The TaskQueue makes it possible to queue up a list of crystals to be run automatically. The program will still pause to let you center a crystal, but will perform all other steps automatically.
To start, you have to 1) define a SIL — a “Sample Information List”, 2) create a puck definition, 3) define puck locations in the dewar, and 4) put crystals into the queue and start the TaskQueue. These steps are desribed below.
A video tutorial on using the Task Queue can be found here.
1. Define a SIL
This can be done either through the WebIce interface (described below) or manually by clicking on the “Create New SIL” menu item from the SIL menu as shown below. This will cause a popup dialogue to ask you to provide a SIL name. An empty SIL will be created and the name will be added to the “My Sils” combo box.
2. Create a PUCK definition
A puck and pins must be defined. This can be done using the “Puck” menu at the top of the BOS gui.
3. Define Puck locations in the dewar
Select the “Center/Robot” menu at the top of the B3 gui. Click on “Dewar”. Click on the field under Puck Name, and a dropdown will allow you to select the pucks that you entered in step 2.
4. Add crystals to the queue and start the queue
To add crystals to the Task Queue, make a query at the top of the table to display your loaded puck contents. (ie “In Dewar” checked and hit return in the Puck Names field.) Select the crystals you want to put in the Q and drag them over to the bottom of the Task Queue Entries panel. The experimental conditions that are set at the top of the panel determine the run parameters.
Note that you have to define the directory path before adding samples to the TaskQueue, otherwise data may be collected to the wrong directory.
To delete crystals from the Task Queue, select the entry and hit the delete key.
The operation of the Q is controlled by the buttons on the bottom left of the BOS gui.
Start – Starts the Q.
Stop – Stops Q.
Pause – Pauses Q.
Resume – Resumes Q after user interaction.
Skip – Skips collection of crystal.
Redo – Performs collection again.
Lastly, crystals can be “Hand mounted” and still tracked by selected a crystal from the task Q list and hitting the “M” button at the top right corner of the interface. This will tell the system which crystal is mounted and allow webice to work.
Entering SILS and Pucks
SILs and PUCKs can be entered directly through the WebIce interface, rather than through the B3 gui. To access WebIce, click here where you can upload an excel spreadsheet with the Crystal/Pin/Puck information.
Most users with a lot of crystals need some mechanism to record their observations regarding the results of the screening/run. Historically, users carry a laboratory notebook or possibly an excel spreadsheet where they keep track of the information. At the bottom right corner of the BOS gui, there is a “Manual Evaluations” panel. This can be used to record basic observations about each crystal. The results are stored in the database and can be viewed on the Task Queue table.
Alternatively, B3 has been extended to use Webice for automatic data processing. One can use Webice several ways.
1) Via the collect tab. Click on the webice checkbox and 2 images will be taken instead of 1 and the data will be processed automatically by Webice.
2) Click on “Use Webice” on the Task Q setup panel.
The results are displayed on the Webice tab in the BOS gui. Use the SIL selection combo to pick a SIL and click on the row of the crystal to load the information and jpegs of the data. Strategies are also generated and can be loaded into the Collect tab by selecting one from the table and hitting the load button.
The results are also available on the BUDS website. Below is a screen shot of the buds/webice gui. This site has the same information as BOS. Additionally, images can be viewed with the Image Viewer.
Click here to watch Raster Scanning instructional video.
In the raster scanning mode, BOS will collect data based on a user-defined grid. This is useful for crystals that have several potential good spots. Additionally, a SIL can be specified and WebIce can be used to evaluate each spot.
As you can see, the amount of signal coming from a crystal varies greatly depending on the location of the crystal in the beam.
The raster tab is similar to the collect page. On the right side of the screen there are some of the same parameters required for standard data collection. In addition to these, there are parameters for defining a grid around the center of the beam. When these fields are filled in, a grid will appear on the video image. A SIL can be specified and if the “WebIce” checkbox is checked the raster screening results will be sent to WebIce for analysis.
The screen shot below shows the result of running a raster scan on a crystal. The results are showing up in the SIL table. Once the run is complete, the crystal can be repositioned back to the corresponding collection position by clicking on the relevant row in the table. You must recenter the sample on that position once selected.
Click here to watch vector scanning instructional video.
In vector collection mode, BOS will perform data collection along a user defined vector path. This is useful for crystals that are tubular and/or vulnerable to beam damage. The vector is defined by centering the crystal at each endpoint and saving the goniometer position. A number of steps between the end points can be specified. BOS will evenly distribute the number of shots taken by the total number of steps in the vector.
This feature can be activated on the Collection tab in the BOS Gui. Once a run tab is created the “Vector Collection” checkbox must be checked. Also, the two endpoints must be set.
To define the endpoints for vector collection, go to the “Center” tab of BOS. On the bottom of the right hand of the GUI there is an area labelled “Vector Positions.” Center the crystal at the first point and click the upper “Set” button. Next, center the crystal at the end point and click the lower “Set” button. Then, select the number of points to collect in the text box below the buttons.
This feature has to be activated on the Collection tab in the BOS Gui. Once a run tab is created the “Vector Collection” checkbox must be checked in order for the defined vector to be used in the run.
Thank you for reading!