NAME

       findligand - find ligands in a protein structure

SYNOPSIS

       findligand [options]

DESCRIPTION

       findligand is a part of the Coot suite of programs.

OPTIONS

       findligand  provides  a  number  of command line arguments for increased flexibility.  The
       options follow the usual GNU command line syntax, with  long  options  starting  with  two
       dashes (-).  A summary of options is included below.

       --pdbin=file
              input PDB file name

       --hklin=file
              MTZ file containing structure factors

       --f=label
              label of MTZ file column containing structure factor amplitudes

       --phi=phi_col_label
              label of MTZ file column containing structure factor phases

       --clusters=nclust
              number of density clusters (potential ligand sites) to search for

       --sigma=level
              density level (in sigma) above which the map is searched for ligands [default 2.0]

       --fit-fraction=frac
              minimum fraction of atoms in density allowed after fit [default 0.75]

       --flexible
              use torsional conformation ligand search

       --samples=nsamples
              the number of flexible conformation samples [default 30]

       --dictionary=file
              name of file containing the CIF ligand dictionary description

       --absolute=level
              Set absolute density level above which to search for ligands

       --script=file
              file name of helper script suitable for use in Coot [default: coot-ligands.scm]

       --pos-x

       --pos-y

       --pos-z

EXAMPLE

       One uses findligand like this:

       $ findligand various-args ligand-pdb-file-name(s)

       i.e.  the example ligand pdb files that you wish to search for are given at the end of the
       command line.

SEE ALSO

       bfactan(1),   coot(1),   density-score-by-residue(1),   findwaters(1),   fix-nomenclature-
       errors(1), lidia(1).

AUTHOR

       findligand is written by Paul Emsley.

       This manual page was written by Morten Kjeldgaard <mok@bioxray.dk>

                                          January, 2011                             FINDLIGAND(1)