UK X-Ray Grimoire


XABS2: A 4-D scale factor for empirical treatment of absorption [J. Appl. Cryst. (1995). 28, 53-56]. It can help under (or over!) correction by face-indexed or multiscan methods, and some effects of anisotropic extinction and scan truncation. Useful as a test for whether face-indexed or multiscan absorption correction was adequate.

RT: An 'R-tensor' that models quality of fit in 3D as an ellipsoid. Small ellipsoids equate to a better overall fit, while low eccentricity means a more isotropic fit over reciprocal space. RT is described in Acta Cryst. (2000) A56, 157-162. RT is intended to guide refinement strategy, e.g. to see if one model or another (twinned vs disordered etc.) is better.

ProtRot: Uses quaternions to find the best rotation to superimpose two protein structure models, using different sets of atoms (e.g. all atoms, backbone only, Cα only etc.). It uses the algorithm described by S.K. Kearsley [Acta Cryst. (1989). A45, 208-210].


shelxl-launcher: Launches SHELXL and more. This version runs ciffix, RT and ciftab-automator (see below and above).

wghtfix: A bash script that automatically optimizes the SHELXL weighting scheme.

ciffix: A bash script that fixes CIFs from SHELXL-2014 (and later) on-the-fly using standard unix tools. Creates CIFs that usually need no further editing.

ciftab-automator: A script that automates the flow of ciftab. It uses Don Libes' expect scripting language to bypass the need for keyboard entry.

sadabs-auto and sadabs-auto-run: Scripts that automate SADABS using bash and expect to bypass all keyboard input.

xp-launcher: SHELXL-2014 (and later) has a bunch of new commands that XP does not understand. This script tricks XP into civilized behaviour.

xprun: An expect script that launches XP. Also sets preferences that can't be changed with the regular 'sxtl.ini' file. Used with xp-launcher.

xp-proj-enabler: A bash script that fixes 'proj' rotation in XP. Called by xp-launcher.

xpdraw: Calls plt2ps to convert XP '.plt' files to '.ps' and '.pdf'. Also makes subtle changes to colours.

xpgrow: Calls ShelXtl XP, reads in a *.res file, 'GROWs' the structure, and writes a new *.ins file.

plt2ps: An expect script that converts '.plt' files created by George Sheldrick's XP program to Adobe PostScript and PDF formats. Called by xpdraw.

isot: A bash script that converts all anisotropic temperature factors in a shelxl file to isotropic.

sfrmhead: A line of bash that extracts the header from a Bruker-AXS *.sfrm X-ray diffraction image file.

awkhkl: A line of awk that extracts experimental reflection data from a SHELXL '.fcf' file and writes a '.hkl' file.

save: Makes a tarball of files needed to continue refinement on a different computer. Invokes secure copy to move the *.tbz.