SSX-PepT Se: Difference between revisions

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mkdir <attendee_name>_SSX (e.g. Greta_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:

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== 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.

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

@@ Line 5: / Line 5: @@
   mkdir <attendee_name>_SSX  (e.g. Greta_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:
@@ Line 63: / Line 62: @@
 == 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.
+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