[ccp4bb] refmac and average B factors

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

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Subject: Re: non ccp4 question
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-10-04

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

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

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.

CCP4bb navigation

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

Previous message:
Subject: Re: non ccp4 question
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-10-04

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