Probably the last update of Jmol for 2010. What a great year! Thank you all
for contributing.
Here's a final list of bug fixes and a few new features in 12.0 summarizing
12.0.23 - 12.0.26.
DRAW command
# 12.0.26 bug fix: draw intersection/polygon without vertices does not clear
existing object
# 12.0.23 bug fix: draw * translucent does nothing
# 12.0.23 bug fix: draw with multiple models can fail to save state
ISOSURFACE command:
# 12.0.26 new feature: isosurface/draw .length (also added to 12.1.27)
# 12.0.26 bug fix: obj/pmesh file reading problems
# 12.0.26 bug fix: failure to create atomicOrbital does not clear that
isosurface
# 12.0.26 bug fix: isosurface slab for plane not working
# 12.0.26 bug fix: undocumented $isosurface1[3] fixed
# 12.0.26 bug fix: isosurface set 0 does not display all sets
# 12.0.23 bug fix: isosurface t.obj should be discernable as OBJ if created
by PyMOL
# 12.0.23 bug fix: isosurface on frame other than first will be incorrect
# 12.0.23 bug fix: isosurface OBJ pymol.obj not reading Pymol output
# 12.0.23 bug fix: relaxing single-model requirement for isosurface for
SELECT option
# as long as only a single model's atoms are selected
# (Jmol 12.1 goes further, allowing for this for preselected atoms)
LOAD command:
# 12.0.26 bug fix: load ... filter "BIOMOLECULE 1" ... broken in 12.0.19
# 12.0.25 bug fix: GenNBO reader does not read MOs properly
# 12.0.25 bug fix: GenNBO reader does not read xxx.31 file P orbitals not in
X Y Z order
# 12.0.25 bug fix: applying unit cell in LOAD command to XYZ file containing
multiple models
# does not convert later model coordinates to fractional ones.
# 12.0.24 bug fix: CIF reader does not recognize -1 for
_atom_site_disorder_group
# 12.0.23 bug fix: Mopac MGF reader upgrade allows orbital subset
# 12.0.23 bug fix: Mopac MGF reader upgrade allows filter "alpha", filter
"beta"
# 12.0.23 bug fix: JME load append does not get saved properly in state
SCRIPT command
# 12.0.24 bug fix: failure to read properly data "connect_atoms" from state
# when struts or hbonds turned OFF
SMILES
# 12.0.25 bug fix: SMILES generator in certain cases may not return
stereochem (c-C(OH)(H)-c)
# 12.0.23 bug fix: find("SMILES", smilesString) does not find Jmol atomIndex
== 0
# 12.0.23 bug fix: find("SMILES", smilesString) does not find [2H]
# 12.0.23 bug fix: SMILES check for c=c can fail.
WRITE command
# 12.0.26 bug fix: write xxx.jmol can fail if the same file is used twice in
two different contexts
# 12.0.25 new feature: (part of write MOL bug fix) write SDF creates
multi-model SDfile based on models of selected atoms
# 12.0.25 new feature: (part of write MOL bug fix) write V3000 creates V3000
file; see http://www.symyx.com/downloads/public/ctfile/ctfile.pdf
# 12.0.25 bug fix: write MOL creates V2000 file
# 12.0.25 bug fix: over-run of SDF, MOL/V2000 reports error
# 12.0.25 bug fix: Web Export and write xx.jmol fail for load XXX:: forcing
file type
# 12.0.24 bug fix: 12.0.19-22 fail to write state properly -- saved settings
not saved
miscellaneous fixes
# 12.0.26 bug fix: popup menu does not show load {1 1 1} options correctly
# 12.0.26 bug fix: space before [ not recognized as significant when
following $xxx or {...}
# 12.0.26 bug fix: set echo myecho [x y] after set echo myecho {3 3 3} does
not work
# 12.0.25 bug fix: assigning array elements using x[i] = pt, where pt is a
# variable that is a cartsian point or a plane does not copy
variable
# 12.0.25 bug fix: pop-up menu after zap 1.1 in set of two models crashes
Jmol
# 12.0.23 bug fix: bondset variables [{1 2 3}] incorrectly shown as atom
bitsets ({1 2 3})
# 12.0.23 bug fix: xxx.yyy when "yyy" has been defined as a local variable
using VAR fails
# 12.0.23 bug fix: appending data to models with unit cells can cause odd
results
--
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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