Frequently Asked Questions


Common questions:

Q1: I want to get the accurate I/sigmaI for the table one using phenix. ...But when I put NO MERGE key word, I get a warning message : "File could be corrupted or it may be a result of a command 'no merge original index". Why?
Q2: When using no merge original index option in scalepack it still comes up with annoying warning message that it doesn't understand the file it is outputting!

A: The 'no merge original index' macro produces a non-standard .sca file. It cannot be used, for example, for structure solution, and therefore gives the warning. You can ignore the warning and use the output file if you just want to calculate Rmerge statistics. 'No merge original index' is available as a checkbutton option on the scale page starting from version 708.

Q: I get the following error

Problem with hardware recognition


Error code: 6

A:Your license key, cr_info, needs to be updated. The error message indicates that the HOST-NAME line in the info file has changed.  This can sometimes happen if you upgrade your operating system.  Please re-run the access_prod program on that computer and send the output (info file) it creates to, so we can generate a new key for you.

Q: Our lab recently collected data at the beamline. I have discovered that I need to reprocess 2 of the data sets, but we do not have the HKL-2000 software in the lab. How do I obtain the HKL-2000 package to do this? and what is the proper procedure?

A: The PI (Principal Investigator) needs to send us a request letter for an HKL-2000 license.  After receiving a confirmation message and installation information from us, the program can be downloaded from our server.  A temporary 30-day HKL-2000 license key (cr_info) can be requested 3 times in a calendar year. See our License Policy for Academic Users  for detailed information.

Q: How do I reference HKL?
A: Any publication arising from use of the HKL/HKL-2000 program package should contain this reference.

Q: When I run  ./HKL2000, I get error message: No such file or directory.
A: You run 32-bit program on 64-bit system without 32-bit support.
Starting from version 706c, HKL-2000 is available as a 32-bit or 64-bit distribution.
For 32-bit systems download package ending with Linux-i386.tar.gz, for 64-bit systems ending with Linux-x86_64.tar.gz.

Q: When I try to launch HKL2000, I get the following error message:
dyld: unknown required load command 0x80000022
Trace/BPT trap
A: HKL-2000 does not support OSX 10.5. Only versions 10.6 and up are supported.

Q: We've installed HKL-2000 (release 704y) on an Ubuntu machine (Ubuntu 12.04 LTS), but can't seem to get the access_prod or any other executables to run, even though permissions are all set correctly. Do you have any suggestions for why this might be or how we might fix the problem?
A: If you run a 32-bit version of HKL-2000 (version 705 and earlier) on a 64-bit system, you have to install the 32-bit libraries. 
In the case of Ubuntu, run as root:
apt-get install ia32-libs xfonts-75dpi

The information is also on our website:

Q: I'm trying to install HKL-2000 v704y on a Linux system (Cent OS 6.4, 64 bit OS), but the program did not run.  It gave the error message: "HKL2000: error while loading shared libraries:  cannot open shared object file: No such file or directory".  What do I do to solve this problem? 
HKL-2000 v704y is a 32-bit distribution.

For Red Hat related systems add 32-bit packages with a command:
yum install glibc.i686 libX11.i686 mesa-libGLU.i686 libXmu.i686 xorg-x11-fonts-75dpi

For Ubuntu:
apt-get install ia32-libs xfonts-75dpi

The information is also on our website:

Q: Does HKL support multi-core processing?
A: The main programs of HKL does not support multi-core processing. The latest versions of HKL-3000 can launch SHELXD in a multi-threaded mode. The number of cores to used can be specified using "Options -> Thread Maximum"  from the main menu.

Question Archive:

See archived questions and answers.