cns_solve < flip_sites.inp > flip_sites.out [< 1 second]The task files for the two independent SAD phasing jobs are identical except for the definitions of the file names for the heavy atom sites and the output file names.
cns_solve < sad_phase2.inp > sad_phase2.out [14 minutes] cns_solve < sad_phase2_flip.inp > sad_phase2_flip.out [14 minutes]For the density modification, it is necessary to have a good estimate of the solvent content. In a preliminary step, the solvent content is estimated by using matthews_coef.inp.
cns_solve < matthews_coef.inp > matthews_coef.out [< 1 second]
The estimated solvent content shown in matthews_coef.list is between 0.53 and 0.55. density_modify.inp and density_modify_flip.inp are modified accordingly by setting the solvent content parameter to 0.54.
cns_solve < density_modify.inp > density_modify.out [27 minutes] cns_solve < density_modify_flip.inp > density_modify_flip.out [28 minutes]The resulting output files are:
density_modify*.list - listing file with statistics for each modification cycle density_modify*.hkl - reflection file with new Hendrickson-Lattman coefficients density_modify*.map - map file with modified electron density density_modify*.mask - file with definition of solvent maskElectron density maps before solvent flipping are computed with modified copies of the fourier_map.inp task file.
cns_solve < fourier_map_sad2.inp > fourier_map_sad2.out [21 seconds] cns_solve < fourier_map_sad2_flip.inp > fourier_map_sad2_flip.out [21 seconds]If you have mapman installed, you can use the command
map_to_omap *.mapto convert the CNS maps to a format which can be read into O. In O, enter @omac to read in the four maps. Portions of these maps are shown below.
Original sites | Flipped sites |
Original sites | Flipped sites |