Precisely, one should not use it! I have seen people do it either
because they dont fully understand what is going on or are not at all
familiar with the documentation.
In phenix the output .mtz contains Fo plus x% Rfree flag=1, so one may
try and do this for refmac because of one of the two above mentioned
reasons (or both)
On Sun, 11 Dec 2011 20:41:48 -0500, Ed Pozharski wrote:
On Sun, 2011-12-11 at 05:28 +0000, Yuri Pompeu wrote:
In refmac however the newly generated refmacX.mtz file contains
phase
info as PHIC calculated from your model. Using this for subsequent
rounds of refinement results in terrific looking maps as they are
now
biased (even more so) by the input model.
PHIC won't be used in refinement unless you specify it, so this can't
happen if you just use the refmac output mtz. AFAIU, the reason the
output mtz should never be used in subsequent refinement is because
the
Fo's are modified. I never understood why one would even have an
idea
of using the output mtz as a new input. Maybe you can explain this
to
me at last.
Cheers,
Ed.
--
Yuri Pompeu
