Align Binding Sites Panel

Align Binding Sites Panel Features

• Use proteins from controls
• Residues for alignment section
• Ignore pairs greater than n Å apart text box
• Structures are prealigned option
• In place (calculate RMSD only) option
• Job toolbar
• Status bar

 

Use proteins from controls

The option menu provides choices of the source of protein structures. The choices are:

• Project Table—Use the entries that are selected in the Project Table for alignment. The first entry in the Project Table (lowest row index) is used as the reference structure.
• Workspace—Use the entries that are included in the Workspace for alignment. The first included entry in the Project Table (lowest row index) is used as the reference structure.
• File—Read the structures from one or more files. The first structure in the first file is used as the reference structure. When you choose File, the Input file text box and Browse button become available, and you can browse for the input files.

Residues for alignment section

In this section you select the residues that are to be used to align the proteins. There are two main options:

Automatically detect binding site residues

Select the binding site residues based on a distance from the ligand. The distance is specified in the Align residues withinNÅ from the ligand text box. Two options are available for specifying the ligand:

• Detect ligand automatically—Detect the ligand by selecting the molecule that is most ligand-like (number of atoms).
• Use molecule number—Specify the ligand by molecule number. You can enter a number in the text box, or select Pick ligand and pick a ligand atom in the Workspace.

Manually select residues

This option allows you to specify individual residues. You can define the residues in one of three ways:

• Enter the residue specification in the Align residues text box, in the format chain:number.

• Click Select residues to open the Atom Selection Dialog Box and define the residues.

• Select Pick a residue to include/exclude and pick residues in the Workspace. Picking an already included residue excludes it.

Ignore pairs greater than N Å apart text box

If the atoms in an atom pair are greater than the specified distance apart, do not use this pair in the alignment process. This test applies to the atom pairs defined by the residues selected for alignment.

Structures are prealigned option

Suppress the global alignment of the protein structures, and align only by using the selected residues.

In place (calculate RMSD only) option

Calculate the RMSD between prealigned protein structures, without doing any alignment.

Job toolbar

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

Status bar

If the panel has a Job toolbar, you can 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.