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
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