Dear phenixbb,

I'm trying to constrain a ligand-metal bond that is continuously getting altered by phenix.refine (my data's only 3.2A). I've added the following restraint but it just doesn't seem to be holding the bond length during refinement.

Could you look in the .geo file to see if the bond restraint was created correctly?

Look for the atom labels exactly as they appear in the PDB file, e.g. search for exactly

O1 ROC L 1

If the restraint is in the .geo file but the bond length is not close to the restraint value after refinement there must be some other force pushing the atoms in the wrong direction. I'll need your input files to find out what that is. (I don't need the mtz, but all the rest; send it to me directly.)

Ralf

Is there a different way of telling phenix.refine not to alter this distance? (I'm doing it all on the command line & by editing the .def file)

refinement.geometry_restraints.edits {
bond {
action = *add
atom_selection_1 = name CA and chain X and resname CA and resseq 1
atom_selection_2 = name O1 and chain L and resname ROC and resseq 1
distance_ideal = 2.380000
sigma = 0.100
}
}

Thanks,

Simon

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Dr Simon Kolstoe
Laboratory for Protein Crystallography
Centre for Amyloidosis & Acute Phase Proteins
UCL Medical School
Rowland Hill Street, London NW3 2PF

Tel: 020 7433 2765
http://www.ucl.ac.uk/~rmhasek
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