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Viewing Poses |
Maestro has a special facility for viewing poses from a pose viewer file
(_pv.maegz) or an ensemble pose viewer file
(_epv.maegz). This facility allows you to step through poses with
the receptor fixed in the Workspace. You can also define and display hydrogen
bonds, contacts, and per-residue interactions, and count hydrogen bonds and
contacts. If you have flexible hydroxyl or thiol groups ("rotatable
groups") in the receptor, these are shown in the correct orientation for
each pose, and you can export the receptor and poses for given orientations of
the rotatable groups. If you have multiple receptors from an ensemble pose
viewer file, the best receptor for each ligand is shown as you step through the
ligands.
To open the Pose Viewer panel, you can:
Choose Applications → Glide → Pose Viewer in the main window.
Choose Entry → View Poses in the Project Table panel.
Choose Tasks → Docking → Pose Viewer in the main window.
Right-click on an entry group in the Project Table panel or the Entry List panel and choose 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.
To start using the pose viewing facility:
Select a single entry group in the Project Table.
The receptor or receptors must be at the beginning of the group, followed by the ligands. This is the normal situation when you import a pose viewer file into the project.
Open the Pose Viewer panel (see above).
Click Set Up
The receptor is fixed in the Workspace, the first ligand entry is included in the Workspace, and the view zooms to the ligand.
If the results are not already imported into the project, do one of the following:
Open the Pose Viewer panel (see above), click Import File, and navigate to and import the pose-viewer file. Setup is performed automatically.
Click the Import toolbar button, ensure that For pose-viewer files, turn on pose viewing is selected, then navigate to and import the pose-viewer file. When the file is imported into the project, the Pose Viewer panel opens and setup is performed automatically.
You can now perform the following actions:
Step through the poses using the right arrow and left arrow keys.
Use the ePlayer to step through the poses, play through the poses automatically, and perform actions on the poses with a script.
For more information, see The ePlayer.
Display non-bonded interactions: hydrogen bonds, halogen bonds, contacts, and pi interactions.
To do so, select the appropriateDisplay options in the Non-bonded interactions section of the panel. The display is turned on for each ligand in the entry group.
You can also set the parameters that define the interactions, by clicking Define in the Non-bonded interactions section. This button opens the Non-Bonded Interactions panel. In this panel you can change the color of the markers and choose the atom sets between which markers are displayed. The panel also provides access to the Non-bonded interactions – Criteria section of the Preferences panel, where the parameters that define each interaction can be changed.
Calculate counts of hydrogen and halogen bonds, contacts, and pi interactions.
To do this, click Create Property in the Non-bonded Interactions section. A dialog box opens, in which you can choose which of the three types of interactions to create properties for. The counts may take a little time to evaluate. They are added as project properties to the entries selected for pose viewing.
Visualize per-residue interactions.
The visualization is turned on by selecting Display in the Per-Residue Interactions section. The per-residue interactions are represented by coloring the residues by the value of the interaction, using a color ramp. To select the residues that are colored and which interactions are visualized, click Define in the Per-Residue Interactions section, and make settings in the Per-Residue Interactions panel.
Per-residue interactions can be set up by selecting Write per-residue interaction scores for residues within N Å of grid center in the Output tab of the Glide Ligand Docking panel.
Export the receptor and poses with particular orientations of rotatable groups in the receptor.
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 coordinates of the receptor in the pose viewer file are for the original orientation, but the receptor includes information on the alternative orientations. This option allows you to write a file with the alternative coordinates.
To do so, you should first include one of the poses that has this orientation in the Workspace. Next, click Export Rotatable Groups. In the Export Rotatable Groups dialog box you can choose whether to export just the receptor, the receptor and the included pose, or the receptor and all poses for which the receptor has that particular orientation of the flexible groups.
To finish viewing poses:
Select any single entry.
Pose viewing finishes because a single entry group is no longer selected.
Choose Entry → Exclude, or type Ctrl+X (⌘X).
The receptor is no longer fixed in the Workspace.
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