Contents

• Finding the Beam Center
• Space Group Table
• HKL/HKL-2000
  • Computers on which HKL/HKL-2000 can be found
  • HKL-2000 beamline/detector def.site files
  • HKL-2000 Hints
  • XdisplayF Aliases
  • Denzo and Scalepack Scripts
  • HKL/HKL-2000 Referencing, Documentation, Availability, and Help
  • HKL Manual
• d*TREK
  • Computers on which d*TREK can be found
  • d*TREK Manual for Beginners, FAQ, and Referencing
• MOSFLM / iMOSFLM
  • Computers on which MOSFLM can be found
  • MOSFLM User Guide, Help and Guidance

• XDS
  • XDS Scripts

Finding the Beam Center

The Beam Center Log is a record of the beam centers used in processing by previous users and is searchable by beamline and data-reduction program. If you encounter trouble indexing your images due to a faulty beam center, it will be worthwhile to try indexing with the latest recorded beam center for your beamline from the log. Once your beam center is determined after refining your data, please enter it into the log for the benefit of later users.

HKL/HKL 2000

• Computers on which HKL/HKL-2000 can be found

  HKL/HKL-2000 can be run from almost any beamline computer that is not the computer running the data-collection software.

  Computers licensed and equipped to run Denzo/HKL/HKL-2000 by beamline:

  • Beamline X12-B:
    • x12b-a.nsls.bnl.gov
    • 
      
  • Beamline X12-C:
    • x12c-a.nsls.bnl.gov
    • x12c-b.nsls.bnl.gov
  • Beamline X25:
    • x25-a.nsls.bnl.gov
    • x25-b.nsls.bnl.gov
  • Beamline X26-C:
    • x26c-a.nsls.bnl.gov
    • x26c-b.nsls.bnl.gov
  • Beamline X29:
    
    • x29-a.nsls.bnl.gov
    • x29-b.nsls.bnl.gov
  • Cyber Café Machines: dunkin, starbucks, yuban, grande, maxwell, java, mocha, beans, coffee, latte, frappe. More information
    
  
  

  In most cases, it is preferable to index, integrate and scale your data while you are collecting at a beamline using the beamline computer. If you need to finish processing your data while you are not at a beamline, you should go to one of your Cyber Café (X12B or X29 vicinity)  or ssh to one of the Cyber Café machine. The data disks upon which you have collected your data will be mounted. 
  

• HKL-2000 detector site def files

  The HKL-2000 detector def.site files are available for the Quantum 4, Quantum 315, B1.3, and B4 detectors. If copying these files, be sure to check the beam center values for accuracy.

  • Quantum 4 def.site for X8c
  • Quantum 4 def.site for X12b
  • Quantum 4 def.site for X26c
  • Quantum 210 def.site for X12c
  • Quantum 315 def.site for X25
  • Quantum 315 def.site for X29
  • B1.3 def.site
  • B4 def.site

• HKL-2000 Hints

  Some observations to make the running of HKL-2000 a little easier:

  • After starting HKL-2000, check the "Site Configuration" to make sure that the beam center is accurate.
  • Under "Main," if using the "Set up Data Files" option to queue a number of data sets to process successively, make sure that the Denzo and Scale buttons are activated (colored red) for each data set only if you want to integrate and scale them together. If the Denzo button is activated for all of them, the data sets will integrate one after another; if the Scale buttons are all activated, each set will be scaled together, which is undesirable if they represent different wavelengths of a MAD collection. To scale them separately, activate Scale and click on "Select" only for the set on which you wish to work.
  • Before indexing, ensure that the wavelength is entered correctly in "Main."
  • Under "Index/Refinement/Integration," select "Fit All" to activate all refinement options before each time you index, refine, or integrate.
• XdisplayF Aliases

  The alias used to run XdisplayF depends on the detector being collected upon:

  hklq4 - alias used for ADSC Quantum 4 Detector.
  hklb4 - alias used for Brandeis B4 CCD Detector.
  hklb1.2 - alias used for Brandeis B1.3 CCD Detector.
  hklq315 - alias used for ADSC Quantum 315 Detector.

  To run xdisplayF, enter from a UNIX shell on a computer that supports HKL the appropriate alias followed by an image name.

• Denzo and Scalepack Scripts

  To instruct the CBASS Data Collection Program to automatically generate Denzo scripts, select File -> Write -> Denzo Command File: "auto.dat" before taking the image. The scripts auto.dat and refine.dat will be written with collection parameters such as wavelength and distance automatically inserted.

  If you are not collecting data at a beamline featuring CBASS, or if you would like to make use of slightly simplified scripts, you may view or copy scripts from the links below.

  • Quantum 4 Detector:
    • index.dat
    • integrate.dat
    • scale.sh
  • Brandeis B4 Detector:
    • index.dat
    • integrate.dat
    • scale.sh
  • Brandeis B1.3 Detector:
    • index.dat
    • integrate.dat
    • scale.sh
  • Quantum 315 Detector:
    • index.dat
    • integrate.dat
    • scale.sh
• HKL/HKL-2000 Referencing, Documentation, Availability, and Help

  Obtain HKL/HKL-2000 information regarding referencing the program in your publications, links to on-line manuals and searchable keyword lists, information on how to acquire licencing to use the HKL package, and local contact information for questions regarding HKL/HKL-2000.

d*TREK

• Computers on which d*TREK can be found

  Currently, d*TREK version 7.0 --no current license--

• d*TREK Manual for Beginners, FAQ, and Referencing

  The d*TREK manual contains information for first-time users, frequently asked questions about d*TREK, and information on how to reference d*TREK in your publications.

MOSFLM / iMOSFLM

• The new GUI for  MOSFLM is called iMOSFLM

  This should be accessible from all beamline machines and cafe machine.

• MOSFLM User Guide, Help and Guidance

  Consult MOSFLM's on-line user guide for information regarding the program.

XDS

• Script to integrate using XDS: XDS.INP

This script has to be in the directory where you intend to start XDS. Modify the script file and  type XDS to start the program.




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Last modified 7 January 2008 by Protein Crystallography Web Master