Closed russell-taylor closed 2 years ago
Note: The determination of C=O is done in fixupHeavyAtomElementType() in Reduce, not in the original name-based look-up.
1.7 that Reduce is doing is not the right answer, it should be the same as probe
This is the backbone Carbonyl -- " C " in the backbone, so should be easy to check
These are also found in other locations -- sidechain chemistry sometimes matches the backbone
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.
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.
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.