jwohlwend
pLDDT reported in _ma_qa_metric_local loop as fraction rather than percent
Output of boltz predict gives the pLDDT as percent (0,100) when reported in the B-factor column, but as a fraction (0,1) in the _ma_qa_metric_local loop.
Yes, pLDDT is (0,1) but we changed it in the B-factor column because many visualization software are used to that scale. Is there any particular reason to also have it as percentage in _ma_qa_metric_local ?
I think that Mol* is taking the pLDDT from _ma_qa_metric_local, so displaying every residue as low confidence. I can tweak this behavior though if the discordance is intentional.
(Annoying that the downstream applications don't have a uniform view of what the range of this parameter should be...)
Thanks, and feel free to close.
ETA: I really appreciate what you've done with Boltz-1. Valuable work.
@MattBrauer Are you sure about this? I thought the whole point of putting it in the b-factor was for mol* and other visualizers.
See attached screenshot. Mol* is evidently taking the pLDDT values from the _ma_qa_metric_local loop, rather than from the b-factor entries.
This might be new behavior though.