Re: [ccp4bb] refmac and average B factors

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: refmac and average B factors
From: Engin Ozkan eozkan {- at -} STANFORD {- dot -} EDU
Date: 2008-10-04

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Date: 2008-10-05

Subject: Re: refmac and average B factors
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-10-05

Hi Engin,

you are correct, you have to run TLSANL and report the corrected B-
factor in your table 1.

Jürgen

On 4 Oct 2008, at 18:32, Engin Ozkan wrote:

> Hi everyone,
>
> I was in the middle of creating a "Table 1" for a finished structure
> and was puzzled by one number. It is the average B factor,
> especially in the case of TLS-refined structures. In this case, the
> average reported by refmac in the header is the average of the B
> factors in the pdb file, which I assume is the residual B factors
> (right?) (A quick Baverage confirmed the number is the average of
> numbers in the B column). If the reported average is really for
> residual B factors, isn't this a bit misleading? In this case, the
> average B was 17, but after I created total B factors with TLSANL,
> average B was 25 A^2.
>
> I think total B factors should be the one reported, but I am afraid
> that might not have been the practice by many. It is such a petty
> point, but with TLS becoming common, shouldn't users be warned more
> about such issues? Or could Refmac report the average for total B
> factors?
>
> Engin
>
> P.S. I hate to bring up the controversy about the reporting of TLS-
> refined B factors (residual vs. full anisotropic, or refmac vs
> PHENIX), but it may come to that.

-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: refmac and average B factors
From: Engin Ozkan eozkan {- at -} STANFORD {- dot -} EDU
Date: 2008-10-04

Next message:
Subject: Re: Clarification of MOLREP logfile
From: Rajan Pillai gene1267 {- at -} GMAIL {- dot -} COM
Date: 2008-10-05