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I agree that grouping/constraining B-factors just to lower the values is a bad thing. You can however play with the B-factor restraint. In REFMAC that sometimes makes a big difference. Keep in mind that your goal should not be to lower the B-factor, but improving the likelihood of your model. This includes having a plausible B-factor distribution. You might end up with higher B-factors for your side-chain atoms, but as the other replies explained this is not necessarily a problem. Cheers, Robbie PS Shameless plug: The pdb_redo server automatically optimises the B-factor restraint weight for REFMAC. Sent from my Windows 10 phone Van: Dale Tronrud<mailto:[log in to unmask]> Verzonden: dinsdag 21 juni 2016 19:15 Aan: [log in to unmask]<mailto:[log in to unmask]> Onderwerp: Re: [ccp4bb] residue with high B-factor I don't quite understand your concern. Do you have some reason to believe that these B factors shouldn't be greater than 100 A^2? Setting the B factor to 0 A^2 would make the statement that you believe that this atom is not moving at all. I really doubt that you believe this. You would only set a parameter w/o refinement if you know what value that parameter should have with much higher reliability than your data could provide on its own. Generally this is not the case for B factors, although there are constraints that are reasonable to apply, such as insisting that a group of atoms all have the same B factor. Such a constraint is not an appropriate tool for simply reducing the size of B's that you don't like by grouping them with atoms with lower B's. Dale Tronrud On 6/21/2016 9:49 AM, chemocev marker wrote: > Hi All > What will be the fate of the residue with the High B-factor. I have some > residues in my structure with B-factor above then 100 and for some of > them there is electron density map as well. > Should I set their value to 0 and refine it or leave it without refinement. > > best > > Jiri