---
name: "findwaters"
section: "1"
platform: "linux"
package: "coot"
version: "1.1.15+dfsg-1+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/findwaters"
---

# findwaters(1)

locate water sites in an electron density map

## 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)](/coot/1.md), [**density-score-by-residue**(1)](/density-score-by-residue/1.md), [**findligand**(1)](/findligand/1.md), [**fix-nomenclature-errors**(1)](/fix-nomenclature-errors/1.md), [**lidia**(1)](/lidia/1.md).\

## AUTHOR

**findwaters** is written by Paul Emsley.

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