Latest revision as of 09:27, 14 May 2019

Visualization of protein and nucleic acid structures is an essential task in structural biology. A variety of visualization tools are available which all differ in functionality and manner of use. Many can be limited by the size of some structures, unable to render the larger complexes in structural archives. Moreover, their use is 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. It can be incorporated as an applet in any web page.

Unlike many visualizers, LiteMol can display extremely large structures containing millions of atoms quickly. Even structures such 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).

LiteMol provides the standard functionality expected of a molecular visualizer such as different representations (cartoon, balls and sticks, Van der Waals spheres, surface, C-α trace), selecting substructures using a simple query language, coloring the parts of the structure etc.

Apart from the atomic models, LiteMol can be used to display electron densities (for X-ray crystallographic data) and cryo-EM data. The validation data from wwPDB validation reports (via the PDBe API) 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 stored locally or downloaded directly from PDBe by entering the PDB ID. Larger structures can also be accessed efficiently using Coordinate Streaming, so the essential data are downloaded immediately and the rest of the data are fetched only when needed, limiting download sizes of files.

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 displayed in the left panel and all available actions will be shown in the right panel. Find more tips on the page on functionality.

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 __NOTOC__
-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.
+Visualization of protein and nucleic acid structures is an essential task in structural biology. A variety of visualization tools are available which all differ in functionality and manner of use. Many can be limited by the size of some structures, unable to render the larger complexes in structural archives. Moreover, their use is 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 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. It can be incorporated as an applet in any web page.
-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.
+Unlike many visualizers, LiteMol can display extremely large structures containing millions of atoms quickly. Even structures such 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).
-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.
+LiteMol provides the standard functionality expected of a molecular visualizer such as different representations (cartoon, balls and sticks, Van der Waals spheres, surface, C-α trace), selecting substructures using a simple query language, coloring the parts of the structure etc.
+Apart from the atomic models, LiteMol can be used to display electron densities (for X-ray crystallographic data) and cryo-EM data. The validation data from wwPDB validation reports (via the PDBe API) 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.
+Data can be uploaded from a CIF file stored locally or downloaded directly from PDBe by entering the PDB ID. Larger structures can also be accessed efficiently using Coordinate Streaming, so the essential data are downloaded immediately and the rest of the data are fetched only when needed, limiting download sizes of files.
 =How to use LiteMol?=
-# Go to [http://add_web_address LiteMol's web page].
+# Go to [http://litemol.org 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 [[LiteMol:Functionality | functionality]].
+# Now you can use all the functions. Just click at any entity in the hierarchy displayed in the left panel and all available actions will be shown in the right panel. Find more tips on the page on [[LiteMol:Functionality | functionality]].