Jmol For Mac

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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. Jmol-Main Menu-Select-None (Needed because 'select all' is the default at load time. Notice the non-zero number in parenthesis after the word select in the main menu. That is the number of items currently selected. Jmol-Main Menu-Set picking-Select Atom Now click an atom once to select, click again to deselect.

Jmol

Applications using Jmol

Jmol users, please add here your favorite Java applications that embed Jmol.

(There is another page for operating systems and software suites that include Jmol.)

  • BioClipse.
  • CaGe (mirror) - the 'Chemical & abstract Graph environment' is a collection of graph generators for GNU Linux and Mac OS X, that uses Jmol as one of its visualizers.
  • ChemPad renders in Jmol 3D models calculated on-the-fly from a formula sketched by hand in a tablet PC.
  • CheS-Mapper - A 3D viewer for small molecule datasets, that preprocesses the dataset. CheS-Mapper can create compound features, it clusters the dataset and embeds the compounds into 3D space.
  • iBabel - A GUI for cheminfomatics toolkit Openbabel, iBabel uses embeded applets to display structures.
  • J-ICE - a Jmol web-Interface for Crystallographic and Electronic Properties. J-ICE can deal with CASTEP, CRYSTAL09 (as well as 06, 03 and 98), QUANTUM ESPRESSO, VASP, Wien2k, FHI-aim, CIF, PDB and many others formats. Watch some videos here.
  • Janocchio is an applet and application; in addition to using Jmol display capabilities, it calculates both H-H and H-C 3-bond NMR coupling constants and NOEs from a three-dimensional structure. © Eli Lilly and Co. Open source and hosted af SF.
  • MoCalc2012 is a Graphical User Interface for MOPAC, GAMESS(US), Firefly and ORCA that uses Jmol for displaying geometries, orbitals, surfaces, animations and vibrations using the Jmol scripting language.
  • Molecular Workbench - A Molecular Simulation Tool.
  • PMOL - A Processing sketch using JMOL to load Molecules, and Processing to visualize them.
  • PFAAT - Protein Family Alignment Annotation Tool.
  • ProteinGlimpse is a free widget for visualizing macromolecules retrieved from the Protein Data Bank or from local disk. It is a dashboard application for Mac OS X that uses the JmolApplet.
  • Raman Data Search and Storage (RDSS) A freeware and user-friendly application developed as an analytical tool for a fast and accurate identification of unknown minerals by comparison of their Raman spectra with the indexed library of data.
  • Sage is a computational platform with the goal of providing a viable free and open-source alternative to Matlab, Maple, Mathematica and Magma. It uses Jmol for its 3D interactive plotting.
  • Spice - Spice is a DAS client for distributed annotation of protein sequences and structures. A java webstart version can be run from online.
  • STRAP - Alignment Program for Proteins and workbench for protein structures.
  • Taverna.
  • TouchMol - molecular visualization on a multi-touch table, allowing up to 4 users to interact with a molecular model using their fingers. Video clips: [1][2][3][4]

Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry. It is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. 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. Jmol for Mac, free and safe download. Jmol latest version: The educational molecular tool. Jmol is a web browser applet that offers an open source molecule viewer that can be integrated in.

Jmol For Mac

How to embed Jmol into an application

  • A very good start is the Integration.java out of Jmol SVN.
  • Here is the previous code ported to Jython
  • To see how Spice is integrating Jmol, please have a look here.
  • A special page is devoted to using Jmol as 3D viewer for CDK based projects: Jmol Cdk Integration.
  • Another example: Programmatic Access to Jmol
Mac

Most interaction with Jmol will happen by sending RasmolScript - like commands to Jmol. This is nicely documented by the Integration.java example. It is also possible to get data back out of Jmol. This can be done by accessing the JmolViewer class. This might be replaced by an Interface in the future.

One example of getting data out of Jmol is by adding a MouseListener to the Panel that contains the JmolViewer instance. e.g.

Jmol For Mac Font

When retreiving the 'seqCode' for an Atom, the Insertion Code of PDB files is appended. Note the Jmol notation of insertion codes: e.g. 122^A, to distinguish from the Rasmol command 122A, which would select residue 122 of chain A.

A Note on JmolStatusListener

If your application needs to be notified of Jmol events, then you must create an interface to Jmol by implementing org.jmol.api.JmolStatusListener. I stumbled for some time before discovering that the notifyFrameChanged() event handler must include updateComputedMenus() on the JmolPopup object. Without this, the menu will mostly contain ghosted items.

Jmol for mac os

Contributors

AngelHerraez, Pierocanepa, Yodah134, Ssorgatem, Mhampton, Kirby, Chris, NicolasVervelle, Pimpim, Nvcleemp, Tzontonel, Christoph.gille, Andorsch, Martin.guetlein

Retrieved from 'http://wiki.jmol.org/index.php?title=Applications_Embedding_Jmol&oldid=9879'

Hi!

I am trying to use the following commands in the notebook:

but Jmol terminates and just returns a black picture. These commands work fine in the command line. I tried this both on my laptop and on the notebook server at sage.lacim.uqam.ca. Is there some configuration necessary to display jmol pictures in the notebook?

Jmol For Mac Download

Thanks,

Anne

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Comments

This is almost certainly to do with your specific configuration. We have had these kinds of issues on a recurring basis. I would suggest searching sage-support (though it's hard to do sometimes) for this. Sometimes it's a Linux thing, sometimes you need to update your Java, and sometimes it's a bug. What version do you have? We did fix some of these things in patches that should be in 4.7.

If you are using Mac OS X + Chrome there is a good thread on sage-support, although that problem was fixed (at least in 4.7.1). You may need to enable your browser to load java applets. Try going to http://jmol.sourceforge.net/demo/alphahelix/ and see if the jmol applet loads.

Thank you for your answers. I am running sage-4.7.1 under Mac OS. The jmol applet loads fine for me when I go to http://jmol.sourceforge.net/demo/alphahelix/ . I am not sure which operating system http://sage.lacim.uqam.ca uses, but the sage version there is sage-4.7. You can get a free account and see whether the problem also occurs for you there.

Thank you for your answers. I am running sage-4.7.1 under Mac OS. The jmol applet loads fine for me when I go to http://jmol.sourceforge.net/demo/alphahelix/ . I am not sure which operating system http://sage.lacim.uqam.ca uses, but the sage version there is sage-4.7. You can get a free account and see whether the problem also occurs for you there.

PS: I am using Firefox.