Re: [phenixbb] Phenix.reflection_file_converter enhancement request

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: [email protected] [mailto:[email protected]] 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 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