Changelog for
jmol-14.29.31-lp151.1.1.noarch.rpm :
* Tue Jan 29 2019 thod_AATTgmx.de- update to 14.29.31
* Sun Jan 27 2019 thod_AATTgmx.de- update to 14.29.30
* Fri Nov 30 2018 thod_AATTgmx.de- update to 14.29.29
* Thu Nov 01 2018 thod_AATTgmx.de- update to 14.29.28
* Mon Oct 29 2018 thod_AATTgmx.de- update to 14.29.27
* Wed Oct 10 2018 thod_AATTgmx.de- update to 14.29.26
* Tue Oct 09 2018 thod_AATTgmx.de- update to 14.29.24
* Mon Sep 10 2018 thod_AATTgmx.de- update to 14.29.22
* Sun Sep 09 2018 thod_AATTgmx.de- update to 14.29.21
* Sat Sep 01 2018 thod_AATTgmx.de- update to 14.29.17
* Fri Aug 31 2018 thod_AATTgmx.de- update to 14.29.19
* Fri Jun 15 2018 thod_AATTgmx.de- update to 14.29.17
* Wed Jun 06 2018 thod_AATTgmx.de- update to 14.29.16
* Thu May 24 2018 thod_AATTgmx.de- update to 14.29.15
* Mon May 14 2018 thod_AATTgmx.de- update to 14.29.14
* Wed Apr 18 2018 thod_AATTgmx.de- update to 14.29.13
* Wed Mar 28 2018 thod_AATTgmx.de- update to 14.29.12
* Sun Mar 25 2018 thod_AATTgmx.de- update to 14.29.11
* Wed Mar 14 2018 thod_AATTgmx.de- update to 14.29.10
* Fri Feb 09 2018 thod_AATTgmx.de- update to 14.29.5
* Thu Feb 08 2018 thod_AATTgmx.de- update to 14.29.4
* Sat Feb 03 2018 thod_AATTgmx.de- update to 14.29.3
* Fri Feb 02 2018 thod_AATTgmx.de- update to 14.29.1
* Tue Jan 30 2018 thod_AATTgmx.de- update to 14.29.2
* Fri Jan 26 2018 thod_AATTgmx.de- update to 14.29.1
* Thu Jan 25 2018 thod_AATTgmx.de- update to 14.28.4
* Fri Jan 19 2018 thod_AATTgmx.de- update to 14.28.3
* Wed Jan 17 2018 thod_AATTgmx.de- update to 14.28.2
* Mon Jan 15 2018 thod_AATTgmx.de- update to 14.28.1
* Sun Dec 17 2017 thod_AATTgmx.de- update to 14.27.2
* Sun Dec 10 2017 thod_AATTgmx.de- update to 14.26.1
* Sun Nov 19 2017 thod_AATTgmx.de- update to 14.25.2
* Sat Nov 11 2017 thod_AATTgmx.de- update to 14.24.2
* Tue Dec 20 2016 thod_AATTgmx.de- update to version 14.8.0 selected new feature:
* fully implemented CIF 2.0 reader
* autocalculation of MMFF94 partial charges
* 3DPrinter-compatible VRML and STL writing
* measure ID \"test\" radius 0.0 font 15.0 SansSerif Plain align CENTER AATT1 AATT2 \"test\"
* allowance for external app loading of binary (mmtf) files or any other file using a simple interface: Viewer.openReader(fullPathName, reader)
* Jmol reads PyMOL 1.8 PSE files with \"set dump_binary, 1\"
* load AUDIO audiofilename -- Java and JavaScript applet can read WAV, MP3, and OGG files -- application can read WAV files
* settable chain string using {atomset}.chain = \"xxx\"
* set hiddenLinesDashed -- when set TRUE, hidden lines in unit cells and boundbox are rendered as dashed lines. -- default is FALSE
* polyhedron -x.x .... -- sets maximum radius for gap calculation to be x.x
* $pbz1_1_.getProperty(x) where x is \"info\", \"faces\", \"faceTriangles\", \"faceCount\", \"face_areas\", \"face_types\", \"face_points\", \"vertices\", ...more... -- polyhedra information
* print unitcell(\"a=...,b=...,c=...,alpha=...,beta=...,gamma=....\")
* load ... unitcell \"a=...,b=...,c=...,alpha=...,beta=...,gamma=....\"
* unitcell \"a=...,b=...,c=...,alpha=...,beta=...,gamma=....\" -- only the numbers are read; everything else is ignored, so order is important here -- uses the format created by show unitcell/a
* unitcell RECIPROCAL 2 -- as integer, multiples of pi
* unitcell reciprocal x.x -- allows scaling of reciprocal cell, similar to unitcell(\"reciprocal\", x.x)
* write CIF -- just a very simple CIF file, P1 format -- allows writing a simple CIF file with changed coordinates after a UNITCELL command
* CONNECT {pair1} {pair2} ATROPISOMER and many bug fixes
* Sat Jul 16 2016 thod_AATTgmx.de- update to version 14.6.1 some bug fixes
* Sat May 28 2016 thod_AATTgmx.de- Improve spec file
* Thu May 26 2016 thod_AATTgmx.de- include current bug fixes
* Fri May 20 2016 thod_AATTgmx.de- update to version 14.6.0 selected new feature:
* CONNECT {pair1} {pair2} ATROPISOMER
* C13 NMR prediction from http://www.nmrdb.org/service/jsmol13c?smiles=CCCC
* Jmol SMILES bond atropisomerism ^nm- and ^^nm-
* SMILES/nonaromatic same as SMILES/noaromatic
* adds SHOW SMILES/bio and {
*}.find(\"SMILES/bio\") options:
* print {
*}.find(\"SMILES/hydrogen/\") adds hydrogen atoms
* Jmol now implements a way of indicating atropisomer chirality.
* full implementation of OpenSMILES and OpenSMARTS in Jmol
* Polyhedra command allows for min and max radius
* draw POINTGROUP SPACEGROUP
* draw SPACEGROUP
* print pointgroup(\"spacegroup\", AATT1)
* show spacegroup/xxxxx
* show symop 3 AATT3 \"atom\"
* show/draw symop AATT1 AATT2
* show/draw symop AATT1 AATT2 n
* symop() options
* symop(3,AATT3,\"atom\")
* getProperty(\"shapeInfo.echo\")
* preliminary MMTF reader
* set window width height
* set window \"xxx.png\"
* setting DSSR on the fly
* show chemical xxx where xxx is a file type and many bug fixes
* Mon Mar 28 2016 thod_AATTgmx.de- include current bug fixes (14.4.4)- split desktop file
* Sun Mar 13 2016 thod_AATTgmx.de- include current bug fixes (14.4.4)
* new feature for SMILES
* Sun Feb 21 2016 thod_AATTgmx.de- include current bug fixes (14.4.3)
* Mon Feb 15 2016 thod_AATTgmx.de- include current bug fixes
* Sat Feb 13 2016 thod_AATTgmx.de- include current bug fixes
* Fri Jan 22 2016 thod_AATTgmx.de- include current bug fixes
* Tue Dec 22 2015 thod_AATTgmx.de- update to version 14.4.1 selected new feature:
* \".\" notation extended to x.[a]
* (undocumented) x.distance.all(y)
* ... PLANE {pt1} {pt2} frac12
* AATTAATT3 for \"atomno=3 and thisModel\"
* AFLOW binary alloy file reader
* AXES TYPE \"a\"|\"b\"|\"c\"|\"ab\"|\"ac\"|\"bc\"|\"abc\"
* CAPTURE \"file.gif\" 10 transparent
* CTRL-PAGE_UP CTRL-PAGE_DOWN in console
* Castep reading of .ts files
* GAMESS input reader
* Legendre polynomials for MSCIF file reading
* MACRO command
* MODEL 1 PROPERTY \"xxx\" x
* MOLDEN extensions [SpaceGroup] [Operators] [Cell]
* MUTATE command
* Molden reader adds [CellAxes] block
* NBO command
* POLYHEDRA
* Raster3D triangle-only file reader (for DSSR cartoon-block representation)
* SHOW DOMAINS
* SYNC nnnn x
* TOPOS Crystal Graph Data (CGD) file reader
* VASP CHGCAR reader
* ZMatrixReader also serves as simple input file reader
* color polyhedra red blue (edge color blue)
* draw POINTS
* draw POLYGON -1
* eval(...)
* extracting array of sequential arrays from array of associative arrays
* frame [1 3 5 6]
* if, for, and while can all operate using no braces for single-line bodies
* image # the current view as an image
* isosurface UNITCELL x.x ....
* magCIF file reading for incommensurately modulated magnetic structures
* modulation
* pmesh files can contain triangle colors
* point(unitcell, {i, j, k})
* polyhedra
* pt.distance(plane,ptRef)
* random(low,high,seed)
* readers for ESS input types: CFILE, VFILE, MOPAC, NWChem, Gaussian, GAMESS, Orca, PQS
* removing empty array values using array.find() and opposite using array.find(\"\")
* reset LIGHTING
* resno is user settable
* show IMAGE
* write IMAGE
* slab/depth setting.
* transparent GIF using WRITE GIFT \"xxx.gif\"
* unitcell() function
* vibration max x.x
* x = plane(pt1, pt2, frac12) and more, in addition many bug fixes
* Sat Jul 11 2015 thod_AATTgmx.de- update to version 14.2.15 selected new feature:
* AFLOW binary alloy file reader
* _argCount, _arguments for functions and scripts
* MACRO command -- runs predefined script, generally defining
* _caller for functions -- a hashtable of local VARs defined in the calling function
* NBO cfi file writer - print data({
*}, \"cfi\")
* calculate symmetry POLYHEDRA
* draw POINTS
* load \"....\" FILL (BOUNDBOX|UNITCELL|..) and more, in addition many bug fixes
* Fri May 29 2015 thod_AATTgmx.de- update to version 14.2.14 new feature:
* \".\" notation extended
* NBO command with no arguments starts NBO panel (Java application only)
* color polyhedra red blue (edge color blue)
* draw polygon [AATT1 AATT2 AATT3...]
* for (var i FROM [a, b]) {...}
* write IMAGE; and various additional options
* print command by itself clears JavaScript and Jmol consoles
* set contextDepthMax
* set showScript -1 and many bug fixes
* Tue Mar 31 2015 thod_AATTgmx.de- update to version 14.2.13 new features:
* AATTAATT3 for \"atomno=3 and thisModel\"
* CGO PostScript option
* CGO SCREEN option
* CGO UVMAP option
* MUTATE command
* Windows BMP image reading
* image
* load MUTATE \"==LYS\"
* load NBO CH3CH2CH3, NBO command with no arguments starts NBO panel (Java application only)
* print data({
*},\"XYZ\", true), print data({
*},\"xyz\")
* random(low,high,seed)
* set zshadePower 0
* show chemical drawing
* show drawing
* show image
* write IMAGE and many bug fixes
* Sat Jan 31 2015 thod_AATTgmx.de- update to version 14.2.12 new features:
* load =cod/1000041 loads Crystallographic Open Database CIF files
* select :\"X\" where quotes are used now forces case sensitivity
* modulation
* CGO (undocumented command from Jmol 13.1.16; never tested)
* NBO command
* x = plane(pt1, pt2, frac12)
* SYNC nnnn x
* reset LIGHTING
* Castep reading of .ts files
* MODEL 1 PROPERTY \"xxx\" x
* readers for ESS input types: CFILE, VFILE, MOPAC, NWChem, Gaussian, GAMESS, Orca, PQS
* NBO .37 archive file coordinate reader (not MOs)
* ZMatrixReader also serves as simple input file reader for Q-Chem, Gaussian, Jaguar, MolPro, and ADF, as produced by NBO6Pro
* isosurface contour 0 \"t.jvxl\" will override contour selected in JVXL file; isosurface CONTOUR n i; isosurface LATTICE {i j k} FIXED; isosurface UNITCELL x.x .... and many bug fixes
* Sat Nov 22 2014 thod_AATTgmx.de- update to version 14.2.9 new feature:
* VASP CHGCAR reader, VASP CHGCAR isosurface reader
* load HISTORY \"saved.his\", CTRL-PAGE_UP CTRL-PAGE_DOWN in console
* capture END
* transparent GIF using WRITE GIFT \"xxx.gif\", GIF images use dithering to approximate full palette
* CAPTURE \"file.gif\" 10 transparent - or CAPTURE \"file.gift\", CAPTURE \"filename0000.png\", CAPTURE \"filename0000.gif\" bug fix:
* set labelOffset {1 2 3} fails
* Molden reader fails to read orbitals if [GEOCONV] is present
* slightly better GIF processing, GIF writer not properly handling large numbers of colors
* GIF and PPM writing broken in JavaScript
* WRITE command should remove \"t\" or \"j\" in WRITE xxx.PNGJ, WRITE xxx.PNGT, WRITE xxx.GIFT
* PDB reader limited to 20 connections per atom
* up-arrow in console may not return command if contains unicode
* antialiasing can subtly change background color
* Mon Oct 13 2014 thod_AATTgmx.de- update to version 14.2.7 feature change:
* DSSR reference to \"lonePairs\" changed to \"isolatedPairs\" -- select within(dssr,\"isolatedPairs\") preferred -- select within(dssr,\"lonePairs\") still OK
* Molden reader adds [CellAxes] block
* TOPOS Crystal Graph Data (CGD) file reader
* load =xxxx/rna3d, load =xxxx/val, load =xxxx/dom, load
*xxxx/dssr, load
*xxxx/rna3d
* Legendre polynomials for MSCIF file reading
* upgrade of application file...export...Gaussian Input File...
* pmesh files can contain triangle colors
* MOLDEN extensions [SpaceGroup] [Operators] [Cell]
* SHOW/WRITE PROPERTIES ... format \"%s %i %f %f %f\" -- allows specifying the format for a set of up to three properties. -- %s is atom name; %i is atom number
* magCIF file reading for incommensurately modulated magnetic structures -- very preliminary only; not tested
* set showModulationVectors true/false -- required now for showing modulation vectors rather than vibration vectors
* vibration max x.x, vector max x.x FEATURE CHANGE:
* atoms without vibration will no longer report out as vxyz = {0 0 0} bug fix:
* msCIF reader incorrectly handling multiple Legendre orders
* msCIF reader incorrectly handling superspace operators with x1,x2,x3 mixed into x4,x5
* CONTACT FULL does not report proper volume (Young ho Jhon)
* (Java only) write FILE fails for string (copy/pasted) data
* set waitForMoveTo not controlling script for ROTATE x.x y.y (finite spin)
* capture command not waiting properly for full spin
* msCIF reader: wave vectors of the form {a -a 0} were being ignored
* isosurface molecular reader misassigning voxel source atom
* JSpecView integration not displaying properly
* CGD reader for fractional coordinates; alternative EDGE syntax
* CGD reader space groups set to Bilbao (origin 2) setting.
* Molden reader overlaying MO info and unit cell info
* interpretation of space group I41 by name only, without operations, drops second (centered) C2 axis.
* exporter generally not allowing creating meshes with PovRAY
* script queue broken in 2014.09.17
* cartoon OFF does not remove nucleic bases from visible set
* and many more...
* Sun Aug 03 2014 thod_AATTgmx.de- update to version 14.2.4 bug fix:
* annotation atom sets not adjusted for added hydrogens
* 14.3.3_2014.08.02 broke mmCIF reader
* BinaryDocument (Spartan file) reading broken in 14.1.12_2014.03.18
* Sun Aug 03 2014 thod_AATTgmx.de- update to version 14.2.3 bug fix:
* 1-letter sequence for water showing as \"I\" not \"?\"
* DSSP analysis not returning information to console
* JSV jsvAddHighlight broken
* Jmol application starts in English regardless of language
* PDB reader not placing compoundSource in model auxiliary info
* SHOW SEQUENCE FALSE not giving 1-letter sequences
* for (i in x) where x is an associative array does not work
* getProperty isosurfaceData fails
* getproperty structureInfo can fail with phosphorus monomers
* model kit menu does not allow setting of new element
* move and moveto cannot be in the same session
* set atomPicking, setDrawPicking, pickLabel, pickingSpinRate all should not be in state
* set pdbAddHydrogens incompatible with mmCIF
*xxxx/val
* write COORD should display untransformed coordinates in XYZ format in the console, but it does not. It writes a JPG file named \"coord\".
* write PDB fails
* x.func(y) as second operand in a boolean \"and\" operation where the first operand evaluates to FALSE (so that x.func(y) is never evaluated), triggers a script error.
* zz = write(\"coord\") should write untransformed coordinates in XYZ format. It is writing untransformed coordinates in MOL format.
* zz = write(\"coord\", \"MOL\") should write transformed coordinates in MOL format. It is writing untransformed coordinates. new feature:
* eval(...)
* getProperty(x,\"[select a,b,c ...
* label %[validation.xxxx]
* load
*1cbs/all, load
*1cbs/dom, load
*1cbs/val, load
*1crs/val, load /pdbe/xxxx
* point({sx,sy,sz}, false) -- FROM screen coordinates
* point({x,y,z}, true) -- TO screen coordinates
* print getProperty(\"domainInfo[select
* where _type=\'SCOP\']\")
* print getProperty(\"validationInfo[select
* where _type=\'clashes\']\")
* select within(annotation, \"\")
* set hoverlabel \"%[validation.xxxx]\"
* show annotation
* SHOW DOMAINS
* SQL NOCACHE flag
* x.in([a,b,c,d])
* x.in(a,b,c,d...) # suggestion of Sameer Velankar
* {
*}.seqid
* Sun Jun 29 2014 thod_AATTgmx.de- update to version 14.2.2 bug fix:
* MCIF reader misreads magnetic symmetry operators involving xyz scaling
* isosurface \"=3hyd\" AS \"3hyd.omap\" fails to save proper file
* Sun Jun 29 2014 thod_AATTgmx.de- update to version 14.2.1 bug fix:
* correction for zz = write(\"coord\"), zz = write(\"coord\", \"MOL\") and write COORD
* MCIF reader not reading magnetic centerings 1/3, 2/3
* JSV jsvAddHighlight broken
* CASTEP phonon .geom file reading broken
* Sat Jun 14 2014 thod_AATTgmx.de- update to version 14.2.0 new feature:
* readers with unit cells may load as trajectories
* protein sidechain minimization bug fix:
* CASTEP reader broken for multiple cells and geometry optimization
* set pdbAddHydrogens fails for structures with ANISOU records
* select x < 0.3 reports error when checking, though it does run when executed
* SMILES for model with nonbonded atoms fails
* 06.09 broke unitcell display
* WebPanel error trapping problem; too long file name for tar file
* Mon Jun 09 2014 thod_AATTgmx.de- update to version 14.0.17
* Sat May 24 2014 thod_AATTgmx.de- correct FSF- add man
* Fri Apr 04 2014 thod_AATTgmx.de- update to version 14.0.13
* Sun Mar 09 2014 thod_AATTgmx.de- update to version 14.0.11
* Fri Feb 21 2014 thod_AATTgmx.de- update to version 14.0.10
* Fri Feb 14 2014 thod_AATTgmx.de- update to version 14.0.8
* Tue Jan 21 2014 thod_AATTgmx.de- update to version 14.0.7
* Fri Jan 10 2014 thod_AATTgmx.de- update to version 14.0.5
* Mon Jan 06 2014 thod_AATTgmx.de- update to version 14.0.4
* Mon Dec 30 2013 thod_AATTgmx.de- update to version 14.0.3
* Sat Dec 21 2013 thod_AATTgmx.de- update to version 14.0.2
* Fri Dec 06 2013 thod_AATTgmx.de- update to version 14.0.1
* Sat Nov 02 2013 thod_AATTgmx.de- update to version 13.2.8
* Wed Oct 02 2013 thod_AATTgmx.de- update to version 13.2.7
* Fri Aug 23 2013 thod_AATTgmx.de- update to version 13.2.4
* Sat Aug 03 2013 thod_AATTgmx.de- update to version 13.2.3
* Sat Aug 03 2013 thod_AATTgmx.de- use hard link- update to version 13.2.0- change icon to 2013 version
* Sat Jul 27 2013 thod_AATTgmx.de- update to version 13.0.18
* Sat Jul 27 2013 thod_AATTgmx.de- update to version 13.0.16
* Sat Jul 27 2013 thod_AATTgmx.de- initial spec file for version 13.0.15
