[phenixbb] Important change in phenix.refine output: MTZ file with data and map coefficients
Pavel Afonine
pafonine at lbl.gov
Thu Mar 3 21:01:49 PST 2011
Hi Everyone,
starting development version dev-686:
http://www.phenix-online.org/download/nightly_builds.cgi
phenix.refine does not output *map_coeffs.mtz file. Instead, it creates
prefix_serial.mtz file (example: lysozime_001.mtz) containing four sections:
- section 1: Original input data (Iobs or Fobs, and HL coefficients if
provided) and flags (as supplied in input);
- section 2: Experimental data used in refinement (labels:
F-obs-filtered, SIGF-obs-filtered). This can be different from "Original
data" due to Iobs->Fobs conversion (if input data are intensities) and
outliers filtering;
- section 3: Contains total model structure factors (labels: F-model,
PHIF-model) used everywhere in refinement (for the formula, see:
http://www.phenix-online.org/documentation/fmodel.htm). In the future,
this section might be extended to explicitly list all contributions to
Fmodel, such as Fcalc (corresponding to atomic model), Fbulk (bulk
solvent contribution), and so on.
- section 4: Fourier map coefficients (exactly the same as used to be in
*map_coeffs.mtz file).
This change is meant to reduce the confusion when people tended to use
*map_coeffs.mtz file for refinement and PDB deposition, and facilitates
the reproduction of refinement statistics (R-factors, for example).
Also, thanks to Jeff Headd, by default phenix.refine now converts input
intensities (Iobs) to amplitudes (Fobs) using French & Wilson method
(Acta Cryst A34, 517, 1978), so no need to run a specific program
(Truncate, for example) to do this.
To see the content of a MTZ file use phenix.mtz.dump command:
phenix.mtz.dump data.mtz
Pavel.
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