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

Pavel Afonine pafonine at lbl.gov
Wed Feb 17 12:41:33 PST 2016

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.


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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