Over 10,000,000 page views! Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. A rich scripting language and a well-developed web API allow easy customization of the user interface. Features include interactive animation and linear morphing. Jmol interfaces well with JSpecView for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD programs for 3D printing (VRML export).
Jmol
Jmol
Active, helpful, world-wide user group; approximately 100,000 downloads/year
HTML5/canvas graphics for all modern browsers, including iOS and mobile
Extremely low footprint option (50K) for simple interactive structure display
Additional server-side Java, stand-alone Java, and signed Java applet options
Full crystallographic symmetry capability
Load many surface formats and creates and displays surfaces on the fly
Easily customizable web-based interface compatible with (and requires) jQuery
Well documented scripting language with over 1000 tokens
Reads over 60 file formats, including PyMOL (PSE) session files
Creates highly compressed (300:1) surface files from volumetric (CUBE) data
Exports to GIF, JPG, PNG, PDF, WRL, POV-Ray, OBJ formats
Uses customized, optimized Java-to-JavaScript compilation for pure HTML5 app
Generalizable JavaScript library for Swing and PDF export in client-side JavaScript
JSpecView module features:
Reading of JCAMP-DX, CML, AnIML formats
Interactive real and predicted 1H NMR spectra
Interactive IR, Raman, NMR, GC/MS, UV/VIS spectra
Spectra generated in PDF format
Jmol is a free, open source viewer of molecular structures useful for students, educators and researchers in chemistry, biochemistry and other fields dealing
Jmol is computer software for molecular modelling chemical structures in 3-dimensions Jmol returns a 3D representation of a molecule that may be used as a
A motion for judgment as a matter of law (JMOL) is a motion made by a party, during trial, claiming the opposing party has insufficient evidence to
Jmol is an open-source viewer for three-dimensional chemical structures, with features for chemicals, crystals, materials and biomolecules
Jmol runs on a Java platform and therefore functions equally well in a PC or Mac environment Because Jmol is freeware and an open source program,
Jmol is an open-source Java viewer for three-dimensional chemiscal structures, with features for chemicals, materials and biomolecules
JmolSQL is a Jmol math syntax that is designed to query this sort of information The idea is that maps, with key/value pairs, and especially arrays of maps,
On-line molecular structure tutorials show their molecular views in the Jmol java applet, a version of Jmol that works only within web browsers
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Jmol Related Questions
What does Jmol stand for?
What is Jmol used for?
Overview. Jmol is a free, open source viewer of molecular structures useful for students, educators and researchers in chemistry, biochemistry and other fields dealing with molecular structure. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.
How do I start Jmol?
The Jmol Console is used to input commands. To access the Console, right click anywhere in the Display Window to bring up the Display Window Menu. In this menu, click on the button 'Console' which will open the Jmol Console.
How do you reference Jmol?
The recommended way to cite Jmol is: Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/ JSmol: an open-source HTML5 viewer for chemical structures in 3D.
How do I change the atom color in jmol?
You can change the default either to the Rasmol "CPK" standard or the Jmol standard, or you can customize any specific element's color. You can explicitly assign atom colors to elements using JavaScript standard color names, octal equivalents, or RGB triples.
Who developed RasMol?
Roger SayleIt is based on the original RasMol that was developed by Roger Sayle at Glaxo, UK. (Reference: Roger A. Sayle and E. J. Milner-White, "RasMol: Biomolecular graphics for all", Trends in Biochemical Science (TIBS), September 1995, Vol.
How do I use jmol console?
To open the console, right click anywhere in the black Jmol window and select "Console" from the menu that appears. You will want to arrange both windows so that they do not overlap, as they will be used at the same time.
How do I move to jmol?
Moving the modelTo rotate the model, just put the mouse pointer over the J(S)mol panel and drag (move the mouse while you hold its button pressed down). To translate or move the model, hold down the Ctrl key while dragging.
How do I download jmol files on Windows?
Installing the application involves nothing more than putting one file, Jmol. jar, on your computer.Download the current Jmol . zip or . Take the one file Jmol. jar from the downloaded package. Windows users should also visit java.com and download the latest version of java. Double-click on the file Jmol.
How do I install J Mol?
StepsDownload the Chem119 compressed folder.Right click the folder and drag it to your Desktop or Documents folder and choose to ExtractOnce it finishes extracting, open the Chem119 folder.Double click Jmol.jar.Jmol should launch, opening to a black screen.
How do I open a PDB file in jmol?
Loading a PDB file for viewing in JMOLRight-click on the Workspace icon.Select "Open File(s)"Select the file type as "PDB File Format".Locate the desired PDB-format file using the file browser (the browser will display files with a ". pdb" filename suffix).The molecular structure will be displayed in Jmol.
Can you download Java for free?
Visit the Java website and download the installer To install Java, you first need to download the installer program from Oracle. Click the "Free Java Download" button. You are then prompted to read and agree with the end user license agreement.
How do I show Sidechains in Jmol?
To select and display only the atoms of the sidechain of a specific amino acid, and not the "bumpy" backbone atoms, you will use the select command followed by the amino acid name/number and end with the and (sidechain or alpha) command.
How do you pick a chain in Jmol?
Select Chain With select :, followed by the letter of the chain you would like to select, only the chain you select will be affected by future commands. Note: The Top 7 protein is a protein with only a single chain, so all atoms are colored red with the commands used above. Hemoglobin based on the file 1a3n.
How do I undo in Jmol?
pdb file in Jmol, or simply click "Undo" on the Jmol Console to revert your model to its original form. This will let you quickly see effect of the change you made in your script.
How do I change my jmol background?
Different Background Color Open Jmol's menu by clicking on Jmol (to the lower right of the molecule; or right-click anywhere in Jmol). Select Color , then Background , then click on a color. This will change the background color only until you click a new View button.
What Colour is an atom?
I hope it's not too long. atoms (as opposed to molecules) do not have colors - they are clear except under special conditions.. you could not see the color of one atom or molecule - not because it is too small - but because the color of one atom would be too faint.
How do I use JSmol?
JSmol Example The structure below is rendered using JSmol, if you click and hold down on the mouse you should be able to rotate it, alt-click rotates in the z-plane, shift-click is zoom (or you can use the scroll wheel on your mouse).
Is RasMol sequence alignment tool?
Rasmol can communicate with other programs via Tcl/Tk on Unix platforms, and via Dynamic Data Exchange (DDE) on Microsoft Windows. With a multiple sequence alignment program, the responsible Java class can be freely used in other applications.
What is PyMOL in bioinformatics?
PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
What is input file format of RasMol?
Currently supported input file formats include Brookhaven Protein Databank (PDB), Tripos' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XMol XYZ format and CHARMm format files.
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