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I would argue strongly that there is no way to predict
what users will do with PDB entries or what programs they
might use. Anyone who has a new idea of how to do something
with coordinates will be creating new code. There is also
no way to educate all of them in the subtleties of PDB entries.
My husabnd, Herbert Bernstein, maintains Rasmol and over
1,000,000 copies have been distributed. In 2006 the PDB had
over 150,000 unique users each month and two entries were
downloaded every second.
My conclusion, therefore, is that no coordinates should
be given for atoms whose positions are not reasonably certain.
If atoms are missing or given in multiple conformations it
is likely to make the user realize that something unusual is
going on in that area. But I quite certain that someone who
is not a crystallographer and is writing a precedure to do
some new calculation will ignore both occupancy and B values.
I would suggest that the people on this discussion list,
who are all basically crystallographers or sophisticated users,
who are advocating including atoms with occupancy 0.0 should
talk to a biologist PDB user down the hall from them and see if
they even understand what a B value is or what an occupancy
of 0.0 means.
Frances Bernstein
P.S. It would certainly be useful to agree on some standards
for the commonly used software on how to flag regions of
uncertainty in a structure. But, as I said above, not
everyone is using the standard packages.
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