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Hi Aaron,<br>
<br>
could you please send us relevant files and tell the steps that lead
to this crash (we need to reproduce this first before we can
comment)?<br>
<br>
Thanks,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/21/19 04:05, Aaron Oakley wrote:<br>
</div>
<blockquote type="cite"
cite="mid:FEBE285A-3774-404F-B4B0-365E04A83CFE@uow.edu.au">
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Phenix.refine used to be able to handle a ligand covalently bound
to cysteine if an appropriate cif dictionary was provided.
<div class=""><br class="">
</div>
<div class="">This now seems to be broken. Re-running a job that
used to work now fails.</div>
<div class=""><br class="">
</div>
<div class=""><font class="" face="Menlo">KeyError :
'link_CYS-MPS'</font></div>
<div class="">
<div class=""><font class="" face="Menlo">Traceback:</font></div>
<div class=""><font class="" face="Menlo">� File
"/usr/local/phenix-1.15.2-3472/modules/cctbx_project/libtbx/runtime_utils.py",
line 180, in run</font></div>
<div class=""><font class="" face="Menlo">� � return_value =
self.target()</font></div>
<div class=""><font class="" face="Menlo"><br class="">
</font></div>
<div class=""><font class="" face="Menlo">� File
"/usr/local/phenix-1.15.2-3472/modules/cctbx_project/libtbx/runtime_utils.py",
line 75, in __call__</font></div>
<div class=""><font class="" face="Menlo">� � result =
self.run()</font></div>
<div class=""><font class="" face="Menlo"><br class="">
</font></div>
<div class=""><font class="" face="Menlo">� File
"/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/runtime.py",
line 79, in run</font></div>
<div class=""><font class="" face="Menlo">� � refine_object =
self._run(args, callback)</font></div>
<div class=""><font class="" face="Menlo"><br class="">
</font></div>
<div class=""><font class="" face="Menlo">� File
"/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/runtime.py",
line 92, in _run</font></div>
<div class=""><font class="" face="Menlo">� �
call_back_handler=callback)</font></div>
<div class=""><font class="" face="Menlo"><br class="">
</font></div>
<div class=""><font class="" face="Menlo">� File
"/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/command_line.py",
line 106, in run</font></div>
<div class=""><font class="" face="Menlo">� � log=log)</font></div>
<div class=""><font class="" face="Menlo"><br class="">
</font></div>
<div class=""><font class="" face="Menlo">� File
"/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/driver.py",
line 224, in __init__</font></div>
<div class=""><font class="" face="Menlo">� �
run_clash_guard=False)</font></div>
<div class=""><font class="" face="Menlo"><br class="">
</font></div>
<div class=""><font class="" face="Menlo">� File
"/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py",
line 1124, in setup_restraints_manager</font></div>
<div class=""><font class="" face="Menlo">� �
assume_hydrogens_all_missing = not self.has_hd())</font></div>
<div class=""><font class="" face="Menlo"><br class="">
</font></div>
<div class=""><font class="" face="Menlo">� File
"/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py",
line 5509, in geometry_restraints_manager</font></div>
<div class=""><font class="" face="Menlo">� � log=self.log)</font></div>
<div class=""><font class="" face="Menlo"><br class="">
</font></div>
<div class=""><font class="" face="Menlo">� File
"/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py",
line 5154, in construct_geometry_restraints_manager</font></div>
<div class=""><font class="" face="Menlo">� � log=log,</font></div>
<div class=""><font class="" face="Menlo"><br class="">
</font></div>
<div class=""><font class="" face="Menlo">� File
"/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/linking_mixins.py",
line 751, in process_nonbonded_for_links</font></div>
<div class=""><font class="" face="Menlo">� � origin_id =
origin_ids['link_%s' % key]</font></div>
<div class=""><font class="" face="Menlo"><br class="">
</font></div>
<div class=""><font class="" face="Menlo">� File
"/usr/local/phenix-1.15.2-3472/modules/cctbx_project/cctbx/geometry_restraints/linking_class.py",
line 35, in __getitem__</font></div>
<div class=""><font class="" face="Menlo">� � raise e</font></div>
<div class=""><br class="">
</div>
</div>
<br>
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