QUATFIT(1OSC)             OSC utilities             QUATFIT(1OSC)



NAME
     quatfit - superimpose atoms of two molecules  given  in  XYZ
     format

SYNOPSIS
     quatfit [ -r _r_e_f-_m_o_l ] [ -f _f_i_t-_m_o_l ] [  -p  _p_a_i_r_s  ]  [  -o
     _f_i_t-_o_u_t ] [ -s _s_t_a_t_f_i_l_e ]

DESCRIPTION
     Program  quatfit  superimposes  specified   atoms   of   two
     molecules  so  they  are  as  close  as possible (in a least
     squares sense). The orientation of the reference molecule is
     kept  fixed,  while  the  fitted  molecule  is  rotated  and
     translated as a rigid body to fulfill the fit. As the  first
     step,  the  reference and fitted molecule are translated, so
     their geometric centers are located at  the  origin  of  the
     coordinate  system. Then the rotation matrix is found by the
     quaternion method and the fitted molecule is  rotated.  Then
     both  molecules are translated to the original center of the
     reference molecule.  If normal modes are present,  they  are
     also  rotated.  The  pairs  of  atoms  to be fitted may have
     assigned weights (the weights represent the onverse  of  the
     atom  pair  distance,  a larger weight will force a thighter
     fit for the pair).  The XYZ format used in the Xmol  program
     (Xmol  is a product of Research Equipment Inc. and Minnesota
     Supercomputer Center, Inc., and is available  via  anonymous
     ftp  at  ftp.msc.edu  in  /pub/xmol) was chosen to represent
     input files for the reference and fitted molecules. The for-
     mat is:
        _l_i_n_e _1: number of atoms
        _l_i_n_e _2: descriptive title
        _l_i_n_e _3, _e_t_c.: Atomic-Symbol X Y Z [ Charge  ]   [  Mode-X
        Mode-Y Mode-Z ]
     If Charge is present, it is in 5th column. If  normal  modes
     are present, they occupy last 3 columns. The file specifying
     atom pairs starts with a line containing the number of  fit-
     ted pairs; the next lines have the format:
        ref-atom fit-atom weight
     where ref-atom is the atom number in the reference molecule,
     fit-atom  is  the corresponding atom in the fitted molecule,
     and weight represents the tightness  of  the  fit  for  this
     pair.  Coordinates  of the superimposed fitted molecule (and
     normal modes, if present) are stored in the _f_i_t-_o_u_t file and
     information about the goodness of fit is stored in the _s_t_a_t_-
     _f_i_l_e which lists distances between fitted  atom  pairs,  the
     RMS,  and dot product of normal modes from the reference and
     the fitted molecule. When any of the I/O options is omitted,
     the  corresponding  file  is  read  from(sent  to)  standard
     input(standard output). The order of files in  the  standard
     input  stream is _r_e_f-_m_o_l, _f_i_t-_m_o_l, _p_a_i_r_s. The order of files
     in the standard output is _f_i_t-_o_u_t, _s_t_a_t_f_i_l_e.




OSC                  Last change: 6 Oct 1992                    1






QUATFIT(1OSC)             OSC utilities             QUATFIT(1OSC)



OPTIONS
     -r _r_e_f-_m_o_l
          The _r_e_f-_m_o_l is a file name of XYZ  file  for  reference
          molecule.  If this option is absent, the information is
          taken from standard input.

     -f _f_i_t-_m_o_l
          The _f_i_t-_m_o_l is an XYZ file with fitted molecule,  i.e.,
          the  molecule  which will be translated and rotated. If
          this option is missing, the information is  taken  from
          the standard input.

     -p _p_a_i_r_s
          The _p_a_i_r_s  is  the  file  with  atom  pairs  and  their
          weights. It starts with the number of fitted pairs as a
          top line and is followed by 3 columns: 1st column is  a
          list of reference molecule atoms, 2nd is a list of fit-
          ted molecule atoms, and 3rd column represents  weights.
          If  -p  _n_o_n_e  is specified, the weights are not read in
          but they are all set to 1.0, and fitted atom pairs  are
          set to consecutive natural numbers, i.e., 1 - 1, 2 - 2,
          3 - 3 ..., up to the number of  atoms  in  the  smaller
          molecule.  You  might want to use -p _n_o_n_e option if you
          compare geometry of the  same  molecule  calculated  by
          different  methods, provided that atom numbering is the
          same.

     -o _f_i_t-_o_u_t
          This  option  specifies  the  output   file   for   the
          transformed  fitted  molecule.   If absent, the file is
          sent to standard output.

     -s _s_t_a_t_f_i_l_e
          The file name for fit statistics.  If  this  option  is
          absent, this information is sent to standard output.

EXAMPLE
     cat rm.xyz fm.xyz | quatfit -o fmmod.xyz -p none > stat.txt
     is equivalent to
     quatfit -r rm.xyz -f fm.xyz -p none -o fmmod.xyz -s stat.txt
     i.e., the reference molecule (kept fixed)  file  is  rm.xyz,
     the  fitted molecule file is fm.xyz, file for translated and
     rotated coordinates of fitted  molecule  is  fmmod.xyz,  and
     stat.txt contains the information about goodness of the fit.
     Atom pairs to be  fitted  and  their  weights  are  assigned
     automatically  by  the  program  in  this  example.   If the
     weights were given explicitly, the command could look like:
     cat  rm.xyz  fm.xyz  pairs.tab  |  quatfit  -o  fmmod.xyz  >
     stat.txt
     which is equivalent to:
     quatfit -r rm.xyz -f fm.xyz -p  pairs.tab  -o  fmmod.xyz  -s
     stat.txt



OSC                  Last change: 6 Oct 1992                    2






QUATFIT(1OSC)             OSC utilities             QUATFIT(1OSC)



     where pairs.tab is the file with fitted pairs and weights.


DIAGNOSTICS
     Most error messages are self-explanatory.

BUGS
     Report bugs to the authors.

AUTHORS
     David Heisterberg, Ohio Supercomputer Center,  1224  Kinnear
     Rd,    Columbus,    OH   43212-1163   e-mail:   djh@ccl.net,
     DJH@OHSTPY.BITNET.  Translation  from  FORTRAN  to   C   and
     input/output  by  Jan Labanowski, Ohio Supercomputer Center,
     1224  Kinnear  Rd,   Columbus,   OH   43212-1163.    e-mail:
     jkl@ccl.net, JKL@OHSTPY.BITNET.

COPYRIGHT
     Program can be copied and distributed freely, provided  that
     the Copyright Notice is not removed from the program source.
     You may acknowledge the use of  this  program  in  published
     material   as:   David  J.  Heisterberg,  1990,  unpublished
     results.
































OSC                  Last change: 6 Oct 1992                    3