SSX-PepT Se
This requires 145 XDS_ASCII.HKL files collected at X06SA (SLS).
generating XSCALE.INP for scaling
mkdir <attendee_name>_SSX (e.g. Greta_SSX) cd <attendee_name>_SSX find ../tutorial_data/PepT_SE_145/ -name xtal* > xscale.inp sed -i s/^/INPUT_FILE=/g xscale.inp sed s/xtal_/"test "/ xscale.inp |sort -n -k2 |sed s/"test "/xtal_/ > XSCALE.INP
paste this into the header:
UNIT_CELL_CONSTANTS= 104.056 110.896 110.369 90 90 90 SPACE_GROUP_NUMBER=20 MINIMUM_I/SIGMA=1 OUTPUT_FILE=all_145.hkl SAVE_CORRECTION_IMAGES=FALSE PRINT_CORRELATIONS=FALSE ! this is not yet in the official BUILT=20171111 WFAC1=1
scale everything together
rm xscale.inp xscale_par
-->have a look at XSCALE.LP
run xscale_isocluster
xscale_isocluster -dim 3 -i all_145.hkl | tee 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:
coot iso.pdb
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.
look at the 4 clusters
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
decide which clusters one would take for structure solution
Here: 1. and 4. cluster
cp XSCALE.INP XSCALE_old.INP
cp XSCALE.LP XSCALE_old.LP
awk '/INPUT_FILE/{ 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.4.INP |grep 'INPUT_FILE'>>temp
sort -nr -k2 temp >temp1
--> look at temp1 , combined clusters ,sorted by strength --> remove lowest (until strength of 0.6)
awk '{print $1}' temp1 > XSCALE.INP
paste this into header:
UNIT_CELL_CONSTANTS= 104.056 110.896 110.369 90 90 90 SPACE_GROUP_NUMBER=20 MINIMUM_I/SIGMA=1 OUTPUT_FILE=1+4.hkl SAVE_CORRECTION_IMAGES=FALSE PRINT_CORRELATIONS=FALSE ! this is not yet in the official BUILT=20171111 WFAC1=1
solve structure with SHELX C/D/E
(use hkl2map)!
other option: run xscale_isocluster with the option -clu 1 and sort by strength, take the upper ones and solve the structure.