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Lines starting with # are comments in cif files. Tools like PyMOL take advantage of this in their cif output, so we should definitely support it. However, BioJava (tested 4.2.8) currently requires data_ on the first line, and throws an exception:
ERROR org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser - This does not look like a valid mmCIF file! The first line should start with 'data_', but is: '# generated by PyMOL 1.8.4.0'
Activity
Solving biojava#704 and adding some tests for biojava#703