Cppxfel Initial Orientation Matrix Refinement: Difference between revisions
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Initial orientation matrix refinement covers the first stage of the dedicated C++ code in ''cppxfel'' and uses an input file which is called <code>integrate.txt</code> by default. This should have been generated during the [[Cppxfel Indexing | previous stage]]. | Initial orientation matrix refinement covers the first stage of the dedicated C++ code in [[Cppxfel|''cppxfel'']] and uses an input file which is called <code>integrate.txt</code> by default. This should have been generated during the [[Cppxfel Indexing | previous stage]]. | ||
== The contents of integrate.txt == | == The contents of integrate.txt == | ||
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This shows an input script along the following lines | This shows an input script along the following lines. This input script is divided into a number of parameters, followed by the line <code>COMMANDS</code>, after which the task(s) for ''cppxfel'' to complete are listed. In this case, ''cppxfel'' should <code>INTEGRATE</code> the data. | ||
<pre> | <pre> | ||
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The initial orientation matrix refinement commands finish with a summary table detailing the main results for each crystal and each image. | The initial orientation matrix refinement commands finish with a summary table detailing the main results for each crystal and each image. | ||
== Output files == | |||
The important files created by running <code>integrate.txt</code> are: | |||
* A new set of orientation matrices which have been refined under three file names: | |||
* * <code>integrate-orientations.dat</code> - this file is to be provided to input files which use the <code>INTEGRATE</code> command, such as <code>integrate.txt</code> generated by <code>cppxfel.input_gen</code> | |||
* * <code>refine-orientations.dat</code> - this file is to be provided to input files which use the <code>REFINE_PARTIALITY</code> command, such as <code>refine.txt</code> generated by <code>cppxfel.input_gen</code> | |||
* * <code>merge-orientations.dat</code> - this file is to be provided to input files which use the <code>MERGE</code> command, such as <code>merge.txt</code> generated by <code>cppxfel.input_gen</code>. | |||
* MTZ files following the format <code>img*.mtz</code>, which contain over-predicted reflection intensities. The first crystal will end in <code>_0.mtz</code>, the second with <code>_1.mtz</code> and so on for the number of lattices indexed in one image. | |||
* <code>shot*.dat</code> files, containing tab-delimited information on the coordinates and intensities of each reflection. | |||
Once these files are generated, it is time to do [[Cppxfel Post-refinement]]. | |||
Revision as of 17:36, 24 November 2015
Initial orientation matrix refinement covers the first stage of the dedicated C++ code in cppxfel and uses an input file which is called integrate.txt by default. This should have been generated during the previous stage.
The contents of integrate.txt
One can look at the contents of integrate.txt by executing:
cat integrate.txt
This shows an input script along the following lines. This input script is divided into a number of parameters, followed by the line COMMANDS, after which the task(s) for cppxfel to complete are listed. In this case, cppxfel should INTEGRATE the data.
ORIENTATION_MATRIX_LIST matrices.dat NEW_MATRIX_LIST orientations.dat SPACE_GROUP 197 UNIT_CELL 105.917757854 105.917757854 105.917757854 90.0 90.0 90.0 FIX_UNIT_CELL ON MM_PER_PIXEL 0.11 BEAM_CENTRE 881.755 881.5075 DETECTOR_DISTANCE 91.0018 INTEGRATION_WAVELENGTH 1.45738121124 PANEL_LIST panels.txt METROLOGY_SEARCH_SIZE 1 SHOEBOX_FOREGROUND_RADIUS 1 SHOEBOX_NEITHER_RADIUS 2 SHOEBOX_BACKGROUND_RADIUS 3 INTENSITY_THRESHOLD 12 ABSOLUTE_INTENSITY OFF REFINE_ORIENTATIONS ON VERBOSITY_LEVEL 1 COMMANDS INTEGRATE
The matrix information from indexing is passed through using the generated file
matrices.dat
under the keyword ORIENTATION_MATRIX_LIST which was produced in the previous stage. One can see the contents of matrices.dat:
head -20 matrices.dat
image shot-s00-20130316165156302 wavelength 1.45690748941 distance 91.0018 centre 881.755 881.5075 unitcell 0.00945122403519 0.0 0.0 -5.78701450245e-19 0.00945122403519 0.0 -5.78701450245e-19 -1.51989185671e-18 0.00945122403519 rotation 0.209524357745 -0.976621953811 0.0480531252429 -0.360236467579 -0.122785692599 -0.924745024923 0.909026529282 0.176446119331 -0.377541436183 image shot-s01-20130316165035212 wavelength 1.45496194705 distance 91.0018 centre 881.755 881.5075 unitcell 0.00944171966033 0.0 0.0 7.80781215281e-18 0.00944171966033 0.0 3.61484632923e-18 2.67460240614e-18 0.00944171966033 rotation -0.351867835054 0.0121912864248 0.935970298241 -0.852741351745 -0.416546104403 -0.315153184867 0.386032658825 -0.909032846184 0.156965190022 image shot-s00-20130316165041011 wavelength 1.45643207192 distance 91.0018 centre 881.755 881.5075 unitcell 0.00943218298265 0.0 0.0 1.51682978341e-18 0.00943218298265 0.0 3.61119512738e-18 5.77535560549e-19 0.00943218298265 rotation -0.21213292526 0.320476950034 0.92319778299 -0.956128815937 -0.263369266933 -0.128274380022 0.202032941263 -0.909907222596 0.362286539789 image shot-s00-20130316165215513 wavelength 1.45673961831 distance 91.0018
The image tag has the name of the image file minus the extension. The values for the detector distance, beam centre and wavelength are over-ridden by the values in the integrate.txt file if they are present, but the over-riding values can be removed if the values vary from one image to another. The orientation matrix is constructed from the unit cell matrix and the rotation matrix listed.
Executing integrate.txt
This integration input file can be executed through cppxfel using the following command:
cppxfel.run -i integrate.txt
Wavelength histograms
The output tracks individual images which execute on different threads as their orientation matrices are refined. An example of a wavelength histogram created is shown below. These wavelength histograms were first described in Ginn et al, Nat Comms 2015.
Wavelength histogram for shot-s00-20130316165134721.img 1.41322 . 1.41759 1.42196 1.42633 . 1.4307 . 1.43508 .. 1.43945 1.44382 .. 1.44819 ..... 1.45256 ......... 1.45693 .................. 1.4613 ...................................................................... 1.46567 ............................................... 1.47004 ..... 1.47441 ....... 1.47878 ... 1.48315 . 1.48752 . 1.4919 .. 1.49627
These integration peaks should be as long and narrow as possible, depending on the extent of over-prediction as determined by the parameter OVER_PRED_BANDWIDTH.
Final integration summary table
The initial orientation matrix refinement commands finish with a summary table detailing the main results for each crystal and each image.
Output files
The important files created by running integrate.txt are:
- A new set of orientation matrices which have been refined under three file names:
- *
integrate-orientations.dat- this file is to be provided to input files which use theINTEGRATEcommand, such asintegrate.txtgenerated bycppxfel.input_gen - *
refine-orientations.dat- this file is to be provided to input files which use theREFINE_PARTIALITYcommand, such asrefine.txtgenerated bycppxfel.input_gen - *
merge-orientations.dat- this file is to be provided to input files which use theMERGEcommand, such asmerge.txtgenerated bycppxfel.input_gen. - MTZ files following the format
img*.mtz, which contain over-predicted reflection intensities. The first crystal will end in_0.mtz, the second with_1.mtzand so on for the number of lattices indexed in one image. shot*.datfiles, containing tab-delimited information on the coordinates and intensities of each reflection.
Once these files are generated, it is time to do Cppxfel Post-refinement.