Opened 8 months ago

Closed 8 months ago

#16860 closed defect (can't reproduce)

Crash drawing scene

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

Description 

The following bug report has been submitted:
Platform:        Linux-6.8.0-38-generic-x86_64-with-glibc2.39
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

Current thread 0x00007498621f7b80 (most recent call first):
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2614 in activate
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1923 in activate_bindings
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 814 in _draw_geometry
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 787 in draw_self
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1554 in draw_opaque
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/view.py", line 259 in _draw_scene
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 153 in resizeEvent
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/apps/chimerax/1.9-noble/usr/lib/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.pdb_lib._load_libs, lxml._elementpath, lxml.etree, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_linux, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath (total: 55)
===== Log before crash start =====
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
> /home/kuhn/bkhare/PDB/FitModelInMap_ChiX_20250213/FitModelInMapChiX_wnv86_20250213/nWNV86_refittedPDB23july.ccp4
> /home/kuhn/bkhare/PDB/FitModelInMap_ChiX_20250213/FitModelInMapChiX_wnv86_20250213/nWNV86rsr063BTF_ssm_MatKUNV.pdb

Opened nWNV86_refittedPDB23july.ccp4 as #1, grid size 72,63,104, pixel 1.73,
shown at level 0.777, step 1, values float32  
Chain information for nWNV86rsr063BTF_ssm_MatKUNV.pdb #2  
---  
Chain | Description  
A C E | No description available  
B D F | No description available  
H | No description available  
L | No description available  
  

> volume #1 level 0.4708

> close #1

> open
> /home/kuhn/bkhare/PDB/FitModelInMap_ChiX_20250213/FitModelInMapChiX_wnv86_20250213/cryosparc_P152_J59_009_volume_map_sharp.mrc

Opened cryosparc_P152_J59_009_volume_map_sharp.mrc as #1, grid size
450,450,450, pixel 1.73, shown at level 0.427, step 2, values float32  

> select /H:124@CB

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,68.952,0,1,0,-49.354,0,0,1,31.697

> view matrix models #2,1,0,0,90.352,0,1,0,-55.937,0,0,1,87.154

> view matrix models #2,1,0,0,161.29,0,1,0,-117.4,0,0,1,63.948

> view matrix models #2,1,0,0,157.49,0,1,0,-107.71,0,0,1,74.853

> ui tool show "Surface Color"

> color radial #1.1 palette 160,#f66151:200,#f9f06b:240,#62a0ea

> color radial #1.1 palette 160,#f66151:200,#f9f06b:240,#62a0ea center
> 389.25,389.25,389.25

> view matrix models #2,1,0,0,173.62,0,1,0,-70.322,0,0,1,120.47

> color radial #1.1 palette 160,#f66151:200,#8ff0a4:240,#62a0ea center
> 389.25,389.25,389.25

> color radial #1.1 palette 180,#f66151:200,#8ff0a4:240,#62a0ea center
> 389.25,389.25,389.25

> color radial #1.1 palette #f66151:#8ff0a4:#62a0ea:#813d9c center
> 389.25,389.25,389.25

> color radial #1.1 palette #f66151:#8ff0a4:#62a0ea:#dc8add center
> 389.25,389.25,389.25

> view matrix models #2,1,0,0,162.49,0,1,0,-64.25,0,0,1,127.24

> volume #1 level 0.3376

> view matrix models #2,1,0,0,114.61,0,1,0,-78.991,0,0,1,104.45

> view matrix models #2,1,0,0,109.41,0,1,0,-82.161,0,0,1,101.14

> select clear

> select /E:273@CD

1 atom, 1 residue, 1 model selected  

> view matrix models #2,1,0,0,114.71,0,1,0,-65.839,0,0,1,131.02

> view matrix models #2,1,0,0,142.23,0,1,0,-67.179,0,0,1,114.02

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.96454,-0.12539,-0.23224,314.35,0.11062,0.99098,-0.075593,-67.918,0.23963,0.047221,0.96972,22.972

> view matrix models
> #2,0.99501,-0.045655,-0.088688,203.99,0.043578,0.99873,-0.025213,-70.53,0.089727,0.021223,0.99574,75.18

> view matrix models
> #2,0.88178,-0.23523,-0.40881,471.13,0.18601,0.96994,-0.1569,-48.457,0.43343,0.062309,0.89903,-19.704

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.88178,-0.23523,-0.40881,413.11,0.18601,0.96994,-0.1569,-121,0.43343,0.062309,0.89903,-134.56

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.91752,-0.36874,-0.14893,295.3,0.325,0.91109,-0.25356,-108.32,0.22919,0.18424,0.95579,-116.94

> view matrix models
> #2,0.80787,-0.46364,-0.36384,479.27,-0.074123,0.53251,-0.84317,466.86,0.58468,0.70815,0.39583,-97.151

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.80787,-0.46364,-0.36384,441.06,-0.074123,0.53251,-0.84317,532.48,0.58468,0.70815,0.39583,-161.42

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.86263,-0.41384,-0.29086,366.96,-0.22596,0.19919,-0.95355,740.82,0.45255,0.88829,0.078321,12.89

> view matrix models
> #2,0.88649,-0.41743,-0.19972,309.61,0.029749,0.48212,-0.8756,522.33,0.46179,0.77027,0.43981,-153.08

> view matrix models
> #2,0.8999,-0.38776,-0.19955,296.29,0.022188,0.49771,-0.86706,516.56,0.43553,0.77584,0.45649,-153.15

> view matrix models
> #2,0.89202,-0.41608,-0.17658,294.65,0.074825,0.5212,-0.85015,480.41,0.44576,0.74514,0.49605,-170.2

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.89202,-0.41608,-0.17658,291.58,0.074825,0.5212,-0.85015,492.94,0.44576,0.74514,0.49605,-176.7

> fitmap #2 inMap #1

Fit molecule nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) to map
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) using 14840 atoms  
average map value = 0.2289, steps = 84  
shifted from previous position = 5.98  
rotated from previous position = 4.16 degrees  
atoms outside contour = 10991, contour level = 0.33763  
  
Position of nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) relative to
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.86652900 -0.44264790 -0.23063028 342.07794690  
0.03247752 0.51109213 -0.85891213 513.87602543  
0.49806897 0.73678197 0.45725226 -171.93803735  
Axis 0.87800349 -0.40095435 0.26142967  
Axis point 0.00000000 499.23776416 337.15194867  
Rotation angle (degrees) 65.32713902  
Shift along axis 49.35509964  
  

> select clear

> select /E:178@CD1

1 atom, 1 residue, 1 model selected  

> view matrix models
> #2,0.86653,-0.44265,-0.23063,337.63,0.032478,0.51109,-0.85891,536.3,0.49807,0.73678,0.45725,-140.06

> view matrix models
> #2,0.86653,-0.44265,-0.23063,336.56,0.032478,0.51109,-0.85891,538.05,0.49807,0.73678,0.45725,-137.3

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.92189,-0.29794,-0.24768,285.12,-0.035773,0.57108,-0.82012,528.16,0.38579,0.76492,0.51581,-131.89

> view matrix models
> #2,0.90969,-0.30951,-0.27688,308.7,-0.03032,0.61545,-0.7876,496.69,0.41417,0.72487,0.55048,-150.98

> view matrix models
> #2,0.93331,-0.29072,-0.21077,258.89,0.0091917,0.60612,-0.79532,487.72,0.35897,0.74034,0.56837,-142.91

> fitmap #2 inMap #1

Fit molecule nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) to map
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) using 14840 atoms  
average map value = 0.2293, steps = 280  
shifted from previous position = 12.5  
rotated from previous position = 22.3 degrees  
atoms outside contour = 11093, contour level = 0.33763  
  
Position of nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) relative to
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.84014699 -0.51790201 -0.16102961 340.83266921  
0.31298607 0.70545069 -0.63590805 256.49193039  
0.44293651 0.48385621 0.75477839 -197.75175593  
Axis 0.73690679 -0.39746467 0.54679998  
Axis point 0.00000000 544.69522603 176.72691995  
Rotation angle (degrees) 49.44421964  
Shift along axis 41.08477358  
  

> hide sel atoms

> select clear

> hide atoms

> show cartoons

> transparency 50

> select add #1

2 models selected  

> select subtract #1

Nothing selected  

> select add #1

2 models selected  

> select subtract #1

Nothing selected  

> select add #1

2 models selected  

> select subtract #1

Nothing selected  

> volume #1 step 1

> transparency 50

> lighting soft

> lighting full

> lighting simple

> select clear

> select #1

2 models selected  

> select clear

> select /L:22

7 atoms, 6 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.84015,-0.5179,-0.16103,333.46,0.31299,0.70545,-0.63591,242.32,0.44294,0.48386,0.75478,-208.28

> view matrix models
> #2,0.84015,-0.5179,-0.16103,333.63,0.31299,0.70545,-0.63591,244.2,0.44294,0.48386,0.75478,-208.1

> fitmap #2 inMap #1

Fit molecule nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) to map
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) using 14840 atoms  
average map value = 0.2335, steps = 180  
shifted from previous position = 8.12  
rotated from previous position = 26.8 degrees  
atoms outside contour = 11144, contour level = 0.33763  
  
Position of nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) relative to
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.68387113 -0.71937057 -0.12176315 429.49522467  
0.65359903 0.67820520 -0.33592561 -36.25260738  
0.32423540 0.15014555 0.93398486 -170.75461999  
Axis 0.31910585 -0.29279817 0.90135492  
Axis point 290.68270401 472.07059276 0.00000000  
Rotation angle (degrees) 49.60671861  
Shift along axis -6.24137961  
  

> view matrix models
> #2,0.68387,-0.71937,-0.12176,429.29,0.6536,0.67821,-0.33593,-36.213,0.32424,0.15015,0.93398,-168.72

> fitmap #2 inMap #1

Fit molecule nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) to map
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) using 14840 atoms  
average map value = 0.2343, steps = 92  
shifted from previous position = 2.38  
rotated from previous position = 1.54 degrees  
atoms outside contour = 11114, contour level = 0.33763  
  
Position of nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) relative to
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.66515987 -0.73762597 -0.11606153 438.49778139  
0.67196425 0.65908969 -0.33773486 -38.31016172  
0.32561696 0.14665848 0.93405829 -170.50052962  
Axis 0.31159484 -0.28411774 0.90674460  
Axis point 295.14751280 463.48330681 0.00000000  
Rotation angle (degrees) 51.01227186  
Shift along axis -7.08219152  
  

> select clear

> ui tool show "Side View"

> select /H:88

7 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.66888,-0.73479,-0.11261,434.43,0.67068,0.66184,-0.3349,-40.055,0.32061,0.14848,0.9355,-169.79

> view matrix models
> #2,0.78442,-0.61199,-0.10083,349.82,0.42508,0.64884,-0.63112,218.98,0.45166,0.4522,0.7691,-213.25

> view matrix models
> #2,0.83288,-0.55074,-0.0547,289.67,0.32211,0.56274,-0.76129,352.29,0.45006,0.61645,0.6461,-190.49

> view matrix models
> #2,0.78626,-0.5991,-0.15125,372.68,0.39688,0.67727,-0.61952,216.3,0.47359,0.42707,0.77027,-215.83

> view matrix models
> #2,0.83375,-0.55203,0.011196,254.36,0.35472,0.51999,-0.77703,359.26,0.42313,0.65182,0.62936,-180.34

> view matrix models
> #2,0.86538,-0.49465,-0.080256,275.6,0.21576,0.51234,-0.83124,445.14,0.45229,0.70202,0.55009,-162.74

> view matrix models
> #2,0.85938,-0.48393,-0.16517,320.61,0.14913,0.54617,-0.82429,458.66,0.48911,0.68375,0.54153,-167.8

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.85938,-0.48393,-0.16517,322.29,0.14913,0.54617,-0.82429,463.52,0.48911,0.68375,0.54153,-161.85

> view matrix models
> #2,0.85938,-0.48393,-0.16517,322.48,0.14913,0.54617,-0.82429,462.75,0.48911,0.68375,0.54153,-162.78

> view matrix models
> #2,0.85938,-0.48393,-0.16517,322.55,0.14913,0.54617,-0.82429,463.49,0.48911,0.68375,0.54153,-161.93

> view matrix models
> #2,0.85938,-0.48393,-0.16517,318.18,0.14913,0.54617,-0.82429,462.28,0.48911,0.68375,0.54153,-162.49

> fitmap #2 inMap #1

Fit molecule nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) to map
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) using 14840 atoms  
average map value = 0.2292, steps = 148  
shifted from previous position = 5.31  
rotated from previous position = 13.9 degrees  
atoms outside contour = 10926, contour level = 0.33763  
  
Position of nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) relative to
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.78294287 -0.58251410 -0.21835242 406.81520055  
0.28298883 0.64607623 -0.70887434 320.38964832  
0.55400161 0.49321682 0.67068576 -200.83066193  
Axis 0.71958943 -0.46234247 0.51810278  
Axis point -0.00000000 576.90943923 190.38628013  
Rotation angle (degrees) 56.64311038  
Shift along axis 40.55925471  
  

> view matrix models
> #2,0.78294,-0.58251,-0.21835,406.99,0.28299,0.64608,-0.70887,321.82,0.554,0.49322,0.67069,-199.68

> view matrix models
> #2,0.78294,-0.58251,-0.21835,410.41,0.28299,0.64608,-0.70887,318.85,0.554,0.49322,0.67069,-203.96

> view matrix models
> #2,0.78294,-0.58251,-0.21835,412.82,0.28299,0.64608,-0.70887,322.02,0.554,0.49322,0.67069,-202.43

> view matrix models
> #2,0.78294,-0.58251,-0.21835,407.73,0.28299,0.64608,-0.70887,319.33,0.554,0.49322,0.67069,-202.21

> fitmap #2 inMap #1

Fit molecule nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) to map
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) using 14840 atoms  
average map value = 0.2291, steps = 48  
shifted from previous position = 1.85  
rotated from previous position = 0.667 degrees  
atoms outside contour = 10913, contour level = 0.33763  
  
Position of nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) relative to
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.78383716 -0.58294503 -0.21394954 404.52302535  
0.29135227 0.64951606 -0.70231242 312.83201079  
0.54837320 0.48816389 0.67895718 -201.78920970  
Axis 0.71622379 -0.45863464 0.52600167  
Axis point 0.00000000 577.28714888 183.53494092  
Rotation angle (degrees) 56.20968096  
Shift along axis 40.11195598  
  

> transparency 0

> view matrix models
> #2,0.78384,-0.58295,-0.21395,394.93,0.29135,0.64952,-0.70231,312.36,0.54837,0.48816,0.67896,-196.89

> fitmap #2 inMap #1

Fit molecule nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) to map
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) using 14840 atoms  
average map value = 0.2291, steps = 68  
shifted from previous position = 4.13  
rotated from previous position = 5.89 degrees  
atoms outside contour = 10753, contour level = 0.33763  
  
Position of nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) relative to
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.76051712 -0.57976679 -0.29237678 441.19955723  
0.21484743 0.64960643 -0.72928188 357.57784693  
0.61274326 0.49181496 0.61859821 -189.78851449  
Axis 0.71194852 -0.52772135 0.46329201  
Axis point 0.00000000 599.21005176 229.53917661  
Rotation angle (degrees) 59.04525509  
Shift along axis 37.48240312  
  

> fitmap #2 inMap #1

Fit molecule nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) to map
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) using 14840 atoms  
average map value = 0.2291, steps = 48  
shifted from previous position = 0.0232  
rotated from previous position = 0.00966 degrees  
atoms outside contour = 10753, contour level = 0.33763  
  
Position of nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) relative to
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.76045686 -0.57989305 -0.29228311 441.19676026  
0.21497720 0.64951625 -0.72932396 357.59329399  
0.61277252 0.49178521 0.61859287 -189.78378331  
Axis 0.71191693 -0.52765505 0.46341604  
Axis point 0.00000000 599.17505934 229.47071769  
Rotation angle (degrees) 59.05045864  
Shift along axis 37.46068523  
  

> view matrix models
> #2,0.76046,-0.57989,-0.29228,443.01,0.21498,0.64952,-0.72932,362.15,0.61277,0.49179,0.61859,-185.71

> view matrix models
> #2,0.76046,-0.57989,-0.29228,443.13,0.21498,0.64952,-0.72932,361.48,0.61277,0.49179,0.61859,-186.52

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.76268,-0.5931,-0.25797,427.38,0.30024,0.67795,-0.671,289.03,0.57286,0.43431,0.69513,-196.48

> view matrix models
> #2,0.80065,-0.59913,0.0016382,274.9,0.42784,0.56982,-0.70161,283.95,0.41942,0.56245,0.71256,-179.48

> fitmap #2 inMap #1

Fit molecule nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) to map
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) using 14840 atoms  
average map value = 0.2212, steps = 100  
shifted from previous position = 7.14  
rotated from previous position = 13 degrees  
atoms outside contour = 10972, contour level = 0.33763  
  
Position of nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) relative to
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.77427023 -0.59226979 -0.22298455 409.84382843  
0.31742784 0.66827240 -0.67279385 285.07001957  
0.54748989 0.45014275 0.70542635 -197.97929011  
Axis 0.68566552 -0.47045199 0.55546172  
Axis point 0.00000000 589.39414844 158.93046511  
Rotation angle (degrees) 54.97145365  
Shift along axis 36.93410565  
  

> select clear

> select /B:34

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view matrix models
> #2,0.7886,-0.57258,-0.22418,399.58,0.36293,0.72771,-0.58199,202.62,0.49638,0.3776,0.78168,-199.35

> view matrix models
> #2,0.57662,-0.77774,-0.25027,551.84,0.61231,0.61418,-0.49786,89.485,0.54091,0.13383,0.83036,-178.01

> fitmap #2 inMap #1

Fit molecule nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) to map
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) using 14840 atoms  
average map value = 0.2227, steps = 112  
shifted from previous position = 4.06  
rotated from previous position = 5.31 degrees  
atoms outside contour = 11127, contour level = 0.33763  
  
Position of nWNV86rsr063BTF_ssm_MatKUNV.pdb (#2) relative to
cryosparc_P152_J59_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.57196302 -0.77309166 -0.27420355 565.72726136  
0.55370729 0.61050904 -0.56629228 153.43175757  
0.60519959 0.17206974 0.77725508 -187.73676586  
Axis 0.42079433 -0.50117401 0.75614598  
Axis point 153.23505677 636.47915023 0.00000000  
Rotation angle (degrees) 61.32350802  
Shift along axis 19.20241123  
  

> view matrix models
> #2,0.49866,-0.74223,-0.44769,679.37,0.22375,0.60921,-0.76079,388.09,0.83742,0.2792,0.46986,-143.13

> view matrix models
> #2,0.34266,-0.48945,-0.80189,863.29,-0.3963,0.69859,-0.59574,520.28,0.85178,0.52193,0.045409,13.961

> view matrix models
> #2,0.3008,-0.49086,-0.81767,888.62,-0.35215,0.73961,-0.57355,480.04,0.88629,0.46047,0.049625,14.481

> view matrix models
> #2,0.37575,-0.79995,-0.46786,754.02,-0.18515,0.42987,-0.8837,662.98,0.90804,0.41868,0.013413,36.453

> view matrix models
> #2,0.57695,-0.65172,-0.49232,648.29,0.25554,0.71653,-0.64906,287.07,0.77577,0.24867,0.57995,-169.67

> view matrix models
> #2,0.70576,-0.53672,-0.46242,550.82,-0.14977,0.52493,-0.83787,599.13,0.69244,0.66059,0.29009,-91.304


===== 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  




OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA GeForce GTX 750 Ti/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=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Supermicro
Model: Super Server
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v3 @ 3.50GHz
Cache Size: 15360 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi        29Gi       9.7Gi       1.7Gi        25Gi        32Gi
	Swap:          8.0Gi       3.0Gi       5.0Gi

Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107 [GeForce GTX 750 Ti] [10de:1380] (rev a2)	
	Subsystem: eVga.com. Corp. GM107 [GeForce GTX 750 Ti] [3842:3751]	
	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, 8 months ago

Cc: Greg Couch added
Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash drawing scene

comment:2 by Tom Goddard, 8 months ago

Resolution: → can't reproduce
Status: assigned → closed

Crashed in OpenGL. Possible remote display or graphics driver issue.

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