School of EPS: Current Staff & Students

EPS Current Students and Staff

Data collection on the X8Apex

  • At the diffractometer, press the square green open door button, then pull handles towards you.

    To check generator settings, open D8 tools, AFTER exiting from BIS. Choose on-line monitor, click on generator. The settings are usually 50kV, 30mA. You should not have to do this every time.

  • On the apexPC start BIS by double clicking on the BIS icon.

The goniometer will drive to zero

  • Double click on APEX2 server icon
  • Under "Instrument" Go to Connect and click on HeriotServer
  • Go to align crystal
  • The video image will come up. (if this takes a while to come up it may be that the video window is still open from the previous run– shut this window and it will open again with the new image.
  • Click on centre – the goniometer drives to a position where goniometer head can be mounted
  • Move beamstop back carefully – if you need to – but you MUST move it back after alignment!
  • Click on center
    • Click on Phi 90. Move the allen bolt on the goniometer head which is facing you to get crystal in the centre and adjust the height using the allen bolt above.

    • Phi 90 to move to other position, then Phi 180 to check if the crystal is centred in that position.
    • To check the height – choose left , then right. To make the adjustments, click to move the goniometer back to the center position.

    NB: SCALE – the rings are approx 0.1mm apart. To put the crosshairs in geometric centre, in the Video program choose tools, options, move center.

Check the beamstop is in the correct position and will not collide with the detector.

Minimise video. Close the doors together and ensure that no alarm light on the enclosure is flashing.

Simple scan

  • Put distance of detector in (usually 50), exposure time in (usually 10) and put 0 for omega Get dark current - new dark image box click on “wide scan” then “drive and scan”.< p> If there’s no response when you click still, change the detector distance or exit apex2 and open it again.

    In the background the BIS window show the status of the instrument – green lights should be on to show client connection.

    - new dark image box click on “wide scan” then “drive and scan”.< p> - new dark image box click on “wide scan” then “drive and scan”.< p>

At the PC in g07:

  • Start database (if its not already started)
  • Open apex2
  • Go to New under the file submenu, for filename GIVE THE NEXT RUN NUMBER e.g. X80102 if the previous run was X80101. See Red folder for run list. Files will be in C:\frames\guest\name.

Click on Instrument which is on the menu bar at the top

  • Connect – will connect to Heriot server (don’t hurry this – check on the BIS window that you have just the two connections lit- if the PC’s slow then exit Apex2 and on X8 PC exit Apex2 and BIS, then reopen BIS and re open apex2)


  • Experiment
  • Set up experiment
  • Append matrix strategy
    • Enter detector distance if you want to have the detector further away than 40mm
    • Change 2theta to 20 rather than have 40
    • Make sure run is shown as active
    • Click execute/resume (bottom right corner)

    (frames should now be collecting in monitor experiment window) – whilst you are waiting enter experimental details in the SETUP – describe menu

Evaluate crystal

  • Once you’ve collected the matrix frames click on Determine unit cell
  • First image – choose matrix_01_0001.sfrm (if you didn’t do a matrix run but went straight onto data collection then click on name_01_0001.sfrm. The default is the first 20 frames in any one run). For the matrix run there will be 20 images if 6degree sweep and 0.3 degree slices
  • Click on "Harvest"
  • Then repeat for next run matrix_02_0001.sfrm and matrix_03_0001.sfrm. (if you want to re –harvest then click clear all reflections)
  • Index – move slider – watch for number of selected spots, then click on index
  • Click on Refine cell, refine , then select Bravais Lattice (not always reliable result), then refine again. Repeat refine until the esd’s don’t change any more. You should have RMS angle < 0.2 for a good crystal


  • Click on Data collection strategy
  • Change exposure time, redundancy, coverage (should be 100)
  • Laue symmetry (if you are confident about your cell being higher than triclinic select that option)
  • detector distance
  • Click on refine strategy , then once you have the completeness, time and redundancy you want click stop, then choose sort runs for completeness
  • Go back to set-up experiment, append strategy. Data collection strategy should be added to the table
  • Add the following line so that the goniometer head is not left under the coldstream

Operation: Position; Active: yes; distance 100; 2 theta: 0 omega: 0; phi: 0 chi: 54.74

If there are any cells coloured pink, it is usually because the angle is greater than 360. This is OK

  • Press validate
  • Press Execute/resume

If you need to interrupt the experiment go to Instrument – choose abort


You need to have determined the unit cell to do this step (If you are unsure of the Laue symmetry – make precession photos, including level 1, from the full dataset – this is under “evaluate crystal”)

  • Click on the abacus icon
  • Find runs (choose root name by clicking on browse and click the name_01_0001.sfrm file. (All the runs should be entered into the table)
  • You may need to change the resolution limit, usually 0.7 is OK. It often sets resolution too low in magnitude
  • Click Start integration

Good data has spot correlation coefficient tending to one

When integration has finished, it will say integration finished in the top right hand corner box


  • Click on scales icon – in this process the next suggested option has a spotted border inside the box
  • Click on the folder icon and click on name_01.raw and click the option “open all with base” Deselect the merged batches option, then the window with all the raw files listed will be in white rather than grey
  • Click next
  • Click refine
  • Click next
  • Determine error model (if it cannot determine an error model that means the data is poor or very incomplete) (NB if one of the runs has a very high Rint value (top left graph), then repeat the scaling but exclude the raw file from the bad run)

    The Rint value should be less than 10%

  • Click Finish – and once the diagnostics box has closed click
  • Exit AXS scale

Evaluate data

  • Click on XPREP icon
  • Choose in the work subdirectory “name_0m.p4p” and “name.hkl” when asked for these files
  • Xprep – space group determination – defaults are usually OK unless it’s a problem structure. Look for Rint and Rsigma in the Intensity output table – it’s a good measure of how good the data is
  • Don’t merge all data when requested (Don’t have the default option A)– let the refinement program do that

Solve (choose either direct methods or Patterson)


Please contact Dr Georgina Rosair for further information.

Links to the other X-Ray Crystallography web pages are also listed here for your convenience:-