The Screening Tab (Fig 1.) provides an interface for automatically screening samples using the SAM system. With this interface, the user selects multiple samples of interest from an embedded spreadsheet and defines the actions to be performed on each sample. Once started, the interface can run with minimal supervision until all of the samples have been screened identically.
[Fig 1] The Screening Tab in Blu-Ice
The screening tab is divided in four different parts (modules or widgets) by one vertical and two horizontal lines. The widgets can be resized by clicking on the resize button on the dividing line and dragging it in the desired direction.
Uploading Crystal Information from an Excel Spreadsheet
Before automatically screening samples in a cassette, the system must first have some basic information about each sample in the cassette. This information is entered into an Excel spreadsheet and then uploaded through a web browser. Templates for the spreadsheet can be downloaded from the SMB website by clicking here: Cassette and Uni-Puck Templates. The template can be edited using Microsoft Excel or the spreadsheet editor which comes with OpenOffice running on a Unix system. Detailed instructions for the content of the spreadsheet can be found in the Users' Guide. Once the information has been entered into the spreadsheet, the spreadsheet is then loaded into Blu-Ice in one of 2 ways:
[Fig 2] Cassette Definition Import Menu
Once the information has been loaded correctly, using either method, the spreadsheet information should be displayed in a table format (Fig. 3).
[Fig 3] Spreadsheet display window
Viewing and Selecting Samples
The Spreadsheet window (Fig. 3) can be used to select the samples to be screened. This window will list the samples in the order that they were defined in the original Excel spreadsheet.
Only three of the columns present in the spreadsheet are used by the screening system as described here:
Other columns are displayed for information purposes. They can be excluded or reordered as explained below.
To the left of the Port column are check boxes used to select samples for screening (the box is blue when selected). These individual check boxes can be clicked to select or deselect all the samples. At the top of this column is a Global selection check box that can be used to select or deselect all the samples. Please note: By default, all samples are selected when the spreadsheet is first loaded into Blu-Ice.
Port Status Indicators
The leftmost column in the Sample Information Widget (Fig. 3) indicates the status of the cassette port.
Customizing the Spreadsheet Layout
After successfully importing the cassette and sample information into Blu-Ice, the spreadsheet is displayed in a table format. The number and format of the spreadsheets displayed can be customized by the user by using the following tools:
Many of the data collection parameters used during screening can be set using the interface on the screening tab shown in Fig. 7.
The Directory entry box specifies where the screening results will be stored. The user's Unix account must have write permissions to this directory, otherwise screening will not start. The Default button changes the directory to the current user's top level data directory. Subdirectories can be added. During screening, the directory will be automatically created if it does not exist. If the sample information contains a directory for each sample, the directories will be subdirectories of this entry box.
The detector mode can be selected, as explained in the Collect Tab documentation
The detector distance and beamstop distance can also be specified. The detector and beamstop will move to the requested distances when images are collected during screening. Clicking on the Update button will change the values in the entry widgets to match the actual physical values of the detector distance and beamstop distance. Clicking on the Update button will not move the detector or beamstop from their current positions.
Attenuation can also be selected to move filters into place during screening to attenuate the beam. Clicking on the Update button will change the value in the entry widget to match the current value of Attenuation. Update will not move any filters into or out of the beam path.Exposure Control (former dose mode) may be chosen via the Enable radio button in the Exposure Control panel.
[Fig 7] Directory and Detector Interface
Screening Action Sequence
The Screening Sequence interface (Fig. 8) allows the user to configure actions to be performed for each sample. The interface consists of a list of actions with a check box next to each action. An action with a selected checkbox indicates that it will be performed during the screening process. Some selections are permanent and will be performed automatically for each sample during screening. These permanently selected actions are "Mount Next Crystal", and the first "Collect Image". The dark green color of these check boxes indicates that they cannot be deselected. "Loop alignment" can be deselected, but if this is done the following "Stop" will become automatically selected; this is done to ensure that the sample is centered, either automatically or by the user, before diffraction shots are collected.
[Fig 8] Screening Action Interface
The following is a summary of the available screening actions:
[Fig 9] Rastering options A: example default settings, B: when the X-ray dose per grid point is increased
[Fig 10] Collect Image
The image filename is constructed as ID_image# with extension .img for Q315 images, extension .mccd for MAR325 images and extension .cbf for Pilatus and Eiger images. The video image file is in JPG format.
Starting and Stopping Screening
Once the samples have been selected for screening and the screening actions have been configured, the screening process can be started. The Screening Control Interface (Fig. 11) is used to control the screening process.
[Fig 11] Screening Control Interface
A summary of each button in the Screening Control Interface is described below:
The screening status is displayed just above the Screening Action Interface.
The left most column in the Screening Action Interface is used to indicate the starting point of screening or the current action. The arrow beside an action will indicate that the screening sequence will start with this action. Once the action sequence is started, a indicator will point to the action currently being carried out. For example, when the robot is in the process of dismounting one crystal and mounting the next, the window will display the following:
during loop alignment the following will be displayed:
and during crystal rotation:
When screening is stopped, the arrow can be moved by clicking in the left column next to a different action. This is useful for repeating or skipping an action.
Additional status indicators can be found to the right of the Screening Task Window (Fig. 12). These indicators are described below:
[Fig 12] Screening Task Window
Screening Task Window
The Screening Task Window (Fig. 12) displays a list of all the samples and actions to be performed based on the crystals and actions selected. Entries displayed in black in this task window will be executed when "Start" is clicked. (If there are no "Stop" actions for example, the entire list will be black and will be carried out to completion.)
The top action in the list will be highlighted in purple if it is currently being executed, and the action will be removed from the list when completed. If there is a "Stop" selected in the Screening Action Interface, the actions up to that point will be black and the remaining actions will be grayed out.
Sample and Hutch Real-Time Video Display
The image of the sample can be viewed in this window by clicking on the Sample Tab. This is the default video display during sample mounting, loop alignment, crystal rotation and image collection.
The sample can be manually centered by 'pointing and clicking' on the part of the sample to center. This behaves exactly the same as the Sample Window in the Hutch Tab. The zoom level can be selected and phi can be rotated from this window.
The Video Snapshot button can be used to save an image of your crystal in jpg format. You will be prompted to enter an image file name.
Selecting Hutch or Robot will display video feeds of the diffractometer, sample surroundings and robot. See the Video Widget documentation for a description of all the video presets.
Data Collection Strategy
[Fig 13] Link to WebIce
Choosing the Web -> Webice option (Fig. 13) will open a browser window and take you to the Screening tab of WebIce. If you have selected "Stop" after collecting two images in the Screening Action Interface (Fig. 8), then the View Strategy button in WebIce will be active, and you will be able to view the results of strategy calculations carried out in mosflm. See the WebIce guide for more information. The Autoindex tab in WebIce can be used to calculate a strategy for any samples for which you have collected two test images using the screening interface.
Collecting Data after Automated Screening
If your sample isn't already mounted on the goniometer, there are two methods for mounting crystals from a cassette and proceeding with data collection:
Once the sample is mounted as described above it is possible to refine the crystal centering; try to improve the diffraction by sample annealing or washing ice off the sample; collect MAD or excitation scans; or collect a data set.
Saving Screening Results
All the information entered into the screening spreadsheet is saved in a database. You may save a spreadsheet to the local file system using the Export button above the spreadsheet display window (Fig. 13). Alternately, you may access the Sample Database via the Crystal server. After logging in, the browser displays a list of the spreadsheets previously uploaded to SSRL together with a link to "Download Results" for each spreadsheet. If a spreadsheet has been used during automatic screening, the image analysis and autoindexing results will be in the spreadsheet.
|Technical questions: Webmaster
questions: Pete Dunten
|Last modified:Tuesday, 30-Apr-2019 12:54:34 PDT.|