MMTSB
Tool Set Documentation

Difference between revisions of "Lsqfit.pl"

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as command line arguments. The fitted structure is written to
 
as command line arguments. The fitted structure is written to
 
standard output in PDB format.<BR>
 
standard output in PDB format.<BR>
 +
 
The fit can be restricted to an inclusive subset of residues with
 
The fit can be restricted to an inclusive subset of residues with
 
<B>-l</B> or exclusive to all residues outside the specified set
 
<B>-l</B> or exclusive to all residues outside the specified set
with <B>-x</B>. By default C-alpha and C-beta atoms are used for
+
with <B>-x</B>. Note, the -l and -x options appear to work with the syntax of the [[Selection]] commands, and thus complex selections can be used to superpose via least-squares fit different atoms in differing chains. By default C-alpha and C-beta atoms are used for
 
the fit. Other atoms can be chosen with <B>-sel</B>. Possible
 
the fit. Other atoms can be chosen with <B>-sel</B>. Possible
 
choices are <font color=#508060>ca</font>, <font color=#508060>cb</font>, <font color=#508060>cab</font>,
 
choices are <font color=#508060>ca</font>, <font color=#508060>cb</font>, <font color=#508060>cab</font>,
 
and <font color=#508060>heavy</font>.<BR>
 
and <font color=#508060>heavy</font>.<BR>
 +
 
By default, atoms in both structures are matched by atom name,
 
By default, atoms in both structures are matched by atom name,
 
residue name, and residue number. If the option <B>-resnumonly</B>
 
residue name, and residue number. If the option <B>-resnumonly</B>
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when fitting structures with different sequences based on the backbone
 
when fitting structures with different sequences based on the backbone
 
atoms.<BR>
 
atoms.<BR>
 +
 
The option <B>-nowarn</B> is available for suppressing warnings about
 
The option <B>-nowarn</B> is available for suppressing warnings about
 
missing atoms.
 
missing atoms.
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; -help : usage information
 
; -help : usage information
 
+
; -l min&#58;max[=...] : fit using only atoms in given residue range
 +
; -x min&#58;max[=...] : fit using atoms that are not in given residue range
 +
; -sel cab|ca|cb|p|heavy... : specify which atoms are used for fitting
 +
; -nowarn : do not print warnings about missing or mismatched atoms
 +
; -resnumonly : match residues by residue number only instead of residue name and number
 +
; -s min&#58;max[=...] min&#58;max[=...] : fit different parts of a given structure separately to the given reference
 +
; -align fasta : provide sequence alignment to fit two structures with different sequences
  
 
== Examples ==
 
== Examples ==

Latest revision as of 22:40, 13 September 2010

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]
Show source


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. Note, the -l and -x options appear to work with the syntax of the Selection commands, and thus complex selections can be used to superpose via least-squares fit different atoms in differing chains. 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
-l min:max[=...] 
fit using only atoms in given residue range
-x min:max[=...] 
fit using atoms that are not in given residue range
-sel cab|ca|cb|p|heavy... 
specify which atoms are used for fitting
-nowarn 
do not print warnings about missing or mismatched atoms
-resnumonly 
match residues by residue number only instead of residue name and number
-s min:max[=...] min:max[=...] 
fit different parts of a given structure separately to the given reference
-align fasta 
provide sequence alignment to fit two structures with different sequences

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

...