[CCP14 Home: (Frames | No Frames)]
CCP14 Mirrors: [UK] | [CA] | [US] | [AU]

(This Webpage Page in No Frames Mode)


Tutorials and Examples

Louis Farrugia's WinGX Single Crystal Suite

GUI based Transforming a Cell, HKL data and Atom Positions with WinGX

The CCP14 Homepage is at http://www.ccp14.ac.uk

[Tutorials page] | [WinGX Tutorial Index]

[Note from Louis Farrugia: "Are Transformations really that simple with WinGX?"

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

To transform the Cell, go into Model Transform to bring up the following options box.

Transformation Option box

Apply the transformation you wish to make. In this case abc-> cab.
You can press the TEST to check that the transformation of the cell is the one intended (c is the unique axis) before continuing.

Transformation Option box

Then select the space group you want to transform to, in this case A 1 2 2/m

Transformation Option box

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.

Transformation output

The resulting A 1 1 2/m based shelx INS file has the following transformed co-ordinates, cell and symmetry operators (and the the A 1 1 2/m based HKL file)

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
SYMM     -X ,    -Y ,     Z

Note from Louis Farrugia: "Are Transformations really that simple with WinGX?"

From: louis@chem.gla.ac.uk
To: Lachlan Cranswick l.m.d.cranswick@dl.ac.uk
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

[Tutorials page] | [WinGX Tutorial Index]

[CCP14 Home: (Frames | No Frames)]
CCP14 Mirrors: [UK] | [CA] | [US] | [AU]

(This Webpage Page in No Frames Mode)

If you have any queries or comments, please feel free to contact the CCP14