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The Autoindex Tab is used to autoindex test diffraction images (with the option to collect the test images too) and to calculate data collection strategies that optimize data completeness. It can also be used to inspect a data collection strategy generated during sample screening.
The autoindex and strategy results for each sample are grouped under as a Run. Each run has got a unique name. The autoindex Tab navigation toolbar contains links to display a summary of all the user's runs (under user Runs), start an interactive application to generate new runs (New Run) or inspect or edit one of the runs (Selected Run)
The Runs page displays a table summarizing all the autoindexing results generated by Web-Ice.
For each run, the following are listed:
The runs can be sorted by alphabetical order or by time of creation. The Update reloads the page (this is useful to display results generated by Web-Ice in the background since the last visit to the page)
Clicking on a run name allows the user to edit and reuse the run or inspect the results. Once a run has been selected, it will be highlighted in the user Runs table. The user can revisit a selected run by clicking on the name, or using the Selected Run link in the navigation toolbar.
To clear the run and all its contents, click the link [Delete] in the Commands column of the user Runs table.
Selecting New Run link in the Autoindex navigation toolbar opens a new run form page. The user has three options: 1) autoindex existing images stored in the MC computers, 2) import a strategy calculated during screening of the currently mounted sample, or 3) to collect and autoindex new test images from a mounted sample. The last two options require the user to connect to a beamline and they can only be used during beamtime.
A name for the run must be chosen. The run name must be a single word of alphanumeric characters.
Pressing the enter key or clicking the Create button will create the run; clicking on the Cancel button will return to the user Runs page.
This option assumes that the user has already used Blu-Ice to collect the diffraction images and, for anomalous dispersion experiments, the fluorescence scans required to characterize the sample. In this case Web-Ice can read these files and supply a data collection strategy to the user.
The option is selected by clicking the ''Autoindex existing images'' button in the new run form page and clicking the Create button. This will take the user to the Setup page which guides the user through the following run set up steps (The Prev and Next buttons can be used to navigate between the various steps):
This option allow the user to collect test images and a fluorescence scan from a sample. In the current version, the sample must be previously mounted by hand, or using the robot via Blu-Ice, and centered by the user. The slit size should also be set to an appropriate value before hand.
The option to collect images and autoindex can be selected from the New Run form after choosing an accessible beamline from the toolbar. Creating the run will take the user to the Setup pages. The Prev and Next buttons can be used to navigate between the following steps:
The multicrystal strategy mode allows to select the optimal starting and final orientation phi in cases where a full data set cannot be collected from a single crystal, often because of radiation damage during data collection of microcrystals, metalloproteins or samples at room temperature. This option can be selected by choosing the multicrystal option in the Other Options setup page.
Upon selecting the multicrystal strategy option, the strategy calculation program will change to MOSFLM and a menu to select multicrystal strategy options will appear.
If the crystal mounted is the first one in the multiple crystal experiment, the Previous run in the multicrystal series input box must be left empty. Once a strategy calculation run has been calculated for the crystal, a file containing information about the orientation of the crystal and the associated strategy is written out in the webice directory for the run. When another crystal in the multicrystal series is mounted, the immediately preceding run must be selected using the drop down menu. This will automatically read in and use the file storing the strategy parameters for all previous crystals in the series and updated with the values determined from the current sample.
The user can specify the expected rotation range that can be collected from the crystal before damage takes place in the rotation angle input box, which defaults to 10 degrees. For the first sample, accurate selection of the rotation range is not critical and could be even left blank -in this case, the program will calculate the standard range to maximize completeness for the crystal symmetry and orientation. However, in general, a fuller completeness will be achieved with a more accurate estimate of the rotation range, based either on the dose calculated by the strategy or the actual decay observed from previous samples.
When a previous run is selected, the program displays the starting and end phi angle determined by the strategy for the previous runs. If these values do not match the data collected from the crystal they can be edited to reflect that data that is actually available (for example, if the crystal was either damaged earlier or lasted longer than the input rotation range)
Note that, for multicrystal MAD and SAD experiments the input angle range will be used, unlike in single crystal mode, where twice as much data are collected by default to improve the multiplicity
If the sample has been mounted and analyzed during a screening experiment, a new run can be created to view the optimal data collection strategy for that sample. To do this from the autoindex tab, follow these steps:
Note: It is also possible to import the strategy from the Screening Tab or by launching the Web-Ice application from the screening tab in Blu-Ice.
Important: The import feature is only enabled if the sample is still mounted on the goniometer. If the sample has been dismounted, the autoindex must be repeated in order to obtain the optimal phi range for data collection.
After the run setup has been completed, a summary of the user's choices is displayed. The user can click the Edit Setup button to change the choices or the Run button to start collecting or autoindexing the images.
The Run Status will be periodically updated in the Run box. Messages will be displayed when autoindexing results are ready for viewing. It is possible to use other Web-Ice tools while the processing is running.
Clicking the Update button will reload the run contents.
The user may choose to abort the data collection or autoindex run by clicking the Abort button displayed after starting autoindexing.
The Selected Run displays a series of links to facilitate viewing all the run analysis results.
The [Scan] page only appears if the Perform Fluorescence Scan option was selected for a MAD/SAD experiment. This page will display a graph showing the raw fluorescence counts as the scan is being carried out, as well as messages from the scan operation. Once the scan is processed with autochooch, a plot of f' and f'' will also be available. The plots can be saved as PNG images by right-clicking on them and selecting the Save Image As... option from the menu.
The [Log] link allows the user to inspect the detailed autoindexing log (with information about each program and version that is run and exit status) and data collection status on the connected beamline. The latter log is shared with Blu-Ice
The [Autoindex Summary] page displays the refined values for the direct beam coordinates (Beam x and Beam y) and the distances; an initial estimate for the mosaicity based on how many of the observed spots are predicted by the best solution; and a list of indexing solutions.
For each indexing solution, the programs displays the following:
A summary of the refinement and integration results for the indexing solution determined by LABELIT is shown at the top of the page. Note that for strong diffraction images the estimated resolution limit may extend well beyond the limits of the detector; in order to collect data to this resolution, you should then move the detector closer to the sample; changing the exposure time by a large amount may have an effect on this estimate.
Note: be aware that the estimated mosaicity value can be underestimated for well diffracting crystals. The estimated value treated as suspect until several contiguous images are available for postrefinement.
The profile fitting for the central region of the images and intensity integration statistics are displayed below the ''Integrated Solution'' table.
To access the entire MOSFLM log and summary file for the integration, see the [Details] link.
To view the predicted spots, click on the [Prediction] tab. This page displays the observed spots, and the predicted spots after autoindexing and integration with MOSFLM for either image used for the autoindexing. The image display parameters can be modified as described in the Image Viewer documentation.
The observed spots used for autoindexing are shadowed in green.
The predicted spots surrounded by a blue circle are fully recorded. The ones surrounded by a yellow circle are partially recorded.
Ice rings and the initial resolution estimate (before autoindexing) are also marked.
[Details] displays the directory tree containing all the files generated by Web-Ice during the autoindex and integration, including scripts, orientation matrix files, logs and output reflection files. Access to these files is useful to validate the image analysis results and to refine the strategy calculation by making changes to the input files and re-running them manually. The contents of non binary files can be displayed by clicking on the file name.
The strategy calculation results are shown under the [Strategy] tab.
The optimal oscillation range for the Laue group determined by LABELIT and the overall completeness are displayed in the ''Space Group'' table. An upper limit for the oscillation per image (delta phi) is also shown in this table. Above this delta phi value, more than 3% reflection in one or more images in the phi range will overlap. Note: The maximum delta value is based on the mosaicity estimation. If the mosaicity is underestimated, the delta phi value will be overestimated.
The full recommended data collection strategy for the determined space group is displayed at the bottom of the page. The BEST strategy calculation results can also be displayed by selecting the appropriate tabs above the data collection strategy table1. Clicking on the phi ranges displayed in the table will toggle between the strategy to optimize anomalous data and unique data completeness.
The Data Collection Strategy table shows all the required input for a Blu-Ice data collection run based on the strategy calculation results. Below is an explanation of how each quantity is determined. If the results are not suitable for the users' experiment it is possible to re-run the calculations as explained in the troubleshooting section.
Important: Web-Ice will recalculate the dose when the exposure time, attenuation or oscillation range are changed in the Export/Collect page. However, the resolution does not change. The resolution corresponds to the diffraction limit of the crystal, and it is difficult to predict the new resolution when the exposure is changed without analyzing another pair of test images first.
|Technical questions: Webmaster
questions: Ana Gonzalez
|Last modified:Tuesday, 13-Aug-2019 14:45:10 PDT.|