EditHeader2

Overview

EditHeader2 is similar to Priism's EditHeader but allows working with the headers of files that use other variants of the MRC file format, include Image 2000 and CCP4 files.

The EditHeader2 dialog consists of two main parts. Along the top is a menu bar for invoking the available operations. The body of the dialog displays the values in the header, with the exception of the labels, common to all MRC variants. You can change those values as you wish. To learn more about the header fields displayed, consult the "Baseline Fields" section below.

The operations available in the menu bar are:

Topics

Overview | Baseline fields | Extension fields | Labels | Defaults

Related Priism Topics

Priism | EditHeader | Priism's variant of the MRC format

Baseline Fields

EditHeader2 displays the values from the MRC header common to all variants within EditHeader2's main dialog (the one exception is the labels and number of labels; to see those, use the "Labels..." option from the View menu).

The values common to all the header variants are:

Number of columns
Is the number of elements along the fastest-varying (i.e. stored adjacent to each other in the file) dimension of the data set.
Start column
Relates the data set stored in the file to a larger data set; this is the column index within the larger data set for the first column stored in this file.
Column mapping
Specifies which spatial axis (X, Y, or Z) corresponds to moving from column to column in the file. If the value in the field is one of the expected values (1, 2, or 3), the menu displays the axis name; otherwise, the menu will show "Nonstandard". The field adjacent to the menu displays the actual value from the header.
Number of rows
Is the number of elements along the second fastest-varying dimension of the data set.
Start row
Relates the data set stored in the file to a larger data set; this is the row index within the larger data set for the first row stored in this file.
Row mapping
Specifies which spatial axis (X, Y, or Z) corresponds to moving from row to row in the file. If the value in the field is one of the expected values (1, 2, or 3), the menu displays the axis name; otherwise, the menu will show "Nonstandard". The field adjacent to the menu displays the actual value from the header.
Number of sections
Is the number of elements along the slowest-varying dimension of the data set.
Start section
Relates the data set stored in the file to a larger data set; this is the section index within the larger data set for the first section stored in this file.
Section mapping
Specifies which spatial axis (X, Y, or Z) corresponds to moving from section to section in the file. If the value in the field is one of the expected values (1, 2, or 3), the menu displays the axis name; otherwise, the menu will show "Nonstandard". The field adjacent to the menu displays the actual value from the header.
Data type
Indicates how each element of the data set is stored within the file. If the format corresponds to one of the formats EditHeader2 recognizes, the menu lists the name of the format. For unrecognized formats, EditHeader2 will display "Nonstandard" in the menu. EditHeader2 uses the field next to the menu to display the numeric code used in the header to represent the data type.
Number of x intervals
Displays the number of intervals along the x spatial dimension.
X length
Displays the cell dimension in the x dimension.
X spacing
Displays the cell dimension in the x dimension divided by the number of intervals in the x dimension. The spacing is a derived quantity that is not directly stored in the header. When you adjust the spacing, EditHeader2 will adjust the cell dimension while leaving the number of intervals constant. When the number of intervals is zero, EditHeader2 disables the spacing field.
Number of y intervals
Displays the number of intervals along the y spatial dimension.
Y length
Displays the cell dimension in the y dimension.
Y spacing
Displays the cell dimension in the y dimension divided by the number of intervals in the y dimension. The spacing is a derived quantity that is not directly stored in the header. When you adjust the spacing, EditHeader2 will adjust the cell dimension while leaving the number of intervals constant. When the number of intervals is zero, EditHeader2 disables the spacing field.
Number of z intervals
Displays the number of intervals along the z spatial dimension.
Z length
Displays the cell dimension in the z dimension.
Z spacing
Displays the cell dimension in the z dimension divided by the number of intervals in the z dimension. The spacing is a derived quantity that is not directly stored in the header. When you adjust the spacing, EditHeader2 will adjust the cell dimension while leaving the number of intervals constant. When the number of intervals is zero, EditHeader2 disables the spacing field.
Axes angles
Display the angles (in degrees, by convention) between the axes of the unit cell.
Intensity statistics
Displays the minimum, maximum, and average element values for the data set, as recorded in the header.
Space group
Displays the space group number recorded in the header.
Extended header size
Displays the number of bytes of extended header that immediately follows the 1024-byte fixed header in the file.

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Extension Fields

To view the portions of the header that vary between the different variants of the MRC format, use the "Extension fields..." option in the View menu of EditHeader2's main dialog. EditHeader2 displays those portions of the header according to the format you've selected in the "Extension format" option of the View menu.

For the Image 2000 extensions the additional header fields are:

Origin
Displays the x, y, and z coordinates for the origin of the data set.
RMS
Displays the root mean square deviation from the mean intensity of the data set, as recorded in the header.

For the CCP4 extensions the additional header fields are:

Has skew
Indicates whether a skew transformation is specified by the header (a nonzero value) or not (a zero value). EditHeader will display the toggle button in an on state when the skew transformation is included. EditHeader2 displays the actual value from the header in the adjacent text field.
Matrix
Displays the 3 x 3 transform matrix for the skew transformation. The first row are, from left to right, the s11, s12, and s13 components of the matrix. The second row are, from left to right, the s21, s22, and s23 components. The third row are, from left to right, the s31, s23, and s33 components.
Translation
Displays the three components of the translation vector for the skew transformation.
RMS
Displays the root mean square deviation from the mean intensity of the data set, as recorded in the header.

For the Priism extensions the additional header fields are:

Origin
Displays the three components (x, y, z) of a translation vector to relate the data set coordinates to another frame of reference.
Tilt angles
Displays the three rotation angles (about x, y, and z; by convention, measured in degrees) to relate the data set coordinates to another frame of reference.
# of times
Displays the number of time points included in the file.
Start time
Relates the time points stored in the file to a longer time series. The value shown in this fields is the time point index within the longer time series for the first time point stored in the file.
# of wavelengths
Displays the number of wavelengths included in the file.
Wavelengths
Displays the wavelengths (in nanometers, by convention) for each of the wavelengths in the file. The header has space to store the wavelengths for up to five wavelengths.
Interleaving
Displays the storage order of z, wavelength, and time within the file. There are three recognized options, ZTW (z varies fastest, time varies second fastest, and wavelength varies slowest), WZT (wavelength varies fastest, z varies second fastest, and time varies slowest), or ZWT (z varies fastest, wavelength varies second fastest, and time varies slowest). If the value in the header is an unrecognized value, EditHeader2 will display "Other" in the menu. EditHeader2 displays the actual value from the header in the text field adjacent to the menu.
Minimum and maximum intensities
Displays the minimum and maximum intensity in each wavelength other than the first (the statistics for the first wavelength use the standard MRC fields in the header for intensity statistics), as recorded in the header. The header has space to store the statistics for up to five wavelengths.
# of resolutions
Displays the total number of resolutions (different versions of the data) present in the file.
Z downsampling
Displays the downsampling factor used in the z dimension applied to each lower resolution data set.
Extended header
For non-crystallographic data, the Priism extended header (if present) contains a set of integer and floating-point attributes for each section of data. The number of integer parameters and floating-point parameters per section is displayed here.
Image type
The Priism header has a field to indicate how the data should be interpreted and four fields (two integers and two fixed point values) for attributes of the data. If the image type indicated in the header is recognized by EditHeader2, it will display a correspond name in the menu next to the "Image type" button; otherwise, EditHeader2 will display "Other" in that menu. EditHeader2 will display the numeric code for the image type in the text field adjacent to the menu.
Lens number
Displays the identification number for the lens used when collecting the data.
Creator ID
Displays the identification tag for the data collection or processing software that generated the data set.

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Labels

To display the number of labels and the contents of the labels from the header, select the "Labels..." option from the View menu in EditHeader2's main dialog. That will open a dialog with the number of labels shown at the top, and the contents of the 10 labels displayed one per line below that. For the display of the labels, EditHeader2 converts any non-printable character to a backslash followed by three digits where the three digits are the character's value as an unsigned decimal value. EditHeader2 also converts any backslash to two backslashes.

Use the "Shift up..." button at the bottom of the dialog to shift the contents of the labels to increasing label number (i.e. move the contents of label nine to label ten, label eight to label nine, ...) and use the "Shift down..." button at the bottom of the dialog to shift the contents of the labels to decreasing label number (i.e. more the contents of label two to label one, label three to label two, ...). Either button displays a dialog where you can enter which labels are shifted and the size of the shift.

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Defaults

Because it is not always possible to distinguish different variants of the MRC format, EditHeader2 makes assumptions about the format when it opens a file. To change the assumptions that EditHeader2 will make when opening files, use the "Set defaults..." option from the Configure menu in EditHeader2's main dialog. Also use that option to change how EditHeader2 detects the ordering of bytes in 2- and 4- byte quantities in the header and the format EditHeader2 uses for new headers.

One key factor affecting EditHeader2's assumptions about an existing file is the 53rd 4-byte word of the file (where the first word in the file is numbered one). The Image2000 and CCP4 formats put "MAP " in that word. The Priism format does not.

The "Set defaults" option opens a new dialog which displays the current set of defaults. You can edit those values. To apply the changes, press the "Apply" button at the bottom of the dialog. Pressing the "Close" button at the bottom of the dialog will discard any changes and close the dialog. If you want EditHeader2 to make the same assumptions when you run it in the future, use the "Save" option from the Configure menu in EditHeader2's main dialog.

The controls at the top of the defaults dialog control how EditHeader2 detects the ordering of multibyte quantities when it opens a file. If the file does not have the characters "MAP " in the 53rd 4-byte word of the file, EditHeader2 chooses the byte ordering depending on how you set the "without MAP field" menu. The available options are:

big endian
Always assume the file is big endian. That is the native byte ordering for IRIX systems and Mac OS X systems with PowerPC processors.
little endian
Always assume the file is little endian. That is the native byte ordering for systems with Intel or AMD Athlon processors.
autodetect
If the number of columns (the first 4-byte word in the file) and the number of rows (the second 4-byte word in the file) are either negative or greater than 65535 when not byte-swapped, assume that all the header entries must be byte-swapped; otherwise, assume the header does not require byte-swapping.

If the file does have the characters "MAP " in the 53rd 4-byte word of the file, EditHeader2 chooses the byte ordering depending on how you set the "with MAP field" menu. The options are the same as above, but the autodetection algorithm works differently. When autodetecting the byte order, EditHeader2 will first look at the first byte of the 54th word in the header and assume the file is big endian if that byte is 17 or little endian if that byte is 68. For any other value in that byte, EditHeader2 will apply the autodetection algorithm for files without "MAP " in the header.

The controls at the bottom of the defaults dialog control how EditHeader2 interprets the values in the header which are not in common to all variants of the MRC format. The menu labeled "new files" controls how EditHeader2 initializes those values when generating a new header. The menu labeled "old files without MAP field" controls how EditHeader2 interprets existing files without "MAP " in the 53rd 4-byte word of the file. The menu labeled "old files with MAP field" controls how EditHeader2 interprets existing files with "MAP " in the 53rd 4-byte word of the file. For all three, the available options are:

Baseline
Assume nothing about the 25th through 55th four-byte words in the header. When creating a new header, fill those values with zeroes.
Image2000
Assume the header of the file is laid out as described at http://www2.mrc-lmb.cam.ac.uk/image2000.html.
CCP4
Assume the header of the file is laid out as described at http://www.ccp4.ac.uk/dist/html/maplib.html#description.
Priism
Assume the header of the file is laid out as described at http://msg.ucsf.edu/IVE/IVE4_HTML/IM_ref2.html.

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