Tutorials

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.

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:

• Simple self calibration of peak positions using Crysfire
  Based around : "New Phases Formed in the Li-Ti-O System under Reducing Conditions",
  I.E. Grey, L. M. D. Cranswick, C. Li, L. A. Bursill, and J. L. Peng,
  Journal of Solid State Chemistry, 138, 74-86 (1998))

• More complicated self calibration of peak positions using 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

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

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.

1. This minor version update includes an updated version of EVA2CRYS (a program for converting EVA DIF peak files into Crysfire CDT files).

1. This minor version update includes EVA2CRYS by Arie van der Lee, a program for converting EVA DIF peak files into Crysfire CDT files.

1. This minor version update fixes a problem when passing large > 100 degree 2-theta values to Dicvol.

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).

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)

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.