generate mask for manual refine

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generate mask for manual refine


This is a really nice GUI. I tried to do supplied masking, following the previous discussion

The process is like this:

1, make_size_map (with input.mrc output.mrc bin_threshold 3.0 interactively)

2, proc3d size_map.mrc output_bin.mrc bin=3

The binarised mask map generated  is then very tiny with voxel size (0.004, open in Chimera), compared to true volume (voxel is 1.04).  Am I doing wrong?



It doesn't sound like you are

It doesn't sound like you are doing anything wrong, instead one of the programs (probably make_size_map) is not writing the correct pixel size out in the header. You should still be able to use this mask as the pixel size in the header is ignored by cisTEM.   One way to check it is to open it in the display (go to the volume assets panel, and select your original 3D and your imported mask and click display).  This will show slices through the 3D and the two should be aligned.

Incidentally, the second binarisation should be a much larger number, as each voxel is replaced with the number of connected voxels in make_size_map this number will usually be in the tens or hundreds of thousands.  



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