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 <[email protected]>