[cctbxbb] iotbx newbie question

[wtempel]

Hello all,
please consider the scenario of a manuscript that, among other things,
describes 20 crystal structures.
Suppose the journal editor requires a Table 1.
I now looking for a tool to prepare such table with high accuracy and
little effort.
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.
My intuition was to combine CSV and IOTBX python modules and produce the
table via input of a list of mmcif files.
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.
After confirming that the example at
http://cctbx.sourceforge.net/iotbx_cif/
works with my cctbx installation,
I attempted to transform that code to read in PDB mmcif coordinates:
<code>
test_structure = iotbx.cif.reader(
  file_path="/tmp/1NXC.cif").build_crystal_structures()["1NXC"]
</code>
which throws an exception:
<output>
Traceback (most recent call last):
  File "1NXC.py", line 3, in <module>
    test_structure =
iotbx.cif.reader(file_path="/tmp/1NXC.cif").build_crystal_structures()["1NXC"]
KeyError: '1NXC'
</output>
How do I need to write the code so that it returns a python object with
access to all the cif items?
Thank you,
Wolfram Tempel
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