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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