Index: pymol-open-source-2.3.0/layer5/main.cpp
===================================================================
--- pymol-open-source-2.3.0.orig/layer5/main.cpp	(revision 4149)
+++ pymol-open-source-2.3.0/layer5/main.cpp	(working copy)
@@ -34,6 +34,11 @@
 #include <dlfcn.h>
 #endif
 
+/* Used for WM_CLASS hack */
+#include <GL/glx.h>
+#include <X11/Xutil.h>
+#include <X11/Xlib.h>
+
 #include "PyMOLGlobals.h"
 #include "PyMOL.h"
 #include "PyMOLOptions.h"
@@ -1025,7 +1030,52 @@
 
 }
 
+/*========================================================================*/
 
+static int IgnoreError(Display *display, XErrorEvent *theEvent)
+{
+  return 0;
+}
+
+static int MainCreateWindow(const char *title)
+{
+  int window;
+  Display *display;
+  GLXDrawable xwin;
+  XClassHint *hint;
+  XErrorHandler oldErrorHandler;
+
+  window = p_glutCreateWindow(title);
+
+  /* Hack to set WM_CLASS hint
+   * This assumes the current drawable is the window we just created which is
+   * a detail of the GLUT implementation. There is no way of getting the XID of
+   * a window using GLUT alone. */
+
+  /* Disable the error handler so in case the assumption fails the program still
+   * works */
+  oldErrorHandler = XSetErrorHandler(IgnoreError);
+
+  display = glXGetCurrentDisplay();
+  if (display) {
+    hint = XAllocClassHint();
+    if (hint) {
+      hint->res_name = "pymol";
+      hint->res_class = "Pymol";
+      xwin = glXGetCurrentDrawable();
+      XSetClassHint(display, xwin, hint);
+      XFree(hint);
+    }
+    /* Make sure all errors are handled before restoring the old error handler */
+    XFlush(display);
+    XSync(display, False);
+  }
+
+  XSetErrorHandler(oldErrorHandler);
+
+  return window;
+}
+
 /*========================================================================*/
 static void MainInit(PyMOLGlobals * G)
 {
@@ -1104,7 +1154,7 @@
       p_glutInitWindowSize(640, 480);
       p_glutInitDisplayMode(P_GLUT_RGBA | P_GLUT_DEPTH | P_GLUT_DOUBLE);
       if(p_glutGet(P_GLUT_DISPLAY_MODE_POSSIBLE)) {
-        theWindow = p_glutCreateWindow("PyMOL Viewer");
+        theWindow = MainCreateWindow("PyMOL Viewer");
         p_glutFullScreen();
         p_glutDestroyWindow(theWindow);
       }
@@ -1604,7 +1654,7 @@
 
       p_glutInitWindowSize(G->Option->winX, G->Option->winY);
 
-      theWindow = p_glutCreateWindow("PyMOL Viewer");
+      theWindow = MainCreateWindow("PyMOL Viewer");
 
       if(G->Option->full_screen) {
         p_glutFullScreen();