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Spi22ccp4

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Adrian Quintana edited this page Dec 11, 2017 · 1 revision

convert_spi22ccp4

Purpose

This program converts XMIPP files from/to CCP4 map format (works with both 2D and 3D data). You can also import MRC tilt series into Xmipp using this command.

The following fields are filled when converting from XMIPP to CCP4

  • map dimensions (nc, nr and ns)
  • data type (mode)
  • index starting values (ncstart, nystart,nsstart)
  • unit cell size (x_length, y_length,z_length). By default x_length=nc, y_length=nr, z_length=ns
  • the correspondence between the x, y and z axes and the fastest, medium and slowest varying dimensions (mapc, mapr and maps). We, follow the EM standard, that is, the 3D data must be stored with the x axis (columns) fastest changing, followed by the y axis (rows) and the z-axis (sections) slowest changing.
  • In order to help programs that work with many formats the map and machst fields in the header should also be filled.
    • map field should contain the string "MAP" and is a "magic" word that identifies CCP4 MAP files
    • machst field describes the way the computer architecture stores the data (machine endianess)

Usage

$ convert_spi22ccp4 -i file_in -o file_out  [-reverse_endian] 
    *    input CCP4/Xmipp file (2D or 3D)
    *   output Xmipp/CCP4 file. In the case of importing a MRC tilt series, this parameter should be a rootname
    * : The format of this file should be the corresponding tilt angle for each image in the series given in -i, with one angle in each line.
    *      by default, output has the same endiannes as input
                                   use this option to change endianness
    *  Cell Dimensions (Angstroms) for x-axis. By default x_length=xdim_image
    *  Cell Dimensions (Angstroms) for y-axis. By default y_length=x_length
    *  Cell Dimensions (Angstroms) for z-axis. By default z_length=1

Examples and notes

In order to convert a xmipp image called img.spi to a ccp4 image type

convert_spi22ccp4 -i img.spi -o img.map

In order to convert a xmipp image called proj00012.spi to a ccp4 image called proj00012.mrc with unit cell dimensions 27x52x2 (in angstroms) type

convert_spi22ccp4  -i proj00012.spi -o proj00012.mrc -x_length 27 -y_length 52 -z_length 2

Converting a MRC tilt series into Xmipp

convert_spi22ccp4  -i tiltSeries.mrc -o rootnam -tilt_angles angles.txt

where angles.txt has the format

-60
-59
-58
...
59
60

Converting a Xmipp selfile into a MRC stack

convert_spi22ccp4  -i tiltSeries.sel -o tiltSeries.mrc -tilt_angles angles.txt

The input is the Selfile with all the images belonging to the tilt series. The output is the MRC stack and the angular file needed by some IMOD programs in the format of one tilt angle per row (see above).

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