>
> I know space is cheap these days, but is there a reason for Refmac to
> generate all those extra columns in the output mtz file? Refmac (as well
> as phenix.refine and buster-tnt) output mtz file is almost always used for
> only one purpose - look at the map in coot. You only need 4 columns for
> that, not 14. Other columns are useful for testing, but why not make them
> optional?
>
a phenix.refine run creates an MTZ file with four kinds of data:
1) Copy of input data. Why? For convenience and consistency. Inputs may not
necessarily be in MTZ format and may be spread across multiple files of
different format.
2) Data that were actually used in refinement. Why? A user has options to
cut resolution from both ends, as well as apply cutting by sigma. Plus,
phenix.refine may choose not to use a handful of reflections as outliers
(Read, 1999). So it may be good to have set of reflections that were used
in given refinement run.
3) Model in reciprocal space: Fmodel. Why? This is a reciprocal space
representation of what's in PDB file except that it is richer because
contains not only atomic model (Fcalc) but also solvent contributions (bulk
and non-uniform) as well as all scales. Fmodel taken from this array and
Fobs from "2)" are expected to reproduce reported R-factor exactly.
4) Fourier map coefficients (2mFobs-DFmodel, mFobs-DFmodel, anomalous map
if applicable).
"1)" and "3)" can be optional:
- with trivial scripting one can obtain Fmodel using data from "2)" and
"4)".
- "1)" duplicates inputs. It's not unreasonable to assume they are
still available by the time you finalize your structure.
But.. as you pointed out space is cheap and personally I find it much
easier to have relevant arrays of data centralized in one place (file)
rather than scattered across hard drive.
All the best,
Pavel
