Re: [ccp4bb]: Bulk solvent model in REFMAC

[Martyn Winn <M.D.Winn@dl.ac.uk>]

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On Mon, 26 Aug 2002, Mark A. White wrote:

> this happen?  In the second case, a moderate resolution structure (2.7
> A) with five-fold NCS was refined with one TLS domain per chain.  The
> B-factors dropped and a large fraction of them were pinned at 2, when
> the default Bbulk value of 200 was used.  I have tried varying the Bbulk

B factors being pinned to 2 (the minimum allowed) is usually
a sign that the TLS refinement has gone awry. Look at the TLS
parameters. The size of L parameters depends on the size of
the TLS group, but if you have diagonal L elements over 100
for molecule-sized groups then be suspicious ....

This can happen if the electron density is poorly defined,
and/or the model is only partially built. In which case,
restrict the TLS group to the well-defined sections, or
refrain from TLS until the model has progressed.

The link with Bbulk is interesting and I don't have a simple
rationalisation for it. But from a practical point of view,
you might not need to fix Bbulk but can let it refine to
an appropriate value. 

Cheers
Martyn

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*                  Dr. Martyn Winn                                       *
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