Prime User Manual - ISP

Chapter 12: Command-Line Utilities
12.4 Structure Alignment: align_binding_sites
This script performs a pairwise superposition of multiple structures using the C-alpha atoms of
selected residues. The reference structure for the alignment is the first structure in the input
file. The C-alpha atoms used for the alignment come from residues within the specified cutoff
distance from the ligand in the reference structure. Alternatively, a list of residues may be
given for the alignment, which must correspond to residues in the reference structure. C-alpha
atoms in the structures that are aligned that are greater than the specified distance from any Calpha
in the reference are not considered in the alignment.
$SCHRODINGER/utilities/align_binding_sites [options] input-file
The options are given in Table 12.2. The Job Control options described in Table 2.1 and
Table 2.2 of the Job Control Guide are supported, with the exception of -INTERVAL.
Table 12.2. Options for the align_binding_sites command.
Option Description
-v[ersion] Show the program version and exit.
-h[elp] Show usage message and exit.
-l[igmol] molnum Molecule number of the ligand. Default is to automatically detect the
ligand.
-c[utoff] value Binding site cutoff distance from the ligand in angstroms. Residues
within this distance of the ligand are used in the alignment. Default: 5.
-d[ist] value Atom pairs greater than this distance are not considered in the alignment
(default=5)
-p[realigned] Structures are prealigned. Do not run global protein structure alignment
(SKA).
-r[es] list Residues for the alignment. This option overrides the use of -cutoff.
Format for a residue is chain:resnum. If there is no chain name, use an
underscore, e.g. _:999 . At least three residues are required. The
comma-separated list should not have spaces.
-j[obname] jobname Jobname to use. The default is based on the input file name.
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