New Crysfire 2002 powder indexing suite by Robin Shirley

L. Cranswick lzc at dl.ac.uk
Sat Aug 3 14:11:48 EST 2002


The Crysfire 2002 powder indexing suite update by Robin Shirley has now been
released (3rd August 2002) and is available on the web.  What's new 
with Crysfire 2002 is mentioned at the tail end of this
message. Major new features include the addition of Ton Spek's LePage
program, Robin Shirley's MMAP program, suggested values for rescaling of
large cells, and pattern extension for datasets containing less than 20
peaks, everything now runs within Crysfire (no need for quitting to
spawn any sub programs) etc, etc, etc.  

While Crysfire is free for not for profit users, a proforma invoice is
provided in the distribution for people wishing to make commercial use
of the Crysfire interface.  (in prior versions - commercial usage was
not possible)

Updated Crysfire Tutorials (showing the new features and methods
of interactiving with Crysfire 2002) are at:

  http://www.ccp14.ac.uk/tutorial/crys/

Downloads:

UK:  http://www.ccp14.ac.uk/ccp/web-mirrors/crys-r-shirley/crysinst.zip
CA:  http://ccp14.sims.nrc.ca/ccp/web-mirrors/crys-r-shirley/crysinst.zip
US:  http://ccp14.semo.edu/ccp/web-mirrors/crys-r-shirley/crysinst.zip
AU:  http://ccp14.minerals.csiro.au/ccp/web-mirrors/crys-r-shirley/crysinst.zip

Be wary to read the install information text files provided with the above
ZIP file, as the method of installing and initialising Crysfire has changed.

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Crysfire also interlinks with the Chekcell graphical helper indexing tool
for Windows by Jean Laugier and Bernard Bochu.  

Chekcell Tutorials
  http://www.ccp14.ac.uk/tutorial/lmgp/index.html#chekcell

Downloads:

UK:  http://www.ccp14.ac.uk/ccp/web-mirrors/lmgp-laugier-bochu/
CA:  http://ccp14.sims.nrc.ca/ccp/web-mirrors/lmgp-laugier-bochu/
US:  http://ccp14.semo.edu/ccp/web-mirrors/lmgp-laugier-bochu/
AU:  http://ccp14.minerals.csiro.au/ccp/web-mirrors/lmgp-laugier-bochu/

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>From the Crysfire 2002 What's New file:

                        Crysfire 2002:  What's New?

Crysfire 2000 users will find that the front-end interface largely
remains familiar, but that the new Crysfire is now a close-coupled
system, faster, more robust and easier to use. Nothing has been lost and
there are several powerful new facilities. The source code for the
command module of Crysfire 2002 is actually four times as large as its
equivalent in Crysfire 2000. 

All facilities can now be run directly from the main command menu,
including programs that previously would only run as standalones.
Another new feature is that on restarting Crysfire in a particular data
directory, the most recently used dataset will automatically reload. 

The online help has been redesigned and extended, supported by a clearer
and more comprehensive manual (twice the size of its predecessor). All
documentation for Crysfire and its supported indexing programs can now
be viewed directly from the Crysfire command menu using new VM (View
Manual) and VF (View File) commands. 

Although Crysfire 2002 will take advantage of the facilities of Windows
when it finds itself running in that environment, it is still
essentially a DOS suite, designed to run on almost any PC anywhere in
the world, including the rather basic equipment that may be all that is
available to students in developing countries. 

Of course, since indexing can be a computationally intensive process,
Crysfire will be seen at its best when running at GHz speeds on a modern
Pentium or Athlon PC, under Windows 95 or later. Nevertheless, it will
still get there eventually on any PC that meets its very basic
requirements (640K RAM, a hard disk of some sort and DOS 5 or later). 

An obvious change, and hopefully an improvement, is the new IN (=index)
command, which launches indexing programs directly (including Mmap - see
below), automatically reloading the current dataset on returning (this
cycle was previously a little clumsy and required several user
commands). 

All previous indexing programs continue to be supported (some with
considerable improvements), plus a completely new program Mmap, which
can be used both for ab initio indexing and for topographical scans of
solution space, since it generates a visual colour-contoured map of the
hills and valleys of figure of merit plotted against lattice parameters.

A merit-surface map provides a clearer picture in which the central peak
reveals itself as likely to be a physically correct solution because of
its narrow and compact cross-section, while others (not shown), which
are merely pseudo-solutions, prove to lie on ridges and other extended
features in solution space. 

The new M1 and M3 commands display the three principal topographic
sections centred on the currently stored cell. M1 displays all three
together as thumbnails within a single screen, while M3 displays three
more detailed consecutive full-screen views. A more general MM command
generates individual maps under more detailed user control. Mmap's
indexing mode can also be accessed from the IN command. 

A new LC (Load Cell) command allows trial solutions to be loaded from
Crysfire or Chekcell summary files to simplify such investigations.
Since the next task is often to assess its topography maps, a shortcut
into the M1/M3 map sequence is provided. 

Another new feature is that, during indexing runs, after the summary
file has been displayed, all solutions are run through a system version
of Ton Spek's Le Page program then redisplayed for comparison in
reduced-cell form. This highlights the relations between trial
solutions, including those which are actually equivalent, though
previously found in different settings (and, equally important, those
that are non-equivalent derivative cells, though their volumes might
have suggested that they were different settings of the same solution). 

Also new is an approximate ab-initio volume estimate which is reported
whenever a dataset is loaded, with a suggested rescale factor if it
seems likely to be outside the volume range for which most indexing
programs have been optimised. This can become important as SDPD attempts
increasingly ambitious structures, even including proteins (e.g. a new
form of zinc insulin: Von Dreele, 2002). 

At the other end of the scale, high-pressure/high-temperature
experiments often unavoidably yield sparse datasets from phases that are
not observable under ambient conditions, and which contain fewer than
the 20 observed lines regarded as the absolute minimum by many indexing
programs. 

A new EP (Extend Pattern) command can automatically extend any sparse
pattern by adding higher orders of observed lines until the total has
been expanded to 20. While this obviously cannot increase the amount of
information present, it permits more programs to run, providing a
broader basis for hypotheses about the cell (or at least sub-cell) that
is present. 

Finally, the logfile has been made considerably more comprehensive, so
that its record now acts more nearly as an automated laboratory notebook
for indexing work on each dataset name. 

                                    Summary

       General Improvements

* Completely rewritten: faster, close-coupled, more robust and easier to
  use.
* Everything runs directly from the main command menu, including
  previous standalone programs.
* On restarting Crysfire, the most
  recently used dataset will automatically  reload.
* Improved online help, and a clearer and more comprehensive manual. 
* All documentation for Crysfire and supported indexing programs can be
  viewed directly using new VM (View Manual) and VF (View File) commands.
* Automatically takes advantage of the facilities of Windows and fast
  modern processors when running in those environments.
* But will still run on a very basic PC anywhere in the world (minimum 
  requirements: 640K RAM, a hard disk of some sort and DOS 5 or later).
* All previous indexing programs still supported (some with considerable 
  improvements).
* Better support for sparse datasets with less than 20 lines from
  high-pressure/high-temperature experiments (including the EP command
  described below). 
* A more comprehensive logfile, now closer to an automated laboratory 
  notebook for indexing work on each dataset. 


       Main New Features

* New IN (=index) command, which launches indexing programs directly,
  automatically reloading the current dataset on returning (this cycle
  previously required several commands). 
* A completely new indexing program Mmap, both for ab initio indexing
  (via the IN command) and for topographical scans of solution space in
  which it generates a visual colour-contoured map of the figure of merit
  surface plotted against lattice parameters.
* New M1 and M3 commands to display the three principal topographic
  sections centred on the currently stored cell - M1 as three thumbnails
  within a single screen, M3 as three more detailed consecutive
  full-screen views.
* A general MM command to generate individual merit-maps under more
  detailed user control.
* New LC (Load Cell) command to load trial solutions from Crysfire or
  Chekcell summary files (since the next task is often to assess its
  topography maps, a shortcut into the M1/M3 map sequence is provided).
* Reduced-cell summaries: after the summary file display in indexing
  runs, all solutions are run through a system version of Ton Spek's 
  Le Page program and redisplayed as a summary table in reduced-cell form.
* An approximate ab-initio volume estimate reported whenever a dataset
  is loaded, with a suggested rescale factor if a large cell seems likely
  (cf Bob Von Dreele's powder structures of proteins!).
* New EP (Extend Pattern) command to automatically extend any sparse
  pattern by adding higher orders of observed lines until the total has
  been expanded to 20 (this obviously cannot increase the amount of
  information present, but it permits more programs to run) 

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-- 
-----------------------
Lachlan M. D. Cranswick

Collaborative Computational Project No 14 (CCP14)
    for Single Crystal and Powder Diffraction
  Birkbeck University of London and Daresbury Synchrotron Laboratory 
Postal Address: CCP14 - School of Crystallography,
                Birkbeck College,
                Malet Street, Bloomsbury,
                WC1E 7HX, London,  UK
Tel: (+44) 020 7631 6850   Fax: (+44) 020 7631 6803
E-mail: l.m.d.cranswick at dl.ac.uk   Room: B091
WWW: http://www.ccp14.ac.uk/





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