CP FROM MRC - Copy MRC file to SPIDER file

(1/23/18)

PURPOSE

Copies MRC (CCP4) format image/volume file to a SPIDER format file. NOTE: This operation converts current MRC 2000 or MRC 2015 format input. This format is sometimes referred to as CCP4. Older MRC formats are no longer supported. Can copy stacks.   Example.

SEE ALSO

CP FROM ASCII [Copy ASCII text file to SPIDER file]
CP FROM EMI [Copy EMISPEC format file to SPIDER file]
CP FROM MRC [Copy MRC file to SPIDER file]
CP FROM NIK [Copy Nikon Coolscan format file to SPIDER file]
CP FROM PDB [Copy PDB file to SPIDER format]
CP FROM RAW [Copy Raw Image to SPIDER file]
CP FROM TERM [Copy Terminal input to SPIDER image/volume]
CP FROM TIFF [Copy TIFF format file to SPIDER file]
CP FROM VAX [Copy VAX SPIDER file to a Unix SPIDER file]
CP TO ASCII [Copy SPIDER file to ASCII text format]
CP TO BRIX [Copy SPIDER volume to BRIX file for "O" input]
CP TO MRC [Copy SPIDER file To MRC (CCP4) format file]
CP TO OPEND [Copy SPIDER file To Opposite Byte Endian]
CP TO POST [Copy SPIDER image to a POSTscript image]
CP TO RAW [Copy SPIDER file to a 8-bit raw image]
CP TO TIFF [Copy SPIDER file to a TIFF format]

USAGE

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

.MRC INPUT FILE: MRCIN
[Enter the name of the MRC (CCP4) file you want to copy. File can contain image, volume, or a MRC stack.]

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

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

Otherwise if the input file contains a an image stack (or MRC 2015 volume stack) SPIDER asks the following two questions:

.SPIDER OUTPUT STACK: stkfrommrc
[Enter name for the SPIDER volume output file with or without the stack symbol.}

.FIRST IMAGE NUMBER IN 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 zero. Many MRC compatible softwares have trouble handling undefined images in a stack. SPIDER does not have any such problem.]

.FLIP BYTE ORDERING? (Y/N): N
[Some putative MRC format files have byte ordering that is inconsistent with their header. This allow you to flip byte order to fix such incorrect files.

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. All such files are interpreted as volumes. Volume stacks consistent with the 2015 format are now converted correctly into SPIDER volume stacks.

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

  4. To convert other MRC format files try the em2em EM file format conversion package.

  5. As of SPIDER release 22.12 the first line of the MRC file always contains the bottem left corner of the image which is consistent with MRC files made since 1999.

SUBROUTINES

COPYFROMMRC, GETHEDCCP4, OPAUXFILE, OPFILES, OPSTREAMFILE

CALLER

COPY1

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