Jmol users,
Jmol 11.6.18 and Jmol 11.7.28 have been released (Thanks, Nico!)
If you have loaded any Jmol since 11.7.25 or so, be sure to use 11.7.28
instead. There were some nasty bugs there (see below).
Jmol 11.6.18 includes some rather obscure bug fixes that I think most people
won't notice. The MO calculation fix, though, reminds me that Jmol may be
the only program around that can display molecular orbital contributions
from SELECTED atoms. Thus, for example, you could display just the
contributions from a carbonyl carbon atom to an antibonding orbital. That
sort of thing. (That's the difference between
ISOSURFACE SELECT {atomno=3} MO LUMO
which accepts a SELECT property, and just
MO LUMO
which does not.)
Jmol 11.7.28
------------------
Jmol 11.7.28 includes these bug fixes plus some additional more significant
bug fixes, plus several new features. Please note that Jmol 11.7.27 had a
bug that made all MOs a single color, but that's fixed here. Also fixed is a
bug in Jmol 11.7.24-26 that made selecting atoms for measurements
impossible.
Also, we never considered what happens when you use MEASURE with the old
format -- just numbers:
measure 3 4 5 6
when there are multiple models. That ambiguity is now resolved to measure
the first matching atoms found in the current frame range rather than the
full set of frames. This seems to be a more intuitive and less surprising
interpretation than what we had up until now, which is "the first matching
atom in the entire set of models" regardless of which frame is being shown.
New features include:
You can now operate on vertex points of an isosurface the way you can with
points relating to DRAW objects. Maybe little application of this, but it
was useful to me. So, for example:
isosurface iplane plane {1 0 0 0};
print $iplane[0];
print $iplane[1];
print distance($iplane[1], $iplane[0]);
Additions to the JVXL file format to allow compressing data that involves
colored faces rather than colored vertices.
isosurface OBJ file reader. Jmol Now reads WaveFront OBJ files (
http://www.eg-models.de/formats/Format_Obj.html) as, for example, created
with pyMol (http://www.pymolwiki.org/index.php/Surface). The OBJ keyword is
required prior to the file name; these objects can then be saved in JVXL
format, if desire and mapped with other data.
isosurface .... MAP CONTOUR [n] [mep|MO homo|etc]
The MAP CONTOUR syntax now delivers a set of lines that correspond to
contours. This was possible in former versions only for planar slices, and
then only with the MESH display option. Now it is possible for any mapped
surface of any kind.
isosurface CONTOURLINES|NOCONTOURLINES
Like mesh/nomesh, fill/nofill, dots/nodots, now we have
contourlines/nocontourlines. The isosurface must have been mapped with
contours. In combination with FILL, contour lines are black against a
colored surface; with NOFILL, the contour lines are colored.
Hovering over an isosurface point for contour and planar plots now reports
the value of the function at that point.
Very preliminary isosurface ED -- electron density. This is a rather
brute-force, slow implementation. All occupied molecular orbitals have to be
read, and the result will not be right for UHF functions, so I'm not putting
in the documentation yet. But you can always store the results as a JVXL
file and then read them back quickly. The expected use is something like:
isosurface molecular map ED
Bob
--------------------------------------------------
#version=11.6.18
# bug fix: line raster not completing lines
# bug fix: (Application) meaurement table not updating properly
# bug fix: subtle MarchingSquares calculation error produces incorrect
contours for mapped plane
# bug fix: isosurface TRIANGLES not turning off when isosurface cleared
# bug fix: remapping colors of translucent isosurface can have incorrect
colors
# bug fix: isosurface sphere 1.0 map molecular not working
# bug fix: MO calculation with selected atoms can fail
# bug fix: Jmol in other applications not initialized the same way can cause
null pointer exception loading file with symmetry
#version=11.7.28
# bug fix: 11.7.27 does not display color for MOs; "color MO" can crash Jmol
# bug fix: line raster not completing lines
# bug fix: measure n1 n2 n3 n4 with just numbers selecting atoms in frame 1
rather than current frame.
# bug fix: toolbar icon for pickMeasure tied to tools "measurements..." item
# bug fix: (Application) meaurement table not updating properly
# bug fix: (Application) measurements toolbar icon does not stay shaded
# bug fix: very subtle code error on lines and cylinders rasterization not
completing line end pixel in most cases
# bug fix: (Application) measurement icon measures angles, not distances.
# bug fix: subtle MarchingSquares calculation error produces incorrect
contours for mapped plane
# bug fix: isosurface TRIANGLES not turning off when isosurface cleared
# bug fix: remapping colors of translucent isosurface can have incorrect
colors
# bug fix: isosurface sphere 1.0 map molecular not working
# bug fix: MO calculation with selected atoms can fail
# bug fix: picked atoms automatically selected -- bug in 11.7.24
# bug fix: JVXL writing after reading JVXL file may not write properly
# bug fix: Jmol in other applications not initialized the same way can cause
null pointer exception loading file with symmetry
--
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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