Advanced Features
BOS has been extended in several ways to allow for automation of the experiment. The goal being to reduce as much as possible the number of manual/error prone tasks required to collect data. Additionally, the overall throughput of the experiment should be increased. (ie screen and analyzed more crystals) These new features can be roughly categorized in the following list.
Contents |
[edit] Preliminaries
In order to use the automation features of BOS. There are a couple basic requirements. First, the "mini" Gui must be used. This program has the additional features used for automation. Type "/prod/BOS/Mini.csh". Secondly, One must login to BOS with a non-shared account. (ie not dcsuser) This prevents people from modifying each others information.
Besides using the BOS Gui at the beamline, some features of BOS can be accessed via the buds/webice website. https://bcsb-xs1.als.lbl.gov/webice3
[edit] Crystal Tracking Database
An important aspect of automated crystallography is the tracking of the crystal throughout it's trip to the beamline. In order for BOS to associate user crystals/pins/pucks with whats on the beamline, a mapping is kept in a MySQL database. The database can be accessed via the BOS gui or the Webice/Buds website.The information that is required for this mapping is
1) A unique crystal identifier/name. This name is associated with an internal key for uniqueness.
This is the "key" used to track the crystal.
2) A unique puck identifier/name.
3) The pin location in the puck of the crystal.
Additionally, the location of the Puck inside the beamline dewar must be specified once the puck is loaded. A puck selection list can me used by clicking on the table in the desired position.
Below is a screen shot of the BOS Gui. This is here to provide a visual reference for the following procedures.
Once this information has been provided to BOS, it can keep track of where the crystal is and which data was generated from it along with any evaluations that are generated by the user or webice. The data that webice generates is stored in something called a SIL (Sample Information List). A SIL can be created several ways. One way, is to create one at the beamline via BOS. This can be done by clicking on the "New SIL" button on the webice tab.
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. If you are working with an empty SIL, a puck and pins must be defined. This can be done using the "Puck" menu at the top of the BOS gui.
Another way to create a SIL is to upload an excel spreadsheet with the Crystal/Pin/Puck information. This can be done using the same panel in BOS or using the website.
[edit] Task Queue
Another aspect of automated crystallography is the reduction of tasks that the user has to perform manually. The basic formula for data collection is
1) Mount Crystal.
2) Center Crystal.
3) Screen. Take some data and determine quality or results.
4) Possibly collect full run on crystal.
5) Unmount Crystal.
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.
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.
[edit] Auto Centering
Once the crystal is mounted, it needs to be positioned in the beam. Normally,
the user will manually move the crystal into the beam path via the Gui. If desired,
the user can optionally use XREC to attempt an auto centering of the crystal. When
crystals are added to the Task Queue the amount of user interaction can be specified
by using the "automation" combo box. The options are
1) Pause for User Centering.
2) Attempt autocentering with user intervention.
3) Coffee time.
[edit] Manual Evaluation of Crystals
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.
[edit] Webice Integration
In addition to subjective analysis of the data. Users will often use programs such as HKL 2000 to determine the quality of the data in order to decide there data collection strategy. BOS 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.
