A small but potentially important correction:
FC_ALL PHIC_ALL from REFMAC are indeed the calculated structure factor
of the coordinates+bulk_solvent, but AFTER multiplying by the likelihood
coefficient "D" (as in 2*m*Fo-D*Fc ). So, if you subtract ( FC_ALL
PHIC_ALL ) from ( FC PHIC ) you will NOT get the bulk solvent
contribution alone. AFAIK there is no way to obtain just the bulk
solvent contribution from REFMAC.
-James Holton
MAD Scientist
On 12/13/2011 6:24 AM, Ed Pozharski wrote:
On Tue, 2011-12-13 at 02:31 +0000, Yuri Pompeu wrote:
Hi Ed,
I just had a chance of looking at your comment more closely.
You are right it only uses PHIC if in refmacs set up you choose to refine "with
prior phase information" -AFAIU.
So what exactly is the info contained in the output refmacX.mtz besides map
coefficients for COOT? If it is not just the raw xray data Fo, is it Fc only,
or Fc that are filled in for missing Fo?
I guess I am not really sure. I was under the impression that model´s PHIC
would cause the problems, if they were present.
Best,
The columns in a standard refmac output mtz file are
H K L FreeR_flag - self-evident
F SIGF - these are modified compared to the input. AFAIU, some of the
scaling is applied to the Fo's as a matter of programming elegance.
Naturally, this makes using them for future refinement cycles
problematic.
FC PHIC - these are Fc's from the atoms present in the model
FC_ALL PHIC_ALL - full Fc's, i.e including the solvent contribution
FWT PHWT DELFWT PHDELWT - this is what you called the "map coefficients
for COOT", although this is historically incorrect since refmac produced
this output before coot was born
FOM - figure-of-merit
As for filling-in missing reflections, it is always on. Not to rekindle
another Hegelian fire, but the idea is that the missing reflections
should always be filled in because Fc's are definitely better estimates
of Fo's than zeros.
HTH,
Ed.
