2010/12/10 Jan Marten Simons <span dir="ltr"><<a href="mailto:marten@xtal.rwth-aachen.de">marten@xtal.rwth-aachen.de</a>></span><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
So from looking at the source I'm pretty confident that cctbx can load a<br>
crystalstructure from a .cif file (like those obtained from COD,<br>
<a href="http://www.crystallography.net/" target="_blank">http://www.crystallography.net/</a>). But so far I've not been able to figure out<br>
how to do this. My experiments included:<br>
<br>
from iotbx import crystal_symmetry_from_any as sym_from_any<br>
from iotbx import file_reader<br>
<br>
file_name = "./xtal_data/9008806.cif"<br>
structure = file_reader.any_file(file_name) #gives an object, but not a structure<br>
# or<br>
structure = sym_from_any.extract_from(file_name) # returns none<br></blockquote><div><br></div><div>The file_reader module is a little misleading - it was written to be used in the Phenix GUI, which is specific to macromolecular crystallography, and thus assumes that any CIF file is specifying geometry restraints. �This may actually be unnecessary for what I'm doing with it, so I'm open to using a more content-neutral API for reading CIFs in iotbx.file_reader. �We should have a reader for actual structures in CIF format, because this is definitely used by the small-molecule parts of CCTBX, but I'm not sure how to use it. �Hopefully one of the other developers can explain.</div>
<div><br></div><div>-Nat</div></div>