degenerate structure

[sitins07@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open X:\Work\Projects\EF-G\g3\Modelling\EF-G_Dom1-ISOLDE.pdb format pdb

Chain information for EF-G_Dom1-ISOLDE.pdb #1  
---  
Chain | Description  
x | No description available  
  
Structure has degenerate atomic coordinates; assigning all 'turn' secondary
structure  

> open X:/Work/Projects/EF-G/g3/512_c4_d4c3_sharpened.mrc

Opened 512_c4_d4c3_sharpened.mrc, grid size 512,512,512, pixel 0.652, shown at
level 4.45, step 2, values float32  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for EF-G_Dom1-ISOLDE.pdb  
---  
Chain | Description  
1.2/x | No description available  
  
Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to EF-G_Dom1-ISOLDE.pdb #1.2  
---  
warnings | Not adding hydrogens to /x ASP 183 CG because it is missing heavy-
atom bond partners  
Not adding hydrogens to /x ASP 183 OD1 because it is missing heavy-atom bond
partners  
notes | No usable SEQRES records for EF-G_Dom1-ISOLDE.pdb (#1.2) chain x;
guessing termini instead  
Chain-initial residues that are actual N termini: /x ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /x PRO 286  
X:\Soft\ChimeraX 1.0\bin\lib\site-packages\chimerax\geometry\plane.py:16:
RuntimeWarning: invalid value encountered in true_divide  
normalize = lambda v: v/norm(v)  
  
Traceback (most recent call last):  
File "X:\Soft\ChimeraX 1.0\bin\lib\site-packages\chimerax\cmd_line\tool.py",
line 258, in execute  
cmd.run(cmd_text)  
File "X:\Soft\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "X:\Soft\ChimeraX 1.0\bin\lib\site-packages\chimerax\atomic\addh\cmd.py",
line 63, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "X:\Soft\ChimeraX 1.0\bin\lib\site-packages\chimerax\atomic\addh\cmd.py",
line 171, in hbond_add_hydrogens  
idatm_type, his_Ns, coordinations, in_isolation)  
File "X:\Soft\ChimeraX 1.0\bin\lib\site-
packages\chimerax\atomic\addh\hbond.py", line 211, in add_hydrogens  
coplanar=[cpa._addh_coord for cpa in coplanar_atoms])  
File "X:\Soft\ChimeraX 1.0\bin\lib\site-
packages\chimerax\atomic\bond_geom.py", line 73, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
File "X:\Soft\ChimeraX 1.0\bin\lib\site-
packages\chimerax\atomic\bond_geom.py", line 129, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
File "X:\Soft\ChimeraX 1.0\bin\lib\site-
packages\chimerax\atomic\bond_geom.py", line 247, in angle_pos  
points.append(xform.inverse() * angle)  
File "X:\Soft\ChimeraX 1.0\bin\lib\site-packages\chimerax\geometry\place.py",
line 187, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File "X:\Soft\ChimeraX 1.0\bin\lib\site-packages\chimerax\geometry\matrix.py",
line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 6, in inv  
File "X:\Soft\ChimeraX 1.0\bin\lib\site-packages\numpy\linalg\linalg.py", line
547, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File "X:\Soft\ChimeraX 1.0\bin\lib\site-packages\numpy\linalg\linalg.py", line
97, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File "X:\Soft\ChimeraX 1.0\bin\lib\site-packages\numpy\linalg\linalg.py", line
97, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 451.67
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GE73VR 7RF
OS: Майкрософт Windows 10 Pro (Build 19041)
Memory: 17,059,950,592
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[pett]

Hi Valentyn,

As per the log message "Structure has degenerate atomic coordinates", one or more of the atoms in EF-G_Dom1-ISOLDE.pdb are directly on top of one another. Many functions in ChimeraX will not work or will throw errors in this situation. You need to correct the structure.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[sitins07@…]

Got it, thanks!
Respectfully yours,
Valentyn Petrychenko


вт, 25 серп. 2020 о 00:49 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> пише: