Cppxfel Statistics - Revision history

Helenginn at 17:56, 25 November 2015

2015-11-25T17:56:03Z

@@ Line 37: / Line 37: @@
 4 44,3396.41,3825.67,2.39429
 4 50,661.039,709.513,2.10893
 </pre>

Helenginn at 17:53, 25 November 2015

2015-11-25T17:53:34Z

← Older revision		Revision as of 17:53, 25 November 2015
Line 120:		Line 120:
	SYMINFO file set to /apps/strubi/ccp4/ccp4-6.5/lib/data/syminfo.lib		SYMINFO file set to /apps/strubi/ccp4/ccp4-6.5/lib/data/syminfo.lib
	Loaded 1520200 reflections (102129 accepted).		Loaded 1520200 reflections (102129 accepted).
			N: lowRes highRes Value Hits Multiplicity
	N: inf 4.28806 0.0138179 1142 3.75862		N: inf 4.28806 0.0138179 1142 3.75862
	N: 4.28806 3.40343 0.0111124 1175 3.62434		N: 4.28806 3.40343 0.0111124 1175 3.62434

Helenginn at 17:46, 25 November 2015

2015-11-25T17:46:18Z

← Older revision		Revision as of 17:46, 25 November 2015
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	One should plot the wavelength on the X axis and both the partiality and percentage columns on separate Y axes, and one hopes that the partiality and percentage graphs match each other as closely as possible.		One should plot the wavelength on the X axis and both the partiality and percentage columns on separate Y axes, and one hopes that the partiality and percentage graphs match each other as closely as possible.

			== R<sub>merge</sub>, R<sub>meas</sub>, R<sub>pim</sub> ==

			The R values R<sub>merge</sub>, R<sub>meas</sub> and R<sub>pim</sub> can be generated from the <code>unmerged*.mtz</code> files generated during refinement (<code>refine.txt</code>) or the <code>unmerged.mtz</code> file generated during the final merge (<code>merge.txt</code>).

			This can be carried out as follows:

			<pre>
			cppxfel.run -rmerge unmerged.mtz
			cppxfel.run -rmeas unmerged.mtz
			cppxfel.run -rpim unmerged.mtz
			</pre>

			These should be used to determine the quality of post-refinement, not the quality of the high resolution data, and should reduce as the post-refinement strategy improves. These will produce appropriate tables:

			<pre>
			$ cppxfel.run -rpim unmerged.mtz
			Running cppxfel...
			Welcome to cppxfel!
			SYMINFO file set to /apps/strubi/ccp4/ccp4-6.5/lib/data/syminfo.lib
			Loaded 1520200 reflections (102129 accepted).
			N: inf 4.28806 0.0138179 1142 3.75862
			N: 4.28806 3.40343 0.0111124 1175 3.62434
			N: 3.40343 2.97317 0.0189678 1223 4.25449
			N: 2.97317 2.70131 0.0270932 1231 4.18195
			N: 2.70131 2.50767 0.0314556 1306 5.0643
			N: 2.50767 2.35981 0.0350953 1306 4.94366
			N: 2.35981 2.24162 0.0398659 1322 5.34516
			N: 2.24162 2.14403 0.0437967 1313 5.49478
			N: 2.14403 2.06148 0.0463546 1319 6.04176
			N: 2.06148 1.99034 0.0486673 1312 6.70868
			N: 1.99034 1.9281 0.0563663 1350 5.81406
			N: 1.9281 1.87298 0.0641532 1291 5.29523
			N: 1.87298 1.82367 0.0746328 1207 4.17778
			N: 1.82367 1.77917 0.0858512 1189 3.44205
			N: 1.77917 1.73872 0.104914 997 2.93709
			N: 1.73872 1.70172 0.127369 826 2.38837
			N: 1.70172 1.66767 0.160804 613 1.98459
			N: 1.66767 1.6362 0.187585 418 1.68597
			N: 1.6362 1.60698 0.266887 163 1.36477
			N: 1.60698 1.57973 0.391058 23 1.17532
			N: * Overall *
			N: 0 1.57973 0.0239934 20726 4.29492
			N: Total time: 0 minutes, 23 seconds (23 seconds).
			</pre>

			This shows an overall Rpim of 2.4%, with significant increase in Rpim after 1.8 Å.

Helenginn: Adding link

2015-11-25T17:23:06Z

Adding link

← Older revision		Revision as of 17:23, 25 November 2015
Line 1:		Line 1:
	There are a number of merging statistics and plots which can be generated using ''cppxfel'' and your favourite graph-drawing software. ''cppxfel'' has a number of commands which generate CSV files which can be plotted elsewhere.		There are a number of merging statistics and plots which can be generated using [[Cppxfel\|''cppxfel'']] and your favourite graph-drawing software. ''cppxfel'' has a number of commands which generate CSV files which can be plotted elsewhere.

	== Correlation between two images ==		== Correlation between two images ==

Helenginn at 17:19, 25 November 2015

2015-11-25T17:19:15Z

@@ Line 9: / Line 9: @@
 </pre>
-This creates a new CSV file named <code>correlation.csv</code> The "first intensity" and "second intensity" columns can be plotted in a suitable program (e.g. R, Veusz, etc.).
+This creates a new CSV file named <code>correlation.csv</code>. This can also be carried out for individual images:
-This can also be carried out for individual images:
+<pre>
 <pre>
-cppxfel.run -cc allMerge5.mtz ref-img-shot-s00-20130316165414164_0.mtz
+h,k,l,wavelength,partiality,percentage,intensity,resolution

Helenginn: Typo

2015-11-25T16:54:22Z

Typo

← Older revision		Revision as of 16:54, 25 November 2015
Line 1:		Line 1:
	There are a number of merging statistics and plots ~~hwich~~ can be generated using ''cppxfel'' and your favourite graph-drawing software. ''cppxfel'' has a number of commands which generate CSV files which can be plotted elsewhere.		There are a number of merging statistics and plots which can be generated using ''cppxfel'' and your favourite graph-drawing software. ''cppxfel'' has a number of commands which generate CSV files which can be plotted elsewhere.

	== Correlation between two images ==		== Correlation between two images ==

Helenginn at 16:54, 25 November 2015

2015-11-25T16:54:09Z

← Older revision		Revision as of 16:54, 25 November 2015
Line 11:		Line 11:
	This creates a new CSV file named <code>correlation.csv</code> The "first intensity" and "second intensity" columns can be plotted in a suitable program (e.g. R, Veusz, etc.).		This creates a new CSV file named <code>correlation.csv</code> The "first intensity" and "second intensity" columns can be plotted in a suitable program (e.g. R, Veusz, etc.).

	~~[[File~~:~~correlation_halves.png\|\|Test]]~~		This can also be carried out for individual images:

	~~This can also be carried out for individual images~~...		<pre>
			cppxfel.run -cc allMerge5.mtz ref-img-shot-s00-20130316165414164_0.mtz

Helenginn: /* Correlation between two images */

2015-11-25T15:45:23Z

Correlation between two images

← Older revision		Revision as of 15:45, 25 November 2015
Line 10:		Line 10:

	This creates a new CSV file named <code>correlation.csv</code> The "first intensity" and "second intensity" columns can be plotted in a suitable program (e.g. R, Veusz, etc.).		This creates a new CSV file named <code>correlation.csv</code> The "first intensity" and "second intensity" columns can be plotted in a suitable program (e.g. R, Veusz, etc.).

			[[File:correlation_halves.png\|\|Test]]

	This can also be carried out for individual images...		This can also be carried out for individual images...

Helenginn: Helenginn moved page Cppxfel Merging statistics to Cppxfel Statistics: More than just merging statistics

2015-11-24T20:33:53Z

Helenginn moved page Cppxfel Merging statistics to Cppxfel Statistics: More than just merging statistics

← Older revision	Revision as of 20:33, 24 November 2015
(No difference)

Helenginn: Created page with "There are a number of merging statistics and plots hwich can be generated using ''cppxfel'' and your favourite graph-drawing software. ''cppxfel'' has a number of commands whi..."

2015-11-24T16:45:30Z

Created page with "There are a number of merging statistics and plots hwich can be generated using ''cppxfel'' and your favourite graph-drawing software. ''cppxfel'' has a number of commands whi..."

New page

There are a number of merging statistics and plots hwich can be generated using ''cppxfel'' and your favourite graph-drawing software. ''cppxfel'' has a number of commands which generate CSV files which can be plotted elsewhere.

== Correlation between two images ==

''cppxfel'' can be used to generate plots of intensities between two images. To calculate the correlation between two halves of the data set in the first merge:

<pre>
cppxfel.run -cc half1Merge0.mtz half2Merge0.mtz
</pre>

This creates a new CSV file named <code>correlation.csv</code> The "first intensity" and "second intensity" columns can be plotted in a suitable program (e.g. R, Veusz, etc.).

This can also be carried out for individual images...