alterheader(1)                                                  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.  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 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.

       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 ori-
       gin 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 opera-
       tion 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 densi-
       ties 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.
       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 multiplied by this value.

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

       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 the X 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


BUGS
       Email bug reports to mast at colorado dot edu.



BL3DEMC                              4.7.3                      alterheader(1)