SPIND Manual

SPIND can work in two modes: CrystFEL-plugin or stand-alone mode, to extract peaks, index pattern and merge intensity.

CrystFEL-plugin mode

For most SFX(Serial Femtosecond Crystallography) users, especially people who are familiar with CrystFEL, plugin mode is recommended. Users should install the modified CrystFEL with SPIND module(crystfel_spind.tar). If not, please see here for installation.

plugin mode

Extract Peaks

indexamajig -i events.lst -o extract_peaks.stream -g detector.geom --peaks=cxi --indexing=spind --felix-options="spind_dir=spind_directory,extract_peaks"

peak_directory is absolute path of work directory for SPIND.

Index with SPIND

There are two steps to index with SPIND.

First, use generate_table.py scripy to generate reference table.

python generate_table.py config.yml

Then perform indexing using SPIND.py script.

python SPIND.py config.yml

All options and parameters are specified in a configuration file.

# configuration example

# lattice information
cell parameters: [103.45,50.28,69.380,90.00,109.67,90.00]  # in A and degree

# exp. parameters
wave length : 1.306098E-10  # in meters
detector distance : 136.4028E-3  # in meters
pixel size : 110.E-6  # in meters

# reference generation parameters
resolution cutoff: 4.5E-10  #  highest resolution for reference, in meters
lattice type: "monoclinic"  # support monoclinic, orthorhombic
centering: "C"  # centering type, optional, support I, A, B, C, P
reference table: "spind_reference.h5"  # table filename

# indexing parameters
peak list directory: "peak_list"  
output directory: "output" 
sort by: "snr"  # peak list sort method, support snr, intensity
seed pool size: 5  # generate seed from this pool. 5 is good for SFX
refine cycles: 10  # refine indexing solution 
seed length tolerance: 3.E+7  # in m^-1, depends on sample and exp. setup
seed angle tolerance: 1.0  # in degrees
seed hkl tolerance: 0.1  # seed hkl tolerence
centering factor: 0.2  # centering weighting factor
eval tolerance: 0.25  # pair peak criterion
multi index: False  # try to index multiple crystal for single pattern?
# first event: 0  # first event for indeixng, optional
# last event: 100  # last event for indexing, optional

hkl file: None  # txt file including all possiable miller indices, optional
hkl constraint: False  # if apply strict hkl constraint, users must specify a hkl file.

Post-processing with CrystFEL

First we need convert SPIND indexing solution into stream files. indexamajig -i events.lst -o spind.stream -g detector.geom --peaks=cxi --indexing=spind --felix-options="spind_dir=peaks_directory" -p prot.cell

Users can also add other options of indexamajig, see details here

When the stream files ready, users can use CrystFEL programs for visualization, merging…

Authors & Contributors: