GPCR Helix Manipulator Panel
Manipulate phi/psi dihedral angles and positions of helices in a GPCR. This panel is intended for manual refinement of GPCR homology models.
To open this panel: click the Tasks button and browse to Protein Preparation and Refinement → Helix Manipulator.
- Using
- Features
- Additional Resources
Using the GPCR Helix Manipulator Panel
When entering values in the text boxes, you can use the up and down arrow keys to change the value, with Shift to increase the increment by a factor of 5, and Ctrl to decrease the increment by a factor of 10.
GPCR Helix Manipulator Panel Features
Plot section
This section displays a Ramachandran plot for the selected helix and provides tools for manipulating the plot and modifying the phi and psi angles.
- Plot toolbar
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The toolbar has tools for manipulating the plot and for saving images. The buttons that are common to all plot toolbars are described in the Plot Toolbar topic.
- Plot area
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Displays the Ramachandran plot for the selected helix. You can pick points on the plot, and the residue you pick is selected in the Workspace.
- Phi and Psi text boxes
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Set the phi and psi angles for the residue that is selected in the plot. The angles are changed in the structure, and one end of the helix is moved to accommodate the change, as determined by the Transform N-terminus and Transform C-terminus options.
You can use the up and down arrow keys to change the value, with Shift to increase the increment by a factor of 5, and Ctrl to decrease the increment by a factor of 10.
- Transform N-terminus option
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When changing the phi and psi angles for the selected residue, adjust the N-terminus of the helix to accommodate the change.
- Transform C-terminus option
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When changing the phi and psi angles for the selected residue, adjust the C-terminus of the helix to accommodate the change.
Helix Selection tab
In this tab, you select the helix you want to manipulate.
- Show Sequence Viewer button
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Show the sequence viewer in the Workspace, if it is not shown.
- Use Sequence Viewer Selection button
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Click this button to use the selection in the sequence viewer to define the helix to manipulate.
- Modify origin/axis choice section
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After picking a helix in the sequence viewer, the mid-point of the selected helix and its axes are detected. These axes are displayed in the Workspace. On of the axes perpendicular to the helix is colored differently.
Plot Tools tab
In this tab, you can save and revert changes to the phi and psi values.
- Pick residue in Workspace to locate in plot option
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Select this option to pick a residue in the Workspace. The picked residue is selected in the plot, and you can then perform actions on it.
- Save Current Position of This Point button
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Save the current values of phi and psi for the residue that is selected in the plot.
- Revert This Point to Saved Position button
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Replace the phi and psi values for the selected residue with the last saved values. This discards the most recent changes to the values.
- Revert This Point to Initial Position button
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Replace the phi and psi values for the selected residue with the original values. This discards all changes to the values.
- Initial and Saved value display
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This display table shows the phi and psi values of the selected residue in the original structure (Initial) and the last saved values. The values shown in the text boxes below the plot are the current values.
Position tab
In this tab you can adjust the overall position and orientation of the helix.
- Translate section
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Translate the helix along its parallel and perpendicular axes.
- Slide helix vertically text box
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Move the helix along its main axis by the specified amount. "Vertical" refers to the direction perpendicular to the membrane in the GPCR, in the standard view where this direction is vertical.
- Shift helix laterally(1) text box
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Move the helix perpendicular to its main axis by the amount specified in the box, in the direction of the first perpendicular axis. This axis is the one that has the same color as the main axis.
- Shift helix laterally(2) text box
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Move the helix perpendicular to its main axis by the amount specified in the box, in the direction of the second perpendicular axis. This axis is the one that has a different color from the other two.
- Rotate section
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Rotate the helix around the origin of the displayed axes.
- Tilt helix text box
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Tilt the helix away from the main axis by the specified amount. The rotation to perform the tilting is done around the first perpendicular axis (colored red).
- Sweep helix text box
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Rotate the helix around the current displayed main axis by the specified amount. Usually this is done after tilting the helix; if there is no tilt, sweeping does the same as rolling.
- Roll helix text box
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Rotate the helix around its actual main axis by the specified amount. This axis differs from the displayed main axis if the helix has been tilted.
- Reset Axes button
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Reset the helix axes to the current position and orientation.
Graphics tab
This tab provides options for the Workspace display.
- Show translation axes option
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Show the axes that will be used for translation of the helix (slide, lateral shift), in blue.
- Show rotation axes option
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Show the axes that will be used for rotation of the helix (tilt, sweep, roll), in red.
- Show hydrophobic moment option
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Display the hydrophobic moment of the helix as an arrow, in green.
- Show bad contacts option
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Show bad contacts between backbone carbon atoms and any other backbone atoms or beta carbons. The contacts are defined in the usual Maestro way (see Pi-Pi and Contact Criteria settings).
- Show backbone H-bonds option
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Show hydrogen bonds between the backbone atoms in the Workspace.
- Display Structure as Backbone Trace button
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Display only the backbone atoms, without the hydrogens and carbonyl oxygens. You can also include the beta carbons by selecting Include C-beta before you click this button.
To change the display back, you will need to use the Style Toolbox (see also Changing Structure Styles).
- Include C-beta option
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Include the beta carbon atoms in the backbone trace.