Thanks Daniel,
yes in fact I get a color gradient with the colors I specify.
I just want to make sure that the white color (center of the gradient) is
set to 0.0, which I can't confirm that it actually happens, as the gradient
won't change even if I set different boundaries to the colorscheme.
It seems to me that whatever one passes with COLOR RANGE or COLOR ABSOLUTE
is just ignored.
Oliver
On Wed, May 23, 2012 at 4:28 PM, Daniel Carbajo <[email protected]>wrote:
> Hi Oliver,
> I haven't had the time to look at your example in depth, but the following
> code works for me on PDB files which I replaced the temperature factor for
> cavity occurrences (discrete from 0 to 10):
> set userColorScheme blue yellow red green cyan orange magenta ghostwhite;
> set isosurfacepropertysmoothing false;
> isosurface NATSAS select {1.1} sasurface 1.2 map color ABSOLUTE 0.0 10.0
> property temperature colorscheme user;
> isosurface NATSOLV select {1.1} solvent 1.2 map color ABSOLUTE 0.0 10.0
> property temperature colorscheme user;
> I'm not sure if the range specified has to span from the min to the max
> found in the selection... I'll have to check.
> Hope this helps.
> Cheers,
> Daniel
>
> 2012/5/24 Oliver Stueker <[email protected]>
>
>> A simpler example:
>> on http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm (12.3.27_dev
>> 2012-05-23)
>>
>> load caffeine.mol
>> calculate partialCharge
>> isosurface vdw map mep color range -1.0 1.0
>> isosurface vdw map mep color range 0.0 1.0
>> isosurface vdw map mep color range -1.0 0.0
>>
>> Output is always:
>> isosurface1 created with cutoff=0.0; isosurface count: 1
>> isosurface full data range -0.15823531 to 0.130531 with color scheme
>> spanning *-0.1 to 0.1*
>>
>>
>> On Wed, May 23, 2012 at 3:56 PM, Oliver Stueker <
>> [email protected]> wrote:
>>
>>> Hi,
>>>
>>> I have the impression that ISOSURFACE ... COLOR RANGE x.xxx y.yyy is
>>> broken:
>>>
>>> the data that I want to map to the surface are stored in .property_xxxand
>>> range from -0.67 to +1.24
>>>
>>> and no matter if I use: (see full commands below or in my previous mail)
>>> ISOSURFACE ... COLOR RANGE -0.35 0.35 # smaller than data range
>>> ISOSURFACE ... COLOR RANGE -1.5 1.5 # larger than data range
>>> ISOSURFACE ... COLOR RANGE 1.5 -1.5 # upper and lower bound switched
>>> ISOSURFACE ... COLOR RANGE 0.0 1.5 # only positive values
>>> ISOSURFACE ... COLOR RANGE -1.5 0.0 # only negative values
>>>
>>> in combination with:
>>> COLORSCHEME "user"
>>> COLORSCHEME user
>>> COLORSCHEME bwr
>>>
>>>
>>> with Jmol versions: 12.1.50, 12.2.0, 12.2.25, 12.3.12, 12.3.25, 12.3.26
>>> (just noticing that 12.1.50 generates the surface much faster than the
>>> newer versions)
>>>
>>> the surfaces always look the same and I get:
>>>
>>> "isosurface full data range -0.67112225 to 1.240843 with color scheme
>>> spanning -0.67112225 to 1.240843"
>>>
>>> which I would interpret that the COLOR RANGE is just ignored.
>>>
>>> Also the isosurface... map property x WITHIN x.y [1]
>>>
>>> just gives me a Syntax-Error:
>>> *script ERROR: {x y z} or $name or (atom expression) required*
>>> ----
>>> isosurface iso_sas2 select { protein } only saSurface 1.4
>>> property_xxx within 1.0 >> colorScheme << "user" color range -1.5 1.5
>>>
>>>
>>>
>>> Thanks,
>>> Oliver
>>>
>>> [1] http://chemapps.stolaf.edu/jmol/docs/examples-12/new2.htm?topic=53
>>>
>>> On Tue, May 22, 2012 at 5:44 PM, Oliver Stueker <
>>> [email protected]> wrote:
>>> > This time sending from the correct address. ;-)
>>> >
>>> > ---------- Forwarded message ----------
>>> >
>>> >
>>> > Hi Bob and other fellow Jmol'ers,
>>> >
>>> > When I run the following commands in Jmol 12.3.25:
>>> >
>>> > {protein}.property_xxx = data(load("data_file.dat"),1,0,1 );
>>> > set userColorScheme deeppink white green ;
>>> > isosurface iso_sas1 SELECT {protein} ONLY SASURFACE 1.4 property_xxx
>>> > COLORSCHEME "user" COLOR RANGE -0.35 0.35 ;
>>> >
>>> > I get :
>>> > iso_sas1 created with cutoff=0.0; isosurface count: 1
>>> > isosurface full data range -0.67112225 to 1.240843 with color scheme
>>> > spanning -0.67112225 to 1.240843
>>> >
>>> > For me it seems that restricting the color range to -0.35 -> 0.35
>>> doesn't
>>> > work.
>>> > Am I doing something wrong here? I would expect that larger values
>>> would be
>>> > mapped to the maximum RANGE values.
>>> >
>>> >
>>> > Related to that I think it would be a nice feature, if Jmol would be
>>> able to
>>> > show a legend of the gradient,
>>> > similar to the one in
>>> > PyMol: http://www.pymolwiki.org/index.php/File:Prot_contact_pot.png
>>> > Plus maybe indicating which color corresponds to 0.0 (in case the lower
>>> > bound is negative and the upper positive)
>>> >
>>> > Oliver
>>> >
>>>
>>
>>
>>
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