Ralf Yes, the whitespace was missing from the continuation line. As for distance-based bond determination, yes, that is exactly what I would like to do. I am looking at the show_distances() method inside the structure class. The usage of some of the optional parameters is a bit unclear to me. Could you provide an example of how the show_distances() method should be used? Thanks, Andrew -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Ralf W. Grosse-Kunstleve Sent: Thursday, January 10, 2008 12:03 PM To: [email protected] Subject: Re: [phenixbb] iotbx.shelx.from_ins
The reason that I was receiving the exception was that the continuation lines in the .RES file were incorrect.
OK. It would still be good for us to produce a clear error message. Was it just the whitespace missing in the continuation line?
As a side question, how would I get bond data from the structure returned from the from_ins function so as to be able to render the bonds between the atoms?
Would distance-based determination work for you? (As opposed to user-defined bonds.) Look for structure.show_distances() in cctbx/cctbx/xray/structure.py to get a start. Let me know if you need more help. It is a fairly complex procedure because of comprehensive handling of special positions. The core data strucutre behind the distance calculations is the pair_asu_table, which is closely tied to the asu_mappings class. Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb