NAME

       findwaters - locate water sites in an electron density map

SYNOPSIS

       findwaters [options]

DESCRIPTION

       findligand is a part of the Coot suite of programs.

OPTIONS

       These  programs  follow the usual GNU command line syntax, with long options starting with
       two dashes (-).  A summary of options is included below.

       --pdbin=file
              name of file containing protein structure

       --hklin=file
              name of input MTZ file. Column labels for F and PHI must be specified using the --f
              and --phi options. Alternatively, an electron density map can be input using option
              --mapin

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

       --phi=label
              label of MTZ file column containing structure factor phase

       --pdbout=file
              output file for waters

       --sigma=level
              sigma level [default 2.0]

       --flood
              fill everything with water molecules (not just water peaks)

       --flood-atom-radius=radius
              adjust contact distance [default 1.4A]

       --chop remove water molecules below a given sigma-level. In this case, the modified  input
              coordinates will be written to the file specified by --pdbout

       --mapin=file
              name of a CCP4 format map file. This option can be used instead of --hklin, --f and
              --phi

SEE ALSO

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

AUTHOR

       findwaters is written by Paul Emsley.

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

                                          January, 2011                             FINDWATERS(1)