If the occupancy is 0.00 there will be no refinement - the output cds
are the same as the input, and I guess that will make for horrible
geometry - COOT will "correct" the geometry of all atoms though so you
can make a prettier picture - but with no more information content re
the model if the occupancies stay 0.00
..
Eleanor
Iain Kerr wrote:
> Dear all,
>
> I'm refining a structure (with TLS, Hs in riding positions) to 2.9A -
> Rfree ~29.9%/Rfac 26.5% in Refmac5 v5.2.0019. Rmsd bonds 0.008A/1.1deg
> angles.
>
> In COOT (0.31) many of the residues whose side chains are (fully or
> partially) set to 0.00 occupancy have really bad geometry...for want
> of a better description, the side-chains literally look like they have
> exploded...a few are intact but have distorted planarity. This occurs
> in 25 residues out of 480 in the ASU.
>
> I have tried:
>
> 1. refining without TLS - no change
> 2. no hydrogens - no change
> 3. refining OVERall B-factors instead of ISOtropic - overall geometry
> much worse (rmsd 0.088 bonds)
> 4. DAMP 0.5 0.5 - no change
> 5. BABINET scaling instead of SIMPLE - no change in geometry, Rfree
> and Rfac increase ~3%
> 6. relaxing geometry (rmsd 0.019A bonds/1.8deg angles)
>
> This occurs with two other structures at higher resolution (~2.5A),
> although only a few violations..it seems to be much worse at low
> resolution.
>
> Any ideas ?
>
> Thanks,
> Iain
>
>
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