A note about 3dmod's coordinate system

Please note that 3dmod places (0,0,0) at the bottom left corner in XY planes, but in the center of the first Z-plane.

For example, this code:

import imodmodel
import pandas as pd
import numpy as np
import mrcfile

df = pd.DataFrame(
    {
        "x": [0, 1, 2, 3],
        "y": [0, 1, 2, 3],
        "z": [0, 1, 2, 3],
    }
)

volume = np.zeros((4, 4, 4), dtype=np.float32)
for i in range(4):
    for j in range(4):
        for k in range(4):
            if (i + j + k) % 2 == 0:
                volume[i, j, k] = 1.0

mrcfile.write("co.mrc", volume, overwrite=True)
imodmodel.write(df, "co.mod")

results in the following:

The resulting position of points in XY slices

The resulting position of (0,0,0) in XYZ slices

Since many other programs place (0,0,0) in the center of the first voxel, one might consider adding (0.5,0.5,0) to the coordinates before saving.