LB67 Thermolysin - Revision history

Tara: /* Detector distance */

2014-09-24T18:08:44Z

Detector distance

← Older revision		Revision as of 18:08, 24 September 2014
Line 83:		Line 83:

	When complete, go to your results directory:		When complete, go to your results directory:
	cd /reg/d/psdm/cxi/~~cxi84914~~/scratch/$USER/dist_trials/r0025		cd /reg/d/psdm/cxi/cxib6714/scratch/$USER/dist_trials/r0025

	Then determine which detz offset is best:		Then determine which detz offset is best:

Tara: /* Detector distance */

2014-09-24T16:55:39Z

Detector distance

← Older revision		Revision as of 16:55, 24 September 2014
Line 72:		Line 72:
	The best way to be sure your detz offset is correct is through a series of trials, testing different values. Create a dist_trials directory in your myrelease folder. cd into it, then generate config files with different candidate detz offsets, thusly:		The best way to be sure your detz offset is correct is through a series of trials, testing different values. Create a dist_trials directory in your myrelease folder. cd into it, then generate config files with different candidate detz offsets, thusly:

	for i in `seq 565 580`; do vi -c "%s/578/$i/g" -c "w LB67-thermolysin_$i.cfg" -c q\! ../LB67-thermolysin.cfg ; done		for i in `seq 565 580`; do vi -c "%s/578/$i/g" -c "w LB67-thermolysin_$i.cfg" \
			-c q\! ../LB67-thermolysin.cfg ; done

	Here, a vi command is executed repeatedly that searches for the number 578 in your config file and replaces it with a number from 565 to 580, then writes out the new file with an appropriate file name. If this seems like a poor window to search, note that the number was originally 572, and has already been optimized to 578 by the authors.		Here, a vi command is executed repeatedly that searches for the number 578 in your config file and replaces it with a number from 565 to 580, then writes out the new file with an appropriate file name. If this seems like a poor window to search, note that the number was originally 572, and has already been optimized to 578 by the authors.

Tara: /* Detector distance */

2014-09-24T16:54:29Z

Detector distance

← Older revision		Revision as of 16:54, 24 September 2014
Line 78:		Line 78:
	Next, submit indexing jobs for each candidate detz offset from your myrelease folder:		Next, submit indexing jobs for each candidate detz offset from your myrelease folder:

	for i in `seq 565 580`; do cxi.lsf -c dist_trials/LB67-thermolysin_$i.cfg		for i in `seq 565 580`; do cxi.lsf -c dist_trials/LB67-thermolysin_$i.cfg \
	-o /reg/d/psdm/cxi/cxib6714/ftc/$USER/dist_trials/ -x cxib6714 -r 30 -q psanacsq -p 8 -t $i; done		-o /reg/d/psdm/cxi/cxib6714/ftc/$USER/dist_trials/ -x cxib6714 -r 30 -q psanacsq -p 8 -t $i; done

Tara: /* Detector distance */

2014-09-24T16:54:16Z

Detector distance

← Older revision		Revision as of 16:54, 24 September 2014
Line 78:		Line 78:
	Next, submit indexing jobs for each candidate detz offset from your myrelease folder:		Next, submit indexing jobs for each candidate detz offset from your myrelease folder:

	for i in `seq 565 580`; do cxi.lsf -c dist_trials/LB67-thermolysin_$i.cfg -o /reg/d/psdm/cxi/cxib6714/ftc/$USER/dist_trials/ \		for i in `seq 565 580`; do cxi.lsf -c dist_trials/LB67-thermolysin_$i.cfg
	-x cxib6714 -r 30 -q psanacsq -p 8 -t $i; done		-o /reg/d/psdm/cxi/cxib6714/ftc/$USER/dist_trials/ -x cxib6714 -r 30 -q psanacsq -p 8 -t $i; done

	When complete, go to your results directory:		When complete, go to your results directory:

Tara: /* Detector distance */

2014-09-24T16:53:41Z

Detector distance

← Older revision		Revision as of 16:53, 24 September 2014
Line 78:		Line 78:
	Next, submit indexing jobs for each candidate detz offset from your myrelease folder:		Next, submit indexing jobs for each candidate detz offset from your myrelease folder:

	for i in `seq 565 580`; do cxi.lsf -c dist_trials/LB67-thermolysin_$i.cfg -o /reg/d/psdm/cxi/cxib6714/ftc/$USER/dist_trials/ -x cxib6714 -r 30 -q psanacsq -p 8 -t $i; done		for i in `seq 565 580`; do cxi.lsf -c dist_trials/LB67-thermolysin_$i.cfg -o /reg/d/psdm/cxi/cxib6714/ftc/$USER/dist_trials/ \
			-x cxib6714 -r 30 -q psanacsq -p 8 -t $i; done

	When complete, go to your results directory:		When complete, go to your results directory:

Aaron: /* Detector distance */

2014-08-22T21:09:27Z

Detector distance

← Older revision		Revision as of 21:09, 22 August 2014
Line 70:		Line 70:
	=== Detector distance ===		=== Detector distance ===

	~~'''UNDER CONSTRUCTION'''~~		The best way to be sure your detz offset is correct is through a series of trials, testing different values. Create a dist_trials directory in your myrelease folder. cd into it, then generate config files with different candidate detz offsets, thusly:

	~~Create a dist_trials directory~~ in ~~your myrelease folder~~. ~~cd into it, then generate config files with different candidate detz offsets:~~		for i in `seq 565 580`; do vi -c "%s/578/$i/g" -c "w LB67-thermolysin_$i.cfg" -c q\! ../LB67-thermolysin.cfg ; done

	for i in ~~`seq~~ 565 580~~`; do vi -c "%s/~~572~~/$i/g" -c "w LB67-thermolysin_$i.cfg" -c q\! ../LB67-thermolysin~~.~~cfg ; done~~		Here, a vi command is executed repeatedly that searches for the number 578 in your config file and replaces it with a number from 565 to 580, then writes out the new file with an appropriate file name. If this seems like a poor window to search, note that the number was originally 572, and has already been optimized to 578 by the authors.

	~~Submit~~ indexing jobs for each candidate detz offset from your myrelease folder:		Next, submit indexing jobs for each candidate detz offset from your myrelease folder:

	for i in `seq 565 580`; do cxi.lsf -c dist_trials/LB67-thermolysin_$i.cfg -o /reg/d/psdm/cxi/cxib6714/ftc/$USER/dist_trials/ -x cxib6714 -r 30 -q psanacsq -p 8 -t $i; done		for i in `seq 565 580`; do cxi.lsf -c dist_trials/LB67-thermolysin_$i.cfg -o /reg/d/psdm/cxi/cxib6714/ftc/$USER/dist_trials/ -x cxib6714 -r 30 -q psanacsq -p 8 -t $i; done

Aaron: /* Detector distance */

2014-08-21T17:34:24Z

Detector distance

← Older revision		Revision as of 17:34, 21 August 2014
Line 81:		Line 81:

	When complete, go to your results directory:		When complete, go to your results directory:
	cd /reg/d/psdm/cxi/~~cxib6714~~/~~ftc~~/$USER/dist_trials/r0025		cd /reg/d/psdm/cxi/cxi84914/scratch/$USER/dist_trials/r0025

	Then determine which detz offset is best:		Then determine which detz offset is best:

Aaron: /* Detector distance */

2014-08-21T17:32:11Z

Detector distance

@@ Line 69: / Line 69: @@
 === Detector distance ===
 === Find candidate hits ===
 === Spotfinding grid searches ===

Aaron: /* Indexing */

2014-08-21T17:17:44Z

Indexing

← Older revision		Revision as of 17:17, 21 August 2014
Line 60:		Line 60:
	tail -f /reg/d/psdm/cxi/cxi84914/scratch/$USER/thermolysin/r0024/000/stdout/s00.out		tail -f /reg/d/psdm/cxi/cxi84914/scratch/$USER/thermolysin/r0024/000/stdout/s00.out

	Individual indexed frames will be deposited in /reg/d/psdm/cxi/cxi84914/scratch/$USER/thermolysin/r0024/000/out and the integrated results will be in /reg/d/psdm/cxi/cxi84914/scratch/$USER/thermolysin/r0024/000/integration. For the parameters provided, around 1923 indexed images.		Individual indexed frames will be deposited in /reg/d/psdm/cxi/cxi84914/scratch/$USER/thermolysin/r0024/000/out and the integrated results will be in /reg/d/psdm/cxi/cxi84914/scratch/$USER/thermolysin/r0024/000/integration. For the parameters provided, around 1923 indexed images are expected.

	== Discovery ==		== Discovery ==

Aaron: /* Indexing */

2014-08-21T17:17:10Z

Indexing

← Older revision		Revision as of 17:17, 21 August 2014
Line 53:		Line 53:
	== Indexing ==		== Indexing ==

	cxi.lsf -c ~~cxi84914/~~LB67-thermolysin.cfg -o /reg/d/psdm/cxi/cxi84914/scratch/~~brewster~~/thermolysin -p 16 -q psanacsq -r 25 -x cxi84914 -i /reg/d/psdm/cxi/cxi84914/xtc/e350		Now that the darks and gain mask are in place, the data is indexed straightforwardly. Copy all the phil files and LB67-thermolysin.cfg to your myrelease folder, then submit the indexing job:

			cxi.lsf -c LB67-thermolysin.cfg -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/thermolysin -p 16 -q psanacsq -r 25 -x cxi84914 -i /reg/d/psdm/cxi/cxi84914/xtc/e350

			You can follow the log of one of the streams using
			tail -f /reg/d/psdm/cxi/cxi84914/scratch/$USER/thermolysin/r0024/000/stdout/s00.out

			Individual indexed frames will be deposited in /reg/d/psdm/cxi/cxi84914/scratch/$USER/thermolysin/r0024/000/out and the integrated results will be in /reg/d/psdm/cxi/cxi84914/scratch/$USER/thermolysin/r0024/000/integration. For the parameters provided, around 1923 indexed images.

			== Discovery ==

			'''UNDER CONSTRUCTION'''

			The indexing results above present already optimized processing parameters. The user will need to explore their data, testing a variety of parameters to extract the best reduced signal. Over the next few sections, techniques for discovering necessary parameters are presented.

			=== Detector distance ===

			=== Find candidate hits ===

			=== Spotfinding grid searches ===