Initial model resizing fixes

[stephen-riggs]

A few issues have come up with the user-supplied initial model:

• The mrc size was not being read from the header
• Box size and downscaling was updated in cryoemservices but not in murfey so they now disagree
• The diameter was given is being given to the box size calculation in angstroms but it wanted pixels
• Relion was not told to force the pixel size, causing 3D classification to crash

[codecov]

Codecov Report

❌ Patch coverage is 0% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 38.51%. Comparing base (c02c9da) to head (e299993).
⚠️ Report is 9 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #709      +/-   ##
==========================================
- Coverage   38.51%   38.51%   -0.01%     
==========================================
  Files          99       99              
  Lines       11663    11664       +1     
  Branches     1542     1542              
==========================================
  Hits         4492     4492              
- Misses       6973     6974       +1     
  Partials      198      198              

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[tieneupin]

The code looks fine as-is, but if you could include a brief summary in the PR description of why you had to change form input_mrc.nx... to input_mrc.header.nx... for future reference, that would be helpful.