You know, the very simplest way to get those points is just to dump the
VRML file. Just
display none
write test.vrl
and take a look. All the vertices will be there in a handy block. There are
other formats as well. Then just read that in with whatever you want to
use.
alternatively, within Jmol you can say:
x = getProperty("isosurfaceInfo.vertices")
Now x contains all the vertices. Although that seems not to be quite
working, as it is just a string list, it seems.
Bob
On Fri, May 4, 2012 at 8:40 PM, Andrew Long <[email protected]>wrote:
> So after some experimenting it seems like "isosurface resolution 1.5
> molecular dots no fill" is the command to generate the perfect mesh. That
> gives me 14606 vertices for azulene for a resolution of 1.5 and 5.8K
> vertices if I use a resolution of 1.0. I think you're right, Using JMOL
> inside a java function seems like it would be the most elegant way to do
> all this plus it keeps all my code in mostly in one place. Is there a
> recommended "api" or set of functions to use to interact with JMOL? so it
> seems like the rough outline of input file generating function goes
> something like this.
>
> 1)initiate JMOL
> 2)pass JMOL the command to load the base molecule
> 3)generate the isosurface using " isosurface resolution 1.5 molecular dots
> no fill"
> 4)return the base molecule (is there an easy way to get JMOL to return a
> neat array of the XYZ data? that's a point3f right? )
> 5)return the set of points on an iso surface(is there an easy way to get
> JMOL to return a neat array of points ala step 4?)
> 6)generate the input files
> 7)?save the isosurface state?
>
> Thanks again
>
> Cheers Andrew
>
> On Thu, May 3, 2012 at 3:16 PM, Robert Hanson <[email protected]> wrote:
>
>> Wow. No kidding!
>>
>> Yes, the resolution can easily be adjusted. That's a good idea.
>>
>> Don't worry about the coloring. That's just an array that can be filled
>> easily; we'll find a simple way to do that. In the end you might want to
>> write a Java app that embeds Jmol, and then we can expose that array for
>> you.
>>
>> Bob
>>
>>
>>
>> On Wed, May 2, 2012 at 1:52 PM, Andrew Long
>> <[email protected]>wrote:
>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
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>> threat landscape has changed and how IT managers can respond. Discussions
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>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Jmol-developers mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> ------------------------------------------------------------------------------
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> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
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>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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