Collaborative Computational Project Number 14

(CCP14)

For Single Crystal and Powder Diffraction
(Freely Available Crystallographic Software for Students and Academia)

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Crysfire on CCP14


Tutorials and Examples

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

What's New with Crysfire


[Tutorials page] | [CRYSFIRE Tutorial Index] | [LMGP Suite Chekcell Index] | [Powder Diffraction Indexing Resources]

Referencing the Crysfire suite: If use of the CRYSFIRE suite makes possible a published paper, then both the CRYSFIRE suite itself and any indexing programs that contributed materially to this result should be cited in the references section of the paper.
CRYSFIRE Suite: R. Shirley , The CRYSFIRE System for Automatic Powder Indexing:

February 2020 New version of Crysfire - Crysfire2020: 
    Crysfire has been rewritten and now runs on Windows (XP-Windows10), Linux, and Macintosh OS X



31st August 2006 New version of Crysfire: 
  1. The latest and Last Version by Robin Shirley is now available.
  2. Both program and source code will be available for download


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 


31st August 2006 New version of Crysfire:

  • Details from What's new file

v9.46.08

 

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.

 

 

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  (** = 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.


20th January 2004 new bugfix version of Crysfire:
  1. A problem with Crysfire involving a "year 2004"/linkfile bug has been fixed.


17th September 2002 new bugfix version of Crysfire:
  1. A wavelength-related constant is now updated correctly from CuKalpha, for example when importing synchrotron datasets from PowderX (this did not affect external indexing runs, but was mysteriously blanking out subsequent topography maps).

  2. MMap no longer halts with an "Invalid Q2A" message if one uses a basis set selected from a basis-set-list file.

  3. CA output correctly repeats by default to the .CFO file (previously it had to be woken up by toggling OF), and the working dataset name is now included in the command-prompt.

15th September 2002 new bugfix and feature Version of Crysfire:
  1. New importer for peak list files generated by Cheng Dong's PowderX program

  2. Added printer/outfile (.CFO) support to SC histograms and tables, and harmonised its Z2Th and SCT dialogues.

  3. Major improvements to self-calibration, including histograms of the suggested corrections and the ability to re-cycle manually until one has converged on a good estimate.

  4. Much tidying and tuning of MMap (both visible and behind the scenes), especially to the solution-refinement phase which now uses dynamic damping and restraints, giving a speed-up in refinement of c.10-20%, with guaranteed non-divergence in certain pathological cases. The user is also now able to advise MMap on the general quality of the dataset (medium/good-lab.data/synchrotron).

Add tutorials on:


29th August 2002 new bugfix Version of Crysfire:
  1. This is a minor bug fix update

  2. Crysfire run under WinXP should now behave in the same way as other versions of windows in bringing up the wordpad program to view results.

  3. Various anomalies in the MMap input defaults.

  4. Other minor bug fixes

3rd August 2002 new Crysfire 2002
  1. Warning: Crysfire 2002 has a new installation method over the old Crysfire 2000 for all versions of Windows except Windows XP. Make sure to read the install.txt and Xpinstal.txt files in the Crysfire DOC directory.

  2. From the Whatsnew.txt 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)


    Robin Shirley


9th July 2002 new Version of Crysfire:
  1. This minor version update includes bugfix versions of the UDI2crys, WF2crys and XF2crys file converter programs. There were circumstances that made them act incorrectly if the user didn't want to overwrite an existing dataset. This has been fixed.

30th April 2002 new Version of Crysfire:
  1. This minor version update includes an updated version of EVA2CRYS (a program for converting EVA DIF peak files into Crysfire CDT files).

22nd March 2002 new Version of Crysfire:
  1. This minor version update includes EVA2CRYS by Arie van der Lee, a program for converting EVA DIF peak files into Crysfire CDT files.

23rd August 2001 new Version of Crysfire:
  1. This minor version update fixes a problem when passing large > 100 degree 2-theta values to Dicvol.

2nd April 2001 new Version of Crysfire:
  1. An updated filtering program is now included that will handle Treor output when less than 20 peaks are present. (e.g., Before it would be reporting that 20 out of 18 peaks were indexed. Now it will correctly report that 18 out of 18 peaks were indexing).

17th December 2000 new Version of Crysfire:
  1. The crysfire suite now includes the "unscale" program for helping to solve on large cells using rescaling. Refer to the tutorials below on how to use this. The rescaling technique was the method used by Bob von Dreele and co-workers to help index proteins from powder data. (Acta Cryst. (2000). D56, 1549-1553)

25th July 2000 updates over previous version of Crysfire:
  1. Self calibration now offers a sample displacement correction option as an alternative to the zero of 2Theta. This is new maths and at the time of release is unpublished. A simulated example dataset SCDISTST is provided to illustrate this facility.
  2. Improved support for KOHL with options to increase user control over the crystal systems searched.
  3. udi2crys - a program for converting Philips UDI peak find data files into CRYS CDT format datasets (programs were already provided to import from Winfit and XFIT formats)
  4. crys2cif - a program to convert a CRYS CDT dataset file into IUCr CIF format (this facility had to be removed from CRYS to make room for the new sample-displacement correction facility).
  5. Various cosmetic improvements and minor bug fixes.

  6. CRYSFIRE continues to support the 8 different indexing programs included with the distribution (TREOR, ITO, DICVOL, TAUP, KOHL, FJZN6, LZON and LOSH), integrating their results into a cumulative line-per-solution summary sorted on lines indexed and figure of merit.

If you have any queries or comments, please feel free to contact the CCP14