Hi Rex,
the command
phenix.superpose_ligands 1.pdb 2.pdb
will do it.
1.pdb and 2.pdb are two PDB files containing the ligands. The output
result will be in overlay_1_pdb_2_pdb.pdb file. The algorithm is based
on graph matching, and it is good for ligand-sized molecules. The atom
labels can be any.
A complete example with input/output files is here:
http://cci.lbl.gov/~afonine/superpose_ligands/
Pavel.
On 9/3/10 4:44 AM, Rex Palmer wrote:
This is not really protein crystallography but we are trying to model
build a ligand into a protein binding site. A similar ligand is
already in place and we want to replace this by initially
superimposing a phenyl ring which is common to both ligands. We
understand that such superpositioning can be done with eg Quanta but
do not have access to this program. Does anyone know of a downloadable
program that we could use instead?
Rex Palmer
Birkbeck College, London