XDSwiki - User contributions [en]

SSX-PepT Se

2017-11-27T12:39:00Z

Shibom: /* decide which clusters one would take for structure solution */

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
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 ==
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 all 4 clusters

== look at the 4 clusters ==

== 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 [[SHELXC/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.

SSX-PepT Se

2017-11-27T12:34:24Z

Shibom: /* color the 4 clusters */

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
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 ==
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 all 4 clusters

== look at the 4 clusters ==

== decide which clusters one would take for structure solution ==
Here: 1. and 4. cluster
cp ../xscale_tut/XSCALE.1.INP .
cp ../xscale_tut/XSCALE.4.INP .

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 [[SHELXC/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.

SSX-PepT Se

2017-11-27T12:24:27Z

Shibom: /* generating XSCALE.INP for scaling */

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
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 ==
grep xtal XSCALE.1.INP |sed s/'INPUT_FILE=..\/kay_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 all 4 clusters

== look at the 4 clusters ==

== decide which clusters one would take for structure solution ==
Here: 1. and 4. cluster
cp ../xscale_tut/XSCALE.1.INP .
cp ../xscale_tut/XSCALE.4.INP .

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 [[SHELXC/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.

SSX-PepT Se

2017-11-27T12:17:02Z

Shibom: /* generating XSCALE.INP for scaling */

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 s/PepT/'INPUT_FILE=..\/PepT'/ xscale.inp >xscale.inp1
sed s/xtal_/"test "/ xscale.inp1 |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
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 ==
grep xtal XSCALE.1.INP |sed s/'INPUT_FILE=..\/kay_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 all 4 clusters

== look at the 4 clusters ==

== decide which clusters one would take for structure solution ==
Here: 1. and 4. cluster
cp ../xscale_tut/XSCALE.1.INP .
cp ../xscale_tut/XSCALE.4.INP .

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 [[SHELXC/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.

SSX-PepT Se

2017-11-27T12:14:09Z

Shibom: /* generating XSCALE.INP for scaling */

This requires 145 XDS_ASCII.HKL files collected at X06SA (SLS).

== generating XSCALE.INP for scaling ==

mkdir <attendee_name>_SSX (e.g. Greta_SSX)
find PepT_SE_145/ (directory with data) -name xtal* > xcale_tut/xscale.inp
cd xscale_tut
sed s/PepT/'INPUT_FILE=..\/PepT'/ xscale.inp >xscale.inp1
sed s/xtal_/"test "/ xscale.inp1 |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
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 ==
grep xtal XSCALE.1.INP |sed s/'INPUT_FILE=..\/kay_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 all 4 clusters

== look at the 4 clusters ==

== decide which clusters one would take for structure solution ==
Here: 1. and 4. cluster
cp ../xscale_tut/XSCALE.1.INP .
cp ../xscale_tut/XSCALE.4.INP .

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 [[SHELXC/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.

SSX-PepT Se

2017-11-27T11:56:26Z

Shibom: /* generating XSCALE.INP for scaling */

This requires 145 XDS_ASCII.HKL files collected at X06SA (SLS).

== generating XSCALE.INP for scaling ==

mkdir xscale_tut
find PepT_SE_145/ (directory with data) -name xtal* > xcale_tut/xscale.inp
cd xscale_tut
sed s/PepT/'INPUT_FILE=..\/PepT'/ xscale.inp >xscale.inp1
sed s/xtal_/"test "/ xscale.inp1 |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
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 ==
grep xtal XSCALE.1.INP |sed s/'INPUT_FILE=..\/kay_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 all 4 clusters

== look at the 4 clusters ==

== decide which clusters one would take for structure solution ==
Here: 1. and 4. cluster
cp ../xscale_tut/XSCALE.1.INP .
cp ../xscale_tut/XSCALE.4.INP .

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 [[SHELXC/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.