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I think Frances is right, i.e. most non crystallographers ignore 
"anything beyond the x, y, z coordinates (i.e. beyond column 54)"
[as Frances wrote]. 
Thus if a crystallographer put in coords that he/she does NOT see,
even with OCC=0, or an enormously large Bfactor, these coords are usually 
treated in just the same way that experimentally observed coords are treated. 
Thus my feeling is that if one does NOT see the coords in the electron
density, they should NOT be included, and let someone else try to model 
them in, but they should be aware that they are modeling them.
Joel L. Sussman



On 3 Apr 2011, at 06:15, Frances C. Bernstein wrote:

Doing something sensible in the major software packages, both
for graphics and for other analysis of the structure, could
solve the problem for most users.

But nobody knows what other software is out there being used by
individuals or small groups.  And the more remote the authors
of that software are from protein structure solution the more
likely it is that they have not/will not properly handle atoms
with zero occupancy or high B values, for example.

I am absolutely positive that there is software that does its
voodoo on ATOM/HETATM records and pays absolutely no attention
to anything beyond the x, y, z coordinates (i.e. beyond column 54).

                   Frances Bernstein

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On Sat, 2 Apr 2011, Jacob Keller wrote:

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?

Some users might pull up the structure, see those atoms, and think
their positions were based on data, which they were not, and then draw
conclusions based on them. I agree that occ=0 is tantamount to the
suggestion you queried, however.

A somewhat key question might be: across the various molecular
visualization programs, what is the default way to handle atoms with
occ=0? Perhaps those programs might be the best place to fix the
problem...

JPK


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