Hi Jim, The speed at which the B-factor converges depends on many factors. The B-factor restraint weight that Herman and I mentioned (the one you should optimise before changing occupancies!) is an important factor. Also the position of your atomic coordinates WRT where they should end up is important. In Refmac, there is a big difference between isotropic and anisotropic B-factors (the latter converge much slower). So all in all it is very difficult to predict when the B-factor converges. The good news however is that more cycles of refinement should not hurt your model (if they do, your refinement settings are non-optimal). So grab a cup of coffee and run enough cycles. In Refmac 30 cycles is enough for most isotropic B-factors, but in some cases I use many more.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Jim Brannigan > Sent: Tuesday, November 20, 2012 10:49 > To: [email protected] > Subject: [ccp4bb] how many cycles to settle B-factor? > > As an adjunct to B-factor vs occupancy thread, i might expect the b-factor to > halve if the occupancy is set to 0.5 (but I'm only a molecular > biologist....), if so > how many cycles of refmac would it take for the value to settle? My limited > experience is that it dosn't exactly halve but i do tend to use fewer cycles > at > later stages of refinement? > > thanks > > Jim Brannigan
