[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,
Pavel
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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