Cppxfel Indexing
This page is under development!
The original version of cppxfel indexed using DIALS, but if the unit cell dimensions are known, cppxfel itself can also be used to index images using the TakeTwo algorithm. This page details how to index using cppxfel.
Downloading test data
Data can be downloaded as a [zip file] from the DIALS website and should be extracted to a new folder.
tar zxvf ginn_jac_cpv17.tgz
Running DIALS spot-finding on the set of 1000 images
The scripts included in cppxfel to run DIALS uses four cores by default. This is to generate the spot-finding parameters for good indexing rates. If you have more cores available on the current machine, this can be edited by setting the environment variable NSLOTS:
export NSLOTS=16
DIALS uses the options found in the two files find_spots.options for spotfinding. These should be generated for find_spots.options with these parameters:
cat > find_spots.options << EOF gain=14.0 min_spot_size=2 global_threshold=100 EOF
Note, in the tcsh shell, this is not a valid way of creating a text file. In this case, create an appropriate file in your favourite text editor with the text gain=14.0 min_spot_size=2 global_threshold=100.
The DIALS scripts can now be run as follows:
cppxfel.run_dials shot*.pickle index=no
The term index=no prevents DIALS from running indexing on these images, as we plan to index using cppxfel.
The spot-finding results made by DIALS should be converted to a new format for reading into cppxfel. This is achieved by running the command:
cppxfel.gen shot*.pickle
This will generate a very simple _XXX_strong.list text file for every _XXX_strong.pickle file, as well as prepare the images for cppxfel. For an easy analysis of the number of spots per image, you can use the command
wc -l *strong.list
This will also create shells of index.txt, integrate.txt, refine.txt and merge.txt.
Preparing for TakeTwo
Have a look at the contents of the index.txt shell.
cat index.txt
The output will look something like this:
ORIENTATION_MATRIX_LIST matrices.dat NEW_MATRIX_LIST indexed.dat # Be sure to set the UNIT_CELL and SPACE_GROUP for indexing. cppxfel cannot index without this knowledge. SPACE_GROUP 0 UNIT_CELL 0 0 0 0 0 0 MM_PER_PIXEL 0.11 BEAM_CENTRE 881.755 881.5075 DETECTOR_DISTANCE 90.9988 INTEGRATION_WAVELENGTH 1.45825667181 PANEL_LIST panels.txt METROLOGY_SEARCH_SIZE 2 # If your crystal is highly mosaic or the detector is quite far back you may need to increase the padding values. SHOEBOX_FOREGROUND_PADDING 1 SHOEBOX_NEITHER_PADDING 2 SHOEBOX_BACKGROUND_PADDING 3 # If you see too many spots, increase the intensity threshold. INTENSITY_THRESHOLD 12 ABSOLUTE_INTENSITY OFF OVER_PRED_BANDWIDTH 0.07 REFINE_ORIENTATIONS ON ROUGH_CALCULATION ON # Specifies maximum multiple lattices to index in total SOLUTION_ATTEMPTS 1 # Maximum reciprocal distance from spot to spot to consider for analysis. # A maximum reciprocal distance of 0.1 would be equivalent separation # between the beam centre and the 10 Angstrom resolution ring. MAX_RECIPROCAL_DISTANCE 0.15 # Initial rlp size: used to determine the tolerances for the vector lengths in the crystal. # For a 1 micron crystal with no mosaicity, the initial rlp size is 0.0001 Ang^-1 (i.e., # 1 / 10000 Ang). To be more strict for indexing, lower this number; to be less strict increase it. INITIAL_RLP_SIZE 0.0001 # If you wish to see more verbose output, change to 1 (moderate), or 2 (debug, usually too much). VERBOSITY_LEVEL 0 COMMANDS INDEX
Note that some parameters have not been initialised. Edit these lines in order to supply the correct information. The edited lines are shown below, but check the entire input. The space group and unit cell are essential for cppxfel indexing: it cannot currently index without a known unit cell and space group.
SPACE_GROUP 197 UNIT_CELL 106.1 106.1 106.1 90 90 90
When the index.txt file is ready, you may run indexing on the data:
cppxfel.run -i index.txt
Wavelength histograms should appear every time an image is successfully indexed:
Wavelength histogram for shot-s00-20130316164947655.img 1.356 1.366 1.377 1.387 ... 1.397 .... 1.407 ...... 1.417 .. 1.428 .... 1.438 .. 1.448 ..... 1.458 ................................................................ 1.468 ................................................................ 1.479 ........ 1.489 .. 1.499 .... 1.509 .... 1.52 ... 1.53 1.54 1.55 1.56
At the end of the run, it should create a file called integrate-indexed.dat which can be fed into integration.