From: Chris Ing (ing.chris_at_gmail.com)
Date: Tue Aug 06 2013 - 15:04:08 CDT

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.
>
>
>