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.inp1
xscale_par

-->have a look at XSCALE.LP

run xscale_isocluster

xscale_isocluster -dim 3 all_145.hkl > XSCALE_ISO.OUTPUT_FILE

--> check output

we obtain 4 clusters

coot iso.pdb & 

--> explain what we see... --> show an INPUT_FILE

color the 4 clusters

color the first cluster:

grep xtal XSCALE.1.INP |sed s/'INPUT_FILE=..\/tutorial_data\/PepT_SE_145\/xtal_//' |sed 's/.HKL//' |awk '{print $1+1}' > selection_1
awk 'FNR==NR {a[$1]=0 ;next}{ if($2 in a){printf "%6s%5i%3s%6s%2s%4s%12.3f%8.3f%8.3f%11s\n",$1,$2,"S",$4,$5,$6,$7,$8,$9,$10} \
                              else{print $0}}' selection_1 iso.pdb  >sel_1.pdb

--> do that for the remaining 3 clusters:

for k in 2 3 4
  do
    grep xtal XSCALE.$k.INP |sed s/'INPUT_FILE=..\/tutorial_data\/PepT_SE_145\/xtal_//' |sed 's/.HKL//' |awk '{print $1+1}' > selection_$k
    awk 'FNR==NR {a[$1]=0 ;next}{ if($2 in a){printf "%6s%5i%3s%6s%2s%4s%12.3f%8.3f%8.3f%11s\n",$1,$2,"S",$4,$5,$6,$7,$8,$9,$10} \
                               else{print $0}}' selection_$k iso.pdb  >sel_$k.pdb
  done

look at the 4 clusters

coot sel_1.pdb 

load sel_2.pdb , sel_3.pdb, sel_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 '{ 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

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
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.