Cppxfel Post-refinement - Revision history

Helenginn at 22:21, 24 November 2015

2015-11-24T22:21:23Z

← Older revision		Revision as of 22:21, 24 November 2015
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	img-shot-s01-20130316165021253_0.mtz 0.991536 0.114612 0.787729 217 0 1.46545 0.0013 -0.0109289 -0.0157625 8.25238e-05 1.5 105.783 105.783 105.783		img-shot-s01-20130316165021253_0.mtz 0.991536 0.114612 0.787729 217 0 1.46545 0.0013 -0.0109289 -0.0157625 8.25238e-05 1.5 105.783 105.783 105.783
	</pre>		</pre>

			== Next steps ==

			After one is happy with the merging statistics for post-refinement, it is time to make a [[Cppxfel Final Merge \| final merge]], with recalculation of sigma values.

Helenginn at 22:19, 24 November 2015

2015-11-24T22:19:29Z

← Older revision		Revision as of 22:19, 24 November 2015
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	== Post-refinement parameter table ==		== Post-refinement parameter table ==

			The parameters used to refine each image are output before each merge. An example is given below. This is also output to a CSV file for each cycle named <code>params_cycle_*.csv</code> so that the data may be analysed by other programs.

			<pre>
			Filename Correl Rsplit Partcorrel Refcount Mosaicity Wavelength Bandwidth hRot kRot rlpSize exp cellA cellB cellC
			img-shot-s00-20130316165428143_0.mtz 0.996824 0.0729367 0.771081 207 0 1.46288 0.0013 -0.00416609 -0.00638984 3.73011e-05 1.5 105.783 105.783 105.783
			img-shot-s01-20130316165101088_0.mtz 0.410825 0.734041 0 179 0 1.46487 0.0013 0.000723228 0.0250253 0.000121815 1.5 105.783 105.783 105.783
			img-shot-s00-20130316165238305_0.mtz 0.40738 0.753037 0 183 0 1.45447 0.0013 0.00706399 -0.0082277 0.000150607 1.5 105.783 105.783 105.783
			img-shot-s00-20130316165159219_0.mtz 0.990674 0.088927 0.865087 216 0 1.46289 0.0013 -0.00286677 -7.7758e-05 6.17136e-05 1.5 105.783 105.783 105.783
			img-shot-s01-20130316165021253_0.mtz 0.991536 0.114612 0.787729 217 0 1.46545 0.0013 -0.0109289 -0.0157625 8.25238e-05 1.5 105.783 105.783 105.783
			</pre>

Helenginn at 22:13, 24 November 2015

2015-11-24T22:13:35Z

@@ Line 31: / Line 31: @@
 This is followed by a number of rounds of post-refinement (approximately 6). The major processing statistics for each image can be followed as they are produced, followed by a large output of all the parameters used in refinement after each cycle. The processing statistics for each subsequent merge are then displayed until refinement ends.
-== Processing statistics output ==
+== Merging statistics output ==
 == Real-time processing statistics ==
 == Post-refinement parameter table ==

Helenginn: Created page with "Post-refinement by cppxfel of integrated intensities occurs after initial orientation matrix refinement. This..."

2015-11-24T17:59:53Z

Created page with "Post-refinement by cppxfel of integrated intensities occurs after initial orientation matrix refinement. This..."

New page

Post-refinement by [[Cppxfel | cppxfel]] of integrated intensities occurs after [[Cppxfel Initial Orientation Matrix Refinement | initial orientation matrix refinement]]. This is the penultimate stage of producing a viable MTZ file for structure solution. This is also the point at which indexing ambiguities are broken (note that only two-fold indexing ambiguities can be broken at the moment without an external reference MTZ).

== Contents of refine.txt ==

This stage is controlled by the input file <code>refine.txt</code> generated by <code>cppxfel.input_gen</code> and uses a number of files generated at the previous stage. The contents of this file:

<pre>cat refine.txt</pre>

<pre>
ORIENTATION_MATRIX_LIST refine-orientations.dat
MATRIX_LIST_VERSION 2.0
NEW_MATRIX_LIST refined.dat

PARTIALITY_CUTOFF 0.2

COMMANDS

REFINE_PARTIALITY
</pre>

== Executing refine.txt ==

This can be executed using the line

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

This begins by generating an initial, merged MTZ file using an initial guess at the parameters of the image. For space group I23, this requires the indexing ambiguity to be broken, which can be followed by the values of the <code>fx:</code> lines during L-BFGS refinement. The processing statistics for the first merge are then displayed.

This is followed by a number of rounds of post-refinement (approximately 6). The major processing statistics for each image can be followed as they are produced, followed by a large output of all the parameters used in refinement after each cycle. The processing statistics for each subsequent merge are then displayed until refinement ends.

== Processing statistics output ==

== Real-time processing statistics ==

== Post-refinement parameter table ==