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

# findligand(1)

find ligands in a protein structure

## NAME

findligand - find ligands in a protein structure

## SYNOPSIS

**findligand** \[*options*\]

## DESCRIPTION

**findligand** is a part of the Coot suite of programs.

## OPTIONS

**findligand** provides a number of command line arguments for increased flexibility. The options follow the usual GNU command line syntax, with long options starting with two dashes (-).  A summary of options is included below.

- **--pdbin=***file*

  input PDB file name

- **--hklin=***file*

  MTZ file containing structure factors

- **--f=***label*

  label of MTZ file column containing structure factor amplitudes

- **--phi=***phi\_col\_label*

  label of MTZ file column containing structure factor phases

- **--clusters=***nclust*

  number of density clusters (potential ligand sites) to search for

- **--sigma=***level*

  density level (in sigma) above which the map is searched for ligands \[default 2.0\]

- **--fit-fraction=***frac*

  minimum fraction of atoms in density allowed after fit \[default 0.75\]

- **--flexible**

  use torsional conformation ligand search

- **--samples=***nsamples*

  the number of flexible conformation samples \[default 30\]

- **--dictionary=***file*

  name of file containing the CIF ligand dictionary description

- **--absolute=***level*

  Set absolute density level above which to search for ligands

- **--script=***file*

  file name of helper script suitable for use in Coot \[default: coot-ligands.scm\]

- **--pos-x**

  - **--pos-y**

  - **--pos-z**

  ## EXAMPLE

One uses findligand like this:

```
$ findligand various-args ligand-pdb-file-name(s)
```

i.e. the example ligand pdb files that you wish to search for are given at the end of the command line.

## SEE ALSO

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

## AUTHOR

**findligand** is written by Paul Emsley.

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