[phenixbb] phenix.refine restraint

[Ralf Grosse-Kunstleve]

On Mon, Sep 12, 2011 at 4:50 AM, Simon Kolstoe <s.kolstoe at ucl.ac.uk> wrote:

> 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
>
> ---------------------------------------------------------------
> 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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