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ReliaSolve / Molprobity2

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Compare hydrogen placement between old and new probe #160

Closed russell-taylor closed 1 year ago

russell-taylor commented 3 years ago

On 1xso with the equivalent of probe -kin -quiet -dumpatominfo "WATER" -DUMPH2O F:\data\Richardsons\1xso.pdb the old code finds a few phantoms that the new does not. The new finds many more than the old; this is in large part due to the 1.05 vs. 1.0 (1+1=2) radius that is used between the two codes.

russell-taylor commented 3 years ago

There are two phantoms found by the old that are not found by the new. Uncommenting the line in AtomTypes.py that adds the carbons in the Histidine back into the _AromaticTable doesn't change this.

russell-taylor commented 3 years ago

It seems likely that this is because some of the atoms are not marked as acceptors in CCTBX that were in Probe. Run ./compare.sh in new_reduce_regression to get a list of these for fragment files.