SSX-PepT Se - Revision history

Kay: /* generating XSCALE.INP for scaling */

2017-11-29T10:57:19Z

generating XSCALE.INP for scaling

← Older revision		Revision as of 12:57, 29 November 2017
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	mkdir <attendee_name>_SSX (e.g. Greta_SSX)		mkdir <attendee_name>_SSX (e.g. Greta_SSX)
	cd <attendee_name>_SSX		cd <attendee_name>_SSX
	find ../tutorial_data/PepT_SE_145/ -name xtal* > ~~xscale~~.~~inp~~		find ../tutorial_data/PepT_SE_145/ -name xtal* > XSCALE.INP
	sed -i s/^/INPUT_FILE=/~~g xscale.inp~~		sed -i s/^/INPUT_FILE=/ XSCALE.INP
	~~sed s/xtal_/"test "/ xscale.inp \|sort -n -k2 \|sed s/"test "/xtal_/ >~~ XSCALE.INP

	paste this into the header:		paste this into the header:

2017-11-29T10:11:33Z

solve structure with SHELX C/D/E

← Older revision		Revision as of 12:11, 29 November 2017
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	== solve structure with [[ccp4com:SHELX C/D/E\|SHELX C/D/E]] ==		== solve structure with [[ccp4com:SHELX C/D/E\|SHELX C/D/E]] ==
	(use [[ccp4com:hkl2map\|hkl2map]])!		(use [[ccp4com:hkl2map\|hkl2map]])! There are 458 residues, out of which 18 are SeMet, in PepT.


			== Notes ==
	other option: run xscale_isocluster with the option -clu 1 and sort by strength, take the upper ones and solve the structure.		other option: run xscale_isocluster with the option -clu 1 and sort by strength, take the upper ones and solve the structure.
			Or

			run xscale_isocluster with the option -clu 1 and sort by strength*cos(angle), take the upper ones and solve the structure.
			That would be

			awk '/INPUT_FILE/{ one = $1 ; getline ; print one " " $7cos($83.14159/180) " " $8;getline}' XSCALE.1.INP \|grep INPUT_FILE >temp
			awk '/INPUT_FILE/{ one = $1 ; getline ; print one " " $7cos($83.14159/180) " " $8;getline}' XSCALE.4.INP \|grep INPUT_FILE >>temp

			sort -nr -k2 temp >temp1

2017-11-29T09:29:35Z

decide which clusters one would take for structure solution

← Older revision		Revision as of 11:29, 29 November 2017
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	PRINT_CORRELATIONS=FALSE ! this is not yet in the official BUILT=20171111		PRINT_CORRELATIONS=FALSE ! this is not yet in the official BUILT=20171111
	WFAC1=1		WFAC1=1

			Alternatively, solve the structure with only cluster 1 !

	== solve structure with [[ccp4com:SHELX C/D/E\|SHELX C/D/E]] ==		== solve structure with [[ccp4com:SHELX C/D/E\|SHELX C/D/E]] ==

2017-11-29T08:36:49Z

2017-11-29T08:34:08Z

← Older revision		Revision as of 10:34, 29 November 2017
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	xscale_isocluster -dim 3 -i all_145.hkl \| tee XSCALE_ISOCLUSTER.LP		xscale_isocluster -dim 3 -i all_145.hkl \| tee XSCALE_ISOCLUSTER.LP

	--> check output on screen (which is saved on XSCALE_ISOCLUSTER.LP)		--> check output on screen (which is saved on XSCALE_ISOCLUSTER.LP). The program says that we obtain 4 clusters. Check with coot:

	~~Comment: we don't really see the clusters as separate when looking at~~ iso.pdb ~~in coot. So let us just take the 4 clusters that xscale_isocluster detects as an opportunity to use groups of data sets for further work, without implying any deeper meaning of the clusters.~~		coot iso.pdb

	~~== we obtain 4~~ clusters ==		We don't really see the clusters as separate when looking at iso.pdb in coot. So let us just take the 4 clusters that xscale_isocluster detects as an opportunity to use groups of data sets for further work, without implying any deeper meaning of the clusters.
	~~coot~~ iso.pdb &
	~~--> explain what we see~~...
	~~--> show an INPUT_FILE~~

	== look at the 4 clusters ==		== look at the 4 clusters ==

	~~coot~~ iso.1.pdb		load iso.1.pdb into coot. Also load iso.2.pdb , iso.3.pdb, iso.4.pdb and use the Display Manager for switching the clusters on/off
	~~also~~ load iso.2.pdb , iso.3.pdb, iso.4.pdb and use the Display Manager for switching the clusters on/off

	== decide which clusters one would take for structure solution ==		== decide which clusters one would take for structure solution ==

2017-11-29T07:30:46Z

look at the 4 clusters

← Older revision		Revision as of 09:30, 29 November 2017
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	coot iso.1.pdb		coot iso.1.pdb
	load iso.2.pdb , iso.3.pdb, iso.4.pdb and use the Display Manager for switching the clusters on/off		also load iso.2.pdb , iso.3.pdb, iso.4.pdb and use the Display Manager for switching the clusters on/off

	== decide which clusters one would take for structure solution ==		== decide which clusters one would take for structure solution ==

2017-11-29T07:30:31Z

run xscale_isocluster

← Older revision		Revision as of 09:30, 29 November 2017
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	--> check output on screen (which is saved on XSCALE_ISOCLUSTER.LP)		--> check output on screen (which is saved on XSCALE_ISOCLUSTER.LP)

			Comment: we don't really see the clusters as separate when looking at iso.pdb in coot. So let us just take the 4 clusters that xscale_isocluster detects as an opportunity to use groups of data sets for further work, without implying any deeper meaning of the clusters.

	== we obtain 4 clusters ==		== we obtain 4 clusters ==

2017-11-29T07:28:27Z

look at the 4 clusters

← Older revision		Revision as of 09:28, 29 November 2017
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	== look at the 4 clusters ==		== look at the 4 clusters ==

	coot ~~sel_1~~.pdb		coot iso.1.pdb
	load ~~sel_2~~.pdb , ~~sel_3~~.pdb, ~~sel_4~~.pdb and use the Display Manager for switching the clusters on/off		load iso.2.pdb , iso.3.pdb, iso.4.pdb and use the Display Manager for switching the clusters on/off

	== decide which clusters one would take for structure solution ==		== decide which clusters one would take for structure solution ==

2017-11-29T07:27:48Z

decide which clusters one would take for structure solution

← Older revision		Revision as of 09:27, 29 November 2017
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	cp XSCALE.LP XSCALE_old.LP		cp XSCALE.LP XSCALE_old.LP

	awk '{ one = $1 ; getline ; print one " " $7 " " $8;getline}' XSCALE.1.INP \|grep 'INPUT_FILE' >temp		awk '/INPUT_FILE/{ one = $1 ; getline ; print one " " $7 " " $8;getline}' XSCALE.1.INP \|grep 'INPUT_FILE' >temp
	awk '{ one = $1 ; getline ; print one " " $7 " " $8;getline}' XSCALE.4.INP \|grep 'INPUT_FILE'>>temp		awk '/INPUT_FILE/{ one = $1 ; getline ; print one " " $7 " " $8;getline}' XSCALE.4.INP \|grep 'INPUT_FILE'>>temp

	sort -nr -k2 temp >temp1		sort -nr -k2 temp >temp1

2017-11-29T07:27:12Z

run xscale_isocluster

← Older revision		Revision as of 09:27, 29 November 2017
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	== run xscale_isocluster ==		== run xscale_isocluster ==
	xscale_isocluster -dim 3 all_145.hkl ~~> XSCALE_ISO~~.~~OUTPUT_FILE~~		xscale_isocluster -dim 3 -i all_145.hkl \| tee XSCALE_ISOCLUSTER.LP

	--> check output		--> check output on screen (which is saved on XSCALE_ISOCLUSTER.LP)

	== we obtain 4 clusters ==		== we obtain 4 clusters ==