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ReliaSolve / Molprobity2

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Probe: Include near contacts in the calculations for both Probe and Reduce #102

Closed russell-taylor closed 3 years ago

russell-taylor commented 3 years ago

Paper says that probe but not reduce gives favorable scores for near contacts

russell-taylor commented 3 years ago

Make this an option, but what should its default value be?

russell-taylor commented 3 years ago

Dave and Jane say to always include them with no option not to. The overall terms are designed for the inside terms to balance the outside terms, so not having them will not follow the Lennard-Jones-like curve

russell-taylor commented 3 years ago

Probe radius defaults to 0.25 Angstroms and is used in Probe to determine the partial and total solvent accessible surface and to determine if points are near. For Reduce, it is used to in a function that determines whether atoms are bumping (CollectBumping) but this function is never called; it is also added to the atom radii to determine which atoms are nearby and should be checked.

In Reduce, the probe radius defaults to 0, which means that it is hit or miss whether further neighbor atoms will be considered (can depend on maximum radius of all atoms found in some cases), which means that not all near-miss dots are considered.

russell-taylor commented 3 years ago

The time taken for reduce -FLIP -RADIUS#.# varies as follows:

Radius 0.0 (default): 2m3.6s Radius 0.25 (Probe default): 2m45.7s Radius 0.5: 3m27.9s

russell-taylor commented 3 years ago

Added to main repository, including fixes for bugs found when implementing.