Re: [ccp4bb] Bfactor is zero?

2010-12-21 Thread Joseph Cockburn
Hi, I saw the same thing once and the cause was that the crystal had been hideously over-exposed during data collection. As a result, essentially all the spots at lower than 2.5A resolution were overloaded. The Wilson plot was thus more or less flat at medium to high resolution and accordingly the

Re: [ccp4bb] Bfactor is zero?

2010-12-20 Thread Nat Echols
On Mon, Dec 20, 2010 at 7:34 AM, Zhibing Lu billz...@gmail.com wrote: Recently I solved a structure in which some water molecules have Bfactors at 0 and overall wilson Bfactor is 0.654 based on PHENIX refinement. Is it possible? Very unlikely - it might be worth trying the latest nightly

Re: [ccp4bb] Bfactor is zero?

2010-12-20 Thread Ralf W. Grosse-Kunstleve
some water molecules have Bfactors at 0 B-factors refining towards zero may be an indication of heavier molecules, e.g. SO4. You have to model them manually. Ralf

Re: [ccp4bb] Bfactor is zero?

2010-12-20 Thread Ezra's gmail
On 12/20/2010 10:34 AM, Zhibing Lu wrote: Hi All, Recently I solved a structure in which some water molecules have Bfactors at 0 and overall wilson Bfactor is 0.654 based on PHENIX refinement. Is it possible? Bill Lu Hi Bill, What resolution are you working with here? An overall Wilson B

Re: [ccp4bb] Bfactor is zero?

2010-12-20 Thread Pavel Afonine
Hi Bill, if you put a water oxygen in place where a heavier atom is, then water oxygen's B-factor will refine to a value close to zero. This is the feature that we currently use as one of many criteria to develop automatic identification and building of metals. Overall Wilson B-factor of 0.6A**2