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Protein Structure Alignment Panel |
Use this panel when you would like to bring two or more proteins into a common frame of reference by structurally aligning (superimposing) them.
It is often difficult to superimpose protein structures. Reasons include:
This panel greatly facilitates the superimposition of protein structures with an algorithm that attempts to align secondary structure elements.
To open the Protein Structure Alignment panel, you can:
Choose Tools → Protein Structure Alignment in the main window.
This panel is dockable, so it opens by default in the Workspace. You can change this behavior in the Preferences panel, under General – Panels.
Structure alignment operates on Project Table entries that have been included in the Workspace or are selected in the Project Table. Include in the Workspace or select two or more protein structures, open the Protein Structure Alignment panel, and click Align to start the alignment calculation. The structure that is the first entry (lowest row number) in the Project Table is used for the frame of reference; to use a different protein's frame of reference, move that protein to the first entry in the Project Table before starting the alignment job.
By default, the alignment includes all residues. However, it is often useful to align a subset of residues that have greater similarity than the structures as a whole, or are more informative to compare. Because this program uses matching of secondary structure elements, the subset should have enough contiguous residues to include at least one helix or strand. Very small numbers of residues do not produce useful alignments.
You might need to try different subsets to obtain the most useful alignment. You can use the picking controls, choose a predefined set of atoms from the selection button menu, or open the Atom Selection dialog box (ASD) to specify subsets. In this dialog box 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. It might also be helpful to display the sequence viewer with the secondary structure assignment, and pick residues in the sequence viewer.
When the alignment calculation is complete, the structures are placed in the same frame of reference in the Workspace, and the results of the calculation are displayed in the Protein Structure Alignment Results panel. The aligned residues are listed and an RMSD and Alignment Score are reported. The RMSD is calculated based only on those residues that are considered to have been successfully aligned, and therefore does not represent an overall comparison of the structures. An Alignment Score greater than about 0.7, or a failure of the structural alignment calculation, indicates there is insufficient structural similarity for a meaningful alignment.
The RMSD and the alignment score are also added to the structures as Maestro
properties, StructAlign RMSD
(r_psp_StructAlign_RMSD) and StructAlign
Score (r_psp_StructAlign_Score).
Choose the source of the proteins to align, from Workspace (included entries) or Project Table (selected entries). The proteins are aligned to the frame of the project entry that has the smallest row number.
Specify the residues in the reference protein to which the other proteins will be aligned, using the standard picking tools. You should specify residues that contain at least one secondary structure element. You must pick residues in the reference protein, which is the project entry with the smallest row number (highest in the table). A warning is displayed if you pick residues in another protein.
Specify the residues in the other proteins that are to be aligned to the reference residue set. If you want to use the same residue definitions as for the reference, choose Use same ASL as reference residues. If you want to define a different set of residues, choose Use separate ASL, and specify the residues with the Residues to align picking tools.
Click this button to start the Protein Structure Alignment job. The Protein Structure Alignment Results panel opens, showing the text "Calculating alignment..." until the alignment is done, when the text is replaced by the results. The text in the results panel is replaced each time you click Align.
Align proteins even if the structures are not sufficiently similar.
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