Prime User Manual - ISP

Chapter 8: Maestro Protein Structure Alignment
The Use proteins from option menu provides choices of the source of protein structures. If you
choose Project Table, the entries that are selected in the Project Table are used. If you choose
File, the Input file text box and Browse button become available, and you can browse for the
input file.
In the Residues for alignment section you select the residues that are to be used to align the
proteins. There are two options, described below.
• Automatically detect binding site residues—Align residues within a specified distance of
the ligand. The distance is specified in the Align residues within N Å 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—Specify the residues to align by using any of the following
methods:
• 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.
The residues are listed in the Align residues text box, which you can edit to remove or add
residues.
The alignment is performed on atom pairs. You can ignore atom pairs in the alignment process
if they are further apart than a specified distance, by entering the distance in the Ignore pairs
greater than N Å apart text box.
If you have proteins that are prealigned, you can select Structures are prealigned to suppress
the global alignment of the protein structures, and align only by using the selected residues.
When you have finished making settings, click Start to start the job.
You can also run a job to align binding sites from the command line—see Section 12.4 on
page 119 for more information.
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