seo wrote:I think I know what you are asking. I believe the ZINCPharmer 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 ZINCPharmer URL. For example: http://zincpharmer.csb.pitt.edu/pharmer.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 query ligand, 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. The Van der Waals surface is a more approximate, slightly faster, molecular surface. 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.
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