id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1547 "Symmetry position atom: LinAlgError(""Singular matrix"")" lpravda@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-12-15) Description Open the attached file; run addh Log: Startup Messages --- notes | FYI: command is replacing existing command: ""ui"" FYI: command is replacing existing command: ""volume"" FYI: command is replacing existing command: ""color"" UCSF ChimeraX version: 0.8 (2018-12-15) How to cite UCSF ChimeraX > open /Users/pett/rm/1dwx_assembly.cif Summary of feedback from opening /Users/pett/rm/1dwx_assembly.cif --- warnings | Missing entity_poly_seq table. Inferring polymer connectivity. Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""HAR"" near line 8067 Unknown polymer entity '5' near line 8067 Chain information for 1dwx_assembly.cif #1 --- Chain | Description A A-2 | nitric oxide synthase > addh Termini for 1dwx_assembly.cif (#1) chain A determined from SEQRES records Termini for 1dwx_assembly.cif (#1) chain A-2 determined from SEQRES records Chain-initial residues that are actual N termini: /A GLN 77, /A-2 GLN 77, /A HAR 906, /A-2 HAR 906 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A GLN 496, /A-2 GLN 496, /A HAR 906, /A-2 HAR 906 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A GLN 496 Missing OXT added to C-terminal residue /A-2 GLN 496 1678 hydrogen bonds Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/cmd_line/tool.py"", line 229, in execute cmd.run(cmd_text) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2587, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/cmd.py"", line 55, in cmd_addh add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/cmd.py"", line 163, in hbond_add_hydrogens idatm_type, his_Ns, coordinations, in_isolation) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/hbond.py"", line 354, in add_hydrogens _do_prune(hbond, pruned, rel_bond, processed, pruned_by) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/hbond.py"", line 1429, in _do_prune other._addh_coord): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/hbond.py"", line 1382, in _tet2_check for pos in bond_positions(tet_pos, 4, 1.0, [], toward=toward, toward2=toward2): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/bond_geom.py"", line 78, in bond_positions return tetra_pos(bondee, bonded, bond_len, toward, away, toward2, away2) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/bond_geom.py"", line 158, in tetra_pos pos = angle_pos(bondee, cur_bonded[0], bond_len, 109.5, coplanar=coplanar) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/bond_geom.py"", line 247, in angle_pos points.append(xform.inverse() * angle) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/geometry/place.py"", line 187, in inverse self._inverse = Place(m34.invert_matrix(self._matrix)) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/geometry/matrix.py"", line 130, in invert_matrix rinv[:, :] = matrix_inverse(r) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/numpy/linalg/linalg.py"", line 532, in inv ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/numpy/linalg/linalg.py"", line 89, in _raise_linalgerror_singular raise LinAlgError(""Singular matrix"") numpy.linalg.linalg.LinAlgError: Singular matrix numpy.linalg.linalg.LinAlgError: Singular matrix File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/numpy/linalg/linalg.py"", line 89, in _raise_linalgerror_singular raise LinAlgError(""Singular matrix"") See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation File attachment: 1dwx_assembly.cif }}} [attachment:""1dwx_assembly.cif""] " defect closed normal Structure Editing fixed all ChimeraX