MxDC (Data Collection)


MXDC IconData collection at the CMCF is carried out on user workstations using the Macromolecular Crystallography Data Collector software (MxDC). An introductory training video is available. Log on to the workstation using your username and password and start MxDC from the desktop by clicking the "Mx Data Collector" icon. 

The MxDC user interface is organized into tabs, each enabling users to perform specific activities. Some of the tools such as the sample and hutch viewers and diffraction image viewer are available on more than one tab.

Occasionally, a change on one tab will change the status of an item on another tab. This is indicated by highlighting the affected tab. If attention is required on another tab this will also be indicated in this way. A bar at the bottom of every screen displays information about the current beamline name, the stored ring current, the state of the shutter, the Mode and readings from intensity monitors along the beamline.

Beamline Setup

Used to restore beam, choose the "Mode", observe video feed from inside the hutch and select beamline parameters (Energy, Attenuation, Detector Distance, Goniometer Omega angle, etc.). The status of beamline components are also found here.

beamline setup tab

The upper left has buttons to restore the beam and choose the Mode. On the right, experimental parameters can be adjusted and an estimate of achievable resolution at the current detector distance is displayed. There is a pane to view the hutch or sample on the lower left. The statuses of beamline components are visible on the lower right. This is the first place to look if you are having problems or if there is no beam.

Restore Beam

To open the shutters, click the Restore Beam button:

  • this needs to be done after locking up the hutch or after an injection
  • you may also need to restore beam at the beginning of a remote session
  • please visit the Beam Optimization section for more information about maintaining optimal beam

Modes

It is critical that you are in Mounting Mode when mounting/dismounting samples. Stay clear of the detector and sample position when changing modes. It is best to change modes from outside the hutch.

  • Mounting Mode You must select this mode before mounting or unmounting a sample manually. Click this button on the workstation computer before going into the hutch to mount your crystal. This is for safety reasons and to help protect the instrumentation from possible damage. The capillary, cryojet, backlight, beamstop and detector will be away from the sample position in this mode to give room for mounting samples.
  • Centering Mode After you mount your sample, select this mode to align your crystal. This will bring the backlight and cryojet into place as well as start moving the detector to a position more appropriate for data collection. Make sure there is nothing in the way of these components.
  • Collect Mode There is no button for Collect Mode. When you start a data collection, the software will move into Collect Mode automatically. In this mode, the backlight will move out of the way and the capillary will be moved into place.
  • Automounter  When using the automounter, the modes will be changed automatically for you. However, please ensure that before beginning a session that the system is in Mounting Mode and that no sample has been inadvertently left on the goniometer.

Experimental Parameters

setup_optionsEach parameter can be adjusted by entering the desired value in the box. (The grey box beside each editable box shows the parameter's current value). You must hit ENTER or click the check mark before the value will be applied. While the parameter changes, you will see its value updated in the current value box, and the check mark will turn into a red stop button that you may use to cancel the parameter change. Some of the values may be set from within the Data Collection tab and such values in the Data Collection tab will override those in the Beamline Setup tab during a data collection.

  • Energy (keV)  Energy changes are fully automated on beamline 08B1-1 and partially automated on beamline 08ID-1. Please see the Energy Changes section for more information.
  • Attenuation (%) The current value of attenuation is calculated based on the actual foils used, taking energy into account. Increase the attenuation if you are getting too many overloaded pixels. You must change the attenuation on the Data Collection tab for it to take effect during a collection.
  • Omega (deg)  Allows you to control the rotation angle in degrees of the sample goniometer. Use this if you want to view your sample at a different angle during centering.
  • Beam Size (microns)  A pull-down menu allows you to control the aperture size on beamline 08B1-1 (20, 50, 100, 150, 200 microns). Note that the beam size is fixed on beamline 08ID-1 (50 microns) and not adjustable through MxDC.
  • Beamstop (mm)  The distance of the beamstop from the sample. Normally this will not need to be adjusted.
  • Detector Distance (mm)  Allows the user to control the distance of the detector from the sample.
    • Beamline 08ID-1 minimum detector distance = 150 mm.
    • Beamline 08B1-1 minimum detector distance = 115 mm. 
  • Detector 2-Theta  Do not use this feature at this time. If you require the detector 2-Theta to be changed, contact the beamline staff.
  • Gonio Kappa, Chi & Phi These can be used on beamline 08B1-1 to change the orientation of the crystal on the Mini-Kappa device. They are not available on beamline 08ID-1.

Samples

Used to load sample information, control the automounter, align samples, verify the beam position and control the cryojet or humidity control device (HC1).

Available Containers and Crystals Pane

From here you can load a sample spreadsheet or your MxLIVE database which contains sample information. You may use this whether mounting manually or when using the SAM Automounter (see Samples & Automounter for more information).

  • Use the icons at the lower left of the pane to load a spreadsheet, load information from MxLIVE, or remove a list which you added previously.
  • If you are using the automounter, staff will help you load the Uni-Pucks (or cassettes). The appropriate position of each Uni-Puck (or cassette) must be entered (ie: L=left, M=middle, R=right). Above, Uni-Puck "UP-2" has been loaded into position Left-A (LA) and Uni-Puck "UP-1" has been loaded into position Left-B (LB). Do not specify positions if you are not using the automounter.
  • Double-clicking on an available crystal will make it the active crystal.

Automounter Pane

Will show a visible representation of the Uni-Pucks or cassettes in either the Left, Middle or Right positions of the automounter. You will only use this pane if you are using the SAM automounter (see Samples & Automounter for more information).

  • Positions that are not coloured have an unknown status. Once probed, they will either be coloured green (sample present), dark grey (no sample) or red (unmountable/port jam).
  • Green or non-coloured positions can be selected then mounted using the "Mount" button. In the example below, sample LC5 has been selected and is ready for mounting. Once mounted, the sample representation turns magenta and the sample will appear in the window next to "Dismount." It can be dismounted by clicking "Dismount".

Sample Camera Pane

Shows a live view of the crystal (or hutch, if desired) and has buttons to align samples. There are two sliders in the lower-left corner pane to control sample lighting to better visualize samples.

  • Beamline Mode. Normally in Centering Mode. If you wish to check the position of the beam, you may select the Beam Mode. Ensure that no samples are mounted when checking the beam position as they may be damaged. Note: this function is not available on beamline 08ID-1 at this time.
  • Zoom Level. If crystal is not visible, decrease zoom level using the zoom level buttons. The three different buttons correspond to three different selectable zoom levels. Normally, use the middle zoom for final centering.
  • Move Sample. The sample needs to be rotated as part of the alignment process to ensure the axis of rotation of the crystal intersects the beam at all angles. There are three preset rotation angles used to accomplish this (-90°, +90º and +180°). To get the crystal in the field of view or for manual centering, you may use the arrow buttons. These buttons allow for small movements in either direction. Normally, the crystal is aligned by centering the crystal as described below. 
  • Centering. Manual point and click centering is activated by selecting the "Click" button within the Sample Camera pane. The crystal is aligned as follows:
    1. Select a low Zoom Level to find the sample.
    2. Ensure "Click" Centering is activated, click on the sample and wait for it to center.
    3. Rotate By +90 (or -90) degrees.
    4. Click on the sample once again to center.
    5. Select a high Zoom Level.
    6. Repeat steps 3 to 4 until crystal is aligned.

    After aligning the crystal you should check the beamline parameters and adjust them if necessary.

Cryojet Stream Pane

You may use this panel to retract the cryojet or restore it to the correct position for data collection, although this is usually done automatically. There is also the capability of annealing your crystals for any desired length of time.

Humidity Control Pane

When using the Humidity Control Device (HC1), the humidity controls and display are available on the Samples Tab in the same pane as the Sample Camera Pane and Cryojet Stream Pane, respectively.

From the Humidity Control pane (shown above), you will see the following items:

  • Status: normally green, but any HC1 technical problems are displayed here
  • Relative Humidity: you can specify any relative humidity above atmospheric humidity up to 99%
  • Sample Temperature: the temperature depends on the humidity selected, not normally controlled by User
  • Region of Interest: Select "Reset" followed by "Define" then outline the area of interest. In the picture above, the green region has been selected as the region of interest and the software automatically finds the widest section of mother liquor in the loop, displayed as the blue line. You may have to reduce/adjust the backlighting.
  • Plot Controls: These control the timescale of the plot and whether temperature or drop size are recorded on the plot. In addition, plotting can be paused or cleared.

Plots of experimental progress are displayed in the Humidity Control pane, where relative humidity is plotted against time. Additionally, you may choose to plot either drop size or temperature:

For additional information on performing a dehydration experiment using the HC1, please see the Humidity Control & XAS page.

Data Collection

Used to set up crystal screening and run parameters for collecting single or multi-wavelength datasets.

There are 3 main areas: the diffraction viewer (left), the run status/control area (centre) and the data collection run tabs (right).

Diffraction Viewer. To zoom into any area, use the left mouse button. The bar below the viewer displays numerous options. These include opening an image file to view, going back to a previous zoom level, returning to the original zoom, adjusting contrast and brightness, colorizing the image, restoring image settings, advancing and going back to previous images, displaying the current image and opening an information panel. The pixel values, intensity and resolution estimate of the mouse arrow position are also displayed on the far right of the bar.  

Status/Control area. The section to the right of the diffraction viewer indicates the current status of beamline parameters, selected crystal (which can be mounted/dismounted from here), the selected strategy (which can be implemented from here). Below this display is the progress of collection and estimated time to completion.

  • Even if you are collecting manually, you can click "Mount" to indicate that you have mounted the indicated crystal. This will associate the indicated crystal name with the dataset.
  • Collect/Pause/Resume Button. After the run parameters have been defined and saved into the queue, data collection may be started by clicking the Collect button. If you neglect to apply the run parameters first (check mark button, see below), nothing will happen! You may pause the run at any time then click the Resume button to Resume. The run may be stopped by clicking the Stop button.

 

Data Collection Run Tabs. On the far right is the Data Collection Run Tab containing parameters that may be adjusted by the user before starting a collection.

  • The MXDC program is capable of handling multiple runs with different parameters (e.g. detector distance, exposure time). The user is free to add and delete tabs except the Run 0 tab, which may be used either for screening or collecting data. Run tabs are added using the Plus button and deleted using the Minus button.
  • If a crystal has been mounted it will be indicated in the "Crystal" box and will be associated with the dataset.
  • The Run 0 tab includes a resolution predictor to assist the user in determining a suitable distance for the detector. If you wish to use other energies you will need to use Run 1 or some other Run besides Run 0.
  • Runs besides Run 0 will also have a "Comments" box. Comments entered here will be associated with that dataset in MxLIVE. 
  • The parameters are as follows:
    • Prefix: The string that will be used at the start of the name of each of the saved image files. For example, in this case, the first image will be named A1b_001.img
    • Folder: This is the file directory where your images will be stored.
    • Distance: The distance between the sample and the detector.
    • Delta: Degree of rotation during exposure (commonly 0.25 - 1 deg on 08B1-1, or 0.1 - 0.2 deg on 08ID-1).
    • Time: Length of exposure time in seconds (typically 0.2s on 08ID-1, or 2 - 15s on 08B1-1).
    • Start: The frame number and omega value assigned to the first image.
    • Total: The frame number and omega value assigned to the final image.
    • Wedge: The omega rotation range that is collected successively at each energy.
    • Skip: The frame numbers to skip (for example if you want to collect a few images starting at 0 deg then a few more at 90 deg).
    • Attenuation: The percentage attenuation (for example "75" will reduce the beam intensity about 75%).
    • Inverse beam: Rotates the crystal by 180° to collect the Friedel pairs for the input omega range. If wedges are used, the inverse beam is collected before changing the energy.
    • Energy: As you enter each new energy, an empty box appears for further energy entries. If more than one energy is used in the data collection, the energy label will be appended to the image prefix.
  • The buttons at the top of the Run tab are to apply the run settings, update parameters (to current positions or current strategy if available), reset parameters to default, activate/deactivate run or delete the run.

Image Information

Info IconBeneath the diffraction image pane is an Informatin Button. Click this anytime to view information about the image currently displayed.

Guidelines for the MARCCD detector (08B1-1): Generally expect an average intensity between 25 and 200 (lower for well diffracting crystals). The maximum intensity should generally be between 20,000 to 50,000 with few or no overloads. This may be lower for SAD data where higher redundancy and very low crystal damage are wanted. On beamline 08B1-1, typical exposure per frame is between 2 and 15 seconds (0.2 - 1 degree oscillations), and the 200 or 100 micron beam size is recommended in most cases. Smaller beam sizes can be used but will have lower flux on the sample.

Guidelines for the Pilatus detector (08ID-1): Generally expect an average intensity between about 10 and 30. On beamline 08ID-1, typical exposure is 0.2 to 0.4 seconds / 0.2 degrees. When choosing an angle increment (delta omega), the time should be chosen to be roughly equivalent to the angle increment (for example 0.1 seconds / 0.1 degrees, or 0.5 seconds / 0.5 degrees). The beam size is fixed at 50 microns.

Info Screen

Screening

Used for automatic screening of crystals using the Automounter or for raster scanning. If using the automounter, be sure to visit the "Samples & Automounters" section for more information.

Sample Selection Pane

This pane is used to choose samples for automatic screening. Simply click the boxes in the "Selected" column to select or deselect which samples to screen automatically. There are "Select All" and "Deselect All" buttons for your convenience.

  • This area has an additional Diffraction Viewer Pane for easier viewing of images collected during screening.

Automatic Screening Pane

Here, you decide what sequence of events the system will follow.

  • In the example below, samples "u-xtal-17" and "u-xtal-29" will be mounted, centered, 2 frames collected at 0, 45 and 90 degrees, and the results analyzed for each. We recommend that you select "pause" after centering to manually verify that each sample has been centered properly. Select an appropriate Parent Folder, Delta, Exposure Time and Detector Distance to be applied to all samples.

  • Be sure to define an appropriate parent folder, usually the date of the experiment.
  • After you are satisfied, click the "Apply" button and the sequence of events will be displayed in the "Screening Tasks" pane.
  • When you select "Start" the screening begins and the status is displayed.
  • If the system has trouble centering a crystal, a message asking for intervention will be displayed.
  • View the diffraction frames using the Diffraction Viewer Pane within the Screening Tab.
  • Results of the analysis are displayed in the Processing Results Tab

Raster Screening Pane

The raster screening option allows you to scan a sample in order to determine the exact location of a crystal, based on diffraction. This is useful, for example, when you have trouble locating your crystal by eye. Before you begin, the sample should be mounted and centred normally. When you select the Raster Screening tab, you will be able to specify various parameters including; prefix, folder, loop size, detector distance and exposure time.

 

  • Gonio Omega can be adjusted by entering an angle.
  • The Beam Aperture is normally set by beamline staff and not adjustable by the User.

Once you are satisfied with the parameters, click "Apply" and the Sample Cameral Pane will be updated with a blue grid overlay.

Each blue circle represents a spot that will be scanned and is the same size as the current beam aperture. The mouse can be used to deselect regions that are not of interest. Only areas covered in blue will be scanned. In the example below, only the loop will be scanned.

After you click "Start" the raster scanning should begin. The sample will move such that an image is collected and analyzed for each blue spot. The results will be displayed in the Results Pane and the spot colour updated such that regions with highest diffraction are coloured red.

Fluorescence Scans

Used for excitation, MAD and EXAFS scans. The excitation scan is used to identify and/or verify the presence of anomalous scatterers in the sample. The MAD scan (or energy scan) is used to select the appropriate wavelengths for anomalous dispersion experiments (optimized SAD and MAD). The EXAFS scan is available on beamline 08B1-1 and is used to characterize the coordination of a metal. Please visit the XAS section for more information.

  • For a MAD or EXAFS scan you must first select the element from the Periodic Table tab by clicking on a particular edge before pressing the Scan button. Only edges available to the beamline you are using are accessible on the table.

  • The scan mode is selected by using the buttons under "Scan Mode:". The results are placed in the chosen directory and the file name is derived from the string entered as the "Prefix."
  • After a MAD scan is complete, peak, inflection and remote energies will be calculated. These values can be used to update the strategy that will be used in the Data Collection tab by clicking the Update Strategy button. If you select New Run, a new Run Tab will be created with the appropriate energies.
  • Results from an EXAFS scan are output using the standardized XAS data interchange specification (.xdi file format) to ensure compatibility with XAS software.

Processing Results

Used for processing datasets or screening using Autoprocess. Results from sample screening with the automounter are also displayed here.

  • Datasets that you have collected will appear in the lower Datasets window
    • You may add datasets using the "Add" button.  To add a dataset, select the corresponding .SUMMARY file.

After selecting a dataset, click either the Screen or Process button.

  • Additionally you can choose Anomalous (to keep Friedel pairs separate) before processing (or obtaining screening results)
  • For merging datasets or processing MAD datasets, choose the appropriate datasets (multiple datasets) then choose Merge or MAD before processing. Multiple datasets may also be chosen without the Merge or MAD options. In these cases they will be processed sequentially as separate datasets.

Once Autoprocess has processed or screened the dataset, it is displayed in the Data Analysis Results window above

  • those identified with a green circle are complete

Double-click the dataset of interest and view the processing or screening results in the right-hand pane

If you wish to use the strategy recommended by a screen, simply click the Select Strategy button and the strategy will become the "selected strategy". The selected strategy can then be applied to the the data collection and implemented by selecting the Update Parameters button in the Run Tab of the Data Collection window.

Interactive Tutorial

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