[phenixbb] lastest phenix.refine reproducible problem

Nathaniel Echols nechols at lbl.gov
Wed May 9 14:25:33 PDT 2012

On Wed, May 9, 2012 at 2:14 PM, 周文昌 <wenchangyu2006 at gmail.com> wrote:
> 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.


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