Below you will find a timeline for new features and things to keep in mind when operating BioMAX. In particular, please check entries posted since your last experiment at BioMAX.

The sample preparation laboratory has been fitted with a blackout roller blind and a light-sealing door to aid in handling light-sensitive samples.

Please contact BioMAX staff in as early advance as possible, in case of interest in handling light-sensitive samples and to discuss any special requirements.

The EDNA framework used for launching auto-processing jobs has been updated. Two major changes are highlighted below:

  • xia2:dials is now automatically run for data collections (xia2, DIALS)
  • autoPROC jobs are now shown as separate results in ISPyB for with/without STARANISO used for anisotropic resolution limit determination (STARANISO)
  • Three papers relating to the BioMAX hardware and software installations have recently been published.

  • BioMAX: BioMAX – the first macromolecular crystallography beamline at MAX IV Laboratory
    DOI: 10.1107/S1600577520008723
  • FragMAX: FragMAX: the fragment-screening platform at the MAX IV Laboratory
    DOI: 10.1107/S205979832000889X
  • SSX: Current status and future opportunities for serial crystallography at MAX IV Laboratory
    DOI: 10.1107/S1600577520008735
  • The BioMAX acknowledgements and references page now also includes a link to the MAX IV user policy page for how to acknowledge BioMAX beamtime in publications.

    Modifications to the ISARA sample changer gripper have been performed to accommodate sample pins outside of the SPINE-standard. More scenarios with pins longer than the length defined in the SPINE-standard should now be possible to mount and unmount safely without staff intervention.

    Modified gripper with cutouts for longer pins

    It is still highly encouraged to avoid sending sample mounts that do not adhere to the SPINE-standard and that one should regularly oversee the state of ones sample mounts to detect issues prior to sample mounting instead of at the beamline. For special experiments requiring other types of sample mounts, please contact beamline staff beforehand.

    For manual data processing jobs and making use of PReSTO software modules, the module loading syntax has been changed to:

    module load gopresto [software to load]

    E.g. module load gopresto XDS

    More details about manual data processing at BioMAX are available here (under “Manual data reduction”)

    User accounts now have write access to the “process” directories generated for each sample collected on. These directories have thereby become suitable for manual processing jobs.

    I.e. / data / visitors / biomax / [proposal] / [date] / raw / [protein] / [sample] / process

    More details about manual data processing at BioMAX are available here (under “Manual data reduction”)

    As previous user cases for accessing the MXCuBE sample changer tab has been put into beamline actions, the sample changer tab has had most of its functionality disabled.

    Diffraction image viewing through adxv (developer page) is available through the terminal with:

    adxv_eiger xxxx_master.h5

    It will read all the necessary meta info and display the correct resolution rings automatically. It’s important to call master file instead of the data file here. When changing to a new dataset, you need to launch the same command from terminal instead of loading another dataset in adxv gui directly (otherwise it uses the meta data from the previous dataset).

    More details about image viewing at BioMAX are available here (under “Image visualization”)

    Annealing is available in beamline actions. This is done by moving the cryo-stream away from the sample and then back. Set a value of at least 1s. Before annealing, it’s better to put the MD3 to centering phase (so one can see the sample) and move the beamline action pop-up window to the side (it is draggable!), and also bring up the beamline diff camera.

    It is to be seen as a “last resort” tool and more details are available here (under “Data collection”)

    User accessible MXCuBE-server restarts. Only for use outside of support hours

    If MXCuBE becomes totally unresponsive (and merely refreshing the browser tab or aborting MD3 do not work) an MXCuBE-server restart can be needed. Contact user support in case of this happening within support hours. If outside support hours, two options are available

    1) Use the beamline action restart_MXCuBE
    or
    2) Open a terminal and run restart_mxcube (needed if beamline actions cannot be accessed)

    Warning! Restarting the server means that you have to resynchronize with ISPyB, redo your queue, etc. The sample overview will also not show which samples that had been collected on prior to the server restart, but that information is still available in ISPyB.

    More details available here (under “Known issues”)

    Energy scans for SAD/MAD or metal characterization are now available.

    Note: Please keep the kappa angle to 0 degrees for such collections.

    More details are available here (Under “Data Collection – Energy scan and SAD/MAD data collection”)

    Data collection strategies can be toggled to be run together with collection of characterization frames.

    More details available here (under “Data collection – Sample characterization”)

    Two new beamline actions:

    empty_sample_mounted – When a sample changer operation resulted in no sample mounted on the goniometer head.
    abort_MD3 – In case the omega axis remains active after a data collection

    More details about these two beamline actions are available here (under “Known issues”)

    Dewar barcodes are scanned upon dewar arrival to MAX IV and ISPyB will report dewars as ‘at MAXIV – BioMAX’

    Flux calculation is available as a beamline action, as well as an automatic measurement before each data collection.
    More details available here (under “Measuring the flux”)

    X-ray fluorescence (XRF) spectra can now be collected.

    Note: Please keep the kappa angle to 0 degrees for such collections.

    More details are available here (Under “Data Collection – XRF scan”)