From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 06 2013 - 16:39:57 CDT

You can do that with less effort.
Take the two grids and set each value to one if it is equal or larger than the desired isovalue or to zero if not.
The sum over all values times the volume of a single voxel is the volume. Now compute the product of the two grids for each point and you have the overlap. Done.
Axel.
--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

-----Original Message-----
From: Chris Ing <ing.chris_at_gmail.com>
Date: Tue, 6 Aug 2013 16:04:08
To: Georgios Gerogiokas<G.Gerogiokas_at_sms.ed.ac.uk>
Cc: John Stone<johns_at_ks.uiuc.edu>; Axel Kohlmeyer<akohlmey_at_gmail.com>; Vmd l<vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: extracting grid points from an isosurface

I'm interested in doing a related task to this. I'd like to compare two
isosurfaces at a particular isovalue and compute the percentage overlap in
volume. I think one strategy to do that would be to use the extracted grid
points at an isovalue, build polygons using a script, and use some
yet-to-be-determined-geometry-magic to determine the intersecting volumes.

 Anyway George, if you make any progress extracting grid points, you should
not hesitate to post your script to VMD-L. Here's an abridged description
of the dx format:
http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html
-Chris


On Tue, Aug 6, 2013 at 11:49 AM, Georgios Gerogiokas <
G.Gerogiokas_at_sms.ed.ac.uk> wrote:

> Hi again,
>
> Thanks, for the quick feedback. I suppose it might be easier to just write
> a script on the file itself then.
>
> Cheers,
> George
>
>
> Quoting John Stone <johns_at_ks.uiuc.edu> on Tue, 6 Aug 2013 09:51:49 -0500:
>
>
>> Hi,
>> As Axel says, there isn't really a way to do this directly, however
>> you can export a triangle mesh to one of the file formats in the
>> File|Render
>> menu and extract the vertices that way if you like. In order to do that
>> an retain the coordinate system of the original molecule, you would also
>> need to set the molecule's view/rotate/centering transformation matrices
>> to identity before exporting. Let me know if you need more help with
>> that.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>>
>> On Tue, Aug 06, 2013 at 01:05:11PM +0200, Axel Kohlmeyer wrote:
>>
>>> On Tue, Aug 6, 2013 at 10:44 AM, Georgios Gerogiokas
>>> <G.Gerogiokas_at_sms.ed.ac.uk> wrote:
>>> > Hi all,
>>> >
>>> > I was wondering if anyone knows how to extract the
>>> > coordinates of the grid points in an isosurface created
>>> > at a particular isovalue, for instance from a dx file during
>>> > a vmd session.
>>>
>>> i dont' think this is possible directly, but there are some dusty
>>> corners in VMD that i have not looked into for a long time. what might
>>> work is to reset view and camera and everything to simple unit
>>> transformation and then output the isosurface to a render program and
>>> parse the resulting file.
>>>
>>> axel.
>>>
>>> >
>>> > Many thanks,
>>> > George
>>> >
>>> > --
>>> > The University of Edinburgh is a charitable body, registered in
>>> > Scotland, with registration number SC005336.
>>> >
>>> >
>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>
>>
>> --
>> NIH Center for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/**Research/vmd/>
>>
>>
>>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>