Pose Viewer Panel

Set up the Workspace for stepping through poses from one or more Glide docking runs with the receptor fixed in the Workspace. The receptor residues can be colored by their values of an interaction with the ligand.

To open this panel, you can:

  • Click the Workflow Action Menu for the entry group and choose View Poses.
  • Click the Visualize link in the banner that is displayed when you import a pose viewer file.
  • Right-click on an entry group in the Project Table panel or the Entry List panel and choose View Poses.
  • Click the Tasks button and browse to Receptor-Based Virtual Screening → Pose Viewer.
  • In the Project Table panel, choose Table → Other Group Actions → View Poses.

This panel is dockable, so it opens by default in the Workspace. You can change this behavior in the Preferences Panel, under General – Panels.

  • Using
  • Features
  • Additional Resources

Using the Pose Viewer Panel

To use the pose-viewing facility to step through poses, you must select a single entry group in the Project Table. The group must contain the receptors at the beginning of the group, followed by the ligands, and the entries in the group must have the appropriate properties. This is the normal situation when you import a pose viewer file or ensemble pose viewer file into the project. Ensemble pose-viewer files have multiple receptors at the beginning of the file, and a property that associates each ligand pose with its receptor. You can create an ensemble pose-viewer file from separate pose-viewer files with the glide_merge utility, using the -epv option. (Hereafter, both kinds of files are referred to as pose viewer files.)

 

For information on different ways of viewing the poses, see Stepping Through Poses.

Pose Viewer Panel Features

Set Up Poses button

Set up the Workspace for viewing poses for the selected entry group. This is done automatically when the panel is opened from an entry group or the import banner for a pose viewer file. If the panel is already open and you select a different entry group, click this button to perform the setup.

Export rotatable groups button menu

If you have defined a set of rotatable groups (hydroxyls in Ser, Thr, and Tyr residues, or thiols in Cys residues) in the receptor, you can export the receptor with different orientations of these groups. The rotatable groups must be defined in the Rotatable Groups tab of the Receptor Grid Generation Panel when you generate the receptor grid. The coordinates of the receptor in the pose viewer file are for the original orientation, but the receptor includes information on the alternative orientations. To perform the export, you must display a pose with the desired orientations of the rotatable groups in the Workspace. You can then click the button and choose the structures to export from the menu:

  • Receptor only—Export only the receptor, with the rotatable groups in the current orientations.

  • Receptor and this pose only—Export the receptor with the rotatable groups in the current orientations and the ligand pose that is currently included in the Workspace. There must be only one ligand pose included in the Workspace.

  • Receptor and all poses for which rotatable groups are in these orientations—Export the receptor with the rotatable groups in the current orientations and all ligand poses in the selected entries for which the receptor adopts this set of orientations.

When you choose one of these options, a file selector opens, so you can export the structures.

Display per-residue interactions option

Visualize the interactions of selected or all residues in the receptor with the ligand. Residues are colored according to the magnitude of a chosen interaction using a color ramp. To use this feature, you must set up the generation of the interactions beforehand, by selecting Write per-residue interaction scores for residues within N Å of grid center in the Output Tab of the Ligand Docking Panel DEPRECATED when you set up the ligand docking run. The features below are not available if this option is not selected.

Type option menu

Select the type of interaction to display:

  • Interaction energy—Total interaction energy between the residue and the ligand from combination of Coulomb, van der Waals and hydrogen bonding terms.
  • van der Waals—Van der Waals interaction between the residue and the ligand.
  • Coulomb—Electrostatic interaction between the residue and the ligand.
  • H-bond energy—Sum of hydrogen bond energies between the residue and the ligand.
  • Minimum distance—Minimum distance between the residue and the ligand.
Colors option menu

Choose the color ramp to use when displaying the interactions. The most negative (favorable) values are mapped to the color at the left end of the ramp, the most positive to the color at the right end.

Range option menu

Choose an option for setting the range of values represented by the color ramp.

  • Auto-detect—use the range available in the data for the selected set of poses.

  • Custom—set the range to be used in the Min. and Max. text boxes. The initial values are taken from the range found in the selected set of poses The values are colored with the colors at the ends of the color ramp, to make relating the colors to values easier.

Apply to option menu

Choose the residues to apply the display of per-residue interactions to.

  • All Residues—apply the display to all residues in the receptor.

  • Selected Residues—apply the display to the residues that are selected in the Workspace. When this option is selected, the Update from Selection button is displayed. After changing the selection in the Workspace, click this button to update the per-residue interaction display.

Tips pane

This pane shows some information about viewing poses.

Tutorials

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