Man page - findwaters(1)

Packages contains this manual

Package:  coot
apt-get install coot

Manuals in package:
• coot-available-comp-id(1)
• coot-fix-nomenclature-errors(1)
• findligand(1)
• coot-mini-rsr(1)
• density-score-by-residue(1)
• fix-nomenclature-errors(1)
• coot-make-shelx-restraints(1)
• findwaters(1)
• coot-bfactan(1)
• lidia(1)
• pyrogen(1)
• coot(1)
• coot-density-score-by-residue(1)
• coot-compare-dictionaries(1)
• coot-identify-protein(1)
• layla(1)
Documentations in package:
• coot

Manual

FINDWATERS

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
AUTHOR

---

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>

---