Author(s)

• phenix.sad_data_from_pdb: Tom Terwilliger

Purpose

phenix.sad_data_from_pdb is a command line tool for downloading coordinates and anomalous structure factor data for a PDB deposition and setting up for running one or more wavelengths of data as SAD datasets.

Usage

How phenix.sad_data_from_pdb works:

phenix.sad_data_from_pdb first uses phenix.fetch_pdb to download the data from the PDB.

Then it converts the structure factor data to Scalepack unmerged original index format, calculates model map coefficients, and identifies the anomalously-scattering atoms in the PDB file, the wavelengths of data collection, and the resolution of the data. If these are not present in the PDB deposition then the procedure will not work.

Examples

Standard run of phenix.sad_data_from_pdb:

Running phenix.sad_data_from_pdb is easy. You can just type:

phenix.sad_data_from_pdb pdb_ids="2etd"

and phenix.sad_data_from_pdb will download the data for 2etd and set up a directory with this data and with subdirectories for each wavelength of data present (w1, w2, and w3 in this case). In each subdirectory a file run_autosol_std.csh will be created that is suitable for running phenix.autosol using that anomalous data.

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all available keywords

• base_directory = None Directory where files are to be located
• pdb_ids = None PDB ID to fetch and use to create SAD datasets
• wavelength_id = None Select only the wavelength specified by wavelength_id
• ha_list = None List of anomalously-scattering atoms (used instead of list extracted from PDB file )
• steps = *fetch *cif_to_sca *fmodel *ha *autosol Steps to carry out: fetch downloads files from the PDB, cif_to_sca converts PDB CIF files to Scalepack unmerged original index, fmodel calculates model structure factors, ha identifies anomalously-scattering atoms in the PDB file, autosol sets up for a run of autosol. To select several steps put them in quotes with the stars: steps='*ha *autosol'
• initialize = None If set, remove any existing data in the PDB directories
• best_only = True Keep only atom with strongest anomalous scattering and ignore the rest
• merge = None If set, merge multiple observations
• replace_full_directory = None You can change the full directory name for a single dataset