Section 25.2.1.11.1. The DOALL procedure

A script to carry out a standard solvent-flattening run is provided along with a description of the expected input files, output files and examples. Not surprisingly, this DOALL procedure does it all. Execution of the script will create a map from an input `anchor' set of phases, typically obtained by MIR, SIR, or MAD methods, and will then create a solvent mask from the map after zeroing out density near heavy-atom sites. This solvent mask is used in four cycles of solvent flattening, combining the map-inverted phase information with the anchor phases. A new solvent mask is then generated, starting from a map produced with the phases after the first four cycles. Four cycles of solvent flattening using the second solvent mask are then carried out, restarting from the original map and combining with the anchor phases. These phases are then used to compute a new map from which a third solvent mask is built. The third mask is then used for eight cycles of solvent flattening, again restarting with the original map and combining with the anchor phases. Supplied in the script, but commented out, are instructions to carry out an arbitrary number of additional phase extension cycles, and then an arbitrary number of phase and amplitude extension cycles, all using the third solvent mask. The combined phases and distribution coefficients are written to a file after all cycles with a given mask are completed.