alterheader(1) General Commands Manual alterheader(1)
NAME
alterheader - to alter header information in an MRC file
SYNOPSIS
alterheader [filename]
DESCRIPTION
Alterheader allows one to alter header information in an MRC file with-
out rewriting the file. The program can be run interactively or with
command-line arguments. When run interactively, for each standard
header entry selected by the user, the program prints the current val-
ues and asks for new values, checking for legality in some cases.
Other operations can be performed as described below. Multiple changes
can be made. When run interactively, 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. The interactive mode is thus much
safer to use, although inconvenient from scripts. The interactive
entries for the different options are not case sensitive but are shown
below in their upper-case form.
Even when running interactively, the file name can be entered on the
command line; if not, the program will ask for it. However, the addi-
tion of any option argument on the command line makes the program
require a filename as well and run without any interaction.
The MRC header stores three pieces of information about size: the num-
ber of pixels in X, Y, and Z, which is output as "columns, rows, sec-
tions", 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.
OPTIONS
When run with command-line arguments, Alterheader uses the PIP package
for input (see the manual page for pip). The order in which options
are entered is not preserved with PIP input. Options are processed in
the same order as they are listed in the brief summary of options when
running interactively, namely: -org, -cel, -dat, -del, -map, -sam,
-tlt, -firsttlt, -rottlt, -mmm, -rms, -fixpixel, -feipixel, -extrafix,
-modefix, -invertorg, -setmmm, -real, -fft, -ispg, -4bit, -toggleorg,
-gridfix, -title.
The following options can be specified either as command line arguments
(with the -) or one per line in a command file or parameter file (with-
out the -). Options can be abbreviated to unique letters; the cur-
rently valid abbreviations for short names are shown in parentheses.
-org (-o) OR -Origin Three floats
(Interactive 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/-invertorg to switch the sign
of the origin values.
-cel (-ce) OR -CellSize Three floats
(Interactive CEL) Change the cell size in X, Y, Z. This will
show up as a change in pixel spacing, as described above.
-del (-d) OR -PixelSize Three floats
(Interactive 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 (-ma) OR -MapIndexes Three integers
(Interactive 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 (-sa) OR -SampleSize Three integers
(Interactive SAM) Set sampling in X, Y, Z. See note above on
IMOD conventions.
-tlt (-tl) OR -TiltCurrent Three floats
(Interactive 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.
-firsttlt (-fir) OR -TiltOriginal Three floats
(Interactive TLT_ORIG) Change original tilt angles. These
angles have no effect in IMOD.
-rottlt (-ro) OR -RotateTilt Three floats
(Interactive 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).
-mmm (-mm) OR -MinMaxMean
(Interactive MMM) Read the file to recompute the minimum, maxi-
mum, and mean densities and the RMS density.
-rms (-rm) OR -RootMeanSquare
(Interactive RMS) Print the current RMS value (root-mean-square
deviation from the mean density) then do the same operation as
MMM/-mmm.
-fixpixel (-fix) OR -FixPixel
(Interactive FIXPIXEL) Set the cell and sample sizes the same
as the image size, resulting in a pixel spacing of 1, 1, 1.
-gridfix (-g) OR -FixGrid
(Interactive FIXGRID) Set the sample size the same as the image
size and modify the cell size so as to preserve the pixel size.
-feipixel (-fe) OR -FeiPixel Integer
(Interactive 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. If the existing pixel spacing
is not 1 but is equal to 2, 3, or 4, this will be assumed to
represent a binning of the data, and the pixel size will be mul-
tiplied by this value. However, if the pixel size has already
been transferred or the pixel spacing does not correspond to a
small integer, the program will transfer the pixel size only if
a positive number is entered for this option. It will exit if 0
or a negative nunber is entered for this option when running
with command-line arguments, or if -1 is entered when running
interactively.
-extrafix (-e) OR -FixExtra
(Interactive FIXEXTRA) Change the flags in the header so that
3dmod no longer interprets the extended header as having piece
coordinates for a montage.
-modefix (-mo) OR -FixMode
(Interactive FIXMODE) Change mode from 1 (signed 16-bit inte-
ger) 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 (-in) OR -InvertOrigin
(Interactive INVERTORG) Invert the signs of the X, Y, and Z
origin values to switch the header between different definitions
of the origin. This operation will not change the flag about
the origin inversion and will invert the origin values seen
inside IMOD programs as well as those stored in the header.
-toggleorg (-to) OR -ToggleOrigin
(Interactive INVERTORG) Invert the signs of the X, Y, and Z
origin values stored in the file header without changing the
values seen inside IMOD programs. This will be done by setting
the flag that determines whether values are inverted on output
to the file or not.
-setmmm (-se) OR -SetMinMaxMean Three floats
(Interactive SETMMM) Set the minimum, maximum, and mean densi-
ties directly with the given values.
-real (-rea) OR -RealMode
(Interactive REAL) Change a mode 4 FFT file to mode 2 and dou-
ble the X size.
-fft (-ff) OR -ComplexMode
(Interactive FFT) Change a mode 2 file to mode 4 and divide the
X size by 2; this can be done only if the X size is two times an
odd number.
-4bit (-4) OR -Change4BitMode Integer
(Interactive 4BIT) For a positive entry, change a mode 0 file
to the 4-bit mode 101 and double the size in X that is stored in
the header. The header listing will look the same if the file
was already recognized as containing 4-bit data packed into
bytes. For a negative entry, change a mode 101 file back to
mode 0 and divide the X size by 2 (X size must be even).
-ispg (-is) OR -SpaceGroup Integer
(Interactive ISPG) Change the space group entry, which should
be 0 for an image stack, 1 for an image volume, and 401 for a
stack with multiple volumes.
-volstack (-v) OR -VolumeStack Integer
(Interactive VOLSTACK) Change the grid sampling in Z to equal
the given number and the space group to 401 to mark the file as
a volume stack with the given number of sections per volume.
Enter 0 to revert from being a volume stack by setting the sam-
ple size equal to the total sections and the space group to 1.
The pixel size will be preserved in these changes. Volume
stacks will be loaded as multiple volumes in 3dmod unless its
-T option is entered.
-title (-ti) OR -TitleToAdd Text string
Add the given string as a new label (title) after all other
labels in the file, unless the -position option is entered with
a specific position. This option is not equivalent to the
interactive LAB option. If there are already 10 labels, the
last one will be replaced. Be sure to quote the whole string
when running from the command line.
-position (-p) OR -PositionForTitle Integer
Position that new title should be placed in, numbered from 1.
Note that a positive number is entered here, unlike the 0 or
negative number entered with the interactive LAB option.
-remove (-rem) OR -RemoveTitles List of integer ranges
List of existing titles to remove, numbered from 1; comma-sepa-
rate ranges may be entered. This option can be used together
with -title and -position; titles will be removed before one is
added with -title.
-copy (-co) OR -CopyFromImage File name
Name of an image file with the same dimensions in X and Y from
which to copy pixel size and origin information. Specifically,
the sampling and cell size for X and Y will be copied from this
file, and appropriately changed for a difference in Z size to
give the same pixel size in Z. The origin and current tilt
angles will also be copied, as well as the unused "start" coor-
dinates. No other options can be entered with this option.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
ADDITIONAL INTERACTIVE OPTIONS
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 opera-
tion in a script, first delete the tenth label, if any, with entries
"lab - 10 - 1 - lab -9 your_new_label".
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.
START - Change the starting coordinates of the volume shown as "Start
cols, rows, sects" in the standard header output. These entries are
not used or managed by any other programs IMOD.
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.
Converted to PIP input, 10/15/14.
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.2.0 alterheader(1)