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Add option in cxs.PengAtomicPotential to fix b factors. #282

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Miro-Astore opened this issue Nov 29, 2024 · 1 comment
Open

Add option in cxs.PengAtomicPotential to fix b factors. #282

Miro-Astore opened this issue Nov 29, 2024 · 1 comment

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@Miro-Astore
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Miro-Astore commented Nov 29, 2024

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.

@mjo22
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mjo22 commented Nov 29, 2024

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?

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