Opened 9 months ago

Closed 9 months ago

#16923 closed defect (nonchimerax)

Many OpenGL errors

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

Description 

The following bug report has been submitted:
Platform:        Linux-6.12.13-200.fc41.x86_64-x86_64-with-glibc2.40
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f2c6c9fb6c0 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/ssl.py", line 1134 in read
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/ssl.py", line 1278 in recv_into
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/socket.py", line 706 in readinto
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/http/client.py", line 279 in _read_status
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/http/client.py", line 318 in begin
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/http/client.py", line 1378 in getresponse
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/urllib/request.py", line 1352 in do_open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/urllib/request.py", line 1391 in https_open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/urllib/request.py", line 496 in _call_chain
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/urllib/request.py", line 536 in _open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/urllib/request.py", line 519 in open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/urllib/request.py", line 216 in urlopen
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/toolshed/available.py", line 62 in load
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 516 in reload_available
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007f2d0f829e80 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/OpenGL/platform/baseplatform.py", line 415 in __call__
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1103 in opengl_version
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/bug_reporter/tool.py", line 622 in opengl_info
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/bug_reporter/tool.py", line 115 in __init__
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/bug_reporter/tool.py", line 369 in show_bug_reporter
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/bug_reporter/crash_report.py", line 217 in _show_bug_report_dialog
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/bug_reporter/crash_report.py", line 45 in _report
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 65 in draw_new_frame
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio (total: 48)
===== Log before crash start =====
Startup Errors  
---  
bug | OpenGL.error.GLError: GLError(  
err = -424,  
baseOperation = glGetError,  
cArguments = (),  
result = 4294966872  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
  
warnings | QRhiGles2: Failed to make context current. Expect bad things to happen.  
QRhiGles2: Failed to make context current. Expect bad things to happen.  
QQuickWidget: failed to create output texture of size 1803x1758  
QRhiGles2: Failed to make context current. Expect bad things to happen.  
QQuickWidget: failed to create depth/stencil buffer of size 1803x1758 and
sample count 1  
QRhiGles2: Failed to make context current. Expect bad things to happen.  
QRhiGles2: Failed to make context current. Expect bad things to happen.  
QRhiGles2: Failed to make context current. Expect bad things to happen.  
QQuickWidget: Failed to begin recording a frame  
QRhiGles2: Failed to make context current. Expect bad things to happen.  
QQuickWidget: Failed to begin recording a frame  
notes | available bundle cache has not been initialized yet  
Traceback (most recent call last):  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 60, in event  
  
self._check_opengl()  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 76, in _check_opengl  
  
e = r.check_for_opengl_errors()  
  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1092, in check_for_opengl_errors  
  
e = GL.glGetError()  
  
^^^^^^^^^^^^^^^  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/OpenGL/platform/baseplatform.py", line 415, in __call__  
  
return self( *args, **named )  
  
^^^^^^^^^^^^^^^^^^^^^^  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
OpenGL.error.GLError: GLError(  
  
err = -424,  
  
baseOperation = glGetError,  
  
cArguments = (),  
  
result = 4294966872  
  
)  
  
  
  
  

QRhiGles2: Failed to make context current. Expect bad things to happen.  

QQuickWidget: failed to create resized output texture of size 1222x1758  

QRhiGles2: Failed to make context current. Expect bad things to happen.  

QQuickWidget: failed to create resized depth/stencil buffer of size 1222x1758  

QRhiGles2: Failed to make context current. Expect bad things to happen.  

[Repeated 1 time(s)]

QQuickWidget: Failed to begin recording a frame  

QRhiGles2: Failed to make context current. Expect bad things to happen.  

QQuickWidget: failed to create resized output texture of size 1222x1726  

QRhiGles2: Failed to make context current. Expect bad things to happen.  

QQuickWidget: failed to create resized depth/stencil buffer of size 1222x1726  

QRhiGles2: Failed to make context current. Expect bad things to happen.  

[Repeated 1 time(s)]

QQuickWidget: Failed to begin recording a frame  

QRhiGles2: Failed to make context current. Expect bad things to happen.  

QQuickWidget: failed to create resized output texture of size 1222x1591  

QRhiGles2: Failed to make context current. Expect bad things to happen.  

QQuickWidget: failed to create resized depth/stencil buffer of size 1222x1591  

QRhiGles2: Failed to make context current. Expect bad things to happen.  

[Repeated 1 time(s)]

QQuickWidget: Failed to begin recording a frame  

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 4v6x.cif

4v6x.cif title:  
Structure of the human 80S ribosome [more info...]  
  
Chain information for 4v6x.cif #1  
---  
Chain | Description | UniProt  
A5 | 28S ribosomal RNA |   
A7 | 5S ribosomal RNA |   
A8 | 5.8S ribosomal RNA |   
AA | 40S ribosomal protein SA | RSSA_HUMAN 1-295  
AB | 40S ribosomal protein S3a | RS3A_HUMAN 1-264  
AC | 40S ribosomal protein S2 | RS2_HUMAN 1-293  
AD | 40S ribosomal protein S3 | RS3_HUMAN 1-243  
AE | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263  
AF | 40S ribosomal protein S5 | RS5_HUMAN 1-204  
AG | 40S ribosomal protein S6 | RS6_HUMAN 1-249  
AH | 40S ribosomal protein S7 | RS7_HUMAN 1-194  
AI | 40S ribosomal protein S8 | RS8_HUMAN 1-208  
AJ | 40S ribosomal protein S9 | RS9_HUMAN 1-194  
AK | 40S ribosomal protein S10 | RS10_HUMAN 1-165  
AL | 40S ribosomal protein S11 | RS11_HUMAN 1-158  
AM | 40S ribosomal protein S12 | RS12_HUMAN 1-132  
AN | 40S ribosomal protein S13 | RS13_HUMAN 1-151  
AO | 40S ribosomal protein S14 | RS14_HUMAN 1-151  
AP | 40S ribosomal protein S15 | RS15_HUMAN 1-145  
AQ | 40S ribosomal protein S16 | RS16_HUMAN 1-146  
AR | 40S ribosomal protein S17 | RS17_HUMAN 1-135  
AS | 40S ribosomal protein S18 | RS18_HUMAN 1-152  
AT | 40S ribosomal protein S19 | RS19_HUMAN 1-145  
AU | 40S ribosomal protein S20 | RS20_HUMAN 1-119  
AV | 40S ribosomal protein S21 | RS21_HUMAN 1-83  
AW | 40S ribosomal protein S15a | RS15A_HUMAN 1-130  
AX | 40S ribosomal protein S23 | RS23_HUMAN 1-143  
AY | 40S ribosomal protein S24 | RS24_HUMAN 1-133  
AZ | 40S ribosomal protein S25 | RS25_HUMAN 1-125  
Aa | 40S ribosomal protein S26 | RS26_HUMAN 1-115  
Ab | 40S ribosomal protein S27 | RS27_HUMAN 1-84  
Ac | 40S ribosomal protein S28 | RS28_HUMAN 1-69  
Ad | 40S ribosomal protein S29 | RS29_HUMAN 1-56  
Ae | 40S ribosomal protein S30 | RS30_HUMAN 1-59  
Af | 40S ribosomal protein S27a | RS27A_HUMAN 77-156  
Ag | Guanine nucleotide-binding protein subunit beta-2-like 1 | GBLP_HUMAN 1-317  
Ah | Plasminogen activator inhibitor 1 RNA-binding protein | PAIRB_HUMAN 1-408  
Az | Elongation factor 2 | EF2_HUMAN 1-858  
B2 | 18S ribosomal RNA |   
BC | E-tRNA |   
CA | 60S ribosomal protein L8 | RL8_HUMAN 1-257  
CB | 60S ribosomal protein L3 | RL3_HUMAN 1-403  
CC | 60S ribosomal protein L4 | RL4_HUMAN 1-427  
CD | 60S ribosomal protein L5 | RL5_HUMAN 1-297  
CE | 60S ribosomal protein L6 | RL6_HUMAN 1-288  
CF | 60S ribosomal protein L7 | RL7_HUMAN 1-248  
CG | 60S ribosomal protein L7a | RL7A_HUMAN 1-266  
CH | 60S ribosomal protein L9 | RL9_HUMAN 1-192  
CI | 60S ribosomal protein L10-like | RL10L_HUMAN 1-214  
CJ | 60S ribosomal protein L11 | RL11_HUMAN 1-178  
CK | 60S ribosomal protein L12 | RL12_HUMAN 1-165  
CL | 60S ribosomal protein L13 | RL13_HUMAN 1-211  
CM | 60S ribosomal protein L14 | RL14_HUMAN 1-215  
CN | 60S ribosomal protein L15 | RL15_HUMAN 1-204  
CO | 60S ribosomal protein L13a | RL13A_HUMAN 1-203  
CP | 60S ribosomal protein L17 | RL17_HUMAN 1-184  
CQ | 60S ribosomal protein L18 | RL18_HUMAN 1-188  
CR | 60S ribosomal protein L19 | RL19_HUMAN 1-196  
CS | 60S ribosomal protein L18a | RL18A_HUMAN 1-176  
CT | 60S ribosomal protein L21 | RL21_HUMAN 1-160  
CU | 60S ribosomal protein L22 | RL22_HUMAN 1-128  
CV | 60S ribosomal protein L23 | RL23_HUMAN 1-140  
CW | 60S ribosomal protein L24 | RL24_HUMAN 1-157  
CX | 60S ribosomal protein L23a | RL23A_HUMAN 1-156  
CY | 60S ribosomal protein L26 | RL26_HUMAN 1-145  
CZ | 60S ribosomal protein L27 | RL27_HUMAN 1-136  
Ca | 60S ribosomal protein L27a | RL27A_HUMAN 1-148  
Cb | 60S ribosomal protein L29 | RL29_HUMAN 1-159  
Cc | 60S ribosomal protein L30 | RL30_HUMAN 1-115  
Cd | 60S ribosomal protein L31 | RL31_HUMAN 1-125  
Ce | 60S ribosomal protein L32 | RL32_HUMAN 1-135  
Cf | 60S ribosomal protein L35a | RL35A_HUMAN 1-110  
Cg | 60S ribosomal protein L34 | RL34_HUMAN 1-117  
Ch | 60S ribosomal protein L35 | RL35_HUMAN 1-123  
Ci | 60S ribosomal protein L36 | RL36_HUMAN 1-105  
Cj | 60S ribosomal protein L37 | RL37_HUMAN 1-97  
Ck | 60S ribosomal protein L38 | RL38_HUMAN 1-70  
Cl | 60S ribosomal protein L39 | RL39_HUMAN 1-51  
Cm | 60S ribosomal protein L40 | RL40_HUMAN 77-128  
Cn | 60S ribosomal protein L41 | RL41_HUMAN 1-25  
Co | 60S ribosomal protein L36a | RL36A_HUMAN 1-106  
Cp | 60S ribosomal protein L37a | RL37A_HUMAN 1-92  
Cq | 60S acidic ribosomal protein P0 | RLA0_HUMAN 1-317  
Cr | 60S ribosomal protein L28 | RL28_HUMAN 1-137  
Cs Ct | 60S acidic ribosomal protein P1 | RLA1_HUMAN 1-114  
Cu Cv | 60S acidic ribosomal protein P2 | RLA2_HUMAN 1-115  
Cz | 60S ribosomal protein L10a | RL10A_HUMAN 1-217  
  

QRhiGles2: Failed to make context current. Expect bad things to happen.  

QQuickWidget: failed to create output texture of size 575x1387  

QRhiGles2: Failed to make context current. Expect bad things to happen.  

QQuickWidget: failed to create depth/stencil buffer of size 575x1387 and
sample count 1  

QRhiGles2: Failed to make context current. Expect bad things to happen.  

[Repeated 2 time(s)]

QQuickWidget: Failed to begin recording a frame  

QRhiGles2: Failed to make context current. Expect bad things to happen.  

QQuickWidget: Failed to begin recording a frame  

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 87, in _expose_event  
self._create_opengl_context()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 120, in _create_opengl_context  
r.initialize_opengl(lw, lh)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1165, in initialize_opengl  
vao = GL.glGenVertexArrays(1)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "src/latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/OpenGL/platform/baseplatform.py", line 415, in __call__  
return self( *args, **named )  
^^^^^^^^^^^^^^^^^^^^^^  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = -424,  
baseOperation = glGenVertexArrays,  
pyArgs = (1, ),  
cArgs = (1, array([0], dtype=uint32)),  
cArguments = (1, array([0], dtype=uint32))  
)  
  
OpenGL.error.GLError: GLError(  
err = -424,  
baseOperation = glGenVertexArrays,  
pyArgs = (1, ),  
cArgs = (1, array([0], dtype=uint32)),  
cArguments = (1, array([0], dtype=uint32))  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event  
self.status(self._last_message, self._last_color)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status  
r.draw_background()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/OpenGL/platform/baseplatform.py", line 415, in __call__  
return self( *args, **named )  
^^^^^^^^^^^^^^^^^^^^^^  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = -424,  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = -424,  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  

Framebuffer incomplete: 0x8cd7  


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

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 4v6x.cif

4v6x.cif title:  
Structure of the human 80S ribosome [more info...]  
  
Chain information for 4v6x.cif #1  
---  
Chain | Description | UniProt  
A5 | 28S ribosomal RNA |   
A7 | 5S ribosomal RNA |   
A8 | 5.8S ribosomal RNA |   
AA | 40S ribosomal protein SA | RSSA_HUMAN 1-295  
AB | 40S ribosomal protein S3a | RS3A_HUMAN 1-264  
AC | 40S ribosomal protein S2 | RS2_HUMAN 1-293  
AD | 40S ribosomal protein S3 | RS3_HUMAN 1-243  
AE | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263  
AF | 40S ribosomal protein S5 | RS5_HUMAN 1-204  
AG | 40S ribosomal protein S6 | RS6_HUMAN 1-249  
AH | 40S ribosomal protein S7 | RS7_HUMAN 1-194  
AI | 40S ribosomal protein S8 | RS8_HUMAN 1-208  
AJ | 40S ribosomal protein S9 | RS9_HUMAN 1-194  
AK | 40S ribosomal protein S10 | RS10_HUMAN 1-165  
AL | 40S ribosomal protein S11 | RS11_HUMAN 1-158  
AM | 40S ribosomal protein S12 | RS12_HUMAN 1-132  
AN | 40S ribosomal protein S13 | RS13_HUMAN 1-151  
AO | 40S ribosomal protein S14 | RS14_HUMAN 1-151  
AP | 40S ribosomal protein S15 | RS15_HUMAN 1-145  
AQ | 40S ribosomal protein S16 | RS16_HUMAN 1-146  
AR | 40S ribosomal protein S17 | RS17_HUMAN 1-135  
AS | 40S ribosomal protein S18 | RS18_HUMAN 1-152  
AT | 40S ribosomal protein S19 | RS19_HUMAN 1-145  
AU | 40S ribosomal protein S20 | RS20_HUMAN 1-119  
AV | 40S ribosomal protein S21 | RS21_HUMAN 1-83  
AW | 40S ribosomal protein S15a | RS15A_HUMAN 1-130  
AX | 40S ribosomal protein S23 | RS23_HUMAN 1-143  
AY | 40S ribosomal protein S24 | RS24_HUMAN 1-133  
AZ | 40S ribosomal protein S25 | RS25_HUMAN 1-125  
Aa | 40S ribosomal protein S26 | RS26_HUMAN 1-115  
Ab | 40S ribosomal protein S27 | RS27_HUMAN 1-84  
Ac | 40S ribosomal protein S28 | RS28_HUMAN 1-69  
Ad | 40S ribosomal protein S29 | RS29_HUMAN 1-56  
Ae | 40S ribosomal protein S30 | RS30_HUMAN 1-59  
Af | 40S ribosomal protein S27a | RS27A_HUMAN 77-156  
Ag | Guanine nucleotide-binding protein subunit beta-2-like 1 | GBLP_HUMAN 1-317  
Ah | Plasminogen activator inhibitor 1 RNA-binding protein | PAIRB_HUMAN 1-408  
Az | Elongation factor 2 | EF2_HUMAN 1-858  
B2 | 18S ribosomal RNA |   
BC | E-tRNA |   
CA | 60S ribosomal protein L8 | RL8_HUMAN 1-257  
CB | 60S ribosomal protein L3 | RL3_HUMAN 1-403  
CC | 60S ribosomal protein L4 | RL4_HUMAN 1-427  
CD | 60S ribosomal protein L5 | RL5_HUMAN 1-297  
CE | 60S ribosomal protein L6 | RL6_HUMAN 1-288  
CF | 60S ribosomal protein L7 | RL7_HUMAN 1-248  
CG | 60S ribosomal protein L7a | RL7A_HUMAN 1-266  
CH | 60S ribosomal protein L9 | RL9_HUMAN 1-192  
CI | 60S ribosomal protein L10-like | RL10L_HUMAN 1-214  
CJ | 60S ribosomal protein L11 | RL11_HUMAN 1-178  
CK | 60S ribosomal protein L12 | RL12_HUMAN 1-165  
CL | 60S ribosomal protein L13 | RL13_HUMAN 1-211  
CM | 60S ribosomal protein L14 | RL14_HUMAN 1-215  
CN | 60S ribosomal protein L15 | RL15_HUMAN 1-204  
CO | 60S ribosomal protein L13a | RL13A_HUMAN 1-203  
CP | 60S ribosomal protein L17 | RL17_HUMAN 1-184  
CQ | 60S ribosomal protein L18 | RL18_HUMAN 1-188  
CR | 60S ribosomal protein L19 | RL19_HUMAN 1-196  
CS | 60S ribosomal protein L18a | RL18A_HUMAN 1-176  
CT | 60S ribosomal protein L21 | RL21_HUMAN 1-160  
CU | 60S ribosomal protein L22 | RL22_HUMAN 1-128  
CV | 60S ribosomal protein L23 | RL23_HUMAN 1-140  
CW | 60S ribosomal protein L24 | RL24_HUMAN 1-157  
CX | 60S ribosomal protein L23a | RL23A_HUMAN 1-156  
CY | 60S ribosomal protein L26 | RL26_HUMAN 1-145  
CZ | 60S ribosomal protein L27 | RL27_HUMAN 1-136  
Ca | 60S ribosomal protein L27a | RL27A_HUMAN 1-148  
Cb | 60S ribosomal protein L29 | RL29_HUMAN 1-159  
Cc | 60S ribosomal protein L30 | RL30_HUMAN 1-115  
Cd | 60S ribosomal protein L31 | RL31_HUMAN 1-125  
Ce | 60S ribosomal protein L32 | RL32_HUMAN 1-135  
Cf | 60S ribosomal protein L35a | RL35A_HUMAN 1-110  
Cg | 60S ribosomal protein L34 | RL34_HUMAN 1-117  
Ch | 60S ribosomal protein L35 | RL35_HUMAN 1-123  
Ci | 60S ribosomal protein L36 | RL36_HUMAN 1-105  
Cj | 60S ribosomal protein L37 | RL37_HUMAN 1-97  
Ck | 60S ribosomal protein L38 | RL38_HUMAN 1-70  
Cl | 60S ribosomal protein L39 | RL39_HUMAN 1-51  
Cm | 60S ribosomal protein L40 | RL40_HUMAN 77-128  
Cn | 60S ribosomal protein L41 | RL41_HUMAN 1-25  
Co | 60S ribosomal protein L36a | RL36A_HUMAN 1-106  
Cp | 60S ribosomal protein L37a | RL37A_HUMAN 1-92  
Cq | 60S acidic ribosomal protein P0 | RLA0_HUMAN 1-317  
Cr | 60S ribosomal protein L28 | RL28_HUMAN 1-137  
Cs Ct | 60S acidic ribosomal protein P1 | RLA1_HUMAN 1-114  
Cu Cv | 60S acidic ribosomal protein P2 | RLA2_HUMAN 1-115  
Cz | 60S ribosomal protein L10a | RL10A_HUMAN 1-217  
  




OpenGL version: 3.3.0 NVIDIA 565.77
OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

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: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 7960 Tower
OS: Fedora Linux 41
Architecture: 64bit ELF
Virtual Machine: none
CPU: 48 Intel(R) Xeon(R) w7-3455
Cache Size: 69120 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi        16Gi        23Gi       853Mi        22Gi        45Gi
	Swap:           71Gi          0B        71Gi

Graphics:
	0000:ac:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104GL [RTX A4000] [10de:24b0] (rev a1)	
	Subsystem: Dell Device [1028:14ad]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (2)

comment:1 by Eric Pettersen, 9 months ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Many OpenGL errors

comment:2 by Tom Goddard, 9 months ago

Resolution: → nonchimerax
Status: assigned → closed

Either a remote display problem or OpenGL driver problem.

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