Jmol

Jmol 13.0 was released Aug 22, 2012. This major release brings to the stable release several very important new features in Jmol developed over the past year.

Jmol 13.0 was released Aug 22, 2012. This major release brings to the stable release several very important new features in Jmol developed over the past year. With well over 500,000 full application downloads (that is, distinct binary downloads by ... [More] application users or developers, not simple applet downloads by users), full server-side Java support for non-Java (iPhone/iPad) or non-applet (Android) mobile devices, and a completely new JavaScript interface, Jmol is well-positioned for the next phase of development of a high-level scripted high-functional HTML5/WebGL user interface. New features (see http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm\) include: APPLET: -- a new OOP JavaScript interface (Jmol-JSO) allowing nonJava options such as ChemDoodle and GLmol as well as JME/JSpecView connectivity (see http://wiki.jmol.org/index.php/Jmol_Javascript_Object\) to be seamlessly integrated into a web page in a platform-aware manner. -- JmolData full "headless" operation for server-side processing allowing image-creation, server processing, and remote cross-domain sourcing for the unsigned applet and applet surrogates such as ChemDoodle and GLmol. BIOPHYSICS: -- COMPARE command FILE READING: -- reading of JCAMP-DX files having structure/spectra assignment data using ##$MODELS and ##$PEAKS (see http://chemapps.stolaf.edu/jmol/jspecview\) -- Gaussian log reading of Natural Transition Orbitals -- automatic PNGJ file caching for immensely faster loading of PNGJ files from remote servers FILE WRITING: -- write PNGJ files encapsulate all model file data into one PNG file -- write image 400 400 PNGJ "http://....." POSTs JMOL or IMAGE or structure to a server as application/octet-stream -- write MOL adds partial charge data as > <JMOL_PARTIAL_CHARGES> in SDF format -- multiple-scene PNGJ files allowing minimal or full data loading and scripted animations ISOSURFACES: -- isosurface caching -- isosurface MOVE [[...matrix4f...]] moves/rotates an isosurface (for the state) MINIMIZATION: -- MMFF94/UFF minimization and energy calculation MOLECULAR DATA: -- show CHEMICAL -- show NMR MOLECULAR PLAYGROUND: -- MolecularPlayground -- remote status and remote control SOLID-STATE PHYSICS: -- solid state physics support SPECTROSCOPY: -- integration of JSpecView into Jmol, including 2D spectral display and manipulation STRUCTURE SEARCHING: -- extended Jmol SMARTS searching -- PubChem search for name (which can be a CAS number), cid, or SMILES using ":" [Less]

Jmol 13.0 was released Aug 22, 2012. This major release brings to the stable release several very important new features in Jmol developed over the past year. With well over 500,000 full application downloads (that is, distinct binary downloads by ... [More] application users or developers, not simple applet downloads by users), full server-side Java support for non-Java (iPhone/iPad) or non-applet (Android) mobile devices, and a completely new JavaScript interface, Jmol is well-positioned for the next phase of development of a high-level scripted high-functional HTML5/WebGL user interface. New features (see http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm\) include: APPLET: -- a new OOP JavaScript interface (Jmol-JSO) allowing nonJava options such as ChemDoodle and GLmol as well as JME/JSpecView connectivity (see http://wiki.jmol.org/index.php/Jmol_Javascript_Object\) to be seamlessly integrated into a web page in a platform-aware manner. -- JmolData full "headless" operation for server-side processing allowing image-creation, server processing, and remote cross-domain sourcing for the unsigned applet and applet surrogates such as ChemDoodle and GLmol. BIOPHYSICS: -- COMPARE command FILE READING: -- reading of JCAMP-DX files having structure/spectra assignment data using ##$MODELS and ##$PEAKS (see http://chemapps.stolaf.edu/jmol/jspecview\) -- Gaussian log reading of Natural Transition Orbitals -- automatic PNGJ file caching for immensely faster loading of PNGJ files from remote servers FILE WRITING: -- write PNGJ files encapsulate all model file data into one PNG file -- write image 400 400 PNGJ "http://....." POSTs JMOL or IMAGE or structure to a server as application/octet-stream -- write MOL adds partial charge data as > in SDF format -- multiple-scene PNGJ files allowing minimal or full data loading and scripted animations ISOSURFACES: -- isosurface caching -- isosurface MOVE [[...matrix4f...]] moves/rotates an isosurface (for the state) MINIMIZATION: -- MMFF94/UFF minimization and energy calculation MOLECULAR DATA: -- show CHEMICAL -- show NMR MOLECULAR PLAYGROUND: -- MolecularPlayground -- remote status and remote control SOLID-STATE PHYSICS: -- solid state physics support SPECTROSCOPY: -- integration of JSpecView into Jmol, including 2D spectral display and manipulation STRUCTURE SEARCHING: -- extended Jmol SMARTS searching -- PubChem search for name (which can be a CAS number), cid, or SMILES using ":" [Less]

Jmol 12.2 introduces over 100 new features in a wide variety of disciplines. For details, see http://chemapps.stolaf.edu/jmol/docs/examples-12/new2.htm

Jmol 12.2 introduces over 100 new features in a wide variety of disciplines. For details, see http://chemapps.stolaf.edu/jmol/docs/examples-12/new2.htm Some highlights include: CONNECTIONS TO OTHER SYSTEMS: direct access to NIH CACTVS server and ... [More] IUPAC name recognition software for small-molecule structures fully verified DSSP calculation of protein secondary structure support for materials science surface first-principles computation visualization (CASTEP, CRYSTAL, QuantumEspresso, VASP, WIEN2K) Molprobity file reading SURFACES: new CONTACT command reversible and extensible isosurface slabbing probability-based atomic orbitals display of linear combinations of molecular orbitals STRUCTURE ANALYSIS AND SEARCHING: structure- and SMILES-based substructure searching using SMARTS bioSMARTS/bioSMILES, and conformational SMARTS searching (Jmol innovations) diasteriomer/enantiomer comparison and checking with structures or SMILES strings ORGANIC CHEMISTRY: easy mechanistic arrows display of 2D drawing images, chemical names, ... and much, much more! The full list: 117. LOAD trajectory extended to vibrations 116. write transparent-background PNG images 115. load "xxx.xxx" [ list of models to load ] 114. set minPixelSetRadius 113. CRYSTAL09 tensor quantities 112. unitcell {xxx yyy scale} 111. Application console commands UNDO, REDO 110. UNDOMOVE/REDOMOVE n 109. set isosurfaceKey 108. SurfaceTool 107. FEATURE CHANGE: "ligand" 106. MolProbity contact dot reader 105. new CONTACT command 104. select within(VDW, xxxx) 103. "picked" variable 102. select/display/hide GROUP ... 101. select/display/hide ADD/REMOVE 100. @n 99. {atomset}.x? 98. measure INTRAMOLECULAR/INTERMOLECULAR 97. measure VDW 96. set measurementUnits VDW 95. calculate HYDROGEN and set pdbAddHydrogens 94. load "==XXX" 93. more information with LOAD 92. isosurface slab n 91. show lighting 90. .count and .count(x) 89. JVXL files return state 88. arbitrary function surfaces 87. isosurface INTERSECTION 86. color isososurface {atom expression} [color] 85. select within(distance, $surfaceID) 84. isosurface slab within x.x {atom expression or point} 83. set defaultLablPDB and set defaultLabelXYZ 82. reversible isosurface slab 81. plane(r, theta, phi) 80. NCI surfaces 79. FEATURE CHANGE -- zshadePower default 78. set zSlab {atom expression or point} 77. quaternion() 76. isosurface PARAMETERS 75. color atoms property VECTORSCALE 74. appletReadyCallback 73. atomMovedCallback 72. connecting surfaces to atoms 71. simple curved mechanistic reaction arrows 70. pointilist atomic/molecular orbitals projected onto planes 69. pointilist molecular orbitals 68. pointilist atomic orbitals 67. loading of structure by IUPAC name 66. show chemical name/inchi/inchikey 65. isosurface remapping 64. set echo ID 63. show drawing 62. for (var x in [...]) {....} 61. for (var x in {...}) {....} 60. SPARTAN READER charge default changed 59. xxx.mass.sum 58. plane(, , true) 57. frame TITLE @someArray 56. load MENU label "null" 55. write COORD XYZVIB filename 54. draw ARROW...BARB 53. isosurface... map property x WITHIN x.y 52. COMMAND-SHIFT-LEFT-DRAG (Macintosh only) 51. expanded XYZ file format 50. mo -n 49. loading of DCD files 48. linear combinations of molecular orbitals 47. write XXX.OBJ 46. intersection() function 45. x.sort, x.reverse 44. V2000 MOL reader reads partial charges 43. write xxxx.XYZRN 42. load filter "|" and "/=" options 41. isosurface spherical slab 40. isosurface MSMS xxxx.vert 39. isosurface/draw .length 38. draw SLAB 37. plane(pt1, pt2) 36. write SDF and write V3000 35. measure LIST 34. CIF file load defaults and load FILTER "MOLECULAR" 33. point(x.y) 32. label %{dataName} 31. set allowMoveAtoms 30. isosurface ROTATE 29. new auxiliaryinfo subset infoUnitCell 28. reset STRUCTURE 27. load OFFSET {x y z} 26. command aliases 25. set defaultStructureDSSP 24. structure HELIX310; structure HELIXPI; select HELIX310; select HELIXPI 23. "xxxx"%9999, "xxxx"%-9999 to upper/lower case 22. show state/xxxx 21. save STRUCTURE 20. calculate structure (DSSP) 19. show DSSP 18. calculate hbonds STRUCTURE 17. load SUPERCELL 16. measureCallback adds unrounded value 15. set structure helix/sheet/turn 14. hide/display bonds 13. color bonds directly using connected() 12. set multipleBondSpacing and set multipleBondRadiusFactor 11. set slabRange -- zoom-independent slab range 10. new SHAPE property 9. lcaoCartoon sp3d, sp3d2 8. "drill-down" properties 7. zSlab, zDepth; slab, depth 6. new NIH/SMILES load $XXXX service 5. new color() function and getProperty shapeInfo.isosurface[n].colorKey 4. isosurface display within 2.0 {...} 3. {*}.find("SMILES", SMILESstring) 2. compare(a,b,"ISOMER") 1. load ... unitcell [ax, ay, az, bx, by, bz, cx, cy, cz] [Less]

Jmol 12.2 introduces over 100 new features in a wide variety of disciplines. For details, see http://chemapps.stolaf.edu/jmol/docs/examples-12/new2.htm Some highlights include: CONNECTIONS TO OTHER SYSTEMS: direct access to NIH CACTVS server and ... [More] IUPAC name recognition software for small-molecule structures fully verified DSSP calculation of protein secondary structure support for materials science surface first-principles computation visualization (CASTEP, CRYSTAL, QuantumEspresso, VASP, WIEN2K) Molprobity file reading SURFACES: new CONTACT command reversible and extensible isosurface slabbing probability-based atomic orbitals display of linear combinations of molecular orbitals STRUCTURE ANALYSIS AND SEARCHING: structure- and SMILES-based substructure searching using SMARTS bioSMARTS/bioSMILES, and conformational SMARTS searching (Jmol innovations) diasteriomer/enantiomer comparison and checking with structures or SMILES strings ORGANIC CHEMISTRY: easy mechanistic arrows display of 2D drawing images, chemical names, ... and much, much more! The full list: 117. LOAD trajectory extended to vibrations 116. write transparent-background PNG images 115. load "xxx.xxx" [ list of models to load ] 114. set minPixelSetRadius 113. CRYSTAL09 tensor quantities 112. unitcell {xxx yyy scale} 111. Application console commands UNDO, REDO 110. UNDOMOVE/REDOMOVE n 109. set isosurfaceKey 108. SurfaceTool 107. FEATURE CHANGE: "ligand" 106. MolProbity contact dot reader 105. new CONTACT command 104. select within(VDW, xxxx) 103. "picked" variable 102. select/display/hide GROUP ... 101. select/display/hide ADD/REMOVE 100. @n 99. {atomset}.x? 98. measure INTRAMOLECULAR/INTERMOLECULAR 97. measure VDW 96. set measurementUnits VDW 95. calculate HYDROGEN and set pdbAddHydrogens 94. load "==XXX" 93. more information with LOAD 92. isosurface slab n 91. show lighting 90. .count and .count(x) 89. JVXL files return state 88. arbitrary function surfaces 87. isosurface INTERSECTION 86. color isososurface {atom expression} [color] 85. select within(distance, $surfaceID) 84. isosurface slab within x.x {atom expression or point} 83. set defaultLablPDB and set defaultLabelXYZ 82. reversible isosurface slab 81. plane(r, theta, phi) 80. NCI surfaces 79. FEATURE CHANGE -- zshadePower default 78. set zSlab {atom expression or point} 77. quaternion() 76. isosurface PARAMETERS 75. color atoms property VECTORSCALE 74. appletReadyCallback 73. atomMovedCallback 72. connecting surfaces to atoms 71. simple curved mechanistic reaction arrows 70. pointilist atomic/molecular orbitals projected onto planes 69. pointilist molecular orbitals 68. pointilist atomic orbitals 67. loading of structure by IUPAC name 66. show chemical name/inchi/inchikey 65. isosurface remapping 64. set echo ID 63. show drawing 62. for (var x in [...]) {....} 61. for (var x in {...}) {....} 60. SPARTAN READER charge default changed 59. xxx.mass.sum 58. plane(<point>, <vector>, true) 57. frame TITLE @someArray 56. load MENU label "null" 55. write COORD XYZVIB filename 54. draw ARROW...BARB 53. isosurface... map property x WITHIN x.y 52. COMMAND-SHIFT-LEFT-DRAG (Macintosh only) 51. expanded XYZ file format 50. mo -n 49. loading of DCD files 48. linear combinations of molecular orbitals 47. write XXX.OBJ 46. intersection() function 45. x.sort, x.reverse 44. V2000 MOL reader reads partial charges 43. write xxxx.XYZRN 42. load filter "|" and "/=" options 41. isosurface spherical slab 40. isosurface MSMS xxxx.vert 39. isosurface/draw .length 38. draw SLAB 37. plane(pt1, pt2) 36. write SDF and write V3000 35. measure LIST 34. CIF file load defaults and load FILTER "MOLECULAR" 33. point(x.y) 32. label %{dataName} 31. set allowMoveAtoms 30. isosurface ROTATE 29. new auxiliaryinfo subset infoUnitCell 28. reset STRUCTURE 27. load OFFSET {x y z} 26. command aliases 25. set defaultStructureDSSP 24. structure HELIX310; structure HELIXPI; select HELIX310; select HELIXPI 23. "xxxx"�99, "xxxx"%-9999 to upper/lower case 22. show state/xxxx 21. save STRUCTURE 20. calculate structure (DSSP) 19. show DSSP 18. calculate hbonds STRUCTURE 17. load SUPERCELL 16. measureCallback adds unrounded value 15. set structure helix/sheet/turn 14. hide/display bonds 13. color bonds directly using connected() 12. set multipleBondSpacing and set multipleBondRadiusFactor 11. set slabRange -- zoom-independent slab range 10. new SHAPE property 9. lcaoCartoon sp3d, sp3d2 8. "drill-down" properties 7. zSlab, zDepth; slab, depth 6. new NIH/SMILES load $XXXX service 5. new color() function and getProperty shapeInfo.isosurface[n].colorKey 4. isosurface display within 2.0 {...} 3. {*}.find("SMILES", SMILESstring) 2. compare(a,b,"ISOMER") 1. load ... unitcell [ax, ay, az, bx, by, bz, cx, cy, cz] [Less]

Jmol 12.0 was released today with over 170 new features compared to the previous release, Jmol 11.8. Full details may be found at http://chemapps.stolaf.edu/jmol/docs/examples-12/new12.htm Generally new capability -- customizable mouse button/action ... [More] bindings -- multi-touch/Kiosk capability using SPARSHUI adaptation (U-Tube video) -- parallel multiprocessor capability for isosurface creation -- drag-and-drop to signed applets and the application -- model kit mode allows rapid construction of simple models -- extensive support for depiction of space groups -- conversion of 2D models (SMILES, JME, MOL) to 3D -- interface to JSDraw for 2D structure input -- interface to Flot for plotting data -- full implementation of Daylight SMILES/SMARTS -- extension of Daylight SMARTS to 3D conformation -- introduction of Jmol bioSMILES and bioSMARTS -- new JmolSmilesApplet.jar. -- JavaScript-like flow commands and TIMEOUT -- JavaScript-like TRY/CATCH error handling -- direct reading of Uppsala electron density maps -- natural bond orbital reading/rendering -- direct logging to files using the LOG command [Less]

Jmol 12.0 was released today with over 170 new features compared to the previous release, Jmol 11.8. Full details may be found at http://chemapps.stolaf.edu/jmol/docs/examples-12/new12.htm

Jmol 12.0 was released today with over 170 new features compared to the previous release, Jmol 11.8. Full details may be found at http://chemapps.stolaf.edu/jmol/docs/examples-12/new12.htm Generally new capability -- customizable mouse button/action ... [More] bindings -- multi-touch/Kiosk capability using SPARSHUI adaptation (U-Tube video) -- parallel multiprocessor capability for isosurface creation -- drag-and-drop to signed applets and the application -- model kit mode allows rapid construction of simple models -- extensive support for depiction of space groups -- conversion of 2D models (SMILES, JME, MOL) to 3D -- interface to JSDraw for 2D structure input -- interface to Flot for plotting data -- full implementation of Daylight SMILES/SMARTS -- extension of Daylight SMARTS to 3D conformation -- introduction of Jmol bioSMILES and bioSMARTS -- new JmolSmilesApplet.jar. -- JavaScript-like flow commands and TIMEOUT -- JavaScript-like TRY/CATCH error handling -- direct reading of Uppsala electron density maps -- natural bond orbital reading/rendering -- direct logging to files using the LOG command [Less]

Jmol 11.8, released August 26, 2009, introduces over 215 new features compared to Jmol 11.6, which was released less than a year previously. Notable new features include greatly expanded scripting capability, extensive quaternion analysis and ... [More] display capability, full support for working with cyrstallographic coordinates and planes, display of point group and cyrstallographic space group symmetry operations, display of Ramachandran planes and dihedral angles, creating of JPG and PNG files with embedded Jmol state so that the 2D image can also be dropped into Jmol and instantly become a 3D object, much expanded VRML and IDTF export capability, trapping of out-of-memory condition errors, and several new readers, including AIMS, Alchemy/3DNA, CASTEP, EFVET, Gromacs, isosurface OBJ, Materials Studio XML, and Wien2k. [Less]