[phenixbb] Phenix.reflection_file_converter enhancement request

[Schubert, Carsten [PRDUS]]

Hi Nat,

I tried that and it chokes on a dtrek reflection file. It doesn't like the I(+) notation, when the output contain I+ and I- separated
Here is the header of the file, which is standard output from dtrek.

3 6 0 5
CRYSTAL_MOSAICITY=1.3945 0.0000 0.0000;
CRYSTAL_ORIENT_ANGLES=101.2180  6.9156  -21.4276;
CRYSTAL_SPACEGROUP=5;
CRYSTAL_UNIT_CELL=98.6333  98.0339  132.5167  90.0000  111.4590  90.0000;
SOURCE_WAVELENGTH= 1.0000  1.0000;
nH
nK
nL
fIntensity
fSigmaI
fIntensity+
fSigmaI+
fIntensity-
fSigmaI-
     0     0     3 18.3045 5.10113 18.3045 5.10113 -1.00000 -1.00000
     0     0     4 5710.08 188.795 5755.10 269.073 5666.41 264.967
     0     0     5 8143.22 236.253 8604.30 351.377 7762.81 319.165
     0     0     6 125.538 22.1897 113.212 28.2108 145.538 35.9342
     0     0     7 7203.69 246.220 7335.97 353.565 7079.14 343.087
....



From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Nathaniel Echols
Sent: Tuesday, April 13, 2010 3:40 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Phenix.reflection_file_converter enhancement request

On Tue, Apr 13, 2010 at 12:07 PM, Ralf W. Grosse-Kunstleve <rwgk at cci.lbl.gov> wrote:
Nat's reflection file editor in the GUI is meant to give you full
flexibility in composing a new mtz file.

. . . however, the current version of the GUI can't make multiple copies of a single data array, unless you fool it by making a copy of the input file and add that.  There is no reason why it can't be modified to allow this - I just need to figure out how to keep the interface simple.

It is tricky to make everything people want to do work from the
command line. -- Nat was working on command-line support for some
of the reflection file editor functionality, but I'm not quite
sure where that stands.

Functional, but not fully tested.  I'm pretty sure it will do what you need here (as long as you don't mind output in MTZ format):

iotbx.reflection_file_editor data.sca dry_run=True

This will print out (among other info) the resulting parameter set, which you can paste into a file and edit to do exactly what you want.  (Specifically, duplicate the block of parameters for the intensity array, and choose "amplitudes" for "output_as" in the second copy.)

-Nat