Re: [ccp4bb]: Structure Resolution!

[Garib N Murshudov <garib@ysbl.york.ac.uk>]

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Just a minor point. Atoms with 0 occupancies are ignored in REFMAC and 
presence or absence should not make any difference. I generally think it is 
better to keep atoms but assign occupancies to 0.


Garib

On Monday 09 Sep 2002 2:32 pm, Dirk Kostrewa wrote:
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>
> Eleanor J. Dodson wrote:
> >>Also, I am not clear as to what kind of differences I would see between
> >>maps calculated with data upto 2.6A and 2.8A.
> >
> > You will just have to look and see. It is a good idea to set the
> > occupancies for some test residue - preferably something big - too 0.00
> > then see how well it comes back in the two maps.
>
> If atoms are present with occupancies set to "0", you must be cautious: if
> you refine your model with a mask bulk solvent correction (CNS, REFMAC5),
> these zero-occupancy atoms cut holes into the bulk solvent mask, very
> likely resulting in positive electron density difference maps around their
> current positions as if they were really there! The reason for this is that
> a hole in the mask has a very low electron density, whereas the real
> structure either has some ordered atoms (in this case the density would be
> correct) or disordered bulk solvent atoms filling this hole (in this case
> the density would be "false positive"). Thus any type of Fobs-Fcalc
> electron density map shows more or less strong positive electron density
> for such holes. There are two ways to circumvent this: either do not use a
> mask bulk solvent correction but a double-exponential bulk solvent
> correction (available in REFMAC5), or remove the atoms in question from
> your coordinate file (works both for CNS and REFMAC5). CNS has also the
> possibility to exclude atoms from the refinement via a selection statement.
>
> Good luck,
>
> Dirk.

-- 
Garib N. Murshudov, Chemistr Department, University of York
Tel: (01904) 328252