Jmol

[Jarom]

Jmol 14.24.1

• new feature: MACRO bz; createWS("p1") -- creates a Wigner-Seitz cell as polygon id "p1" -- requires current unit cell to be primitive to work correctly -- polyhedron can be shifted using POLYHEDRA OFFSET -- default ID "pbz1_1_" for just CREATEWS()
• new feature POLYHEDRA edgesOnly
• -- shows just edges -- operates on ALL polyhedra -- complements edges, noEdges, frontEdges
• new feature: select within(d, $p1) where $p1 is a polyhedron ID -- d = 0 is "on or within the polyhedron" -- d < 0 is "-d angstroms within polyhedron" -- d > 0 is "within d angstroms of polyhedron"
• bug fix: POLYHEDRA edges should inherit color, not use black as default
• bug fix: calculate CHIRALITY may fail to show Z for some seqCis systems
• new macros: "aflow", "
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  ", "AFLOW macros", "bz", "
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  ", "Brillouin Zone/Wigner-Seitz macros" code: biomodel classes are being loaded prematurely due to @cystine definition involving cys.sg instead of cys and atomname=sg

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[Jarom]

Jmol 14.24.2

• bug fix: invertSelected was not clearing chirality
• bug fix: JmolAppletSigned0.jar fails -- missing org/apache/tools
• bug fix: SHOW SMILES sometimes missing allene chirality
• bug fix: hbondsDistanceMaximum should not be limited by 2.5 max; increased maximum to 3.5
• bug fix: hbondsDistanceMaximum and hbondsAngleMinimum should not be in state
• code: moved scriptEval.cmdInvertSelected to scriptext.cmdExt

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[Jarom]

Jmol 14.27.2

Jmol.___JmolVersion="14.27.2" new feature: frame MO - goes to first frame with a molecular orbital bug fix: [UNK] missing in atom identities, even when part of actual structures such as 3A0B bug fix: polyhedra ID p1 @11 to {connected(@11)} not working -- allows for $p1.getProperty(....) bug fix: load(filename, "JSON") should allow for files that start with "[" rather than "{" bug fix: JSJSON parser fails for leading whitespace in map values code: additions to QCJSONWriter and QCJSONReader - working with Jmol-datafiles/qcjson/preliminary - "QCJSON 0-0-0.Jmol_14.27.2__2017-12-11_09:38", JmolVersion="14.27.1" released 2017.12.11 new feature: functions write("zip") and write("jmol") - allows creating a binary variable containing zip data - does not include preview.png (unlike write xxx.zip or xxx.jmol) - includes any local files (as for WRITE command) - "zip" does not include remote-access files - "jmol" DOES include remote-access files - allows use of .pop() and .push() to remove, modify, or add files - same as write xxx.zip; x = load("xxx.zip",true) -- except includes no preview.png - for example: load $caffeine x = write("jmol") x.push("mydata","testing") write var x "test.zip" y = load("test.zip", true) print y.keys ... print y.mydata testing load test.zip ... load $caffeine x = write("jmol") zap load var x bug fix: CIPChirality adds "mancude system" averaging of atomic numbers in Rule 1a JmolVersion="14.26.1" new feature: experimental qcjson write format - ALPHA only bug fix: decimal formatter failing for 9.9999999 to 5 digits bug fix: Jaguar reader not reading MOs; (working, but still does not read STO-3G) bug fix: direct call to sun.audio on some systems fails; -- moved to class openscience.jmol.jmolPanel.JmolAudio -- accessed by reflection, so not loaded unless needed. code - synchronized with NBOServe project. (2017.11.10) JmolVersion="14.25.2" bug fix: DCD (trajectory) reader failing when periodic lattice info is present JmolVersion="14.25.1" >> TODO NEEDS DOCUMENTING: new feature: polyhedra WIGNER // Wigner-Seitz cell new feature: polyhedra BRILLOUIN // 1st Brillouin zone new feature: polyhedra BRILLOUIN 1 // 1st Brillouin zone new feature: polyhedra BRILLOUIN 2 // 2nd Brillouin zone new feature: polyhedra BRILLOUIN -1 // Wigner-Seitz cell new feature: polyhedra scale 3.0 BRILLOUIN 1 // scaled 1st Brillouin zone bug fix: MOL file reader should not autobond if number of bonds is 0.

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[Jarom]

Jmol 14.29.3

Jmol.___JmolVersion="14.29.3"
bug fix: mac cut/paste enabled for Macs
bug fix: set autobond corrected
bug fix: changing an atom's element should delete all partial charges
bug fix: load AUDIO "xxx.wav" broken in Java
bug fix: load AUDIO "xxx.wav" broken in JavaScript
bug fix: loading of pdb file does not report HET = .... to console
bug fix: CONTACT leading to no contacts crashes Jmol.
bug fix: load FILES with filter does not work
bug fix: load =xxxx/val with filter does not save in state
solution was to change "+" to "-" to indicate special two-file loading in this case

new feature: set label picking icon in application
new feature: set label picking does not require shift for drag
new feature: set label picking allows double-click to set the label

new feature: drag-drop of PNGJ into script opens editor (for movie.spt; use not implemented)

new feature: set allowAudio (default TRUE)

new feature: AUDIOcallback
- used to continue after completion of an audio clip
- parameter is a hashtable with information about the audio clip

new feature: load AUDIO "xxx.wav" FILTER "...options..."
- filter options include:
- id='....' an identifier for this audio clip
- loop loop until told to stop
- start='...', play='...', stop='...', ended='...' callback scripts allowed
- single word arguments allowed - for example, id=a2 ended=audioDone()

note: These features will be included in a future AUDIO command

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[Jarom]

Jmol 14.29.5

Jmol.___JmolVersion="14.29.5" // released 2018.02.08
bug fix: (Java application only) Incorrect class file in Jmol.jar causes BOUNDBOX ON to fail

JmolVersion="14.29.4" // released 2018.02.07
bug fix: set hbondsrasmol false fails with O atom-only HOH group
bug fix: calculate pointgroup does not change with new atom positions

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