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 >
