[sdpd] Re: Time for an indexation Round Robin ?

[L.M.D.Cranswick... @dl.ac.uk (L. Cranswick)]

One of the potential advantages of CRYSFIRE relates to
it producing a summary file with one result per line.

This in theory means a Le Bail extraction program could
be made to automatically crunch through the CRYSFIRE
results to give a FOM based on parameters such 
as Rwp, etc - and maybe be used to automatically
suggest possible spacegroups as well once "decent"
cells have been suggested.

Also, if CRYSFIRE has found no single correct solution -
but may have all the elements of a correct solution in
the summary list - a mixing algorithm (genetic - whatever) 
could then be used to possibly obtain the correct result
 from the CRYSFIRE list.

Has this been attempted to try and sort things out?

------

Just a suggestion from me but I think this is where
indexing software of the future has to go - passing
results to automatic Le Bail fitting and possible
optimisation/mixing of results to get a list of
possible good cells based on a global fit "up to
decently high angle".

The present state of Powder Indexing would possibly be
analogous to only being able to perform single crystal
structure solution with manual interpretation of 
Patterson maps???

Rather than challenge people's ability to interpret problem 
powder patterns with traditional methods - perhaps it 
is time to see if some new tools might be feasible to
enable powder indexing to routinely go into new areas(?).

I have been interacting with a few CCP14 users on similar
types of problems.  Not sure if there would be agreement
on my conclusions which have been of the sort:
  - try and put more effort into growing good crystals 
    (even micro-crystals that could be run on beamlines 
    such as the Darebsury 9.8 Smart single crystal system)
  - only as a last resort go to powders with these types of
    problems.

This is mainly based on possible large cells, purity of
sample not guaranteed, and that powder indexing tools not 
being up to the job and not getting to the point of 
worrying about "solving" the structure.

Lachlan.

> 
> Dear SDPD Subscribers,
> 
> At Glasgow IUCr XVIII were shown only successful
> studies. Nobody will invite you if you intend to talk
> about failure.
> 
> So, now that the IUCr meeting is closed, let us discuss
> of really difficult cases ;-).
> 
> The SDPD Round Robin last year was certainly presenting
> really difficult examples, however, cells were given.
> 
> It is well known that indexation can be a problem. The
> recent CRYSFIRE suite is undoubtedly a big step toward
> a more simple life for people facing indexation challenges.
> But the example distributed with the package, with a cell
> volume of 200A**3 is rather trivial.
> 
> Now, the question is : can the indexing programs provide
> cells that do not need any confirmation by a subsequent good
> WPPF with cell constraint, and ultimately, a successful
> structure determination ?
> 
> One of the most difficult cases for indexation is when
> two parameters are large and the third is small.
> 
> As a possible preliminary Indexation Round Robin (which
> I will certainly not organize), I have a vicious case to
> submit to your attention.
> 
> The sample is an organometallic compound containing Bi.
> 
> I failed to index quite good data from a Bruker D8 powder
> diffractometer producing minimal FWHM lower than 0.06°
> (2-theta). In fact, there were some clues that more than
> the 20 first reflections could be indexed in a cell with :
>   a = 33.163(3) , b= ?, c = 11.4179(9), alpha=?,
> beta = 90.637(5), and gamma=?
> 
> One year later, I could record a synchrotron pattern (ESRF,
> BM02 beamline). The FWHM is now 0.017° (wavelength
> = 0.79764 A). Maybe the sample was not happy to wait for
> a year since a few weak reflections that were not seen on the
> CuKalpha1+2 pattern are now there. Anyway, I continue to
> fail, but the above parameters were nicely fitting the data.
> 
> Below is a cell parameters refinement by the ERACEL 
> software (data in °theta) :
> 
>   H   K   L TH(OBS)  TH-ZERO  TH(CALC)   DIFF.
> 
>   2   0   0   1.378    1.379    1.378    .000
>   1   0  -1   2.109    2.111    2.110    .001
>   1   0   1   2.122    2.123    2.124   -.001
>   2   0  -1   2.417    2.418    2.418    .000
>   2   0   1   2.441    2.442    2.443   -.001
>   4   0   0   2.757    2.758    2.757    .000
>   3   0  -1   2.861    2.862    2.862    .000
>   3   0   1   2.894    2.895    2.895    .000
>   4   0  -1   3.389    3.391    3.390    .000
>   4   0   1   3.425    3.426    3.426    .000
>   5   0  -1   3.968    3.969    3.968    .001
>   1   0  -2   4.058    4.059    4.058    .002
>   1   0   2   4.071    4.072    4.073   -.001
>   6   0  -1   4.577    4.579    4.578    .000
>   6   0   1   4.617    4.618    4.619    .000
>   8   0   0   5.520    5.521    5.521    .000
>   6   0  -2   5.732    5.733    5.732    .000
>   8   0  -1   5.853    5.855    5.854    .001
>   1   0  -3   6.046    6.047    6.047    .000
>   1   0   3   6.061    6.062    6.063   -.001
>   3   0   3   6.385    6.386    6.385    .001
>   9   0  -1   6.507    6.508    6.510   -.001
>   9   0   1   6.552    6.554    6.552    .001
>   4   0  -3   6.593    6.594    6.593    .000
>   4   0   3   6.649    6.650    6.649    .001
>   6   0  -3   7.271    7.272    7.272    .000
>   6   0   3   7.346    7.347    7.348   -.001
>   9   0   2   7.440    7.441    7.440    .001
>  11   0  -1   7.840    7.842    7.843   -.001
>   0   0   4   8.031    8.032    8.032    .000
>   2   0   4   8.165    8.166    8.166   -.001
>  12   0   0   8.297    8.298    8.298   -.001
> 
> With such data, you should not use the default values in
> CRYSFIRE. If you tolerate an error of +-0.06°, you will
> obtain nothing (MATH error with TREOR and so on).
> The max error should be +-0.003 or +-0.002, and the
> zeropoint becomes quite decisive at the apparently
> negligible value of 0.002° (2-theta) ...
> 
> OK, I cannot ensure full purity : this is an experimental case,
> you know.
> 
> OK, I obtained figures of merit M20 >200 for at least 300
> different cells ! Which is the good one ? None was really
> satisfying at the stage of WPPF with cell constraint.
> 
> I would be happy to obtain experts point of view.
> 
> If this challenge interests you, the two powder patterns are
> available at :
> 
> http://www.cristal.org/sdpd/indexrr.zip
> 
> Once unzipped, you will obtain two files : biesrf.rit and
> bid8.rit in a format that can be read by DMPLOT or other
> software.
> 
> Good luck !
> 
> 
> Armel Le Bail - Universite du Maine, Laboratoire des Fluorures,
> CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
> http://www.cristal.org/
> 
> 
> 
> 


-- 
Lachlan M. D. Cranswick

Collaborative Computational Project No 14 (CCP14)
    for Single Crystal and Powder Diffraction
Daresbury Laboratory, Warrington, WA4 4AD U.K
Tel: +44-1925-603703  Fax: +44-1925-603124
E-mail: l.cranswick... @dl.ac.uk  Ext: 3703  Room C14
                           http://www.ccp14.ac.uk