Common Questions

Question: None of our SGI computers with Irix 5.3 are able to run the new version. Only SGIs with Irix 6.5 runs the program. Is there are fix for this problem? 

New HKL version does not support the old operating system.


Question: Our lab recently collected data at the APS on the SBC 19ID beamline. I have discovered that I need to reprocess 2 of the data sets . Is it possible to obtain the HKL-2000 package to do this? and what is the proper procedure?

The HKL-2000 package is not available in general distribution yet. Developmental version can be obtained by academic users directly from the program Authors. The user needs to send us a request (info file) for the computer he wishes to use for data processing. After receiving a confirmation message from one of the Authors, the appropriate license key (cr_info) will be released.


Question: We have been using denzo/scalepack on our dec alpha, but up to now we have only run it as jobs in background, we are now trying to use the display program and we are having problems. Xdisp comes up OK, and we can run denzo and with a command file, but when we get to the point where it should put up the predicted pattern, xdisp crashes with this error message: 'Segmentation fault (core dumped)' . We are using adsc unsupported-q4 type images. We have tried rebooting the system and using unlimit to increase the amount of memory available, but neither of these helped.

Try not to run anything else (like Netscape), but xdisp. 


Question: Problem with version Denzo1.96 for DEC Alpha station: When we run xdisp. After several seconds it displays  '> Image Ready' in a command window. And everything works good unless one executes probably the most important command, Peak Search, when the program terminates with a message: '> Floating exception (core dumped)'. I hope You know, how can we deal with this problem?

This problem has been fixed in release 1.96.3. You must have an earlier version of the program. Please download the newest version.


Question: What are the hardware / operating systems requirements?

Please visity our Hardware and Operating System Recommendations


Question: I get the following error

Problem with hardware recognition


Error code: 6

HOST-NAME line in the info file must have changed. Please re-run the access_prod program on that computer and send to Your access file, cr_info, needs to be updated.


Question: When I ran 

xdisp ccd adsc unsupported-q4 xxx2_1_001.img 1.

I received the following error: 'timer error or current directory name too long, error code -2'

Timer error means that the checking program found that the time of your computer has been changed. Usually it happens when  the system clock is set backward. Check /etc directory, if you do not have files that have the dates 'in the future'.


Question: When I increased the swap partition on the alpha to 1.5 megablocks (running tru64 4.0F, BTW) and I now get an error that says /sbin/loader fatal error program datasize exceeds process datasize limit.

On OSF (Digital Unix) operating system you have to set all resources (as it was on VMS) to the appropriate level. The best is to increase datasize to 'unlimited'.


Question: When I process my virus data I frequently have more then the set limit of 99999 rejections. Normally I simply modify the "write reject file" value so that I reject less then 100,000 reflections, is there a better way to do this, perhaps a version of the program that can accept greater then 100,000 rejections?

You should expect less than  0.1% reflections rejected. It means that you should have problems only when you collect 1 billion reflections. You have some other problem that should be fixed before you request version with the larger number of rejections.


Question: I'm processing a data set with the 'ccd adsc unsupported-q4' format. It seems to integrate fine with chi sq. lower than 1 and mosaicity ~1, but when I try to scale even a few frames the mosaicity goes beyond 6 and the program finds few reflections to scale. What may be wrong?

Probably the spindle axis is not set properly. Please consult manual.


Question: Hello, would you mind refreshing my memory about meaning of each of these

  • scalepackbig*
  • scalepackenormous*
  • scalepackhuge*
  • scalepackmanyframes*
  • scalepacknorm*
  • scalepacksmall*
  • scalepackverybig*

In version 1.96.5 new names for Scalepack versions were introduced. The table explains scalepack mutations limits.


Question 1: In the new 1.96 version of the HKL-package, we have problems displaying the predictions of the x file in xdisp (i.e. when typing "xdisp format image.ipf xfile.x").

Question 2: In the new HKL version 1.96.1, I can not display the raxis image file with integrated list of reflections to see the predictions using the command shown below: 

xdisp raxis raxis2_001.osc raxis2_001.x

It gives the error "Unrecognized frame format in command line: raxis2_001.osc". I can do the same for raxis4 file and it works:

xdisp raxis4 100 raxis4_001.osc raxis4_001.x

If you would like to display predictions from Raxis-IIc data you have to give a command like: 

xdisp raxis p24nat###.osc 2 p24nat###.x

In that case sector 2 is displayed. p24nat002.x represents the name of the file, which contains a list of reflections in Denzo output format. Now if you click 'update pred', you will get predictions. 
To display only the image, you have two alternative ways: 

xdisp raxis p24nat###.osc 2   (STRONGLY recommended) 

or, for some detectors (like Raxis-IV): 

xdisp raxis4 100 lys002.osc 

still works.


These changes were introduced for the functionality that has been used in HKL2000. Similarly you are doing that for other instruments. The old versions of the program used a little different convention:

xdisp raxis xtal001.osc [hklpredictions]

Communication between Denzo and XdisplayF is achieved by using hklpredictions and .test files. This explains why the programs must be started in the same directory. The program version number is stored in these files, so you should delete them when switching to a new version of the programs. hklpredictions is a name of the file, which Denzo creates. It contains the predicted reflections. The use of hklpredictions file is now a default, therefore it is put here in parentheses [ ]. The old convention still works for some detectors. The change of convention has been forced by the variety of naming schemes used by detector vendors and developers.

The new convention has to be applied to display predictions from Denzo output files. To display predictions from xtal150.x file one has to type:

xdisp raxis xtal###.osc 150 xtal###.x

where xtal150.x represents the name of the file, which contains a list of reflections in Denzo output format. You need to click the Update Pred option in the Image Window for predictions to appear on the screen.