This article provides a very brief introduction to getting started, hardware requirements, finding and downloading free protein models, and basic navigation for various viewers.
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Examining how real proteins are modeled can help novices to intuitively learn how the various 3D protein structures are naturally positioned and arranged in the real world. Many scientists offer their research free of charge on the Internet for anyone to download and study, and the tools to view and examine proteins are also often free. Some of the example objects are ridiculously huge in the tens of thousands of atoms, and so are not offered as a complete structural download since a supercomputer would be needed to model it fully, and not everyone can afford that.
Instead, the huge objects are usually constructed of smaller protein blocks that repeat over and over, and it is these sections that are offered for download. PDB files are nothing more than simple text files that describe all atoms in a structure, and which list the interconnections between each atom. The three letter extension generally identifies it as a protein structure to be opened with a special viewer.
If a viewer such as Avogadro or Chimera is installed, usually a PDB will be automatically associated with the viewer and will auto-open as a 3D view. The PDB may also contain heading information that is plain text and is directly readable from any simple text editor such as Windows Notepad. However, a PDB over kilobytes can contain thousands of lines of data, and Windows Notepad can seem to hang Not responding for several seconds to several minutes while an extremely large text file is opened.
Small proteins can load quickly into the viewer, but the load time increases dramatically as the number of atoms increases. It is normal to try to open a protein in a viewer and for the viewer to seem to hang with Not responding in the Windows title bar. It is working hard, so please wait patiently.
There are a number of free resources available, and some are better suited for general access by students and the public than others. The naming of proteins can be arcane and difficult for a newcomer to understand, but there are websites that have made an attempt to highlight some of the more interesting proteins and structures that have been investigated.
For a typical example, such as the Tobacco Mosaic Virus, click on the image or article name to bring up the detailed description of the virus. From here, the text usually refers to what seem to be randomly named strings of numbers and letters, which are how proteins are named.
Click on the protein name to bring up a page devoted to describing it. On the protein page at the top is the protein name, and a row of icons, one with a downward pointing arrow. Click on this icon to download the PDB file. Next to it is an icon that looks like a page of text. This allows you to view the text of the PDB file directly in your web browser.
The University of Massachusetts Amherst microbiology department has created an Atlas of Macromolecules to document some of the more interesting molecular structures. It offers flexible high quality rendering and a powerful plugin architecture.
Many consider this best for all platforms ArgusLab contains: An interactive 3D molecule builder that allows the user to build and manipulate complex structures; and, a rich suite of computational methods, both quantum mechanical and molecular mechanical, for calculating ground and excited states properties.
The program is free for academic use.
Mage requires the use of Kinemage files. Because of the large number of Kinemage files available to the public this makes for an interesting teacher tool. The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
Commercial users must obtain permission for its use. The crystallographic software can solve, refine and examine small molecule crystal structures. Software for Powder pattern simulation and the detection and display of voids is also available. PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard PCs.
Viewing real protein models
The initial level stage can be downloaded free. Jmol and Jsmol is a free, open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet.
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Jmol is a collaboratively developed visualization and measurement tool for scientists and educators. New features being added on an ongoing basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project. Toggle navigation.