Next: Screening Crystals
Previous: Autoindex and strategy calculation
The tab Process is used to process data sets and, optionally, to attempt structure solution by molecular replacement. Data autoindexing and integration are carried out with LABELIT and XDS. The data are analyzed with POINTLESS and XTRIAGE, scaled and merged with AIMLESS (previously with SCALA, and transformed to amplitudes with TRUNCATE. A free R-set is also generated using 5% of the reflections.
If a PDB file is supplied, MOLREP is run, and the best solution is refined with REFMAC5. Selected statistics and graphical output from these programs is displayed on the results pages; Input scripts and full log files are written to disk, under the /data/$USER/webice/process directory. These files can also be inspected via the web-ice application.
Since June 2017, Web-Ice is used to process automatically the data from the runs in the Blu-Ice Collect tab, if a minimum of 5 images are collected. Older processed data are stored in a separate directory, which can also be browsed from Web-Ice.
See the introduction to Web-Ice for the appropriate software references.
When the Process tab is selected, the user is shown the User Datasets page (it will be empty if Web-Ice processing has never been used before. Once a data set has been processed, this page will list the user supplied dataset name, creation time, the name of the first image in the set and other information about the job status. the Delete link can be used to clear the results from the /data/''user''/webice directory and delete the dataset name; the images will not be deleted.
The processing run results can be browsed by clicking on the Dataset Name of interest.
The runs can be sorted by ascending or descending alphabetical order or by the time of creation. The Update reloads the page and displays any new results generated since the last visit to the page.
Once data processing has been started, the run parameters cannot be modified. In order to change processing parameters, a new run must be started from scratch.
After approximately one week, old processed datasets are moved to a different directory. The list of these datasets can be displayed by clicking on the Old Processed Datasets link.
Clicking on the New Dataset link in the Process navigation toolbar open the data processing input form. If a form has been filled in previously for another run, the form will be pre-populated with the same values.
Once the dataset form have been filled up, processing is initiated by clicking on the Create Run button. The browser will display the results page, which shows the status of the job and links to summarized results and plots by all the different programs.
If automated data processing is enabled at a given beamline, Blu-Ice will automatically start a data processing run when each data collection run is finished, for the purpose of providing quick feedback about the data quality.
The processing run will be given a unique name, based on the collected images root names, and displayed in the User Datasets list. Clicking on the run name will show a summary of the input and links to the summarized results and plots. Note that automatic data processing runs with no resolution or I/sigmaI cutoffs. The scaling and merging statistics in the Summary page will provide an estimate of the resolution limit of the data, which may then be applied on manual reprocessing.
The Logs page links to a time-stamped log listing the programs that have been run, and the log file. The Log can be refreshed while the processing is running by clicking on the Update Log button.
Hint: In the log, search for the ISigma asymptotic (ISa) value in the CORRECT.LP XDS job. Usable data sets tend to have a ISa above 10. The higher this number, the better the data are.
The Error Log lists fatal errors during execution of a program or script. It can be useful to trace the ultimate cause of a problem during processing.
The Summary page displays a summary of the data statistics after scaling and merging, analysis with XTRIAGE, space group and unit cell determination with POINTLESS and refinement (only if a model has been supplied).
Hint: In the scaling statistics summary, look at the lowest resolution bin numbers, since an overoptimistic sample to detector distance setting during data collection can result in very poor high resolution and overall statistics. Usable data sets tend to have R factors lower than 0.05, Mn(I/sd(I)) higher than 10, a correlation coefficient close to 1 and completeness between 95 and 100% in this resolution bin. Also, if you expect an anomalous signal and the program detects none, you probably need higher quality diffraction or a higher multiplicity.
This page lists the L and Z test plots from XTRIAGE, useful to determine if the crystal is twinned and, if a model has been provided, the change in R-factor after some cycles of refinement.
The Details link can be used to browse the command files, output files and full logs from the processing job, stored under the /data/''user''/webice/process/''DatasetName'' directory. The DataProcessing_0. directory contains subdirectories for each program used for processing. Each of these subdirectories, in turn, contains the command file (''run.csh''), output files and logs (''stdout.txt'') for each program run.
Other directories less interesting to the user are the scratch directory, which contains intermediate output files; plots, containing the data displayed in the browser ''Plots'' page, and _metadata with input and results related to the processing software framework.
The command files written to the webice/process/ subdirectories can used for reprocessing the data set with different input parameters. If you are not familiar with the programs used for processing, consult the documentation available online in the software pages or consult with the beamline support person.
|Technical questions: Webmaster
questions: Ana Gonzalez
|Last modified:Tuesday, 13-Aug-2019 14:45:10 PDT.|