Frieda,
Whew! That took all day!
The short answer is that, yes, if you are mapping data, what is selected
prior to the isosurface command determines which atoms are mapped. it should
give just a surface fragment.
The longer answer is that in Jmol 11.8 and the currently released versions
of Jmol 12 you can't map selected atom property data onto JVXL surfaces, at
least not properly. This should be fixed for Jmol 12.0.11 and 12.1.9.
Coloring is now tied to the setting:
set rangeSelected TRUE/FALSE
Note also that
isosurface select {helix} sasurface map property temperature
and
select {helix}
isosurface sasurface map property temperature
are the same, but they aren't quite the same as
isosurface sasurface map select {helix} property temperature
where the select is AFTER the map keyword.
In both cases you get a fragment, but in the first case, a partial surface
is created first, then it is mapped; in the second case a full surface is
created (or, perhaps, read from a JVXL file), and then the property is
mapped for the specific selected atoms only (and any surface closer to other
atoms is then removed). It's not a big difference, but it is noticeable.
The first is faster, but the second is your only option if you have saved a
JVXL file and are now mapping it (or RE-mapping it). What's happening is
that when you create a surface for the whole model you are limited in the
resolution you can get, but the making of a surface fragment will generally
run at much higher default resolution.
Bob
On Sun, Aug 29, 2010 at 12:46 AM, Frieda Reichsman <frieda...@mac.com>wrote:
> Hi,
>
> Does the display of an isosurface (the area it covers) vary depending on
> what is selected at the time you call the jvxl file? I don't recall this,
> but it is true in 12.0.8 and 12.0.10. I expect the surface in a jvxl file to
> be the same surface all the time... but perhaps somehow I have been lucky
> enough not to trip over this before.
>
> Or perhaps it varies when you are mapping something to the surface, e.g.,
> isosurface surf1 "3d/finalsurface.jvxl" map property_x color translucent -1
> colorscheme "user";
> but then I would expect the color might vary with the selection, but not
> the surface itself.
>
> Frieda
>
>
>
> On Aug 27, 2010, at 3:47 PM, Robert Hanson wrote:
>
> Jmol users --
>
> The isosurface/JVXL problems in 12.0 and 12.1 have been fixed. (Jmol 12
> could crash opening older nonXML JVXL files.)
>
> http:/chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
>
> 12.0.10 will have that in it, probably next week.
>
> -- Bob
>
> On Mon, Aug 23, 2010 at 8:41 AM, Pshemak Maslak <p...@chem.psu.edu> wrote:
>
>> Hello,
>>
>>
>> 4. 12.08 has difficulty in displaying jvxl file written by 11.8. It does
>> it very slowly (several minutes) and --after finally loading -- the
>> model cannot be interacted with. I have encountered only one example of
>> this difficulty, and the jvxl file re-written with 12.08 Jmol works
>> fine. Could this have anything to do with the changes in the spartan
>> file reader? (my jvxl files are based on smol spartan files)
>>
>>
>> PM
>>
>>
>>
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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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--
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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