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Tutorials and Examples

CRYSFIRE Powder Indexing System for DOS/Windows by Robin Shirley et al

Importing an XFIT Peak Listing into Crysfire

The CCP14 Homepage is at http://www.ccp14.ac.uk
[Tutorials page] | [CRYSFIRE Tutorial Index] | [Crysfire What's New] | [LMGP Suite Chekcell Index] | [Powder Diffraction Indexing Resources]

This run through will use the peak list file obtained on the y2o3 example file provided with the CCP14 software distribution of XFIT. XFIT is not that easy to use by default and thus there is a tutorial at the CCP14 site. XFIT Tutorial and Download Page

There is also an XFIT tutorial on saving an XFIT peak result file in a Crysfire, Chekcell, etc export happy format

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.

Note: The following is just a single example of using CRYSFIRE. There are other methods of interacting with the program and doing the following.

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 [l.m.d.cranswick@dl.ac.uk]
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 that has the xfit.txt peak list file. In this case example, c:\crysfire\cf_exmp\y2o3.

In the old Crysfire 2000, you just ran the program XF2CRYS to start the xfit.txt peak importing utility. However, in the new Crysfire 2002, this is done via the Crysfire IM (IMport) menu.

To start Crysfire, from the DOS Prompt type crysfire, agree to the Licencing conditions by typing Y for Yes to eventually be given the following style of menu.

Now run IM to go into the import facility of Crysfire 2002. This will tell you what file importing facilities are available.

Select XF for importing Xfit files.

If you have a "not enough memory" problem, you might be running out of DOS memory and may have to add the following style of command to your c:\config.sys file. 

dos=high,umb
device=c:\windows\himem.sys /testmem:off
device=c:\windows\emm386.sys  ram

Also, if not all the peaks get converted, it could imply that you are also running out of DOS memory.

When prompted by XF2crys, input the XFIT filename, title, wavelength and other required information.

When asked if you want to load the converted dataset, type Y for yes and then load the newly created Crysfire CDT file.

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.

As described by Robin in the beginning of this tutorial, be wary that Crysfire 2002 does not like non-descriptive names like "crys" (as shown below). Thus I will enter a file name of crys1 - which is descriptive enough for Crysfire 2002 to accept. You are advised to enter a filename that is meaningful to you and your specific problem.

Crysfire will then prompt you if you want to open the CDT file you just created into Crysfire.

Now carry on with running all the indexing programs as shown in the Crysfire Basic tutorial.

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