[phenixbb] Fwd: Sorry: Fatal problems interpreting model file

Alejandro Virrueta alejandro.virrueta at yale.edu
Wed Feb 17 11:50:30 PST 2016


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
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.

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