align command won't work

[yakomaxa]

When executing "align protein1, protein2" the session crashes.

[yakomaxa]

Note that "super" runs.

[yakomaxa]

I guess this is because pymol cannot access permutation matrix.

[yakomaxa]

For reference, I cite original source code

https://github.com/schrodinger/pymol-open-source/blob/d59041b68ce95fc9f72c54a3cce72437fe679b3e/modules/pymol/fitting.py#L380

[hikarino-my]

This is because PYMOL_PATH environment variable is not set by guess_pymol_path.
https://github.com/schrodinger/pymol-open-source/blob/d59041b68ce95fc9f72c54a3cce72437fe679b3e/modules/pymol/__init__.py#L175
https://github.com/schrodinger/pymol-open-source/blob/d59041b68ce95fc9f72c54a3cce72437fe679b3e/modules/pymol/__init__.py#L207
PYMOL_PATH is usually /lib/python3.10/site-packages/pymol/pymol_path.
This will be created by install_pymol_path.
https://github.com/schrodinger/pymol-open-source/blob/d59041b68ce95fc9f72c54a3cce72437fe679b3e/setup.py#L198

So, adding pymol/pymol_path/data folder into pymol-2.6.0a0-cp39-cp39-emscripten_3_1_46_wasm32.whl will solve this.

I checked it by unzipping whl, adding data folder and re-zipping it.

[yakomaxa]

Thank you for suggesting the solution. I'll try your workaround when I have time. Your workaround will also solve some of other problem related to data directory.