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Hi Alex,<br>
<br>
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.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 2/17/16 11:50, Alejandro Virrueta
wrote:<br>
</div>
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<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>
<br>
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<br>
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