[phenixbb] B-factors

Ed Pozharski epozh001 at umaryland.edu
Sat Apr 6 08:13:46 PDT 2013


On 04/06/2013 05:00 AM, Pavel Afonine wrote:
> A quick comment on "B-factor problem" recently brought to attention: 
> in fact it is not a bug at all, but a conflict of philosophies. It all 
> boils down to whether you want to keep meaningless bulk overall 
> B-factor in ATOM records in your PDB file (current phenix.refine 
> behavior) or you say it is junk and keep it in overall scale factors 
> (previous behavior that many of you called a bug). Personally I would 
> prefer to keep in overall scale factors.

While my useless comment has a potential to start an endless and equally 
useless discussion, I'd like to nevertheless point out that from my 
understanding overall B-factor is not entirely meaningless. While some 
of it is due to overall static disorder which is truly of little 
interest, figuring out what part of it is contributed by true thermal 
motion (whether real at 100K or frozen out from 300K) is not exactly 
trivial.  I appreciate your opinion that from mathematical standpoint it 
does not matter where this contribution goes, but having B=0 for some 
atoms because min(B) was subtracted and placed into a header comment 
line is at least equally meaningless.  I do not see how B-min(B) is a 
better assessment of the "true atomic B-factor".



Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
                                                 Julian, King of Lemurs

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