Hey Lorenz!

Maybe something like this works? runscript /Users/artem.kushner/Desktop/threshold90.py

```python
from chimerax.map import Volume
from chimerax.core.commands import run

def thresh_90_all():
    for model in session.models:
        if isinstance(model, Volume):
            max_val = model.data.matrix().max()
            threshold_90 = 0.9 * max_val
            run(session, f"volume #{model.id_string} level {threshold_90}")
            print(f"Map '{model.name}': max={max_val:.2f}, 0.9 threshold is {threshold_90:.3f}")

thresh_90_all()
```




On Tue, Aug 26, 2025 at 5:25 PM Grundmann,Lorenz Emanuel via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX-Team and all,


I want to visualize multiple cryoEM maps in a comparative manner. Therefore, I would like to display them with a threshold level of e.g. 90% their maximum voxel value.

Is this possible in chimerax? Any help would be greatly appreciated. Thank you.


Best,
Lorenz
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