RLatt 3.0

[eldorado]

Does anybody know about twinning problem resolving with new RLatt 3.0?
Who can supply a valid copy of subroutine for me?

[johnewarren]

Hi eldorado

Sorry for not responding sooner, I hoped that someone from Bruker would post but it would appear not.

To the best of my knowledge RLatt in its current python based form and its earlier java incarnation is propriety software purchased from Bruker-AXS.

I don't think you can get RLatt without buying it from Bruker and perhaps only then if you own Bruker hardware.

Hopefully someone will post to the contrary.

[eldorado]

Hmm..., looks convincingly... I have thought it not so problematically.
I would be gratefull if someone creates temporary remote user account for data processing with RLATT (I think its practically possible) and, in this way, all Bruker AXS agreements would be abided.

[ALThompson]

For this to work I would imagine you would have to find someone running the Bruker software on a Linux machine and sadly, there are very few of those as fas as I know.

A.

[johnewarren]

Hmmm, indeed looks like I am one but a few of them and my machine is heavily guarded by STFC and DL firewalls of death.

[ALThompson]

But Swindon Town Football Club have a notoriously bad record for defence - I shouldn't be too concerned by any wall they put up...



A.

[jchrist]

Does anybody know about twinning problem resolving with new RLatt 3.0?
Who can supply a valid copy of subroutine for me?

What format is your data? Depending on the format of the original data there are freeware and even open source programs available to do twin indexing.
(judging from the discussion it is not a Bruker format).

/Jeppe

[johnewarren]

I think I am allowed to provide a tool given out by Bruker that can convert bruker frames to other formats as long as it is for academic use, if that helps.

[eldorado]

Does anybody know about twinning problem resolving with new RLatt 3.0?
Who can supply a valid copy of subroutine for me?

What format is your data? Depending on the format of the original data there are freeware and even open source programs available to do twin indexing.
(judging from the discussion it is not a Bruker format).

/Jeppe

Several datasets integrated in P1 to retain all possible reflections ( *.p4p + *.hkl or *.raw). The problem seems like "Rubik Cube": unable to define correct cell - both single crystal and powder examing showed high reflection overlapping. ABSEN, XPREP, TWINROTMAT, ROTAX... All 230 groups are possible!!! (Arh!!!) I suppose "manual" search of cell and twin components with RLatt is something promising.

[pmueller]

Do you think it could be a non-merohedral twin? If so, have you tried cell_now?

Cheers,

Peter

[eldorado]

Looks like a merohedral twinning. xprep data reduction procedure is given below:
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ XPREP - Reciprocal space exploration - Version 2003/1 for Windows +
+ Copyright(C) 2003 Bruker-AXS All Rights Reserved +
+ z81sh started at 13:07:58 on 10-Mar-2009 +
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


Original cell in Angstroms and degrees:

13.762 13.762 13.762 90.00 90.00 90.00

169514 Reflections read from file z81sh.hkl; mean (I/sigma) = 9.18


Lattice exceptions: P A B C I F Obv Rev All

N (total) = 0 84623 84555 84350 63149 126764 113234 113004 169514
N (int>3sigma) = 0 28154 28245 28261 622 42330 37854 37801 56423
Mean intensity = 0.0 3.4 3.3 3.3 0.2 3.3 3.2 3.2 3.2
Mean int/sigma = 0.0 9.7 9.6 9.5 0.6 9.6 9.3 9.3 9.2

Lattice type: I chosen Volume: 2606.19

-------------------------------------------------------------------------------

DETERMINATION OF REDUCED (NIGGLI) CELL

Transformation from original cell (HKLF-matrix):
0.5000 0.5000 -0.5000 -0.5000 0.5000 0.5000 0.5000 -0.5000 0.5000

Unitcell: 11.918 11.918 11.918 109.47 109.47 109.47

Niggli form: a.a = 142.04 b.b = 142.04 c.c = 142.04
b.c = -47.35 a.c = -47.35 a.b = -47.35

-------------------------------------------------------------------------------

Search for higher metric symmetry
Identical indices and Friedel opposites combined before calculating R(sym)
------------------------------------------------------------------------------
Option A: FOM = 0.000 deg. CUBIC I-lattice R(sym) = 0.095 [ 19680]
Cell: 13.762 13.762 13.762 90.00 90.00 90.00 Volume: 2606.19
Matrix: 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000

Option A selected

-------------------------------------------------------------------------------

SPACE GROUP DETERMINATION


Lattice exceptions: P A B C I F Obv Rev All

N (total) = 0 84623 84555 84350 63149 126764 113234 113004 169514
N (int>3sigma) = 0 28154 28245 28261 622 42330 37854 37801 56423
Mean intensity = 0.0 3.4 3.3 3.3 0.2 3.3 3.2 3.2 3.2
Mean int/sigma = 0.0 9.7 9.6 9.5 0.6 9.6 9.3 9.3 9.2


Crystal system C and Lattice type I selected

Mean |E*E-1| = 0.580 [expected .968 centrosym and .736 non-centrosym]

Chiral flag NOT set



Systematic absence exceptions:

41/43 a-- --d

N 103 4799 6524
N I>3s 20 3157 3961
<I> 0.5 3.3 3.4
<I/s> 7.2 14.5 15.2


Identical indices and Friedel opposites combined before calculating R(sym)

Option Space Group No. Type Axes CSD R(sym) N(eq) Syst. Abs. CFOM

[A] Im-3 #204 centro 1 4 0.095 19680 0.0 / 7.2 36.43
[B] I23 #197 chiral 1 4 0.095 19680 0.0 / 7.2 23.82
[C] I2(1)3 #199 chiral 1 1 0.095 19680 0.0 / 7.2 53.82
[D] Im-3m #229 centro 1 20 0.096 20572 0.0 / 7.2 21.23
[E] I-43m #217 non-cen 1 19 0.096 20572 0.0 / 7.2 8.85
[F] I432 #211 chiral 1 0 0.096 20572 0.0 / 7.2 103.85

Option [E] chosen

-------------------------------------------------------------------------------

As for my poor experience, |E*E-1| criteria gives reasons for twin (merohedral) suggestion, however, I'm doubting that cell settings correspond to "real" cell. Could anybody advise well procedure to find it?

[Rudi]

About a year later?

Original cell in Angstroms and degrees:

13.762 13.762 13.762 90.00 90.00 90.00

It seems that the cell refinement and data reduction were carried out with symmetry constraints for the cubic system.

I would suggest that you go back to the data reduction program and reindex the data and refine the cell and process the data without any symmetry constraints, outlier rejections and absorption corrections. Then reinspect the data and try to solve the structure.

[eldorado]

Hi, Rudi!

Thanks for your answer. I have the several sets of intergration results as well with symmetry constraints (-4m3, m-3 + absorption corections) and without it (P1 + direction cosines). However, given above example of xprep run is typical for all experiments. Cubic lattice is proposed as more suitable, but I am getting smashed after several hours trying to solve it.

[Rudi]

Did you try to solve only with cubic symmetry?

I think you should try to solve with lower symmetry, may be even in P1.Try different methods (if possible) and programs. These are common strategies. But to be honest if direct methods fail mostly somthing is wrong with the unit cell.

But of course it's difficult to evaluate wihout to see the data.

[Rudi]

by the way: Did you confirm the sum formula or at least the elements present by a chemical analysis?

And did you search the ICSD for possible isostructural compounds?