WinGX allows you to transform a cell, the HKL data and the atomic
positions using a user friendly menu system. In this case,
we will transform a "b" unique (C 2/m) monoclinic
structure to "c" unique (A 1 1 2/m).
The reason for this particular transformation is to make it easier
to see structural relationships with related crystal structures.
This example uses the structure of Li0.92Ti2.88O6 as published in (I.E. Grey, L. M. D. Cranswick, C. Li, L. A. Bursill, and J. L. Peng, "New Phases Formed in the Li-Ti-O System under Reducing Conditions", Journal of Solid State Chemistry, 138, 74-86 (1998)).
The initial co-ordinates are taken from part of the tutorial on using WinGX for Powder Diffraction Extracted Intensities for Structure Solution and Space Group Assignment, which was then passed through the Assembling Residues with WinGX tutorial.
The initial C 2/c based shelx INS file has the
following co-ordinates, cell and symmetry operators (and the the C 2/c based HKL file)
TI1 3 0.00000 0.00000 0.00000 0.25000 0.05811 TI2 3 0.14428 0.50000 0.52050 0.50000 0.03427 O3 2 0.09437 0.00000 0.25602 0.50000 0.05397 O4 2 0.22759 0.00000 0.68766 0.50000 0.13380 O5 2 0.08152 0.50000 0.89990 0.50000 0.00001 CELL 1.54184 14.09600 2.95200 4.89170 90.0000 92.1700 90.0000 ZERR 2 0.00200 0.00200 0.00100 0.0000 0.0500 0.0000 LATT 7 SYMM -X,Y,-Z
To transform the Cell, go into Model Transform to bring up the following options box.
Apply the transformation you wish to make. In this case abc-> cab.
Then select the space group you want to transform to, in this case A 1 2 2/m
Then press OK to continue leading to the following output and a new.ins and new.hkl with transformed, cell, co-ordinates and HKL data.
Ti1 3 0.00000 0.00000 0.00000 0.25000 0.05811 Ti2 3 0.52050 0.14428 0.50000 0.50000 0.03427 O3 2 0.25602 0.09437 0.00000 0.50000 0.05397 O4 2 0.68766 0.22759 0.00000 0.50000 0.13380 O5 2 0.89990 0.08152 0.50000 0.50000 0.00001 CELL 1.54184 4.8917 14.0960 2.9520 90.000 90.000 92.170 ZERR 2 0.0010 0.0020 0.0020 0.000 0.000 0.050 LATT 5 SYMM -X , -Y , Z
Note from Louis Farrugia: "Are Transformations really that simple with WinGX?"
From: email@example.com To: Lachlan Cranswick firstname.lastname@example.org Subject: Re: Some tutorials to vet(?) - Transformation?? Date: Thu, 24 Sep 1998 13:26:45 +0100 >One thing I am wondering if you could check a tutorial on Cell >transformation I have done - but not announced or linked yet at: > http://www.ccp14.ac.uk/tutorial/wingx/tranform/ > >Is it really that simple with WinGX? - it is very unnerving as I am used to >transformation (for me) being a very nasty and painful experience. And most >often with clueless arithmetic and matrix mistakes in it. Yes it is that easy, in fact in my current version it is even easier Say you had collected a structure in the non-standard orthorhombic setting C2cb and wish to transform it to the standard setting. Using the menu option SPGR INFO (which incidentally is new and uses the GETSPEC algorithm) you type in C2cb (spaces in string are no longer necessary!) and you will see that C2cb is space group 41 with setting -cba. Then got to transform menu and click on the -cba button (this dialog box has also changed slightly to reflect the common matrices required for orthorhombic settings - sorry !) and select the standard setting of space group 41 Aba2. Then click OK - thats it!!!! The HKL file (possibly with direction cosines), the INS file CELL ZERR, LATT and SYMM and any OMIT instructions with HKL's on them plus all atoms and adp's are correctly transformed. The orientation matrix file name .OMX is also transformed, so that (most) absorption corrections may be carried out in the new setting. Incidentally it is also now possible to enter alternative settings using the conventions listed in file sginfo.dat (in files directory) so that the space group R-3 can be indicated as R-3:h for hexagonal axes or R-3:r for rhombohedral axes. SPGR INFO wil give the correct LATT and SYMM cards now for both options - remember when you are starting a structure using Initialise Files to give the space group with its setting