Local contact information

Aperture alignment

Before aligning the apertures, verify that the beam is well aligned on centered position (do Centre beam if unsure)

Normally there is no need to realign Beam defining Aperture (your LC has done it in the morning).

Apertures alignment is performed inside the MD2 software. Put the scintillator in, aperture in (in mxCuBE -> Instruments --> Scintillator and Aperture), open safety shutter and fast shutter.

Access the MD2 software (windows PC, VNC to Microdiff or vncviewer microdiff29new) go to Devices-->Aperture and align each of the aperture using the X and Y scrolling (it is safer to use the arrows for tiny movements). When the beam and the apertures are aligned click on Set to Current. Repeat this operation for each of the aperture.

Be careful, wrong settings might impair the correct realignment of the five aperture.

MD2 v4 aperture

NB: When centering a sample, apertures are taken out for better lighting, they will be inserted at data collection starting. When aligning the apertures they need to be inserted manually (MxCuBE --> Instruments --> Aperture)

Minikappa calibration

Mounting of the minikappa

If specifically requested in advance by users LC can remove the single axis goniohead and mount the minikappa following this procedure:

1. Switch off the MD2-PMAC controller (red button)

2. unmount the goniohead (unscrew it and unplug the internal connector)

3. mount the minikappa available on the beamline (be careful as it can fit only in one position) and screw it progressively.

4. Switch on the PMAC controller (green button)

5. in spec type SCKappaOn

MiniKappa should be ready for use. Calibration may be needed

When mounting the minikappa freshly on the minidiff (all beamlines but ID29), make sure to switch off the DPAP(s) for the kappa1 and kappa2 motors.

Calibration of the minikappa

the GONIOMETER TRANSLATION CALIBRATION is needed to make sure that the sample does NOT move out of the cryo during a rotation. This procedure together with the GONIOMETER ROTATION CALIBRATION needs to be done ONLYduring the START-UP of the beamline if the minikappa has been unmounted on the control PC (e.g. id29control) make sure that within the file /users/opidxy/STAC/config/BCM.dat the two following lines are correct (if you change anything, save the old file to BCM.dat.date):

      I)  BCM_PLUGIN BMC_PLUGIN_esrf_safe

     II)  SPECVERSION lid292:exp (or the equivalent for any other beamline)

run the program by typing STAC into a x-terminal on the control PC.

if you really want to do the full calibration (i.e. I) Translation Calibration and II) Rotation Calibration, you need to activate these 2 tabs in SPEC first under the tab OPTIONS


  you need to have an alignment device that allows you to carefully centre (e.g. an acupuncture needle mounted in a pin)

  1. initialise motors

  2. move (0;0;0)

  3. centre tip (3 click centering) very carefully (do this at zoom 6; do NOT change the focus!)

  4. reset translation

  the next three steps need to be repeated for every phi translation made

  5. set phi translation

     (do this for phi = 90, 180 and 270 degree)

  6. centre tip

  7. get translation

  8. set kappa translation

     (do this for kappa = 80, 160 and 240 degree)

  9. centre tip

10. get translation

11. calculate (if nothing is selected, everything will be taken for the calculation)

             these are the values to check:

                        I           DIFF TO CURRENT should be ≤ 0.7º

                        II          the calculated axis for phi should be close to x=0; y=0; z=1

                        III         RECONSTRUCTION ERROR should be less than 0.012 mm


 12. UPDATE when everything is fine.


     1. initialise motors

     2. move (0;0;0)

     3. centre crystal (3 click centering) very carefully

     4. collect four subsequent images (oscillation start musst be 0)

easiest is to use the automatically generated mosflm.inp or XDS.INP files. If you like to do the
indexing manually, make sure that you generate also the bestfile.par (which is needed by STAC).

     5. index the images

     6. open the xxx.mat (when using MOSFLM) or the CORRECT.LP (when using XDS) into the space

     7. move (0;0;P)

     8. make sure that the oscillation start is 0 and repeat steps 3.-6.

     9. move (0;K;P)

   10. make sure that the oscillation start is 0 and repeat steps 3.-6.

   11. move (O;K;P)

   12. here the oscillation start corresponds to the value of O; repeat steps 3.-6.


            these are the values to check:

                  I           the calculated axes for phi and omega should be close to x=0; y=0; z=1

                  II          the calculated angle should be close to calibration values (∆ ≤ 0.7º)

                  III         DIFF TO CURRENT should be ≤ 0.7º


   14. UPDATE


    1. mount a crystal

    2. centre crystal (3 click centering) very carefully

    3. collect four subsequent images

    4. index the images

    5. read in the xxx.sav file from the MOSFLM output and press LOAD

    the current angles and the translation plus the OM (orientation matrix) will be filled in automatically.

    6. NEXT (you know will automatically jump to the VECTOR EVALUATION tab)

    7. select whatever orientation you would like to have and press MvSel

    8. start data collection or press NEXT to calculate a strategy calculation.