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FINDLIGAND(1) General Commands Manual FINDLIGAND(1)

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.

input PDB file name

MTZ file containing structure factors

label of MTZ file column containing structure factor amplitudes

label of MTZ file column containing structure factor phases

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

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

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

use torsional conformation ligand search

the number of flexible conformation samples [default 30]

name of file containing the CIF ligand dictionary description

Set absolute density level above which to search for ligands

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

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), density-score-by-residue(1), findwaters(1), fix-nomenclature-errors(1), lidia(1).

AUTHOR

findligand is written by Paul Emsley.

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

January, 2011