wow. no kidding. OK! Now I understand Angel's suggestion. Yes, in fact you
should only need eight points in the mapping cube file. Here it is:
simple cube file
z-based coloring for isosurface
-1 -500 -500 -500 ANGSTROMS
2 1000 0 0
2 0 1000 0
2 0 0 1000
1 1.000000 .000000 .000000 .000000
1 just a cube
-1 1
-1 1
-1 1
-1 1
That's because Jmol just needs to interpolate the position of the point --
and that just require once cube! Just make sure the range of the points
extends beyond your other data.
Bob
On Mon, Apr 6, 2009 at 1:14 PM, Sergey Levchenko <[email protected]> wrote:
> Dear Angel and Bob,
>
> Thanks for your help. Bob is right, if I specify the same file as a map, I
> get a uniform color again. But following Angel's example, I generated a CUBE
> file that has the same header, but instead of my volumetric data contains
> values of z-coordinate for a given grid point. When I use it as a map, I get
> the desired color scheme.
>
> Bob, I use this to create a constant-current STM image. I have current as a
> function in space, then I plot an isosurface, and the hight of that
> isosurface in the direction perpendicular to the crystal surface is an STM
> image.
> Best regards,
>
> Sergey.
> On Mon, Apr 6, 2009 at 5:44 PM, Robert Hanson <[email protected]> wrote:
>
>> I don't think that will work, Angel. The cube file value being mapped will
>> be the same as the cube file generating the isosurface - iso meaning "same
>> value" so that the same value will be mapped. It will just look like a blur.
>>
>>
>> Sergey, there's no simple way to do this. If using the applet you can use
>> MAP FUNCTIONXY and then provide a function that simply returns the Z value.
>> It's an odd request. May I ask what use that would be?
>>
>> Bob
>>
>> 2009/4/6 Angel Herráez <[email protected]>
>>
>> Hi Sergey
>>>
>>> Yes, it think it can be done. I haven't worked with cube files, but I
>>> have done coloring by Z in
>>> math functions. You must use the keyword "map" in "isosurface" and, after
>>> that, repeat the
>>> parameters given for the surface.
>>> There should be info on this in the jmol-users list archive.
>>>
>>> This is my example, see if you can adapt it to your case:
>>>
>>> isosurface myS functionXY "myF" {x y z} {-50 1 0 0) {50 0 1 0} {23 0 0 1}
>>> fullyLit map functionXY "myF" {x y z} {-50 1 0 0) {50 0 1 0} {23 0 0 1}
>>>
>>> So, you may try something like
>>>
>>> isosurface value -0.6 "filename.cube" map "filename.cube"
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> _______________________________________________
>>> Jmol-users mailing list
>>> [email protected]
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>
>>
>>
>> --
>> 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
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
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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
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