On Mon, 2014-03-10 at 10:09 -0400, Brian Radak wrote:
> Deleting this line fixes the problem. Is this an overly strict
> implementation in gridData or is this frivolous output from rism3d?
There are 3 dx writers implemented in Amber: one in RISM, one in PBSA,
and one in cpptraj all designed to write grid data. I believe the dx
writers were designed to allow the grid data to be displayed in PyMol
and VMD (I know this to be true for the cpptraj DX writer since I wrote
it for that purpose).
Each of the other writers (PBSA and cpptraj) write out a similar string
at the end of the grid data (for cpptraj I was using a DX file printed
by VMD as a template). Since the overwhelming majority of use-cases for
grid data printed by Amber is visualization of that density in either
pymol or VMD, it seems logical to support their parsers.
So I would say the scipy DX parser is overly strict. I have a DX file
parser written in Python I can share that I've used to parse these
densities. It returns a 3-D ndarray subclass that has some helpful
methods for dealing with grid data.
> Is this
> output supposed to mean something?
I don't know that VMD or PyMol does anything with this information, but
that's hardly a definitive answer.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 10 2014 - 08:00:02 PDT
