Indexing strategy of indexing with less than 20 peaks

1. First index on the native 15 peaks using the programs that work with less than 20 peaks: Dicvol, Taup, Kohl and Treor

2. Then use Crysfire's Pattern Extension to extend the number of peaks out to 20, then run All the programs again.

   As noted by Robin:

   From: Robin Shirley [R.Shirley@surrey.ac.uk]
   Date: Wed, 10 Jul 2002 16:31:23 GMT
   
   Jon and fellow Rietvelders/sdpd-ers
   
   > Does this just mean dividing the observed d-spacings by 2 (or 3,4..)
   > to get more "observed" values, or am I missing a more cunning trick?
   
   In essence that's exactly what lies behind it, though perhaps a bit more
   systematically than most humans would consider worth grinding through.
   
   For example, it works iteratively, making overlap-avoidance tests at each
   step, and produces the minimum extension set using the lowest available
   orders.
   
   But the bottom line is that no more information is injected into the
   pattern by this process - it would be impossible for things to be
   otherwise, since to win more degrees of freedom you have to make more
   actual observations (which is sometimes not experimentally possible).
   
   At least it would be impossible to conjure up more information (i.e.
   degrees of freedom) just through working from a fixed set of observed
   peak positions - in principle there might be more information to be
   found buried beneath the profile, though in practice it is usually very
   low-grade.
   
   In fact, not only does pattern extension *not* add more information, but
   if the original data contained systematic errors, then the extra
   higher-order lines will not reproduce these in a self-consistent way -
   all available correction and calibration should always be done *before*
   pattern extension.
   
   Having said all that, it is still a great convenience to be able to
   extend unavoidably sparse patterns from High-P/High-T experiments in a
   few seconds to give a format that none of the indexing programs will
   object to.  For good (though sparse) data, this can open the door to
   getting cell (or at least sub-cell) information that can otherwise be
   hard to lock onto.
   
   The authentic pattern that Lachlan supplied me for testing these issues
   (yes, it was Lachlan's turbo-charged lobbying on behalf of his
   High-P/High-T clientele that lay behind this) originally contained only
   7 lines.  As you can imagine, it was tough to interpret in that form,
   but becomes significantly more stable after pattern-extension, yielding
   some quite interesting possible solutions (or partial solutions).
   
   But it's certainly a case of caveat emptor, and is intended specifically
   for folk who know what they're doing.
   
   I'll try to put together a short paper on this when a bit more experience
   has been gained on how it usefully it performs.
   
   Robin Shirley
   

Refer to the following tutorials on how to load peak positions into Crysfire;

• Inputting a list of peaks / observations into Crysfire

• Importing an XFIT Peak Listing into Crysfire and creating a CDT file (Winfit, Philips and Bruker files can also be imported 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 [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

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.

• Taup
• Dicvol - high symmetry
• Treor
• Dicvol - low symmetry

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)

• Taup
• Dicvol - high symmetry
• ITO
• Fjzn
• Treor
• Kohl
• Dicvol - low symmetry
• Lzon

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: