At this point I usually chime in with an explanation of why
the Protein Data Bank made some choice or other in the early
days but on the matter of U vs. B I have not information to
contribute.
I can point out the at that time characters were stored in
display code on a CDC 6600 and display code used 6 bits so
'bytes' at that time were less obese. 6 bits per character
explains, of course, why lower case characters were not
routinely used.
Frances
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On Wed, 12 Oct 2011, James Holton wrote:
> I think the PDB decided to store "B" instead of "U" because unless the
> B factor was > 80, there would always be a leading "0." in that
> column, and that would just be a pitiful waste of two bytes. At the
> time the PDB was created, I understand bytes cost about $100 each!
> (But that could be a slight exaggeration)
>
> -James Holton
> MAD Scientist
>
> On Wed, Oct 12, 2011 at 2:56 PM, Phil Evans <[log in to unmask]> wrote:
>> Indeed that paper does lay out clearly the various definitions, thank you, but I note that you do explicitly discourage use of B (= 8 pi^2 U), and don't explain why the factor is 8 rather than 2 (ie why it multiplies (d*/2)^2 rather than d*^2). I think James Holton's reminder that the definition dates from 1914 answers my question.
>>
>> So why do we store B in the PDB files rather than U? :-)
>>
>> Phil
>>
>> On 12 Oct 2011, at 21:19, Pavel Afonine wrote:
>>
>>> This may answer some of your questions or at least give pointers:
>>>
>>> Grosse-Kunstleve RW, Adams PD:
>>> On the handling of atomic anisotropic displacement parameters.
>>> Journal of Applied Crystallography 2002, 35, 477-480.
>>>
>>> http://cci.lbl.gov/~rwgk/my_papers/iucr/ks0128_reprint.pdf
>>>
>>> Pavel
>>>
>>> On Wed, Oct 12, 2011 at 6:55 AM, Phil Evans <[log in to unmask]> wrote:
>>> I've been struggling a bit to understand the definition of B-factors, particularly anisotropic Bs, and I think I've finally more-or-less got my head around the various definitions of B, U, beta etc, but one thing puzzles me.
>>>
>>> It seems to me that the natural measure of length in reciprocal space is d* = 1/d = 2 sin theta/lambda
>>>
>>> but the "conventional" term for B-factor in the structure factor expression is exp(-B s^2) where s = sin theta/lambda = d*/2 ie exp(-B (d*/2)^2)
>>>
>>> Why not exp (-B' d*^2) which would seem more sensible? (B' = B/4) Why the factor of 4?
>>>
>>> Or should we just get used to U instead?
>>>
>>> My guess is that it is a historical accident (or relic), ie that is the definition because that's the way it is
>>>
>>> Does anyone understand where this comes from?
>>>
>>> Phil
>>>
>>
>
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