On Mar 10, 2014, at 7:34 AM, Jason Swails <jason.swails.gmail.com> wrote:
> 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.
Specifically w.r.t. the 3D-RISM DX writer, there is a typo in the line you mentioned it. The ‘call’ is supposed to be ‘class’. It wasn’t picked up before because gridData seems to be one of the few DX readers that reads this line. This will be fixed in the next release (or shortly thereafter).
In summary, you can safely delete the line and in the future you shouldn’t have to.
Tyler
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Received on Mon Mar 10 2014 - 10:00:02 PDT
