LiteMol:Introduction: Difference between revisions
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=How to use LiteMol?= | =How to use LiteMol?= | ||
# Go to [http:// | # Go to [http://add_web_address LiteMol's web page]. | ||
# Find “Molecule from PDBe” in the right panel, enter the PDB identifier (such as 1CBS) of your molecule, and click “Add”. | # Find “Molecule from PDBe” in the right panel, enter the PDB identifier (such as 1CBS) of your molecule, and click “Add”. | ||
# Your molecule has been downloaded from the server and should be visible in the center of the screen. | # Your molecule has been downloaded from the server and should be visible in the center of the screen. | ||
# Now you can use all the functions. Just click at any entity in the hierarchy in the left panel and its available actions will be shown in the right panel. Find more tips on the page on [[LiteMol:Functionality | functionality]]. | # Now you can use all the functions. Just click at any entity in the hierarchy in the left panel and its available actions will be shown in the right panel. Find more tips on the page on [[LiteMol:Functionality | functionality]]. | ||
Revision as of 18:35, 20 June 2016
Visualization of protein and nucleic acid structures is a typical task in structural biology. A variety of visualization tools are/is? available today. They differ in provided functionality and manner of use and are often limited by the size of visualized structures. Moreover, their use often troublesome because of installation, system requirements, or licence purchase.
What is LiteMol?
LiteMol is a visualization tool designed to be user-friendly yet flexible, interactive, and very fast even for extremely large protein structures. LiteMol can be run directly from your web browser without any installation and it does not require any plugins. Moreover, it can be incorporated as an applet in other web pages.
LiteMol provides standard functionality of visualization tools, such as different modes of visualization (cartoon, balls and sticks, vdW spheres, surface, C-α trace), selecting substructures using a simple query language, coloring the parts of the structure etc. The main advantage of LiteMol is the capability of visualizing extremely large structures containing up to millions of atoms. Even such structures as virus capsids can be shown in a few seconds. The degree of detail can be adjusted from rather coarse (but fast) to very smooth (though slower).
Apart from the structures, LiteMol can be you used to display electron densities and cryo-EM data. The validation data from PDBe as well as annotation data from several databases are available and can be mapped to the 3D structure and shown as distinctive coloring. Another feature of LiteMol is its extended interactivity. Interesting regions of the structure can be inspected in more detail by a single click.
Data can be uploaded from a CIF file or downloaded directly from PDBe by entering the PDB ID. Larger structures can also be accessed using Coordinate Streaming, so the essential data are downloaded immediately and the rest of the data are fetched only when needed.
How to use LiteMol?
- Go to LiteMol's web page.
- Find “Molecule from PDBe” in the right panel, enter the PDB identifier (such as 1CBS) of your molecule, and click “Add”.
- Your molecule has been downloaded from the server and should be visible in the center of the screen.
- Now you can use all the functions. Just click at any entity in the hierarchy in the left panel and its available actions will be shown in the right panel. Find more tips on the page on functionality.