Hi Matt,
PyMOL does not currently allow you to export the data mapped to the surface.
However, the dx format is very straightforward. It follows a subset of the
OpenDX standard, as described on the APBS site (
http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data
).
I don't know much about surface file formats, but the PyMOL wiki mentions (
http://www.pymolwiki.org/index.php/Surface#Exporting_Surface.2FMesh_Coordinates_to_File)
that you can save surface coordinates to a file. It might be possible for a
developer (you?) to convince PyMOL to write out the electrostatic potential
along with whatever else it's writing to the .wrl file.
Hope that helps,
-Michael
On Mon, Jan 31, 2011 at 7:03 PM, Matteo Pendleton wrote:
> Greetings,
>
> I'm looking to use an electrostatic surface map for downstream calculations
> and was wondering whether it's currently possible (after using APBSv2 to
> calculate a surface potential map) to export a mesh of data points in a list
> format with each data point's associated potential? If not, does anyone have
> an outline of the file layout for the pymol-generated.dx file so I could
> write my own script to do it?
>
> Thank you kindly,
>
> Matt Pendleton
>
> Independent Researcher
> New York, NY
>
>
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