment further.

Conrad is investigating getting Delphi to work on Windows and will be  
following up.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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