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Subsections
Screening Crystals
The Screening tab provides an interface to view the results of
automated screening with the Blu-Ice/DCS
software. The
screening tab allows viewing and editing of the spreadsheet containing
sample information and diffraction analysis results and also detailed
inspection of the images and results obtained for each screened
sample.
When clicking on the Screening Tab for the first time in the
session, the browser displays the User Cassettes, a list
of the spreadsheets previously uploaded to SSRL by the
user. When a beamline is selected, the Beamline Cassettes will list the spreadsheets currently assigned to
each cassette position in the beamline.
The search tool at the top makes it easy to locate a specific
spreadsheet. The search input box allows use of the wild-card ''*''; in
this case all the spreadsheets matching the partial name will be displayed.
The spreadsheet contents are accessed by clicking on one of the following links:
- Summary: Displays the selected spreadsheet in a table
format. It also allows access to a tool to edit the spreadsheet
contents.
- Details: Allows detailed inspection of the diffraction
image analysis and autoindex results for each sample.
- Download Excel: Allows the user to download the
spreadsheet to the user's computer. If the spreadsheet has been used
in the automatic screening, the image analysis and autoindexing results
will be in the spreadsheet.
The link Upload new spreadsheet directs to the
Screening System Database (usually to upload a new spreadsheet).
Figure 25:
Spreadsheet list with links to the screening results, Excel
spreadsheet file and the Screening Database interface.
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Once a cassette has been selected, it is possible to revisit the
results for that cassette by clicking on the Cassette Summary
and Cassette Details links in the Screening Tab navigation toolbar.
Cassette Summary
In the Cassette Summary view, the spreadsheet is
displayed in a table
format. All rows (each corresponding to a sample)
are displayed. The columns and the contents displayed can be controlled by the
display options set in the Preferences Tab.
Figure 26:
Cassette Summary: the users' spreadsheet is displayed in
table format.
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Screening Results
If the user collects two images during screening, autoindexing
of the images will be carried out automatically. The following columns
will be shown in the Cassette Summary - Results
view and appended to the user's spreadsheet:
- Unit cell and Bravais lattice. Note that the
symmetry is, at this point just an educated guess. The actual Laue
group and the presence of pseudo-symmetry can only be detected during
scaling. Sometimes, particularly if the diffraction is poor, a lower
symmetry than the correct one can be chosen by
LABELIT.
- Mosaicity: The initial mosaicity estimate by MOSFLM. The
estimate is based on how many observed spots are predicted and it is
good enough for strategy calculation and sample characterization. A more
accurate value can be obtained after post-refinement using a larger
number of images.
- Rmsr: Root mean square deviation between the observed and
predicted spots, as calculated by MOSFLM after image integration. It
is usually around 0.05 or less for good crystals.
- Resolution: The diffraction limit of the crystal at the
used exposure time based on the
values. The limit is set at
If the diffraction is very strong, the resolution may
extend beyond the limit set by the detector area and sample to
detector distance used during screening.
- Score: Calculated as
, where is
the resolution limit in Å, rmsr (described above) is in mm, and
is the mosaicity in degrees. A score of 0.4-0.6 indicates
borderline quality. Good crystals usually have a score of
about 0.8 or higher. This score is meant to be used as an
initial indicator of the sample quality; although it has been
found to agree reasonably well with human assessment in many
cases, it is recommended to inspect the diffraction before
choosing a sample for data collection.
- Image: Diffraction image name.
- System Message: If the autoindexing fails, the error
message from LABELIT will be displayed in this column.
A second set of results are appended to the Excel file as a
separate column for each diffraction image, regardless of whether
autoindexing has been performed or not. In the Cassette
Summary page they can be seen by going to the
Preferences Tab and setting the Image Display Type
set to ''Show all Crystal Links'' (for all samples) or ''Show
Selected Images'' (only for one sample). If a group of two or
more contiguous images are collected at each crystal orientation,
results are given only for the last image in each group.
These values are particularly useful if the autoindex
fails. Having an independent quality assessment for each image is
then useful to determine if the sample merits further inspection
or it can be safely discarded.
- Crystal JPEG: Snapshot file name.
- Spot Shape: Mean value of the longest spot dimension
divided by the shortest one. It is between 1.5 and 2 for good crystals.
- DISTIL Resolution: Resolution estimate by the LABELIT
SPOTFINDER module,
based on the number of spots in resolution shells.
- Ice rings: Number of ice rings.
- Diffraction Strength: Average spot intensity.
- Score: The score for the individual image. 0 or 1 usually indicate no
useful diffraction. A sample scoring higher than 4-5 may merit
inspection. Very different scores for images at different orientation
indicate anisotropic diffraction or a badly centered crystal; this can
be confirmed by inspection of the Crystal JPEG.
A sample is selected by clicking the radio button in the port
column; only one button can be selected at a time.
Figure 27:
Selecting the sample row A1.
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Data collection strategy
A data collection strategy will be calculated during screening if
the sample stays mounted on the goniometer head3 after the
screening shots (i.e., by inserting a ''Stop'' in the screening task
sequence in Blu-Ice - see the Blu-Ice User
Manual). In
this case, the View Strategy button will direct
the user to the Autoindex Tab, from which the
strategy results can be viewed once the strategy calculation is
complete. If the strategy calculation has not been finished, the
Update button in the Autoindex Tab to update the contents of the run.
The Analyze Crystal button can be used to re-run the
analysis and autoindexing software for a selected sample. This is
useful if the test images for that sample have been recollected or in
case of a software crash or server time-out during the first analysis.
While a sample is being re-analyzed the Analyze Crystal
button will be disabled. Use the Update
button to display the new analysis results.
To access the sample editing tool, select a crystal as described
above; then, click the Edit crystal
button at the top of the spreadsheet table. This will link to the
the Edit crystal tool page (shown in
figure 28). The selected sample row is displayed and
only certain fields are editable. Click Set Crystal to save the
changes. To cancel the changes, simply exit the page by clicking the
Cassette Summary button (to return to the spreadsheet table) or
All Cassettes or Cassette Details to access the user's
spreadsheet list or the detailed screening result viewer
respectively.
Figure 28:
Sample editing tool
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Some column headers are displayed as links. Clicking on
will result in column sorting, toggled between ascending
and descending. For example, to sort the samples by score, click on
the Score column header.
Note: The sorting affects the table display only.
The actual Excel spreadsheet is always sorted by port ID unless the
user edits the Excel file directly.
Updating the Spreadsheet
The spreadsheet is updated with the latest available screening
results automatically every 5 seconds by
default; this can be changed from the Preferences Tab.
The Update button can also be used to reload the spreadsheet from the
crystals server.
Cassette Details
The Details page is similar to the Image Viewer
tab;
but instead of using the file browser to locate the image file, the
user uses the cassette browser.
The top left frame displays one of the images of the selected
crystal. Like in the Image Viewer, the user can zoom, pan,
and adjust the brightness. The Analyze Image button displays
the image with highlighted spots picked by SPOTFINDER. The user
can toggle between Analyze Image and Image Only
to display or hide the highlighted spots.
The top right frame contains various tabs that display
information about the image and the autoindexing results:
- Header: The Header tab displays the image header.
- Analyze Image: This tab displays the image
analysis results. The analysis results (logs and JPEG
images) are stored together with the user's data under the directory
crystal-analysis.
- Crystal Image: The Crystal Image tab displays
the crystal snapshot JPEG file.
- Autoindex: This tab displays the autoindex
results from LABELIT. Autoindex will be carried out if two
images at different crystal orientations are collected. Image or
images collected at a third orientation will not be used for the autoindex.
- Details: The Details tab lists all the output files from
autoindexing. The results are stored together with the user's data
in the directory listed at the top of the Details view. The
files named indexXX and indexXX_S. mat are the MOSFLM input script
and matrix used for solution number XX. By clicking on a file name,
the contents will be displayed on a separate browser window.
The bottom frame contains the cassette
browser tool. It displays an array corresponding to the
ports in the cassette (or unipuck). The ports that contain valid crystal id are displayed with
links, otherwise they are grayed out. When the user clicks one of the
ports, the first image collected for that port will be displayed.
The Analyze and View Strategy buttons
have the same functionality as in the Cassette Summary
page.
Note: The Update function and button only activate the link to
the latest sample for which results are available. It does not update
the images and results displayed.
Footnotes
- ... head3
- Typically,
the crystal orientation will be different after each sample remount,
so the collection strategy will change accordingly.
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