id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20825 align command warns about complex values discarding imaginary part Eric Pettersen Tom Goddard "Begin forwarded message: From: Eric Pettersen Subject: align_points ComplexWarning Date: August 5, 2026 at 2:51:57 PM PDT To: Tom Goddard Hi Tom, Whilst working on the Metal Geometry tool I noted that chimerax.geometry.align_points() sometimes elicits a ComplexWarning, e.g.: /Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-packages/chimerax/geometry/align.py:68: ComplexWarning: Casting complex values to real discards the imaginary part tf[:,:3] = R /Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-packages/chimerax/geometry/align.py:69: ComplexWarning: Casting complex values to real discards the imaginary part tf[:,3] = ref_center - dot(R,center) /Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-packages/chimerax/geometry/align.py:76: ComplexWarning: Casting complex values to real discards the imaginary part rms = sqrt(rms2/len(Si)) if rms2 >= 0 else 0 So I inserted a print statement at the top of align_points() to print out its parameters, and I don't see anything suspicious, and it's only one of a zillion calls to align_points() that elicits the warning. This is my personal build using numpy 2.4.6. I've attached a file of the output (since it's voluminous). --Eric" defect closed moderate Core fixed all ChimeraX