[Jmol-users] Jmol 14.4.0 released

[Robert H. <ha...@st...>]

Happy to report the release of Jmol 14.4.0.

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.0/

Jmol 14.4.0 culminates 16 months of work. Thank you all for great ideas,
great feedback, and great testing.

Onward, ho!



summary of 200+ new features for Jmol 14.4 -- June, 2014 - Oct. 2015 -- Bob
Hanson

development highlights include:

 -- new MUTATE command allows easy modification of protein residues, which
along with set picking dragMinimize allows easy tweaking of the mutated
group

 -- biomolecule annotations including DSSR, RNA3D, EBI sequence domains,
and PDB validation data

 -- additional math functions for working with arrays, data tables, planes
and polyhedra

 -- simplified JmolSQL for working with annotations and other array-based
data

 -- new DRAW and CGO options, including simple PostScript graphics reading

 -- new capability to display images in pop-up windows or within locations
on a web page

 -- integration into NBO (still in development)

 -- several important new load options, including volume filling
    (rather than unit cell filling) of crystal data, lattice scaling,

 -- significant enhancements in relation to polyhedra, including extension
of stereochemical SMILES and SMARTS to atom environments, polyhedra
matching, and the polyhedra() function.

 -- addition of Legendre polynomials for modulated structure CIF file
loading

 -- integration into AFLOW computational solid state physics project

Not all of this is fully documented in the Interactive Documentation, but
it can all be found in
http://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.0/README-14.4.0_2015.10.13.properties/download

new feature:  getProperty(x,"[select a,b,c ....
new feature:  x.dot(y) for planes and points
new feature:  x.in([a,b,c,d])
new feature:  x.in(a,b,c,d...)
new feature: "." notation extended to x.[a]
new feature: "...".split("\t",true) // tab split of string to array of
arrays
new feature: "....".split("",true) // CSV split of string to array of arrays
new feature: ".[a]" notation extended to x.. and allows mixing with .a.
new feature: (undocumented) x.distance.all(y)
new feature: ... PLANE {pt1} {pt2} frac12
new feature: @@3 for "atomno=3 and thisModel"
new feature: [...].split("",true) // CSV split of array to array of arrays
new feature: [...].split("\t",true) // tab split of array to array of arrays
new feature: [...][...].col(n)
new feature: [...][...].join("",true) // CSV join to array of lines
new feature: [...][...].join("\t",true) // tab join to array of lines
new feature: [array].pivot
new feature: [Font] button added to Console
new feature: [Font] button added to ScriptEditor
new feature: _.currentModelIndex  _  shortcut for
@{getProperty("auxiliaryInfo", "")}
new feature: _argCount, _arguments for functions and scripts
new feature: _caller for functions
new feature: _m.xxx   _m shortcut for
@{getProperty("auxiliaryInfo.models[<currentModel>]")}
new feature: {*}._(...)  same as {*}._getProperty(...)
new feature: {*}.find("MF", TRUE)
new feature: {*}.getProperty("atomInfo.xxx") alternative for
getProperty("atominfo.xxx", {*})
new feature: {*}.getProperty("bondInfo.xxx") alternative for
getProperty("bondinfo.xxx", {*})
new feature: {*}.getProperty("xxx")  same as
{*}.getProperty("atomInfo.xxx")
new feature: {*}.seqid
new feature: {atomset}.bondcount({atomset2})
new feature: {cell=555}.find("CellFormula");
new feature: {cell=555}.find("CellFormula", TRUE);
new feature: {xxx}.find("MF","CH2O")
new feature: AFLOW binary alloy file reader can filter "list=xx" to produce
a list of values
new feature: AFLOW binary alloy file reader centers unit cells in all
frames at the same point
new feature: AFLOW binary alloy file reader reading -- DATA -- block into
associative arrays:
new feature: AFLOW binary alloy file reader selective for a given
composition:
new feature: array of sequential arrays formatting using
array.format("format")
new feature: array.getProperty("xxxx")
new feature: associative array binning:
new feature: AXES TYPE "a"|"b"|"c"|"ab"|"ac"|"bc"|"abc"
new feature: calculate symmetry POLYHEDRA
new feature: CAPTURE "file.gif" 10 transparent
new feature: CAPTURE "filename0000.gif"
new feature: CAPTURE "filename0000.png"
new feature: capture END
new feature: Castep reading of .ts files
new feature: CGO (undocumented command from Jmol 13.1.16; never tested)
new feature: CGO PostScript option
new feature: CGO SCREEN option
new feature: CGO UVMAP option
new feature: color polyhedra red blue (edge color blue)
new feature: CTRL-PAGE_UP CTRL-PAGE_DOWN in console
new feature: draw POINTS [ array of points ]
new feature: draw POINTS <list of points or array of points>
new feature: draw polygon [@1 @2 @3...]
new feature: draw POLYGON <list of points or array of points> -1
new feature: eval(...)
new feature: extracting array of sequential arrays from array of
associative arrays
new feature: for (var i FROM [a, b]) {...}
new feature: for msCIF (modulated structure files), setting modulation or
using vibration ON
new feature: frame [1 3 5 6]
new feature: frame align [modelNo] [pt]
new feature: frame align {atoms} FIXED
new feature: GAMESS input reader
new feature: Gaussian Input File creation defaults to "opt pop=full
gfprint" to generate orbital information by default.
new feature: getProperty shapeInfo.polyhedra
new feature: getProperty("ShapeInfo.polyhedra") includes keys
new feature: GIF images use dithering to approximate full palette.
new feature: image             # the current view as an image
new feature: image "" close    # close the current view image
new feature: image "c:/temp/t.bmp" # image from a file
new feature: image "c:/temp/t.bmp" close # close image from a file
new feature: image 300 400     # adjustable size
new feature: image CLOSE       # close all
new feature: image ID ...
new feature: isosurface "==1blu"
new feature: isosurface contour 0 "t.jvxl" will override contour selected
in JVXL file
new feature: isosurface CONTOUR n i
new feature: isosurface LATTICE {i j k} FIXED
new feature: isosurface RMSD (same as SIGMA)
new feature: isosurface UNITCELL x.x ....
new feature: Jmol Application Tools|NBO... (Experimental Only; requires
NBOServer)
new feature: JSmol  <div id=JmolApplet0_console></div>  sets a place on the
page for the JSmol console.
new feature: JSmol  Jmol._persistentMenu = true
new feature: label %[validation.xxxx]
new feature: label %O
new feature: Legendre polynomials for MSCIF file reading
new feature: load "...." FILL
new feature: load "...." FILL [o va vb vc]
new feature: load "...." FILL [o vabc]
new feature: load "...." FILL BOUNDBOX
new feature: load "...." FILL UNITCELL
new feature: load *1cbs/all
new feature: load *1cbs/dom
new feature: load *1crs/val
new feature: load *xxxx/dssr
new feature: load *xxxx/rna3d
new feature: load /pdbe/xxxx
new feature: load =cod/1000041  loads Crystallographic Open Database CIF
files
new feature: load =xxxx/dom
new feature: load =xxxx/rna3d
new feature: load =xxxx/val
new feature: load HISTORY "saved.his"
new feature: load MUTATE "==LYS"
new feature: load NBO CH3CH2CH3
new feature: load quartz.cif supercell "2a,2b+a,c;1/2,0,0"
new feature: load xxx filter "latticeScaling=1.2"
new feature: load(filename, asbinary, async)
new feature: MACRO command
new feature: magCIF file reading for incommensurately modulated magnetic
structures
new feature: MODEL 1 PROPERTY "xxx" x
new feature: modulation occupancy settable using {*}.occupancy =
{*}.modulation('O',t)
new feature: modulation Q {q1 q2 q3}
new feature: modulation Q n
new feature: modulation T {t1 t2 t3}
new feature: modulation T x.x
new feature: MOLDEN extensions [SpaceGroup] [Operators] [Cell]
new feature: Molden reader adds [CellAxes] block
new feature: MUTATE command
new feature: NBO .37 archive file coordinate reader (not MOs)
new feature: NBO cfi file writer
new feature: NBO command
new feature: NBO command with no arguments starts NBO panel (Java
application only)
new feature: NBO TYPE <nboType>
new feature: pmesh files can contain triangle colors
new feature: point({sx,sy,sz}, false)
new feature: point({x,y,z}, true)
new feature: POLYHEDRA 12 UNITCELL
new feature: POLYHEDRA 4-16
new feature: polyhedra highlight with select ON or set selectionHalos ON
new feature: polyhedra ONLY
new feature: polyhedra properties "smiles" and "smarts"
new feature: polyhedron(smarts)
new feature: polyhedron(smiles)
new feature: preliminary AFLOW AaBb binary file reader
new feature: print  command by itself clears JavaScript and Jmol consoles
new feature: print data({*},"xyz")
new feature: print data({*},"XYZ", true)
new feature: print getProperty("domainInfo[select * where _type='SCOP']")
new feature: print getProperty("validationInfo[select * where
_type='clashes']")
new feature: print getProperty("validationInfo[select * where
_type='clashes']", atomset)
new feature: pt.distance(plane,ptRef)
new feature: random(low,high,seed)
new feature: readers for ESS input types: CFILE, VFILE, MOPAC, NWChem,
Gaussian, GAMESS, Orca, PQS
new feature: removing empty array values using array.find() and opposite
using array.find("")
new feature: reset LIGHTING
new feature: resno is user settable
new feature: select :"X"  where quotes are used now forces case sensitivity
new feature: select POLYHEDRA
new feature: select polyhedra(4)
new feature: select within(annotation, "<query>")
new feature: select within(validation, "clashes where value>3")
new feature: set contextDepthMax
new feature: set edsUrlFormatDiff
new feature: set hoverlabel "%[validation.xxxx]"
new feature: set labeloffset range expanded to [-500,500]
new feature: set labelOffsetAbsolute x y
new feature: set legacyJavaFloat
new feature: set showModulationVectors true/false
new feature: set showScript -1
new feature: set zshadePower 0
new feature: show annotation
new feature: show chemical drawing
new feature: SHOW DOMAINS
new feature: SHOW DOMAINS "<annotationRecordIinfo> all"
new feature: SHOW DOMAINS "<annotationRecordIinfo> mappings"
new feature: SHOW DOMAINS "<annotationRecordIinfo>"
new feature: SHOW DOMAINS "some info"
new feature: show drawing
new feature: show IMAGE
new feature: show IMAGE "filename"
new feature: show image 300 400     # adjustable size
new feature: show image CLOSE                 # "all" presumed
new feature: show image CLOSE ""              # the model image
new feature: show image CLOSE "c:/temp/t.bmp" # the image for this file
new feature: show image none        # closes all image panels
new feature: show pointgroup POLYHEDRON
new feature: SHOW/WRITE PROPERTIES ... format "%s %i %f %f %f"
new feature: smiles2.find("SMILES",smiles1, asMap, allMappings)
new feature: SQL "drilling" in associative arrays for sub arrays with a
given property
new feature: SQL NOCACHE flag
new feature: SYNC nnnn {type:"command",  "command" : command, "var": vname,
"data":vdata}
new feature: SYNC nnnn x
new feature: TOPOS Crystal Graph Data (CGD) file reader
new feature: transparent GIF using WRITE GIFT "xxx.gif"
new feature: upgrade of application file...export...Gaussian Input File...
new feature: VASP CHGCAR default cutoff set to 0.5
new feature: VASP CHGCAR isosurface reader
new feature: VASP CHGCAR reader
new feature: vector max x.x  // alternative; the same
new feature: vibration max x.x
new feature: Windows BMP image reading
new feature: write IMAGE
new feature: write IMAGE 500 500
new feature: x = plane(pt1, pt2, frac12)
new feature: x.find("SMILES","*")
new feature: ZMatrixReader also serves as simple input file reader






-- 
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