HKL2MAP 0.2

HKL2MAP is a graphical user-interface for macromolecular phasing.

The current version (0.2 as of 08-Jul-05) connects several programs from the SHELX-suite to guide the user from analysing scaled diffraction data (SHELXC), via substructure solution (SHELXD) and phasing (SHELXE) to displaying an electron density map (Xfit).

To use HKL2MAP, you need to have licenced versions of SHELXC/D/E and Xfit in the executable path of your computer.

Reference

Thomas Pape & Thomas R. Schneider
HKL2MAP: a graphical user interface for phasing with SHELX programs
J. Appl. Cryst. 37:843-844 (2004).

Tutorial

FAQ

• please check that the script was properly detached from the email. the first line should be: '#!/usr/bin/wish' the last line should be: 'focus .project.entry'
• please check that you have Tcl/Tk with a version number equal or greater than 8.3: from the UNIX-command line:
  UNIX> /usr/bin/wish
  % puts $tk_version
  
• If you get an error message along the lines of ': Bad interpreter', your mail-program may have added or removed something when saving the attachment. Please check the HKL2MAP-script by using the unix-command wc. For hkl2map-0.1.dist, wc should give the following result:
  > wc hkl2map-0.1-dist
  5132 19687 155608
  You may get away buy deleting the last character of each line by the following unix-command:
  > sed 's/.$//g' hkl2map-0.1-dist > hkl2map
  On some systems, you may also find a utility program called dos2unix or dos2unix.pl to repair the changes made by the mail program (thanks to Bradley Ford for pointing this option
• Please remember that HKL2MAP has been tested only under Linux

• Unfortunately, this is not possible with the distributed version. You'll have to rerun the respective jobs. However, as the seeds etc. are explicitly set, the results should be absolutely reproducible if you run the jobs on the same computer.

• A good place to look is: http://www.activestate.com/activetcl .

Related Programs

• A program mtz2sca (written by Tim Gruene) to convert mtz-files to something that can be used by HKL2MAP is available at: mtz2sca.html
• The SHELX-programs used by HKL2AMP, shelxc, shelxd, and shelxe are available from the SHELX-site
• Duncan McRee's molecular graphics program xfit is available as part of the XtalView-system from the San Diego Super Computer Center .
• A shell-script to convert phs-files containing phased reflections to mtz-format is available: phs2mtz.

Non-Linux operating systems

MAC OS X

• MAC-versions of SHELXC/D/E are available from the SHELX-server
• Xfit for MAC is available from: Xfit for MAC down any executable.
  Please let me know if you have information about this.
• Make sure that Tcl/Tk is installed on your MAC by typing which wish.
  If you don't have Tcl/Tk on your computer, a good place to download a current version is: http://www.apple.com/downloads/macosx/unix_open_source/tcltkaqua.html.
• Copy the hkl2map-script into some generally accessible directory. A possible location is /usr/bin
• Now you should be able to use HKL2MAP by typing wish /usr/bin/hkl2map from a UNIX-command line.
• Known problems:
  • After running SHELXC, an error message 'Abnormal termination of SHELXC ... ... Child process exited abnormally' is generated. This can be ignored.
  • Similar messages appear when SHELXD and SHELXE finish. These can also be ignored.
  • Resizing windows belonging to HKL2MAP can be very slow.
  • Various other problems were reported when HKL2MAP was used on Intel-based MACs

SGI IRIX

• You may need to change the first line of hkl2map-script to contain the proper path for 'wish' on your system.
• There is a problem with assigning "inf" to an internal variable. To avoid this, you can add the following lines to HKL2MAP-0.2 (in procedure Max, at line 464, before the line containing return $maximum:

      if { $maximum == "inf"} {
        set maximum 9999999
      }

  Thanks to Ingrid Vetter for fixing this one.

True64

• Chris Roome reported that HKL2MAP runs under Tru64

Release Notes

Version 0.2 - Jul 2005

• A help file has been integrated. It can be displayed by clicking the Help-Button in the Main-Window
• d'-values as a function of resolution (as evaluated by SHELXC) are now displayed properly.
• Some other small bugs have been fixed.

Version 0.1 - Sep 2003

• The very first version of HKL2MAP as released during the SHELX-Workshop in Goettingen.

Contact

Last Update: 05/02/2009

Pages on this server were created by Thomas R. Schneider (thomas.schneider at embl-hamburg.de). and Roberto Mosca (roberto.mosca at embl-hamburg.de) RM and TRS accept full responsibility for the content of these pages, for which EMBL is not responsible by any means.