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I wonder if this is due to the late residue number. Could you try again reducing that to something smaller. I seem to remember SFALL stores a flag to recall which residue contributed to which density and there could be a limit on its size.

Will test when I get near a working system 
Eleanor

On 6 July 2015 at 22:53, Jens Kaiser <[log in to unmask]> wrote:
All,
  We seem to have stumbled upon a problem in sfall. The two attached pdb
files are nearly identical, except the coordinates and b-factors for the
two atoms are swapped. When calculating Fs with sfall, we get
drastically different mtz files. Upon calculating the corresponding
Fcalc maps, it seems that the second atom in a.pdb gets ignored, whereas
both atoms in b.pdb are included. There is nothing obvious in the log
files to hint to what is happening (i.e. both files state
"Number of atoms input            =             2
 Number of atoms in sort          =           2
 Number in density generation     =      2
 Number completely within fft box =      2
     Minimum B =     5.91
     Maximum B =     5.97
     Average B =     5.94
"
We observed this behavior on mac and on Linux.

Cheers,

Jens