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lsqfit.pl
Usage
usage: lsqfit.pl [options] refPDB cmpPDB
options: [-l min:max[=...]]
[-x min:max[=...]]
[-sel cab|ca|cb|p|heavy]
[-nowarn]
[-resnumonly] [-useseg]
[-s min:max[=...] min:max[=...]]
[-align fasta]
[-mem]
[-showmatrix]
Description
This script performs least square fits of a structure with respect
to a reference. Both structures, the reference first, are expected
as command line arguments. The fitted structure is written to
standard output in PDB format.
The fit can be restricted to an inclusive subset of residues with
-l or exclusive to all residues outside the specified set
with -x. By default C-alpha and C-beta atoms are used for
the fit. Other atoms can be chosen with -sel. Possible
choices are ca, cb, cab,
and heavy.
By default, atoms in both structures are matched by atom name,
residue name, and residue number. If the option -resnumonly
is given only atom name and residue number are used. This is necessary
when fitting structures with different sequences based on the backbone
atoms.
The option -nowarn is available for suppressing warnings about
missing atoms.
Options
- -help
- usage information
Examples
lsqfit.pl 1vii.exp.pdb 1vii.exp.min.pdb
performs a least squares fit of 1vii.exp.min.pdb with respect
to the reference structure in 1vii.exp.pdb.
ATOM 1 HT1 MET 1 3.095 -10.784 -1.764 1.00 0.00 PRO0 ATOM 2 HT2 MET 1 3.675 -9.380 -1.095 1.00 0.00 PRO0 ATOM 3 N MET 1 3.271 -9.786 -1.958 1.00 0.00 PRO0 ATOM 4 HT3 MET 1 3.992 -9.706 -2.688 1.00 0.00 PRO0 ATOM 5 CA MET 1 2.034 -9.103 -2.277 1.00 0.00 PRO0 ATOM 6 CB MET 1 1.412 -9.597 -3.593 1.00 0.00 PRO0 ATOM 7 CG MET 1 2.178 -9.233 -4.861 1.00 0.00 PRO0 ATOM 8 SD MET 1 1.401 -9.893 -6.359 1.00 0.00 PRO0 ATOM 9 CE MET 1 0.297 -8.563 -6.743 1.00 0.00 PRO0 ATOM 10 C MET 1 1.064 -9.364 -1.134 1.00 0.00 PRO0 ...
lsqfit.pl -l 10:21 1vii.exp.pdb 1vii.rebuilt.10:21.pdb
perform a least squares fit of residues 10 through 21 in 1vii.rebuilt.10:21.pdb
with respect to the reference structure 1vii.exp.pdb
ATOM 1 N MET 1 2.161 -9.498 -1.381 1.00 0.00 ATOM 2 CA MET 1 1.212 -8.350 -1.288 1.00 0.00 ATOM 3 C MET 1 0.403 -8.465 0.005 1.00 0.00 ATOM 4 O MET 1 -0.103 -9.518 0.344 1.00 0.00 ATOM 5 CB MET 1 0.277 -8.353 -2.501 1.00 0.00 ATOM 6 CG MET 1 0.840 -7.419 -3.578 1.00 0.00 ATOM 7 SD MET 1 0.865 -8.278 -5.177 1.00 0.00 ATOM 8 CE MET 1 0.004 -7.006 -6.137 1.00 0.00 ATOM 9 N LEU 2 0.292 -7.389 0.735 1.00 0.00 ATOM 10 CA LEU 2 -0.459 -7.420 2.019 1.00 0.00 ...
lsqfit.pl -sel ca -x 10:21 1vii.exp.pdb 1vii.exp.min.pdb
perform a least squares fit of all residues except for 10 through 21 in
1vii.min.pdb with respect to the reference structure
1vii.exp.pdb. Only C-alpha atoms are used for the fit.
ATOM 1 HT1 MET 1 2.778 -10.861 -1.943 1.00 0.00 PRO0 ATOM 2 HT2 MET 1 3.373 -9.462 -1.278 1.00 0.00 PRO0 ATOM 3 N MET 1 2.938 -9.859 -2.130 1.00 0.00 PRO0 ATOM 4 HT3 MET 1 3.628 -9.763 -2.886 1.00 0.00 PRO0 ATOM 5 CA MET 1 1.684 -9.182 -2.388 1.00 0.00 PRO0 ATOM 6 CB MET 1 1.013 -9.662 -3.684 1.00 0.00 PRO0 ATOM 7 CG MET 1 1.724 -9.273 -4.977 1.00 0.00 PRO0 ATOM 8 SD MET 1 0.892 -9.917 -6.452 1.00 0.00 PRO0 ATOM 9 CE MET 1 -0.237 -8.591 -6.772 1.00 0.00 PRO0 ATOM 10 C MET 1 0.763 -9.468 -1.211 1.00 0.00 PRO0 ...
lsqfit.pl -sel ca -resnumonly 1poa.exp.pdb 1vii.exp.pdb
perform a least squares fit of C-alpha backbone atoms of all residues
in 1vii.exp.pdb with respect to the backbone atoms in the
reference structure 1poa.exp.pdb. Since the option
-resnumonly is given, it does not matter that both structures
have completely different amino acid sequences.
ATOM 1 N MET 1 22.014 91.744 10.128 1.00 0.00 PRO0 ATOM 2 CA MET 1 23.347 91.475 9.514 1.00 0.00 PRO0 ATOM 3 C MET 1 23.200 90.399 8.436 1.00 0.00 PRO0 ATOM 4 O MET 1 22.565 89.381 8.639 1.00 0.00 PRO0 ATOM 5 CB MET 1 24.331 91.013 10.593 1.00 0.00 PRO0 ATOM 6 CG MET 1 25.135 92.217 11.095 1.00 0.00 PRO0 ATOM 7 SD MET 1 25.110 92.252 12.910 1.00 0.00 PRO0 ATOM 8 CE MET 1 26.897 92.396 13.163 1.00 0.00 PRO0 ATOM 9 1H MET 1 21.376 90.943 9.940 1.00 0.00 PRO0 ATOM 10 2H MET 1 22.125 91.867 11.156 1.00 0.00 PRO0 ...