AddH on 1trz: Singular matrix

[lpravda@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-11-19)
Description
addh hbonds true command. Also happens on Red Hat Linux 7.4.

Log:
UCSF ChimeraX version: 0.8 (2018-11-19)  
How to cite UCSF ChimeraX  

> open 1qyl fromDatabase pdbe_updated

1qyl title:  
GCATGCT + Vanadium [more info...]  
  
Chain information for 1qyl #1  
---  
Chain | Description  
A | 5'-D(*GP*CP*ap*TP*GP*CP*T)-3'  
  
1qyl mmCIF Assemblies  
---  
1| author_defined_assembly  
  
  

> addh hbond true

Termini for 1qyl (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A DG 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A DT 7  
Chain-final residues that are not actual C termini:  
124 hydrogen bonds  
171 hydrogens added  

> open 1trz fromDatabase pdbe_updated

Summary of feedback from opening 1trz fetched from pdbe_updated  
---  
notes | Fetching compressed mmCIF 1trz from http://www.ebi.ac.uk/pdbe/entry-
files/download/1trz_updated.cif  
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif  
  
1trz title:  
Crystallographic evidence for dual coordination around zinc In the T3R3 human
insulin hexamer [more info...]  
  
Chain information for 1trz #2  
---  
Chain | Description  
A C | insulin  
B D | insulin  
  
1trz mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| software_defined_assembly  
4| software_defined_assembly  
5| software_defined_assembly  
6| software_defined_assembly  
7| software_defined_assembly  
8| software_defined_assembly  
9| software_defined_assembly  
  
  

> delete #1

Expected a keyword  

> addh hbond true

Termini for 1trz (#2) chain C determined from SEQRES records  
Termini for 1trz (#2) chain A determined from SEQRES records  
Termini for 1trz (#2) chain D determined from SEQRES records  
Termini for 1trz (#2) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /C GLY 1, /A GLY 1, /D PHE
1, /B PHE 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /C ASN 21, /A ASN 21, /D THR
30, /B THR 30  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /D THR 30  
295 hydrogen bonds  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 225, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2581, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/hbond.py", line 630, in add_hydrogens  
toward=toward_pos, toward2=toward2, away2=away2)  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/geometry/place.py", line 182, in inverse  
self._inverse = Place(m34.invert_matrix(self.matrix))  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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
"/Applications/ChimeraX.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  
  




OpenGL version: 4.1 ATI-2.2.8
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tristan Croll]

Forgive my chiming in, but the culprit here appears to be an error in the model: a water oxygen (/D:34@O) is occupying exactly the same position as a chloride ion (/D:32@CL).

[Eric Pettersen]

Yes, as Tristan pointed out, it seems like an error in the model. While atoms /D:34@O and /D:32@CL are not exactly at the same position, they are only 0.28 angstroms apart, and they are exactly collinear with /D:31@ZN.

--Eric