[chimerax-users] MLP value of the ASP and GLU carboxylate

[Zhijie Li]

Hello,


I noticed that the lipophilic atomic potentials of OD2 and OE2 are set to very positive values in mlp.py:


 'ASP': {'C': -0.54,
         'CA': 0.02,
         'CB': 0.45,
         'CG': 0.54,
         'N': -0.44,
         'O': -0.68,
         'OD1': -0.68,
         'OD2': 0.53}
 'GLU': {'C': -0.54,
         'CA': 0.02,
         'CB': 0.45,
         'CD': -0.54,
         'CG': 0.45,
         'N': -0.44,
         'O': -0.68,
         'OE1': -0.68,
         'OE2': 0.53},


As as result the hydrophobic surface representation always show hydrophobic patchs on the carboxylates, which look quite odd to me.   Is there a justification for this setting?  In addition, aren't the two oxygens in the carboxylate equal considerting that they are in resonance?


Zhijie
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