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Hi Jan, Did you use the TLS refinement for your data? I have had the similar problem with the multi-group TLS refinement. After the first run the resulting pdb file contained unreasonably small atomic B factors for many atoms comparing to the Wilson plot B factor. They seemed to be the TLS-B factors instead of the expected residual B factors. The TLSANL could have not produced the total nor residual B factors when given that file (plus the .tls file from that Refmac run). Moreover, I couldn't use this file as an input for the next Refmac refinement as it was not stable. Interestingly, I have had no problem when using one group only in the TLS step. The version of Refmac was 5.2.0019. Do you observe by chance a similar case? Aleks On 11 Nov 2008, at 01:36, Jan Abendroth wrote: > Hi all, > I have a number of low-ish resolution data sets that show a strange > B-factor behaviour: > All are just better than 3AA resolution, collected on a strong > synchrotron beamline. Some, yet not tremendous radiation decay. > Wilson scaling, obviously not very reliable at this resolution, gives > me a Wilson B of about 40, already a low number. Refinement in refmac5 > (5.5.0053) with individual B-factors refinement leads to an average B > factor of around 16 with several individual B factors hitting the B=2 > limit... > When I convert Is to Fs in truncate simply using the square root, > things get even a bit worse, the average B now is 14. > When I try to do an overall B-factor refinement, still individual > B-factors appear in the output file. > > refinement details: 2.8AA resolution,medium ncs for two ncs related > chains, no riding hydrogens, simple scaling, MKLF target, isotropic B > factors > Rwork: 0.206, Rfree=0.286, bonds=0.018, angles=1.89 ... obviously I > could retrain a bit more... > > Any ideas how to handle this? Basically, my question is: how do I get > the overall B factor to realistic numbers? > Thanks a lot for any hints > > Jan > -- > Jan Abendroth > deCODE biostructures > Seattle / Bainbridge Island, WA, USA > work: JAbendroth_at_decode.com > home: Jan.Abendroth_at_gmail.com > ------------------------------------------------------------------------ -------------------------------------------------- Aleksander W. Roszak, PhD E-mail: [log in to unmask] Protein Crystallography Web: www.chem.gla.ac.uk/~aleks University of Glasgow Fax: +44-(0)141-330 3779 Level 3 Room B 317 Tel (office): +44-(0)141-330 4476 Glasgow Biomedical Research Centre Tel (X-ray lab): +44-(0)141-330 3589 120 University Place Mobile: +44-(0)780 9559996 Glasgow G12 8TA Scotland, UK