Opened 13 months ago

Closed 13 months ago

#15986 closed defect (limitation)

The X11 connection broke

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: Tom Goddard, Zach Pearson
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-113-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007efdcc258740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.linalg._flinalg, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 123)
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/alphafold/Downloads/194_fit.pdb

Chain information for 194_fit.pdb #1  
---  
Chain | Description  
B | No description available  
  

> open
> /home/net/shared/scripts/processing_server/uploads/processing/wss205/240904_1716_run_class001_emready/run_class001_emready.mrc

Opened run_class001_emready.mrc as #2, grid size 448,448,448, pixel 1.21,
shown at level 0.388, step 2, values float32  

> open /alphafold-
> libs/otter/shared/jumbo_phage/baseplate/J1716/model_angelo/model_angelo.cif

Summary of feedback from opening /alphafold-
libs/otter/shared/jumbo_phage/baseplate/J1716/model_angelo/model_angelo.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for model_angelo.cif #3  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
9 | No description available  
A0 | No description available  
A1 | No description available  
A3 AN | No description available  
A5 AM An | No description available  
AA | No description available  
AB | No description available  
AC | No description available  
AD | No description available  
AE | No description available  
AF | No description available  
AG | No description available  
AH | No description available  
AI | No description available  
AK | No description available  
AL | No description available  
AQ | No description available  
AR BS | No description available  
AV | No description available  
AW | No description available  
AY | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Ah | No description available  
Al | No description available  
Am | No description available  
Ap | No description available  
Aq | No description available  
Ar | No description available  
As | No description available  
At | No description available  
Ax | No description available  
Ay | No description available  
Az | No description available  
B | No description available  
B0 | No description available  
B5 | No description available  
B7 | No description available  
BE | No description available  
BG | No description available  
BJ | No description available  
BQ | No description available  
BR | No description available  
BT | No description available  
BU | No description available  
BV | No description available  
Bd | No description available  
Bg | No description available  
Bi | No description available  
Bn | No description available  
Bp CX | No description available  
Bs | No description available  
Bv | No descriAn error occurred in drawing the scene. Redrawing graphics is
now stopped to avoid a continuous stream of error messages. To restart
graphics use the command "graphics restart" after changing the settings that
caused the error.  
  
GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_BACK,)  
)  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw  
self._draw_scene(camera, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 272, in _draw_scene  
draw_highlight_outline(r, highlight_drawings, color = self._highlight_color,  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1625, in draw_highlight_outline  
r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1927, in finish_rendering_outline  
r.pop_framebuffer()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 764, in pop_framebuffer  
fb.activate()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 2313, in activate  
GL.glDrawBuffer(self._draw_buffer)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_BACK,)  
)  
  

The X11 connection broke (error 1). Did the X11 server die?  

le  
C9 Ca DR | No description available  
CC | No description available  
CD | No description available  
CF | No description available  
CM | No description available  
CN | No description available  
CO | No description available  
CP Cs | No description available  
CT | No description available  
Cc Co | No description available  
Cn | No description available  
Cp | No description available  
Ct | No description available  
D | No description available  
D0 | No description available  
D1 | No description available  
D2 | No description available  
D3 | No description available  
D4 | No description available  
D5 | No description available  
D6 | No description available  
D7 | No description available  
D8 | No description available  
D9 | No description available  
DE | No description available  
DX | No description available  
Da | No description available  
Db | No description available  
Dc | No description available  
Dd | No description available  
De | No description available  
Df | No description available  
Dg | No description available  
Dh | No description available  
Di | No description available  
Dj | No description available  
Dk | No description available  
Dl | No description available  
Dm | No description available  
Dn | No description available  
Do | No description available  
Dp | No description available  
Dq | No description available  
Dr | No description available  
Ds | No description available  
Dt | No description available  
Du | No description available  
Dv | No description available  
Dw | No description available  
Dx | No description available  
Dy | No description available  
Dz | No description available  
E | No description available  
EA | No description available  
EB | No description available  
EC | No description available  
ED | No description available  
EE | No description available  
EF | No description available  
EG | No description available  
EH | No description available  
EI | No description available  
EJ | No description available  
EK | No description available  
EL | No description available  
EM | No description available  
EN | No description available  
EO | No description available  
EP | No description available  
EQ | No description available  
ER | No description available  
ES | No description available  
ET | No description available  
EU | No description available  
EV | No description available  
EW | No description available  
EX | No description available  
EY | No description available  
EZ | No description available  
Ea | No description available  
Eb | No description available  
Ec | No description available  
Ed | No description available  
Ee | No description available  
Ef | No description available  
Eg | No description available  
Eh | No description available  
Ei | No description available  
Ej | No description available  
Ek | No description available  
El | No description available  
Em | No description available  
En | No description available  
Eo | No description available  
Ep | No description available  
Eq | No description available  
Er | No description available  
Es | No description available  
Et | No description available  
Eu | No description available  
Ev | No description available  
I | No description available  
J | No description available  
K | No description available  
N | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #3 models

> show #3 models

> ui mousemode right "translate selected models"

> select #2

2 models selected  

> select clear

> select add #3

21751 atoms, 21935 bonds, 2750 residues, 1 model selected  

> view matrix models #3,1,0,0,117.72,0,1,0,165.49,0,0,1,180.34

> view matrix models #3,1,0,0,170.79,0,1,0,177.03,0,0,1,176.62

> view matrix models #3,1,0,0,172.93,0,1,0,180.94,0,0,1,177.31

> fitmap sel inMap #2

Fit molecule model_angelo.cif (#3) to map run_class001_emready.mrc (#2) using
21751 atoms  
average map value = 6.627, steps = 80  
shifted from previous position = 7.81  
rotated from previous position = 0.0291 degrees  
atoms outside contour = 85, contour level = 0.3881  
  
Position of model_angelo.cif (#3) relative to run_class001_emready.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.99999996 -0.00020506 -0.00019871 180.20542513  
0.00020514 0.99999989 0.00042043 180.10928148  
0.00019862 -0.00042047 0.99999989 180.20410645  
Axis -0.82725970 -0.39088368 0.40354843  
Axis point 0.00000000 569497.86960935 -291798.36669057  
Rotation angle (degrees) 0.02912054  
Shift along axis -146.75737908  
  

> mmaker #1 to #3/Ef

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker model_angelo.cif, chain Ef (#3) with 194_fit.pdb, chain B (#1),
sequence alignment score = 93.1  
RMSD between 12 pruned atom pairs is 0.931 angstroms; (across all 54 pairs:
26.522)  
  

> hide #3 models

> volume #2 step 1

> volume #2 level 4.45

> volume #2 color #ffffb233

> fitmap #1 inMap #2

Fit molecule 194_fit.pdb (#1) to map run_class001_emready.mrc (#2) using 2284
atoms  
average map value = 3.401, steps = 176  
shifted from previous position = 2.23  
rotated from previous position = 10.2 degrees  
atoms outside contour = 1531, contour level = 4.4501  
  
Position of 194_fit.pdb (#1) relative to run_class001_emready.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.99996287 0.00574574 -0.00642282 71.04367735  
-0.00574121 0.99998326 0.00072290 205.97723342  
0.00642687 -0.00068600 0.99997911 113.82964563  
Axis -0.08147242 -0.74305538 -0.66425217  
Axis point 6546.55547341 0.00000000 8049.29374242  
Rotation angle (degrees) 0.49541553  
Shift along axis -234.45218106  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for 194_fit.pdb  
---  
Chain | Description  
1.2/B | No description available  
  

> isolde set simFidelityMode Lowest/Fastest

ISOLDE: setting sim fidelity mode to Lowest/Fastest  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = False  

> isolde set simFidelityMode Lowest/Fastest

ISOLDE: setting sim fidelity mode to Lowest/Fastest  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = False  

> addh #1

Summary of feedback from adding hydrogens to 194_fit.pdb #1.2  
---  
notes | Termini for 194_fit.pdb (#1.2) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 194_fit.pdb #1.2/B ALA 3  
Chain-final residues that are actual C termini: 194_fit.pdb #1.2/B PRO 147  
Chain-final residues that are not actual C termini:  
122 hydrogen bonds  
0 hydrogens added  
  

> isolde sim start #1.2/B

> clipper associate #2 toModel #1

Opened run_class001_emready.mrc as #1.1.1.1, grid size 448,448,448, pixel
1.21, shown at step 1, values float32  

> isolde sim start #1.2/B

ISOLDE: started sim  

> hide sel atoms

> show sel cartoons

> ui mousemode right "isolde tug residue"

> show #3 models

> select add #3

24035 atoms, 24248 bonds, 2895 residues, 3 models selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> hide #3 models

> show #3 models

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 8 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start #3/A,B,C,D,E,F-z,0-9,AA-Az,A0-A9,BA-Bz,B0-B9,CA-
> Cz,C0-C9,DA-Dz,D0-D9,EA-Ev #1.2/B

ISOLDE: started sim  

> hide sel atoms

> show sel cartoons

> ui mousemode right "isolde tug residue"

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> hide sel atoms

> show sel cartoons

> show sel atoms

> style sel stick

Changed 24035 atom styles  

> isolde sim start #3/A,B,C,D,E,F-z,0-9,AA-Az,A0-A9,BA-Bz,B0-B9,CA-
> Cz,C0-C9,DA-Dz,D0-D9,EA-Ev #1.2/B

ISOLDE: started sim  

> select clear

> select H

1139 atoms, 145 residues, 1 model selected  

> hide sel atoms

> ui mousemode right "isolde tug residue"

> hide sel atoms

> select clear

> hide atoms

> show cartoons

> select #3/ET

372 atoms, 378 bonds, 48 residues, 1 model selected  

> show sel atoms

> select #1/B

2284 atoms, 2313 bonds, 145 residues, 1 model selected  

> show sel atoms

> select H

1139 atoms, 145 residues, 1 model selected  

> hide sel atoms

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 6 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1/B:1-120

1865 atoms, 1886 bonds, 118 residues, 1 model selected  

> select H

1139 atoms, 145 residues, 1 model selected  

> hide sel atoms

> isolde sim start #1.2/B

ISOLDE: started sim  

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> ui mousemode right "isolde tug residue"

> show sel atoms

> select H

1139 atoms, 145 residues, 1 model selected  

> hide sel atoms

> select add #3

22890 atoms, 21935 bonds, 2895 residues, 2 models selected  

> show sel atoms

> select clear

> select #1/B:1-110

1701 atoms, 1720 bonds, 108 residues, 1 model selected  

> select #1/B:110-200

603 atoms, 613 bonds, 38 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> select #1

2284 atoms, 2313 bonds, 145 residues, 21 models selected  

> isolde sim start #1.2/B

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start #1.2/B

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start #1.2/B:36

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start #1.2/B:33-39

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start #1.2/B:129

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1

2284 atoms, 2313 bonds, 145 residues, 21 models selected  

> isolde sim start #1.2/B

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> hide sel atoms

> show sel cartoons

> isolde sim start #1.2/B

ISOLDE: started sim  

> show sel cartoons

> ui mousemode right "isolde tug residue"

> show sel atoms

> select #1

2284 atoms, 2313 bonds, 145 residues, 21 models selected  

> select H

1139 atoms, 145 residues, 1 model selected  

> hide sel atoms

> ui mousemode right "isolde tug atom"

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> hide #3 models

> isolde sim start #1.2/B

ISOLDE: started sim  

> show sel cartoons

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> isolde sim start #1.2/B

ISOLDE: started sim  

> show sel atoms

> show #3 models

> hide sel atoms

> select clear

> hide atoms

> show cartoons

> ui mousemode right "isolde tug residue"

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> hide atoms

> show atoms

> hide #!1 models

> show #!1 models

> select #1

2284 atoms, 2313 bonds, 145 residues, 21 models selected  

> isolde sim start #1.2/B

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start #1.2/B

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /home/alphafold/Downloads/194_fit.pdb models #1

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_BACK,)  
)  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw  
self._draw_scene(camera, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 272, in _draw_scene  
draw_highlight_outline(r, highlight_drawings, color = self._highlight_color,  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1625, in draw_highlight_outline  
r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1927, in finish_rendering_outline  
r.pop_framebuffer()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 764, in pop_framebuffer  
fb.activate()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 2313, in activate  
GL.glDrawBuffer(self._draw_buffer)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_BACK,)  
)  
  

The X11 connection broke (error 1). Did the X11 server die?  


===== Log before crash end =====

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA RTX A5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 48 AMD Ryzen Threadripper 3960X 24-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          125Gi       3.3Gi       119Gi        25Mi       3.1Gi       121Gi
	Swap:          15Gi       145Mi        15Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2231] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:147e]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.3
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.2.2
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    pprintpp: 0.4.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (3)

comment:1 by pett, 13 months ago

Cc: Tom Goddard Zach Pearson added
Component: Unassigned → Platform
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → The X11 connection broke

comment:2 by Tom Goddard, 13 months ago

This is quite interesting as I've seen this Linux glDrawBuffer(GL_BACK) invalid operation error reported dozens of time but never saw the "The X11 connection broke (error 1). Did the X11 server die?" message. Possibly when the X11 server disconnects this glDrawBuffer(GL_BACK) call is the first place our code fails. That would explain why I have only ever seen this OpenGL error on Linux.

comment:3 by Greg Couch, 13 months ago

Resolution: → limitation
Status: assigned → closed

Sometimes the graphics driver crashes taking the X11 server with it.

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