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Opened 17 months ago
Closed 17 months ago
#15215 closed defect (duplicate)
Crash in python_instances_of_class
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.0-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202403271703 (2024-03-27 17:03:08 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 0x00007ff84d093e80 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 2636 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in include_state
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 260 in discovery
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 641 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 917 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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.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, 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, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 60)
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{
"uptime" : 1100000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 213944,
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"captureTime" : "2024-05-15 13:03:51.3543 +0200",
"codeSigningMonitor" : 0,
"incident" : "54D14E13-218D-42D8-BB4A-AF17392CDEB8",
"pid" : 82618,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-05-15 12:40:38.5137 +0200",
"procStartAbsTime" : 1114942001930540,
"procExitAbsTime" : 1116334801867905,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"0A66F1B3-3BBD-5766-A05A-47C82466196B","thirdParty":true},
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"crashReporterKey" : "7DAF7761-BC1D-32F0-F7DC-21A113FACD02",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 11049,
"bridgeVersion" : {"build":"21P365","train":"8.0"},
"sleepWakeUUID" : "2DE832EF-D130-43F6-81BE-15A87DB97CEA",
"sip" : "enabled",
"vmRegionInfo" : "0x900e is not in any region. Bytes before following region: 4507987954\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10cb30000-10cb34000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x000000000000900e","rawCodes":[1,36878],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000900e"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":82618},
"vmregioninfo" : "0x900e is not in any region. Bytes before following region: 4507987954\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10cb30000-10cb34000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/adriasogues/Desktop/PS2/EM_ready_maps/J314_EMREADY_map.mrc
Opened J314_EMREADY_map.mrc as #1, grid size 425,425,425, pixel 1, shown at
level 1.95, step 2, values float32
> open /Users/adriasogues/Downloads/fold_2024_05_13_14_53_model_0.cif
Chain information for fold_2024_05_13_14_53_model_0.cif #2
---
Chain | Description
A B C | .
> select add #2
10100 atoms, 10254 bonds, 1304 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,212.41,0,1,0,242.67,0,0,1,70.728
> view matrix models #2,1,0,0,202.89,0,1,0,250.55,0,0,1,197.65
> view matrix models
> #2,0.19256,-0.036876,-0.98059,215.38,0.080823,0.99649,-0.021603,249.13,0.97795,-0.075095,0.19486,179.71
> view matrix models
> #2,0.1863,0.01981,-0.98229,216.11,0.747,-0.65228,0.12852,219.71,-0.63818,-0.75772,-0.13632,199.16
> view matrix models
> #2,0.034107,0.37422,-0.92671,222.65,-0.33039,-0.8709,-0.36384,235.1,-0.94323,0.31859,0.093937,216.42
> view matrix models
> #2,0.68736,-0.015707,-0.72615,207.45,-0.2335,-0.95147,-0.20045,232.69,-0.68776,0.30733,-0.65767,211.42
> view matrix models
> #2,0.68736,-0.015707,-0.72615,173.24,-0.2335,-0.95147,-0.20045,220.28,-0.68776,0.30733,-0.65767,219.7
> view matrix models
> #2,0.68736,-0.015707,-0.72615,189.39,-0.2335,-0.95147,-0.20045,227.25,-0.68776,0.30733,-0.65767,215.91
> view matrix models
> #2,0.64131,0.0019978,-0.76728,190.33,-0.22059,-0.9573,-0.18687,226.98,-0.73489,0.28909,-0.61348,216.53
> fitmap #2 inMap #1
Fit molecule fold_2024_05_13_14_53_model_0.cif (#2) to map
J314_EMREADY_map.mrc (#1) using 10100 atoms
average map value = 3.574, steps = 772
shifted from previous position = 6.66
rotated from previous position = 15 degrees
atoms outside contour = 3798, contour level = 1.9468
Position of fold_2024_05_13_14_53_model_0.cif (#2) relative to
J314_EMREADY_map.mrc (#1) coordinates:
Matrix rotation and translation
0.44322148 0.04476165 -0.89529387 186.26280257
-0.14517933 -0.98198256 -0.12096782 231.39400328
-0.88457769 0.18359370 -0.42873730 219.56236830
Axis 0.84813335 -0.02984209 -0.52894165
Axis point 0.00000000 106.27249284 180.26530415
Rotation angle (degrees) 169.65655898
Shift along axis 34.93473299
> fitmap #2 inMap #1
Fit molecule fold_2024_05_13_14_53_model_0.cif (#2) to map
J314_EMREADY_map.mrc (#1) using 10100 atoms
average map value = 3.574, steps = 400
shifted from previous position = 0.0118
rotated from previous position = 0.0154 degrees
atoms outside contour = 3797, contour level = 1.9468
Position of fold_2024_05_13_14_53_model_0.cif (#2) relative to
J314_EMREADY_map.mrc (#1) coordinates:
Matrix rotation and translation
0.44304587 0.04482735 -0.89537750 186.25390131
-0.14501257 -0.98201320 -0.12091914 231.40128956
-0.88469301 0.18341372 -0.42857636 219.56019884
Axis 0.84808305 -0.02977444 -0.52902610
Axis point 0.00000000 106.27741091 180.26641164
Rotation angle (degrees) 169.66379058
Shift along axis 34.91585805
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 step 1
> volume #1 level 4
> fitmap #2 inMap #1
Fit molecule fold_2024_05_13_14_53_model_0.cif (#2) to map
J314_EMREADY_map.mrc (#1) using 10100 atoms
average map value = 3.574, steps = 292
shifted from previous position = 0.0133
rotated from previous position = 0.0159 degrees
atoms outside contour = 6382, contour level = 4
Position of fold_2024_05_13_14_53_model_0.cif (#2) relative to
J314_EMREADY_map.mrc (#1) coordinates:
Matrix rotation and translation
0.44326887 0.04479280 -0.89526886 186.25007005
-0.14511365 -0.98199065 -0.12098095 231.39155490
-0.88456472 0.18354282 -0.42878583 219.55184435
Axis 0.84814782 -0.02981274 -0.52892010
Axis point 0.00000000 106.27014887 180.25055560
Rotation angle (degrees) 169.65803365
Shift along axis 34.94379055
> open
> /Users/adriasogues/Desktop/PS2/FINAL_Strucutre/Full_good_seq_real_space_refined_009-coot-5.pdb
Summary of feedback from opening
/Users/adriasogues/Desktop/PS2/FINAL_Strucutre/Full_good_seq_real_space_refined_009-coot-5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP G 12 ASP G 14 1 3
Start residue of secondary structure not found: HELIX 2 2 GLU G 28 GLN G 46 1
19
Start residue of secondary structure not found: HELIX 3 3 VAL G 50 ALA G 56 1
7
Start residue of secondary structure not found: HELIX 4 4 GLU G 71 ALA G 128 1
58
Start residue of secondary structure not found: HELIX 5 5 PRO G 139 THR G 141
1 3
4 messages similar to the above omitted
End residue of secondary structure not found: HELIX 10 10 VAL G 255 GLU G 287
1 33
Start residue of secondary structure not found: HELIX 11 11 LEU G 302 ALA G
333 1 32
Start residue of secondary structure not found: HELIX 12 12 ASP G 348 VAL G
372 1 25
Start residue of secondary structure not found: HELIX 13 13 GLN G 374 GLU G
429 1 56
Start residue of secondary structure not found: HELIX 14 14 ASP H 12 ASP H 14
1 3
Start residue of secondary structure not found: HELIX 15 15 GLU H 28 GLN H 46
1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 23 23 VAL H 255 GLU H 287
1 33
Start residue of secondary structure not found: HELIX 24 24 LEU H 302 ALA H
333 1 32
Start residue of secondary structure not found: HELIX 25 25 ASP H 348 VAL H
372 1 25
Start residue of secondary structure not found: HELIX 26 26 GLN H 374 GLU H
429 1 56
Start residue of secondary structure not found: HELIX 27 27 ASP I 12 ASP I 14
1 3
Start residue of secondary structure not found: HELIX 28 28 GLU I 28 GLN I 46
1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 VAL I 255 GLU I 287
1 33
Start residue of secondary structure not found: HELIX 37 37 LEU I 302 ALA I
333 1 32
Start residue of secondary structure not found: HELIX 38 38 ASP I 348 VAL I
372 1 25
Start residue of secondary structure not found: HELIX 39 39 GLN I 374 GLU I
429 1 56
Start residue of secondary structure not found: HELIX 40 40 ASP J 12 ASP J 14
1 3
Start residue of secondary structure not found: HELIX 41 41 GLU J 28 GLN J 46
1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 49 49 VAL J 255 GLU J 287
1 33
Start residue of secondary structure not found: HELIX 50 50 LEU J 302 ALA J
333 1 32
Start residue of secondary structure not found: HELIX 51 51 ASP J 348 VAL J
372 1 25
Start residue of secondary structure not found: HELIX 52 52 GLN J 374 GLU J
429 1 56
Start residue of secondary structure not found: HELIX 53 53 ASP K 12 ASP K 14
1 3
Start residue of secondary structure not found: HELIX 54 54 GLU K 28 GLN K 46
1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 62 62 VAL K 255 GLU K 287
1 33
Start residue of secondary structure not found: HELIX 63 63 LEU K 302 ALA K
333 1 32
Start residue of secondary structure not found: HELIX 64 64 ASP K 348 VAL K
372 1 25
Start residue of secondary structure not found: HELIX 65 65 GLN K 374 GLU K
429 1 56
Start residue of secondary structure not found: HELIX 66 66 ASP L 12 ASP L 14
1 3
Start residue of secondary structure not found: HELIX 67 67 GLU L 28 GLN L 46
1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 75 75 VAL L 255 GLU L 287
1 33
Start residue of secondary structure not found: HELIX 76 76 LEU L 302 ALA L
333 1 32
Start residue of secondary structure not found: HELIX 77 77 ASP L 348 VAL L
372 1 25
Start residue of secondary structure not found: HELIX 78 78 GLN L 374 GLU L
429 1 56
Start residue of secondary structure not found: HELIX 79 79 ASP M 12 ASP M 14
1 3
Start residue of secondary structure not found: HELIX 80 80 GLU M 28 GLN M 46
1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 88 88 VAL M 255 GLU M 287
1 33
Start residue of secondary structure not found: HELIX 89 89 LEU M 302 ALA M
333 1 32
Start residue of secondary structure not found: HELIX 90 90 ASP M 348 VAL M
372 1 25
Start residue of secondary structure not found: HELIX 91 91 GLN M 374 GLU M
429 1 56
Start residue of secondary structure not found: HELIX 92 92 ASP N 12 ASP N 14
1 3
Start residue of secondary structure not found: HELIX 93 93 GLU N 28 GLN N 46
1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 101 101 VAL N 255 GLU N
287 1 33
Start residue of secondary structure not found: HELIX 102 102 LEU N 302 ALA N
333 1 32
Start residue of secondary structure not found: HELIX 103 103 ASP N 348 VAL N
372 1 25
Start residue of secondary structure not found: HELIX 104 104 GLN N 374 GLU N
429 1 56
Start residue of secondary structure not found: HELIX 105 105 ASP O 12 ASP O
14 1 3
Start residue of secondary structure not found: HELIX 106 106 GLU O 28 GLN O
46 1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 114 114 VAL O 255 GLU O
287 1 33
Start residue of secondary structure not found: HELIX 115 115 LEU O 302 ALA O
333 1 32
Start residue of secondary structure not found: HELIX 116 116 ASP O 348 VAL O
372 1 25
Start residue of secondary structure not found: HELIX 117 117 GLN O 374 GLU O
429 1 56
Start residue of secondary structure not found: HELIX 118 118 ASP P 12 ASP P
14 1 3
Start residue of secondary structure not found: HELIX 119 119 GLU P 28 GLN P
46 1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 127 127 VAL P 255 GLU P
287 1 33
Start residue of secondary structure not found: HELIX 128 128 LEU P 302 ALA P
333 1 32
Start residue of secondary structure not found: HELIX 129 129 ASP P 348 VAL P
372 1 25
Start residue of secondary structure not found: HELIX 130 130 GLN P 374 GLU P
429 1 56
Start residue of secondary structure not found: HELIX 131 131 ASP Q 12 ASP Q
14 1 3
Start residue of secondary structure not found: HELIX 132 132 GLU Q 28 GLN Q
46 1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 140 140 VAL Q 255 GLU Q
287 1 33
Start residue of secondary structure not found: HELIX 141 141 LEU Q 302 ALA Q
333 1 32
Start residue of secondary structure not found: HELIX 142 142 ASP Q 348 VAL Q
372 1 25
Start residue of secondary structure not found: HELIX 143 143 GLN Q 374 GLU Q
429 1 56
Start residue of secondary structure not found: HELIX 144 144 ASP R 12 ASP R
14 1 3
Start residue of secondary structure not found: HELIX 145 145 GLU R 28 GLN R
46 1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 153 153 VAL R 255 GLU R
287 1 33
Start residue of secondary structure not found: HELIX 154 154 LEU R 302 ALA R
333 1 32
Start residue of secondary structure not found: HELIX 155 155 ASP R 348 VAL R
372 1 25
Start residue of secondary structure not found: HELIX 156 156 GLN R 374 GLU R
429 1 56
Start residue of secondary structure not found: HELIX 157 157 ASP S 12 ASP S
14 1 3
Start residue of secondary structure not found: HELIX 158 158 GLU S 28 GLN S
46 1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 166 166 VAL S 255 GLU S
287 1 33
Start residue of secondary structure not found: HELIX 167 167 LEU S 302 ALA S
333 1 32
Start residue of secondary structure not found: HELIX 168 168 ASP S 348 VAL S
372 1 25
Start residue of secondary structure not found: HELIX 169 169 GLN S 374 GLU S
429 1 56
Start residue of secondary structure not found: HELIX 170 170 ASP T 12 ASP T
14 1 3
Start residue of secondary structure not found: HELIX 171 171 GLU T 28 GLN T
46 1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 179 179 VAL T 255 GLU T
287 1 33
Start residue of secondary structure not found: HELIX 180 180 LEU T 302 ALA T
333 1 32
Start residue of secondary structure not found: HELIX 181 181 ASP T 348 VAL T
372 1 25
Start residue of secondary structure not found: HELIX 182 182 GLN T 374 GLU T
429 1 56
Start residue of secondary structure not found: HELIX 183 183 ASP U 12 ASP U
14 1 3
Start residue of secondary structure not found: HELIX 184 184 GLU U 28 GLN U
46 1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 192 192 VAL U 255 GLU U
287 1 33
Start residue of secondary structure not found: HELIX 193 193 LEU U 302 ALA U
333 1 32
Start residue of secondary structure not found: HELIX 194 194 ASP U 348 VAL U
372 1 25
Start residue of secondary structure not found: HELIX 195 195 GLN U 374 GLU U
429 1 56
Start residue of secondary structure not found: HELIX 196 196 ASP V 12 ASP V
14 1 3
Start residue of secondary structure not found: HELIX 197 197 GLU V 28 GLN V
46 1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 205 205 VAL V 255 GLU V
287 1 33
Start residue of secondary structure not found: HELIX 206 206 LEU V 302 ALA V
333 1 32
Start residue of secondary structure not found: HELIX 207 207 ASP V 348 VAL V
372 1 25
Start residue of secondary structure not found: HELIX 208 208 GLN V 374 GLU V
429 1 56
Start residue of secondary structure not found: HELIX 209 209 ASP W 12 ASP W
14 1 3
Start residue of secondary structure not found: HELIX 210 210 GLU W 28 GLN W
46 1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 218 218 VAL W 255 GLU W
287 1 33
Start residue of secondary structure not found: HELIX 219 219 LEU W 302 ALA W
333 1 32
Start residue of secondary structure not found: HELIX 220 220 ASP W 348 VAL W
372 1 25
Start residue of secondary structure not found: HELIX 221 221 GLN W 374 GLU W
429 1 56
Start residue of secondary structure not found: HELIX 222 222 ASP X 12 ASP X
14 1 3
Start residue of secondary structure not found: HELIX 223 223 GLU X 28 GLN X
46 1 19
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 231 231 VAL X 255 GLU X
287 1 33
Start residue of secondary structure not found: HELIX 232 232 LEU X 302 ALA X
333 1 32
Start residue of secondary structure not found: HELIX 233 233 ASP X 348 VAL X
372 1 25
Start residue of secondary structure not found: HELIX 234 234 GLN X 374 GLU X
429 1 56
Chain information for Full_good_seq_real_space_refined_009-coot-5.pdb #3
---
Chain | Description
G H I J K L M N O P Q R S T U V W X | No description available
> volume flip #1
Opened J314_EMREADY_map.mrc z flip as #4, grid size 425,425,425, pixel 1,
shown at step 1, values float32
> hide #2 models
> open
> /Users/adriasogues/Desktop/PS2/EM_ready_maps/J331_volume_map_emready.mrc
Opened J331_volume_map_emready.mrc as #5, grid size 638,638,638, pixel 0.5,
shown at level 1.9, step 4, values float32
> close #5
> open
> /Users/adriasogues/Desktop/PS2/EM_ready_maps/J251_volume_map_emready.mrc
Opened J251_volume_map_emready.mrc as #5, grid size 425,425,425, pixel 1,
shown at level 2.04, step 2, values float32
> close #5
> open /Users/adriasogues/Desktop/PS2/J187_008_volume_map_emready.mrc
Opened J187_008_volume_map_emready.mrc as #5, grid size 425,425,425, pixel 1,
shown at level 2.41, step 2, values float32
> close #5
> fitmap #3 inMap #4
Fit molecule Full_good_seq_real_space_refined_009-coot-5.pdb (#3) to map
J314_EMREADY_map.mrc z flip (#4) using 60516 atoms
average map value = 1.734, steps = 64
shifted from previous position = 1.16
rotated from previous position = 0.206 degrees
atoms outside contour = 50443, contour level = 4
Position of Full_good_seq_real_space_refined_009-coot-5.pdb (#3) relative to
J314_EMREADY_map.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.99999367 -0.00348350 -0.00072970 0.94159048
0.00348390 0.99999378 0.00055008 -0.78879295
0.00072778 -0.00055262 0.99999958 -1.19098117
Axis -0.15308567 -0.20233920 0.96727639
Axis point 292.81227133 219.82120369 0.00000000
Rotation angle (degrees) 0.20635432
Shift along axis -1.13654825
> fitmap #3 inMap #4
Fit molecule Full_good_seq_real_space_refined_009-coot-5.pdb (#3) to map
J314_EMREADY_map.mrc z flip (#4) using 60516 atoms
average map value = 1.734, steps = 40
shifted from previous position = 0.0162
rotated from previous position = 0.000561 degrees
atoms outside contour = 50441, contour level = 4
Position of Full_good_seq_real_space_refined_009-coot-5.pdb (#3) relative to
J314_EMREADY_map.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.99999367 -0.00348378 -0.00072301 0.94617357
0.00348417 0.99999378 0.00054294 -0.80248619
0.00072112 -0.00054545 0.99999959 -1.19169198
Axis -0.15119054 -0.20060805 0.96793483
Axis point 296.10053537 221.77510796 0.00000000
Rotation angle (degrees) 0.20623029
Shift along axis -1.13554747
> fitmap #3 inMap #4
Fit molecule Full_good_seq_real_space_refined_009-coot-5.pdb (#3) to map
J314_EMREADY_map.mrc z flip (#4) using 60516 atoms
average map value = 1.734, steps = 40
shifted from previous position = 0.00935
rotated from previous position = 0.000166 degrees
atoms outside contour = 50447, contour level = 4
Position of Full_good_seq_real_space_refined_009-coot-5.pdb (#3) relative to
J314_EMREADY_map.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.99999367 -0.00348364 -0.00072377 0.93717834
0.00348404 0.99999378 0.00054574 -0.80096961
0.00072186 -0.00054826 0.99999959 -1.19102781
Axis -0.15195093 -0.20079070 0.96777787
Axis point 295.65501627 219.01195315 0.00000000
Rotation angle (degrees) 0.20625591
Shift along axis -1.13422824
> fitmap #3 inMap #4
Fit molecule Full_good_seq_real_space_refined_009-coot-5.pdb (#3) to map
J314_EMREADY_map.mrc z flip (#4) using 60516 atoms
average map value = 1.734, steps = 44
shifted from previous position = 0.00475
rotated from previous position = 0.000247 degrees
atoms outside contour = 50445, contour level = 4
Position of Full_good_seq_real_space_refined_009-coot-5.pdb (#3) relative to
J314_EMREADY_map.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.99999368 -0.00347956 -0.00072330 0.93897869
0.00347996 0.99999380 0.00054446 -0.80369398
0.00072140 -0.00054698 0.99999959 -1.19141007
Axis -0.15177408 -0.20089778 0.96778340
Axis point 296.81168593 219.84960829 0.00000000
Rotation angle (degrees) 0.20601300
Shift along axis -1.13407918
> fitmap #3 inMap #4
Fit molecule Full_good_seq_real_space_refined_009-coot-5.pdb (#3) to map
J314_EMREADY_map.mrc z flip (#4) using 60516 atoms
average map value = 1.734, steps = 44
shifted from previous position = 0.0194
rotated from previous position = 0.00533 degrees
atoms outside contour = 50436, contour level = 4
Position of Full_good_seq_real_space_refined_009-coot-5.pdb (#3) relative to
J314_EMREADY_map.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.99999335 -0.00357217 -0.00073086 0.96239838
0.00357257 0.99999347 0.00054710 -0.80463091
0.00072890 -0.00054971 0.99999958 -1.19231633
Axis -0.14873289 -0.19794947 0.96886250
Axis point 288.74202640 221.45169453 0.00000000
Rotation angle (degrees) 0.21126059
Shift along axis -1.13905460
> fitmap #3 inMap #4
Fit molecule Full_good_seq_real_space_refined_009-coot-5.pdb (#3) to map
J314_EMREADY_map.mrc z flip (#4) using 60516 atoms
average map value = 1.734, steps = 40
shifted from previous position = 0.00672
rotated from previous position = 0.00504 degrees
atoms outside contour = 50446, contour level = 4
Position of Full_good_seq_real_space_refined_009-coot-5.pdb (#3) relative to
J314_EMREADY_map.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.99999367 -0.00348421 -0.00072792 0.94850418
0.00348461 0.99999378 0.00054728 -0.78983534
0.00072601 -0.00054981 0.99999959 -1.19137722
Axis -0.15231121 -0.20185240 0.96750034
Axis point 292.96349554 221.96275739 0.00000000
Rotation angle (degrees) 0.20634856
Shift along axis -1.13769552
> fitmap #3 inMap #4
Fit molecule Full_good_seq_real_space_refined_009-coot-5.pdb (#3) to map
J314_EMREADY_map.mrc z flip (#4) using 60516 atoms
average map value = 1.734, steps = 40
shifted from previous position = 0.00827
rotated from previous position = 0.000416 degrees
atoms outside contour = 50443, contour level = 4
Position of Full_good_seq_real_space_refined_009-coot-5.pdb (#3) relative to
J314_EMREADY_map.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.99999364 -0.00349042 -0.00072976 0.94321022
0.00349082 0.99999376 0.00055054 -0.78744788
0.00072784 -0.00055308 0.99999958 -1.19050510
Axis -0.15292627 -0.20197654 0.96737740
Axis point 291.74791894 219.88718158 0.00000000
Rotation angle (degrees) 0.20674290
Shift along axis -1.13686336
> select add #3
70616 atoms, 71760 bonds, 9080 residues, 2 models selected
> show sel & #3 cartoons
> hide sel & #3 atoms
> view matrix models
> #2,0.40101,0.28658,-0.87009,182.05,-0.011869,-0.9481,-0.31775,224.79,-0.916,0.13775,-0.3768,222.05,#3,0.96879,-0.23777,0.070124,41.132,0.24011,0.97037,-0.026912,-38.545,-0.061648,0.042909,0.99718,3.4924
> fitmap #3 inMap #4
Fit molecule Full_good_seq_real_space_refined_009-coot-5.pdb (#3) to map
J314_EMREADY_map.mrc z flip (#4) using 60516 atoms
average map value = 2.626, steps = 116
shifted from previous position = 1.98
rotated from previous position = 4.88 degrees
atoms outside contour = 45292, contour level = 4
Position of Full_good_seq_real_space_refined_009-coot-5.pdb (#3) relative to
J314_EMREADY_map.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.96077592 -0.27732570 -0.00028715 67.47750746
0.27732578 0.96077590 0.00029738 -50.76762454
0.00019342 -0.00036535 0.99999991 -0.98771428
Axis -0.00119487 -0.00086643 0.99999891
Axis point 213.21243886 213.15450325 0.00000000
Rotation angle (degrees) 16.10067931
Shift along axis -1.02435319
> transparency #4.1 50
> show sel & #3 atoms
> style sel & #3 stick
Changed 60516 atom styles
> style sel & #3 ball
Changed 60516 atom styles
> color sel & #3 byhetero
> select clear
> fitmap #3 inMap #4
Fit molecule Full_good_seq_real_space_refined_009-coot-5.pdb (#3) to map
J314_EMREADY_map.mrc z flip (#4) using 60516 atoms
average map value = 2.626, steps = 48
shifted from previous position = 0.0228
rotated from previous position = 0.00198 degrees
atoms outside contour = 45302, contour level = 4
Position of Full_good_seq_real_space_refined_009-coot-5.pdb (#3) relative to
J314_EMREADY_map.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.96078039 -0.27731020 -0.00030092 67.49605681
0.27731028 0.96078038 0.00027005 -50.74896731
0.00021423 -0.00034290 0.99999992 -0.99507006
Axis -0.00110518 -0.00092882 0.99999896
Axis point 213.16645852 213.24359019 0.00000000
Rotation angle (degrees) 16.09975390
Shift along axis -1.02252742
> volume flip #4
Opened J314_EMREADY_map.mrc z flip z flip as #5, grid size 425,425,425, pixel
1, shown at step 1, values float32
> select add #3
60516 atoms, 61506 bonds, 7776 residues, 1 model selected
> view matrix models
> #3,0.044014,0.99903,-0.0021503,-8.569,0.99868,-0.043941,0.026684,3.4783,0.026563,-0.0033219,-0.99964,451.89
> view matrix models
> #3,0.044014,0.99903,-0.0021503,-20.994,0.99868,-0.043941,0.026684,13.526,0.026563,-0.0033219,-0.99964,430.55
> view matrix models
> #3,0.044014,0.99903,-0.0021503,-17.176,0.99868,-0.043941,0.026684,-6.1799,0.026563,-0.0033219,-0.99964,427.3
> view matrix models
> #3,0.044014,0.99903,-0.0021503,-10.99,0.99868,-0.043941,0.026684,11.835,0.026563,-0.0033219,-0.99964,417.49
> view matrix models
> #3,-0.25762,0.96528,-0.043097,69.814,0.9656,0.25882,0.024989,-45.194,0.035276,-0.035176,-0.99876,422.22
> fitmap #3 inMap #5
Fit molecule Full_good_seq_real_space_refined_009-coot-5.pdb (#3) to map
J314_EMREADY_map.mrc z flip z flip (#5) using 60516 atoms
average map value = 6.303, steps = 164
shifted from previous position = 8.2
rotated from previous position = 7.76 degrees
atoms outside contour = 17170, contour level = 4
Position of Full_good_seq_real_space_refined_009-coot-5.pdb (#3) relative to
J314_EMREADY_map.mrc z flip z flip (#5) coordinates:
Matrix rotation and translation
-0.13539419 0.99079157 0.00069453 30.68346357
0.99079166 0.13539452 -0.00045775 -26.73415927
-0.00054757 0.00062616 -0.99999966 425.08189089
Axis 0.65749814 0.75345617 0.00005588
Axis point 27.12267611 -0.00000000 212.53355486
Rotation angle (degrees) 179.95277303
Shift along axis 0.05505464
> select clear
> open /Users/adriasogues/Downloads/fold_2024_05_13_14_53_model_0.cif
Chain information for fold_2024_05_13_14_53_model_0.cif #6
---
Chain | Description
A B C | .
> select add #6
10100 atoms, 10254 bonds, 1304 residues, 1 model selected
> select clear
> hide #!5 models
Drag select of 1 atoms, 2 residues, 1 bonds
Alignment identifier is 3/L
> select #3/L:343
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/L:343
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/B:111
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 1 atoms, 2 bonds
Alignment identifier is 6/B
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Already setting window visible!
> select #3/L:372-373
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/L:372-375
31 atoms, 30 bonds, 4 residues, 1 model selected
> show #!5 models
> select #6/B:255@OG
1 atom, 1 residue, 1 model selected
> select #3/L:372
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/L:372-375
31 atoms, 30 bonds, 4 residues, 1 model selected
> select #3/L:285
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/L:285-288
30 atoms, 29 bonds, 4 residues, 1 model selected
> view matrix models
> #3,-0.13539,0.99079,0.00069453,30.223,0.99079,0.13539,-0.00045775,-27.191,-0.00054757,0.00062616,-1,425.31
> undo
> ui tool show "Side View"
Drag select of 73 atoms, 29 residues, 61 bonds
Drag select of 235 atoms, 54 residues, 201 bonds
Drag select of 17 atoms, 107 residues, 11 bonds
> ui tool show Matchmaker
> matchmaker #6 & sel to #3 & sel
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 Full_good_seq_real_space_refined_009-coot-5.pdb, chain L (#3) with
fold_2024_05_13_14_53_model_0.cif, chain B (#6), sequence alignment score =
326.1
RMSD between 63 pruned atom pairs is 0.735 angstroms; (across all 63 pairs:
0.735)
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select #6/B:255
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/B:255-259
36 atoms, 35 bonds, 5 residues, 1 model selected
> style sel stick
Changed 36 atom styles
> select clear
> style #3,6 stick
Changed 70616 atom styles
> show #3,6 atoms
Drag select of 16 atoms, 7 residues, 13 bonds
> select up
59 atoms, 53 bonds, 10 residues, 2 models selected
> select up
79 atoms, 73 bonds, 10 residues, 2 models selected
> select up
1574 atoms, 1604 bonds, 196 residues, 2 models selected
> select up
6726 atoms, 6835 bonds, 864 residues, 2 models selected
> select ~sel & ##selected
63890 atoms, 64925 bonds, 8216 residues, 2 models selected
> delete sel
> hide #6 models
> show #6 models
> show #!4 models
> hide #!4 models
> show #!5 models
> select #6/B:255
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/B:255-260
47 atoms, 46 bonds, 6 residues, 1 model selected
> select #6/B:255
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/B:255
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/B:112@OD1
1 atom, 1 residue, 1 model selected
> select add #3/L:282@OE2
2 atoms, 2 residues, 2 models selected
> hide #!5 models
> select add #6/B:255@OG
3 atoms, 3 residues, 2 models selected
> view sel
> show #!5 models
> show #2 models
> mmaker #2 to #6
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 fold_2024_05_13_14_53_model_0.cif, chain B (#6) with
fold_2024_05_13_14_53_model_0.cif, chain A (#2), sequence alignment score =
2207.4
RMSD between 411 pruned atom pairs is 0.544 angstroms; (across all 432 pairs:
0.868)
> close #6
> save /Users/adriasogues/Desktop/PS2/AF3_Ca++/superpositions_V1.cxs
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/adriasogues/Downloads/fold_2024_05_13_14_53_model_0.cif
Chain information for fold_2024_05_13_14_53_model_0.cif #1
---
Chain | Description
A B C | .
OpenGL version: 4.1 INTEL-22.1.27
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2,3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2020.0.1.0.0 (iBridge: 21.16.365.0.0,0)
OS Loader Version: 580~439
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 37 days, 5 hours, 40 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
MSI MP271Q:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: PA3T161900078
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 5,06
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
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: 2.12.1
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: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
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: 1.8.dev202403271703
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
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: 1.1.1
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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-PICKLUSTER: 0.5
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
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-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
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: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 17 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class |
comment:2 by , 17 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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