findligand is a stand-alone command-line program that uses the libraries of Coot.
findligand provides a number of command line arguments for increased flexibility:
--pdbin pdb-in-filename
where pdb-in-filename is the protein (typically)
--hklin mtz-filename
--f f_col_label
--phi phi_col_label
--clusters nclust
where nclust is the number of density clusters (potential ligand sites) to search for
--sigma sigma-level
where sigma-level the density level (in sigma) above which the map is searched for ligands
--fit-fraction frac
where frac is the minimum fraction of atoms in density allowed after fit [default 0.75]
--flexible
means use torsional conformation ligand search
--samples nsamples
nsamples is the number of flexible conformation samples [default 30]
--dictionary cif-dictionary-name
the file containing the CIF ligand dictionary description
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.