MergeLysozyme.csh - Revision history

Tara at 22:38, 30 September 2014

2014-09-30T22:38:25Z

← Older revision		Revision as of 22:38, 30 September 2014
Line 1:		Line 1:
	<pre>		<pre>
	~~$ vi bt_allmerge.csh~~
	#!/bin/csh -f		#!/bin/csh -f

			set trial1=${1}
	set trial1=${11}		set trial2=${2}
	set trial2=${4}
	set datadir1 = /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e239		set datadir1 = /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e239
	set datadir2 = /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e240		set datadir2 = /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e240
	set runs1 = 27, 28, 29, 31		set runs1 = 27,28,29,31
	set runs2 = 3, 4, 5 ,6, 7~~, 8, 9~~, 10, 12, 14~~, 15~~, 16, 17 , 18 , 19 , 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40		set runs2 = 3,4,5,6,7,10,12,14,16,17,18,19,21,24,25,26,27,28,29,30,32,33,34,35,36,37,38,39,40
	set datastring1= `python -c "print ' '.join(['data=${datadir1}/r%04d/${trial1}/integration'%i for i in [${~~runs~~}]])"`		set datastring1=`python -c "print' '.join(['data=${datadir1}/r%04d/${trial1}/integration'%i for i in [${runs1}]])"`
	set datastring2= `python -c "print ' '.join(['data=${datadir2}/r%04d/${trial2}/integration'%i for i in [${~~runs~~}]])"`		set datastring2=`python -c "print' '.join(['data=${datadir2}/r%04d/${trial2}/integration'%i for i in [${runs2}]])"`
	set tag = last_BT_${~~trial~~}		set tag=last_BT_${trial1}_${trial2}_1.8_

	set effective_params = ~~“d_min~~=1.8" \		set effective_params="d_min=1.8 \
	output.n_bins=10 \		output.n_bins=20 \
	${datastring1} \		${datastring1} \
	${datastring2} \		${datastring2} \
Line 21:		Line 19:
	target_space_group=P43212 \		target_space_group=P43212 \
	nproc=16 \		nproc=16 \
	merge_anomalous=~~True~~ \		pixel_size=0.11\
			merge_anomalous=False \
	merging.refine_G_Imodel=True\		merging.refine_G_Imodel=True\
	plot_single_index_histograms=False \		plot_single_index_histograms=False \
	raw_data.sdfac_auto=True \		raw_data.sdfac_auto=True \
			backend=FS\
	mysql.runtag=${tag} \		mysql.runtag=${tag} \
	mysql.passwd=terp888 \		mysql.passwd=terp888 \
	mysql.user=~~tara~~ \		mysql.user=nick \
	mysql.database=xfelnks \		mysql.database=xfelnks \
	scaling.mtz_file="Gd-Lysozyme.mtz" \		scaling.mtz_file="Gd-Lysozyme.mtz" \
Line 36:		Line 36:
	set_average_unit_cell=True \		set_average_unit_cell=True \
	rescale_with_average_cell=True \		rescale_with_average_cell=True \
	output.prefix=${tag}”		output.prefix=${tag}"

	cxi.merge ${effective_params}		cxi.merge ${effective_params}
	cxi.xmerge ${effective_params}		cxi.xmerge ${effective_params}

	~~$ ./bt_allmerge.csh 001~~
	</pre>		</pre>

Tara at 22:05, 29 September 2014

2014-09-29T22:05:51Z

← Older revision		Revision as of 22:05, 29 September 2014
Line 3:		Line 3:
	#!/bin/csh -f		#!/bin/csh -f

	~~#setting trial number that is not yet used by either run~~
	set ~~trial~~=${13}		set trial1=${11}
			set trial2=${4}
	set datadir1 = /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e239		set datadir1 = /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e239
	set datadir2 = /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e240		set datadir2 = /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e240
	set runs1 = 27, 28, 29, 31		set runs1 = 27, 28, 29, 31
	set runs2 = 3, 4, 5 ,6, 7, 8, 9, 10, 12, 14, 15, 16, 17 , 18 , 19 , 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40		set runs2 = 3, 4, 5 ,6, 7, 8, 9, 10, 12, 14, 15, 16, 17 , 18 , 19 , 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40
	set datastring1= `python -c "print ' '.join(['data=${datadir1}/r%04d/${~~trial~~}/integration'%i for i in [${runs}]])"`		set datastring1= `python -c "print ' '.join(['data=${datadir1}/r%04d/${trial1}/integration'%i for i in [${runs}]])"`
	set datastring2= `python -c "print ' '.join(['data=${datadir2}/r%04d/${~~trial~~}/integration'%i for i in [${runs}]])"`		set datastring2= `python -c "print ' '.join(['data=${datadir2}/r%04d/${trial2}/integration'%i for i in [${runs}]])"`
	set tag = last_BT_${trial}		set tag = last_BT_${trial}

Tara at 18:51, 29 September 2014

2014-09-29T18:51:00Z

← Older revision		Revision as of 18:51, 29 September 2014
Line 17:		Line 17:
	${datastring1} \		${datastring1} \
	${datastring2} \		${datastring2} \
	target_unit_cell=39,78,78,90,90,90 \		target_unit_cell=79,79,38,90,90,90 \
	target_space_group=P43212 \		target_space_group=P43212 \
	nproc=16 \		nproc=16 \

Tara at 18:49, 29 September 2014

2014-09-29T18:49:08Z

← Older revision		Revision as of 18:49, 29 September 2014
Line 17:		Line 17:
	${datastring1} \		${datastring1} \
	${datastring2} \		${datastring2} \
	target_unit_cell=~~81.8~~,~~94.0~~,~~123.0~~,90,90,90 \		target_unit_cell=39,78,78,90,90,90 \
	target_space_group=P43212 \		target_space_group=P43212 \
	nproc=16 \		nproc=16 \

Tara at 18:40, 29 September 2014

2014-09-29T18:40:44Z

← Older revision		Revision as of 18:40, 29 September 2014
Line 21:		Line 21:
	nproc=16 \		nproc=16 \
	merge_anomalous=True \		merge_anomalous=True \
	merging.refine_G_Imodel=~~False~~		merging.refine_G_Imodel=True\
	plot_single_index_histograms=False \		plot_single_index_histograms=False \
	raw_data.sdfac_auto=True \		raw_data.sdfac_auto=True \

Tara: Created page with "

 $ vi bt_allmerge.csh #!/bin/csh -f  #setting trial number that is not yet used by either run set trial=${13} set datadir1 = /reg/d/psdm/cxi/cxi84914/scratch/$USER/result..."

2014-09-29T18:22:19Z

Created page with "<pre> $ vi bt_allmerge.csh #!/bin/csh -f #setting trial number that is not yet used by either run set trial=${13} set datadir1 = /reg/d/psdm/cxi/cxi84914/scratch/$USER/result..."

New page

<pre>
$ vi bt_allmerge.csh
#!/bin/csh -f

#setting trial number that is not yet used by either run
set trial=${13}
set datadir1 = /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e239
set datadir2 = /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e240
set runs1 = 27, 28, 29, 31
set runs2 = 3, 4, 5 ,6, 7, 8, 9, 10, 12, 14, 15, 16, 17 , 18 , 19 , 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40
set datastring1= `python -c "print ' '.join(['data=${datadir1}/r%04d/${trial}/integration'%i for i in [${runs}]])"`
set datastring2= `python -c "print ' '.join(['data=${datadir2}/r%04d/${trial}/integration'%i for i in [${runs}]])"`
set tag = last_BT_${trial}

set effective_params = “d_min=1.8" \
output.n_bins=10 \
${datastring1} \
${datastring2} \
target_unit_cell=81.8,94.0,123.0,90,90,90 \
target_space_group=P43212 \
nproc=16 \
merge_anomalous=True \
merging.refine_G_Imodel=False
plot_single_index_histograms=False \
raw_data.sdfac_auto=True \
mysql.runtag=${tag} \
mysql.passwd=terp888 \
mysql.user=tara \
mysql.database=xfelnks \
scaling.mtz_file="Gd-Lysozyme.mtz" \
scaling.show_plots=True \
scaling.algorithm=mark1 \
scaling.log_cutoff=3. \
scaling.mtz_column_F=f-obs \
set_average_unit_cell=True \
rescale_with_average_cell=True \
output.prefix=${tag}”

cxi.merge ${effective_params}
cxi.xmerge ${effective_params}

$ ./bt_allmerge.csh 001
</pre>