I may be wrong here (and please by all means correct me), but I think
it's not entirely true that experimental errors are not used in modern
map calculation algorithm.  At the very least, the 2mFo-DFc maps are
calibrated to the model error (which can be ideologically seen as the
"error of experiment" if you include model inaccuracies into that).  And
I quote from Acta D53:240,

"REFMAC also includes the sigma_E0 in the derivation of these terms (m
and D) which usually leads to improved behavior.  In fact in several
cases when this has not been so it has been shown that the sigma_I0 were
wrongly estimated during data processing."

Thus, the experimental errors do affect the maps (albeit indirectly).  I
have not done extensive (or any for that matter) testing, but my
evidence-devoid gut feeling is that maps not using experimental errors
(which in REFAMC can be done either via gui button or by excluding SIGFP
from LABIN in a script) will for a practicing crystallographer be
essentially indistinguishable.

The reason for this is that "model errors" as estimated by various
maximum likelihood algorithms tend to exceed experimental errors.  It
may be that these estimates are inflated (heretical thought but when you
think about it uniform inflation of the SIGMA_wc may have only
proportional impact on the log-likelihood or even less so when they
correlate with experimental errors).  Or it may be that the experimental
errors are underestimated (another heretical thought).

Nevertheless, the perceived situation is that "our models are not as
good as our data", and therefore experimental errors don't matter.  Now
I am playing another devil's advocate and I know how crazy this sounds
to an unbiased experimental scientist (e.g. if they don't matter, why
bother improving data reduction algorithms?).

I guess maps produced in phenix do not use experimental errors in any
way given that the maximum likelihood formalism implemented there does
not.  Although phenix is not immutable and my understanding may be
outdated.  But this is not the right forum for pondering this specific
question.

Cheers,

Ed.

PS.  I fully realize that Francisco's question was more practical (and
the answer to that is to run REFMAC without SIGFP record in LABIN), but
isn't thread-hijacking fun? :)

On Wed, 2012-05-23 at 10:05 +0300, Nicholas M Glykos wrote:
> Hi Francisco,
> 
> I'll play devil's advocate, but a measurement without an estimate of its 
> error is closer to theology than to science. The fact that the standard 
> deviations are not used for calculating an electron density map via FFT is 
> only due to the hidden assumption that you have 100% complete, error-free 
> data set, extending to sufficient high (infinite) resolution. When these 
> assumptions do not apply (as is usually the case with physical reality), 
> then the simple-minded FFT is not the correct inversion procedure (and the 
> data do not univocally define a single map). Under these conditions other 
> inversion mathods are needed (such as maximum entropy) for which the 
> standard deviations are actively being used for calculating the map.
> 
> My twocents,
> Nicholas
> 
> 
> On Tue, 22 May 2012, Francisco Hernandez-Guzman wrote:
> 
> > Hello everyone,
> > 
> > My apologies if this comes as basic, but I wanted to get the expert's 
> > take on whether or not the sigmaF values are required in the calculation 
> > of an electron density map. If I look at the standard ED equation, 
> > sigma's don't appear to be a requirement but all the scripts that I've 
> > looked at do require sigma values.
> > 
> > I wanted to calculate the electron density for PDB id: 1HFS but the 
> > structure file only lists the Fo's, Fc's and Phases, but no sigmas. 
> > Would such structure factor file be considered incomplete?
> > 
> > Thank you for your kind explanation.
> > 
> > Francisco
> > 
> 

-- 
"I'd jump in myself, if I weren't so good at whistling."
                               Julian, King of Lemurs