Downloading data from PDB and setting up for SAD structure determination with phenix.sad_data_from_pdb



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.


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.


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:


Additional information

List of all available keywords