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Hi Iain,
I know there are (at least) two schools of thought and both have their
justification, and my suggestion does not explain you phenomenon.
However, instead of setting the occupancy to zero, I would rather delete
the affected atoms/ residues.
In my point of view this would make your submitted structure less error
prone, especially to non-crystallographers, because they usually just
look at the PDB file with a graphics viewer rather than the PDB file
itself (and most viewers, unlike coot, do not highlight atoms with zero
occupancy).
Omitting these residues should help correct interpretation of you data by
others than you.
As a side effect, it would solve your problem of bonds becoming distorted.
Tim
- --
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Mon, 15 Oct 2007, 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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