[phenixbb] Important change in phenix.refine output: MTZ file with data and map coefficients

Schubert, Carsten [PRDUS] CSCHUBER at its.jnj.com
Fri Mar 4 04:38:54 PST 2011

Hi Pavel,

how will this affect coot? It is very convenient to just point to an
mtz_mapcoeff file and have coot produce a map automatically. Has this
been verified to work? I would rather have the autoload feature retained
as a convenience for the general user base to make their work load more
efficient than try to cater to a minority who quite frankly shouldn't be
doing what they are doing when they don't know the difference between
map-coefficients and structure factors. 

I guess I need to coffee, realize I'm getting cranky early in the
morning ....


> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
> bounces at phenix-online.org] On Behalf Of Pavel Afonine
> Sent: Friday, March 04, 2011 12:02 AM
> To: PHENIX user mailing list
> Subject: [phenixbb] Important change in phenix.refine output: MTZ file
> with data and map coefficients
>   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
> 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
> the reproduction of refinement statistics (R-factors, for example).
> Also, thanks to Jeff Headd, by default phenix.refine now converts
> 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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