PdbStructure passes element EP to PDBFile, rather than any extraParticleIdentifier

wrappers/python/simtk/openmm/app/internal/pdbstructure.py

@@ -797,7 +797,9 @@ class Atom(object):
         except ValueError: self.formal_charge = None
         # figure out atom element
         if self.element_symbol == extraParticleIdentifier:
-            self.element = self.element_symbol
+            self.element = 'EP'
+        elif not self.element_symbol and extraParticleIdentifier is None:
+            self.element = 'EP'
         else:
             try:
                 # Try to find a sensible element symbol from columns 76-77

wrappers/python/simtk/openmm/app/pdbfile.py

@@ -108,7 +108,7 @@ class PDBFile(object):
                         atomName = atomReplacements[atomName]
                     atomName = atomName.strip()
                     element = atom.element
-                    if element == extraParticleIdentifier:
+                    if element == 'EP':
                         element = None
                     elif element is None:
                         # Try to guess the element.