Closed caleblareau closed 9 months ago
I have now added this. This gets saved alongside the other scores like pae_interaction
. There is binder_aligned_rmsd
which is the RMSD of the predicted binder aligned to the initial design model of the binder. And there is also target_aligned_rmsd
which is the RMSD of the predicted binder when the two complexes are aligned on the target structure, this is a more stringent alignment metric and is the same as what is calculated in af2_complex_rmsd
awesome-- thanks for adding the feature and clarifying the metric.
@nrbennet Just to clarify
target_aligned_rmsd
You first align the initial and final targets, and then calculate the RMSD of the binder only? So it is more stringent because if they are actually far away from each other (i.e not binding) then the score will be large? binder_aligned_rmsd
You first align binders and then calculate the rmsd of the binders only?
Apologies if I missed this somewhere, but is there an easy way to get the RMSD following the execution of the
dl_binder_design/af2_initial_guess/predict.py
script? Or does that require running another piece of the workflow? I see the various plddt and pae outputs in the.silent
file but not theaf2_complex_rmsd
metric discussed in the methods. Thanks!