SSX-PepT Se: Difference between revisions

From XDSwiki
Jump to navigation Jump to search
 
(10 intermediate revisions by 2 users not shown)
Line 5: Line 5:
  mkdir <attendee_name>_SSX  (e.g. Greta_SSX)
  mkdir <attendee_name>_SSX  (e.g. Greta_SSX)
  cd <attendee_name>_SSX
  cd <attendee_name>_SSX
  find  ../tutorial_data/PepT_SE_145/ -name xtal* > xscale.inp
  find  ../tutorial_data/PepT_SE_145/ -name xtal* > XSCALE.INP
  sed -i s/^/INPUT_FILE=/g xscale.inp
  sed -i s/^/INPUT_FILE=/ XSCALE.INP
sed s/xtal_/"test "/ xscale.inp |sort -n -k2 |sed s/"test "/xtal_/ > XSCALE.INP


paste this into the header:  
paste this into the header:  
Line 20: Line 19:


== scale everything together ==
== scale everything together ==
  rm xscale.inp xscale.inp1
  rm xscale.inp  
  xscale_par
  xscale_par
-->have a look at XSCALE.LP  
-->have a look at XSCALE.LP  


== run xscale_isocluster ==
== run xscale_isocluster ==
  xscale_isocluster -dim 3 all_145.hkl > XSCALE_ISO.OUTPUT_FILE
  xscale_isocluster -dim 3 -i all_145.hkl | tee XSCALE_ISOCLUSTER.LP


--> check output  
--> check output on screen (which is saved on XSCALE_ISOCLUSTER.LP). The program says that we obtain 4 clusters. Check with coot:


== we obtain 4 clusters ==
  coot iso.pdb
  coot iso.pdb &
--> explain what we see...
--> show an INPUT_FILE


== color the 4 clusters ==
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.
 
color the first cluster:
<pre>
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 $0}}' selection_1 iso.pdb  >sel_1.pdb
</pre>
--> do that for the remaining 3 clusters:
<pre>
for k in 2 3 4
  do
    grep xtal XSCALE.$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
</pre>


== look at the 4 clusters ==
== look at the 4 clusters ==


coot sel_1.pdb
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
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 ==
== decide which clusters one would take for structure solution ==
Line 62: Line 41:
  cp XSCALE.LP XSCALE_old.LP
  cp XSCALE.LP XSCALE_old.LP
   
   
  awk '{ 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.1.INP |grep 'INPUT_FILE' >temp
  awk '{ one = $1 ; getline ; print one " "  $7 " " $8;getline}' XSCALE.4.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
  sort -nr -k2 temp >temp1
Line 79: Line 58:
  PRINT_CORRELATIONS=FALSE    ! this is not yet in the official BUILT=20171111
  PRINT_CORRELATIONS=FALSE    ! this is not yet in the official BUILT=20171111
  WFAC1=1
  WFAC1=1
Alternatively, solve the structure with only cluster 1 !


== solve structure with [[ccp4com:SHELX C/D/E|SHELX C/D/E]] ==
== solve structure with [[ccp4com:SHELX C/D/E|SHELX C/D/E]] ==
(use [[ccp4com:hkl2map|hkl2map]])!  
(use [[ccp4com:hkl2map|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.
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

Latest revision as of 12:57, 29 November 2017

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
Retrieved from "https://wiki.uni-konstanz.de/xds/index.php?title=SSX-PepT_Se&oldid=3651"