2017 prime tutorial - Revision history

Mona at 20:38, 14 February 2017

2017-02-14T20:38:21Z

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	Post-refine and Merge Sample Data Set with PRIME (2017 Tutorial)		Post-refine and Merge Sample Data Set with PRIME (2017 Tutorial)

	In this tutorial, we will work on the integration results from the first of Tutorial 2 (Myoglobin Data). Before proceeding to running the program, we'll consider making the input file for PRIME based on the situation of this data set.		In this tutorial, we will work on the integration results from the first part of Tutorial 2 (Myoglobin Data). Before proceeding to running the program, we'll consider making the input file for PRIME based on the situation of this data set.

	== Generating Input File ==		== Generating Input File ==

Mona: /* Generating Input File */

2017-02-14T20:37:23Z

Generating Input File

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	data = /net/viper/raid1/mu238/XfelProject/dials17/extracted		data = /net/viper/raid1/mu238/XfelProject/dials17/extracted

	Note that you supply data as a multiple arguments. The value of the parameter can be a file containing list of integration results, a folder~~, or a wildcard argument~~.		Note that you can supply data parameter as multiple arguments. The value of the parameter can be a file containing list of integration results or a folder.

	* Unit cell information		* Unit cell information

Mona: /* Running the Program */

2017-02-14T20:02:38Z

Running the Program

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	[https://commons.wikimedia.org/wiki/File:Dials17_myo_indexing_ambiguity.png Results of Running Indexing Ambiguity with Boostrap]		[https://commons.wikimedia.org/wiki/File:Dials17_myo_indexing_ambiguity.png Results of Running Indexing Ambiguity with Boostrap]

	[https://commons.wikimedia.org/wiki/File:Dials17_indexing_ambiguity_clustering.gif Results of Image Clustering]		[https://commons.wikimedia.org/wiki/File:Dials17_indexing_ambiguity_clustering.gif Results of Image Clustering]

Mona: /* Running the Program */

2017-02-14T20:02:10Z

Running the Program

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	[https://commons.wikimedia.org/wiki/File:Dials17_myo_indexing_ambiguity.png Results of Running Indexing Ambiguity with Boostrap]		[https://commons.wikimedia.org/wiki/File:Dials17_myo_indexing_ambiguity.png Results of Running Indexing Ambiguity with Boostrap]
			[https://commons.wikimedia.org/wiki/File:Dials17_indexing_ambiguity_clustering.gif Results of Image Clustering]

	PRIME will select on of these two clusters and merge it to get a reference set for the Bootstrap step. Here, the remaining images will get assigned with a basis that makes it correlate best with the reference set.		PRIME will select on of these two clusters and merge it to get a reference set for the Bootstrap step. Here, the remaining images will get assigned with a basis that makes it correlate best with the reference set.

Mona: /* Running the Program */

2017-02-14T19:56:35Z

Running the Program

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	For this tutorial, PRIME will score the randomly selected 1,000 images then select the best 100 for running Brehm & Diederichs algorithm in Bootstrap mode. If you run the program with flag_plot=True, you'll see a plot showing two separated clusters, each representing images with matching assigned basis.		For this tutorial, PRIME will score the randomly selected 1,000 images then select the best 100 for running Brehm & Diederichs algorithm in Bootstrap mode. If you run the program with flag_plot=True, you'll see a plot showing two separated clusters, each representing images with matching assigned basis.

	[[File:~~Dials17 myo indexing ambiguity~~.png~~\|thumb\|left\|Solving indexing ambiguity program in XFEL Crystallography.]~~]		[https://commons.wikimedia.org/wiki/File:Dials17_myo_indexing_ambiguity.png Results of Running Indexing Ambiguity with Boostrap]

	PRIME will select on of these two clusters and merge it to get a reference set for the Bootstrap step. Here, the remaining images will get assigned with a basis that makes it correlate best with the reference set.		PRIME will select on of these two clusters and merge it to get a reference set for the Bootstrap step. Here, the remaining images will get assigned with a basis that makes it correlate best with the reference set.

Mona: /* Running the Program */

2017-02-14T19:49:22Z

Running the Program

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	Once all images are assigned with appropriate basis, PRIME will proceed to scaling and post-refinement steps. After three post-refinement cycles (default value), the process is done and here is the output of the program.		Once all images are assigned with appropriate basis, PRIME will proceed to scaling and post-refinement steps. After three post-refinement cycles (default value), the process is done and here is the output of the program.


	Isotropic B-factor: 5.30		Isotropic B-factor: 5.30

Mona: /* Running the Program */

2017-02-14T19:47:35Z

Running the Program

← Older revision		Revision as of 19:47, 14 February 2017
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	For this tutorial, PRIME will score the randomly selected 1,000 images then select the best 100 for running Brehm & Diederichs algorithm in Bootstrap mode. If you run the program with flag_plot=True, you'll see a plot showing two separated clusters, each representing images with matching assigned basis.		For this tutorial, PRIME will score the randomly selected 1,000 images then select the best 100 for running Brehm & Diederichs algorithm in Bootstrap mode. If you run the program with flag_plot=True, you'll see a plot showing two separated clusters, each representing images with matching assigned basis.

			[[File:Dials17 myo indexing ambiguity.png\|thumb\|left\|Solving indexing ambiguity program in XFEL Crystallography.]]
	PRIME will select on of these two clusters and merge it to get a reference set for the Bootstrap step. Here, the remaining images will get assigned with a basis that makes it correlate best with the reference set.		PRIME will select on of these two clusters and merge it to get a reference set for the Bootstrap step. Here, the remaining images will get assigned with a basis that makes it correlate best with the reference set.

Mona: /* Generating Input File */

2017-02-14T19:22:04Z

Generating Input File

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	uc_tolerance = 5		uc_tolerance = 5
	}		}

	indexing_ambiguity {		indexing_ambiguity {
	mode = Auto		mode = Auto

Mona at 19:18, 14 February 2017

2017-02-14T19:18:28Z

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	Total calculation time: 542.00 seconds		Total calculation time: 542.00 seconds
	Finished: Tuesday 14. February 2017 10:53:18		Finished: Tuesday 14. February 2017 10:53:18

			== Obtaining the Output ==

			Your output will be in Prime_Run_n (where n is the number of run).

			-bash-4.1$ ls Prime_Run_1/ -l
			total 9076
			-rw-r--r-- 1 mu238 camb 879638 Feb 14 10:53 crystal.o
			drwxr-xr-x 2 mu238 camb 104 Feb 14 10:46 index_ambiguity
			drwxr-xr-x 2 mu238 camb 6 Feb 14 10:44 isoform_cluster
			-rw-r--r-- 1 mu238 camb 32704 Feb 14 10:53 log.txt
			-rw-r--r-- 1 mu238 camb 324556 Feb 14 10:47 mean_scaled_merge.hkl
			-rw-r--r-- 1 mu238 camb 157260 Feb 14 10:47 mean_scaled_merge.mtz
			-rw-r--r-- 1 mu238 camb 15753 Feb 14 10:53 pickle.stat
			-rw-r--r-- 1 mu238 camb 324381 Feb 14 10:49 postref_cycle_1_merge.hkl
			-rw-r--r-- 1 mu238 camb 157260 Feb 14 10:49 postref_cycle_1_merge.mtz
			-rw-r--r-- 1 mu238 camb 324515 Feb 14 10:51 postref_cycle_2_merge.hkl
			-rw-r--r-- 1 mu238 camb 157260 Feb 14 10:51 postref_cycle_2_merge.mtz
			-rw-r--r-- 1 mu238 camb 324716 Feb 14 10:53 postref_cycle_3_merge.hkl
			-rw-r--r-- 1 mu238 camb 157340 Feb 14 10:53 postref_cycle_3_merge.mtz
			-rw-r--r-- 1 mu238 camb 6412200 Feb 14 10:53 rejections.txt

			File log.txt contains all the merging stats. The final merged reflection set is postref_cycle_3_merge.mtz (or .hkl).

Mona: /* Running the Program */

2017-02-14T19:12:54Z

Running the Program

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	10 2.59 - 2.50 100.0 759 / 759 92.53 78.61 14.72 96.51 759 0.00 0 0.00 0 1.36 312.4 218.8 2.07		10 2.59 - 2.50 100.0 759 / 759 92.53 78.61 14.72 96.51 759 0.00 0 0.00 0 1.36 312.4 218.8 2.07
	--------------------------------------------------------------------------------------------------------------------------------------------------		--------------------------------------------------------------------------------------------------------------------------------------------------
	TOTAL 100.0 7735 / 7735 119.73 75.51 10.45 97.21 7735 0.00 0 0.00 0 3.02 527.3 176.9 2.56		TOTAL 100.0 7735 / 7735 119.73 75.51 10.45 97.21 7735 0.00 0 0.00 0 3.02 527.3 176.9 2.56
	--------------------------------------------------------------------------------------------------------------------------------------------------		--------------------------------------------------------------------------------------------------------------------------------------------------

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	10 2.59 - 2.50 94.44 97.81 96.67 249.0 400.1 236.2 42 36 40		10 2.59 - 2.50 94.44 97.81 96.67 249.0 400.1 236.2 42 36 40
	----------------------------------------------------------------------------------------------------------		----------------------------------------------------------------------------------------------------------
	total 97.57 97.74 94.58 494.1 446.0 619.4 410 390 415		total 97.57 97.74 94.58 494.1 446.0 619.4 410 390 415
	----------------------------------------------------------------------------------------------------------		----------------------------------------------------------------------------------------------------------