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.
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 labels. You will a numbered list of labels and can enter a
range (comma-separated list) of numbers to delete.
MMM - Read the file to recompute the minimum, maximum, and mean
densities and the RMS density.
RMS - Print the current RMS value 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.
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.
SETMMM - Set the minimum, maximum, and mean densities directly with the
given values.
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