Jmol.___JmolVersion="14.9.1"
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.9/Jmol%2014.9.1/
new feature: set nboCharges (default true)
- determines whether formal charges are also displayed with LABEL %[nbo]
new feature: connect NBO
- connect atoms in the currently visible model using a resonance
structure configuration found in an NBO .46 or .nbo file
- where is one of
alpha|beta|46|46a|46b|nrtstr_n|nrtstra_n|topo_n|topoa_n|topob_n
new feature: label %[nbo];
- label an atom using a resonance structure configuration found in an
NBO .46 or .nbo file
- requires a previous connect NBO
new feature: quintuple and sextuple bonds.
-- connect @1 @2 quintuple
-- connect @1 @2 sextuple
-- readily saved in state
-- adding MOL file bond type 15 and 16 for these -- a bit of a hack, of
course.
new feature: Viewer.runScriptCautiously(String) replacement name for older
Viewer.runScript(String)
new feature: plugin main menu item.
- allows integrated additions to Jmol
- Just has NBO at this time; could have more, as it is a simple interface.
- created automatically from reading
org/openscience/jmol/app/plugins/plugin.properties,
which just contains a list of name=class pairs:
# plugin.properties
NBO=org.gennbo.NBOPlugin
new feature: startup options -U nbo or --plugin nbo
- starts Jmol in NBO mode, as if the Plugins...NBO menu item had been
clicked
- could be generalized, but do not that more than just nbo in place at
this time
- case insensitive
new feature: NBO n BETA - for GenNBOReader nth beta orbital; could be
expanded
bug fix: SHOW CHEMICAL JME (from NCI CIR) does not properly return formal
charges
bug fix: JSpecView, when open in application, does not allow ZAP
bug fix: draw POINTGROUP crashes Jmol if model is not first model
bug fix: DRAW circle rendering broken (load $2-butene ; draw pointGroup)
bug fix: NBO/ISOSURFACE command - Displaying BETA orbitals for NBO types
(NHO, PNBO, etc.) that
are from a file other than the current file causes read failure
and no orbital display.
bug fix: Viewer.runScript(String) now uses evaluateExpression(T[])
Lesson learned: Never mix viewer.runScript() and viewer.runScriptQueued()
calls.
What will happen is that the unqueued calls will corrupt
the
queued calls. However, if you use
viewer.evaluateExpression("script('')"),
that is also synchronous, and it uses a new ScriptEval() to
isolate it from
the script being queued. You still have the problem that
the scripts could
mess up each other, but at least it will not cause
catastrophic failure.
bug fix: *.CA should pick up calcium in a PDB file
bug fix: cfi format (for NBOPro) writing broken
- from using the command
x = data({*}, 'cfi')
bug fix: La and Ac should be in transitionmetal
bug fix: GenNBO reader not recognizing FILTER "BETA"
code: NBO options extended using the NBO VIEW or NBO OPTIONS "..." command
options
protected boolean jmolOptionNOZAP = false; // do no zap between modules
protected boolean jmolOptionNOSET = false; // do not use NBO settings by
default
protected boolean jmolOptionVIEW = false; // present only the VIEW option
protected boolean jmolOptionNONBO = false; // do not try to contact
NBOServe
noting previously undocumented:
set fontscaling true; font label 10 arial plain 0.020
- last number is a fontscaling factor that allows one to set a font size
for
- labels in angstroms. Roughly, this pointSize * factor is in Angstroms.
- if label is changed, one must use set fontscaling FALSE; label ;
fontScaling TRUE;
--
Robert M. Hanson
Larson-Anderson Professor 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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