findwaters - locate water sites in an electron density map
findligand is a part of the Coot suite of programs.
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
bfactan(1), coot(1),
density-score-by-residue(1), findligand(1),
fix-nomenclature-errors(1), lidia(1).
findwaters is written by Paul Emsley.
This manual page was written by Morten Kjeldgaard
<mok@bioxray.dk>