Difference: FileConversion (1 vs. 8)

Revision 829 Jul 2009 - Main.DavidStokes

 
META TOPICPARENT name="ComputerProcessing"
Changed:
<
<		How to Plot 1D CTF profile of an image
>
>		How to Plot 1D CTF profile of an image
 
Changed:
<
<		This can now be done more simply using EmIP
>
>		This can now be done more simply using EmIP
Added:
>
>
 

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

Revision 729 Jul 2009 - Main.DavidStokes

 
META TOPICPARENT name="ComputerProcessing"
Changed:
<
<		File Conversion
>
>		How to Plot 1D CTF profile of an image
Added:
>
>		This can now be done more simply using EmIP
 

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

Revision 601 Jun 2007 - Main.DavidCowburn

 
META TOPICPARENT name="ComputerProcessing"
File Conversion

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

Changed:
<
<
  • 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)
>
>		 
 
    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
Added:
>
>		 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

Revision 522 Sep 2006 - Main.BillRice

 
META TOPICPARENT name="ComputerProcessing"
File Conversion

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
Changed:
<
<
    • OR - use /cryoem/script/subbkgctf.pl - no need to do above editing.
>
>
    • 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

Revision 422 Sep 2006 - Main.BillRice

 
META TOPICPARENT name="ComputerProcessing"
Changed:
<
<		File Conversion

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
    • 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

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

>
>		File Conversion

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/subbkgctf.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

Added:
>
>

Revision 319 Jan 2006 - Main.BillRice

 
META TOPICPARENT name="ComputerProcessing"
File Conversion

Contents

Setup Linux computer

  • login
  • startx -- -depth 8
Changed:
<
<
  • cd /home/nsfhome/kderr/pds . . .
>
>
  • 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
Changed:
<
<
    • source /cryoem/IMOD/IMOD-linux.csh
>
>
    • source /dl380/cryoem/IMOD/IMOD-linux.csh
 
    • tiff2mrc filename.tif filename.mrc
    • 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

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

Added:
>
>		-- BillRice - 19 Jan 2006
 

Revision 222 Mar 2005 - Main.DavidStokes

 
META TOPICPARENT name="ComputerProcessing"
File Conversion

Contents

Setup Linux computer

  • login
  • startx -- -depth 8
Changed:
<
<
  • cd /home/nsfhome/kderr/pds-?
>
>
  • cd /home/nsfhome/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 /cryoem/IMOD/IMOD-linux.csh
    • tiff2mrc filename.tif filename.mrc
    • 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

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

Added:
>
>

Revision 118 Mar 2005 - Main.DavidStokes

 
META TOPICPARENT name="ComputerProcessing"
File Conversion

Contents

Setup Linux computer

  • login
  • startx -- -depth 8
  • cd /home/nsfhome/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 /cryoem/IMOD/IMOD-linux.csh
    • tiff2mrc filename.tif filename.mrc
    • 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

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

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