# hydrophobic interactions ------------------------- select :a and not nad define ~target selected select not selected and not solvent and not hetero define ~non_target selected select (~non_target and (carbon,sulfur,selenium) and within(4.0, (~target and (carbon,sulfur,selenium)))) define ~nontarget_phobic selected define ~aas within(group,~nontarget_phobic) select (~target and (carbon,sulfur,selenium) and within(4.0, (~non_target and (carbon,sulfur,selenium)))) define ~target_phobic selected select ~target_phobic or ~nontarget_phobic define ~all_phobic selected connect 4.5 (~target_phobic) (~nontarget_phobic) hbond modifyOrCreate color hbonds magenta hbonds off # hbonds -------------------------------- select :a and not nad define ~target selected select not selected and not solvent and not hetero define ~non_target selected select (~non_target and (oxygen, nitrogen) and within(3.5, (~target and (oxygen, nitrogen)))) define ~nontarget_hbonders selected define ~aas within(group,~nontarget_hbonders) select (~target and (oxygen, nitrogen) and within(3.5, (~non_target and (oxygen, nitrogen)))) define ~target_hbonders selected select ~target_hbonders or ~nontarget_hbonders define ~all_hbonders selected connect 3.5 (~target_hbonders) (~nontarget_hbonders) hbond modifyOrCreate color hbonds blue hbonds off