[3dem] Re: different mrc formats in relion-1.2 and xmipp-3.???

Anchi Cheng acheng at scripps.edu
Mon Jul 15 12:58:42 PDT 2013

Hi, all,

I want to modify what Roberto stated about distinguishing
single image, stack of images, single volume, stack of volumes in MRC format.

A couple of us made an effort to resolve some mrc conflict with ccp4 library recently.
To look into the future, we designated the ISPG 401 NZ / MZ = N object so not to alter
the original ccp4 definition of MZ ( number of grid (sampling) in a unit cell ).  None of us is
aware of the use of MRC format as volume stack, yet.  Hopefully when this becomes a
practice, we will all use the same convention.

In short, using the wording of IMGIC 4D

pixel size in Z = CELL(Z) / MZ
single image:  ISPG=0 NZ = MZ = 1
image stack: ISPG=0 NZ = N object
single volume: ISPG=1 NZ = MZ = Z slices
volume stack: ISPG=401 MZ = Z slices; NZ / MZ = N object

If any of you have been writing stack of mrc volume and/or have concern over this,
please let me know.  I will assemble them to  present to the group, or add you to
the discussion if you prefer.

I've presented as a side bar of my poster at 3D-EM GRC the essence of our conclusions.
The full conclusion of the effort will be given in full later after we figure out of a
few of details on handling extended header used in some variant.


Anchi Cheng

Others in the discussion group:
Bridget Carragher (TSRI-Leginon)
Martyn Winn (STFC-CCP4)
Richard Henderson (MRC)
David Matronarde (UColorado-IMOD)
Remco Schoenmakers (FEI)
David Agard (UCSF)
Steven Ludtke (Baylor-EMAN)
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