On Wed, May 9, 2012 at 2:14 PM, 周文昌
I did a search, by heart, in order to find Ralf's great comment but I did not find it. Could you send the link if you have a way to find it?
The problem is that the precision of the atomic properties in the PDB file is limited to 0.001 for coordinates and 0.01 for B-factors. Internally, the precision is much greater, but some of this is lost when writing them out. For example, the B-factor for an atom might refine to 36.0423947, but it will be written out as 36.04. The cumulative effect of this on every atom results in the slight difference in R-factors. Jeff and I found a similar "problem" with running phenix.refine from command-line arguments only versus running it from a parameter file - the map grid used for FFT structure factor calculations is spaced resolution * 1/3, but this gets written out to the parameter file as 0.3333333333, and this is enough to result in slightly different final models and R-factors. I used scare quotes around "problem", because these kinds of R-factor differences aren't meaningful anyway. -Nat