CCP14 Homepage - Tutorials and Examples - Example refinement of an Inorganic Phase Using CAOS - CAOS - Single "Crystal Analysis Operating System" for Windows and UNIX

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Tutorials and Examples

CAOS - Single "Crystal Analysis Operating System" for Windows and UNIX

Example refinement of an Inorganic Phase Using CAOS

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

[Tutorials page] | [CAOS Tutorial Index]

This example uses the raw hkl data used to determine the crystal structure of Cs₂TiSi₆O₁₅ as published in I.E. Grey, R.S. Roth, M.L. Balmer, Journal of Solid State Chemistry, 131, 38-42 (1997).

CAOS works based on a scripting language; that can be issued manually from the keyboard, or invoked from files.
The manual, available for download off the web, describes the command set that is available and provides examples on using the program.

Place the data in a subdirectory under the c:\caos directory (in this case c:\caos\csti). Each structure should have it's own subdirectory.
Run CAOS from either the Windows explorer or the CAOS Icon.
This leads to the CAOS Screen that will prompt you to give the directory, and the control filename.
CAOS remembers the most recent structure it worked on so we will be over riding this. When prompted for Current work file directory is:, enter CSTI and when prompted to the binary file, type CSTI. If the binary file does not exist, CAOS will create it. When prompted for the current input and output filename, just press enter.
As the binary file does not exist, CAOS will prompt whether you want to crate it. Enter Y to create the binary file.
At this point, maximise the screen text window so that the command prompt is always visible on the screen (otherwise it might be one line below the screen)

It is possible to see the state of the information inside the CAOS program by displaying LIST numbers which are in the manual.

LIST TYPE NUMBER   IDENTIFYING STRING        TYPE OF DATA

      1                CELL                 cell parameters
      2                SYMMETRY             space group symmetry
      3                FORM                 form scattering factors and cell content
      4                WEIGHTING            weighting parameters
      5                ATOMS                atomic parameters
      6                REFLECTIONS          reflections 
     12                DREFINEMENT          refinement instructions
     14                LIMITS               fourier directives
     15                PEAK                 peaks localised from the map
     18                CONDITIONS           min & max values of the data
     35                                     peaks interpreted by the program.

Before we import the Shelx INS format starting structure and HKL file, we have to tell CAOS the spacegroup of the structure as the Shelx INS file does not have an explicitely stated spacegroup symbol. The spacegroup is C 2/c so in CAOS, type at the # prompt read 2 c 2/c (this information is available via the manual - telling CAOS to put the Spacegroup information into LIST 2 (the first 2 being the LIST number) (an alternative is to use read symm c 2/c as symm is an alias for "LIST 2".
To now import the Shelx INS format starting structure and HKL (FoSQ HKLF 4) file, type at the # prompt read file shelx. Then when prompted for the file name, enter csti (for csti.ins and csti.hkl)
Thus it is possible to see the atom list (LIST 5) by doing one of the following command (subject to conditions on page 4 of the manual) at the # prompt:
- list 5
- or dump 5 (prompts for a filename for the results to be dumped into)
Following is the result of a LIST 5 command. (press enter twice to get the list)

To do some cycles of refinement (by default the imported atoms will refine positions and isotropic thermals), at the # prompt type LSQ then [enter] and if you want to refine to convergence, type ## then [enter].

In the above output, CAOS warns that one atom (O(9)) has an isotropic thermal greater than 11.5. Doing a LIST 5 (or a DUMP FILE to dump all the list contents to a file for evaluation) shows that the O(9) thermal (of 192!) is most likely a spurious atom and should be deleted.

While CAOS has its own structure viewer in-built into the program, it is possible to use external structure viewers that can input CIF files. To output a CIF file, at the # prompt, type CIF and when prompted, enter a file name. Then import the CIF file into a structure viewer such as Loius Farrugia's Ortep-3 or GUI WinSTRUPLO. If CAOS refuses to create a CIF file stating that "no list of type 14 stored"; the way around this is at the # prompt type FOURIER [enter] and ## [enter] and this will populate LIST 14 such that you can now routinely create CIF files.

Importing the outputted CIF file into Ortep-3 graphically shows that o(9) is definitely got a problem.

To delete the offending Oxygen atom:
- At the # prompt type update atoms [enter]
- at the > prompt type delete o(9) [enter]
- at the > prompt type end [enter]

To again to least squares until convergence
- At the # prompt type LSQ [enter]
- at the > prompt type ## [enter]
Remember that you can write out a CIF file at any time and view the structure with Ortep-3 or GUI WinSTRUPLO to keep a graphical track of the structure. If you write to the identical file name, you can do a reload of the structure to view the update.

To now set the heavy Cs and Ti atoms refinding anisotropic:
- At the # prompt type update atoms [enter]
- at the > prompt type aniso cs ti [enter]
- at the > prompt type end [enter]

To again apply least squares until convergence
- At the # prompt type LSQ [enter]
- at the > prompt type ## [enter]
Remember that you can write out a CIF file at any time and view the structure with Ortep-3 or GUI WinSTRUPLO to keep a graphical track of the structure. If you write to the identical file name, you can do a reload of the structure to view the update.

To now set the Si atoms refinding anisotropic:
- At the # prompt type update atoms [enter]
- at the > prompt type aniso si [enter]
- at the > prompt type end [enter]

To again apply least squares until convergence
- At the # prompt type LSQ [enter]
- at the > prompt type ## [enter]
Remember that you can write out a CIF file at any time and view the structure with Ortep-3 or GUI WinSTRUPLO to keep a graphical track of the structure. If you write to the identical file name, you can do a reload of the structure to view the update.

To now set the O atoms refinding anisotropic:
- At the # prompt type update atoms [enter]
- at the > prompt type aniso o [enter]
- at the > prompt type end [enter]

To again apply least squares until convergence
- At the # prompt type LSQ [enter]
- at the > prompt type ## [enter]
Remember that you can write out a CIF file at any time and view the structure with Ortep-3 or GUI WinSTRUPLO to keep a graphical track of the structure. If you write to the identical file name, you can do a reload of the structure to view the update.

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