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Omid, how necessary is it that you do TLS refinement? I.e. are you just doing it to improve your Rs a bit or is the density really getting better? If the density is not improving, I would just refine without TLS and avoid any posterior temperature factor analysis difficulties. While I am sure there are cases where TLS refinement really helps (cf. published examples), my experience in our structures is that it does not really make a difference. Also, in my opinion the TLS model you define must make some physical sense, i.e. some logical explanation why your structure or domains of your structure may have internally consistent anisotropic Bs. Mark On 8 Aug 2013, at 23:01, Ethan Merritt wrote: > On Thursday, August 08, 2013 01:51:34 pm Omid Haji-Ghassemi wrote: >> 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. > > You have only told us about an increase in average B, not whether it is > uniformly inflated. Possibly the output from analysis by the Parvati server > http://skuld.bmsc.washington.edu/parvati > would indicate specific parts of your structure that are behaving > badly during refinement. > > Ethan > >> >> 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: [log in to unmask] >>> 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 >>>> >>> >> > > -- > Ethan A Merritt > Biomolecular Structure Center, K-428 Health Sciences Bldg > University of Washington, Seattle 98195-7742