Is there a script I could use that reports the results of structural alignment? Using the Atom Selection interface I can readily identify the residue number, but is there a command to do this, so I can write a script that outputs the corresponding residue numbers?

You could run Protein Structural Alignment from the command line:

$SCHRODINGER/utilities/structalign reference.pdb file1.pdb file2.pdb ...

The output is formatted to look like a sequence alignment, so you should be able to find corresponding residues numbers for all structures.

Keywords: structural alignment , structalign, Maestro

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