diff --git a/avogadro/qtplugins/customelements/customelements.cpp b/avogadro/qtplugins/customelements/customelements.cpp
index 6a561056fb..2d3342b227 100644
--- a/avogadro/qtplugins/customelements/customelements.cpp
+++ b/avogadro/qtplugins/customelements/customelements.cpp
@@ -16,11 +16,18 @@
 
 #include "customelements.h"
 
+#include <avogadro/qtgui/backgroundfileformat.h>
 #include <avogadro/qtgui/customelementdialog.h>
+#include <avogadro/qtgui/fileformatdialog.h>
 #include <avogadro/qtgui/molecule.h>
 
+#include <QtCore/QSettings>
+#include <QtCore/QThread>
 #include <QtWidgets/QAction>
+#include <QtWidgets/QMessageBox>
+#include <QtWidgets/QProgressDialog>
 
+using Avogadro::QtGui::BackgroundFileFormat;
 using Avogadro::QtGui::Molecule;
 
 namespace Avogadro {
@@ -28,16 +35,20 @@ namespace QtPlugins {
 
 CustomElements::CustomElements(QObject* parent_)
   : Avogadro::QtGui::ExtensionPlugin(parent_), m_molecule(nullptr),
-    m_reassignAction(new QAction(tr("Reassign &Custom Elements..."), this))
+    m_reassignUsingTool(nullptr), m_reassignFromFile(nullptr),
+    m_fileReadThread(nullptr), m_threadedReader(nullptr),
+    m_fileReadMolecule(nullptr), m_progressDialog(nullptr)
 {
-  connect(m_reassignAction, SIGNAL(triggered()), SLOT(reassign()));
+  m_reassignUsingTool = new QAction(tr("Reassign &Custom Elements..."), this);
+  m_reassignFromFile =
+    new QAction(tr("&Import Coordinate/Topology File..."), this);
+  connect(m_reassignUsingTool, SIGNAL(triggered()), SLOT(reassign()));
+  connect(m_reassignFromFile, SIGNAL(triggered()), SLOT(importMapFile()));
 
   updateReassignAction();
 }
 
-CustomElements::~CustomElements()
-{
-}
+CustomElements::~CustomElements() {}
 
 QString CustomElements::description() const
 {
@@ -46,7 +57,7 @@ QString CustomElements::description() const
 
 QList<QAction*> CustomElements::actions() const
 {
-  return QList<QAction*>() << m_reassignAction;
+  return QList<QAction*>() << m_reassignUsingTool << m_reassignFromFile;
 }
 
 QStringList CustomElements::menuPath(QAction*) const
@@ -86,9 +97,129 @@ void CustomElements::reassign()
   }
 }
 
+bool CustomElements::openFile(const QString& fileName, Io::FileFormat* reader)
+{
+  if (fileName.isEmpty() || reader == nullptr) {
+    delete reader;
+    return false;
+  }
+
+  QString ident = QString::fromStdString(reader->identifier());
+
+  // Prepare the background thread to read in the selected file.
+  if (!m_fileReadThread)
+    m_fileReadThread = new QThread(qobject_cast<QWidget*>(parent()));
+  if (m_threadedReader)
+    m_threadedReader->deleteLater();
+  m_threadedReader = new BackgroundFileFormat(reader);
+  if (m_fileReadMolecule)
+    m_fileReadMolecule->deleteLater();
+  m_fileReadMolecule = new Molecule(qobject_cast<QWidget*>(parent()));
+  m_fileReadMolecule->setData("fileName", fileName.toLocal8Bit().data());
+  m_threadedReader->moveToThread(m_fileReadThread);
+  m_threadedReader->setMolecule(m_fileReadMolecule);
+  m_threadedReader->setFileName(fileName);
+
+  // Setup a progress dialog in case file loading is slow
+  m_progressDialog = new QProgressDialog(qobject_cast<QWidget*>(parent()));
+  m_progressDialog->setRange(0, 0);
+  m_progressDialog->setValue(0);
+  m_progressDialog->setMinimumDuration(750);
+  m_progressDialog->setWindowTitle(tr("Reading File"));
+  m_progressDialog->setLabelText(
+    tr("Opening file '%1'\nwith '%2'").arg(fileName).arg(ident));
+  m_progressDialog->setCancelButton(nullptr);
+  connect(m_progressDialog, SIGNAL(canceled()), m_fileReadThread, SLOT(quit()));
+  connect(m_fileReadThread, SIGNAL(started()), m_threadedReader, SLOT(read()));
+  connect(m_threadedReader, SIGNAL(finished()), m_fileReadThread, SLOT(quit()));
+  connect(m_threadedReader, SIGNAL(finished()),
+          SLOT(backgroundReaderFinished()));
+
+  // Start the file operation
+  m_fileReadThread->start();
+  m_progressDialog->show();
+
+  return true;
+}
+
+void CustomElements::backgroundReaderFinished()
+{
+  QString fileName = m_threadedReader->fileName();
+  if (m_progressDialog->wasCanceled()) {
+    delete m_fileReadMolecule;
+  } else if (m_threadedReader->success()) {
+    if (!fileName.isEmpty()) {
+      m_fileReadMolecule->setData("fileName", fileName.toLocal8Bit().data());
+    } else {
+      m_fileReadMolecule->setData("fileName", Core::Variant());
+    }
+    setMapFromMolecule(m_fileReadMolecule);
+  } else {
+    QMessageBox::critical(qobject_cast<QWidget*>(parent()), tr("File error"),
+                          tr("Error while reading file '%1':\n%2")
+                            .arg(fileName)
+                            .arg(m_threadedReader->error()));
+    delete m_fileReadMolecule;
+  }
+  m_fileReadThread->deleteLater();
+  m_fileReadThread = nullptr;
+  m_threadedReader->deleteLater();
+  m_threadedReader = nullptr;
+  m_fileReadMolecule = nullptr;
+  m_progressDialog->hide();
+  m_progressDialog->deleteLater();
+  m_progressDialog = nullptr;
+}
+
+void CustomElements::setMapFromMolecule(QtGui::Molecule* mol)
+{
+  if (mol->atomCount() != m_molecule->atomCount()) {
+    QMessageBox::critical(
+      qobject_cast<QWidget*>(parent()), tr("Error"),
+      tr("Atom count mismatch.\nExpected %1 atoms, found %2.")
+        .arg(m_molecule->atomCount())
+        .arg(mol->atomCount()));
+  } else {
+    size_t n = m_molecule->atomCount(), i;
+    for (i = 0; i < n; ++i) {
+      m_molecule->atom(i).setAtomicNumber(mol->atom(i).atomicNumber());
+    }
+    n = m_molecule->bondCount();
+    for (i = 0; i < n; ++i) {
+      m_molecule->addBond(mol->bond(i).atom1(), mol->bond(i).atom2(),
+                          mol->bond(i).order());
+    }
+    m_molecule->emitChanged(Molecule::Atoms | Molecule::Modified);
+  }
+}
+
+void CustomElements::importMapFile()
+{
+  QSettings settings;
+  QString dir = settings.value("MainWindow/lastOpenDir").toString();
+
+  QtGui::FileFormatDialog::FormatFilePair reply =
+    QtGui::FileFormatDialog::fileToRead(qobject_cast<QWidget*>(parent()),
+                                        tr("Open Molecule"), dir);
+
+  if (reply.first == NULL) // user cancel
+    return;
+
+  dir = QFileInfo(reply.second).absoluteDir().absolutePath();
+  settings.setValue("MainWindow/lastOpenDir", dir);
+
+  if (!openFile(reply.second, reply.first->newInstance())) {
+    QMessageBox::information(
+      qobject_cast<QWidget*>(parent()), tr("Cannot open file"),
+      tr("Can't open supplied file %1").arg(reply.second));
+  }
+}
+
 void CustomElements::updateReassignAction()
 {
-  m_reassignAction->setEnabled(m_molecule && m_molecule->hasCustomElements());
+  m_reassignUsingTool->setEnabled(m_molecule &&
+                                  m_molecule->hasCustomElements());
+  m_reassignFromFile->setEnabled(m_molecule && m_molecule->atomCount());
 }
 
 } // namespace QtPlugins
diff --git a/avogadro/qtplugins/customelements/customelements.h b/avogadro/qtplugins/customelements/customelements.h
index 00c215e12d..27cd029528 100644
--- a/avogadro/qtplugins/customelements/customelements.h
+++ b/avogadro/qtplugins/customelements/customelements.h
@@ -19,7 +19,15 @@
 
 #include <avogadro/qtgui/extensionplugin.h>
 
+class QProgressDialog;
+class QThread;
+
 namespace Avogadro {
+
+namespace QtGui {
+class BackgroundFileFormat;
+}
+
 namespace QtPlugins {
 
 /**
@@ -43,12 +51,21 @@ public slots:
 private slots:
   void moleculeChanged(unsigned int changes);
   void reassign();
+  void importMapFile();
+  void backgroundReaderFinished();
 
 private:
   QtGui::Molecule* m_molecule;
-  QAction* m_reassignAction;
+  QAction* m_reassignUsingTool;
+  QAction* m_reassignFromFile;
+  QThread* m_fileReadThread;
+  QtGui::BackgroundFileFormat* m_threadedReader;
+  QtGui::Molecule* m_fileReadMolecule;
+  QProgressDialog* m_progressDialog;
 
   void updateReassignAction();
+  bool openFile(const QString& fileName, Io::FileFormat* reader);
+  void setMapFromMolecule(QtGui::Molecule* mol);
 };
 
 } // namespace QtPlugins