[phenixbb] Average B-factors when using TLS
Pavel Afonine
pafonine at lbl.gov
Wed Oct 13 14:41:25 PDT 2010
Hi Phil,
I'm replying since I implemented TLS refinement in phenix.refine.
Honestly, I've never done such comparisons, so I can't really comment on
this thoroughly. The ADP refinement in phenix.refine is described here:
http://www.phenix-online.org/newsletter/CCN_2010_07.pdf
starting at page 23 (this is the very latest source), and here (older)
http://www.ccp4.ac.uk/newsletters/newsletter45/articles/Tmax-CCP4_Afonine-Urzhumtsev_2006_arial.pdf
and here (oldest):
http://www.phenix-online.org/papers/ccp4_july_2005_afonine.pdf
and for completeness:
http://journals.iucr.org/d/issues/2005/07/00/gx5040/index.html
I'm happy to further discuss it, see your suggestions and do tests if it
comes to it (although I'm in travel now, and I will return back from UK
and France sometime around Octber 20, so I may not be interactively
responsive during this time). I'm interested in feedback and
constructive suggestions.
Thanks for questions and all the best!
Pavel.
On 10/13/10 11:20 AM, Phil Jeffrey wrote:
> I'm having a discussion with a colleague here about what we expect to
> see on a model with and without TLS being used. I had the expectation
> that if you'd compared both models the Biso values reported in the
> ATOM line for the same atom w/ and w/o TLS would be somewhat
> comparable. Not the same, because the ADP model is different, but
> similar.
>
> However in the case of the TLS-refined model the average B-factors are
> systematically higher over the whole structure (86 A^2 vs 69A^2 for
> one polypeptide chain). Is this reasonable ? Expected ?
>
> Phil Jeffrey
> Princeton
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