2017 cxi merge tutorial: Difference between revisions

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This is an updated, worked example of data merging using cxi.merge.  Previous documentation sets are [[Merging | here]] and [[Advanced Merging | here]].
This is an updated, worked example of data merging using cxi.merge.  Previous documentation sets are [[Merging | here]] and [[Advanced Merging | here]].


In this example, we are given integrated still-shot data collected by Danny Axford at Diamond, for P6 myoglobin, PDB code [http://www.rcsb.org/pdb/explore/explore.do?structureId=5M3R 5M3R].
In this example, we are given integrated still-shot data collected by Danny Axford at Diamond, for P6 myoglobin, PDB code [http://www.rcsb.org/pdb/explore/explore.do?structureId=5M3S 5M3S].


* /net/dials/raid1/aaron/zurich0038/jr_006_batches/split_reintegrated/extracted # cctbx-style integration pickles  
* /net/dials/raid1/aaron/zurich0038/jr_006_batches/split_reintegrated/extracted # cctbx-style integration pickles  
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* Unit cells are variable but do seem to cluster around 91.4 91.4 45.9 90 90 120
* Unit cells are variable but do seem to cluster around 91.4 91.4 45.9 90 90 120


  phenix.fetch_pdb --mtz 5m3r
  phenix.fetch_pdb --mtz 5m3s


Merge command file:
Merge command file:
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  backend=FS \
  backend=FS \
  nproc=1 \
  nproc=1 \
  model=5m3r.pdb \
  model=5m3s.pdb \
  merge_anomalous=True \
  merge_anomalous=True \
  plot_single_index_histograms=False \
  plot_single_index_histograms=False \
  scaling.algorithm=mark0 \
  scaling.algorithm=mark0 \
  raw_data.sdfac_auto=False \
  raw_data.sdfac_auto=False \
  scaling.mtz_file=5m3r.mtz \
  scaling.mtz_file=5m3s.mtz \
  scaling.show_plots=False \
  scaling.show_plots=False \
  scaling.log_cutoff=None \
  scaling.log_cutoff=None \

Revision as of 00:21, 9 February 2017

cxi.merge for the 2017 Berkeley Lab tutorial

This is an updated, worked example of data merging using cxi.merge. Previous documentation sets are here and here.

In this example, we are given integrated still-shot data collected by Danny Axford at Diamond, for P6 myoglobin, PDB code 5M3S.

  • /net/dials/raid1/aaron/zurich0038/jr_006_batches/split_reintegrated/extracted # cctbx-style integration pickles
  • /net/dials/raid1/aaron/zurich0038/jr_006_batches/sig_filter/split_reintegrated/extracted # same data, with per-image resolution cutoff during integration

Unix ls reveals 5031 *.pickle files in each directory.

Immediately there is a problem:

$ cxi.print_pickle /net/dials/raid1/aaron/zurich0038/jr_006_batches/sig_filter/split_reintegrated/extracted/*.pickle

...fails on image 0059 with a traceback; it looks like the file is corrupted.

So focus on the data without integration resolution cutoff:

$ cxi.print_pickle /net/dials/raid1/aaron/zurich0038/jr_006_batches/split_reintegrated/extracted/*.pickle

Some conclusions with the aid of grep:

  • all integration pickles have space group P6 (good)
  • distance and beam center is fixed throughout the integrated dataset
  • Unit cells are variable but do seem to cluster around 91.4 91.4 45.9 90 90 120
phenix.fetch_pdb --mtz 5m3s

Merge command file:

#!/bin/csh -f

set effective_params = "d_min=DMIN \
data=/net/dials/raid1/aaron/zurich0038/jr_006_batches/split_reintegrated/extracted/*.pickle \
output.n_bins=10 \
pixel_size=0.172 \
backend=FS \
nproc=1 \
model=5m3s.pdb \
merge_anomalous=True \
plot_single_index_histograms=False \
scaling.algorithm=mark0 \
raw_data.sdfac_auto=False \
scaling.mtz_file=5m3s.mtz \
scaling.show_plots=False \
scaling.log_cutoff=None \
scaling.mtz_column_F=i-obs \
scaling.report_ML=True \
set_average_unit_cell=True \
rescale_with_average_cell=False \
significance_filter.apply=True \
significance_filter.min_ct=30 \
significance_filter.sigma=0.2 \
include_negatives=NEG \
postrefinement.enable=True \
postrefinement.algorithm=rs \
output.prefix=TAG"
set tag = p6m
set dmin = 2.5
set neg = True
set eff = `echo $effective_params|sed -e "s,FS,Flex,g"|sed -e "s,DMIN,$dmin,g"|sed -e "s,NEG,$neg,g"|sed -e "s,TAG,$tag,g"`

cxi.merge ${eff}
exit
cxi.xmerge ${eff}