CP FROM MRC - Copy MRC file to SPIDER file

(1/2/20)

PURPOSE

Copies MRC format image/volume file to a SPIDER format file. NOTE: This operation converts current MRC 2000 or MRC 2014+ format input. Older MRC formats are no longer supported. Can copy stacks.   Example.

SEE ALSO

USAGE

.OPERATION: CP FROM MRC
    <or>
CP FROM MRCV [The operation 'CP FROM MRCV' can be used to force conversion of a MRC volume to a SPIDER volume. This is necessary with some variants of 'MRC' format files which have non-standard headers.]

.INPUT FILE NAME OR TEMPLATE (E.G. STK@****): MRCIN.mrc
[Enter the name of the MRC file you want to copy. File can contain image, volume, or a MRC stack. Name should include extension. Valid extensions inlude: 'mrc', 'MRC', 'mrcs', 'MRCS', 'map', and 'MAP'.]

If the input contains a single MRC image or volume SPIDER asks:

.SPIDER OUTPUT FILE: spi_imgfrommrc
[Enter the name of the SPIDER output file. MRC 2000 volume stacks are always considered to be simple volumes here.]

If the input contains an image/volume stack SPIDER asks the following two questions:


.SPIDER OUTPUT FILE OR TEMPLATE (E.G. STK@****): spi_stkfrommrc
[Enter name for the SPIDER volume output file with or without the stack symbol.}

.FIRST IMAGE NUMBER IN SPIDER STACK: 1
[Enter the number for the image in SPIDER output file. This can be used to place multiple MRC stacks in a single SPIDER stack. This emphasizes to the user that SPIDER stacks begin with image number one and MRC stacks may begin with image number one or zero. Note: many MRC compatible softwares have trouble handling undefined images in a stack. SPIDER does not have any such problem.]

If the input contains MRC image(s) SPIDER asks:

.DATA ORIGIN CORNER (UL/LL): UL
[Relion, Cryosparc and ImageJ MRC files have a data origin of 'UL' (upper left corner) whereas IMOD, Chimera and some other softwares usually use 'LL' (lower left corner).]

Alternatively if the input contains MRC volume(s) SPIDER asks:

.DATA ORIGIN CORNER (UL/LL) & HANDEDNESS (L/R) : UL L
[Relion, Cryosparc and ImageJ MRC files have a data origin of 'UL' (upper left corner) whereas IMOD, Chimera and some other softwares usually have 'LL' (lower left corner). SPIDER only handles left-handed volumes which are produced by Relion & Cryosparc at this time but right handed volumes for some other softwares may supported in future releases.]

NOTES

  1. Works for MRC modes: 0, 1, 2, & 6. Does not copy MRC Fourier format files.

  2. Prior to the 2015 MRC format revision there was no way to specify a volume stack other than using the '.mrcs' extension. Volume stacks consistent with the 2015 format are now converted correctly into SPIDER volume stacks.

  3. This operation can copy a whole MRC volume or stack. It can not copy just particular slices from a MRC volume.

  4. The simple 'CP' operation can now be used to copy to/from MRC files by just specifying the MRC extension.

  5. The MRC format is sometimes referred to as CCP4.

SUBROUTINES

COPYFROMMRC, OPFILES, OPSTREAMFILE

CALLER

COPY1

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