This is a NOTE for CXIDB ID 64.
Written by Keitaro Yamashita, RIKEN SPring-8 Center.

Publication:
 T. Tosha et al. (2017) Nature Communications
 "Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate"
 doi: 10.1038/s41467-017-01702-1
 Related PDB ID to this entry: 5Y5H

We used slightly-modified version of cctbx.xfel for data processing, which is available at https://github.com/keitaroyam/cctbx_fork/tree/for_sacla_sfrox
The details are described in Shimada et al. (2017) Sci. Adv. 3, e1603042. doi: 10.1126/sciadv.1603042. (see the "XFEL data processing" section in MATERIALS AND METHODS)

Instructions to reproduce our result
====================================

1. Indexing and integration using cxi.index

 * Here is the script to process each image:

cctbx.python /PATH-TO-CCTBX-PROJECT-DIR/xfel/command_line/cxi_image2pickle_mod.py \
 -c -x ${xy[0]} -y ${xy[1]} data_01.img --bkgpix ../../BKGPIX.cbf 

cxi.index -d -o . data_01.pickle target=index.phil

 * index.phil is:

distl_highres_limit = 1.5
force_method2_resolution_limit = 1.5
distl.res.outer = 1.5

distl.minimum_spot_area=2
distl.minimum_signal_height=2
known_setting=5
target_cell=54.9 75.7 101.6 90 90 90
target_cell_centring_type=P

integration.detector_gain=0.2798
integration.mask_pixel_value=-2
integration.background_factor=2

integration.model=user_supplied
integration.mosaic.refinement_target=ML

difflimit_sigma_cutoff=2

 * $xy is the beam center coordinates pre-optimized for each experiment:

  20150220_sacla1: 1530.59 1565.42
  20150615_sacla2: 1490.89 1567.54
  20150622_sacla2: 1490.98 1567.43

 * BKGPIX.cbf is prepared using XDS to mask shadows of instruments


2. Merging using prime.postrefine

 * phil file for prime.postrefine is:

pixel_size_mm=0.073242

target_unit_cell=54.9 75.7 101.6 90 90 90
target_space_group=P222

scale.d_max=25
postref.scale.d_max=25
postref.crystal_orientation.d_max=25
postref.reflecting_range.d_max=25
postref.unit_cell.d_max=25
postref.allparams.d_max=25
merge.d_max=25
iotacc.d_max=25

scale.d_min=1.5
postref.scale.d_min=1.5
postref.crystal_orientation.d_min=1.5
postref.reflecting_range.d_min=1.5
postref.unit_cell.d_min=1.5
postref.allparams.d_min=1.5
merge.d_min=1.5
iotacc.d_min=1.5

n_residues=400

run_no=1
n_processors=16
n_postref_cycle=7

data = all_files.lst
swap_xy_in_polarization_correction = true

 * all_files.lst is the list file of int_*.pickle given by cxi.index

 * After prime.postrefine, B-factor needs to be applied to the result (see our paper) 
   Following bash script may be uesful.
   apply_b_factor.py can be found at: https://github.com/keitaroyam/yamtbx/blob/master/cctbx_progs/apply_b_factor.py

bs=(`grep "B:     " ../prime.log | awk '{print $2/4.}'`)
n=-1
for mtz in mean_scaled_merge.mtz postref_cycle_*_merge.mtz
do
 n=$((n+1))
 cctbx.python apply_b_factor.py $mtz -b ${bs[$n]}
done