Hi Alex, you need to supply a CIF file with restraints definitions for unknown (to Phenix) part of the PDB file. eLBOW or ReadySet are the tools to use for this. See documentation for more details. Pavel On 2/17/16 11:50, Alejandro Virrueta wrote:

Hello,

How can I successfully execute the following command:

phenix.refine pdb_1jbe_res_ALA_resID_101_del.pdb 1jbe.mtz main.number_of_macro_cycles=5 output.write_eff_file=False output.write_geo_file=False output.write_def_file=False refinement.input.xray_data.r_free_flags.generate=True --overwrite

Currently, I am getting the following error:

Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 8 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary.

I'm not a crystallographer, so I don't fully understand the error. I'm simply trying to automate this procedure for many PDBs, and this particular error has come up quite a few times. Can I resolve this issue by providing additional files or command line flags? Other files I have available are 1jbe.cif and 1jbe-sf.cif. File 'pdb_1jbe_res_ALA_resID_101_del.pdb' is similar to 1jbe.pdb, except that the occupancies for ALA 101 are set to 0.

Thanks, Alex

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