Upstream just committed a workaround to avoid these crashes as this is a
non-fatal OpenGL error and doesn't prevent the APBS Electrostatic plugin
from rendering the electrostatic surfaces as long as the terminate is
avoided...

https://github.com/schrodinger/pymol-open-
source/commit/8efe9948200ec07e565ff7fb385a3786e3121de9

From 8efe9948200ec07e565ff7fb385a3786e3121de9 Mon Sep 17 00:00:00 2001
From: Jarrett Johnson <[email protected]>
Date: Fri, 4 Apr 2025 11:27:40 -0400
Subject: [PATCH] Dont crash on GL error

---
 layer0/GraphicsUtil.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/layer0/GraphicsUtil.cpp b/layer0/GraphicsUtil.cpp
index e2f2f9766..7ab9d1bd7 100755
--- a/layer0/GraphicsUtil.cpp
+++ b/layer0/GraphicsUtil.cpp
@@ -45,7 +45,6 @@ bool CheckGLErrorOK(PyMOLGlobals* G, std::string_view 
errString)
     } else {
       printf("GL_ERROR : 0x%04x %s\n", err, errString.data());
     }
-    std::terminate();
 #endif
   }
   return err == 0;

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https://bugs.launchpad.net/bugs/2106189

Title:
  pymol-3.1.0+dfsg wayland regressions

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