[phenixbb] iotbx.shelx.from_ins

Foelker, Andrew Andrew.Foelker at bruker-axs.com
Thu Jan 10 12:46:12 PST 2008


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?


-----Original Message-----
From: phenixbb-bounces at phenix-online.org
[mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Ralf W.
Sent: Thursday, January 10, 2008 12:03 PM
To: phenixbb at phenix-online.org
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.

phenixbb mailing list
phenixbb at phenix-online.org

More information about the phenixbb mailing list