Re: [Jmol-developers] label formatting options ("temperature factor")

[Bob H. <ha...@st...>]

Would the best then be to remove %t from the documentation and just list 
%b as B-factor? Surely anyone who cares to use this will know what it 
is, and %t can still be there, just not documented?

Bob


Dr P. Murray-Rust wrote:

> On Jun 13 2004, Bob Hanson wrote:
>
>> so we have:
>>
>> (I looked up B-factor/temperature factor. They are the same. See
>>
>> http://bmbiris.bmb.uga.edu/wampler/danfip-pres/sld010.htm
>>
>> )
>
>
> Technically not. From the CIF core dictionary , B is:
>
>   Isotropic atomic displacement parameter, or equivalent isotropic
>   atomic displacement parameter, B(equiv), in angstroms squared,
>   calculated from anisotropic temperature factor parameters.
>
>   B(equiv) = (1/3) sum~i~[sum~j~(B^ij^ a*~i~ a*~j~ a~i~ a~j~)]
>
>   a     = the real-space cell lengths
>   a*    = the reciprocal-space cell lengths
>   B^ij^ = 8 pi^2^ U^ij^
>
>   Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
>        775-776.
>
>   The IUCr Commission on Nomenclature recommends against the use
>   of B for reporting atomic displacement parameters. U, being
>   directly proportional to B, is preferred.
>
> Although it doesn't say so here, the use of "temperature factor" is 
> deprecated. There are many physical effects contributing to the ADPs 
> and temperature is only one. You will not find "temperature factor" in 
> the CIF dictionaries and it would be useful to discourage the term.
>
> Best
>
> P.
>
>
>
>
>
>
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-- 

-- Robert M. Hanson, ha...@st..., 507-646-3107 
Professor of Chemistry, St. Olaf College 
1520 St. Olaf Ave., Northfield, MN 55057 
mailto:ha...@st... 
http://www.stolaf.edu/people/hansonr