Hi, I apologize sincerely since I imagine this comes up often on the mailing list.

I'm basically wondering if it's possible to import just the `core` functionality from a chimerax installation into a custom python environment and bypass the GUI and the binary completely.

Example: I don't think it matters whether it's linux, mac, or source build, but let's say i installed a clean chimerax via my package manager (`yay i chimerax`). It's at `/opt/chimerax` and looks like this:

(venv) ᢹ ritual.rtviii[ /opt/chimerax ] ls -la
total 24
drwxr-xr-x 6 root root 4096 May 1 16:08 .
drwxr-xr-x 10 root root 4096 May 1 16:58 ..
drwxr-xr-x 4 root root 4096 May 1 16:51 bin
drwxr-xr-x 8 root root 4096 May 1 16:51 include
drwxr-xr-x 4 root root 4096 May 1 16:51 lib
drwxr-xr-x 6 root root 4096 May 1 16:51 share

If I launch `chimerax` at the command line, i get a functional GUI etc. It works. I create a fresh custom `virtualenv` with the same python that this chimerax ships:

virtualenv --python='/opt/chimerax/bin/python3.11' venv

Then i do something ugly in the name of science: i symlink the chimerax folder from the installation into my virtualenv:

ln -s /opt/chimerax/lib/python3.11/site-packages/chimerax /home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax

i also tried:
for P in $(ls /opt/chimerax/lib/python3.11/site-packages/); do ln -s /opt/chimerax/lib/python3.11/site-packages/$P /home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/$P; done

This enables me to import chimerax modules into my python code that uses this virtualenv:

```/home/rtviii/dev/try_chimerax/test.py

from chimerax.core.commands import run
from chimerax.core.session import Session
import chimerax.mmcif.mmcif as mmcif

s = Session("Hi")
print(s)
run(s,"open 1ubq.cif")

```

However, this is where i'm struggling a little to use any actual functionality (especially interested in cutting, merging structures and operations treating density maps and mmcif structures) because the Session wouldn't initialize well:

```
<chimerax.core.session.Session object at 0x70472673b5d0>
NOTE: Traceback (most recent call last):
  File "/home/rtviii/dev/try_chimerax/test.py", line 9, in <module>
    run(s,"open 1ubq.cif")
  File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
    results = command.run(text, log=log, return_json=return_json)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2849, in run
    _compute_available_commands(session)
  File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2431, in _compute_available_commands
    ts.register_available_commands(session.logger)
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute'register_available_commands'
BUG: AttributeError: 'NoneType' object has no attribute'register_available_commands'
File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2431, in _compute_available_commands
ts.register_available_commands(session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_See log for complete Python traceback._
```

I had some success with a similar approach in PyMol in this regard, but can't quite get this to work in ChimeraX. I really appreciate any advice for achieving this scripting decoupling from GUI/binary if that's possible at all:

- either how to "pull in" ChimeraX library code properly (i realize mine is an ugly hack)

- how to use library code otherwise

- how to bypass the dependence of a lot of commands on the Session object or how to initialize it outside of the gui properly: an example of how to use selections to open a local density map and perform a smoothing, for example.

Kindest regards and huge thanks for the monumental application.

Artem,

UBC Vancouver