MergeLysozyme.csh: Difference between revisions

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


#setting trial number that is not yet used by either run
set trial1=${1}
set trial=${13}
set trial2=${2}
set datadir1 = /reg/d/psdm/cxi/cxi84914/scratch/$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/${trial}/integration'%i for i in [${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/${trial}/integration'%i for i in [${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} \
${datastring2} \
target_unit_cell=39,78,78,90,90,90 \
target_unit_cell=79,79,38,90,90,90 \
target_space_group=P43212 \
target_space_group=P43212 \
nproc=16 \
nproc=16 \
merge_anomalous=True \
pixel_size=0.11\
merge_anomalous=False \
merging.refine_G_Imodel=True\
merging.refine_G_Imodel=True\
plot_single_index_histograms=False \
plot_single_index_histograms=False \
raw_data.sdfac_auto=True \
raw_data.sdfac_auto=True \
backend=FS\
mysql.runtag=${tag} \
mysql.runtag=${tag} \
mysql.passwd=terp888 \
mysql.passwd=terp888 \
mysql.user=tara \
mysql.user=nick \
mysql.database=xfelnks \
mysql.database=xfelnks \
scaling.mtz_file="Gd-Lysozyme.mtz" \
scaling.mtz_file="Gd-Lysozyme.mtz" \
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set_average_unit_cell=True \
set_average_unit_cell=True \
rescale_with_average_cell=True \
rescale_with_average_cell=True \
output.prefix=${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>

Latest revision as of 22:38, 30 September 2014

#!/bin/csh -f

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

set effective_params="d_min=1.8 \
output.n_bins=20 \
${datastring1} \
${datastring2} \
target_unit_cell=79,79,38,90,90,90 \
target_space_group=P43212 \
nproc=16 \
pixel_size=0.11\
merge_anomalous=False \
merging.refine_G_Imodel=True\
plot_single_index_histograms=False \
raw_data.sdfac_auto=True \
backend=FS\
mysql.runtag=${tag} \
mysql.passwd=terp888 \
mysql.user=nick \
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}