Importing structures from the PDB


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Importing structures from the PDB

Using the PHENIX GUI
Command-line use
Output

Unlike most other reflection formats, the CIF files used by the PDB to store experimental data are not supported for direct input to PHENIX. phenix.cif_as_mtz is a simple utility for importing these files, and can automatically identify and fix several errors common in the PDB, such as incorrectly labeled intensities in place of amplitudes. Unfortunately, many structures fail to parse properly, so this tool is not guaranteed to work in all cases.

Using the PHENIX GUI

Open the main GUI and click "Import CIF structure factors" under the "Reflection tools" category. Only the CIF file is required, but a PDB file will often be necessary to obtain the correct symmetry information. Click "Use model to guess data type" if you want PHENIX to do a sanity check on the labeled amplitudes (which may not really be amplitudes!).

If you know the PDB ID but haven't downloaded the necessary files yet, you can simply enter the ID into the box in the upper right corner and click "Run", and the PDB and CIF files will be fetched automatically from the RCSB web server.

Command-line use

The output of phenix.cif_as_mtz without arguments is show below:

Usage: phenix.cif_as_mtz [reflection_cif_file] [options]

Options:
  -h, --help            show this help message and exit
  --unit-cell=10,10,20,90,90,120|FILENAME
                        External unit cell parameters
  --space-group=P212121|FILENAME
                        External space group symbol
  --symmetry=FILENAME   External file with symmetry information
  --output-file-name=OUTPUT_FILE_NAME
                        Output mtz file name.
  --use-model=USE_MODEL
                        Use PDB model to make better guess about reflection
                        data type.
  --wavelength-id=WAVELENGTH_ID
                        Extract data set with given wavelength_id.
  --crystal-id=CRYSTAL_ID
                        Extract data set with given crystal_id.
  --show-details-if-error
                        Show data details for some errors.
  --show-log            Show some output.

Example: phenix.cif_as_mtz r1o9ksf.ent --symmetry=pdb1o9k.ent

The --symmetry argument is frequently required due to missing symmetry information; in these cases you should use the equivalent PDB file. Most of the other options are usually not necessary, but --use-model is often helpful to get the data type right.

As a shortcut to download the files from the RCSB (or mirror) website, PHENIX includes a tool for fetching data for a given PDB code:

phenix.fetch_pdb 2hr0 phenix.fetch_pdb -x 2hr0

The argument "-x" specifies that the structure factors should be downloaded instead of the PDB file. (This will only work if the authors deposited their data.)

Output

Assuming that the data were successfully extracted, the program will create an MTZ file with columns FOBS, SIGFOBS (these will be treated as group by most applications in PHENIX), and R-free-flags. In many cases there will be fewer reflections in the output than data lines in the CIF file; this is due to the presence of non-numeric or otherwise unintelligible values.