MXCuBE

MXCuBE2

MXCuBE2 is the Beamline Control environment used at MX beamlines. MXcube2 provides a completely redesigned GUI that simplifies user interaction and opens to more complex experiments in an automated way.

   MXcube2 interface has been completely redesigned to permit simpler operation of more complex experiments.

mxcube_1.png

The interface is virtually divided in four areas. The first one (see figure - 1) contains the data collection queue, below the usual login menu, the second one (2) the sample view and motors control, the third one (3) some subtabs with the Collection methods, (Discrete - i.e. normal data collection, Characterization - aka Edna, Energy scan - on tunable beamlines, Helical data collection and Advanced (i.e. workflows for meshes, line scan, crystal reorientation, dehydration, etc). The last and forth one (4) contains ring current, photon flux, cryo temperature, control for shutters and beamstops and remote access menu.

 

 

The queue contains:
- Sample changer content
- Sample list from ISPyB
- Data collection queue for each sample
- History of data collection for each sample
- Results of characterization, energy scan, meshes etc for each sample.

 

  Start MXCuBE2

To start MXCuBE2 use the icon on the left screen "MXCuBE2.0" or, remotely, type "mxcube2" in a terminal on the control PC

Data Collection Queue

The queue is organized with the hierarchy: Sample - Data collection group - Data collection. In a simple view it is possible to follow the status of the experiment, showing what has been collected, characterized (successfully or not) and what is still be be collected and on which sample.

queue.pngsample.png

collection.png

A Data Collection Group is grouping together data collection of the same kind that should be linked together. This is particularly relevant for multi-positional data collection. A data collection can be a Characterization, a Discrete, a Helical, an Energy scan and an Advanced data collection. Each line of the queue is preceded by a checkbox. Selected checkbox will be executed after clicking on Collect queue, at the buttom of the window.

MXCuBE2 permits to (pre-)fill the collection queue with any of the data collection method, and on any crystal contained in the sample changer. How to fill the queue: The sequence is the same for any kind of data collection. (1) Select the sample in the queue (by clicking on it) and a centered position and (2) add a data collection method by clicking add to queue button, at the bottom. This procedure is needed in order to permit the data collection on multiple sample and on multiple positions. To collect all checked elements click in (3) Collect queue.

 

Sample centering and Saving position

Sample is loaded with right-click on it and select mount. While executing the queue, a sample "checked" will be mounted. After sample load, loop is autocentered, then user can accept or improve the centring using the three-click procedure. Save the position by clicking on Save button. A mark (in bold green in the figure) indicate the saved position. More than one position can be saved, by re-centering (in thin yellow in figure). There is no limit to the number of positions. To move from one centered position to another it is sufficient to double click on them. Centered position can be selected by clicking on them. The figure above shows two saved positions, on of them is selected (in bold green). The selected position will be associated with the data collection method, when clicking add to queue (see below).

N.B. Position saving is not mandatory. If no position is saved, MXCuBE2 will either wait for a position to be specified (using the procedure described above) or continue after clicking the Continue button.

Add to Queue

Add to queue add a desired data collection to the selected sample and the data colletion will be performed on the selected position. Right-click on the data collection gives access to all details of the data collection, even those not available in Collection method menu.

Collect queue

Clicking on Collect queue will execute all tasks that are checked (mind the difference between checking - from checkbox - and selecting - highlighting a sample or a Data collection). Resuming any kind of Data collection can be performed with the sequence:

Select sample ---> Select saved position ---> Add to queue data collection ---> Collect queue

This is the most simple sequence. More complex data collection scenario can be built, using the same logic and sequence, without limitations.

It is possible to select more than one position, two for example, then add to queue. This will add the same data collection to the two points, and the two data collection will belong to the same data collection group (see below).

Modify Data collection parameters

The content of each data collection can be modified anytime before collecting data. Any Data collection parameters can always be modified by editing any parameter directly in the Collection method menu. o do this select (i.e. highlight) the data collection, you will see that the selected position will be highlighted and the parameters displayed. At this stage you can modify any of the parameter, without the need to replace the data collection with a new one, and you can even change the position. The position at which the Data collection will be performed can also be changed just by selecting another saved position.

Selecting multiple samples

By selecting multiple samples the same data collection will be added to each of the sample (so-called pipeline mode). In this case a "sample centering" task is added to the queue, for each sample. While executing the queue, MXCuBE asks for user intervention after mounting the sample and automatically centered the loop.

It is important to notice that, even in this case, the prefilled queue can always be modified, either by centering in more than one position, by adding another to the queue. If you do not need to add or modify any centered position you can just click on the continue button, at the bottom right of the data collection queue.

This way is particularly convenient for screening a large number of crystals or to perform routinely the same data collection on multiple crystals.

Collection methods

Discrete

Discrete data collection is just a normal data collection with standard parameters.

Characterization

Characterization Data collection make use of the software described in the EDNA paper. If the characterization is successful a Data collection plan is proposed as a new data collection node. To collect with th suggested plan, check the corresponding box in the queue tree and click on Collect queue. Also in this case it is possible to modify the results, by selecting the data collection and modify the parameters.

Data collection plan results are preserved at sample level.

Click on sample characterized, Discrete tab contains as parameters the result. This can be used for different purpose, such as, making a MAD experiment, (by checking the MAD checkbox and selecting the desired energy, in case an energy scan was performed on the same sample), or use the same strategy to modify the data collection to an inverse beam geometry.

Energy scan

Energy scan is now considered by all means a Data collection. To perform an Energy scan, select the element, and add to queue. To see the scan and the Chooch result right-click on the Energy scan in the queue and select Details (or double click on the Energy scan in the queue). Results from Chooch (i.e. peak, inflection point and high energy remote) are available in the other Data collection method by checking the MAD box and select the Energy.

Helical

In order to perform a Helical data collection two centered position should be save. Then select both positions (holding ctrl) and click on "+" in the helical menu. This adds a line between the two points. Then add to queue the helical data collection.