[3dem] RE: mrc format

[Anchi Cheng]

Dear Michael,

As I may have mentioned in my e-mail the proposal I posted was put forward to a
number of people including MRC/CCP4/IMOD representative and we are
in the process of finalizing it which include another important change.  I was
put charge of writing the initial draft of the proposal to the larger community but am
a bit slow in doing so.  I apologize for it.

Our proposal actually did not mean to make MZ number of objects (nor number of 
volumes in Roberto's wording) but as number of sections in each volume in your words.

I should explain that there is a reason for defining MZ as number of sections
in Z for each single 3D volume in the 3D stack.  In crystallography context where MRC
format first derived from from CCP4, MX,MY,MZ represents number of the grid points for sampling
the result of Fourier synthesis in a unit cell.  "Number of intervals along Z" really meant
number of intervals along Z in the unit cell.  I intend to preserve this definition by
rationalizing that we think each of the volume in the 3D stack or each of the image
in the 2D stack as our "unit cell".


I made a picture to give an example.

http://www.scripps.edu/~acheng/NZMZ.png

The "unit cell" here has MX=3, MY=2, and MZ=2
NX,NY,NZ that all current program read as total number of data in each direction is
NX = 3, NY=2, and NZ = 6

Accompany to the new (or restored) definition of MZ, one more definition needs to be
clarified:  Since single 3D volume as defined previously has NZ = MZ, there was no formal
definition on how pixel size is derived from 3rd CELLA (long word 13) and these integers.
We propose that from now on it will be defined as

pixel size in Angstrom in Z = 3rd CELLA  /  MZ

so as to avoid having to change 3rd CELLA value if more volumes are appended to the 3D Stack.
If we use your and Roboto's definition of 3D volume stack, NZ, MZ, as well as 3rd CELLA
need to be changed if a new volume is appended to an existing one.

I didn't realize that Roberto has decided on his MRC format of 3D stack in new XMIPP until he posted it
on 3DEM.  Martyn Wimm who represents CCP4 in our effort suggests that we add
him in our primary circulation of proposal.  Would you like to join in?  It is best that those
of us with interest in this find out possible problems with this before we all start using it.

Best,

Anchi