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 <friedar22@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 <pm@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