[cctbxbb] Bug in structure.expand_to_p1?

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Tue Jun 21 09:49:36 PDT 2011

Hi Marten,
Your idea is fine. Please go ahead.

2011/6/21 Jan Marten Simons <marten at xtal.rwth-aachen.de>:
> Am Montag 20 Juni 2011 19:16:16 schrieb Nat Echols:
>> 2011/6/20 Jan Marten Simons <marten at xtal.rwth-aachen.de>
>> > It bothers me that there are x,y,z not in [0, 1[. Shouldn't the newly
>> > expanded
>> > cell only contain atoms within the unit cell?
>> I can't speak for Ralf, but FYI, this is exactly the opposite of what
>> macromolecular crystallographers would expect - for us, the current
>> behavior makes the most sense.
> I see your point with mmcrystals where molecules might span the cell boundary
> quite often. But for inorganic crystallogrphy one usually just wants to have
> all atoms inside the asymmetric unit (even after expansion to P1 where the
> asymmetric unit is the unit cell).
> Would any of you object if I add an optional parameter to expand_to_p1 to have
> all atoms inside the unit cell (defaulting to false of course)? I suppose the
> desired result can be achieved by calling
> .sites_mod_positive().sites_mod_short() on the result. The optional parameter
> would just be additional comfort and a little warning that by default
> expand_to_p1 will return scatterers with possible negative or bigger than 1
> fractional coordinates.
> With regards,
>  Dipl. Phys.
>  Jan M. Simons
> Institute of Crystallography
> RWTH Aachen University
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