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CCP4i: Graphical User Interface |
| Data Reduction Module |
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The layout of each task window, i.e. the number of folders present, and whether these folders are open or closed by default, depends on the choices made in the Protocol folder of the task (see Introduction). Although certain folders are closed by default, there are specific reasons why you should or may want to look at them. These reasons are described in the Task Window Layout sections below.
Data which has not been scaled and merged is saved in a 'multi-record' MTZ file. The multi-record file contains several columns which do not appear in a standard MTZ file, for example M/ISYM BATCH. The Scala program does the scaling and merging of data and outputs a standard MTZ file. Data imported from Mosflm is in a 'multi-record' MTZ format but any other imported unscaled data will need to be converted to the MTZ multi-record format. Imported scaled data is converted directly to standard MTZ format.
Data columns within the standard MTZ file are labelled with a 'project name' and a 'dataset name'. The dataset name should be used to distinguish data from native or derivative structures within the MTZ file. When importing data or converting to the standard MTZ format you will be required to provide a dataset name for the data. You are strongly recommended to use this facility carefully, both to help you keep your data organised but also because some 'down-stream' programs such as SCALEIT (Scale Datasets in the Experimental Phasing module) require that input MTZ files have consistent dataset naming.
Data from Denzo (Import Scaled Denzo Data) or d*TREK (Import Scaled d*TREK Data) are already scaled and, once converted to standard MTZ format, will need converting from intensities to structure factors (see below) and, possibly, passing through the 'uniqueify' process (see below). There are options to convert to SFs and Uniqueify in the Import task in the Reflection Data Utilities module, which is the preferred route after importing scaled data from Denzo or d*TREK.
See program documentation: SCALEPACK2MTZ, dTREK2MTZ.
The most common imported unscaled data is probably from Mosflm which is already in the multi-record MTZ format and so can be used directly in the Scale Experimental Intensities task. But other, less likely, formats can be imported through this task and then used in Scale Experimental Intensities. It is possible to 'import' standard MTZ format files for conversion to the multi-record format.
See program documentation: Combat.
There are some editing functions which you may need to apply to multi-record MTZ files prior to scaling - particularly changing the space group or reindexing might be necessary if the initial reflection indexing is suspect. There is also an option to reset the batch numbers for sets of reflections. This should only be necessary if they were wrongly or not recorded at the time of data collection or if you suspect that some sets of reflections need special treatment by Scale Experimental Intensities and need identifying as a separate batch.
Note that there is an option in the Reflection Data Utilities to reindex standard MTZ files.
See program documentation: Sortmtz, REINDEX, Rebatch.
The Interface for Scala is quite large. Many of the options are only needed if detailed optimisation of the scaling is required. For this, the program documentation of Scala gives numerous hints, which will be incorporated in the Task Window Layout section below.
By default, data which has been scaled and merged by Scala is then converted from intensities to structure factures (see below) and usually passed through the Uniqueify process (see below). The data is then in a standard MTZ format and suitable for input to molecular replacement or experimental phasing.
Scala is one of the Data Harvesting programs. See Data Harvesting in CCP4i.
Coming soon.
See program documentation: Scala
The detwin program will either analyse the data to determine the twinning fraction or generate detwinned data.
See program documentation: Detwin
The program Truncate is used to obtain structure factor amplitudes from intensities. This conversion is performed by default when importing scaled data or running Scala (Scale Experimental Intensities). There is an explicit interface to the Truncate program which includes some less commonly used options. By default, if you use this task interface then the data will also be passed through the Uniqueify process (see below).
Truncate is one of the Data Harvesting programs. See Data Harvesting in CCP4i.
Features to look out for in the Truncate Task are:
| Folder title | Importance | Comment |
|---|---|---|
| Usual Parameters | Use truncate protocol to calculate Fs | default YES, see description |
| Define Cell | Define unit cell contents | program will not work without some description of cell contents |
| Log File Output | Draw Wilson plot to file | default through Interface YES, compare PLOT OFF |
See program documentation: Truncate
By default this process is applied to all data after it has been converted to structure factors in any of the tasks which import scaled data or scale the data. The process will ensure that all reflections are unique and will 'fill in' any missing reflections. It will add a column of FreeR indicators or optionally import the FreeR column from an existing MTZ file. The data can also optionally be extended to higher resolution (this is recommended if you expect to have data to higher resolution in future and should set up a full FreeR set from the start).
If you are processing derivative data and you want to add it to the MTZ file for the native data, you should NOT run the Uniqueify options but use the Merge MTZ Files task in the Reflection Data Utilities module.
See also: Convert to MTZ & Standardise.
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