findligand - find ligands in a protein structure
findligand is a part of the Coot suite of programs.
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
-
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.
bfactan(1), coot(1),
density-score-by-residue(1), findwaters(1),
fix-nomenclature-errors(1), lidia(1).
findligand is written by Paul Emsley.
This manual page was written by Morten Kjeldgaard
<mok@bioxray.dk>