Torsion Profile Analysis Panel

Torsion Profile Analysis Panel Features

Use structures from option menu

Choose the structure source for torsion profile analysis.

• Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries. When this option is selected, a Load button is displayed to the right.
• Workspace (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries. When this option is selected, a Load button is displayed to the right.

Open Project Table button

Open the Project Table panel, so you can select or include the entries for the structure source.

Analyze trajectory option

Analyze the frames in the trajectory associated with the structure. This enables plotting of the profile as a function of simulation time in the Torsion Profile Analysis Viewer Panel. This option is not available if the input structure does not have periodic boundary conditions and a trajectory.

Trajectory Frames button

Set the range and interval of trajectory frames to use in the analysis. The total number of frames to be used and the time range (in ns) corresponding to the selected frames are shown to the right of the button. Opens the Trajectory Frames dialog box, in which you can set the following:

• Frame range text boxes—Set the range of frames to use. You can also use the slider to select the range.
• Step size text box—Set the interval at which trajectory frames are taken. For a step size of n, every n^th frame is taken within the selected range. The first and last frames are always included. Increasing the step size decreases the number of frames to be used and the computational time needed.
• Frames text—Lists the corresponding frame numbers of the selected frame range and step size.
• Time text—Lists the corresponding time range and interval (in ns) of the selected frame range and step size.
• OK button—Apply the selected trajectory frame range and step size and close the dialog box.

Torsion definition tools

These tools allow you to define torsion types in terms of SMARTS patterns. All torsions defined by the SMARTS pattern are included in the analysis.

Torsion label and count text

This text identifies the torsion by number and reports the number of torsions found. Clicking on it shows or hides the torsion definition tools.

torsion definition management buttons

These buttons perform display and ordering operations on the torsion definition. They allow for easy duplication and rearrangement of torsion definitions.

	Show or hide the contents of the torsion definition. When hidden, only the torsion definition number, label (if any) and these buttons are displayed. This is useful when you have a number of torsion definitions and want to compare two separate torsion definitions, for example.
	Move the torsion definition up or down one place in the list.
	Duplicate the torsion definition. This is useful for creating similar torsion definitions with variations on the settings.
	Delete the torsion definition.

Torsion SMARTS text box and Use Workspace Selection button

Enter the SMARTS pattern for defining the torsional angle in the text box, or select the atoms in the Workspace for the SMARTS pattern and click Use Workspace Selection. When you click the button, a SMARTS pattern is generated for the Workspace selection and replaces the contents of the SMARTS text box. You can modify the SMARTS pattern after it is obtained from the Workspace. You can use the names of coarse-grained particles in brackets, e.g. [cg1], instead of atomic symbols to define a SMARTS pattern for coarse-grained particles.

Torsion atom option menus A, B, C, D

Select the atoms from the SMARTS pattern that define the torsion A-B-C-D. The menus are populated from the SMARTS pattern and a default selection is made.

Add Torsion button

Add a set of torsion definition tools below the last set.

Find BackboneTorsion button

Find the torsion for the backbone of the structure and add a torsion definition tool set. The SMARTS pattern is populated automatically. The backbone is defined as usual for structures such as polymers and proteins; for other structures it is the shortest path between the farthest non-hydrogen atoms in a molecule.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Torsion Profile Analysis - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

Use the Reset button to reset the panel to its default settings and clear any data from the panel. If the panel has a Job toolbar, you can also reset the panel from the Settings button menu.

If you can submit a job from the panel, the status bar displays information about the current job settings and status for the panel. The settings include the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

The status bar also contains the Help button , which opens an option menu with choices to open the help topic for the panel (Documentation), launch Maestro Assistant, or if available, choose from an option menu of Tutorials. If the panel is used by one or more tutorials, hover over the Tutorials option to display a list of tutorials. Choosing a tutorial opens the tutorial topic.

Related Topics

• Torsion Profile Analysis Viewer Panel
• Torsion Profile Analysis - Job Settings Dialog Box