https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.2/
Jmol.___JmolVersion="14.4.2_2016.02.05"
FEATURE NOTE: Prior to this version if the MO command was issued after use
of
rotateSelected, the orbitals were calculated improperly,
because the
basis functions always must be applied for the original file
coordinate
frame, not the rotated frame. In addition, if MOs were
calculated prior to
use of rotateSelected or translateSelected, then they would
not "track"
with the modified atom positions. So MOs and
rotate/translateSelected
were completely incompatible. Jmol 14.4.2 fixes this issue.
It should be
possible now to produce correct MOs before or after use of
rotateSelected.
Note that ALL atoms in a specified model must be moved in
order for this
tracking of MOs to take place. This functionality was
introduced in
14.4.1_2016.01.28, but that version (never released) does not
properly
check to see that ALL the atoms in a model have been involved
in the rotation.
FEATURE NOTE: If rotateSelected or translateSelected is used to move all
atoms in a
model, and after that the state is saved, then Jmol 14.4.2
will save a state that is not readable in 14.4.1. This is
necessary
because of the added FRAME ORIENTATION command, which is used
in the states
to indicate the relationship of a model to its file
coordinates. The MO
reader requires this so that it can rotate the coordinates
back to their
original position prior to doing its calculation.
new feature: variable _versionDate
$ show _versionDate
_versionDate = "14.4.1_2016.01.16 2016-01-15 17:25"
bug fix: LOAD $benzene; SHOW smiles should give c1ccccc1 not c1=cc=cc=c1
bug fix: LOAD FILES "$caffeine" ":caffeine";print {1.1}.find("SMARTS",{2.1})
should give atoms, but it does not. Problem is with aromatic
structure
to SMILES shows c=c instead of just cc. (SMARTS searching with c=c
does
not match
bug fix: JVXL files saved from models that involve full model
rotate/translateSelected
do not get restored properly.
bug fix: molecular orbitals do not move with atoms
when full molecule is moved using rotateSelected or
translateSelected
bug fix: IboView/Molpro XML reader validated for multi-molecule XML files
-- to concatenate Molpro XML files, you must supply a new root tag as well
as
remove all <?...?> directives.
-- DOS CMD file example:
catxml.bat ibo*.xml test.xml
where catxml.bat is:
copy /b %1 _temp
echo ^<OUTER^> > %2
type _temp | find /V "<?" >> %2
echo ^</OUTER^> >> %2
bug fix: IboView/Molpro XML Reader validated for reading orbitals
bug fix: MOs need to move with atoms and be restored from state properly
after use of ROTATESELECTED.
-- note that fix for 14.4 does not include state saving, as that would
break previous subversions
bug fix: Spartan file reader not working properly after MacSpartan
-> Spartan14 upgrade
bug fix: mol, xyz readers not reporting model name like other readers
bug fix: d = [start:1,end:10] fails due to reserved word "end" (also
"select", "case", "default", "if", "for", etc.)
bug fix: color "chain" (with quotes) should work, allowing for x="chain";
color @x
bug fix: inappropriate use of REGEX in ["a","b"].find("x")
bug fix: ".xxx" should be allowed as a math continuation:
print script("show spacegroup all")
.split()
.find("Hall symbol:")
bug fix: labels, echos, and measurements improperly shaded when z-shaded
with nonblack background
bug fix: rendering error when set zshade followed by set antialiasdisplay
bug fix: labels, echos, and measurements disappear when z-shaded
code: better loading of surfaces -- no longer requires javajs.util.XmlUtil
code: removal of unnecessary api interfaces MinimizerInterface,
VolumeDataInterface, QuantumPlaneCalculationInterface,
MOCalculationInterface, MepCalculationInterface
code: new abstract reader XmlMOReader
code: JmolZipUtilities interface removed
code: JmolBinary reduced to just all Spartan-related methods
code: polyhedra, pointgroup, load =ams/, load "xxxx#_DOCACHE_" features
from 14.5 added to 14.4
code: (JavaScript) refactoring to allow faster, cleaner load for biomodels
code: (JavaScript) refactoring to reduce extraneous file download
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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