[phenixbb] phenix.refine problems with my pdb

[Joao Renato Carvalho Muniz]

Hi Matthew,

Did you try to run phenix like that (see below)? for instance:

phenix.refine data.hkl model.pdb elbow._you_ligand_name.pdb.001.cif

I mean, supplying the cifs file in the same line?

Regards,

Joao Muniz.

On 3/15/07, Matthew Bowler <mwb at mrc-dunn.cam.ac.uk> wrote:
>
> Dear All,
>         I am trying to run phenix.refine but I keep getting the message:
>
>
> Sorry: Fatal problems interpreting PDB file:
>    Number of atoms with unknown nonbonded energy type symbols: 308
>    Please edit the PDB file to resolve the problems and/or supply a
>    CIF file with matching restraint definitions. Note that
>    elbow.builder is available to create restraint definitions.
>
> I have run my ligands through elbow and used the output .cif but I
> still get the same message.  I can find no info on this problem in
> the manual or the BB, can anyone help?  Thanks in advance, yours, Matt.
>
>
>
>
>
> Matthew Bowler
> MRC Dunn Human Nutrition Unit
> Wellcome Trust / MRC Building
> Hills Road
> Cambridge CB2 2XY
> Tel: 0044 (0) 1223 252826
> Fax: 0044 (0) 1223 252825
>
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