With 7c31_single_hydrogen_rotatorFH.pdb (attached), we get very different potential dot counts and surface areas.
The Probe2 command line was probe2.py ignore_lack_of_explicit_hydrogens=True outputs/7c31_single_hydrogen_rotator.orig.pdb output.filename=outputs/7c31_single_hydrogen_rotator.orig.txt output.overwrite=True output.count_dots=True and the Probe1 command line was probe -mc -count -self "ogt10" c:\tmp\7c31shrFH.pdb.
With 7c31_single_hydrogen_rotatorFH.pdb (attached), we get very different potential dot counts and surface areas.
The Probe2 command line was
probe2.py ignore_lack_of_explicit_hydrogens=True outputs/7c31_single_hydrogen_rotator.orig.pdb output.filename=outputs/7c31_single_hydrogen_rotator.orig.txt output.overwrite=True output.count_dots=Trueand the Probe1 command line wasprobe -mc -count -self "ogt10" c:\tmp\7c31shrFH.pdb.https://app.zenhub.com/files/298640964/870c5873-b540-479c-b883-dab5a9f1d301/download