<div dir="ltr">Hello all,<div>please consider the scenario of a manuscript that, among other things, describes 20 crystal structures.</div><div>Suppose the journal editor requires a Table 1.</div><div>I now looking for a tool to prepare such table with high accuracy and little effort.</div>
<div>My PDB deposition workflow includes the preparation of mmcif coordinates with pdb_extract. The mmcif file is complete in the sense that after upload to RCSB-ADIT, virtually no additional information is required for deposition.</div>
<div>My intuition was to combine CSV and IOTBX python modules and produce the table via input of a list of mmcif files.</div><div>The current phenix table_1 tool provides some, but not all of that functionality, and I thought once familiar with the python modules, I would quickly write the script.</div>
<div>After confirming that the example at</div><div><a href="http://cctbx.sourceforge.net/iotbx_cif/">http://cctbx.sourceforge.net/iotbx_cif/</a><br></div><div>works with my cctbx installation,</div><div>I attempted to transform that code to read in PDB mmcif coordinates:</div>
<div><code></div><div><div>test_structure = iotbx.cif.reader(</div><div>� file_path="/tmp/1NXC.cif").build_crystal_structures()["1NXC"]</div></div><div></code><br></div><div>which throws an exception:</div>
<div><output></div><div><div>Traceback (most recent call last):</div><div>� File "1NXC.py", line 3, in <module></div><div>� � test_structure = iotbx.cif.reader(file_path="/tmp/1NXC.cif").build_crystal_structures()["1NXC"]</div>
<div>KeyError: '1NXC'</div></div><div></output></div><div>How do I need to write the code so that it returns a python object with access to all the cif items?</div><div>Thank you,</div><div>Wolfram Tempel</div>
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