Hi Tim, no, in the cases I remember there was no significant difference in geometry - of course, we do tend to work on rather stable, rocky proteins... Mark
On 9 Aug 2013, at 16:33, Tim Gruene wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Hi Mark, > > does your experience also include the geometry of the model? There > might be improvements, as e.g. reported from molprobity, because of a > better modelling of the temperature factors. > > I am asking because you mention improvements of the electron density, > whereas some improvements in the geometry, like the Ramachandran plot, > may not be directly visible in the electron density. > > Cheers, > Tim > > On 08/09/2013 04:27 PM, Mark J van Raaij wrote: >> 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: >>>>> 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 >>>>>> >>>>> >>>> >>> >>> -- Ethan A Merritt Biomolecular Structure Center, K-428 Health >>> Sciences Bldg University of Washington, Seattle 98195-7742 >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.14 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFSBP3LUxlJ7aRr7hoRAo2eAKDoDFsAnywjd3GIc2S+d7UZw1PU2QCffIn4 > UZiFSH1yXDMexQQIkzyBSqI= > =Y4ad > -----END PGP SIGNATURE-----
