Helenginn at 17:25, 25 November 2015

2015-11-25T17:25:20Z

← Older revision		Revision as of 17:25, 25 November 2015
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	This uses the file allMerge5.mtz calculated using in the previous stage, and the merge-orientations.dat list which refer to the refined MTZ files (<code>ref-img*.mtz</code>) generated by post-refinement. This will produce a final merge and associated merging statistics.		This uses the file allMerge5.mtz calculated using in the previous stage, and the merge-orientations.dat list which refer to the refined MTZ files (<code>ref-img*.mtz</code>) generated by post-refinement. This will produce a final merge and associated merging statistics.

	If <code>MERGE_ANOMALOUS</code> is set to <code>ON</code> then an anomalous data set will be generated instead of a normal merge.		If <code>MERGE_ANOMALOUS</code> is set to <code>ON</code> then an anomalous data set will be generated instead of a normal merge. This creates I(+), SIGI(+), I(-) and SIGI(-) columns containing the anomalously merged intensities.

	== Output of merge.txt ==		== Output of merge.txt ==

	In the output of merge.txt the correlations in each indexing hand are displayed for each image. The log file ends with new merging statistics. The correlation coefficient can be heavily altered due to the new recalculated sigma values and may appear less high than one would like. If in doubt, plot the intensities of the half-data sets against each other ~~as explained in [[Cppxfel Statistics\|cppxfel statistics]]~~ to confirm their successful correlation.		In the output of merge.txt the correlations in each indexing hand are displayed for each image. The log file ends with new merging statistics. The correlation coefficient can be heavily altered due to the new recalculated sigma values and may appear less high than one would like. If in doubt, [[Cppxfel Statistics#Correlation between two images\|plot the intensities]] of the half-data sets against each other to confirm their successful correlation.

	The two halves of the data set are output to <code>half1Merge.mtz</code> and <code>half2Merge.mtz</code>, and the final merged data set will be output to <code>remerged.mtz</code>, which should be used in further structure solution. If the merge was set to merge anomalous information, then the appropriate file will be saved as <code>anomalous_diff.mtz</code>.		The two halves of the data set are output to <code>half1Merge.mtz</code> and <code>half2Merge.mtz</code>, and the final merged data set will be output to <code>remerged.mtz</code>, which should be used in further structure solution. If the merge was set to merge anomalous information, then the appropriate file will be saved as <code>anomalous_diff.mtz</code>.

Helenginn: Created page with "The final merge in cppxfel is carried out in order to choose the final rejection criteria and recalculate the sigmas so that they better reflect the precision of i..."

2015-11-24T20:38:04Z

Created page with "The final merge in cppxfel is carried out in order to choose the final rejection criteria and recalculate the sigmas so that they better reflect the precision of i..."

New page

The final merge in [[Cppxfel|cppxfel]] is carried out in order to choose the final rejection criteria and recalculate the sigmas so that they better reflect the precision of individual reflections. This is carried out after [[Cppxfel Post-refinement|post-refinement]] and is the final stage in generating a suitable MTZ file.

== Contents of merge.txt ==

The contents of <code>merge.txt</code> from <code>cppxfel.input_gen</code> can be displayed.

<pre>cat merge.txt</pre>

<pre>
ORIENTATION_MATRIX_LIST merge-orientations.dat
MATRIX_LIST_VERSION 2.0
INITIAL_MTZ allMerge5.mtz

OUTLIER_REJECTION_SIGMA 1.6
MERGE_ANOMALOUS OFF
RECALCULATE_SIGMA ON
CORRELATION_THRESHOLD 0.9

COMMANDS

MERGE
</pre>

This uses the file allMerge5.mtz calculated using in the previous stage, and the merge-orientations.dat list which refer to the refined MTZ files (<code>ref-img*.mtz</code>) generated by post-refinement. This will produce a final merge and associated merging statistics.

If <code>MERGE_ANOMALOUS</code> is set to <code>ON</code> then an anomalous data set will be generated instead of a normal merge.

== Output of merge.txt ==

In the output of merge.txt the correlations in each indexing hand are displayed for each image. The log file ends with new merging statistics. The correlation coefficient can be heavily altered due to the new recalculated sigma values and may appear less high than one would like. If in doubt, plot the intensities of the half-data sets against each other as explained in [[Cppxfel Statistics|cppxfel statistics]] to confirm their successful correlation.

The two halves of the data set are output to <code>half1Merge.mtz</code> and <code>half2Merge.mtz</code>, and the final merged data set will be output to <code>remerged.mtz</code>, which should be used in further structure solution. If the merge was set to merge anomalous information, then the appropriate file will be saved as <code>anomalous_diff.mtz</code>.

Cppxfel Final Merge - Revision history

Helenginn at 17:25, 25 November 2015

Helenginn: Created page with "The final merge in cppxfel is carried out in order to choose the final rejection criteria and recalculate the sigmas so that they better reflect the precision of i..."