Jmol - Visualization of Molecular Models
Jmol is a free source code and distribution program for the representation of three-dimensional molecular models, offered under the GLPL (GNU Lesser General Public License). Jmol allows a variety of chromatic renderings, translation and rotation movements of molecules, visual magnification, calculations of distances, angles, structures and surfaces, molecular optimizations, and animations, among others.
The program is multiplatform (Windows, Mac OS X, Linux, Unix) developed in Java environment, and can be executed both in closed version (standalone), as well as integrated with other Java applications, or even with internet search engines with the help of an applet. When installed, Jmol can run both from a directory folder containing its files, as well as from a hard disk or removable media (pendrive).
The contents developed with Jmol for Biochemistry and related topics can be viewed in Structural Biochemistry Guided by Jmol. This is a work for autonomous learning of the main molecular structures in Biochemistry, prepared in an itemized format, and allowing progressive monitoring of the topics covered with the help of the viewer.
The models contained in the ebook are obtained from this LINK, separated by chapters of the ebook, or in single compressed file (zip), containing the renderable images. The figures can be opened in any image viewer in static form, or rendered three-dimensionally by Jmol.
Quick usage tip!
Jmol is accessed online by several Structural Biology sites, such as First Glance in Jmol from Proteopedia, or St. Olaf College.
This quick tutorial in video illustrates a tip for another site as well.
So, just go to the link, right-click on the empty space (canvas), search for File->Load->Open from PDB, and type in a code from the online database Protein Data Bank such as 5cyt (cytochrome C).
On the other hand, if you wish to study any figure from the ebook, download the desired file from the link image library and drag it to the FGJM window to automatically render the structure in 3D.
On the other hand, if you wish to study any figure from the ebook, download the desired file from the link image library and drag it to the FGJM window to automatically render the structure in 3D.
Structural Biochemistry Guided By Jmol
The links below allow you to try out a material under construction completely online for learning Biochemistry and using Jmol. This material is being ported and adapted from the ebook on this page.
Other programs for viewing molecular models
There are several programs for three-dimensional rendering of atomic models, both standalone, for mobile devices (Android, iPhone), and online. A quick internet search allows you to access programs such as: