Cppxfel Indexing - Revision history

Helenginn at 14:26, 4 May 2016

2016-05-04T14:26:12Z

← Older revision		Revision as of 14:26, 4 May 2016
Line 27:		Line 27:
	</pre>		</pre>

	Note, in the tcsh shell, this is not a valid way of creating a text file. In this case, create an appropriate file in your favourite text editor with the text <code>gain=14.0 min_spot_size=1 global_threshold=100</code>.		Note, in the tcsh shell, this is not a valid way of creating a text file. In this case, create an appropriate file in your favourite text editor with the text <code>gain=14.0 min_spot_size=2 global_threshold=100</code>.

	The DIALS scripts can now be run as follows:		The DIALS scripts can now be run as follows:
Line 35:		Line 35:
	</pre>		</pre>

	The term <code>index=no</code> prevents DIALS from running indexing on these images, as we plan to index using ~~DIALS~~.		The term <code>index=no</code> prevents DIALS from running indexing on these images, as we plan to index using cppxfel.

	The spot-finding results made by DIALS should be converted to a new format for reading into ''cppxfel''. This is achieved by running the command:		The spot-finding results made by DIALS should be converted to a new format for reading into ''cppxfel''. This is achieved by running the command:

2016-05-04T01:23:04Z

← Older revision		Revision as of 01:23, 4 May 2016
Line 1:		Line 1:
	This page is under development!		This page is under development!

	The original version of cppxfel indexed using DIALS, but if the unit cell dimensions are known, cppxfel itself can also be used to index images. This page details how to index using cppxfel.		The original version of cppxfel indexed using DIALS, but if the unit cell dimensions are known, cppxfel itself can also be used to index images using the TakeTwo algorithm. This page details how to index using cppxfel.

	== Downloading test data ==		== Downloading test data ==
Line 51:		Line 51:
	This will also create shells of <code>index.txt</code>, <code>integrate.txt</code>, <code>refine.txt</code> and <code>merge.txt</code>.		This will also create shells of <code>index.txt</code>, <code>integrate.txt</code>, <code>refine.txt</code> and <code>merge.txt</code>.

	== Preparing ~~and running indexing with cppxfel~~ ==		== Preparing for TakeTwo ==

	Have a look at the contents of the <code>index.txt</code> shell.		Have a look at the contents of the <code>index.txt</code> shell.

2016-05-04T01:21:22Z

Editing cppxfel indexing to be actual cppxfel indexing

2016-05-04T01:13:21Z

minor edits

2016-05-04T01:05:24Z

minor edits

2016-03-22T21:14:54Z

Tcsh shell warning

← Older revision		Revision as of 21:14, 22 March 2016
Line 24:		Line 24:
	EOF		EOF
	</pre>		</pre>

			Note, in the tcsh shell, this is not a valid way of creating a text file. In this case, create an appropriate file in your favourite text editor with the text <code>gain=14.0 min_spot_size=1 global_threshold=100</code>.

	This should be similarly created for <code>index.options</code>. This is an appropriate options file for a DIALS distribution built after 20th Feb:		This should be similarly created for <code>index.options</code>. This is an appropriate options file for a DIALS distribution built after 20th Feb:
Line 32:		Line 34:
	EOF		EOF
	</pre>		</pre>

			Note, in the tcsh shell, this is not a valid way of creating a text file. In this case, create an appropriate file in your favourite text editor with the text <code>unit_cell=106.1,106.1,106.1 space_group=I23 minimum_number_of_reflections=20 detector.fix=all beam.fix=all recycle_unindexed_reflections=1 refinement.reflections.outlier.algorithm=null refinement_protocol.n_macro_cycles=1 refinement.reflections.weighting_strategy.override=stills</code>

	The DIALS scripts can now be run as follows:		The DIALS scripts can now be run as follows:

2016-03-06T16:53:39Z

Updating indexing options for recent DIALS distribution.

← Older revision		Revision as of 16:53, 6 March 2016
Line 25:		Line 25:
	</pre>		</pre>

	This should be similarly created for <code>index.options</code>:		This should be similarly created for <code>index.options</code>. This is an appropriate options file for a DIALS distribution built after 20th Feb:

	<pre>		<pre>
	cat > index.options << EOF		cat > index.options << EOF
	~~outlier.algorithm=null indexing.method=fft3d~~ unit_cell=106.1,106.1,106.1 space_group=I23 minimum_number_of_reflections=20 detector.fix=all beam.fix=all		unit_cell=106.1,106.1,106.1 space_group=I23 minimum_number_of_reflections=20 detector.fix=all beam.fix=all recycle_unindexed_reflections=1 refinement.reflections.outlier.algorithm=null refinement_protocol.n_macro_cycles=1 refinement.reflections.weighting_strategy.override=stills
	EOF		EOF
	</pre>		</pre>

2016-02-26T15:26:54Z

Removed reference to recycle_unindexed_reflections which has changed in the DIALS API.

← Older revision		Revision as of 15:26, 26 February 2016
Line 29:		Line 29:
	<pre>		<pre>
	cat > index.options << EOF		cat > index.options << EOF
	outlier.algorithm=null indexing.method=fft3d unit_cell=106.1,106.1,106.1 space_group=I23 minimum_number_of_reflections=20 detector.fix=all beam.fix=all ~~recycle_unindexed_reflections=True~~		outlier.algorithm=null indexing.method=fft3d unit_cell=106.1,106.1,106.1 space_group=I23 minimum_number_of_reflections=20 detector.fix=all beam.fix=all
	EOF		EOF
	</pre>		</pre>

2015-11-24T21:58:49Z

← Older revision		Revision as of 21:58, 24 November 2015
Line 29:		Line 29:
	<pre>		<pre>
	cat > index.options << EOF		cat > index.options << EOF
	indexing.method=~~real_space_grid_search~~ unit_cell=106.1,106.1,106.1 space_group=I23 minimum_number_of_reflections=20 detector.fix=all beam.fix=all recycle_unindexed_reflections=True		outlier.algorithm=null indexing.method=fft3d unit_cell=106.1,106.1,106.1 space_group=I23 minimum_number_of_reflections=20 detector.fix=all beam.fix=all recycle_unindexed_reflections=True
	EOF		EOF
	</pre>		</pre>

2015-11-24T17:37:09Z

← Older revision		Revision as of 17:37, 24 November 2015
Line 1:		Line 1:
	This covers the generation of indexing solutions using DIALS within the ''cppxfel'' distribution. This assumes a successful [[Cppxfel Installation \| installation of cppxfel]] including the DIALS dependency.		This covers the generation of indexing solutions using DIALS within the [[Cppxfel\|''cppxfel'' distribution]]. This assumes a successful [[Cppxfel Installation \| installation of cppxfel]] including the DIALS dependency.

	== Downloading test data ==		== Downloading test data ==