[phenixbb] B-factors

Pavel Afonine pafonine at lbl.gov
Sat Apr 6 12:45:09 PDT 2013

Hi Ed,

that's all right. Both ways have clear pros and cons (I have a few pages 
long email that I wrote a year ago to someone that carefully lists them 
all), but are ok as long as a) things are self-consistent, and b) track 
about what was done is recorded. The only reason I made that remark is 
to point out that the previous behavior was not strictly speaking a bug, 
that's all. At some point Garib made a very nice comment about this (in 
ccp4bb list).

All the best,

On 4/6/13 8:13 AM, Ed Pozharski wrote:
> Pavel,
> 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".
> Cheers,
> Ed.

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