You already finished alignments, and think you cannot improve the quality of your last alignment anymore using FEI Inspect3D. Then you can try the following steps to improve your structure using the script file tomo-super-refine.sh.

 

•         Step 1: create a folder to contain the data in the /datadisk/silo/share/ under your name directory.  For example: create a folder named PrvTomo20 under /datadisk/silo/share/whui

 

•         Step 2:  within the folder you just created, create 4 folders named raw, clean, align and out. Go to the folder raw, copy the final alignment result from Inspect3D to here. For example: copy  PrvTomo20-4.ali into folder raw, then rename it to tomo20.mrc

 

•         Step 3: unstack the stack file you just copied.

Then you will see tomo20.mrc is unstacked to tomo20_000.img,   tomo20-001.img …….

 

•         Step 4: go to the folder clean, copy a file named tomo-clean.sh from /datadisk/silo/share/whui/template/, then make tomo-clean.sh executable.

 Then run tomo-clean.sh

 

•         Step 5: go to folder align, copy files  tomo-super-refine.sh, Set##-01.param, Set##-01.tlt from /datadisk/silo/share/whui/template/,  then rename  Set##-01.param and  Set##-01.tlt as you wish.               For example: rename them as Set20-01.param & Set20-01.tlt

•         Step 6: update the tlt file and param file you just renamed:

 

1)      Open tlt file, then change TILT SERIES from “daitomo20” to a name you wish

2)      Change FILE names from tomo20_000, tomo20_001 … to files names you find in your folder clean accordingly.

3)      Change TILT ANGLE accordingly.

4)      Update the number in the red circles accordingly, save and close tlt file.

 

5)  Open param file and update the number on line 11 accordingly, save and close  param file

•         Step 7: copy the tlt file within the same folder, the name of new file with suffix as “-super”. For example: copy Set20-01.tlt  to   Set20-01-super.tlt

 

•         Step 8: make tomo-super-refine.sh executable and run this script file.

      Command:     chmod  +x  tomo-super-refine.sh

 

•         Step 9: after normal end of tomo-super-refine.sh, do a backprojection reconstruction.

      Command :       tomo-map.sh Set20-01.param   Set20-01-super.tlt

 

•         Step 10: go to the folder out, convert the output file to MRC format.