 |
 |
 | VIDA
User Manual | ||||
 |
 |
 |
 |
||||
The first view is the Docking View, the results of which can be seen in Figure 5.24(a). This view sets up the protein's active site (the region around the reference ligand) with a cropped electrostatic surface and the nearby molecular structure. Optionally, it will also display the protein's associated ribbon. Finally, it labels the c-alpha carbons on the protein with residue information.
The Docking View then places the reference ligand in the active site and colors the carbons using the ``Reference Color" (the default is green). Finally, it loads the optional results and makes the first molecule in that list the Focused molecule.
The Docking View has several optional parameters, as shown in Figure 5.23. Hydrogen bonds, protein ribbons, residue labels, and the protein surface can all be toggled using the checkboxes at the bottom of the dialog. Furthermore, there are additional preferences with respect to the distance cutoffs used that can be found in the application preferences (see chapter 12).
[An EON Results View]
[A ROCS Results View]
 |
|
|
| VIDA
User Manual | ||||
|
|
|
|
||||