diff --git a/prody/atomic/flags.py b/prody/atomic/flags.py index c3fcc2316..63768d466 100644 --- a/prody/atomic/flags.py +++ b/prody/atomic/flags.py @@ -148,7 +148,7 @@ 'pyrimidine': set(['CYT', 'C', 'THY', 'T', 'URA', 'U']), 'water': set(['HOH', 'DOD', 'WAT', 'TIP3', 'H2O', 'OH2', 'TIP', 'TIP2', - 'TIP4', 'SPC', 'SOL']), + 'TIP4', 'SPC']), 'ion': set(['AL', 'BA', 'CA', 'CD', 'CL', 'CO', 'CS', 'CU', 'CU1', 'CUA', 'HG', 'IN', 'IOD', 'K', 'MG', 'MN', 'MN3', 'NA', 'PB', 'PT', 'RB', @@ -503,7 +503,7 @@ def changeBackbone(flag, names): water indices `HOH`_ and `DOD`_ recognized by *PDB* and also WAT, TIP3, H2O, - OH2, TIP, TIP2, and TIP4 recognized by molecular dynamics (MD) force + OH2, TIP, TIP2, TIP4 and SPC recognized by molecular dynamics (MD) force fields. .. _HOH: http://www.pdb.org/pdb/ligand/ligandsummary.do?hetId=HOH @@ -511,7 +511,8 @@ def changeBackbone(flag, names): .. _DOD: http://www.pdb.org/pdb/ligand/ligandsummary.do?hetId=DOD Previously used water types HH0, OHH, and SOL conflict with other - compounds in the *PDB*, so are removed from the definition of this flag. + compounds in the *PDB*, so are removed from the definition of this flag + except SOL (restored) as compound SOL (L-sorbose) is only used 3 times. ion