reflection file editor - only 1 dataset#
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/
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
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participants (2)
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Pavel Afonine
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vincent Chaptal