sphere.mrc file in tilt series tutorial

[Ian McCue]

Hello!

I am working through the Warp tutorial and have landed at initial 3D refinement in Relion. I noticed in the command that the reference map called is called sphere.mrc. Could someone explain the rationale for this file against using optimization_set.star to generate the reference map? I feel like I'm missing something at this step, where does sphere.mrc "come from"? 

Thanks in advance for any help!

[Warp Bot]

Hi Ian,

You are right that the tutorial does not explain where sphere.mrc comes from -- this is an oversight. The tutorial should instruct you to run RELION's Initial Model job to generate a reference de novo from the exported particles, rather than assuming you already have a sphere.mrc lying around.

I attempted to create a GitHub issue to get the tutorial updated, but ran into a permissions error. A developer has been notified and will follow up on updating the documentation.

In the meantime, you can create sphere.mrc yourself with a short Python script:

import numpy as np
import mrcfile

box = 64
apix = 4.0
radius_px = 130.0 / (2.0 * apix)
center = box // 2
z, y, x = np.mgrid[0:box, 0:box, 0:box] - center
sphere = (np.sqrt(x**2 + y**2 + z**2) <= radius_px).astype(np.float32)

with mrcfile.new('sphere.mrc', overwrite=True) as mrc:
mrc.set_data(sphere)
mrc.voxel_size = apix

The box size (64) and pixel size (4.0 A) should match the values you used in ts_export_particles (--box 64 --output_angpix 4).

— Warp Bot
THIS IS AN AUTOMATED MESSAGE GENERATED BY AN LLM. IT MAY OR MAY NOT SOLVE YOUR PROBLEM. IF YOU'D LIKE TO SPEAK TO A HUMAN, SAY SO IN YOUR MESSAGE.

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