<div dir="ltr"><div class="gmail_quote"><div dir="ltr"><div class="gmail_quote"><div dir="ltr"><div>Hello,</div><div><br></div><div>How can I successfully execute the following command:</div><span class="">
<div><br></div><div>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<br></div><div><br></div><div>Currently, I am getting the following error:</div><div><br></div>Sorry: Fatal problems interpreting model file:<br> Number of atoms with unknown nonbonded energy type symbols: 8<br> Please edit the model file to resolve the problems and/or supply a<br> CIF file with matching restraint definitions, along with<br> apply_cif_modification and apply_cif_link parameter definitions<br> if necessary.<div><br></div>I'm not a crystallographer, so I don't fully understand the error.<div>I'm simply trying to automate this procedure for many PDBs, and this particular error has come up quite a few times.<br>Can I resolve this issue by providing additional files or command line flags?</div></span><div>Other files I have available are 1jbe.cif and 1jbe-sf.cif.</div><div>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.<br><div><br></div><div>Thanks,<br>Alex</div></div></div></div></div></div></div>