Jmol Changelog

New in version 14.3.10_2014.11.27 Beta

November 27th, 2014
  • bug fix: SPIN BRANCH {atomno=2} {atomno=1} does not work code: scriptExt.IsoExt splits CmdExt into two parts -- (note this will require changes to build_03_tojs_stable)
  • code: simplification of SurfaceGenerator
  • bug fix: JVXL files do not record selected contour bug fix: isosurface CONTOUR -n broken (in Jmol 12)
  • bug fix: isosurface "t.jvxl" loading of contoured planes broken
  • bug fix: isosurface plane xy map property atomno broken every other time used
  • new feature: isosurface contour 0 "t.jvxl" will override contour selected in JVXL file
  • new feature: isosurface CONTOUR n i -- n contours; i-th only
  • FEATURE CHANGE: For the ISOSURFACE command, there is an undocumented syntax that the CUTOFF keyword prior to a number is optional, as in "ISOSURFACE 2.0". This was never documented and was never shown in any examples. This change is to require the CUTOFF keyword
  • new feature: isosurface LATTICE {i j k} FIXED -- creates an isosurface from periodic volumetric data with the specified number of unit cells -- "fixed" in the sense that the operation is at load time not at rendering, allowing slabbing and use of WITHIN
  • new feature: isosurface UNITCELL x.x .... -- for periodic lattices only -- adjusts grid by x.x in fractional coordinates -- caution is advised, as the grid is expanded in this process, leading to more grid points and more memory required -- negative x.x results in a selection of a subset of the data centered on the center of the unit cell

New in version 14.3.9_2014.11.23 Beta (November 24th, 2014)

  • bug fix: isosurface slab plane -xy not recognizing "-"
  • bug fix: PNGJ writing broken bug fix: VASP CHGCAR reader not recognized for primitive cell
  • bug fix: Euler ZYZ and ZXZ for quaternion({0 0 1},theta) where theta < 0 in error

New in version 14.2.9 (November 19th, 2014)

  • new feature: VASP CHGCAR reader
  • new feature: VASP CHGCAR isosurface reader
  • new feature: load HISTORY "saved.his" (Gabor Oszlanyi)
  • loads command history with script in saved.his
  • new feature: CTRL-PAGE_UP CTRL-PAGE_DOWN in console (Gabor Oszlanyi)
  • searches for next instance of current start of command up or down command history
  • new feature: capture END
  • closes capture without annoying popup message
  • also for capture CANCEL and just CAPTURE
  • new feature: transparent GIF using WRITE GIFT "xxx.gif"
  • new feature: GIF images use dithering to approximate full palette.
  • new feature: CAPTURE "file.gif" 10 transparent
  • or CAPTURE "" -- "gift" automatically changed to "gif"
  • new feature: CAPTURE "filename0000.png"
  • captures set of PNG files
  • 0000 is not required
  • new feature: CAPTURE "filename0000.gif"
  • captures set of GIF files
  • 0000 IS required in order to distinguish this from animated GIF
  • bug fix: set labelOffset {1 2 3} or set labelOffset [1 2 3 4 5 6 7]
  • fails if selection does not contain a label at each selected atom
  • bug fix: Molden reader fails to read orbitals if [GEOCONV] is present
  • bug fix: JmolVersion 14.3.3_2014.07.27 broke ligand bond reading when fetching ligands.
  • mmCIF reader was not being selected by the Resolver
  • Requires an increment of version number to 14.3.9
  • bug fix: slightly better GIF processing
  • bug fix: GIF writer not properly handling large numbers of colors
  • use of CIE L*a*b for color quantification
  • nearly identical to GIMP
  • uses MEAN_cut (not MEDIAN_cut)
  • uses Floyd-Steinberg dithering
  • will not discolor background (as GIMP will do)
  • bug fix: GIF and PPM writing broken in JavaScript
  • initial putString improperly forces string buffer mode in OC (Output Channel)
  • bug fix: WRITE command should remove "t" or "j" in WRITE xxx.PNGJ, WRITE xxx.PNGT, WRITE xxx.GIFT
  • specifically when no PNGJ, GIFT, or PNGT designation is made.
  • bug fix: PDB reader limited to 20 connections per atom
  • bug fix: up-arrow in console may not return command if contains unicode
  • bug fix: antialiasing can subtly change background color
  • bug fix: working on GIF writer -- some success with 256 colors using median-cut with RGB
  • bug fix: GIFT (transparent-background GIF) dithering transparent background
  • bug fix: Legendre for U not implemented in msCIF reader - preliminary
  • bug fix: Legendre for D,U in Jana2006 reader not implemented - preliminary
  • code: code clean-up in GData, Graphics3D, and Export3D
  • code: PDB reader CONECT efficiency

New in version 14.3.7_2014.10.13 Beta (October 15th, 2014)

  • new feature:
  • modulation occupancy settable using {*}.occupancy = {*}.modulation('O',t)
  • bug fix: msCIF reader superspace group operators with mixing of x1,x2,x3 into x4,x5 was still not quite correct.
  • bug fix: data "occupancy set" spelled wrong in state

New in version 14.2.7 (October 13th, 2014)

  • feature change: DSSR reference to "lonePairs" changed to "isolatedPairs"
  • select within(dssr,"isolatedPairs") preferred
  • select within(dssr,"lonePairs") still OK
  • bug fix: msCIF reader incorrectly handling multiple Legendre orders
  • bug fix: msCIF reader incorrectly handling superspace operators with x1,x2,x3 mixed into x4,x5
  • bug fix: CONTACT FULL does not report proper volume (Young ho Jhon)
  • bug fix: (Java only) write FILE fails for string (copy/pasted) data

New in version 14.3.6_2014.08.17 Beta (August 18th, 2014)

  • bug fix: modulated magnetic moment scaling by VECTORS MAX x.x not saved in state for modulations that are 0,0,0.
  • bug fix: magnetic CIF reader not automatically showing modulation
  • bug fix: load SUPERCELL {x y z} not working correctly in terms of packing
  • bug fix: load SUPERCELL not working correctly with modulation or magnetic

New in version 14.2.4 (August 4th, 2014)

  • bug fix: annotation atom sets not adjusted for added hydrogens
  • bug fix: 14.3.3_2014.08.02 broke mmCIF reader
  • bug fix: BinaryDocument (Spartan file) reading broken in 14.1.12_2014.03.18
  • new feature: point({x,y,z}, true) TO screen coordinates
  • new feature: point({sx,sy,sz}, false) FROM screen coordinates
  • bug fix: move+moveto/zoomto still an issue.
  • new feature: load *1cbs/dom
  • new feature: load *1cbs/val
  • new feature: load *1cbs/all
  • ew feature: label %[validation.xxxx]
  • new feature: set hoverlabel "%[validation.xxxx]"
  • new feature: select within(validation, "clashes where value>3")
  • new feature: print getProperty("validationInfo[select * where _type='clashes']", atomset)
  • new feature: print getProperty("domainInfo[select * where _type='SCOP']")
  • new feature: SQL NOCACHE flag
  • new feature: SHOW DOMAINS "some info"
  • new feature: SHOW DOMAINS " all"

New in version 14.2.2 (June 30th, 2014)

  • bug fix: MCIF reader misreads magnetic symmetry operators involving xyz scaling
  • bug fix: isosurface "=3hyd" AS "3hyd.omap" fails to save proper file (error in seek() method of javajs.util.binaryDocument)

New in version 14.2.1 (June 30th, 2014)

  • bug fix: zz = write("coord") should write untransformed coordinates in XYZ format. It is writing untransformed coordinates in MOL format.
  • bug fix: zz = write("coord", "MOL") should write transformed coordinates in MOL format. It is writing untransformed coordinates.
  • bug fix: write COORD should display untransformed coordinates in XYZ format in the console, but it does not. It writes a JPG file named "coord".
  • bug fix: MCIF reader not reading magnetic centerings 1/3, 2/3
  • bug fix: JSV jsvAddHighlight broken
  • bug fix: JSmol HTML5 console broken for Safari and Chrome
  • bug fix: CASTEP phonon .geom file reading broken