Well - REFMAC and I think other refinement programs simply read in an
atom with occupancy 0.00 and write it out again in exactly the same
place.. All refinement contributions for atoms both Xray and geometrical
are weighted by the atom occupancy so such an atom will not shift.
The assumption is that you do not know where such an atom is placed, and
will rebuild it later if the electron density gives an indication.
I think an improvement would be if COOT automatically included such a
residue in the category of one which "contains missing atoms". Then you
could use the useful coot extension to check out all such residues as
soon as you read in the new map.
Eleanor
I think this is reasonable, but On 01/17/2011 09:28 AM, Marcus Fislage
wrote:
> Dear all,
>
> I might excuse myself for the silly question but it is the first time I
> solve an x-ray structure.
>
> After modell building in coot and running of refmac with restrained
> refinement I have the problem that the pdb output file contains
> distances between e.g. ILE Cb and Cg that are so long that the Cg is
> displayed as single atom (distance ~1.64 A instead of 1.5 A). This seems
> to happen to me for aminoacid sidechains where I added an alternative
> conformation (especially if the 2nd conformation is oriented not far
> away from the first one) and if I set the occupancy of sidechains like
> Glu for Cd and further to zero (Here refmac gives a bond break between
> the last atom with occupancy 0 and the first with occupancy 1). I can
> adjust it of course in coot back to normal but after the next refmac run
> the same happens again. The option card in refmac for geometric
> restraints I kept untouched.
> Am I missing to set on an option in refmac, or is there something else
> going wrong?
>
> Thanks a lot for the help
>
> Marcus
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