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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
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Switzerland                      Internet: http://www.sb.psi.ch
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