align_binding_sites Command Help
Command: $SCHRODINGER/utilities/align_binding_sites
Usage: align_binding_sites [options] <input file>
NOTE: If more than one input file is specified, then the first
structure from the first input file is used as reference,
and structures from other files are aligned.
Supported input formats: Maestro and PDB.
Supported output formats: Maestro and PDB.
Description: This script performs a pairwise superposition of multiple
structures using the C-alpha atoms of selected residues. If one input file
specified, the reference structure for the alignment is the first structure in
the input file. If more than one file is specified, then the reference
structure is taking from the first file. The C-alpha atoms for the alignment
are 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 mobile structure greater than the specified distance from
any C-alpha in the reference are not considered in the alignment. Copyright
Schrodinger LLC, All Rights Reserved.
Options:
-v, -version Show the program's version and exit.
-h, -help Show this help message and exit.
-l int, -ligmol int Molecule number of the ligand (default auto)
-c float, -cutoff float
Binding site cutoff distance from the ligand in
Angstrom (default=5)
-d float, -dist float
Atom pairs greater than this distance are not
considered in the alignment (default=5)
-p, -prealigned Structures are prealigned. Do not run Protein
Structure Alignment (SKA)
-inplace Do not align the structures, but only report the RMSD
between the input structures. Also triggers the
-prealigned flag.
-r list, -res list Residues for the alignment. This option overrides the
use of -c/-cutoff. Format for a residue is
chain:resnum. If there is no chain name, use "_". For
example, A:123,A:456,_:999 for residue numbers 123 and
456 from chain A and residue number 999 from a blank
chain. At least three residues are required. The
comma-separated list should not have spaces. (no
default)
-j JOBNAME, -jobname JOBNAME
Jobname to use (default: input file basename)
-o OUTFILE, -outfile OUTFILE
How to name the output file (default: <jobname>-align-
final.maegz); allowed formats are Maestro and PDB.
-color Color the binding side based on the CA RMSD value (not
compatible with -inplace option)
-rmsdasl RMSDASL Group of atoms over which to compute the RMSD matrix.
The default is Calpha carbons, and ASL can be used to
calculate RMSD. This option does NOT affect the actual
atoms used for alignment nor the RMSD values that are
reported as "Post-SKA RMSD" or "Final RMSD" in the
.log file - only the RMSD matrix values reported in
the .log and -matrix.csv file are affected by this
flag. The "Post-SKA RMSD" and "Final RMSD" values
reported in the .log file during the alignment step
are for the Calpha atoms actually used in the
alignment. Note that sidechain, heavy, and all should
only be used if all proteins will have identical
residue types in the binding site.
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-WAIT Do not return a prompt until the job completes.
-LOCAL Do not use a temporary directory for job files. Keep
files in the current directory.
-D, -DEBUG Show details of Job Control operation.
-TMPDIR TMPDIR The name of the directory used to store files
temporarily during a job.
-NOJOBID Run the job directly, without Job Control layer.