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#Jmol color scheme mac os#

Under Mac OS X, only Netscape 4 in Mac Classic mode is compatible with Chime.

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Despite this, full compatibility was only assured for Netscape 3 or 4 under Windows and Macintosh operating systems. These plug-ins were later supported by Microsoft Internet Explorer, and MDL made several updates of Chime to allow a greater compatibility with this browser. The birth of Chime was based on the plug-in architecture (complementary modules for the web browser) developed by Netscape. have also been using Rasmol and Chime as viewers. The abbreviation used is: PDB, Protein Data Bank. Worldwide structure databases such as the Protein Data Bank (PDB) 1 1 The ability to create a model in a predefined rendering, surrounded by descriptive text and material, including controls interacting with the model, all of it available through an intranet or the internet, has led to the creation through the years of innumerable tutorials and educational websites using Chime (see Ref.

#Jmol color scheme for free#

Although proprietary and copyrighted, Chime has been available for free after registration with MDL.

This allowed one to put molecular models inside web pages (initially for viewing with Netscape 3 and 4, later with Microsoft Internet Explorer, too). Its extensive spread among the scientific and teaching communities is well known and needs no further explanation here.Ĭhime was an implementation of Rasmol code in the form of a web browser plug-in, done at MDL (Molecular Design Limited, currently Elsevier MDL ).

It is fast in operation, remarkably low on system requirements (the executable file is only 342–473 kb, depending on the version), and endowed with an extensive command language (“Rasmol scripts”) that allows interaction with the molecular model (for a review, see Refs. This article does not pretend to review all of them, but instead will focus on two that are available for free and have been extensively used during the last 10–15 years, becoming fairly de facto standards, and a recent one that promises to become an advantageous replacement for them.įirst of all is Rasmol (by Roger Sayle and later by Herbert Bernstein in the form of OpenRasmol ), a standalone program running under Unix/Linux, Windows, and MacOS operating systems. Many programs exist that allow one to view and manipulate molecular models, both commercial and free. Most notably, the models are interactive, in the sense that the user (and the instructor programming the materials) can choose all sorts of actions to be performed on the model: the aforementioned rotation, changing the rendering, focusing on a part of the molecule, measuring its geometry, and so forth … To this end, some programs add lighting, shading, and perspective for a depth effect. Of course, it offers three-dimensional perception, through the possibility of rotating the model in any direction, both automatically and through manipulation by the user. It allows the use of diverse representations of a molecule: wireframe, sticks, balls and sticks, spheres (space-filling) and, crucial for proteins and nucleic acids, schematic renderings (such as several variants of ribbons and cylinders and the structures usually dubbed “cartoons”). It offers unlimited availability of “items” (atoms, bonds), helping one to avoid running out of materials, which frequently occurs with plastic models. Also, students are more likely to have individual access to a computer than to a physical model for each molecule.

It allows molecular models to be displayed in front of a wide audience, by means of multimedia projectors in the classroom or lecture hall. This pedagogical tool offers several advantages, as compared with classical physical molecular models, among which we can highlight:

#Jmol color scheme software#

The use of molecular models on a personal computer is nowadays commonplace, thanks to the availability of easy-to-use software (two inspired historical reviews have been written by Voet and Martz and Francoeur ).