Dear Robbie, Marcus and Reginald, Thanks again for your replies, I truly appreciate the help.
The B-factors was set to 20 when performing TLS refinement so I don't think that is the problem. I also tried Marcus's suggestion using output from coot, with no luck. The only thing left to try is to test alternative TLS group as Reginald have suggested. Cheers Omid > Hi Omid, > > Sometimes the choice of TLS groups and to a lesser extent the initial > B-factor matter a lot. You should try a few other TLS group selections and > see if these give nicer results. Things to try: TLSMD, including or > excluding ligands and carbohydrates, other common-sense or gut-feeling > structure partitionings. If you have a lot of different groupings to > test, you can reset the B-factor and do pure TLS refinement (i.e. 0 cycles > of restrained refinement) for all of them. You can then use the best one > for your 'final' refinement. It's much faster then trying your final > refinement with all TLS groups selections. > > Cheers, > Robbie > > Sent from my Windows Phone > ________________________________ > Van: Omid Haji-Ghassemi > Verzonden: 8-8-2013 21:55 > Aan: CCP4BB@JISCMAIL.AC.UK > Onderwerp: Re: [ccp4bb] TLS refinement and ANISOU records > > 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 >> >
