[PyMOL] Compatibility Issue: Cartoon Representation Disappears After Ray Tracing When Opening Old PSE Files in New PyMOL Versions

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Dear PyMOL Community,

I am encountering a version compatibility issue with PyMOL and would appreciate your insights. The problem occurs when opening legacy session files (.pse) created in older PyMOL versions in newer releases (3.1.5.1).

Observed Behavior:


In the original environment (older PyMOL):


Session contains objects with simultaneous cartoon and surface representations



Both have active transparency settings



ray command correctly renders both semi-transparent elements(ray by original version.png)




In newer PyMOL versions (3.1.5.1):



Session loads without errors



ray command execution causes cartoon representation to completely disappear(ray by new version.png)



surface and other representations (e.g., sticks) render normally



Transparency settings appear preserved in GUI but ignored during rendering



The following prompt message appears when loading the PSE file:
PyMOL(TM) 3.1.5.1 - Incentive Product
Copyright (C) Schrodinger, LLC
This Executable Build integrates and extends Open-Source PyMOL.
Detected OpenGL version 2.1. Shaders available.


 Tessellation shaders not available
 Detected GLSL version 1.20.
 OpenGL graphics engine:
  GL_VENDOR:   Apple
  GL_RENDERER: Apple M2
  GL_VERSION:  2.1 Metal - 76.3
 License Expiry date: 2025-12-01 
Appreciate any guidance on resolving this rendering discrepancy while maintaining visualization integrity across versions.

Best regards,
[eva]