findligand1

Usage

Overview

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

Examples

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.