Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

ALTERHEADER(1)							ALTERHEADER(1)

NAME
  alterheader - to alter header information in an MRC file

SYNOPSIS
  alterheader

DESCRIPTION
  Alterheader allows one to alter header information in an MRC file 
  without rewriting the file.  For each standard header entry selected by
  the user, the program prints the current values and asks for new values,
  checking for legality in some cases.  Other operations can be performed
  as described below.  Multiple changes can be made.  The header is not
  written to the file until you enter DONE to exit the program, so you can
  interrupt with Ctrl-C to discard changes.  Entries are not case
  sensitive.

  The file name can be entered on the command line; if not, the program
  will ask for it.

  The MRC header stores three pieces of information about size: the number
  of pixels in X, Y, and Z, which is output as "columns, rows, sections",
  the sample grid size, output as "grid x,y,z", and the cell size, which is
  not directly output in the standard printing of the header.  The pixel
  spacing in Angstroms is defined to be the ratio of the cell size to the
  sample size in each dimension.  Programs in IMOD generally try to keep
  the sample size the same as the image size, and to set the cell size to
  achieve an appropriate pixel spacing.

  The options to the program are as follows:

  ORG - Change the origin in X, Y, Z.  In IMOD, the origin is defined as the
  coordinates of the origin relative to the lower-left corner of the first 
  section in the file, in units scaled by the pixel size.  The origin is
  defined in the opposite way in UCSF Chimera; use INVERTORG to switch the
  sign of the origin values.

  CEL - Change the cell size in X, Y, Z.  This will show up as a change in
  pixel spacing, as described above.

  DAT - Change data type, which is defined as 0 for normal data, 1 for tilt
  series, 2 for stereo pairs, 3 for averaged data, 4 for averaged stereo
  pairs.  The only non-zero value that could be useful in IMOD is 1; with
  this value you can set a starting angle and increment that will be
  accepted by the Tilt program instead of entering angles from a file.

  DEL - Change the pixel size in X, Y, Z to given values.  The program will
  change the cell size so that the ratio of cell to sample size will give
  the entered pixel size.

  MAP - Set mapping from X, Y, Z to rows, columns, sections.  The only
  effect of this in IMOD is to reorder the sample grid and pixel spacing
  values by the given mapping.  Do not use it.

  SAM - Set sampling in X, Y, Z.  See note above on IMOD conventions.

  TLT - Change current tilt angles to given alpha, beta, gamma.  These
  values will be used to apply a rotation to a model loaded into 3dmod
  along with the image.

  TLT_ORIG - Change original tilt angles.  These angles have no effect in
  IMOD.

  TLT_ROT - Rotate current tilt angles by the given alpha, beta, and gamma
  values, where the rotations are applied the order gamma (around Z), beta
  (around Y), alpha (around X).

  LAB - Delete a list of labels, or add a label.  You will see a numbered list
  of existing labels.  To delete some labels, enter a range (comma-separated
  list) of the numbers to delete.  To add a label, enter the negative of the
  label number after which you want the new label to appear.  Enter 0 to have
  the new label become the first one, or -9 to have it added after the last
  one.  Then enter the complete label (the date/time stamp will not be
  added).  If you need to program this operation in a script, first delete the
  tenth label, if any, with entries "lab - 10 - 1 - lab -9 your_new_label".

  MMM - Read the file to recompute the minimum, maximum, and mean
  densities and the RMS density.

  RMS - Print the current RMS value (root-mean-square deviation from the mean
  density) then do the same operation as MMM.

  FIXPIXEL - Set the cell and sample sizes the same as the image size,
  resulting in a pixel spacing of 1, 1, 1.

  FEIPIXEL - Set the pixel spacing in X, Y, Z from the value for the pixel
  size of the first section in an Agard/FEI-style extended header.

  FIXEXTRA - Change the flags in the header so that 3dmod no longer
  interprets the extended header as having piece coordinates for a montage.

  FIXMODE - Change mode from 1 (signed 16-bit integer) to 6 (unsigned) or
  from 6 to 1.  The program will warn if the current minimum and maximum
  densities indicate that there are values that will not be interpreted
  correctly after the change.

  INVERTORG - Invert the signs of the X, Y, and Z origin values to switch
  the header between different definitions of the origin.

  SETMMM - Set the minimum, maximum, and mean densities directly with the
  given values.

  REAL - Change a mode 4 FFT file to mode 2 and double the X size.

  FFT - Change a mode 2 file to mode 4 and divide X the size by 2; this can be
  done only if the X size is two times an odd number.

  HELP - print a summary of these options.

  DONE - Write the modified header to the file and exit.

HISTORY
  Written by David Mastronarde 10/24/88; ported to SGI 12/7/94