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Bill
CNS doesn't have to choose anything. You provide it with a structural model
in a predefined unit cell. Assuming the positioning in the unit cell
corresponds to the choice of structure factor indexing, the Fobs and Fcalc
will match. The position of the model in the cell was determined using the
observed data (by either experimental phasing or molecular replacement) and
therefore the position will again match whatever setting your data processing
program choose to use. So what I'm trying to say is that the indexing of Fobs
defines one of several possible settings and the structure solution procedure
will automatically match whatever setting that is because it finds the
correct solution relative to the choosen setting.
My main point is that if you simply take a pdb file from say a hexagonal
crystal, put it into a trigonal cell, use (eg) CNS to calculate Fcalcs,
there is no way to know in advance which way to index a native data set
that never sees or knows about any of this.
I hope that helps. If not, try coffee or something a bit stronger :)
May I try some of yours?
Bill
