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Computational Crystallography Toolbox
https://cctbx.github.io
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Add the Phantom Hydrogen radius and distance changes to Probe2 and Reduce2 #171

Closed russell-taylor closed 2 years ago

russell-taylor commented 2 years ago

See if there are different values in Reduce for H placement on an OH that is not a Phantom Hydrogen.

Compare this against the chem_data value and see if they agree. Also compare this against the OH distance of 0.84 value for electron-cloud and 0.98 value for neutron maps that Jane found from her paper.

We'll use the 1.05 radius for electron cloud and 1.0 for neutron maps for the added Hydrogen.

Let Jane know

russell-taylor commented 2 years ago

(done) The Phantom Hydrogen placement code in Probe already has an @todo that we may want to replace the 1.0 values it used with these; we'll want to replace them throughout.

russell-taylor commented 2 years ago

(done) Re-run the regression test code for Probe2 and modify the expected output to match the new values.

russell-taylor commented 2 years ago

(done) Before adjusting this, see why the Phantom Hydrogen is not backing off when the acceptor atom approaches. See the behavior when running Probe or Probe2 on oo.pdb. How is it that it was backing off on some of the other models for water-water and water-other interactions?

1xso has some that are between waters that are slightly shorter. Fe_1brf_rubredoxin_0.new.self.kin has some that are very short between waters.

Hmm... when we bring the Oxygen all the way back to 1A from the Water in Probe, the Phantom Hydrogen dots show up again on the Oxygen and indicate that it has backed up to the origin even though the line showing the Hydrogen bond is 1A long. The dots are all 1.05A from the Oxygen. For Probe2, we get strong collisions between the heavy atoms and no Hydrogen overlap dots when we are that far in.

The H dots are only 0.766 from the 1A Hydrogen line end, so the PH is being pulled back.

We appear to be seeing all of the placed hydrogens on all models in all models. Indeed, it is being reported before the 'group dominant' command.

Adjusted the way the output is handled to provide master control for the bonds and to also group them by model.

russell-taylor commented 2 years ago

Added in Probe version 2.1.0.