The heavy-atom sites are usually found using an automated method (see previous tutorial). It is important to remember that there is a hand ambiguity in the location of the sites. The search procedures are based purely on amplitude information. However, a given heavy-atom configuration and its inverse image give rise to identical diffraction amplitudes. The hand ambiguity can be resolved by SAD phasing with both choices, followed by inspection of the resulting electron density maps. Only the correct hand will produce an interpretable map.
SAD phasing, like MAD phasing, is performed with the CNS task file mad_phase.inp. Because in this case only one wavelength is used, for clarity the file name is changed to sad_phase.inp.
cns_solve < sad_phase.inp > sad_phase.out [12 minutes]
The output files are:
sad_phase.summary
sad_phase.fp
sad_phase.sdb
sad_phase.hkl
sad_phase_grad.hkl
The sad_phase.summary file contains information about the
progress of the SAD phasing procedure. The refined f' and f" can be
found in the sad_phase.fp file, and the refined heavy-atom
parameters are stored in the sad_phase.sdb site database file.
The refined phases are written to the sad_phase.hkl file as
Hendrickson-Lattman coefficients, and also as centroid phases and
corresponding figures of merit. The Fourier coefficients for the
gradient map are stored in the sad_phase_grad.hkl file.
The use of the hkl file for the detection of additional
heavy-atom sites is shown in the following tutorials.