Jmol

Software Screenshot:
Jmol
Software Details:
Version: 14.29.14 updated
Upload Date: 22 Jun 18
Distribution Type: Freeware
Downloads: 93

Rating: nan/5 (Total Votes: 0)

Jmol is an open source, cross-platform and free graphical software that has been originally designed to act as molecular viewer for 3D chemical structures. It runs in four standalone modes, as a HTML5 web app, a Java program, a Java applet, and a "headless" server-side component.

Feaures at a glance

Key features include high-performance 3D rendering support without requiring any high-end hardware, exports files to JPG, PNG, GIF, PDF, WRL, OBJ and POV-Ray formats, supports basic unit-cells, support RasMol and Chime scripting languages, as well as the JavaScript library.

In addition, the software supports animations, surfaces, vibrations, orbitals, measurements, symmetry and unit cell operations, and schematic shapes.

Supported file formats

Currently, the application supports a wide range of file formats, among which we can mention MOL MDL, V3000 MDL, SDF MDL, CTFile MDL, CIF, mmCIF, CML, PDB, XYZ, XYZ+vib, XYZ-FAH, MOL2, CSF, GAMESS, Gaussian, MM1GP, HIN HIN / HIV, MOLPRO and MOPAC.

Additionally, the CASTEP, FHI, VASP, ADF, XSD, AGL, DFT, AMPAC, WebMO, PSI3, CRYSTAL, MGF, NWCHEM, odydata, xodydata, QOUT, SHELX, SMOL, GRO, PQR and JME are also supported.

Supports all major web browsers

The software has been successfully tested with all major web browsers, including Mozilla Firefox, Google Chrome, Internet Explorer, Opera and Safari. The aforementioned browser apps have been tested on all the mainstream operating systems (see the next section for supportes OSes).

Supports all mainstream operating systems

Being written in the Java programming language, Jmol is a platform-independent application designed to support all GNU/Linux distributions, the Microsoft Windows and Mac OS X operating systems, and any other OS where the Java Runtime Environment is installed.

What is new in this release:

  • bug fix: Jmol SMILES not allowing for insertion-code search -- adds "^" for insertion code: [G#129^A.*]

What is new in version :

  • bug fix: Jmol SMILES not allowing for insertion-code search -- adds "^" for insertion code: [G#129^A.*]

What is new in version 14.20.3:

  • bug fix: Jmol SMILES not allowing for insertion-code search -- adds "^" for insertion code: [G#129^A.*]

What is new in version 14.6.5:

  • bug fix: Jmol SMILES not allowing for insertion-code search -- adds "^" for insertion code: [G#129^A.*]

What is new in version 14.6.1:

  • bug fix: Jmol SMILES not allowing for insertion-code search -- adds "^" for insertion code: [G#129^A.*]

What is new in version 14.4.4 Build 2016.04.22:

  • 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

What is new in version 14.4.4 Build 2016.04.14:

  • 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

What is new in version 14.4.4 Build 2016.03.31:

  • 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

What is new in version 14.4.3 Build 2016.03.02:

  • 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

What is new in version 14.4.3 Build 2016.02.28:

  • 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

What is new in version 14.4.2 Build 2016.02.05:

  • 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

What is new in version 14.4.0 Build 2015.12.02:

  • 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

What is new in version 14.2.15:

  • 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

What is new in version 14.2.13:

  • 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

What is new in version 14.2.12:

  • 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

What is new in version 14.1.8 Beta:

  • new feature - set cartoonRibose:
  • draws in ribose rings, with facets showing puckering
  • connects via C4'-C5'-O5'-P explicitly
  • shows C3'-O3' for reference.
  • disables cartoonBaseEdges (Leontis-Westhof Edges)
  • disabled by SET cartoonBaseEdges ON
  • suggested by Rick Spinney, Ohio State
  • new feature: anim frame [a,b,c,d] works with negative numbers to indicate ranges:
  • anim frame [1, -5, 10, -6] --> [1,2,3,4,5,10,9,8,7,6]
  • read as "1 through 5 and then 10 through 6"
  • new feature: Tinker file reader (and FoldingXYZ reader upgrade):
  • Can use Tinker:: but this is only required if first line is JUST an atomCount
  • accommodates older Tinker format with n-1 atoms for atomCount
  • allows for trajectories and desired model number
  • new feature: (actually 13.1 but undocumented) animation frame [ 51 50 49 48 47 46 45 (etc) 27 1 2 3 4 5 6 7 (etc)....]
  • new feature: x = compare({atomset1}, {atomset2}, "MAP")
  • new feature: x = compare({atomset1}, {atomset2}, "MAP", "all")
  • new feature: x = compare({atomset1}, {atomset2}, "MAP", "best")
  • new feature: x = compare({atomset1}, {atomset2}, "MAP", "H")
  • new feature: x = compare({atomset1}, {atomset2}, "MAP", "allH")
  • new feature - x = compare({atomset1}, {atomset2}, "MAP", "bestH"):
  • generates one or more correlations lists based on non-aromatic SMILES
  • optionally includes H atoms
  • optionally generates all possible atom mappings
  • returns int[][] = [ [a1 b1],[a2 b2],[a3 b3],... ]
  • where an and bn are integer atom indices or list when "all" option is chosen.
  • the following will generate one atom correlation map for two structures including hydrogen atoms: load files "a.mol" "b.mol" x = compare({1.1} {2.1} "MAP" "H")
  • the following compares the model of caffeine from NCI to that from PubChem:
  • load $caffeine;load append :caffeine;frame *
  • select 2.1; label %[atomIndex]
  • compare {1.1} {2.1} SMILES rotate translate
  • x = compare({1.1}, {2.1}, "MAP" "bestH")
  • for (a in x) {a1 = a[1];a2=a[2];select atomindex=a1;label @a2}
  • new feature: compare {model1} {model2} SMILES:
  • no need to give SMILES; Jmol can generate it from {model1}
  • new feature: x = {*}.find("SMILES", "H"):
  • generates SMILES with explicit H atoms
  • bug fix: substructure() function using SMILES instead of SMARTS, so only full structures;
  • bug fix: better error trapping and messages in SMILES-related methods
  • bug fix: make webexport discovery of path to Jmol.jar and jsmol.zip more robust.
  • bug fix: getProperty extractModel not honoring subset
  • bug fix: set pdbGetHeader TRUE does not capture REMARK3 REMARK290 REMARK350
  • bug fix: getProperty("JSON",....) should wrap value in {value:...}
  • bug fix: MO persistent translucency broken in 11.x
  • bug fix: show MENU write MENU load MENU all broken in 12.2
  • bug fix: {*}[n] should be empty if nAtoms

What is new in version 14.0.7:

  • Bug fix: 14.0.6 fatally bugged -- unitcell and echo rendering, getProperty

What is new in version 14.0.5:

  • Bug fix: LCAOCartoon translucency broken
  • Bug fix: translucent backbone broken
  • Bug fix: pqr,p2n readers broken
  • Bug fix: isosurface map property xxx can fail if surface is a fragment that (somehow) has a point not associated with an underlying atom.

What is new in version 14.1.5 Beta:

  • bug fix: LCAOCartoon translucency broken
  • bug fix: translucent backbone broken
  • bug fix: pqr,p2n readers broken
  • bug fix: isosurface map property xxx can fail if surface is a fragment that (somehow) has a point not associated with an underlying atom.

What is new in version 14.0.4:

  • Bug fix: rockets broken
  • Bug fix: PDB byChain, bySymop not supported.

What is new in version 14.0.2:

  • bug fix: modulation not distinguishing between q and t;
  • bug fix: modulated measurements not working
  • bug fix: not skipping set defaultLattice "{NaN NaN NaN}"
  • bug fix: isosurface map atomic orbital fails
  • bug fix: vibrational display of modulation with distances doesn't update
  • bug fix: vibration off causes unnecessary warning in console
  • bug fix: draw symop broken
  • bug fix: array.mul(matrix3f) crashes Jmol
  • bug fix: select symop=1555 broken
  • bug fix: set picking dragSelected not working
  • code: refactored CifReader, separating out MMCifReader and MSCifReader code: minor renaming/refactoring of methods in SV
  • code: adds javajs.api.JSONEncodable interface
  • super-simple implementation in org.jmol.script.SV
  • allows implementations of javajs to deliver custom JSON results

What is new in version 14.1.2 Beta:

  • new feature: JavaScript: JSmol api Jmol.evaluateVar(applet, expression):
  • better than Jmol.evaluate because result is a JavaScript variable, not a string.
  • DEPRECATING JSmol api Jmol.evaluate(applet, expression)
  • new feature: getProperty("JSON", ....):
  • returns JSON code for property
  • allows JavaScript: x = Jmol.getPropertyAsArray("variableInfo","some expression")
  • new feature: getProperty variableInfo :
  • allows retrieval of variables in Java or JSON format
  • evaluates expression
  • defaults to "all"
  • new feature: modulation adjustable by q and t, up to d=3:
  • modulation on/off (all atoms)
  • moduation {atom set} on/off
  • modulation int q-offset
  • modulation x.x t-offset
  • modulation {t1 t2 t3}
  • modulation {q1 q2 q3} TRUE
  • new feature: pickedList:
  • ordered array of recently picked atoms
  • can be used the same as the PICKED variable, but that is ordered sequentially, not temporally
  • twice clicking off structure clears the list
  • @{pickedList}[0] last-picked atom
  • @{pickedList}[-1] next-to-last-picked atom
  • @{pickedList}[-1][0] last two picked atoms
  • new feature: array.pop(), array.push() - similar to JavaScript
  • new feature: modulation scale x.x
  • new feature: caption "xxxxx" x.x - number of seconds to run
  • new feature: modulation 0.2 // sets t-value
  • new feature: array.pop(), array.push(x)
  • a=[];a.push("testing");print a.pop()
  • new feature: select ON/OFF atom-set:
  • turns selection halos on or off as well as doing the selection
  • convenience only
  • new feature: pt1.mul3(pt2):
  • returns {pt1.x*pt2.x, pt1.y*pt2.y, pt1.z*pt2.z}
  • if both are not points, reverts to simple multiplication
  • new reature: array.mul3(pt2) - applies mul3 to all elements of array
  • new feature: {atomset}.modulation(type, t):
  • delivers P3 (displacement modulation)
  • implemented only for type="D" (optional)
  • optional t is 0 by default
  • bug fix: modulation not distinguishing between q and t;
  • bug fix: modulated measurements not working
  • bug fix: not skipping set defaultLattice "{NaN NaN NaN}"
  • bug fix: isosurface map atomic orbital fail
  • bug fix: vibrational display of modulation with distances doesn't update
  • bug fix: vibration off causes unnecessary warning in console
  • bug fix: draw symop broken
  • bug fix: array.mul(matrix3f) crashes Jmol
  • bug fix: select symop=1555 broken bug fix: set picking dragSelected not working
  • code: refactored CifReader, separating out MMCifReader and MSCifReader
  • code: minor renaming/refactoring of methods in SV
  • code: adds javajs.api.JSONEncodable interface:
  • super-simple implementation in org.jmol.script.SV
  • allows implementations of javajs to deliver custom JSON results

What is new in version 14.0.1:

  • new feature: Jmol._j2sLoadMonitorOpacity (default 55)
  • new feature: load() function, as in print load("xxx"), limited local file reading in applet:
  • no root-directory files
  • no files without extension
  • no files with any "/." in path
  • new feature: JAR files securely signed
  • new feature: applet JAR files include JNLPs (Java Network Launch Protocols) for local file loading
  • new feature: JSmol URL options _USE= _JAR= _J2S= overrides for Info data
  • new feature: (was present but undocumented) print quaternion([array of quaternions]) - returns spherical mean a la Buss and Fillmore
  • new feature: print quaternion([array of quaternions], true):
  • returns standard deviation for spherical mean a la Buss and Fillmore
  • units are angular degrees
  • new feature - named quaternion modulus values:
  • print quaternion(1,0,0,0)%"matrix"
  • options include w x y z normal eulerzxz eulerzyz vector theta axisx axisy axisz axisangle matrix
  • ew feature - set celShadingPower:
  • sets strength of cel shading
  • integer values
  • default 10 is a thick line
  • 5 is a fine line
  • 0 turns cel shading off
  • negative value removes interior shading -- outline only
  • operates on pixel based on normal to light source (power > 0) or user (power < 0)
  • sets color to background contrast (black or white) when normal_z < 1 - 2^-(|celShadingPower|/10)
  • new feature: mmCIF reading reports _citation.title in Jmol scripting console
  • new feature: minimize SELECT {atomset} ONLY - ONLY option excludes all other atoms
  • new feature: minimize {atomset} - implicit SELECT and ONLY
  • new feature -"extensions" directories in JSmol for contributed JS and SPT scripts:
  • jsmol/js/ext
  • jsmol/spt/ext
  • new feature: load ... filter "ADDHYDROGENS" - local set pdbAddHydrogens just for one load command
  • new feature: compare {1.1} {2.1} BONDS SMILES
  • new feature: list = compare({atomset1} {atomset2} "SMILES" "BONDS")
  • new feature: write JSON xxx.json
  • new feature: [#210] JSON {"mol":...} reader
  • ew feature - set particleRadius :
  • global radius for atoms over the max radius value (16.0)
  • defaults to 20.0
  • new feature - CIF and PDB filters "BYCHAIN" and "BYSYMOP" for virus particulation:
  • creates just one atom per chain or per symop
  • size can be scaled larger than the max of 16 Angstroms using, for example:
  • set particleRadius 30;
  • spacefill 30; // any number over 16 here uses particleRadius instead
  • new feature: list = compare({atomset1} {atomset2} SmartsString "BONDS")
  • new feature: symop() function allows symmetry from biomolecule filter for PDB and mmCIF
  • new feature - isosurface SYMMETRY:
  • applies symmetry operators to isosurface
  • more efficient rendering and creation
  • default selection is {symop=1} only
  • default coloring is to color by symop based on propertyColorScheme
  • example:
  • load 1stp filter "biomolecule 1"
  • color property symop
  • isosurface sa resolution 0.8 symmetry sasurface 0
  • new feature - new atom property: chainNo:
  • sequentially from 1 for each model;
  • chainNo == 0 means "no chain" or chain = ''
  • new feature - new propertyColorScheme "friendly":
  • color-blindness-friendly color scheme
  • used at RCSD
  • new feature: JSpecView completely Java-free; includes 2D nmr and PDF printing of spectra
  • new feature - WRITE PDF "xxx.pdf" quality > 1 requests landscape mode:
  • uses efficient custom PDF creation classes
  • sizes image to fit if too large
  • new feature: JSpecView adds PDF and 2D NMR for JavaScript
  • new feature: load "==xxx" FILTER "NOIDEAL" - Chemical component load from PDB using the "nonideal" coordinate set
  • bug fix: write CD removed; ChemDoodle has changed formats; use JSON instead
  • bug fix: PDB and CIF files indicated assemblies such as PAU as large negative number
  • bug fix: COMPARE with no rotation starts infinite loop
  • bug fix: looping problem with delay(-1)
  • bug fix: Mouse wheeling for Chrome in JavaScript
  • bug fix: JavaScript popup menu fix for language changes
  • bug fix: JavaScript core components not being processed; Jmol._debugCode not recognized
  • bug fix: unitcell offset incorrectly for biomolecules; origin incorrect for axes.
  • bug fix: isosurface/mo FRONTONLY broken
  • bug fix: language localization broken in JavaScript
  • bug fix: ADF reader not reading MO output from DIRAC Build 201304052106
  • bug fix: Safari reports yellow Jmol info instead of asking to accept applet
  • -- tag needed to be
  • bug fix: CIF reader not handling _pdbx_struct_assembly_gen.assembly_id properly
  • -- wrong atom set for load =3fsx.cif filter "ASSEMBLY 1"
  • bug fix: [#558 Compatibility issue with ChemDoodle] JSmol error in definition of Number.toString()
  • bug fix: mouse wheel not working properly
  • bug fix: JavaScript J2S compiler error does not coerce int += float to integer
  • bug fix: JavaScript WEBGL option broken
  • bug fix: JavaScript NMRCalculation does not access resources
  • bug fix: JavaScript stereo not implemented
  • bug fix: MOL reader fix for multiple-model file (just 13.3.9_dev)
  • bug fix: MOL reader error with load APPEND -- does not continue atom numbers
  • bug fix: CIF modulation reader not reading linear combinations of cell wave vectors
  • bug fix: CIF reading with filter "BIOMOLECULE 1" fails if only the identity operation
  • bug fix: mmCIF reader not reading all _pdbx_struct_assembly_gen.oper_expression options
  • bug fix: PDB CRYST entry 1.0 1.0 1.0 90 90 90 should mean "no unit cell" regardless of biomolecule filter
  • bug fix: isosurface slab not adapting well for flat molecules such as HEM
  • bug fix: print userfunc() may fail (userfunc() by itself is fine)
  • bug fix: within(helix) not implemented for C-alpha-only polymers
  • bug fix: _modelTitle not updated when a new file is loaded or zapped
  • bug fix: {*}.symop.all not delivering symmetry operator appropriately
  • bug fix: for triple bond in SMILES in URLs
  • bug fix: build.xml missing PDF creation classes
  • bug fix: following Java update, adding proper path check for local signed applet
  • bug fix: {xxx}.property_xx not saved in state (broken 8/7/2013 rev 18518)
  • bug fix: Manifests updated for signed and unsigned applet JAR files
  • bug fix: write fails
  • bug fix: applet scriptWait() method broken
  • bug fix: PyMOL session may display unit cell after read from saved state
  • bug fix: MMCIF reader fails for multiple assembly types
  • bug fix: CIF reader "biomolecule 1" translating to "molecular" rather than "assembly"
  • bug fix: load trajectory with multiple files not working
  • bug fix: JS applet popup menu not closing properly upon language change
  • bug fix: HTML checkbox id attribute not assigned
  • code: refactoring of applet/appletjs code; org.jmol.util.GenericApplet
  • code: refactoring, simplification of buffered readers and buffered input streams.
  • code: JavaScript refactoring, better build_...xml
  • code: JavaScript Integer, Long, Short, Byte, Float, Double all reworked
  • code: disambiguation of GT._
  • code: Refactored all unnecessarily inner classes to top level
  • code: isolated util/ModulationSet using api/JmolModulationSet
  • code - All applet language localization read from plain .po files :
  • as for JavaScript already
  • no need to compile class files for applet languages
  • no language .jar files
  • new jsmol/idioma directory holds .po files for both Java and HTML5
  • code: faster isosurface rendering adding implicit "frontonly" with select {xxx} ONLY
  • code: faster isosurface rendering with implicit "isosurfacepropertySmoothing FALSE" in relevant (integer) cases
  • code: JmolBinary.getBufferedReaderForResource() - consolidates all references to URL.getContent() and Class.getResource()
  • code: JavaScript work around for inner class problem with variable name reassignment
  • code: work-around for eval(functionName) not working in JavaScript.
  • code: experimenting with ambient occlusion
  • code: Required manifests added for Java Ju51 (January, 2014).
  • code: JmolOutputChannel moved to javajs.util.OutputChannel
  • code: jsmol.php fixed to allow " in saveFile method
  • code: refactoring Parser into javajs.util
  • code: DSSP moved to org.jmol.dssx, reducing JSmol bio load by 20K
  • code: iText package jettisoned, no longer nec, as I wrote my own PDF creator

Requirements:

  • Oracle Java Standard Edition Runtime Environment

Similar Software

AREM
AREM

11 May 15

VULCAN
VULCAN

20 Feb 15

AHREA
AHREA

11 May 15

Staden Package
Staden Package

12 May 15

Comments to Jmol

Comments not found
Add Comment
Turn on images!