Cppxfel Initial Orientation Matrix Refinement - Revision history

Helenginn at 23:12, 25 November 2015

2015-11-25T23:12:44Z

← Older revision		Revision as of 23:12, 25 November 2015
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	METROLOGY_SEARCH_SIZE 1		METROLOGY_SEARCH_SIZE 1

	~~SHOEBOX_FOREGROUND_RADIUS~~ 1		SHOEBOX_FOREGROUND_PADDING 1
	~~SHOEBOX_NEITHER_RADIUS~~ 2		SHOEBOX_NEITHER_PADDING 2
	~~SHOEBOX_BACKGROUND_RADIUS~~ 3		SHOEBOX_BACKGROUND_PADDING 3

	INTENSITY_THRESHOLD 12		INTENSITY_THRESHOLD 12

Helenginn at 18:00, 25 November 2015

2015-11-25T18:00:31Z

← Older revision		Revision as of 18:00, 25 November 2015
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	* 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.		* 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.		* <code>shot*.dat</code> files, containing tab-delimited information on the coordinates and intensities of each reflection.
			* <code>integration.csv</code>, which contains the information in the final integration summary table which can be imported into other graph-drawing software suites.

	Once these files are generated, it is time to do [[Cppxfel Post-refinement]].		Once these files are generated, it is time to do [[Cppxfel Post-refinement]].

Helenginn at 22:03, 24 November 2015

2015-11-24T22:03:13Z

← Older revision		Revision as of 22:03, 24 November 2015
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	<pre>		<pre>
	head -20 matrices.dat		head -21 matrices.dat
	</pre>		</pre>

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	</pre>		</pre>

	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 <code>integrate.txt</code> 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.		The image tag has the name of the image file minus the extension. The values for the detector distance, beam centre and wavelength are overridden by the values in the <code>integrate.txt</code> file if they are present, but the overriding 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. The unit cell matrix is the inverse of the real space unit cell matrix, and the unit cell matrix is multiplied by the rotation matrix before use (rotation × unit cell matrix).

	== Executing integrate.txt ==		== Executing integrate.txt ==
Line 142:		Line 142:
	</pre>		</pre>

	The "score" column is the result of the minimisation function used to refine the horizontal and vertical rotations, which are listed in the following two columns. In general, a score of 3 or less is good, though will be higher for low resolution data.		The "score" column is the result of the minimisation function used to refine the horizontal and vertical rotations, which are listed in the following two columns. This is a weighted combination of the total number of reflections and the standard deviation of the Ewald sphere wavelengths. In general, a score of 3 or less is good, though will be higher for low resolution data, using the standard setting for <code>ORIENTATION_SCORE</code>. The horizontal and vertical rotations show the rotations in degrees required to find the optimal solution.

	== Output files ==		== Output files ==

Helenginn at 17:44, 24 November 2015

2015-11-24T17:44:13Z

@@ Line 115: / Line 115: @@
 == 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.
+The initial orientation matrix refinement commands finish with a summary table detailing the main results for each crystal and each image. It will start with something like this:
 == Output files ==

Helenginn at 17:36, 24 November 2015

2015-11-24T17:36:54Z

← Older revision		Revision as of 17:36, 24 November 2015
Line 1:		Line 1:
	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 ==
Line 9:		Line 9:
	</pre>		</pre>

	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>
Line 116:		Line 116:

	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]].

Helenginn at 17:05, 24 November 2015

2015-11-24T17:05:40Z

← Older revision		Revision as of 17:05, 24 November 2015
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	<pre>		<pre>
	Wavelength histogram for shot-s00-~~20130316165215513~~.img		Wavelength histogram for shot-s00-20130316165134721.img
	1.~~41304~~ ..		1.41322 .
	1.~~41741~~		1.41759
	1.~~42178~~ .		1.42196
	1.~~42615 .~~.		1.42633 .
	1.~~43052~~ .		1.4307 .
	1.~~43489~~		1.43508 ..
	1.~~43926~~		1.43945
	1.~~44363~~ ..		1.44382 ..
	1.~~448~~ .......		1.44819 .....
	1.~~45237~~ ...		1.45256 .........
	1.~~45674~~ ......		1.45693 ..................
	1.~~46111~~ ...........................................		1.4613 ......................................................................
	1.~~46548~~ ...................................................		1.46567 ...............................................
	1.~~46985~~ ..........		1.47004 .....
	1.~~47422~~ ...		1.47441 .......
	1.~~47859~~ ...		1.47878 ...
	1.~~48296~~ ...		1.48315 .
	1.~~48733~~ ....		1.48752 .
	1.~~4917~~ .		1.4919 ..
	1.~~49607~~ ..		1.49627
	1.~~50044~~
	</pre>		</pre>

			These integration peaks should be as long and narrow as possible, depending on the extent of over-prediction as determined by the parameter <code>OVER_PRED_BANDWIDTH</code>.

			== 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.

Helenginn at 17:01, 24 November 2015

2015-11-24T17:01:54Z

@@ Line 80: / Line 80: @@
 <pre>
 cppxfel.run -i integrate.txt
 </pre>

Helenginn at 16:59, 24 November 2015

2015-11-24T16:59:00Z

← Older revision		Revision as of 16:59, 24 November 2015
Line 1:		Line 1:
	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'' 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 ==

Helenginn at 16:58, 24 November 2015

2015-11-24T16:58:38Z

← Older revision		Revision as of 16:58, 24 November 2015
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	INTEGRATE		INTEGRATE
			</pre>

			The matrix information from indexing is passed through using the generated file <pre>matrices.dat</pre> under the keyword <code>ORIENTATION_MATRIX_LIST</code> which was produced in the previous stage. One can see the contents of <code>matrices.dat</code>:

			<pre>
			head -20 matrices.dat
			</pre>

			<pre>
			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
			</pre>

			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 <code>integrate.txt</code> 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:

			<pre>
			cppxfel.run -i integrate.txt
	</pre>		</pre>

Helenginn: Created page with "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 defa..."

2015-11-24T16:48:25Z

Created page with "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 defa..."

New page

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]].

== The contents of integrate.txt ==

One can look at the contents of integrate.txt by executing:

<pre>
cat integrate.txt
</pre>

This shows an input script along the following lines:

<pre>
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
</pre>