lsqfit.pl Show Source
lsqfit.pl [options] refPDB cmpPDB
options: [-l min:max[=...]]
[-x min:max[=...]]
[-sel cab|ca|cb|p|heavy]
[-nowarn]
[-resnumonly]
[-s min:max[=...] min:max[=...]]
[-align fasta]

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.

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
ATOM     11  O   MET     1       1.007 -10.473  -0.588  1.00  0.00      PRO0
ATOM     12  N   LEU     2       0.289  -8.349  -0.753  1.00  0.00      PRO0
ATOM     13  H   LEU     2       0.298  -7.522  -1.282  1.00  0.00      PRO0
ATOM     14  CA  LEU     2      -0.669  -8.471   0.334  1.00  0.00      PRO0
ATOM     15  CB  LEU     2      -0.458  -7.417   1.426  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          
ATOM     11  C   LEU     2      -1.934  -7.718   1.767  1.00  0.00          
ATOM     12  O   LEU     2      -2.703  -6.846   1.414  1.00  0.00          
ATOM     13  CB  LEU     2      -0.325  -6.065   2.712  1.00  0.00          
ATOM     14  CG  LEU     2       0.628  -6.208   3.896  1.00  0.00          
ATOM     15  CD1 LEU     2       2.067  -6.287   3.384  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
ATOM     11  O   MET     1       0.737 -10.586  -0.679  1.00  0.00      PRO0
ATOM     12  N   LEU     2      -0.004  -8.465  -0.783  1.00  0.00      PRO0
ATOM     13  H   LEU     2      -0.023  -7.631  -1.300  1.00  0.00      PRO0
ATOM     14  CA  LEU     2      -0.916  -8.611   0.339  1.00  0.00      PRO0
ATOM     15  CB  LEU     2      -0.670  -7.572   1.438  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
ATOM     11 3H   MET     1      21.610  92.610   9.715  1.00  0.00      PRO0
ATOM     12  HA  MET     1      23.718  92.381   9.057  1.00  0.00      PRO0
ATOM     13 1HB  MET     1      23.785  90.573  11.415  1.00  0.00      PRO0
ATOM     14 2HB  MET     1      25.006  90.282  10.176  1.00  0.00      PRO0
ATOM     15 1HG  MET     1      26.153  92.141  10.751  1.00  0.00      PRO0
...
GenUtil.pm  Molecule.pm  Analyze.pm
Michael Feig, Brooks group, TSRI