L498 Thermolysin - Revision history

Aaron at 23:11, 18 August 2026

2026-08-18T23:11:51Z

← Older revision		Revision as of 23:11, 18 August 2026
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			{{Archived}}

	In this tutorial, we assume that we are handed an SFX dataset containing thermolysin diffraction, but are not told anything else. We will have to go through all the data runs, figure out which one is to be used for dark subtraction, and account for untrusted pixels and detector metrology. At this point, we will be prepared to integrate and merge the data. Finally, we will perform simple molecular replacement and ask whether there is any Zn signal in the anomalous difference Fourier.		In this tutorial, we assume that we are handed an SFX dataset containing thermolysin diffraction, but are not told anything else. We will have to go through all the data runs, figure out which one is to be used for dark subtraction, and account for untrusted pixels and detector metrology. At this point, we will be prepared to integrate and merge the data. Finally, we will perform simple molecular replacement and ask whether there is any Zn signal in the anomalous difference Fourier.

Tara: /* Discovery of data collection parameters */

2014-09-15T22:36:35Z

Discovery of data collection parameters

← Older revision		Revision as of 22:36, 15 September 2014
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	mkdir -p cxi84914		mkdir -p cxi84914

	List out the thermolysin XTC files ~~(in two separate experiment directories)~~:		List out the thermolysin XTC files:
	ls /reg/d/psdm/cxi/cxi84914/xtc/e157		ls /reg/d/psdm/cxi/cxi84914/xtc/e157

Tara: Undo revision 623 by Tara (talk) accidentally edited this page instead of Gd-Lysozyme

2014-09-15T22:31:21Z

Undo revision 623 by Tara (talk) accidentally edited this page instead of Gd-Lysozyme

← Older revision		Revision as of 22:31, 15 September 2014
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	=Prepare to mask out the untrusted pixels=		=Prepare to mask out the untrusted pixels=
	We'll now calculate dark-subtracted averages.		We'll now calculate dark-subtracted averages.
	for m in ; \		for m in 17 18 19 20 21 22 23 24 25 26 27; \
	do echo $m; cxi.lsf -c ~/myrelease/cxi84914/~~mkavg_e239~~.cfg \		do echo $m; cxi.lsf -c ~/myrelease/cxi84914/mkavg_e157.cfg \
	-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e157/ \		-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e157/ \
	-i /reg/d/psdm/cxi/cxi84914/xtc/~~e239~~ -q psanacsq -s -p 8 -x ~~239~~ -r ${m} -t 0; done		-i /reg/d/psdm/cxi/cxi84914/xtc/e157 -q psanacsq -s -p 8 -x 157 -r ${m} -t 0; done

	This repeats exactly the same averaging calculations as before, except the dark average from run 31 is subtracted.		This repeats exactly the same averaging calculations as before, except the dark average from run 31 is subtracted.
	The dark image to be subtracted (along with its std deviation) is defined in the configuration file [[~~mkavg_e239~~.cfg]].		The dark image to be subtracted (along with its std deviation) is defined in the configuration file [[mkavg_e157.cfg]].

	Now we'll figure out which pixels are untrusted, and thus should not be integrated. Three criteria will be used:		Now we'll figure out which pixels are untrusted, and thus should not be integrated. Three criteria will be used:

Tara: /* Prepare to mask out the untrusted pixels */

2014-09-05T16:54:37Z

Prepare to mask out the untrusted pixels

← Older revision		Revision as of 16:54, 5 September 2014
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	=Prepare to mask out the untrusted pixels=		=Prepare to mask out the untrusted pixels=
	We'll now calculate dark-subtracted averages.		We'll now calculate dark-subtracted averages.
	for m in ~~17 18 19 20 21 22 23 24 25 26 27~~; \		for m in ; \
	do echo $m; cxi.lsf -c ~/myrelease/cxi84914/~~mkavg_e157~~.cfg \		do echo $m; cxi.lsf -c ~/myrelease/cxi84914/mkavg_e239.cfg \
	-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e157/ \		-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e157/ \
	-i /reg/d/psdm/cxi/cxi84914/xtc/~~e157~~ -q psanacsq -s -p 8 -x ~~157~~ -r ${m} -t 0; done		-i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -s -p 8 -x 239 -r ${m} -t 0; done

	This repeats exactly the same averaging calculations as before, except the dark average from run 31 is subtracted.		This repeats exactly the same averaging calculations as before, except the dark average from run 31 is subtracted.
	The dark image to be subtracted (along with its std deviation) is defined in the configuration file [[~~mkavg_e157~~.cfg]].		The dark image to be subtracted (along with its std deviation) is defined in the configuration file [[mkavg_e239.cfg]].

	Now we'll figure out which pixels are untrusted, and thus should not be integrated. Three criteria will be used:		Now we'll figure out which pixels are untrusted, and thus should not be integrated. Three criteria will be used:

Nicksauter: /* Discovery of data collection parameters */

2014-09-04T21:10:15Z

Discovery of data collection parameters

← Older revision		Revision as of 21:10, 4 September 2014
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	\| style="padding: 2px;"\| Events		\| style="padding: 2px;"\| Events
	\| style="padding: 2px;"\| Wall clock <br> 000 psanacsq <br> 6 cores		\| style="padding: 2px;"\| Wall clock <br> 000 psanacsq <br> 6 cores
			\| style="padding: 2px;"\| Wall clock <br> 001 psanaq <br> 6 cores
	\|-		\|-
	\| style="padding: 2px;"\| 16		\| style="padding: 2px;"\| 16
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	\| style="padding: 2px;"\| weak powder		\| style="padding: 2px;"\| weak powder
	\| style="padding: 2px;"\|		\| style="padding: 2px;"\|
	\| style="padding: 2px;"\| ~~33685~~		\| style="padding: 2px;"\| 39313
	\| style="padding: 2px;"\| 60:36		\| style="padding: 2px;"\| 60:36
			\| style="padding: 2px;"\| 36:20
	\|-		\|-
	\| style="padding: 2px;"\| 17		\| style="padding: 2px;"\| 17
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	\| style="padding: 2px;"\| weak powder		\| style="padding: 2px;"\| weak powder
	\| style="padding: 2px;"\|		\| style="padding: 2px;"\|
			\| style="padding: 2px;"\| 66647
			\| style="padding: 2px;"\| 72:32
			\| style="padding: 2px;"\| 62:16
	\|-		\|-
	\| style="padding: 2px;"\| 18		\| style="padding: 2px;"\| 18
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	\| style="padding: 2px;"\| weak powder		\| style="padding: 2px;"\| weak powder
	\| style="padding: 2px;"\|		\| style="padding: 2px;"\|
			\| style="padding: 2px;"\| 47297
			\| style="padding: 2px;"\| 77:21
			\| style="padding: 2px;"\| 45:28
	\|-		\|-
	\| style="padding: 2px;"\| 19		\| style="padding: 2px;"\| 19

Nicksauter: /* Discovery of data collection parameters */

2014-09-03T23:40:48Z

Discovery of data collection parameters

← Older revision		Revision as of 23:40, 3 September 2014
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	\| style="padding: 2px;"\| Comments		\| style="padding: 2px;"\| Comments
	\| style="padding: 2px;"\| Events		\| style="padding: 2px;"\| Events
	\| style="padding: 2px;"\| Wall clock-000 psanacsq		\| style="padding: 2px;"\| Wall clock <br> 000 psanacsq <br> 6 cores
	\|-		\|-
	\| style="padding: 2px;"\| 16		\| style="padding: 2px;"\| 16

Nicksauter: /* Discovery of data collection parameters */

2014-09-03T21:30:03Z

Discovery of data collection parameters

← Older revision		Revision as of 21:30, 3 September 2014
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	\| style="padding: 2px;"\| Diffraction		\| style="padding: 2px;"\| Diffraction
	\| style="padding: 2px;"\| Comments		\| style="padding: 2px;"\| Comments
			\| style="padding: 2px;"\| Events
			\| style="padding: 2px;"\| Wall clock-000 psanacsq
	\|-		\|-
	\| style="padding: 2px;"\| 16		\| style="padding: 2px;"\| 16
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	\| style="padding: 2px;"\| weak powder		\| style="padding: 2px;"\| weak powder
	\| style="padding: 2px;"\|		\| style="padding: 2px;"\|
			\| style="padding: 2px;"\| 33685
			\| style="padding: 2px;"\| 60:36
	\|-		\|-
	\| style="padding: 2px;"\| 17		\| style="padding: 2px;"\| 17

Tara at 17:41, 27 August 2014

2014-08-27T17:41:29Z

← Older revision		Revision as of 17:41, 27 August 2014
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	List out the thermolysin XTC files (in two separate experiment directories):		List out the thermolysin XTC files (in two separate experiment directories):
	ls /reg/d/psdm/cxi/cxi84914/xtc/~~e239~~		ls /reg/d/psdm/cxi/cxi84914/xtc/e157
	~~ls /reg/d/psdm/cxi/cxi84914/xtc/e240~~

	Notice that there are numerous runs in the directory. Now we will create composite averages for each run. Grab this configuration file: [[mkdark.cfg]] and put it in your cxi84914 directory. For one run only:		Notice that there are numerous runs in the directory. Now we will create composite averages for each run. Grab this configuration file: [[mkdark.cfg]] and put it in your cxi84914 directory. For one run only:

Tara at 17:40, 27 August 2014

2014-08-27T17:40:21Z

← Older revision		Revision as of 17:40, 27 August 2014
Line 15:		Line 15:
	mkdir -p cxi84914		mkdir -p cxi84914

	List out the thermolysin XTC files:		List out the thermolysin XTC files (in two separate experiment directories):
	ls /reg/d/psdm/cxi/cxi84914/xtc/~~e157~~		ls /reg/d/psdm/cxi/cxi84914/xtc/e239
			ls /reg/d/psdm/cxi/cxi84914/xtc/e240

	Notice that there are numerous runs in the directory. Now we will create composite averages for each run. Grab this configuration file: [[mkdark.cfg]] and put it in your cxi84914 directory. For one run only:		Notice that there are numerous runs in the directory. Now we will create composite averages for each run. Grab this configuration file: [[mkdark.cfg]] and put it in your cxi84914 directory. For one run only:

Nicksauter: /* Solve the structure */

2014-08-26T22:16:00Z

Solve the structure

← Older revision		Revision as of 22:16, 26 August 2014
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	pdb="CA CA A 320 " : 1.08 sigma		pdb="CA CA A 320 " : 1.08 sigma
	pdb="CA CA A 321 " : 0.20 sigma		pdb="CA CA A 321 " : 0.20 sigma
			</pre>

	Better results from trial 005:		Better results from trial 005:
			<pre>
	pdb="ZN ZN A 317 " : 7.66 sigma		pdb="ZN ZN A 317 " : 7.66 sigma
	pdb="CA CA A 318 " : 1.10 sigma		pdb="CA CA A 318 " : 1.10 sigma

← Older revision		Revision as of 21:10, 4 September 2014
Line 62:		Line 62:
	\| style="padding: 2px;"\| Events		\| style="padding: 2px;"\| Events
	\| style="padding: 2px;"\| Wall clock <br> 000 psanacsq <br> 6 cores		\| style="padding: 2px;"\| Wall clock <br> 000 psanacsq <br> 6 cores
			\| style="padding: 2px;"\| Wall clock <br> 001 psanaq <br> 6 cores
	\|-		\|-
	\| style="padding: 2px;"\| 16		\| style="padding: 2px;"\| 16
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	\| style="padding: 2px;"\| weak powder		\| style="padding: 2px;"\| weak powder
	\| style="padding: 2px;"\|		\| style="padding: 2px;"\|
	\| style="padding: 2px;"\| ~~33685~~		\| style="padding: 2px;"\| 39313
	\| style="padding: 2px;"\| 60:36		\| style="padding: 2px;"\| 60:36
			\| style="padding: 2px;"\| 36:20
	\|-		\|-
	\| style="padding: 2px;"\| 17		\| style="padding: 2px;"\| 17
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	\| style="padding: 2px;"\| weak powder		\| style="padding: 2px;"\| weak powder
	\| style="padding: 2px;"\|		\| style="padding: 2px;"\|
			\| style="padding: 2px;"\| 66647
			\| style="padding: 2px;"\| 72:32
			\| style="padding: 2px;"\| 62:16
	\|-		\|-
	\| style="padding: 2px;"\| 18		\| style="padding: 2px;"\| 18
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	\| style="padding: 2px;"\| weak powder		\| style="padding: 2px;"\| weak powder
	\| style="padding: 2px;"\|		\| style="padding: 2px;"\|
			\| style="padding: 2px;"\| 47297
			\| style="padding: 2px;"\| 77:21
			\| style="padding: 2px;"\| 45:28
	\|-		\|-
	\| style="padding: 2px;"\| 19		\| style="padding: 2px;"\| 19

← Older revision		Revision as of 23:40, 3 September 2014
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	\| style="padding: 2px;"\| Comments		\| style="padding: 2px;"\| Comments
	\| style="padding: 2px;"\| Events		\| style="padding: 2px;"\| Events
	\| style="padding: 2px;"\| Wall clock-000 psanacsq		\| style="padding: 2px;"\| Wall clock <br> 000 psanacsq <br> 6 cores
	\|-		\|-
	\| style="padding: 2px;"\| 16		\| style="padding: 2px;"\| 16

← Older revision		Revision as of 21:30, 3 September 2014
Line 60:		Line 60:
	\| style="padding: 2px;"\| Diffraction		\| style="padding: 2px;"\| Diffraction
	\| style="padding: 2px;"\| Comments		\| style="padding: 2px;"\| Comments
			\| style="padding: 2px;"\| Events
			\| style="padding: 2px;"\| Wall clock-000 psanacsq
	\|-		\|-
	\| style="padding: 2px;"\| 16		\| style="padding: 2px;"\| 16
Line 66:		Line 68:
	\| style="padding: 2px;"\| weak powder		\| style="padding: 2px;"\| weak powder
	\| style="padding: 2px;"\|		\| style="padding: 2px;"\|
			\| style="padding: 2px;"\| 33685
			\| style="padding: 2px;"\| 60:36
	\|-		\|-
	\| style="padding: 2px;"\| 17		\| style="padding: 2px;"\| 17