6. How to collect data

While collecting data you should keep in mind the following two limitations. 1) The fastest mechanical rotation speed of the goniometer should be no more than 10 degrees per second. 2) The minimum sample-detector distance is 120mm (see beamline personnel to move detector in the range 160-120mm). The detector can be moved up or tilted for collection of ultra-high resolution data or to increase the spots separation (this procedure is done only by the beamline personnel). We do not recommend using the exposure time less than 0.5 seconds because of the shutter/goniometer synchronization issues or more than 5 seconds (possible beam positional instability). If you have a BIG crystal – use attenuators. One second exposure is the most commonly used.

Safety note: The front of the expensive ADSC detector is protected now by a laser curtain. Anytime a foreign object (finger, clothes, etc) is coming close to the front of the detector, the alarm will sound and a record will be put in the logbook.

Now sit in front of left ADSC computer (see first figure), open new terminal; in most cases you are collecting data in /24ID-C/users/your_home_institution/your_PI_date/images (unless instructed otherwise by the beamline personnel). Next, close any previous ADSC windows, if any are open. To be sure that there is no ADSC daemon running, type " ps –e | grep ccd", and "ps -e |grep det" if any ccd or det processes are running - kill them. Now create a new directory for your new data/crystal, go there, and type "ccdsys startup". Typing "ccdsys" only will show all other available options for ADSC software.

ADSC control windows (ADX and ADX-Status) should appear in a while – figure below.

Figure 19

Note: ADSC software should be restarted every time the beam control software on the "master" computer is restarted (konzuu2 script on the rightmost monitor), or if MD2 comwrapper server is restarted.

Now you should use SETUP → Snapshot (to collect snapshots), SETUP → Manual (to manually move the ADSC detector to the desired position within the range 120-1200mm and to move phi angle, don't try to move other motors), SETUP → Run (to setup the script to collect your data). Additional help is available by pressing help in the top-right corner of the corresponding window.
The screenshot with ADSC software ready for data collection is presented on the figure 20.

Figure 20. Screenshot of ADSC computer display

    Snapshots details: specify the directory name where to collect data, usually you don’t need to change the file prefix, input the desired sample to detector distance and the exposure time, 2q offset is not supported as well as kappa/omega axes, use 2x2 binning unless you expect a very sharp reflections or poor spots separation (file size increases for unbinned image from 18Mb to 72Mb ), collect new detector dark current every time you change the exposure time, D-phi is the oscillation range and the dezinger "on" should be used only with long exposures (more than one minute -- never happened on 24ID). Binning type: HW – hardware binning by summation of four pixels, it is claimed to make slightly lower noise; SW (default) – software binning by averaging of four pixels, thus increasing the dynamical range of the image.
    Runs details: specify the valid directory name where to collect data and meaningful image prefix, don’t use any compression and collect in time mode only, input as much comment as possible (will be saved in the "LOGFILE" –very helpful in one year after data collection). To change the binning mode/type go to the "Config" pulldown-menu, choose option ccd. "Anomalous" - if yes ticked the "inverse beam" mode is activated; you need to specify the number of frames per wedge collected (usually ~20-30 frames) before the goniometer is rotated 180^o to collect the same number of frames; this decreases the impact of the radiation damage on the precision of the anomalous signal), and "MAD" – if yes checked, you may specify up to five different energies to collect your MAD data. The "MAD" mode in ADSC software is NOT recommended because of common radiation damage. We suggest processing all data in a real time and adjust strategy of data collection manually.
    In the run window you setup different parameters for your data collection. You may specify several different runs from the same crystal ( i.e. run #1 to collect low resolution data with short exposure and run #2 for high resolution data with long exposure etc) . You need to input total number of frames, desired distance, starting phi angle, oscillation range and exposure time. Check dezinger is"N". Please don’t touch 2q, kappa and omega or change any rotation axis.
Hit "Collect" only once (no double click) to collect your data or "cancel" to close the Runs window. If the "collect" button is hit multiple times, the software will redo the same runs over again, overwriting your previous images.
    If you decide to stop the data collection before it is over, you may choose STOP –> "after current image". The GUI of MD2 windows may remain locked until you press "UNLOCK" button (right lower side of the MD2 window). Make sure the gripper of the robot is NOT protruding into MD2 before clicking on "unlock" button, as severe mechanical damage will result.