Viewer Control

Controlling the JMol visualization.

Viewer Control

Postby dkoes » Mon Jan 17, 2011 3:31 pm

AnchorQuery uses Jmol for visualization. Many additional visualization options are available through the standard Jmol menus (right-click on the viewer). To enable file system access, add ?SIGNEDJMOL=1 to the anchorquery URL. For example: http://anchorquery.ccbb.pitt.edu/anchorquery.html?SIGNEDJMOL=1

Click and drag to rotate. Cntrl-right-click to translate. Use the mouse wheel to zoom. Further mouse controls are described here.

A selection of molecule styles and color schemes is available for the anchor residues (those uploaded with the Load Residues button), the receptor residues, and the result compounds. Additionally, the visualization of the pharmacophore features can be enabled/disabled.

The molecular surface or solvent accessible surface of the receptor can be visualized. A gradient mapping of partial charges is available when the receptor is specified using a pdb file. Disabling the receptor surface can result in a substantial boost in viewer responsiveness.
dkoes
 
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