[cctbxbb] Bug in cif file parser? (was: How to load a structure from a .cif file?)

Jan Marten Simons marten at xtal.rwth-aachen.de
Tue Dec 14 04:28:02 PST 2010

Am Samstag 11 Dezember 2010 14:16:37 schrieb Richard Gildea:
> Hi Jan,
> This should be fairly straightforward:
> from cctbx import xray
> xs = xray.structure.from_cif(file_path="my.cif")
> This will return you an instance of xray.structure. If you have more than
> one data block in your cif, you can specify which structure you want to
> extract using the block_heading keyword (by default it just returns the
> first structure it can successfully extract from the cif). There is also
> similar functionality that can be used to extract miller arrays from fcf or
> hkl formats.

Ok, my code is now like this:
file_name = "./xtal_data/9008806.cif"
#file_name = "./xtal_data/9010017.cif"
structure = xray.structure.from_cif(file_path=file_name)

> Please let me know if you have any further questions about this.

I've tested it with 2 cif files chosen at will from COD:

* http://www.crystallography.net/cif/9/9010017.cif
works like expected.

* http://www.crystallography.net/cif/9/9008806.cif
gives an error:

./xtal_data/9008806.cif(43)  : error 3 : ()* loopback of 150:8: ( ( WHITESPACE 
)+ ( data_items | save_frame ) )*, at offset 0
    near _
     : cannot match to any predicted input...

Traceback (most recent call last):
  File "Check_F_calc.py2", line 12, in <module>
    structure = xray.structure.from_cif(file_path=file_name)
  File "/home/marten/Arbeit/cctbx-
latest/cctbx_sources/cctbx/xray/structure.py", line 1366, in from_cif
AttributeError: 'NoneType' object has no attribute 'structure'

This either suggests an error in the .cif file or in the cif file parser of 
cctbx. From taking a look at both cif files I'm not sure why it breaks on the 
2nd one.

With regards,

 Jan Simons

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