SSX-PepT Se

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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=/ 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

Alternatively, solve the structure with only cluster 1 !

solve structure with SHELX C/D/E

(use 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. 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 " "  $7*cos($8*3.14159/180) " " $8;getline}' XSCALE.1.INP |grep INPUT_FILE  >temp
awk '/INPUT_FILE/{ one = $1 ; getline ; print one " "  $7*cos($8*3.14159/180) " " $8;getline}' XSCALE.4.INP |grep INPUT_FILE >>temp

sort -nr -k2 temp >temp1