[phenixbb] phenix.refine problems with my pdb
Joao Renato Carvalho Muniz
jrcmuniz at gmail.com
Thu Mar 15 06:26:28 PDT 2007
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?
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
> phenixbb mailing list
> phenixbb at phenix-online.org
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