Cartoon representation disappear in extracted molecules when chain IDs are not set

[ErikPoppleton]

Thank you for keeping PyMol available open source! I have encountered an issue with the cartoon representations.

Describe the bug

When loading a file without chain identifiers (for example, a Gromacs .gro file) the cartoon representation is initially drawn well:

You can change the cartoon representation and everything works as expected:

However, if you extract the molecule, the cartoon representation breaks in a really strange way:

This does not happen if you set chain identifiers with this script BEFORE you run extract (doing it after doesn't fix anything):

I have tested this with both proteins and RNA. With proteins all strands except the first one disappear, with RNA, the behavior is inconsistent. Sometimes backbones disappear, sometimes parts of structures disappear.

Here's an RNA structure in .gro format to test with (extension changed to .txt so GitHub will accept it)
RNA_test.txt

Expected behavior

Cartoon representation shouldn't be different when atoms have been extracted to a new object. Also it was very challenging to create chain identifiers to fix the problem, but that's a feature request more than a bug.

Environment

• PyMOL Version: 3.2.0a
• PyMOL Source: Compiled from this repo
• Operating System: MacOS 15.5

[JarrettSJohnson]

Thank you for the detailed report! I could also reproduce this behavior after running sort immediately following loading of the file. I'll investigate soon.

[JarrettSJohnson]

For now, if you don't want any disruption in your reps from this, use set retain_order, 1 before issuing extract.