Beamline Inductions

If you are new to the MX beamlines or your beamline induction has expired (check by logging into Portal, under Dashboard, Exams/Inductions) then you will need a beamline induction by a beamline scientist before starting your experiment.

Please e-mail beamline staff ahead of time to arrange a beamline induction. Typically, beamline inductions are run at 10am (MX1 experiments) and 2pm (MX2 experiments) at the start of your experiment. If you are cannot be present at these times, please let the beamline staff know ahead of schedule so that an alternative time can be arranged.

Experimental Authorisation (EA) Form

Before arriving at the Australian Synchrotron, check that you are on the user list for the experiment. You can do this by accessing the experimental authorisation (log into User Portal Experimental Authorisations, upcoming - Manage EAs for scheduled beamtime). Prior to your experiment, you should also receive an email titled: “Important information for your upcoming Australian Synchrotron Beamtime”

Start time

Experiments for MX1 (9am to 9am) and MX2 (1pm to 9am) include a 1 hour set up time by the beamline scientist. This means that you can expect to start collecting data at 10am for MX1 or 2pm for MX2 experiments. The set up time can vary depending on how well the beamline is functioning, excessive delays will be communicated by the beamline scientist. Once a Beamline Ready email has been received, the experiment has officially begun!

Check your CAPs user schedule

For larger CAPs comprising of multiple labs, communicate with the CAP to organise a schedule for users and coordinate when each user will take over access to data collection and the length of time for each user. Communicate with the users for the experiment when you have taken over access, when you have finished, and whether there are any delays, for example, if the beamline staff are fixing issues on the beamline. If there are more than 12 pucks in your CAPs schedule, please send a copy of your schedule including puck order to the MX staff.

Remote Access (for those logging in remotely)

If you are collecting data remotely, you will need to log into our remote access server, Guacamole. The credentials for remote access login are provided in the Beamline Ready email. There is an initial ASWebMX user and password prompt, and then finally a randomised password for the experiment. You will have access to 3 different connections or monitors to access the different GUIs for data collection.

Change User via CAP User Changer

All data collected will be collected and saved under the user that is selected in CAP User Changer. To access CAP User Changer, click on Quick Access in the Toolbar (bottom left), and select ‘CAP internal user changer’ in the Quick links prompt. Click the user you wish your data to be saved under.

Locate your sample pucks

It’s important to have a list of which pucks (ASP####) your samples are associated with. These pucks are loaded into the sample dewar that contain 3 adaptors (Left, Middle, Right). Pucks list can be access via Quick Access in the Toolbar (bottom left), and select ‘Robot Dewar Content’ in the Quick links prompt. The pucks can also be viewed from your Beamline Ready email by click on the hyperlink ‘Pucks List’.

If you don’t see your pucks and your CAP has sent more than 12 pucks to the beamline, it’s possible that you will need to request an adaptor change from the AS operators. Their contact details are in the Beamline Ready email, or on a laminated poster stuck on the wall.

Collecting Data

This is the general workflow in collecting data on your protein crystals. You will need to launch 3 GUIs and a webpage. In the Toolbar, you will find the icons for: ‘MX Shutter Flux’, ‘MX Robot’, ‘MX Collect’. The Processing webpage can be opened from the Quick Access button in the toolbar, select ‘All processing results (dataset and indexing)’. It can also be reached by typing ‘processing/processing’ into a web browser.

1. Take over access of the MX robot

It’s a good time to let your CAP know that you are taking over data collection. The MX Robot interface is designed so that only one location (either on site or remote access) can control the robot at any given time.

In the MX Robot GUI (webpage), on the top right corner. If access is currently set to inactive, take over robot access by clicking on the button to change it to active.

2. Add samples to your mount queue

You can add sample pins to your mount queue by clicking on them individually. Otherwise, the ‘ALL’ button on the top right of each puck will add the entire puck to the Mount Queue.

You can remove sample pins from the mount queue by clicking on the ‘cross’ icon. If you want to remove the entire queue, you can click on the ‘Clear Queue’ button on the right.

3. Mounting your sample and other robot tools

The ‘Mount and Prefetch’ button can be broken into two actions:

“Mount” - robot fetches your next sample pin (sample on the top of the queue) directly from the puck or from the prefetch area and mounts it onto the goniometer (the instrument that rotates).

While the robot is mounting, the robot status will read:
'Goniometer motors locked for mount or collection'

“Prefetch” - robot prefetches your 2nd sample pin (sample second from the top) and places it in a slot that the robot can quickly retrieve.

While the robot is prefetching:
'Robot is busy but safe to collect'

It is safe to start collecting data whilst the robot is prefetching.

Entering the Hutch

If you need to go into the hutch. Make sure you ’Park' the robot. The robot status might read:

‘Robot is idle: Must be parked prior to hutch entry’

Avoid going into the hutch whilst the robot is moving, especially during mount and prefetch stages. For your safety, the robot will cease its movement when the hutch is unlocked and open and can cause it to stall. Parking the robot will take some time, when it is parked the following text should show up on the robot status:

‘Robot parked: Safe for hutch entry’

4. Sample Centering

At the top of the page, navigate to the ‘Sample Centering' tab. Most users prefer to use the 'Three Click Centering’ tool, just follow the prompts and pick a particular spot on your crystal.

The ‘Sample Position’ button allows you to move the centering by small amounts. Whilst the tweak angle button allows you to do small angle rotations via entering a custom step size.

5. Screening and Collecting

In the collection GUI, there are multiple tabs for data collection. You should use the ‘screening’ tab to screen your sample (20 degree wedge) to get an estimate on the resolution of your diffraction, the quality of the reflections, and possible space group and unit cell determination.

For larger crystals, it may be worth centering and screening multiple sites to find the best point for data collection

Once you are happy with your choice, navigate to the ‘collection’ tab. We recommend 1s exposure per 10 degrees (i.e. 36s exposure for 360 degree wedge). For most protein crystallography experiments, a 180 degree collection will be enough with proper sample centering and a good quality crystal, but when in doubt: collect 360 degrees.

The distance input determines the distance between your sample crystal and the detector. If your crystal diffracts all the way to the edge, consider moving the detector closer so that all reflections are accounted for. If the your crystal diffracts into a small area in the center, consider if your crystal is worth collection, and if so, move the detector further out.

6. Data Processing

The Data Processing page can be reached using any synchrotron browser by typing in:
processing/processing

It will show a list of auto-processed data by XDS for each of the samples that you have screened or collected. An excel spreadsheet export of all of the auto-process data is automatically uploaded to the EPN folder on our FTP server.

Finished collecting

When you have finished mounting and collecting your data, it is common courtesy and good beamline etiquette to 'Dismount and Park' the robot for the next user or for the beamline scientists.

It is good practise to communicate with your CAP group 15 minutes before you intend to finish to alert the next user that they can get ready to take over. If you are the last user for your experiment, it would be appreciated if you could reply to the beamline ready email and let the beamline scientists know that you are the last user and you are done with collection.