SSX-PepT Se: Difference between revisions

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Revision as of 12:57, 29 November 2017

638 bytes added , 29 November 2017

→‎generating XSCALE.INP for scaling

Kay

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@@ Line 4: / Line 4: @@
   mkdir <attendee_name>_SSX  (e.g. Greta_SSX)
-  find  PepT_SE_145/ (directory with data) -name xtal* > xcale_tut/xscale.inp
+ cd <attendee_name>_SSX
- cd xscale_tut
+  find  ../tutorial_data/PepT_SE_145/ -name xtal* > XSCALE.INP
-  sed s/PepT/'INPUT_FILE=..\/PepT'/ xscale.inp  >xscale.inp1
+  sed -i s/^/INPUT_FILE=/ XSCALE.INP
- sed s/xtal_/"test "/ xscale.inp1 |sort -n -k2 |sed s/"test "/xtal_/ > XSCALE.INP
 paste this into the header:
@@ Line 16: / Line 15: @@
   OUTPUT_FILE=all_145.hkl
   SAVE_CORRECTION_IMAGES=FALSE
-  PRINT_CORRELATIONS=FALSE
+  PRINT_CORRELATIONS=FALSE   ! this is not yet in the official BUILT=20171111
   WFAC1=1
 == scale everything together ==
-  rm xscale.inp xscale.inp1
+  rm xscale.inp
   xscale_par
 -->have a look at XSCALE.LP
 == 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.
- 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 ==
+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_tut/XSCALE.1.INP .
+  cp XSCALE.INP XSCALE_old.INP
-  cp ../xscale_tut/XSCALE.4.INP .
+  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
@@ Line 62: / Line 56: @@
   OUTPUT_FILE=1+4.hkl
   SAVE_CORRECTION_IMAGES=FALSE
-  PRINT_CORRELATIONS=FALSE
+  PRINT_CORRELATIONS=FALSE    ! this is not yet in the official BUILT=20171111
   WFAC1=1
-== solve structure with [[SHELXC/D/E]] ==
+Alternatively, solve the structure with only cluster 1 !
-(use [[hkl2map]])!
+== solve structure with [[ccp4com:SHELX C/D/E|SHELX C/D/E]] ==
+(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.
+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