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"
>>
>>
>>
>>
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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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