diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/by-name/ro/root/package.nix
similarity index 99%
rename from pkgs/applications/science/misc/root/default.nix
rename to pkgs/by-name/ro/root/package.nix
index 7352c16d312e..19d61c405c76 100644
--- a/pkgs/applications/science/misc/root/default.nix
+++ b/pkgs/by-name/ro/root/package.nix
@@ -37,7 +37,7 @@
 , nlohmann_json
 , pkg-config
 , procps
-, python
+, python3
 , which
 , xxHash
 , zlib
@@ -104,7 +104,7 @@ stdenv.mkDerivation rec {
     patchRcPathCsh
     patchRcPathFish
     patchRcPathPosix
-    python.pkgs.numpy
+    python3.pkgs.numpy
     tbb
     xrootd
   ]
diff --git a/pkgs/applications/science/misc/root/setup-hook.sh b/pkgs/by-name/ro/root/setup-hook.sh
similarity index 100%
rename from pkgs/applications/science/misc/root/setup-hook.sh
rename to pkgs/by-name/ro/root/setup-hook.sh
diff --git a/pkgs/applications/science/misc/root/sw_vers.patch b/pkgs/by-name/ro/root/sw_vers.patch
similarity index 100%
rename from pkgs/applications/science/misc/root/sw_vers.patch
rename to pkgs/by-name/ro/root/sw_vers.patch
diff --git a/pkgs/applications/science/misc/root/tests/default.nix b/pkgs/by-name/ro/root/tests/default.nix
similarity index 100%
rename from pkgs/applications/science/misc/root/tests/default.nix
rename to pkgs/by-name/ro/root/tests/default.nix
diff --git a/pkgs/applications/science/misc/root/tests/test-thisroot.nix b/pkgs/by-name/ro/root/tests/test-thisroot.nix
similarity index 100%
rename from pkgs/applications/science/misc/root/tests/test-thisroot.nix
rename to pkgs/by-name/ro/root/tests/test-thisroot.nix
diff --git a/pkgs/applications/science/misc/root/disable_libc_dicts_root5.patch b/pkgs/by-name/ro/root5/disable_libc_dicts_root5.patch
similarity index 100%
rename from pkgs/applications/science/misc/root/disable_libc_dicts_root5.patch
rename to pkgs/by-name/ro/root5/disable_libc_dicts_root5.patch
diff --git a/pkgs/applications/science/misc/root/5.nix b/pkgs/by-name/ro/root5/package.nix
similarity index 100%
rename from pkgs/applications/science/misc/root/5.nix
rename to pkgs/by-name/ro/root5/package.nix
diff --git a/pkgs/applications/science/misc/root/purify_include_paths_root5.patch b/pkgs/by-name/ro/root5/purify_include_paths_root5.patch
similarity index 100%
rename from pkgs/applications/science/misc/root/purify_include_paths_root5.patch
rename to pkgs/by-name/ro/root5/purify_include_paths_root5.patch
diff --git a/pkgs/applications/science/misc/root/root5-python311-fix.patch b/pkgs/by-name/ro/root5/root5-python311-fix.patch
similarity index 100%
rename from pkgs/applications/science/misc/root/root5-python311-fix.patch
rename to pkgs/by-name/ro/root5/root5-python311-fix.patch
diff --git a/pkgs/by-name/ro/root5/setup-hook.sh b/pkgs/by-name/ro/root5/setup-hook.sh
new file mode 100644
index 000000000000..7affd21012eb
--- /dev/null
+++ b/pkgs/by-name/ro/root5/setup-hook.sh
@@ -0,0 +1,19 @@
+thisroot () {
+    # Workaround thisroot.sh dependency on man
+    if [ -z "${MANPATH-}" ]; then
+        MANPATH=:
+    fi
+    local oldOpts="-u"
+    shopt -qo nounset || oldOpts="+u"
+    set +u
+    source @out@/bin/thisroot.sh
+    set "$oldOpts"
+}
+
+postHooks+=(thisroot)
+
+addRootIncludePath() {
+    addToSearchPath ROOT_INCLUDE_PATH $1/include
+}
+
+addEnvHooks "$targetOffset" addRootIncludePath
diff --git a/pkgs/applications/science/misc/root/sw_vers_root5.patch b/pkgs/by-name/ro/root5/sw_vers_root5.patch
similarity index 100%
rename from pkgs/applications/science/misc/root/sw_vers_root5.patch
rename to pkgs/by-name/ro/root5/sw_vers_root5.patch
diff --git a/pkgs/development/libraries/physics/hepmc3/default.nix b/pkgs/development/libraries/physics/hepmc3/default.nix
index c622d7562001..f7f281af74f3 100644
--- a/pkgs/development/libraries/physics/hepmc3/default.nix
+++ b/pkgs/development/libraries/physics/hepmc3/default.nix
@@ -11,7 +11,7 @@ let
   pythonVersion = with lib.versions; "${major python.version}${minor python.version}";
   withPython = python != null;
   # ensure that root is built with the same python interpreter, as it links against numpy
-  root_py = if withPython then root.override { inherit python; } else root;
+  root_py = if withPython then root.override { python3 = python; } else root;
 in
 
 stdenv.mkDerivation rec {
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 1ca157fd8a65..f6a847b642dd 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -18234,12 +18234,6 @@ with pkgs;
 
   ns-3 = callPackage ../development/libraries/science/networking/ns-3 { python = python3; };
 
-  root = callPackage ../applications/science/misc/root {
-    python = python3;
-  };
-
-  root5 = lowPrio (callPackage ../applications/science/misc/root/5.nix { });
-
   rink = callPackage ../applications/science/misc/rink {
     inherit (darwin.apple_sdk.frameworks) Security;
   };