Dear Ethan,
Thank you for your reply.
I will try to review my refinement protocol once more; however, I am still
perplexed at what lies at the heart of the problem.
Overestimation of average B-factor using TLS is perfectly sound, but I am
not sure why all my structures the average increases tremendously.
In one case it increases from 16.36 to 73.02 for a 2.3Ang structure.
I already tried changing weights and number of TLS rounds, which resulting
in only a small change in average B.
Omid
> On Thursday, August 08, 2013 11:39:22 am Omid Haji-Ghassemi wrote:
>> Dear all,
>>
>> I was about to deposit a few structures to the pdb when I noticed the
>> mean
>> B-factors were larger than one might expect.
>>
>> All the structures were refined using TLS refinement.
>>
>> During refinement in Refmac the average temperature factors for each
>> structure is reasonable. For example, a structure at 2.75� has a mean
>> B-factor of 40; however, after adding the ANISOU records as required by
>> the PDB, I noticed the average B-factors double.
>
> Please see my paper:
> E. A. Merritt (2011).
> "Some Beq are more equivalent than others". Acta Cryst. A67, 512-516.
> <http://skuld.bmsc.washington.edu/parvati/ActaA_67_512.pdf>
>
> In short, the quantity stored in the "B" field of a PDB file after TLS
> refinement is Beq, which overestimates what the isotropic B factor would
> have been if you had refined without TLS. So in general the "average B"
> after TLS refinement is always higher than the "average B" without TLS.
> The problem is that the two quantities marked "average B" are not
> directly comparable.
>
> Having said that, the overestimate is not usually as much as a factor of
> 2.
> So something else may indeed be causing a problem in your case.
>
> Ethan
>
>
>>
>> Is this normal?
>>
>> Sincerely,
>> Omid
>>
>> ---------------------------------------------------
>> ---------------------------------------------------
>> Omid Haji-Ghassemi, Graduate Student
>> Department of Biochemistry & Microbiology
>> University of Victoria
>> PO Box 3055 STN CSC
>> Victoria, BC, V8W 3P6
>> CANADA
>>
>> Tel: 250-721-8945
>> Fax: 250-721-8855
>>
>
> --
> Ethan A Merritt
> Biomolecular Structure Center, K-428 Health Sciences Bldg
> University of Washington, Seattle 98195-7742
>
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