The MiniKappa is mounted on all beamlines (except the microfocus beamline ID23-2) and can be used in association with the STAC software suite for the re-orientation of crystals for an optimal data collection strategy. The reorientation options depend on the type of experiment to be carried out. Options include aligning a crystallographic axis along the rotation axis such that Bijvoet mates can be measured on the same image for the optimal measurement of anomalous differences in MAD/SAD phasing experiments. Other options include optimising the spot separation for a particularly large unit cell axis, minimising the total oscillation range needed and the collection of a complete dataset from multiple crystals. 

The MiniKappa is a highly precise instrument with a sphere of confusion of ~4 microns.  It should not be removed or interfered with without the permission of the Beamline Scientist. 

Please note that in Kappa geometry, as implemented on our beam-lines, the rotation axis during data collection is termed omega. Phi is a reorientation angle.

 

Calculations of crystal reorientations

 

The following is a quick guide to using the Minikappa to reorient your crystal along a specific axis/crystal direction.  For more detailed information please contact the Beamline Scientist or Sandor Brockhauser (brockhauser@embl.fr).

 

  1. Click the init button in the mini kappa section of mxCuBE.
  2. Mount a crystal and centre very carefully
  3. Collect four consecutive images (no overlap).  This will automatically create a 'process' directory in your current directory.  Within this directory you will find subdirectories containing input files for Mosflm (mosflm.inp) and XDS (xds.inp).  Run your chosen program in the relevant directory using the input file, index the images, save (using default file names) and exit.  Verify that the following files are present in the process directory - mosflm: bestfile.par, mosflm.inp, matrix file (xxx.mat); XDS: CORRECT.LP; DENZO: .x file.
  4. Now click the STAC_KAPPA icon on the control computer right screen.  This is the reorientation software - STrategic Alignment of Crystals.  You should see the following GUI open:
    (or Open a shell on the beamline control computer and type stac (this is the reorientation software - STrategic Alignment of Crystals) you should see the following GUI open:)

 

 

 stac_3-resize640x401.png

 

5. Now click NEW XTAL button and then the folder button for the descriptor file and choose the location and name of the descriptor file (e.g mosflm.descr from Mosflm (or mosflm.sav))

6. Press the load button.  The current crystal orientation matrix file will be displayed in the GUI with the current motor values:

 

 stac_4-resize640x401.png
 

7. Highlight the crystal orientation that you require (usually select all). In case of looking for best approaching orientation even if the exact alignment is not possible, also check the appropriate checkbox Close.

 

8. After click  NEXT (you now will automatically jump to the VECTOR EVALUATION tab):

 

 stac_6-resize640x401.png

 

All possible alignments are displayed in the table.  In the case of impossible reorientations a popup window will describe them.

 

8. The allowed reorientations will be displayed.  Select the crystal orientation you would like to have and press MvSel

 

 stac_7-resize640x401.png

 

9. The MiniKappa will now move to the selected position.  Check the centreing of the crystal and re-centre if necessary. 

10. Click  NEXT to view the calculated data collection strategy for the new orientation (see image below).

Note: Strategies  will almost always  contain two-sweeps  due to blind regions of the diffraction pattern which cannot be accessed when a crystal is aligned in a particular orientation.

An alternative to using STAC data collection strategies is to calculate them using DNA, BEST etc. after collecting 2 reference images in the new orientation.

 

 stac_8-resize640x401.png