Prime User Manual - ISP

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Chapter 8: Maestro Protein Structure Alignment
Prime 2.1 User Manual
Figure 8.1. The Protein Structure Alignment panel.
To run a default alignment job, include two or more protein structures in the Workspace, open
the Protein Structure Alignment panel, and click Align to start the alignment calculation.
The Protein Structure Alignment panel provides some tools for controlling which parts of the
protein are aligned and how they are aligned. These tools are described below.
Residues to align Section
Alignment can be performed for all residues or for a subset of residues. You might need to try
different subsets to obtain the most useful alignment. You can use the picking controls, Workspace
selection, or the Atom Selection dialog box to specify subsets. Subsets should include at
least one secondary structure element (helix or strand). Clicking the Select button opens the
Atom Selection dialog box to the Residue tab. Here you can select a range of residue numbers,
specify portions of the residue sequence, or click Secondary Structure in the list of options on
the left to choose residues based on their location in Helix, Strand, or Loop structures. Subsets
can be combined, intersected, or otherwise modified in the Atom Selection dialog box.