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By default cxs.PengAtomicPotential(atom_positions, atom_identities, b_factors) won't read in an atom with a b factor of 0.
Many pieces of software such as VMD and MDAnalysis will by default use a bfactor of 0. This adds an extra step when reading in PDBs made by these other softwares where you need to set the bfactor to 1.
Adding a fix_bfactors = True option would be very useful.
The text was updated successfully, but these errors were encountered:
The default is b_factors = None, which is the same as them being zero. However, it should be possible to directly pass in b_factors = jnp.zeros((n_atoms,), dtype=float). Do you get an error when you try this?
By default cxs.PengAtomicPotential(atom_positions, atom_identities, b_factors) won't read in an atom with a b factor of 0.
Many pieces of software such as VMD and MDAnalysis will by default use a bfactor of 0. This adds an extra step when reading in PDBs made by these other softwares where you need to set the bfactor to 1.
Adding a
fix_bfactors = True
option would be very useful.The text was updated successfully, but these errors were encountered: