News archive

Release 721 introduces many new features to both HKL-2000 & HKL-3000:

  • Support for the Bruker Photon III M28 detector format (please note that these detectors are often shipped with a Metaljet system, which uses Ga Ka radiation)
  • Support for the HyPix-6000HE modified format [785 x 813 pixels].
  • Support for the PAD4M format using the new Oxford frame format.
  • For MicroED Users: this release allows the processing of data collected with the Thermo Fisher Scientific CETA-D Micro ED detector.
  • The distribution includes the program “rename_frames” (in the bin directory). This can be useful in cases where the name template does not match the convention expected by HKL-2000/HKL-3000.
  • An internal editor was added - it is now the default editor [see Options tab ->Text editor, also nano editor was added as an option.
  • The warning: "Old HKL (XDisp, Denzo, etc.) program versions" was updated; it also has a 'Do not show again" option

Additionally, the new release includes a number of new features exclusive to HKL-3000:

  • Support for CCP4 7.1 
  • Support for ACHESYM, a standard position model placing program 
  • A new validation bar chart for map cc (RSCC)
  • Auto phasing was improved
  • The model report was updated

A short-term license for the HKL-3000 software may be obtained free of charge by academic users who collected data at synchrotron beamlines and need to reprocess their data at home. The license will be valid only for data collected at facilities where HKL-3000 or HKL-2000 is available to users. The license can be granted for one computer up to 3 times per year. The request for a short-term license should be written on the institution's letterhead and provide: Start Date, End Date, Beamline, Detector, Name of the Principal Investigator, Grant Support, and Contact Information. It should be signed by the Principal Investigator and faxed to 434-979-6381. The following template letter may be used to request the license: 

To HKL Research, Inc.

The members of my research group collected X-Ray diffraction data at the _______________ beamline at _______________ on _______________. The beamline has an HKL-2000 or HKL-3000 license. This research is supported by grants: _______________.

As an academic, non-profit organization, we currently (check one): ( ) have a permanent, academic HKL license for our lab, ( ) do not have a license for the HKL software.

We would like to obtain a temporary license to use the HKL-3000 software to process data collected at the synchrotron site on home computers. The HKL-3000 software will be used exclusively by me and/or members of my group and only for projects that I control as a Principal Investigator, for "non-commercial use" as defined on your web site. I understand that HKL Research does not provide a site definition file (; I will obtain one from the beamline support staff.


Principal Investigator

Release 720 includes several new features and updates:

  • Support for the Eiger2 format (detectors 16M, 9M, 4M, 1M)
  • Support for the h5 nexus format for Diamond beamlines
  • Scaling statistics for different .sca files can be displayed to visually compare results
  • Starting and ending frame numbers for .x data sets can be edited
  • Model building with "HKL Builder" allows refining the structure with the twinning mode enabled 
  • "HKL update" for HKL-3000 Linux/Mac allows to download and install the new version of the program (beta version; stability not yet tested in all environments)
  • hkl_auto ("Auto" tab) was updated


Version 719 brings several new features and updates:

  • An option to merge frames (also in h5 format) - it allows combining frames for peak searching, indexing, and integration, which reduces the number of data files (.x files) for scaling. This option improves the speed of the processing and allows data sets with a large number of frames to be scaled. The procedure is intended mainly for data collected with an oscillation width smaller than 0.1 degrees.
  • "Check for Updates" was added to the main "Help" menu. It allows the user to check if a new version of the program is available. The new version still has to be downloaded and installed manually.
  • Function "Check in PDB", which determines if your unit cell has been seen before in PDB, has been updated (and made available in HKL-2000).
  • Model building with SHELEXE was implemented (HKL-3000). It may improve phasing with MLPHARE and model building when the option to use a starting model is used.
  • The installer now checks if additional fonts are necessary.
  • The ”Auto” tab has been updated, the MAR345 format was added.
  • The "Check Space Group" procedure was improved.
  • The communication with Xdisp Qt was improved. The program does no longer needs to restart to display a different frame.
  • An option to handle spot splitting caused by silver anodes was added for small molecules.

HKL-2000 v718 distribution was released for Linux, Linux 32 and Mac. Changes include:
- update of the auto mode ("Auto" tab),
- improvement in indexing procedure
- new option to integrate and scale in P1 as an intermediate step in data processing
- multiple, dated site files can be placed in the site file directory. HKL-2000 automatically chooses the site file that has the date closest to the date of data collection specified in the header of processed data.

Version 717 is the first release of HKL with an automatic mode, further simplifying the process of determining a structure. Both HKL-2000 and HKL-3000 can process and scale your data, and HKL-3000 can determine and build your structureautomatically. The "Auto" tab allows automatic indexing, integration, and scaling of data using the hkl_auto program. In benchmark tests on a batch of several thousand data sets, the automatic mode had the success rate of ~83% for indexing and integration and ~76% for space group determination (success was determined by comparison with processing reported in PDB). The automatic mode uses the CCP4 program "pointless" for final space group determination (CCP4 setup needs to be sourced before running HKL). In HKL-3000, the "Auto" feature of the Structure tab will attempt to phase your data and build your model. Please note that some formats or constructs supported in the manual mode are not yet available in the automatic mode.

Other new features of release 717 include the new options to invert beam position read from the frame header. Beam position options have been added to "Site Configuration" window in the "Advanced" tab. You may now 1) always read the beam position from the header or 2) invert it. Also, the 3D Window (the number of frames that will be processed together for indexing and integration) is now calculated based on the frame width and memory limits of the denzo_3d program.

The latest version 716.1 can handle data collected by the new Eiger 16M detector at the Shanghai Synchrotron Research Facility, beamline 17U1.

New features include:

- "Site included" option allows one to place the file in the data (frames) or processing directories - instead of in a directory in the hklint sites directory. This option is available in the initial site selection window,

- scalepack with auto corrections generates 6 additional scaled (.sca) files that are tuned for various tasks like: displaying radiation damage and anomalous maps, structure refinement, generating statistics,

- Xdisp Qt is now the default frame display program. Old Xdisp is available in the 'Options/XDisp/XDisp X' main menu,

- "Check Space Group" is integrated with the "pointless" program from CCP4 and allows to apply the selected space group for the next scaling. It also auto generates required re-indexing matrix,

- new 'Merge' tab allows combining 2 or more .sca files together.

The changes from HKL-2000 v714 to v715 are:

  • handling of NeXus (.h5) data was improved. Read times are around 2x faster - support for variable 32-bit/16-bit data was added to NeXus format (.h5). This resolved issues in earlier versions (Xdisp Qt displayed black bars and higher percentage of reflections were rejected during scaling)
  • Linux 32-bit distribution now works with NeXus lz4 bitshuffle format
  • option to read beam position from frame header was moved to the 'Advanced' tab of the 'Site Configuration' window
  • reading the beam position from frame header was enabled for NeXus (.h5) format
  • Rigaku PAD4M, Rigaku Oxford Atlas, Rayonix mx170hs and Pilatus 1M detector formats were added
  • indexing and integration handling procedures were improved
  • 'Short Version' option was added to scaling report. It does not include tables for integration statistics
  • reindexing window was updated
  • option to keep original lattice symmetry was added to 'Check Space Group' window
  • input to 'Check Space Group' was updated to handle primitive orthorhombic groups to keep "unique" axis along c.

Diffraction images from Eiger detectors are written as .h5 files (NeXus format), in which multiple images may be compressed into one file. HKL-2000 release 714 can process .h5 files directly, thereby sidestepping the need to extract images manually and convert them into individual .cbf files. From the user's perspective, processing is handled just like any other file format (.cbf, .img, etc).