That's strange... I've never tried user color schemes on continues values,
but the following with bwr gradient works for me:
set isosurfacepropertysmoothing false;
isosurface NATSAS select {1.1} sasurface 1.2 map color ABSOLUTE 0 120
property temperature colorscheme bwr;
If the colors don't change maybe your are specifying a range different from
what can be seen in the structure; if in the region you want to color for
example according to temperature the values go from 0 to 1 and the
different ranges you specify are 0-90, 0-90 or 0-100, the coloring wouldn't
change.
I'm sorry I did this long ago and I'm not of much help, I just can confirm
that the code I wrote works properly.
2012/5/24 Oliver Stueker <[email protected]>
> 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
>>>> >
>>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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/
>>> _______________________________________________
>>> Jmol-users mailing list
>>> [email protected]
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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/
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> ------------------------------------------------------------------------------
> 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/
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
------------------------------------------------------------------------------
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/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
