findwaters1

Usage

Overview

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