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RE: [sdpd] STX/RIET/CCP14: Latest Crysfire powder indexing suite
I agree. This is precisely the technique used by Crysfire's rescale
facility, except that it is more general, allowing any user-specified
rescale ratio.
However, the consequences of using a fictitious "working" wavelength
are that the resulting cells in the solutions list will also be
rescaled in that same proportion, and so need scaling back to their
true dimensions.
The new UNSCALE program merely provides a convenient and robust way
to do this simultaneously for all the possible solutions in a
Crysfire summary list, while minimising any loss of precision during
the transformation.
Best wishes
Robin Shirley
-----------------------------
To: <sdpd...@egroups.com>
From: "Peter Y. Zavalij" <zavalij...@binghamton.edu>
Date: Sun, 17 Dec 2000 01:06:53 -0500
Reply-to: sdpd...@egroups.com
Subject: RE: [sdpd] STX/RIET/CCP14: Latest Crysfire powder indexing suite for proteins and other large cell data
The simple and easy way to rescale (I used successfully to index relatively
large cells) is to assign wrong wavelength, for example:
1) MoKa instead of CuKa gives scale of about 2
2) AgKa instead of CuKa - 3, etc.
It works perfectly well with any already existing indexing software ...
-----Original Message-----
From: L. Cranswick [mailto:L.M.D.Cranswick...@dl.ac.uk]
Sent: Saturday, December 16, 2000 7:08 PM
To: Rietveld Mailing List; CCP14 Software Hints Mailing List;
Crystallography Newsgroup; SDPD Structure Solution Mailing List
Subject: [sdpd] STX/RIET/CCP14: Latest Crysfire powder indexing suite
for proteins and other large cell data
Latest Crysfire powder indexing suite for proteins and other large cell data
There is a new version of the Crysfire for DOS (and Windows) powder
indexing suite by Robin Shirley. This now includes a program
called "unscale"
An tutorial using this on a large celled inorganic that
does not solve using the raw peak find data (collected on a Philips
1050/1710 medium resolution (173 mm goniometer radius) laboratory
powder X-ray diffractometer - not a synchrotron) is at:
http://www.ccp14.ac.uk/tutorial/crys/rescale.htm
More information on "rescaling" and "unscaling" on large cells
(as well educated guesswork on volume ranges that the various
indexing programs have been optimised for) is at:
http://www.ccp14.ac.uk/tutorial/crys/rescale_info.htm
Rescaling was the method used by Bob von Dreele and co-workers
on synchrotron powder data to help index proteins: - e.g.
a b c al be ga
81.2780 81.2780 73.0390 90.000 90.000 120.000
(R. B. Von Dreele, P. W. Stephens, G. D. Smith and R. H. Blessing,
"The first protein crystal structure determined from high-resolution
X-ray powder diffraction data: a variant of T3R3 human insulin-zinc
complex produced by grinding", Acta Cryst. (2000). D56, 1549-1553.)
============================================================
Crysfire comes with and links seemlessly into:
Treor90 (Per-Eric Werner)
Ito12 (Jan Visser)
Dicvol91 (D. Louër)
Taup (Daniel Taupin) (also called Powder -
Daniel Taupin's Index-Permutation program)
Kohl (Franz Kohlbeck)
FJZN (Jan Visser & R. Shirley)
Lzon (Robin Shirley, Daniel Louer & Jan Visser)
LOSHFZRF (Daniel Louer & Robin Shirley)
Summary files are generated with one solution per line making
it easy to scope the solution space of the cells:
Crysfire also includes the extra programs:
xf2crys - program for importing "Coehlo and Cheary's" XFIT Peak Profile
files into CRYSFIRE CDT format. (default filename xfit.txt)
wf2crys - program for importing "Stefan Krumm's" Winfit Peak Profile
files into CRYSFIRE CDT format. (default filename winfit.dat)
udi2crys - program for Philips UDI peak find data files into CRYSFIRE
CDT format.
MERGESUM Program: Merges the CRYSFIRE summary files for different
dataset names.
============================================================
Crysfire can be downloaded from:
UK: http://www.ccp14.ac.uk/ccp/web-mirrors/crys-r-shirley/
CA: http://ccp14.sims.nrc.ca/ccp/web-mirrors/crys-r-shirley/
AU:
ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/crys-r-sh
irley/
General tutorials on installing and running Crysfire:
http://www.ccp14.ac.uk/tutorial/crys/
============================================================
>From a large celled Inorganic:
Top result on trying to index on un-rescaled data
(no true solution is found)
I20 Merit Volume V/V1 BL IndexProg Date Time Pedig
20 35.15 1740.311 1.00 I KOHLv6.20i 27Sep00 18:33:15 27
a b c alpha beta gamma
16.9217 23.9262 4.2992 90.000 91.084 90.000
Top result with Indexing on "rescaled" data - factor of .3 -
I20 Merit Volume V/V1 BL IndexProg Date Time Pedig
20 40.78 369.668 1.00 F TAUPv3.2c 16Dec00 17:29:52 Cub__1
a b c alpha beta gamma
7.1769 7.1769 7.1769 90.000 90.000 90.000
After unscaling using "unscale" - factor of .3 - to give the real
result (confirmed originally using single crystal data)
I20 Merit Volume V/V1 BL IndexProg Date Time Pedig
20 40.78 13691.390 1.00 F TAUPv3.2c 16Dec00 17:29:52 Cub__1
a b c alpha beta gamma
23.9230 23.9230 23.9230 90.000 90.000 90.000
============================================================
For graphically evaluating Crysfire results: the Chekcell for Windows
program by Jean Laugier and Bernard Bochu can be very convenient and
allows selection of possible true cells using the principle of
"parsimony of extra reflections" by allow manual and automatic
Best Cell solution by going through all applicable cell/spacegroup
combinations.
Tutorials:
http://www.ccp14.ac.uk/tutorial/lmgp/index.html#chekcell
Download:
http://www.ccp14.ac.uk/ccp/web-mirrors/lmgp-laugier-bochu/
http://ccp14.sims.nrc.ca/ccp/web-mirrors/lmgp-laugier-bochu/
ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/lmgp-laug
ier-bochu/
There are also bleeding_edge_beta_versions of the latest Chekcell
(latest beta version is quite well tested) which now has:
LePage for Windows (from original Fortran code by A.L.Spek
and A. Meetsma - ftp://xraysoft.chem.uu.nl/pub/unix/lepage/ )
for obtaining the reduced cell and searching for sub and super cells.
GUI based cell transformation (Hex <-> Rhom, Obverse <-> Reverse,
manually define the transformation matrix, etc);
HKL to peak assignment tolerance wizard,
Improved Truecell (potentially superceded by the more effecient LePage)
Ability to add and save manually inserted, transformed, Le page and
Truecell found cells to the summary list.
Sorting of the summary list as well as ellimination of unwanted cell
types (e.g., elliminating a few 1000 triclinic trial cells from a
summary list). Saving a new summary list.
Other convenience features.
Beta versions of Chekcell are located in the bleeding_edge_beta_versions
subdirectory of the above download sites.
The above Chekcell features help get around the bias in powder
indexing programs that favour low volume low symmetry cells.
There is also a pre-release stand alone version of Le Page for Windows
in the above mentioned bleeding_edge_beta_versions sub-directory.
============================================================
Using LePage for Windows can help get around the problem described by
Buerger ('Reduced Cells', M.J. Buerger, (Zeitschift fur Kristallographie,
BD 109, S. 42-60 (1957)) where most powder indexing programs use
the Delaunay reduction which does not reliably give the "reduced cell"
Relevant extracts at:
http://www.ccp14.ac.uk/solution/indexing/reduced_cell.html
e.g.,
"Several authors have erroneously stated that the endpoint of the
Delaunay reduction is the reduced cell, although Delaunay himself was
well ware of the literature on reduced cells and avoided using the
term in connection with his reduction"
.
.
.
"A short time ago Ito presented a method by which powder photographs
of crystals of any symmetry can be indexed. His method indexes the
reflections on the basis of an arbitrary primitive cell of the lattice.
In order to interpret the results, this cell must be transformed into
some easily recognised standard cell. Ito chose, as standard, one of
four cells provided by the Delaunay reduction, specificially that cell
which is based on the three shortest axes of the four homogenious axes
corresponding to Delaunay reduced form. In two places, Ito referrred
to this cell as the "reduced cel", and this practise has been copied by
Henry and Lonsdale and by Donnay. This is an unfortunate slip, since
the term "reduced cell" was already well established, and had been
defined in a different way."
------
Lachlan.
--
Lachlan M. D. Cranswick
Collaborative Computational Project No 14 (CCP14)
for Single Crystal and Powder Diffraction
Daresbury Laboratory, Warrington, WA4 4AD U.K
Tel: +44-1925-603703 Fax: +44-1925-603124
E-mail: l.cranswick...@dl.ac.uk Ext: 3703 Room C14
http://www.ccp14.ac.uk
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