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