Difference: FileConversion (5 vs. 6)

Contents

Setup Linux computer

• login
• startx -- -depth 8
• cd /dl380/home/kderr/pds . . .
  • this is dl380 directory

Convert Files

• from PDS
  • Change .HDR and .IMG files to lowercase
  • mv HDR filename.hdr
  • pds2mrc (for PDS)
  • title: description #-film mag scanner pixelsize date speed initials

• from Zeiss
  • Open another shell
  • source /dl380/cryoem/IMOD/IMOD-linux.csh
  • tiff2mrc filename.tif filename.mrc
  • May need to first filter file with gimp, by opening and resaving as tif
  • title: description #-film mag scanner pixelsize date speed initials

Fourier Transform

• fftrans filename.mrc filename.fft
• mrcdisp filename.fft
  • display fft (can also display original image: filename.mrc)

Rotational average for display of CTF rings

• sctravgft (sector average ft)
  • ALL defaults OK
  • Enter file name [def.fft] filename
  • Sector [def 5]
  • Enter output name [def filename.ctf](ctf=contrast transfer function)
  • Table size [def 1024]
  • All sectors using defocus amount [def N]
• If have background file can subtract background and calculate S/N
  • subctfbkg
    • Use sed to remove parenthesis with dialog on third line
    • Must rename file
    • Control C to exit
    • Use mv to move data back into original file
  • OR - use /cryoem/script/subctfbkg.pl - no need to do above editing.
    • Can also usr /cryoem/script/fix_ctf.pl - to extract data in format suitable for plotting with gnuplot

Plot results with gnuplot

Visit Cryo EM Web site at http://www.nysbc.org/facilities/CEM

-- DavidStokes - 18 Mar 2005

-- BillRice - 19 Jan 2006

• Set ALLOWTOPICCHANGE = CemfacGroup