Hi Bob, Jmol'ers I just noticed that if I make sure that my atom properties are all negative (e.g. by subtracting a certain offset) I get a larger planar isosurface. (compare attached figure to the one attached on my June 8th mail)
To me it seems, all positive (or rather non-negative) are ignored by
ISOSURFACE PLANE MAP.
(with Jmol 12.2.28, 12.3.28)
Is this intended behavior?
Best,
Oliver
On Thu, Jun 14, 2012 at 12:07 PM, Oliver Stueker <
revilo2...@users.sourceforge.net> wrote:
> Is there any way to map the "potential" of custom atom-properties to a
> planar (square) isosurface as a color gradient?
>
> Oliver
>
>
> On Fri, Jun 8, 2012 at 6:12 PM, Oliver Stueker wrote:
>
>> Hi Jmol-Community,
>>
>> it seems I am again kind of stuck. :-/
>>
>> I have some correlation data for a protein (1 value per residue) that
>> I want to map on different isosurfaces.
>>
>> I have succeeded in mapping the data on Molecular (or VDW, SAS)
>> surfaces, but now I am interested how things look like inside the
>> protein by mapping these values onto cross-sections through the
>> protein.
>>
>> But:
>> ISOSURFACE my_iso PLANE {0 0 15} {0 1 15} {1 1 15} molecular MAP
>> FULLPLANE property_correl
>>
>> gives me only a partial surface (see attached figure), although I
>> would expect FULLPLANE would result in a bigger, square or rectangle
>> plane.
>>
>> As a test case I have attached a Jmol-script that demonstrates this
>> and the data-file needed.
>>
>> What I would like to see is something like:
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=6
>> or
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?topic=28
>> ( http://chemapps.stolaf.edu/jmol/docs/examples-11/img/molslice.jpg )
>>
>> I hope someone can enlighten me. :-)
>>
>> Best,
>> Oliver
>>
>
>
<<attachment: iso_plane_map_fullplane_prop_negative.jpeg>>
iso_plane_test2.spt
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cdata.dat
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