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google-deepmind / alphafold

Open source code for AlphaFold.
Apache License 2.0
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Side chain Frame constrcution #187

Open wangleiofficial opened 3 years ago

wangleiofficial commented 3 years ago

For example:

# psi-frame to backbone
    mat = _make_rigid_transformation_4x4(
        ex=atom_positions['C'] - atom_positions['CA'],
        ey=atom_positions['CA'] - atom_positions['N'],
        translation=atom_positions['C'])
    restype_rigid_group_default_frame[restype, 3, :, :] = mat

From paper: For the side chain frames, we use the atom before the torsion bond as x1, the atom after the torsion bond as x2 and the next atom after that as x3. but here, CA atom is the origin of the Psi frame, can you help me to explain this code?

YiyuHong commented 1 year ago

@wangleiofficial Hi, Did you figure it out? I don't quite understand this part either.