diff --git a/pkgs/applications/science/chemistry/pymol/default.nix b/pkgs/applications/science/chemistry/pymol/default.nix
index 1733ba2f236c..295ac7e14cb2 100644
--- a/pkgs/applications/science/chemistry/pymol/default.nix
+++ b/pkgs/applications/science/chemistry/pymol/default.nix
@@ -2,7 +2,6 @@
 , lib
 , fetchFromGitHub
 , makeDesktopItem
-, python3
 , python3Packages
 , netcdf
 , glew
@@ -50,7 +49,7 @@ python3Packages.buildPythonApplication rec {
 
   postPatch = ''
     substituteInPlace setup.py \
-      --replace-fail "self.install_libbase" '"${placeholder "out"}/${python3.sitePackages}"'
+      --replace-fail "self.install_libbase" '"${placeholder "out"}/${python3Packages.python.sitePackages}"'
   '';
 
   build-system = [
@@ -63,10 +62,10 @@ python3Packages.buildPythonApplication rec {
 
   postInstall = with python3Packages; ''
     wrapProgram $out/bin/pymol \
-      --prefix PYTHONPATH : ${lib.makeSearchPathOutput "lib" python3.sitePackages [ pyqt5 pyqt5.pyqt5-sip ]}
+      --prefix PYTHONPATH : ${lib.makeSearchPathOutput "lib" python3Packages.python.sitePackages [ pyqt5 pyqt5.pyqt5-sip ]}
 
     mkdir -p "$out/share/icons/"
-    ln -s $out/${python3.sitePackages}/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg"
+    ln -s $out/${python3Packages.python.sitePackages}/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg"
   '' + lib.optionalString stdenv.hostPlatform.isLinux ''
     cp -r "${desktopItem}/share/applications/" "$out/share/"
   '';
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 16102d8ee87b..1f5d7d009ecf 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -36819,7 +36819,9 @@ with pkgs;
 
   pdb2pqr = with python3Packages; toPythonApplication pdb2pqr;
 
-  pymol = callPackage ../applications/science/chemistry/pymol { };
+  pymol = callPackage ../applications/science/chemistry/pymol {
+    python3Packages = python311Packages;
+  };
 
   quantum-espresso = callPackage ../applications/science/chemistry/quantum-espresso {
     hdf5 = hdf5-fortran;