Hydrogen orientations differ slightly between Reduce and Reduce2

[russell-taylor]

Team,

The hydrogens attached to nd2basn c 51 are at different orientations in Reduce and Reduce2, they are aligned with the ray from cg to cb in Reduce2 but with the ray from cg to od1 in Reduce. This is also true for basn d 51 and (with a much smaller difference between them) in asn d 137. In asn c 68, the Reduce2 hydrogens are not aligned with either in its flipped configuration (presumably due to a difference in alignment and distorted geometry).

For basn d 51, Reduce2 leaves it unflipped, so the hydrogen placement is the one performed by hydrogenate.

When Reduce2 does a flip, it attempts to place the hydrogens in the plane of the N-C-O rather than the N-C-C, which will be inconsistent with their initial placement with respect to N-C-C by hydrogenate.

When the two planes N-Cg-Cb and N-Cg-Od1 disagree, which one should be followed? We'll want to make Reduce2 consistently follow the same one for both flipped and unflipped.

Thanks,

Russ

p.s. The Reduce (.orig) and Reduce2 (.new) PDB files are attached, with different flips performed by each (presumably due to the hydrogen angle discrepancy).

https://app.zenhub.com/files/298640964/040aa871-cee5-473e-b2f4-200b742515f1/download