[phenixbb] reflection file editor - only 1 dataset#

[Pavel Afonine]

Hi Vincent,

I don't think Reflection File Editor can do that but I just wrote a 
cctbx based script to do that. Save lines below (between ****) into a 
file convert.py:

****

from iotbx import mtz
from iotbx import reflection_file_reader

def run(file_name = "1yjp_refine_001.mtz"):
   miller_arrays = reflection_file_reader.any_reflection_file(file_name =
     file_name).as_miller_arrays()
   mtz_dataset = None
   for ma in miller_arrays[1:]:
     label = ma.info().label_string()
     if "," in label: label = label[:label.index(",")]
     if mtz_dataset is None:
       mtz_dataset = ma.as_mtz_dataset(column_root_label = label)
     else:
       mtz_dataset.add_miller_array(ma, column_root_label = label)
   mtz_dataset.mtz_object().write("output.mtz")

if __name__ == '__main__':
   run()

****

then put the correct file name instead of 1yjp_refine_001.mtz and run

phenix.python convert.py

The output output.mtz file will have all the arrays in one data block.

Good luck!
Pavel


On 9/28/23 07:36, vincent Chaptal wrote:
> Hi,
>
> I have a reflection file generated by phenix.refine, which contains  
> HKL, I, Rfree, SIGI, Fs..., Fmodel... and map coeffs. All these arrays 
> are placed in several dataset#.
> I would like to place them all in a single Dataset#. Is it possible to 
> do that using the reflection file editor? I've tried to modify the 
> output with "edit arrays" but I can't figure out how to do that?
>
> Thank you.
> Best
> Vincent
>
> -- 
>
> Vincent Chaptal, PhD
>
> Director of GdR APPICOM
>
> Drug Resistance and Membrane Proteins Lab
>
>
> MMSB -UMR5086
>
> 7 passage du Vercors
>
> 69007 LYON
>
> FRANCE
>
> +33 4 37 65 29 01
>
> http://www.appicom.cnrs.fr
>
> http://mmsb.cnrs.fr/en/
>
>
>
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