phenix.sad_data_from_pdb is a command line tool for downloading coordinatesand anomalous structure factor data for a PDB deposition and setting upfor running one or more wavelengths of data as SAD datasets.
and phenix.sad_data_from_pdb will download the data for 2etd and set upa directory with this data and with subdirectories for each wavelengthof data present (w1, w2, and w3 in this case). In each subdirectorya file run_autosol_std.csh will be created that is suitable for runningphenix.autosol using that anomalous data.
base_directory = None Directory where files are to be locatedpdb_ids = None PDB ID to fetch and use to create SAD datasetswavelength_id = None Select only the wavelength specified by wavelength_idha_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 directoriesbest_only = True Keep only atom with strongest anomalous scattering and ignore the restmerge = None If set, merge multiple observationsreplace_full_directory = None You can change the full directory name for a single dataset 041b061a72