Hi Tim
Sorry I can't help you with Phenix, I would just like to point out that
from a theoretical standpoint it's very difficult to say a priori what
the value of the ADP variance should be. Since the resolution is 2.4 I
assume you're talking about isotropic ADP's. Essentially all of the
contribution to the differential isotropic ADP comes from transverse
librational motion, i.e. perpendicular to the bond, and it's almost
impossible to place a limit on the magnitudes of the libration
amplitudes. Measured bond vibration amplitudes parallel to the bond
direction are 1 or 2 orders of magnitude lower than those usually
observed in proteins (they are even an order of magnitude lower than
those observed in small molecules where the average B is around 5 to
10), so the bonds are effectively rigid. The isotropic ADP is of course
the mean of the principal components of the anisotropic ADP tensor, so
all one can say is that the isotropic ADP difference is the mean of 3
numbers, 1 of which is zero and the other 2 you don't really know!
-- Ian
> -----Original Message-----
> From: [log in to unmask]
> [mailto:[log in to unmask]] On Behalf Of Tim Gruene
> Sent: 30 January 2008 13:42
> To: [log in to unmask]
> Subject: ADP variance restriction in phenix
>
> -----BEGIN PGP SIGNED MESSAGE-----
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>
> Good day,
>
> we are currently refining a 2.4 protein structure using phenix.refine.
>
> I would like to know how to reduce the adp-variance. We have
> jumps from 60
> to 90 and back between adjacent residues and I do not like it.
>
> I scanned the documentation I found on the web but did not
> find what I was
> looking for.
>
> Cheers, Tim
>
> - --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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