Obtaining and installing CRYSFIRE
NOTE: A graphical program for MS-Windows that links into CRYSFIRE to help check trial cells and determine spacegroups is the Chekcell software - part of the LMGP suite for Windows by Jean Laugier and Bernard Bochu.
Why Bother Rescaling your Peak list?
A quick summary without mentioning all the details on why you might consider rescaling your peak list data is that the various indexing programs work best in the 500 - 1500 A**3 range. Thus for large or very small cells that are not indexing with the native peak list data, rescaling into this range (by fudging/changing the wavelength) may help index the cell - which can then be unscaled back to real size later.
The new Crysfire 2002 will recommend the use of Rescaling and propose a Rescale value to try.
About this sample
A default run of Crysfire does not solve the cell (which is a 23.92 Angstrom Cubic phase as shown by single crystal CCD analysis).
Appropriately rescaling the data based on Crysfire's recommended rescaling factor (i.e., 0.5 rescaling) does make it solvable by running Crysfire with defaults. This means you can index larger cells that would fail by running in standard / unscaled mode.
Obtaining Peak Positions from the powder diffraction pattern
This run through used peaks obtained on a dataset run on a Philips 1050/1710 standard laboratory diffractometer with a Copper X-ray tube. The peaks were profiled for peak positions using XFIT in fundamental parameters mode providing the peak positions for CuKalpha1 (1.54056 Angstrom). Refer to: Lithium Titanate Fundamental Parameters Peak Profiling Tutorial for how to use XFIT in fundamental parameters mode.
Converting the XFIT file into Crysfire format
Crysfire can import the following peak listing format.
EV = Bruker Socabim EVA format (EVA2Crys: Arie van der Lee) UD = Philips UDI format (UDI2Crys: Robin Shirley) WF = WinFit format (WF2Crys: Robin Shirley) XF = XFit format (XF2Crys: Robin Shirley)
The following assumes you have already created a Crysfire CDT file. Available, example tutorials for importing data into Crysfire are:
Rescaling the peak list data
As per the above screen dump, Crysfire has recommended using a rescaling factor of 0.5. Bear in mind that you might have to play with this and try a variety of rescaling values.
To rescale the data, type RS. Choose a rescale factor that you would expect the cell to then move into the 500 - 1500 A**3 range. At first, try the value recommended by Crysfire (in this case 0.5). Remember this value as you will need it to unscale the data after running all the indexing programs.
After rescaling, Crysfire will prompt to save the file with an R2 appended to the filename so as to distinguish this from the starting CDT file.
Now Run all the relevant Crysfire based indexing programs as per the Crysfire Basic tutorial (via the IN (Indexing) command)
Analyse your scaled results using MMAP
Due to the MMAP defaults not liking very large cells, it is best to run MMAP on the "scaled" data before unscaling the summary file.
Too evalute solutions with MMAP, first make sure you have the relevant CDT file loaded into memory (using the LO command).
Then use the Load Cell command (LC) to load a trial cell into Crysfire's memory. The following screen dump gives the type of prompt you will encounter. (remember that you are using scaled results)
Tell Crysfire you wish to load a cell from the Crysfire summary file on which you will be given the Summary file list.
Select Cell the top FOM solution by typing 1. After accepting this and the various Crysfire information, you will be prompted to Display the 3 principal M1-map sections for this cell. Type Y for Yes.
Following is a MMAP Merit Map from solution 3 (a cubic cell).
Unscaling the results via the MS menu (Modify SUM files)
After you have run all the relevant indexing programs, you now need to unscale the results in the summary file via the MS (Modify SUM files) menu system.
When prompted, give the name of the Crysfire run you wish to unscale (in this example, crys1r2, the output file (try adding us to the filename - crys1), and the scaling factor you used (0.5 for this example). When prompted, you may like to give a file description making it obvious that this data has been scaled, then unscaled.
Analyse your unscaled results
Now try Chekcell
Now might be a good time to pass the results over to the Chekcell graphical indexing helper tool by Jean Laugier and Bernard Bochu and see which might be the best solution.
Make sure you peruse the following tutorial: Using Ton Spek's Lepage within Chekcell to find super-cells and better trial cell solutions
Crysfire Log file
Crysfire creates a Log file of all the major functions you run, opening the relevant *.LOG file will display what you did.