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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