Hi Jan,
Thanks for pointing out the problem. There is a fix now on the svn, so you
can either grab the updates off sourceforge, or for now just comment
out (with a #) the offending line (43, beginning _[local]), since this line
is of no use (to the cctbx) anyway.
Cheers,
Richard
2010/12/14 Jan Marten Simons
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) print(str(structure)) structure.show_summary().show_scatterers()
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 data_structure_builder=builders.crystal_structure_builder).structure 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 _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb