Structure Morpher Panel

Structure Morpher Panel Features

• Use structures from option menu
• Open Project Table button
• File name text box and Browse button
• Output file text box and Browse button
• Number of intermediate frames text box
• Coordinates to use for morphing options
• Superimpose option
  • Interval text box
  • Structure text box and Browse button
• Append ligand options
• Structure Equivalency Test button
• Job toolbar
• Status bar

Use structures from option menu

Choose the structure source for the transformation.

• 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.
• 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.
• Files—Use structures from the specified files. When this option is selected, the File names text box and Browse button are displayed. The allowed file types are: Maestro, PDB, SD.

Open Project Table button

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

File names text box and Browse button

Enter the file names in this text box, or click Browse and navigate to the files. The names of the files you selected is displayed in the text box. You must choose an even number of files. Each pair of files (taken in the order given) defines an initial and a final structure for morphing. Only the first structure from each file is used.

Output file text box and Browse button

Specify the name of the output file in this text box, or click Browse and navigate to the file. If a name is not provided, the job name is used to construct the file name.

Number of intermediate frames text box

Specify the number of intermediate structures ("frames", as in a trajectory) to generate between the two input structures. This number does not include the input structures. Each frame is a linear interpolation between the two structures, along the chosen coordinates.

Coordinates to use for morphing options

Select an option for the coordinate type to use for morphing.

• Internal—Perform the interpolation on the internal coordinates of the structures. This choice allows for rotation of bonds, giving a more chemically intuitive interpolation.
• Cartesian—Perform the interpolation on the Cartesian coordinates. If the two structures are at different locations, you can select Perform translations, to effectively perform a superposition of the structures, so that the translational component is removed.

Superimpose option

Superimpose each frame on a reference structure. This is useful for eliminating translational and rotational changes between the structures.

Interval text box

Superimpose each Nth frame on the reference by entering N in this text box.

Structure text box and Browse button

Specify the file that contains the reference structure for the superposition. The first structure in the file is used as the reference structure.

Append ligand options

Choose an option for how to treat the ligand (if present) when doing the interpolation.

• Morph ligand along with protein—Include the initial ligand in the interpolation procedure with the protein.
• Remove ligand from the intermediate protein structures—Do not include the ligand in the interpolation, and only include it in the initial and final structures.
• Add ligand from the final structure to the intermediate protein structures—Add the ligand from the final structure to each interpolated structure. The ligand is placed in each frame at interpolated Cartesian coordinates. This option is useful if the initial and final ligands are different.

Structure Equivalency Test button

Check that the structures are equivalent, i.e. have the same atoms and connectivity.

Job toolbar

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

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes 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.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.