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
