>
>Just create a new tag, say _atom_site.imaginary_site, which is either
true or false for every atom. Then everyone would be able to either
filter out the fake atoms or leave them in, without ambiguity or
confusion.
>
Aside from being a binary rather than continuous parameter, how exactly
does this suggestion differ from the occupancy column of the pdb, that
we already have?
I guess I missed it in the flurry of replies to this thread over the
last few days, but what exactly is so terrible about keeping the atoms
(since you have chemical evidence from protein sequence that they are
there, and even if there is X-ray damage they were originally there and
are likely still there in a subset of the molecules), but changing
occupancy to zero as an acknowledgment that your data does not provide
evidence to support a specific atomic position for these atoms?
Evette S. Radisky, Ph.D.
Assistant Professor
Mayo Clinic Cancer Center
Griffin Cancer Research Building, Rm 310
4500 San Pablo Road
Jacksonville, FL 32224
(904) 953-6372
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