Prepare and validate files for deposition

The final stage of the crystallographic structure solution is the deposition of the final structure and the observations in the Protein Data Bank (PDB). The PDB require that the files be provided in a standard form, specifically the observations and the atomic model must be in CIF format. This task will automatically prepare the required files in the appropriate formats.

Input

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Firstly, the contents of the asymmetric unit must be supplied (1). This must contain the complete sequences of all macromolecule chains present in the coordinate file i.e. including parts present in the crystallized species but not modelled.

Next add the coordinates from the final refinement job (2). At this point all the information from this job will be harvested from the database and the related files section will be populated.

You may choose not to send the data and coordinates to the wwPDB Validation Service (3). In this case the task will prepare the files but you will not receive a validation report.

The option to add statistics from data reduction (4) is described below.

If you have run the data reduction task in this CCP4i2 project this task should be able to identify the correct job that produced the data that were used in refinement and add data reduction statistics to the coordinate mmCIF file.

There are two reasons why this automatic detection does not work. Firstly, data reduction was not done within CCP4i2. However, if data reduction was done within CCP4i2 but the space group used differs from that of the refined structure the detection will fail. In both cases this pop-up will appear.

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How to proceed depends on whether data reduction was done within CCP4i2.

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If data reduction was done within CCP4i2 you can locate the output XML from Aimless that contains the data reduction statistics (5). Alternatively you can choose to not add data reduction statistics to the coordinate mmCIF file (4) and instead enter this information into the wwPDB OneDep system.

Results

If you chose to send the coordinates and data to the wwPDB Validation Service the task will take at least five minutes (but often much longer) to run as it waits until the Validation Service returns the validation report.

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If you chose to add data reduction statistics a summary of these is provided and/or chose to send the coordinates and data to the wwPDB Validation Service a summary is shown (1).

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You can view and export the coordinates (2), reflection data (3), and validation report (4). You can also run a Coot job (5) to inspect issues highlighted in the validation report.