diff --git a/avogadro/qtplugins/applycolors/applycolors.cpp b/avogadro/qtplugins/applycolors/applycolors.cpp
index 4ca45fc4a7..28c5f66fd6 100644
--- a/avogadro/qtplugins/applycolors/applycolors.cpp
+++ b/avogadro/qtplugins/applycolors/applycolors.cpp
@@ -12,10 +12,12 @@
 #include <avogadro/core/vector.h>
 #include <avogadro/qtgui/molecule.h>
 
-#include <QStringList>
 #include <QAction>
 #include <QColorDialog>
 #include <QInputDialog>
+#include <QStringList>
+
+#include <QDebug>
 
 using namespace tinycolormap;
 
@@ -248,14 +250,14 @@ void ApplyColors::applyChargeColors()
 
   // populate the dialog to choose the model and colormap
   ChargeColorDialog dialog;
-  for (const auto &model : identifiers) {
+  for (const auto& model : identifiers) {
     auto name = Calc::ChargeManager::instance().nameForModel(model);
     dialog.modelCombo->addItem(name.c_str(), model.c_str());
   }
   dialog.exec();
   if (dialog.result() != QDialog::Accepted)
     return;
-  
+
   // get the model and colormap
   const auto model = dialog.modelCombo->currentData().toString().toStdString();
   const auto colormapName = dialog.colorMapCombo->currentText();
@@ -267,6 +269,12 @@ void ApplyColors::applyChargeColors()
   float maxCharge = 0.0f;
   auto charges =
     Calc::ChargeManager::instance().partialCharges(model, *m_molecule);
+  // check if the model string is already a partial charge type
+  if (m_molecule->partialChargeTypes().find(model) !=
+      m_molecule->partialChargeTypes().end()) {
+    charges = m_molecule->partialCharges(model);
+  }
+
   for (Index i = 0; i < numAtoms; ++i) {
     float charge = charges(i, 0);
     minCharge = std::min(minCharge, charge);
@@ -568,4 +576,4 @@ void ApplyColors::applyShapelyColors()
   m_molecule->emitChanged(QtGui::Molecule::Atoms);
 }
 
-} // namespace Avogadro
+} // namespace Avogadro::QtPlugins
diff --git a/avogadro/quantumio/orca.cpp b/avogadro/quantumio/orca.cpp
index 4a317db3f8..52c15598f6 100644
--- a/avogadro/quantumio/orca.cpp
+++ b/avogadro/quantumio/orca.cpp
@@ -60,14 +60,6 @@ bool ORCAOutput::read(std::istream& in, Core::Molecule& molecule)
     return false;
   }
 
-  // add the partial charges
-  if (m_partialCharges.size() > 0) {
-    for (auto it = m_partialCharges.begin(); it != m_partialCharges.end();
-         ++it) {
-      molecule.setPartialCharges(it->first, it->second);
-    }
-  }
-
   if (m_frequencies.size() > 0 &&
       m_frequencies.size() == m_vibDisplacements.size() &&
       m_frequencies.size() == m_IRintensities.size()) {
@@ -143,6 +135,17 @@ bool ORCAOutput::read(std::istream& in, Core::Molecule& molecule)
   basis->setMolecule(&molecule);
   load(basis);
 
+  // we have to do a few things *after* any modifications to bonds / atoms
+  // because those automatically clear partial charges and data
+
+  // add the partial charges
+  if (m_partialCharges.size() > 0) {
+    for (auto it = m_partialCharges.begin(); it != m_partialCharges.end();
+         ++it) {
+      molecule.setPartialCharges(it->first, it->second);
+    }
+  }
+
   molecule.setData("totalCharge", m_charge);
   molecule.setData("totalSpinMultiplicity", m_spin);
   molecule.setData("dipoleMoment", m_dipoleMoment);