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 in the Lithium Titanate Fundamental Parameters Peak Profiling Tutorial. (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))
However, given the sample was degrading/decomposing, it would be best to remove the most dodgy or uncertain of peaks (53.040, 53.277, 66.1785 two-theta).
The two-theta peak positions from the CuK alpha1 (1.54056 Angstrom) radiation follow
12.5831 18.1218 21.7033 22.5138 25.2850 30.6924 31.8536 35.9363 36.2206 36.6577 38.3112 39.4055 40.1827 40.8568 42.0205 43.3337 44.1743 44.4603 45.9253 47.8406 48.8522 51.6880 52.8706 55.1945 57.9764 58.4374 59.1862 61.6021 62.8889 63.7227 65.3320 65.8139 67.6632 68.5040
Also, note that depending on the problem, manual optimisation of each Index input file may be required (i.e., manual insertion, deletion of peaks, change default volume range, restrict to certain cell types, etc.) This run through gives a generic run that (in one case) just happens to work (and it is a real, recently published structure solution).
Note: The following is just a single example of using CRYSFIRE. There are other methods of interacting with the program and doing the following.
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
If running under Windows, go into a DOS Prompt and create/enter the appropriate
subdirectory where you wish to perform the indexing. In this case example, C:\crysfire\cf_exmp\liti.
Type CRYSFIRE, when prompted, agree to the Licence to give the following the menu interface.
Typing Help leads to a help system including the commands that it
recognises (organised in several different ways).
To enter a new set of peak positions, type OB (as per the help
menu), when prompted, input T for peaks listed in 2-theta,
then accept the defaults for the queries the program offers.
Rather than type in the peak positions by hand (introducing errors in the process),
use the Windows Edit copy, edit paste at this point. Just select and Edit, Copy the column of
peak positions and Edit, Paste into CRYSFIRE (Windows allows you to do this for DOS "Windows")
It is best to avoid manual typing in of values as this always introduces errors; edit copy, edit
pasting is a much better option. There is no need to specify the wavelength as CRYSFIRE uses
Copper K Alpha as the default.
Note that on some Windows systems, you may have to wiggle the mouse for the paste to occur. If you do Edit, Paste and nothing happens, try wiggling the mouse. If nothing happens, Edit, Copy the peak positions and try again.
Pressing the Enter Key twice after the last peak position then prompts for further information such as the filename for the dataset.
In this case, we will call the filename crys. This will create a file called crys.cdt
It should be noted that to save the Crysfire CDT file, you use the SA
command (no extension is needed). When in doubt, make sure to save the CDT file
using this command so you do not lose anything.
Self Calibration and running the Indexing programs
Normally you would try an indexing run (and failing) before trying Self Calibration. However, for this example, we are going to show Self Calibration being performed out of the normal indexing sequence.
Self-calibrate the sample for a possible two-theta offset or sample displacement. (in this case we will be using the two-theta offset option but it would be best to play around with both avaiable options as sample displacement is potentially a better thing to use)
It would be best to have used either a very well calibrated/aligned diffractometer and a silicon internal standard, but in this case, non-optimal data collection conditions on this degrading sample were used.
Thus type (again check the help if you cannot remember these) the SC command for self-calibration. Crysfire now prompts whether we wish to go with the default of a two-theta offset correction or sample displacement. For flat plate Bragg-Bretano data, it would be best to go with the sample displacement option by typing T.
Select the default then CRYSFIRE should provide a list of two-theta offset pairs for selection.
In this case, the lowest angle (with the lowest risk of peak overlap) is probably the best one to select. However, you may like to check whether the self calibration is telling a consistent story with respect to peak offset/sample displacement. Tell Crysfire you wish to accept one of the values by typing T, then select the 1st trial pair by typing 1. Doing a LIST command in CRYSFIRE confirms that the 2-theta offset correction has been applied (in the case of this screen dump: 0.00030116).
Be very wary of applying the Self Calibration option; especially if you are confident that the diffractometer is well aligned and the sample well prepared and collected. Misapplying self calibration may put you in a world of pain by applying inappropriate offsets to you data. If you believe your data has problems, it can be far more effective to recollect a "good" dataset.
Crysfire will then suggest you save the file with SCT (Self Calibration T option) appended to the filename so that it is obvious what data correction process has been applied. Plus Crysfire will add an SCT comment to the title, in this case, SCT=0.000301
From: Robin Shirley [R.Shirley@surrey.ac.uk] Organization: Psychology Dept, Surrey Univ. U.K. To: Lachlan Cranswick [firstname.lastname@example.org] Date: Mon, 7 Sep 1998 19:22:30 GMT Subject: Re: CRYS and Tutorial on CCP14 site "Referring again to the tutorial example, I think there may be some additional ramifications re the -0.0349 2Theta correction which has been applied following self-calibration: a) Firstly, a brief cautionary note may be helpful re relying on just the first line-pair for the 2theta correction. While it's true that this pair will carry the lowest risk of line-overlap problems, it's also true that (unless based on a line profile based on fundamental instrumental parameters) the first and therefore lowest-angle line is the most likely to be affected by various abberrations which can shift its apparent position relative to the rest of the pattern. and hence liable to be one of the least accurately measured. While there is certainly no harm in trying out the effect of applying a zero correction based on a single line-pair, personally I like to see values from two line pairs, that more or less agree with each other, before placing too much confidence in the resulting correction, since with such small numbers it is quite easy to get an apparent "second order" matching which actually arises by chance."
You are now ready to try the Indexing programs inside Crysfire