Preliminary Checklist

plusCryoPin Specifications
  • The beamline is setup for use with "18mm" pins

 

plusPre-Arrival
  • Apply for beamtime through the User Services office.
  • Arrange for shipping of samples Dewars. Keep shipping/receiving department as well as CMCF staff informed.
  • Determine what tools you will need. A list of user tools available at the CMCF is here. If you require one or more tools that are not listed and which you feel should be stocked, please let us know.
  • Complete required safety training (exam to be completed at CLS).
  • Obtain computer account from CMCF staff.

plusArrival

plusBeamline Specific Orientation
    Upon arrival you will be given an orientation of the beamline that includes the following topics:

  • Location and posting of permit.
  • Attended/Unattended beamline procedures.
  • Contact numbers.
  • Safety and first-aid.
  • Guidelines (Food and Drink).
  • Beamline lockup procedure.
  • Data collection procedure.
  • LN2 safety.
  • Crystal mounting procedures.

Beamline

plusLayout
  • The beamline is approximately 50 m in length, and its endstation is located in the South-East corner of the building. There are exits at each corner of the building along with access card readers to allow entry. There is a water fountain along the South wall not too far from the exit. There is a washroom located at the west side of the beamline hall near shipping and receiving and several on the mezzanine level. There is a user lounge on the mezzanine level near the South-West corner with comfortable seating, a table,  refrigerator, microwave oven, a vending machine, and a kitchen sink.
plusLockup Procedure
  • The first two hutches are normally locked. If they need to be locked up please contact the floor coordinator.
  • The endstation hutch lockup procedure is as follows:

    Push the green button on lock up station 1 (upstream wall).

    Push the green button on the lock up station 2 (inboard wall down-stream end

    Evacuate the hutch, and press and hold the red "MAIN DOOR" CLOSE button on the endstation panel (labelled 08ID1 BEAMLINE A.C.I.S. PANEL SOE-1).
     

  • After the hutch is secure following the 15 second warning, you may open the end-station safety shutters using the SHUTTERS OPEN button on the endstation panel (labelled 08ID1 BEAMLINE A.C.I.S. PANEL SOE-1).
plusBeamline Parameters
    The following describes a number of beamline parameters and how they are controlled

  • Energy:
    • Energy selection is done by entering the energy in the data collection application. This will automatically change the undulator gap (to be implemented) and the double crystal monochromator Bragg angle.
  • Attenuators:
    • The intensity of the beam may be adjusted by selecting the percent transmission desired. The appropriate foils will be inserted to achieve the closest match to the desired value and the actual value will be displayed.
  • Beam Size (Slits):
    • JJ slits are located in the endstation just downstream from the attenuators. The beam size is represented by lines in the sample visualization GUI in the data collection application. The beam size may be adjusted by entering the desired values for the horizontal and vertical dimensions.

  Computing

plusComputers
  • There are a numbers computers on the beamline. The computers designated as operator interfaces (or OPIs) are running the Linux operating system (Scientific Linux to be exact).
    • The monitors are labelled with the hostnames: OPI1608-001, OPI1608-002, OPI1608-003, OPI1608-004 (endstation hutch) and IOC1608-301 (data processing server). The data processing server is accessed from the 'Data Processing' desktop icon on any of the other user terminals.
  • Computer Accounts
    • CMCF staff will setup user accounts under the name of the experimenter's PI.
  • Data Backup and Transfer
    • The most convenient method of backing up your data is to bring your own USB external hard drive. Ensure that any external hard drive is properly configured before coming to the beamline.
    • Experimental data backups on the CMCF beamline have limited server space. The oldest backups of data are removed from the server as required (currently about one month, but this is expected to decrease).
plusTransferring Data
Here are a number of ways to transfer your data:
  • Fire-wire drive mounting procedure:
    • To mount a firewire drive, simply connect the drive to the firewire port located on the front of either OPI1608-001 or OPI1608-002.
  • USB drive mounting procedure:
    • To mount a USB drive, simply connect the drive to the USb port located on the front of either OPI1608-001, OPI1608-002 or OPI1608-003.
  • Burning DVD (not recommended):
    • DVD burners are located on all the computers. The software used for burning DVDs is called K3b and can be found by clicking on Applications → Sound & Video → K3b.
  • Secure copy (scp).
    • This is the command to recursively copy a whole directory (not allowed in SFTP) from the local computer to a remote computer using secure copy:
      scp -r LocalDirectory <username>@<Remote Computer>:/<Absolute Path>
      e.g.: scp -r /data/directory001 user@computer.usask.ca:/home/user/directory (at which point it asks for a password).
  • CANARIE Lightpath
    • Implimentation in progress.

Data Collection

plusData Collection
  • Data collection is done using the Macromolecular Crystallography Data Collection (MXDC) GUI (follow the link for more details).
  • Directory structure (where and how to create directories):
    • Typically data is stored in the /data/permit_number/prefix directory, where prefix is a string descriptor (e.g. protein name) that is entered in the data collection application.
  • Images file naming conventions:
    • Each data file in your selected run sequence is named in the following way: 'file prefix'_'run number'_'energy number'_'image number'.img.
    • For example, a file could be named data_1_E2_003.img. This image is in the 3rd frame collected in Run 1 at the 2nd input energy.
    • With only one energy level selected, the file would be name 'file prefix'_'run number'_'image number'.img.
  • Entering hutch and mounting crystals.
    • Click "Mount Xtal" using the data collection application GUI to cause the beamstop and the CCD detector to move away from the sample staging region.
    • To enter the hutch, press and hold the red "MAIN DOOR" OPEN button on the endstation panel (labelled 08ID1 BEAMLINE A.C.I.S. PANEL SOE-1).
    • Rotate the protective cover over the sample camera.
    • Physically mount the cryo-pin onto the goniometer. Once the sample has been mounted and no further adjustments are required remember to again rotate the cover away from the camera. (Take special care not to touch or disturb the camera in anyway).
  • Aligning crystals and loop centering.
    • Align the crystal using the Sample viewing GUI from inside the experimental hutch or from the user terminals
  • Exit the hutch and lock up following the lock up procedure above (the safety shutter for the endstation should be opened).
  • Click "Finished Mounting" to reset the beamstop position to default and move the CCD detector to a distance of 300mm.
  • Taking the first image (Run 0)
    • Run tab 0 is for taking snapshots to test crystals and plan strategies for data collection.
    • All other Run tabs can be used for collecting a data set.
  • Adjusting data collection parameters (Run 1, Run 2, etc...).
  • View and process data using autoxds by typing autoxds or autoprocess and specifying the number of frames. It is very necessary to collect 4 degrees of data to obtain a correct strategy.
  • Enter parameters into the data collection application such as the directory you wish to store your data in, prefix for the image file names, distance of detector, omega delta, start frame and end frame. The following is a list of parameters and definitions:
    • delta: Degree of rotation during exposure (commonly 1 or 0.5 deg, depending on spot overlapping).
    • time:  Length of exposure time in seconds.
    • start: The number and omega value assigned to the first image.
    • end: The number and omega value assigned to the final image.
    • inverse beam: Rotates the crystal by 180 deg to collect the Friedel pairs for the input omega range. If wedges are used, the inverse beam is collected before changing the energy.
    • wedge: The omega rotation range that is collected successively at each energy.
    •  energy: As you enter every new energy, an empty box appears for further energy entries.

 

plusBeam Centre
  • How the diffraction images are displayed:
    • MARCCD data collection program: The image is as seen looking in the downstream direction of the beam. Up on image is up in reality with the origin in the upper left corner.
    • XDS(VIEW): The image is seen looking in the downstream direction of the beam. The image is flipped vertically such that up on the image is down in reality with the origin in the lower left corner.
    • Mosflm: The image is seen looking at the upstream direction of the beam (from the detector towards the crystal). Left on image is down in reality, with the origin in the lower right corner.
    • Fit2d: Image seen as in the MARCCD data collection program but with the origin in the lower left corner.
  • Image coordinates:
    • The following method is used to calculate beam center parameters from the fit2d refined beam center.

      x_marccd = x_xds = x_fit2d = y_mosflm
      y_marccd = y_xds = IMAGE_SIZE - y_fit2d = x_mosflm

      Detector data for our detectors:
      MAR 225: 3072 x 3072 pixels, pixel size 0.073242 mm
plusData Processing Software
  • See