Xtal News

August 2005: Sweeping a little dust. Reworked the documentation to use CSS, DocBook Website and XML based dtds. Can embed manuals in the ToC. The technology is described here.

April 2003: Released Gnu Xtal System 3.7.2. Probably it should have been 3.8, but the theory was that by 4.0 the system would have been irreversibly reworked.

November 2002: The facilities offered by sourceforge.net may offer a stable and accessible environment for stimulating collaborative new development work in Xtal (or not, as the case may be).

March 1 2001: Minor fixes to several programs are included in this release. Most of which you won't notice. The biggest change for unix platforms is that the PIG and PREVUE graphics interface text entry modes are now implemented as Tcl/Tk widgets. These have complex key bindings which are documented under the tcl entry man page ( man 3 entry).

Feb 1 2001: A bug was detected in the reporting of sigma values in the structure factor factor listings for Frel, F²rel and Irel. Unfortunately instead of reporting sigma in each case it is sigma², appropriately scaled. A bug fix wil be made available.

The download page for Xtal version 3.7 has been installed. The executable modules for other platforms will be added as they become available. Users are also able to do their own installations using the supplied source codes.

As Announced at the Society of Crystallographers in Australia (SCA) Crystal XXI meeting in Threadbo, 1st-4th Feb, The Xtal System is going the Free Software route!

It is envisaged that by March 2000 Xtal3.7 will be ready for distribution in the form of binary executables for a range of architectures. Hopefully soon thereafter, the sources will also be publicly available.

Xtal3.7 is progressing more and more along the free software path, with interfaces to XFIG added in PLOTX , POV-Ray and RasMol in PIG, and with the adoption of Tcl/Tk based graphics for all graphical programs. The new graphics interface has greatly facilitated development of a new Powder diffraction pattern calculating routine, POWGEN and an associated new program ADDPAT for reading various Powder diffractometer files.

August 99: Improvements to Xtal3.6.1 ADDATM reads LINK lines for adding H atom calculation constraints to the archive for the CRILSQ "riding atom" refinements. PLINK can be used to purge link lines from archive in update mode.

Generation of LINK lines by BONDAT (for CRILSQ)

BONDAT may be used to generate LINK lines for calculated sites for addition to the archive file for the CRILSQ "riding atom" refinements.

Improvement to the filled-contour facility in CONTRS

The filled contour facility in CONTRS has been improved by sorting all contours by area to place the smallest areas on top - instead of being overwritten by larger contours in Xtal3.6. There remains a fundamental flaw in the algorithm in that re-entrant contours have the wrong colour by one shade, and if the zero contour is not a good baseline (inflection point), the contours may appear incorrect. By and large, filled contours are intended for glossy slide shows rather than the precision requirements of publications.

New least squares refinement program CRILSQ

A new Least squares program CRILSQ has been added to 3.6. CRILSQ is a full-matrix F**2 refinement program which permits linked-atom sites as a "riding-atom" model. Details of this are given in the writeup but suffice it to say that the initial geometry constrained (i.e. "linked") sites may be generated using the PIG "build/auto H-atom" option. This step generated the required LINK information which is stored in the archive for subsequent ADDATM and CRILSQ calculations. The same LINK information can be generated using BONDAT. The current version of CRILSQ does not refine or apply Restraints. It does however refine the Flack parameter.

Improvements to the speed and versatility of CRISP

Modifications to CRISP have led to some improvements in speed of solution, more stable block-diagonal least squares refinement for peak elimination, improved random phase generator and assorted bug fixes.

Improvements to PIG

An auto-hydrogen building feature has been added to PIG which auto- matically adds H-atom sites to the atom list where this can deduced from the chemistry and the geometry. *Caution* may need to be exercised when when parent C-atom geometries are unusual. H-atom sites generated with this option are accompanied by LINK line information which is loaded into the archive file via ADDATM (intended for the CRILSQ "riding atom" model). Note that LINK information is NOT generated if H atoms are assigned directly from peak sites. The addition of LINK information may be switched off if the riding atom features of CRILSQ are not being used via the 'PIG nolink' option PIG can now generate a POV-Ray control file (.pov) and automatically spawn a background POV-Ray process to display the file on UNIX platforms at least. The POV-Ray program needs to installed as per the implementation instructions. Users have some control over the image size and type generated, with mean squared displacements represented by ellipsoids at various probability levels. Read the PIG manual pages for an explanation of how to use/configure this feature.

New CIF validation program PREPUB

A program has been added to 3.6 which applies a subset of the IUCr CIF data validation tests (as per CIFCHECK) to all data blocks in a user supplied CIF. The tests applied are:

             SYMMG_01
             SYMMG_02
             CELLZ_01
             CHEMW_03
             REFLT_03
             STRVAL_02

March 99: Xtal3.6 is released but with the new least squares routine CRILSQ ommitted. It is intended to distribute a free upgrade (3.6.1) to existing 3.6 users early in June of 1999.

Y2K conformance

Xtal makes no use of file access times whatsoever. Nucleus routines do get the current time and date for storing as auxilliary information in certain files, so if your operating system supplies this incorrectly, it will certainly be recorded. However, the time stamp is purely for users information, and is not used by xtal to control archive updates or file read/writes. Xtal output listings continue to record the year as a 2 digit number.

Xtal3.6 will be released starting in January 1999.