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