<div dir="ltr">Oleg<div><br></div><div>I tried to reproduce the problem but it seems to be your exact files. Can you send them all off list?</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709     Email : NWMoriarty@LBL.gov<br>Fax   : 510-486-5909       Web  : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, May 3, 2019 at 7:22 AM &lt;<a href="mailto:oleg@quantumbioinc.com">oleg@quantumbioinc.com</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">phenix-1.15.2-3472 crashes at the very end of the refinement when multiple CIF&#39;s are given at the command line (see below).<br>
<br>
Please have a look.<br>
<br>
Thanks<br>
<br>
Oleg Borbulevych, Ph.D.<br>
Staff Scientist<br>
QuantumBio, Inc.<br>
2790 W. College Ave.<br>
State College, PA 16801<br>
E-mail: <a href="mailto:oborbulevych@yahoo.com" target="_blank">oborbulevych@yahoo.com</a>, <a href="mailto:oleg@quantumbioinc.com" target="_blank">oleg@quantumbioinc.com</a><br>
Linkedin Professional Profile: <a href="https://www.linkedin.com/in/oleg-borbulevych-b8045422" rel="noreferrer" target="_blank">https://www.linkedin.com/in/oleg-borbulevych-b8045422</a><br>
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============================== Exporting results ==============================<br>
<br>
Writing refined structure to PDB file:<br>
  /home/oleg/TEST2/astex/full_set/astex_oniom_qm5_5_01_19/1N2J/1N2J-H_refine_001.pdb<br>
n_use            =  9639<br>
n_use_u_iso      =  9639<br>
n_use_u_aniso    =  0<br>
n_grad_site      =  0<br>
n_grad_u_iso     =  0<br>
n_grad_u_aniso   =  0<br>
n_grad_occupancy =  0<br>
n_grad_fp        =  0<br>
n_grad_fdp       =  0<br>
total number of scatterers =  9639<br>
<br>
Writing refined structure to CIF file:<br>
  /home/oleg/TEST2/astex/full_set/astex_oniom_qm5_5_01_19/1N2J/1N2J-H_refine_001.cif<br>
Traceback (most recent call last):<br>
  File &quot;/home/oleg/phenix-1.15.2-3472/build/../modules/phenix/phenix/command_line/refine.py&quot;, line 11, in &lt;module&gt;<br>
    command_line.run(command_name=&quot;phenix.refine&quot;, args=sys.argv[1:])<br>
  File &quot;/home/oleg/phenix-1.15.2-3472/modules/phenix/phenix/refinement/command_line.py&quot;, line 162, in run<br>
    refine_object.write_model_cif_file(f_cif_model)<br>
  File &quot;/home/oleg/phenix-1.15.2-3472/modules/phenix/phenix/refinement/driver.py&quot;, line 984, in write_model_cif_file<br>
    additional_blocks=[cif_block])<br>
  File &quot;/home/oleg/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py&quot;, line 964, in model_as_mmcif<br>
    restraints = self.extract_restraints_as_cif_blocks()<br>
  File &quot;/home/oleg/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py&quot;, line 862, in extract_restraints_as_cif_blocks<br>
    if &#39;_chem_comp_plane_atom.comp_id&#39; in loop.keys():<br>
AttributeError: &#39;NoneType&#39; object has no attribute &#39;keys&#39;<br>
<br>
<br>
<br>
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</blockquote></div>