Hi All –


Francesco is correct; you can only select points from the OpenDX file based on potential value.  I would recommend looking only at points outside of the molecular or solvent-accessible surface.  You can then assemble a histogram of electrostatic potential values from these points and select the best ranges of potential values for your particular system.


Good luck,


Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997



From: francesco oteri [mailto:francesco.oteri@gmail.com]
Sent: Monday, April 16, 2012 2:28 AM
To: Francois Berenger
Cc: apbs-users@lists.sourceforge.net
Subject: Re: [apbs-users] post processing of the dx file


Hi Francois,

as far as I know, each grid point holds the potential in that point so there is no hydrophobic point. 

You can only select basing on the positive or negative value. 





Il giorno 16 aprile 2012 11:04, Francois Berenger <berenger@riken.jp> ha scritto:


I'd like to process the dx output file after having run
apbs on a protein.

I'd like to know which points are negative, which
points are positive and which ones are hydrophobic
(in the 3D grid stored in the .dx file).

Are there some standard values to do this kind of

I am OK to be pointed out to some articles/literature
as I am just a software guy. ;)

Thanks a lot,

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Cordiali saluti, Dr.Oteri Francesco