Resolution of the enantiomorph ambiguity

This tutorial shows how to compute electron density maps based on the results of MAD phasing runs, and how to use them to resolve the enantiomorph ambiguity.

The enantiomorph ambiguity can be resolved by MAD phasing with the original heavy atom configuration and its inverse image, followed by inspection of the resulting electron density maps. Only the correct enantiomorph will produce an interpretable map.

The electron density maps are computed with the observed structure factors measured at a remote wavelength, and MAD phases. The input files are derived from the fourier_map.inp task file in the inputs directory. 

      cns_solve < fourier_map_elec.inp > fourier_map_elec.out            [18 seconds]
      cns_solve < fourier_map_elec_flip.inp > fourier_map_elec_flip.out  [18 seconds]
The two resulting map files are: 
      fourier_map_elec.map       fourier_map_elec_flip.map
If you have mapman installed, you can use the command 
      map_to_omap *.map
to convert the CNS maps to a format which can be read into O. In O, enter @omac to read in the maps. Use the Objects menu to turn the maps on and off individually.

Experimental MAD phased map,
sites as found (incorrect) 		Experimental MAD phased map,
inverted sites (correct)
The electron density map based on the inverted sites (fourier_map_elec_flip.map) clearly shows a contrast between protein regions and solvent regions. The electron density in the map based on the original sites is much more evenly distributed in the asymmetric unit of the unit cell. This means, we have established that the inverted heavy atom configuration is the correct choice.

Sometimes, for example if there are problems with the quality of the data or only a small subset of the heavy atom sites is known, neither of the two electron density maps shows a clear contrast between protein regions and solvent regions. In such a case, density modification should be performed and the new electron density maps inspected.

Script to run this tutorial

Back to tutorials   Previous section   Next section