JMOL DOCUMENTATION PDF

Jmol is a free, open source molecule viewer for students, educators, and researchers in For the most up-to-date scripting documentation see the Jmol/ JSmol. Documentation of Jmol’s scripting language can be found here: http://chemapps. This is the official. JSmol is a fully functional implementation of Jmol that does not Various ways to create surfaces and more documentation on surfaces.

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The recommended way to cite Jmol is: Includes atomic, van der Waals and ionic radii. Shaded images are calculated and cached, so performance should not be an issue except when dealing with very large protein molecules.

Jmol Documentation

In addition to an extensive description of all commands and options, it provides excellent demonstrations and examples. Table of Contents Testing results. The applet is tested and working with Internet Explorer, Netscape, Opera, Mozilla and derivatives and Konqueror on various platforms.

It is ideal for development of web-based courseware and web-accessible chemical databases. They cover the basic functionality of both application and applet, documentaation they have not been updated recently particularly, documentaion features in version 11 of Jmol. So if you make the atom sizes large you will get disappointing results. For up-to-date details or instructions for adding your language, see the Wiki. Documentation for the JavaScript Library Jmol.

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Jmol in an Android tablet. Particularly, if you are learning how to use JmolApplet and scripting, you are encouraged to only use the JavaScript library. In addition, the Jmol rendering engine does not currently handle intersecting spheres. A list of literature describing Jmol can be found at Jmol Wiki. Support and operating systems.

Jmol Applet Documentation

Colors Used by Jmol This document specifies which colors Jmol uses for elements, chains, chain direction, charge, hydrogen documentatiion, isosurfaces, positional variability, residues, nucleotides, and secondary structure.

Web pages without writing code by using the Jmol “Export to Web” function. More dynamical and frequently updated than this web site! A short script included as an applet parameter which is executed as soon as the applet is loaded.

If you would like to have multiple instances of the applet on a single page then you should give them unique names. Supported Browsers Testing results 3. By default, documrntation are rendered with perspective depth. Scripting Scripting References Ways to integrate scripts.

To get things to run on an installed base of older Netscape and IE browsers you may want to consider looking for ‘old’ documentation rather documentwtion ‘up to date’ documentation. Renders atoms and bonds as shaded spheres and cylinders. The Jmol Applet Guide describes the Jmol applet.

Backward compatibility changes of behavior across versions Features added since version 10 Users mailing list and a mirror.

Jmol links Website Sourceforge. Unfortunately, the news is not good for Macintosh OS X.

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Jmol – Research Computing Documentation

We recommend that you use the name ‘jmol’ as in:. Scripting for Jmol Scripting Documentation This interactive online documentation is the reference guide for all commands that form the Jmol scripting language. Jmol is an open-source viewer for three-dimensional chemical structures, with features for chemicals, crystals, materials and biomolecules.

Views Page Discussion View source History. You should use them only if you are experienced and you know precisely what you need. A user-maintained site collecting a lot of information about the use of Jmol. Using buttons to call javascript methods, each of which is driving a jmol animate script. Documentation for Surfaces This documentation describes and compares the different options available in Jmol scripts for generating surfaces, either based on the molecule or geometric.

These are official guides for Jmol. It also provides a testing and demonstration page. The JmolViewer can be integrated as a component into other Java applications. This documentation describes and compares the different options available in Jmol scripts for generating surfaces, either based on the molecule or geometric.

With some browser versions you can sneak by without starting object references with ‘document’. Verified Error on jmol-applet.

Running Jmol using Java Web Start.