Viewer (Jmol) control

Getting the most out of ZINCPharmer

Viewer (Jmol) control

Postby dkoes » May 27th, 2011, 1:30 pm

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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Re: Viewer (Jmol) control

Postby smokyjohn » November 2nd, 2012, 1:07 pm

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.


Hello,

I cannot zoom because my mouse wheel seems to be broken. Is there another way to zoom?
Last edited by smokyjohn on November 9th, 2012, 1:04 pm, edited 1 time in total.
smokyjohn
 

Re: Viewer (Jmol) control

Postby dkoes » November 3rd, 2012, 6:19 pm

Zoom in / out Shift + drag vertically drag vertically

More controls are described at the web page linked above.
dkoes
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Posts: 24
Joined: May 27th, 2011, 11:29 am


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