Unix scripts for use with Xtal data

This page identifies some unix shell scripts which could be useful for a variety of Xtal related data handling tasks. Most users will NEVER need to use these scripts, but they are given here as examples of how to set up some specialised processing if you are inclined to do this locally. None of these examples are guaranteed to work on your OS version (especially if you use Windows! :-) and no liability is accepted for any damages or losses incurred in their use.

  • xtal.sh xtal invokation script under unix

  • xtal.bat xtal invokation script under Win32 DOS console

  • xtal.com xtal invokation under VMS

Xtal_3.6 refinement scripts

  • start Ever wanted to check STARTX for consistency with every space group in the SYMMAP space group listing? This script lets you do it! (well - almost every space group)

  • newabs James R. Hester's method of repeatedly running ABSORB and SORTRF to optimize the crystal shape according to the reflection Merging R-factor.

  • newabs1 An alternative method of the same.

  • rfactors A unix awk script to strip out the vital statistics from a CRYLSQ listing and list then on standard out

  • extscal Run repeated least squares structural refinments, varying the scale factor and the extinction parameter (notoriously correlated) to determine a 2D R-factor map.

  • shiftm and shiftit2 These two scripts combined permit you to specify atomic positional parameters which will be "wiggled" by +/- some fixed amount in order to escape from some envisaged local minimum in the CRYLSQ least squares surface.

CIF browsers interfacing to Netscape

  • These scripts are described elsewhere but permit browsing and editing of CIF data downloaded using Netscape, with molecular structure viewing using Xtal.

Utilities for presenting bond lists, etc.

  • bonds Some trivial reformatting of the BONDLA .lst list file using awk.

  • eigenvectors Strip the Uij vibration tensors from a CRYLSQ .pch refined parameter punch file and pipe them into a MathematicaTM process for eigenvector/eigenvalue decomposition.

  • spam Some trivial reformatting of the CRYLSQ .pch list file using awk

  • conpsfilt Scale and translate pre xtal3.6 CONTRS postscript files such that the bounding box is set to a user specified dimension (in pt - 72pt/inch), the map borders are translated to the bounding box origin and the map is scaled to fit in the bounding box- preserving the aspect ratio.

  • conps36.pl A perl script to do for xtal3.6 CONTRS postscript images what conpsfilt.csh does for pre xtal3.6 postscript images.


  • Heard a report of a lisp module for running xtal under emacs. Anybody have any info?