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Opened 5 months ago
Closed 5 months ago
#17807 closed defect (can't reproduce)
Crash in python_instances_of_class saving session
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.1.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00007ff84b706b40 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 52 in
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 61 in
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 61 in python_instances_of_class
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 2642 in
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 290 in
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 290 in include_state
File "/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 646 in save
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 922 in save
File "/Applications/ChimeraX-1.8.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-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.8.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-1.8.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-1.8.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-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 61)
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{
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"procRole" : "Foreground",
"version" : 2,
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"captureTime" : "2025-05-26 12:47:53.2627 +0200",
"codeSigningMonitor" : 0,
"incident" : "C21D0F1E-38A7-49FC-932B-D3E49B42A61F",
"pid" : 1697,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-26 12:42:07.5712 +0200",
"procStartAbsTime" : 890372039269,
"procExitAbsTime" : 1236015526779,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"crashReporterKey" : "DB56B5AD-0CD9-2D16-8E96-8D112F6D657A",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"codeSigningTrustLevel" : 4294967295,
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"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4380901376\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1051f4000-1051f8000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":1697},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4380901376\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1051f4000-1051f8000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> mousemode shift leftMode "translate selected models"
> mousemode shift middleMode "rotate selected models"
> mousemode rightMode zoom
> mousemode control wheelMode "contour level"
> mousemode setting "contour level" speed 0.1
> mousemode shift wheelMode "rotate selected models"
> camera ortho
> set bgColor grey
> lighting shadows false
> lighting depthCue false
> graphics silhouettes true
> lighting simple
> functionkey F1 cofr sel
> functionkey F2 mousemode rightMode 'mark surface'
> functionkey F3 mousemode rightMode 'move markers'
> functionkey F4 mk 3 1
> functionkey F5 view
> functionkey F6 view sel pad 0.92 clip false
> functionkey F7 mousemode rightMode 'delete markers'
> functionkey F8 mousemode rightMode zoom
> functionkey F9 sequence chain sel
> functionkey F10 transparency sel 65
> functionkey F11 transparency sel 0
> functionkey F12 tool show 'Fit in Map'
> color name f01graublau #BADBED
Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed
> color name f02silber #F6FAFC
Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc
> color name f03muschel #FFFFE5
Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5
> color name f04beige #F3F3A9
Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9
> color name f05gelb #f2b701
Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701
> color name f06orange #e68310
Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310
> color name f07rotorange #FF6A25
Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25
> color name f08rot #dd3d2d
Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d
> color name f09lachs #f97b72
Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72
> color name f10flieder #D57AD5
Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5
> color name f11violett #cf1c90
Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90
> color name f12lila #4b148f
Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f
> color name f13dunkelblau #2E2EF7
Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7
> color name f14blau #00AAFF
Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff
> color name f15cyan #60e2d6
Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6
> color name f16blaugrün #30ffa6
Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6
> color name f17grün #00FF00
Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00
> color name f18dunkelgrün #228B22
Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22
> color name f19hellgrau #DCDCDC
Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc
> color name f20grau #B2B2B2
Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2
> color name f21anthrazit #323F45
Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45
> alias localres color sample #$1 map #$2 offset 0.0 update true palette
> "#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"
> range $3,$4
> alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1
> $2'
> alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4
> 'quickmk $1 $2'
> alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3
> alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep
> $3
> alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep
> $3
> alias consurf color byattr seq_conservation protein palette cyanmaroon
> novalue yellow
> alias chaininfo preset custom chaininfo
> alias foto save browse format tiff height 4000 width 5500 supersample 4
> transparentBackground false
> alias durch save browse format tiff height 4000 width 5500 supersample 4
> transparentBackground true
> alias session save browse format session includeMaps true compress lz4
> alias nomapsession save browse format session includeMaps false compress lz4
> alias splitup color zone #$1 near sel sharpEdges true distance $2
> alias quicksplitup color zone #$1 near sel sharpEdges false distance $2
> alias spalt volume splitbyzone #$1
> alias undust surface undust #$1
> alias dust surface dust #$2 size $1
> alias dust1 surface dust #$1 size 1
> alias dust2 surface dust #$1 size 2
> alias dust3 surface dust #$1 size 3
> alias dust4 surface dust #$1 size 4
> alias dust5 surface dust #$1 size 5
> alias dust6 surface dust #$1 size 6
> alias dust7 surface dust #$1 size 7
> alias dust8 surface dust #$1 size 8
> alias dust9 surface dust #$1 size 9
> alias dust10 surface dust #$1 size 10
> alias dust11 surface dust #$1 size 11
> alias dust12 surface dust #$1 size 12
> alias dust13 surface dust #$1 size 13
> alias dust14 surface dust #$1 size 14
> alias dust15 surface dust #$1 size 15
> alias dust20 surface dust #$1 size 20
> alias dust25 surface dust #$1 size 25
> alias dust30 surface dust #$1 size 30
> alias dust35 surface dust #$1 size 35
> alias dust40 surface dust #$1 size 40
> alias dust45 surface dust #$1 size 45
> alias dust50 surface dust #$1 size 50
> alias sunset color sample #$1 map #$2 offset 0.1 update true palette
> "#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026"
> range $3,$4
> alias nicemap volume #$1 subdivideSurface true surfacesmoothing true
> smoothLines true squareMesh false meshLighting true
> alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false
> smoothLines false squareMesh true meshLighting true
> alias figure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ;
> camera ortho
> alias tryfigure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.01 ; set bgColor white ;
> camera ortho; cartoon style width 2.4 thickness 0.4; lighting
> ambientintensity 1.2 fillIntensity 0.4
> alias abbild sel zone sel 1 #$1 residues true extend true
> alias abbild+ sel zone sel 1 #$1 residues true extend true; show sel; sel
> intersect #$1; style sel stick; sel compound; sel zone sel 7 #$1 residues
> true extend true; sel intersect :HOH:MG:K:ZN:SPD:SPM; show sel; sel
> intersect :MG; style sel ball; size sel ballscale 0.5
> alias network sel zone sel $1 #$2 residues true extend true
> alias network34 sel zone sel 3.4 #$1 residues true extend true
> alias network4 sel zone sel 4 #$1 residues true extend true
> alias network10 sel zone sel 10 #$1 residues true extend true
> alias wasser sel zone #$1 3.4 #$2 residues true extend true; sel intersect
> #$2:HOH; sel add #$1; sel zone sel 3.4 #$2 residues true extend true
> alias 1st-wasser sel zone #$1 3.4 #$2 residues true extend true; sel
> intersect #$2:HOH
> alias farben color sel f14; sel #$1 & nucleic; color sel f20; sel #$1 &
> protein; color sel f07; sel #$1:HOH; color sel red; sel #$1:MG; color sel
> f17; sel #$1:K; color sel f15
> alias magnesiumcluster sel zone sel 2.7 #$1 extend true; sel intersect
> #$1@o*:HOH:MG
> alias magnesiumcluster4 sel zone sel 4 #$1 extend true; sel intersect
> #$1@o*:HOH:MG
> alias upsplit color zone #$1 near #$3 sharpEdges true distance $2
> alias weihwasser sel zone #$1 3.4 #$2 residues true extend true; sel
> intersect #$2:HOH; sel add #$1; sel subtract badwaters; sel zone sel 3.4 #$2
> residues true extend true; sel subtract badwaters
> alias fixall size pseudobondRadius 0.075; sel :MG; style sel ball; size sel
> ballscale 0.5
> alias fix size pseudobondRadius 0.075; da $1; sel intersect :MG; style sel
> ball; color sel f17; size sel ballscale 0.5; da $1; sel intersect
> ##name="K"; color sel blueviolet
> alias pixel zoom pixelsize 0.04
> alias da sel #$1 @@display
> alias neu hide #$1; da $2; sel intersect ligand; mm #$1 to #$2 matrix
> Nucleic; network10 $1,$2; mm #!$1 & sel to #$2 & sel matrix Nucleic; da $2;
> abbild+ $1
> alias neu2 da $1; sel intersect ligand; farben $1; da $1; color sel byhet;
> hbonds sel color f05 restrict both interModel false intraMol false intraRes
> false; sel intersect :HOH; style sel stick; combine #$1; da $1; sel
> intersect :HOH; name frozen temp sel; hide sel; da $1; sel intersect
> ##name="hydrogen bonds"; del pbonds sel; sel temp; show sel; da $2; sel
> intersect :HOH; hide sel; da $2; sel intersect nucleic; sel intersect
> ##name="hydrogen bonds"; hide sel; da $2; sel intersect protein; sel
> intersect ##name="hydrogen bonds"; hide sel; da $1; sel intersect
> ##name="hydrogen bonds"; color sel f15
> alias kalium da $1; sel intersect :K; style sel ball; size sel ballscale
> 0.3; name frozen temp sel; sel zone sel 3.5 #$1 extend true; sel intersect
> @o*,n*:K; contacts sel restrict temp overlapCutoff -3.0 color #8A2BE2 name K
> log true
> alias magnesium da $1; sel intersect :MG; style sel ball; size sel ballscale
> 0.5; name frozen temp sel; magnesiumcluster $1; contacts sel restrict temp
> overlapCutoff -0.8 color #00FF00 name Mg log true
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/max/Documents/Projects/MKM/Figure/Supplementary_figure/SX17_congeners/SX17.cxs
Opened PP_70S_AP_adjusted copy.mrc as #2, grid size 432,432,432, pixel 0.822,
shown at level 0.0256, step 1, values float32
Opened PP_70S_AP_adjusted copy.mrc 5 as #3.6, grid size 432,432,432, pixel
0.822, shown at level 0.0179, step 1, values float32
Opened PP_70S_AP_adjusted copy.mrc 6 as #3.7, grid size 432,432,432, pixel
0.822, shown at level 0.0181, step 1, values float32
Opened PP_70S_AP_adjusted copy.mrc 2 1 as #6.2, grid size 432,432,432, pixel
0.822, shown at level 0.0185, step 1, values float32
opened ChimeraX session
> open
> /Users/max/Documents/Projects/MKM/Modelling/MKM_cifs/MKM_E_50S-coot-4.pdb
Chain information for MKM_E_50S-coot-4.pdb #9
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
95 atoms, 97 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
89189 atoms, 96970 bonds, 282 pseudobonds, 6404 residues, 3 models selected
> delete sel
> select #9/8:6228@C1
1 atom, 1 residue, 1 model selected
> select up
95 atoms, 97 bonds, 1 residue, 1 model selected
> select up
600545 atoms, 651592 bonds, 44010 residues, 10 models selected
> select down
95 atoms, 97 bonds, 1 residue, 1 model selected
> color sel #00a9ffff
> color sel byhetero
> select clear
> hide #!7 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> close #7
> save
> /Users/max/Documents/Projects/MKM/Figure/Supplementary_figure/SX17_congeners/SX17.cxs
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> mousemode shift leftMode "translate selected models"
> mousemode shift middleMode "rotate selected models"
> mousemode rightMode zoom
> mousemode control wheelMode "contour level"
> mousemode setting "contour level" speed 0.1
> mousemode shift wheelMode "rotate selected models"
> camera ortho
> set bgColor grey
> lighting shadows false
> lighting depthCue false
> graphics silhouettes true
> lighting simple
> functionkey F1 cofr sel
> functionkey F2 mousemode rightMode 'mark surface'
> functionkey F3 mousemode rightMode 'move markers'
> functionkey F4 mk 3 1
> functionkey F5 view
> functionkey F6 view sel pad 0.92 clip false
> functionkey F7 mousemode rightMode 'delete markers'
> functionkey F8 mousemode rightMode zoom
> functionkey F9 sequence chain sel
> functionkey F10 transparency sel 65
> functionkey F11 transparency sel 0
> functionkey F12 tool show 'Fit in Map'
> color name f01graublau #BADBED
Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed
> color name f02silber #F6FAFC
Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc
> color name f03muschel #FFFFE5
Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5
> color name f04beige #F3F3A9
Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9
> color name f05gelb #f2b701
Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701
> color name f06orange #e68310
Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310
> color name f07rotorange #FF6A25
Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25
> color name f08rot #dd3d2d
Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d
> color name f09lachs #f97b72
Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72
> color name f10flieder #D57AD5
Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5
> color name f11violett #cf1c90
Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90
> color name f12lila #4b148f
Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f
> color name f13dunkelblau #2E2EF7
Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7
> color name f14blau #00AAFF
Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff
> color name f15cyan #60e2d6
Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6
> color name f16blaugrün #30ffa6
Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6
> color name f17grün #00FF00
Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00
> color name f18dunkelgrün #228B22
Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22
> color name f19hellgrau #DCDCDC
Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc
> color name f20grau #B2B2B2
Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2
> color name f21anthrazit #323F45
Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45
> alias localres color sample #$1 map #$2 offset 0.0 update true palette
> "#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"
> range $3,$4
> alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1
> $2'
> alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4
> 'quickmk $1 $2'
> alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3
> alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep
> $3
> alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep
> $3
> alias consurf color byattr seq_conservation protein palette cyanmaroon
> novalue yellow
> alias chaininfo preset custom chaininfo
> alias foto save browse format tiff height 4000 width 5500 supersample 4
> transparentBackground false
> alias durch save browse format tiff height 4000 width 5500 supersample 4
> transparentBackground true
> alias session save browse format session includeMaps true compress lz4
> alias nomapsession save browse format session includeMaps false compress lz4
> alias splitup color zone #$1 near sel sharpEdges true distance $2
> alias quicksplitup color zone #$1 near sel sharpEdges false distance $2
> alias spalt volume splitbyzone #$1
> alias undust surface undust #$1
> alias dust surface dust #$2 size $1
> alias dust1 surface dust #$1 size 1
> alias dust2 surface dust #$1 size 2
> alias dust3 surface dust #$1 size 3
> alias dust4 surface dust #$1 size 4
> alias dust5 surface dust #$1 size 5
> alias dust6 surface dust #$1 size 6
> alias dust7 surface dust #$1 size 7
> alias dust8 surface dust #$1 size 8
> alias dust9 surface dust #$1 size 9
> alias dust10 surface dust #$1 size 10
> alias dust11 surface dust #$1 size 11
> alias dust12 surface dust #$1 size 12
> alias dust13 surface dust #$1 size 13
> alias dust14 surface dust #$1 size 14
> alias dust15 surface dust #$1 size 15
> alias dust20 surface dust #$1 size 20
> alias dust25 surface dust #$1 size 25
> alias dust30 surface dust #$1 size 30
> alias dust35 surface dust #$1 size 35
> alias dust40 surface dust #$1 size 40
> alias dust45 surface dust #$1 size 45
> alias dust50 surface dust #$1 size 50
> alias sunset color sample #$1 map #$2 offset 0.1 update true palette
> "#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026"
> range $3,$4
> alias nicemap volume #$1 subdivideSurface true surfacesmoothing true
> smoothLines true squareMesh false meshLighting true
> alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false
> smoothLines false squareMesh true meshLighting true
> alias figure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ;
> camera ortho
> alias tryfigure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.01 ; set bgColor white ;
> camera ortho; cartoon style width 2.4 thickness 0.4; lighting
> ambientintensity 1.2 fillIntensity 0.4
> alias abbild sel zone sel 1 #$1 residues true extend true
> alias abbild+ sel zone sel 1 #$1 residues true extend true; show sel; sel
> intersect #$1; style sel stick; sel compound; sel zone sel 7 #$1 residues
> true extend true; sel intersect :HOH:MG:K:ZN:SPD:SPM; show sel; sel
> intersect :MG; style sel ball; size sel ballscale 0.5
> alias network sel zone sel $1 #$2 residues true extend true
> alias network34 sel zone sel 3.4 #$1 residues true extend true
> alias network4 sel zone sel 4 #$1 residues true extend true
> alias network10 sel zone sel 10 #$1 residues true extend true
> alias wasser sel zone #$1 3.4 #$2 residues true extend true; sel intersect
> #$2:HOH; sel add #$1; sel zone sel 3.4 #$2 residues true extend true
> alias 1st-wasser sel zone #$1 3.4 #$2 residues true extend true; sel
> intersect #$2:HOH
> alias farben color sel f14; sel #$1 & nucleic; color sel f20; sel #$1 &
> protein; color sel f07; sel #$1:HOH; color sel red; sel #$1:MG; color sel
> f17; sel #$1:K; color sel f15
> alias magnesiumcluster sel zone sel 2.7 #$1 extend true; sel intersect
> #$1@o*:HOH:MG
> alias magnesiumcluster4 sel zone sel 4 #$1 extend true; sel intersect
> #$1@o*:HOH:MG
> alias upsplit color zone #$1 near #$3 sharpEdges true distance $2
> alias weihwasser sel zone #$1 3.4 #$2 residues true extend true; sel
> intersect #$2:HOH; sel add #$1; sel subtract badwaters; sel zone sel 3.4 #$2
> residues true extend true; sel subtract badwaters
> alias fixall size pseudobondRadius 0.075; sel :MG; style sel ball; size sel
> ballscale 0.5
> alias fix size pseudobondRadius 0.075; da $1; sel intersect :MG; style sel
> ball; color sel f17; size sel ballscale 0.5; da $1; sel intersect
> ##name="K"; color sel blueviolet
> alias pixel zoom pixelsize 0.04
> alias da sel #$1 @@display
> alias neu hide #$1; da $2; sel intersect ligand; mm #$1 to #$2 matrix
> Nucleic; network10 $1,$2; mm #!$1 & sel to #$2 & sel matrix Nucleic; da $2;
> abbild+ $1
> alias neu2 da $1; sel intersect ligand; farben $1; da $1; color sel byhet;
> hbonds sel color f05 restrict both interModel false intraMol false intraRes
> false; sel intersect :HOH; style sel stick; combine #$1; da $1; sel
> intersect :HOH; name frozen temp sel; hide sel; da $1; sel intersect
> ##name="hydrogen bonds"; del pbonds sel; sel temp; show sel; da $2; sel
> intersect :HOH; hide sel; da $2; sel intersect nucleic; sel intersect
> ##name="hydrogen bonds"; hide sel; da $2; sel intersect protein; sel
> intersect ##name="hydrogen bonds"; hide sel; da $1; sel intersect
> ##name="hydrogen bonds"; color sel f15
> alias kalium da $1; sel intersect :K; style sel ball; size sel ballscale
> 0.3; name frozen temp sel; sel zone sel 3.5 #$1 extend true; sel intersect
> @o*,n*:K; contacts sel restrict temp overlapCutoff -3.0 color #8A2BE2 name K
> log true
> alias magnesium da $1; sel intersect :MG; style sel ball; size sel ballscale
> 0.5; name frozen temp sel; magnesiumcluster $1; contacts sel restrict temp
> overlapCutoff -0.8 color #00FF00 name Mg log true
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac19,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3,7 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Memory: 32 GB
System Firmware Version: 2069.0.0.0.0
OS Loader Version: 582~2132
SMC Version (system): 2.46f13
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B91)
Kernel Version: Darwin 24.1.0
Time since boot: 21 minutes, 34 seconds
Graphics/Displays:
Radeon Pro 580X:
Chipset Model: Radeon Pro 580X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D0008A-042
VBIOS Version: 113-D0008A1X-009
EFI Driver Version: 01.B1.042
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2412M:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: YPPY075P29KS
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 1.0.5
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: 1.8
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: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
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-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
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: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
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: 2.0.1
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: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class saving session |
comment:2 by , 5 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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