[cctbxbb] reflection conditions for non-standard settings

[David Waterman]

Thanks for the suggestions. The application is for selection of rows in a
table of reflections where particular reflections are systematically absent.
The catch is that this is in a language (R) that is "vector oriented" and is
much more efficient at applying a single subset condition (derived from the
ITvA reflection condition) over the entire table in a vectorised operation
rather than explicitly looping through and checking each hkl. Variety is the
spice of life, etc.

So, I would need absence conditions for every setting. I have all the
standard conditions already. As was suggested, it does seem like it would be
a manageable amount of work to use the change of basis operations in
syminfo.lib to figure out the mapping between h, k and l in the standard
setting with h, k, and l in other settings and adapt the absence conditions
accordingly.

I had a quick look through absences.py, but as I'm just starting out with
cctbx I need a strong coffee and a bit more time to achieve familiarity.

Best wishes

-- David


On 4 June 2011 21:12, Petrus Zwart <phzwart at lbl.gov> wrote:

> This could be of use perhaps:
>
> http://cci.lbl.gov/cctbx_sources/mmtbx/scaling/absences.py
>
> I use it in xtriage for spacegroup determination. I'm not sure what your
> application is you have in mind, it might nit be suitable of course.
>
> Hth
> P
>
>
>
> Verstuurd vanaf mijn iPhone
>
> Op Jun 4, 2011 om 13:04 heeft "Ralf W. Grosse-Kunstleve" <rwgk at yahoo.com>
> het volgende geschreven:
>
> Hi David,
>
> cctbx does not include lists of reflection conditions as you find them in
> the International Tables.
>
> It is very easy and fast to derive the reflection condition for a given hkl
> directly from the symmetry operations. See the code near the top of
> cctbx/sgtbx/miller.cpp. This is what we use for all practical applications.
> For example:
>
>   from cctbx import sgtbx
>   sg = sgtbx.space_group_info("19").group()
>   print sg.is_sys_absent((1,2,3))
>   print sg.is_sys_absent((0,0,3))
>
>  I have C code given to me by Maxim Larine and Slava Klimkovich in 1997
> which computes the conditions, but it involves inefficient grid searches.
>
> I think a good solution would be to tabulate the conditions for the 230
> reference settings and figure out the transformation law to obtain the
> conditions for arbitrary settings via a change of basis. But I yet have
> to find a practical motivation for spending the effort implementing this.
>
> If you find that Phil has a solution, it would be nice to move it into
> cctbx.
>
> Ralf
>
> ------------------------------
> *From:* David Waterman <dgwaterman at gmail.com>
> *To:* <cctbxbb at phenix-online.org>cctbxbb at phenix-online.org
> *Sent:* Saturday, June 4, 2011 3:28 AM
> *Subject:* [cctbxbb] reflection conditions for non-standard settings
>
> Hi,
>
> I'm new to cctbx and to this mailing list, so please let me first apologise
> if the answer to this question should be obvious, or lies in the archive.
>
> I want a list of general reflection conditions for all space groups and
> settings listed in the CCP4 file syminfo.lib. At first I thought I could get
> this information from the online version of ITC vol A, but I soon realised
> that only certain standard settings are included. To avoid deriving them all
> by hand from the symop and cenop lines, I wonder if there is a foolproof way
> I can get this information from cctbx, but I don't know where to begin.
> Perhaps something in sgtbx?
>
> Many thanks
>
> -- David
>
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