I agree that zero occupancy is a bit ugly, but useful when not sure
whether you will ever see that LYS..
But I dont think it wlll displace bulk solvent - at least not in REFMAC
where an atom with occ=0.0 will not contribute to the atom map. And I
expect this is true for all other structure factor calculations using
various programs..
Eleanor
Ed Pozharski wrote:
On Thu, 2010-08-12 at 08:57 +0000, MARTYN SYMMONS wrote:
Zero occupancy is generally a deprecated way of dealing with missing
density as it is confusing for less experienced user of the
coordinates. I think zero occupancy can be useful during refinement as
the atoms help fill space (or for example satisfy NCS restraint
format requirement) but then these atoms can be stripped out before
deposition. They should in any case never be included in B-factor
refinement as they will skew the statistics and possibly the B-factor
restraint model.
Zero occupancy may be a bad idea for yet another reason - the atoms will
displace bulk solvent and produce what is essentially a hole in the
structure. It may be justified if you are trying to fill the empty
internal cavities, but for atoms missing from density it seems like a
wrong approach.
