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Re: [ccp4bb]: Structure Resolution!
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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.
--
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Dirk Kostrewa
Paul Scherrer Institut E-mail: dirk.kostrewa@psi.ch
Life Sciences, OSRA/007 Phone: +41-56-310-4722
CH-5232 Villigen PSI Fax: +41-56-310-4556
Switzerland Internet: http://www.sb.psi.ch
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