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mergehklf5 is program to merge so-called hklf5 files.

If performing a TWIN refinement with an hklf5 file using shelxl merging must be surpressed with MERG 0 ( Herbst-Irmer & Sheldrick,(1998) Acta Cryst. B54, 443-449). Therefore it is advisable to merge the hklf5 file before entering shelxl
mergehklf5 is made for this purpose and takes into account the point group symmetry and the hklf5 batch numbers. Several weighting schemes for merging intensities and sigmas may be selected.

Features: Remarks:
  1. If you intend to perform an absorption correction on your data, you should do this before using mergehklf5.
  2. Depending on the geometry of the diffraction experiment, it may happen that, for a given h,k,l, there are overlapping and non-overlapping reflections available. From our experience with eval14 and eval15, it is advisable to use, in such a case, only the non-overlapping equivalents.

Download and Installation

Obtaining MERGEHKLF5

The program (version 3-nov-2011) is distributed as source code in the form of a tar file for Unix/Linux platforms.
You can obtain the tar file (~850Kb) via anonymous ftp.
Compressed (~300K) and gzipped (~175K) tar files are also available.

Installing mergehklf5

  1. Copy the file mergehklf5src.tar into an empty directory, for example /usr/local/src/mergehklf5
  2. Untar the file with the command tar -xvf mergehklf5.tar
  3. Edit the Makefile and (un)comment the lines for your operating system.
  4. Compile the source code by typing make all
  5. Create with your editor a file /usr/local/bin/mergehklf5 (or somewhere else in your searchpath). This file should contain two lines:
    exec /usr/local/src/mergehklf5/mergehklf5 "$@"
  6. Make this file executable: chmod ugo+x /usr/local/bin/mergehklf5
  7. You should now be able to use mergehklf5

How does it work

Equivalent reflections will be merged.


You have to specify the pointgroup. The program can handle the following pointgroups:
   2      m    2/m
 222    mm2    2mm   m2m    mmm
   4     -4    4/m
 422    4mm   -42m  -4m2  4/mmm
   3     -3
 312    321    31m   3m1   -31m    -3m1
   6     -6    6/m
 622    6mm   -6m2  -62m  6/mmm
  R3    R-3
 R32    R3m   R-3m
  23     m3
 432   -43m    m3m

Reflections are considered equivalent if the indices of the main AND the indices of the overlapping lattice follow the pointgroup symmetry AND if the batchnumbers are equal.

Intensity merging

To calculate the average intensity Imean of every group of equivalent reflections, you must select one of three weighting schemes
 Imean = ——————
  1. Unit Weights
     wi = 1
  2. Statistical weights
     wi = 1/σi²
  3. Shelx weights (taken from the SHELXL-97 source code)
     if Iii > 3
     wi = Iii²
     wi = 3/σi

Sigma merging

For calculating the final sigma, you must select a sigma weighting scheme, a formula for the Internal Sigma, a formula for the External Sigma and a formula for the Final Sigma.

Input and Output files

Both the input file and output file are ascii files in shelx format:
 h k l Intensity σ batchnr

see shelx manual
Optional direction cosines in the input file are not transfered to the output file.


By typing help at the Mergehklf5> command prompt, a webbrowser will be launched to display this page.

How to use mergehklf5

Final Notes

Disclaimer: you use mergehklf5 freely, but at your own responsibility completely.

Please do report failures, give comments and ask questions, preferable via e-mail. We will help you as much as possible.
Email: or
Postal address: Laboratory for Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Padualaan 8, NL-3584 CH Utrecht, The Netherlands.