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Receptor Grid Generation — Excluded Volumes Tab |
In this tab you can define spherical regions of space from which ligand atoms should be excluded during docking, by applying a penalty. The penalty ramps up from zero at the sphere surface to its maximum value at a small distance from the surface. This provides a "soft" surface to the sphere, rather than having a hard cutoff.
This table lists each sphere, with its name, the coordinates of its center, and its radius. You can select multiple rows in the table to delete. All the table cells are editable, so you can change the characteristics of the excluded volume after adding it to the table.
Click this button to add a new excluded volume sphere. The New Excluded Volume dialog box opens, so you can define the sphere center and radius and provide a name. The sphere center is placed at the centroid of the atoms that you pick in the Workspace.
Import excluded volumes from a Phase hypothesis. Only the sphere center
and sphere radius are imported. Opens a dialog box, in which you can navigate to
the desired .xvol file.
Note: You must ensure that the hypothesis is in the same frame of reference as the receptor. No translation or rotation of the coordinate frame is done when the excluded volumes are imported.
You can check the alignment by including in the Workspace the native ligand for the receptor and the reference ligand for the hypothesis, to see if they are properly superimposed. If there is no reference ligand for the hypothesis, include the hypothesis in the Workspace and ensure that the sites in the hypothesis are placed at appropriate locations on the native ligand. If you don't see a reasonable alignment, the excluded volumes are likely to be of little value.
Select table rows and click Delete to delete the selected volumes. Click Delete All to delete all the excluded volumes.
Select this option to display the excluded volume spheres in the Workspace. The selected volumes are colored red; the unselected volumes are colored yellow.
Label the excluded volumes in the Workspace with the names listed in the table.
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