|Python-based Hierarchical ENvironment for Integrated Xtallography|
SAD and MR-SAD phasing with the Phaser GUI
Since the two Phaser GUIs use a common base, much of the experimental phasing
interface is similar to the Phaser-MR GUI. This section
only covers features unique to SAD phasing, including instructions for MR-SAD.
Input files and mandatory parameters
Phaser requires a reflections file (any format) containing anomalous data, and a file containing heavy atom sites, in either PDB or SHELX format. Either the wavelength or the energy used is also required. To run an MR-SAD experiment, change the mode to "MR-SAD phasing", and enter a partial model (PDB file) and the expected variance from the actual structure (RMSD or percent identity). If you are using normal SAD mode, you may choose whether to use the given enantiomer ("hand") of the heavy-atom sites or the inverse or both; in MR-SAD, the chirality of the partial model restricts the sites to the given enantiomer.
The input for composition is identical to the Phaser-MR GUI. Heavy atoms may be either standard elements from the periodic table, or cluster compounds such as tantalum bromide or tungsten clusters.
Depending on the choice of hand, Phaser will output one or two sets of files containing the heavy atom sites (PDB format) and phased reflections (MTZ), including map coefficients and Hendrickson-Lattman phase distributions (useful for refining with experimental phase restraints). This map is usually very noisy and difficult to interpret, and typically requires density modification to become useful.