H-Bonds: Singular matrix

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/danadayan/Downloads/Q8NFU3_0_fullatom37.pdb

Summary of feedback from opening
/Users/danadayan/Downloads/Q8NFU3_0_fullatom37.pdb  
---  
warning | Ignored bad PDB record found on line 1  
PARENT N/A  
notes | Combining 44 symmetry atoms into MET /A:0 CE  
Combining 37 symmetry atoms into ARG /A:12 NE  
Combining 33 symmetry atoms into GLU /A:10 OE1  
  
Chain information for Q8NFU3_0_fullatom37.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> dockprep

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A MET 0: phi none, psi 78.8 trans  
/A GLU 10: phi -65.8, psi -44.2 trans  
/A ARG 12: phi -61.0, psi -44.8 trans  
/A ARG 19: phi -96.6, psi -13.5 trans  
/A ARG 21: phi -103.5, psi 123.6 trans  
/A PHE 23: phi -124.6, psi 113.8 trans  
/A ARG 26: phi -75.3, psi 167.0 trans  
/A ARG 28: phi -58.2, psi -37.6 trans  
/A GLU 29: phi -65.5, psi -46.2 trans  
/A GLU 30: phi -62.0, psi -43.0 trans  
/A GLU 46: phi -111.2, psi -3.8 trans  
/A GLU 48: phi -57.7, psi -49.9 trans  
/A GLN 52: phi -97.9, psi -2.4 trans  
/A MET 53: phi -68.4, psi 152.4 trans  
/A GLU 54: phi -64.8, psi 151.4 trans  
/A PHE 58: phi -60.4, psi -44.3 trans  
/A GLN 59: phi -62.4, psi -40.7 trans  
/A TYR 62: phi -111.3, psi -4.0 trans  
/A GLU 65: phi -63.9, psi 131.8 trans  
/A LYS 66: phi -60.7, psi 132.2 trans  
/A LYS 68: phi -95.4, psi 153.9 trans  
/A GLU 70: phi -87.3, psi -6.0 trans  
/A GLU 72: phi -98.1, psi 143.3 trans  
/A HIS 73: phi 72.2, psi 45.2 trans  
/A PHE 76: phi -103.6, psi 136.6 trans  
/A PHE 77: phi -147.1, psi 159.9 trans  
/A GLN 79: phi -80.0, psi -43.1 trans  
/A MET 80: phi -128.7, psi -3.0 trans  
/A LYS 82: phi -70.7, psi -51.5 trans  
/A ARG 83: phi -65.9, psi -30.8 trans  
/A GLN 86: phi -57.8, psi -44.8 trans  
/A GLN 89: phi -65.6, psi -43.0 trans  
/A ARG 92: phi -66.7, psi -36.3 trans  
/A TYR 96: phi -72.1, psi 82.0 trans  
/A ARG 100: phi -136.8, psi 150.6 trans  
/A TYR 102: phi -86.7, psi 93.1 trans  
/A TYR 106: phi -64.4, psi -26.8 trans  
/A ARG 107: phi -65.1, psi -47.3 trans  
/A GLU 108: phi -63.2, psi -41.4 trans  
/A TRP 109: phi -60.4, psi -45.9 trans  
/A GLU 111: phi -71.9, psi -33.2 trans  
/A LYS 112: phi -110.0, psi -20.4 trans  
/A GLU 113: phi -117.9, psi -15.6 trans  
/A SER 114: phi -96.0, psi none trans  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 170, in dock_prep_cmd  
dock_prep_caller(session, structures, memorization=memorize, nogui=True, **kw)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 96, in prep  
swap_aa(session, targets, "same", rot_lib=style)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 122, in swap_aa  
process_hbonds(session, res, by_alt_loc, False, None, None, hbond_relax,  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 805, in process_hbonds  
hbonds = { hb: color for hb in find_hbonds(session, target_models,
intra_model=False,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 585, in find_hbonds  
donor_hyds = hyd_positions(donor_atom)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hydpos.py", line 77, in hyd_positions  
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 84, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 140, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 258, in angle_pos  
points.append(xform.inverse() * angle)  
^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,6
      Model Number: MRX33HB/A
      Chip: Apple M3 Pro
      Total Number of Cores: 11 (5 performance and 6 efficiency)
      Memory: 18 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4.1 (24E263)
      Kernel Version: Darwin 24.4.0
      Time since boot: 161 days, 14 hours, 47 minutes

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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[Eric Pettersen]

Pretty sure it's a problematic structure (e.g. "Combining 37 symmetry atoms into ARG /A:12 NE")