On 16 Oct 2007, at 8:44, Tim Gruene wrote:
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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).
Oh - its been a year since we did not have "Episode 17: The return of
the Positionally Challenged" !
Although I am confident Garib will clear the landscape soon (0 occ
atoms are ignored for for everything, including restraints; it is an
old PROLSQ 'feature' that has been adopted by REFMACx as far as I know).
I personally btw like to leave the atoms there and let B's go high,
with similar arguments like Tim's, and with similar 'side-effects'.
Better be clear that a long side chains is there, rather than think
its Alanine. But, I am sure the archive has loads on that, including
all the arguments that counter the above.
Maybe I will set up a ballot in the (coming soon!) ARP/wARP blog ;-)
Tassos
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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