Before any reader goes into a rant about the dangers of indexing based on such a small number of peaks; in some areas of research, this can be all you get. Unfortunately, the real data could not be used (has not been published yet) so the following uses some quickly obtained "contrived" peak profile data.
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.
This run through will use the peak list file obtained from high pressure experiments -
using XFIT to profile the peaks. XFIT is not that easy to use by default and
thus there is a tutorial at the CCP14 site.
There is also an XFIT tutorial on saving an XFIT peak result file in a Crysfire, Chekcell, etc export happy format
|Note: The following is just a single example of using CRYSFIRE. There are other methods of interacting with the program and doing the following.|
Indexing strategy of indexing with less than 20 peaks
Note: The following is just a single example of using CRYSFIRE. There are other methods of interacting with the program and doing the following.
Refer to the following tutorials on how to load peak positions into Crysfire;
A comment from Robin Shirley about filenames and descriptive text
From: Robin Shirley [R.Shirley@surrey.ac.uk] Organization: Psychology Dept, Surrey Univ. U.K. To: Lachlan Cranswick [email@example.com] Date: Mon, 22 Jul 2002 18:43:55 GMT Incidentally, in this context, could you please emphasise in your tutorials the importance of spending the few seconds that it takes to give each new dataset a well-chosen name and some helpful brief descriptive text in its description field, seeing that whatever is used there will remain the default throughout the rest of the analysis? Careful dataset naming really is important for keeping track of progress in any serious study that can involve several dataset variants, and such distinctive names have been assumed throughout Crysfire as the basis of its data organisation. Users shouldn't rely just on having kept each problem separate within its own data directory (folder). While that's important, it's *not* sufficient, because (a) doing that only identifies the directory, not the files within it, and (b) as the study progresses, it's likely that several datasets and dataset variants will be required, for example after recalibration, applying estimated Z2theta or specimen-displacement corrections, rescaling, etc. These will all need to be kept in the same directory so that, for example, their trial cells can easily be loaded and examined (LC, M1, etc), but if they aren't given different names (and preferably also different description fields - see below) then complete confusion will quickly result. Since the description field gets appended to every summary-file solution line, an important opportunity is lost if its contents can't act as an aide memoire of the characteristics of the particular dataset or dataset variant that was used for that trial solution. This becomes particularly relevant when datasets are merged and/or rescaling/unscaling is used, as was discussed above and as is increasingly likely to happen in response to the new volume estimates and rescaling prompts in CF2002. I'm already regretting that I short-sightedly left it far too easy in WF2crys and XF2crys for users to default to an undistinctive and meaningless dataset name like Crys.cdt (I've noticed that you are yourself a frequent offender in this regard!), and I may well look at ways to prevent this in the next revisions of those programs. As things stand, it's too easy for a moment's impatience on the part of the user at this basic choice point to handicap all subsequent work on that sample with a basically null name (and description) - I really should have had the foresight to protect users from this pitfall. (A bit of a rant, perhaps, but I do think the point needs making.) With best wishes Robin
From (in this case) the C:\crysfire\examples\7peak directory, run Crysfire.
Then type IM to go into the IMport area; followed by XF to import the XFIT file, type in the filename (default is xfit.txt), then answer the questions such as the value of the wavelength. When prompted, load the newly created Crysfire CDT file using the LO command. Crysfire will warn that with less than 20 peaks, not all the indexing programs will run - though it does advise the EP Pattern Extension command is available.
Be wary that if you are low on DOS RAM - the last few peaks may not get imported into the CDT file. Check this out after running the importing routine.
Indexing on the 7 peaks
Run all the relevant Crysfire based indexing programs as per the Crysfire Basic tutorial (via the IN (Indexing) command)
Due to there only being 15 peaks, only the following programs can be run.
Crysfire will explain this in the IN Indexing menu option, as showing in the following screen dump.
Crysfire summary file on the 7 peaks. - Taup, Dicvol - high symmetry, Treor, Dicvol - low symmetry
Performing Pattern Extension in Crysfire
To extend the pattern to 20 peaks, run the EP (Extend Pattern) command.
Crysfire recommends and prompts the saving of the modified data to a CDT file with EP to the filename (e.g., in this case, crys1ep.CDT).
CDT file BEFORE pattern extension
"CRYS v9.30c dataset, saved as crys1 by XF2CRYS v1.7b on 27Jul02 at 22:04:33" "" "To use with CRYS versions prior to v9.30, delete these first 3 lines" "crys1",7,0,0,0,0,1.54056,0,1,"P" 0,0,0,0,28.3464,4837.0742 0,0,0,0,47.1625,1766.6555 0,0,0,0,55.976,1277.9629 0,0,0,0,68.95010000000001,297.0331 0,0,0,0,76.22929999999999,627.768 0,0,0,0,87.8663,497.7363 0,0,0,0,94.7882,0
CDT file AFTER pattern extension
"Crysfire 9.45.15 dataset, saved as crys1EP on 27Jul02 at 22:19:52" ",EP20" "To use with CRYS versions prior to v9.30, delete these first 3 lines" "crys1EP",20,0,0,0.0000000000000,0,1.00000000,0.0000000000000,0,"P" 1010.4546292934787, 0, 0, 0, 18.2905470936284,4837.07400000 2697.3010526759795, 0, 0, 0, 30.1018819434549,1766.65500000 3711.7534113792990, 0, 0, 0, 35.4707042567356,1277.96200000 5400.1797717844256, 0, 0, 0, 43.1143594758309,297.03300000 6421.0603898682257, 0, 0, 0, 47.2385889019994,627.76000000 8113.2459397443172, 0, 0, 0, 53.5345671495925,497.73600000 9130.4188302460898, 0, 0, 0, 57.0792110165363, 0 4041.8185171739146, 0, 0, 0, 37.0691050114265, 0 9094.0916636413076, 0, 0, 0, 56.9551462930426, 0 10789.2042107039178, 0, 0, 0, 62.5780553697409, 0 14847.0136455171960, 0, 0, 0, 75.0693734135128, 0 16167.2740686956586, 0, 0, 0, 78.9517079662539, 0 21600.7190871377024, 0, 0, 0, 94.5906323740015, 0 24275.7094740838147, 0, 0, 0,102.3442834511437, 0 25261.3657323369662, 0, 0, 0,105.2522015900592, 0 25684.2415594729027, 0, 0, 0,106.5117564386302, 0 32452.9837589772687, 0, 0, 0,128.5098513240440, 0 33405.7807024136928, 0, 0, 0,132.0893765605785, 0 36376.3666545652304, 0, 0, 0,144.9666786397511, 0 36521.6753209843591, 0, 0, 0,145.6985228337022, 0
Indexing on the 20 Pattern Extended peaks
Now run all the Crysfire based indexing programs as per the Crysfire Basic tutorial (via the IN (Indexing) command)
As per the example shown in the Crysfire Basic tutorial, it would be good to now run MMap and evaluate the trial solutions for both the raw data, and extended data using Chekcell to obtain the best cell and spacegroup. However: