Collaborative Computational Project Number 14
For Single Crystal and Powder Diffraction
(Freely Available Crystallographic Software for Students and Academia)
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August 2006 New version
| Robin Shirley 1941-2005
It is with great sadness that I have to announce that Robin died in hospital on Sunday, 27th March 2005.
Robin Shirley 1941-2005
August 2006 New version
Crysfire 2004: What's New?
(including Latest enhancements)
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 286 or newer x86-family processor, 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 and McMaille - 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, which are merely pseudo-solutions, are more likely 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.
From v9.46 (April 2003), Armel Le Bail's new McMaille program (v3) is also supported, in its automated "Black Box" mode. This uses Monte Carlo search with profile-based solution-matching (using an idealised profile for greater speed). A copy of McMaille is included in the Crysfire distribution – to check whether a later release is available see Armel's website.
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.
Exploratory indexing work is assisted (from v9.45.27) by new HO (Higher/Lower Orders Analysis) and ZT (Zone Transformation) commands, and (from v9.46.01) by enhancements to the CA command to allow the exclusion of obs lines that are not indexed within specified obs-calc difference limits in 2Theta or Q. A new PS (Pattern Separation) command can then be used to save either the excluded or non-excluded lines to disk as a separate dataset. A new S (Strip low intensity lines) option has been added to the ED (Edit) command, to delete lines below a specified intensity threshold.
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.
* 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 (** = enhancements since the original release in August 2002)
* 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.
** Armel Le Bail's new McMaille whole-profile indexing program (v3) is now supported (from v9.46.04).
* 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)
** An enhanced SC (Self-Calibration) command, which now includes histogram displays of 2Theta-zero or specimen-displacement corrections, and supports iterative use.
** New HO (Higher/Lower Orders Analysis) command to search the observed pattern for possible higher or lower orders (harmonics) of each line.
** New ZT (Zone Transformation) command to double or centre an hk0 zone prior to use as a basis zone by Mmap.
** Enhancements to the CA (Calculate Pattern) command, to exclude unindexed observed lines based on user-specified limits in 2Theta or Q.
** A new PS (Pattern Separation) command to save either the excluded or remaining lines (after CA) to disk as a separate dataset, and thus help to separate patterns from mixed phases into their components.
** New S option in the ED (Edit) command, to strip out any observed lines that are below a specified intensity threshold.
** The DI (Direct Indexing) command now works correctly.
January 2004 new bugfix
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September 2002 new
bugfix version of Crysfire:
September 2002 new
bugfix and feature Version of Crysfire:
Add tutorials on:
August 2002 new bugfix
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August 2002 new Crysfire
July 2002 new Version of
April 2002 new Version
March 2002 new Version
August 2001 new Version
April 2001 new Version
December 2000 new
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July 2000 updates over
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