Determine what radius to use for C=O (carbonyl) atoms

[russell-taylor]

Probe has an adjustable dot point set for C=O Carbonyl atoms, which supports a command-line settable CORadScale, which converts it from 1.75 to 1.65 angstrom radius by default -- can we ignore -COSCALE?

There is a comment in Reduce from 7/3/98 JMW saying that the C=O radius changes from 1.75 to 1.65 but there is no corresponding 1.65 in the code, and the table entry for C=O specifies 1.70. It was changed in a later commit.

We'll need to decide what to do for the CCTBX-native Probe VDW table and also perhaps modify this in CCTBX proper.

[russell-taylor]

Note: The determination of C=O is done in fixupHeavyAtomElementType() in Reduce, not in the original name-based look-up.

[russell-taylor]

1.7 that Reduce is doing is not the right answer, it should be the same as probe

• Make it a multiplier that applies to both electron-cloud and neutron distance
• Enable a Phil parameter to change the ratio in the CCTBX Probe/Reduce

This is the backbone Carbonyl -- " C " in the backbone, so should be easy to check

• This should definitely be changed to 1.65 for the hydrogen tests we do
• The Richardsons may not have looked at heavy atom contacts with these atoms. We may need to look at a distribution of contact distances in good structures to find out what to do in this case.

These are also found in other locations -- sidechain chemistry sometimes matches the backbone

• The Richardsons may not have looked at sidechain cases, so we don't know if these cases should change

[russell-taylor]

Both the electron-cloud and neutron distances were 1.70, so switched both to 1.65 in the CCTBX Reduce code that duplicates in Python the C++ code.

[russell-taylor]

Modified this in the ReliaSolve Reduce master, upgrading the version number to 4.8 and did a pull request into the rlabduke repository. Asked them when it is ready to merge.