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Jmol is computer software for molecular modelling of chemical structures in 3 dimensions. [2] It is an open-source Java viewer for chemical structures in 3D [3]. The name originated from ava (the programming language) + [mol]ecules, and also the mol file format. JSmol is an implementation in JavaScript of the functionality of Jmol. [4]
To display molecules with Jmol, your browser needs to be Java enabled. Two examples of Jmol images in a wiki are here and here. These use Jmol to show medium sized molecules with buttons to control the rotation of the molecules. The right mouse button opens a Jmol menu while the left mouse button can be used to move the image.
Currently, web-integrated crystal structure visualization is based on Java applets from open-source projects such as Jmol. [35] Web-integrated crystal structure visualization is tailored for examining crystal structures in web browsers, often supporting wide color spectra (up to 32 bit) and window size adaptation. However, web-generated crystal ...
the collaborative, 3D encyclopedia of proteins and other molecules. A wiki that contains a page for every entry in the PDB (>100,000 pages), with a Jmol view that highlights functional sites and ligands. Offers an easy-to-use scene-authoring tool so you don't have to learn Jmol script language to create customized molecular scenes.
The site contains a page for all of the entries in the Protein Data Bank (PDB), as well as pages that are more descriptive of protein structures in general such as acetylcholinesterase, [5] hemoglobin, [6] and the photosystem II [7] with a Jmol view that highlights functional sites and ligands. It employs a scene-authoring tool so that users do ...
Chime largely has been superseded by Jmol, [5] a non-proprietary open-source Java molecular visualization application and JavaScript applet that has maintained most Chime command compatibility while adding numerous features.
An addition that I think would be useful for the Wiki: rather than directly adding a Jmol applet in a MediaWiki page (which requires loading the applet when viewing the page), I have added the possibility to add a button opening a new window with the Jmol applet in it (the applet will only be loaded for people that want to see the molecule in 3D).
The XYZ file format is a chemical file format.There is no formal standard and several variations exist, but a typical XYZ format specifies the molecule geometry by giving the number of atoms with Cartesian coordinates that will be read on the first line, a comment on the second, and the lines of atomic coordinates in the following lines. [1]