Difference: FileConversion (6 vs. 7)

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

 
    gnuplot
    Plot "filename.ctf"
    Set xrange[0:512]
    Set yrange[0:250]
    replot
    set title "collection parameters, date, initials"
    replot
    set term postscript color
    set output "filename.ctf.ps"
    replot
    set term x11
    quit
    lpr filename (to print)

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

-- DavidStokes - 18 Mar 2005

-- BillRice - 19 Jan 2006

• Set ALLOWTOPICCHANGE = CemfacGroup