Man page - findligand(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

FINDLIGAND

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLE
SEE ALSO
AUTHOR

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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), 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>

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