Interesting. I will have to puzzle over the commands to really parse
this out. I don't really follow the set rangeSelected bit, but I can
look at the documentation later. Thanks for looking at this, Bob!
Frieda
On Aug 30, 2010, at 5:20 PM, Robert Hanson wrote:
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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phone: 507-786-3107
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it is better to take what answer we get.
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