I'm sorry for the trouble! You can check to see if ligand fitting is generally working on your computer with a test that comes with your phenix installation. You can type in a command window:
phenix_regression.list LigandFit_std
This will print out something like this:
Listing of available Phenix regression tests
Total of 1705 tests available.
Listing 1 tests matching of the following strings: LigandFit_std
libtbx.python "/Users/terwill/unix/PHENIX/build_2020-04-24/modules/phenix_regression/wizards/LigandFit_tests/test_LigandFit_std/tst_LigandFit_std.py"
Try running the test that is printed out...it should run and say "OK" when it is done. If not...let me know!
Then to address your question more directly...by "recently", do you mean that you have a new version of Phenix, or new data, or both?
If new data, best thing to try is rerun with old data, then change things until you are running with new data and see when something fails. If that doesn't show what the problem is, I'm happy to help (if you send the data and log file I can debug it here)
If you have a new version of Phenix and the same data that worked with an old version does not work any more, let me know as above.
If you have a new version of Phenix and new data, can you run with old data, old version, then old/new, then new/old, then new/new and see which one causes the problem.
Thanks!
-Tom T