Thomas Holder

The problem is that the models are not homogeneous. ATOM 1 from the first model is different from ATOM 1 in the second model, and bonds are specified by atom...

The easiest way to load this is to replace `MODEL` by `HEADER` (search and replace using your favorite text editor), then PyMOL will load 5 independent objects.

I like this suggestion. Something similar exists already: [cmd.extendaa](https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/commanding.py#L578). Using type-annotations looks nicer of course. What do you mean by "automated usage help"?

Hi Pedro - does it work if you first activate the conda environment? The bundle contains a `Conda-Prompt.bat` launcher, can you try that? _EDIT: FYI, activating the environment will add...

Thanks a lot @pslacerda for the env comparison. PyMOLWin.exe is a very thin wrapper which does: - unsetting environment variables which are known to cause problems (`TCL_LIBRARY`, `PYMOL_PATH`, `PYMOL_DATA`, `PYTHONHOME`,...

Didn't find anything. This code works reliably for me, no matter how PyMOL was launched: ```python args = ['install', 'mypackage'] import subprocess, sys process = subprocess.Popen( [sys.executable, '-m', 'pip', '--disable-pip-version-check']...

I was about to suggest `transparency_mode` 1 or 3 (multi-layer), but I hit a different (maybe related) bug, some spheres become fully opaque: 

Can reproduce in PyMOL 1.8.2 but not in 1.8.0. However, there are almost no changes to the ray tracer or the spheres representation between those versions :thinking:

In my understanding, MMCIFIO is doing the right thing. The PDB chain id is preserved as `auth_asym_id`, this is consistent with .pdb and .cif downloads from rcsb.org. E.g. `chain=H` from...

Which "original file"? The `pdb_file`? It does not contain a `label_asym_id` equivalent.