MxCube overview                     How to center your sample with MxCube                     Collecting single wavelength data                     Collecting Mad data

MxCube Overview

MxCube provides a unified beamline control module for the PX station and ties togeather all the operations involved in collecting data for PX experiments in a single user friendly interface.

To launch the GUI, click on the MxCube icon on the desktop of BM16mach. An image of the BM16 MxCube interface is shown below.

You also need to have a PX Spec session running to use MxCube (to start a PX session click on the PX icon on the desktop of bm16mach).

Centering your sample in MxCube

You can center your sample using SampleVideo in the experimental hutch or by using MxCube in the control hutch. Follow the steps below to carry out a 3-click alignment in MxCube...

The blue box represents the beam profile at maximum zoom the red cross represents the rotation axis.

1. click on the arrow next to the Zoom button and select Zoom 0 from the drop down menu
   
2. if you still cannot see your sample or loop when the camera is at minimum zoom (Zoom 0) the sample is off the edge of the screen and should be translated horizontally to bring it into the cameras field of view. To do this input a new value into the box marked gonioz in the Sample Manipulation brick, and press return or use the arrows next to the gonioz box to translate the sample horizontally in small steps until it is roughly centered on the small red cross.

   Note: you can change the speed of each of the gonio motors by clicking on the box next to the motor and selecting a different step-size or by typing a new value in the step size box and pressing return (fastest speed 0.5 mm/step)

3. once the sample is aligned horizontally you can rotate it by clicking on the Phi buttons which allow you to make absolute movements to 0, 90, 180 or 270 degrees phi or relative movements of +/- 90 or +/-1 degrees phi. The current position of the phi is displayed at all times in the Phi box.

   Tip: you can also rotate the phi motor freely rotated to any value you input into this box.

4. to be begin centering your sample select the 3-Click button
5. a line will appear at the top of the screen asking you to click on the center of your crystal. When you have done this a small yellow cross will appear at the point you click and the crystal will be rotated by 90 degrees.
6. when the crystal stops moving click on the center of the crystal again and it will be rotated by another 90 degrees

   Note: if your crystal doesnt move read the message on the screen to check that your last click has been accepted.

7. when the crystal stops moving make the final click on the center of the crystal and your sample will be aligned horizontally and vertically
8. after this rough alignment at minimum zoom select Zoom 8 from the Zoom box and redo the 3 click alignment at the highest magnification
9. at maximum zoom the beam profile is given by the blue box on the screen and the rotation axis by a red cross. Both these parameters will be set by your LC at the beginning of your beamtime.

For more on 3-click sample centering click here.

Single-wavelength data

For a single-wavelength experiment follow the steps below :!

1. Login with your proposal name and password (e.g. mx 666 password zzmx666 or bm161 666 and password zzbm161666). Click on the arrow next to the Code: box to change the proposal type.

2. Fill in the exposure time, start position, osillation range and No of frames etc in the data collection parameters section of the MxCuBe (see following image)

Note: typical exposure times on BM16 are form 1 to 20 seconds

3. Give a directory and image pre-fix (the default directory path is suggested by MxCube and should start with /data/bm16/external/)
4. Start the data collection with the Collect data button!

MAD data

Click on the Energy scan tab in top left of the MxCuBe GUI.

This will open a tab containing a periodic table listing the available edges you can scan. Then just click on the edge you wish to scan...

When you have selected the element of interest - check the directory pathway is correct then click Start scan and MxCuBe will automatically select the appropriate level of attenuation, perform the edge scan and run AutoChooch to calculate the experimental anomalous scattering factors for your sample. All data related to the scan are saved in the current data collection directory from which you launched the scan. However you can change the directory into which the scans are written, or change the prefix, by clicking on the parameters button and browsing for a new directory. More details on carrying out fluorescence scans at BM16 are given here and a typical selenium K edge  scan should look like this

The raw fluorescence scan will be displayed live and the values of F'' maxima and F' minima, calculated by Chooch, will be piped into the boxes labelled Peak and Inflection respectively. MxCube will also suggest a value for the remote wavelength usually 1KeV above the peak wavelength.

If you click Accept these values will then be piped into the data collection brick.

When you begin a data colllection the program will then automatically set up sub directories for your pk, ip and rm datasets, and will collect the data according to the parameters you set, into the appropriate directory.

Note: The program will automatically change the energy and optimise the intensity before collecting each wavelength.

You can change the order that the wavelengths are collected by clicking on the MAD energies button and selecting the order you prefer from the pull down list. The wavelengths for your MAD experiment will then be displayed in order and you can click on the box next to each wavelength to select or deselect a data collection for this wavelength.

If you want to do a SAD experiment you should click (ie select) only the pk wavelength and deselect the other datatsets. To collect a 2 wavelegth MAD experiment you should click next to either the pk and rm or ip and rm datasets.