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Opened 2 years ago
Closed 6 months ago
#10215 closed defect (can't reproduce)
Crash in garbage collection while fetching mmCIF
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | chimerax-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1.1-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202307312254 (2023-07-31 22:54:15 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007000139d1000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff854ac4b40 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/plistlib.py", line 174 in parse
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/plistlib.py", line 875 in load
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/platform.py", line 425 in _mac_ver_xml
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/platform.py", line 448 in mac_ver
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/fetch.py", line 332 in html_user_agent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/fetch.py", line 153 in retrieve_url
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/fetch.py", line 88 in fetch_file
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 97 in fetch
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 454 in remember_data_format
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 483 in collated_open
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 154 in provider_open
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 119 in cmd_open
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 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 893 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 1044 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 52)
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{
"uptime" : 260000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 505,
"deployVersion" : 210,
"modelCode" : "iMac19,1",
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"build" : "23B81",
"releaseType" : "User"
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"captureTime" : "2023-11-23 14:17:38.9647 +0100",
"codeSigningMonitor" : 0,
"incident" : "7DCF7CC3-3BCF-4EE1-A185-6D05B0A92DCB",
"pid" : 80118,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-11-23 12:49:04.6241 +0100",
"procStartAbsTime" : 263396419666003,
"procExitAbsTime" : 268710496478484,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E4C15149-BA40-3306-9A73-C2C570B476AC",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487699799\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff60000-7ffffff61000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":80118},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737487699799\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff60000-7ffffff61000 [ 4K] r-x\/r-x SM=SHM ",
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"faultingThread" : 0,
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===== Log before crash start =====
> 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
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Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9
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Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701
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Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310
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Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25
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Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d
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Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72
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Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5
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Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90
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Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f
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Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7
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Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff
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Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6
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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 0.1 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 supersample 4
> transparentBackground false
> alias durch save browse format tiff height 4000 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 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
UCSF ChimeraX version: 1.7.dev202307312254 (2023-07-31)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/Haaris/Desktop/Modelling_Ksg/postprocess_masked.mrc
> /Users/Haaris/Desktop/Modelling_Ksg/run_class001.mrc
Opened postprocess_masked.mrc as #1.1, grid size 400,400,400, pixel 0.832,
shown at level 0.0108, step 2, values float32
Opened run_class001.mrc as #1.2, grid size 400,400,400, pixel 0.832, shown at
level 0.00636, step 2, values float32
> open /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot11.pdb
Chain information for Haaris_Kasugamycin_Coot11.pdb #2
---
Chain | Description
A | No description available
D | No description available
E | No description available
F | No description available
H | No description available
K | No description available
L | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
T | No description available
U | No description available
W | No description available
X | No description available
> show cartoons
> hide atoms
> set bgColor white
> volume #1.2 step 1
> volume #1.1 step 1
> volume #1.2 level 0.008035
> hide #!1.1 models
> volume #1.2 level 0.005687
> open /Users/Haaris/Desktop/Modelling_Ksg/J142_cluster_004.mrc
Opened J142_cluster_004.mrc as #3, grid size 140,140,140, pixel 2.4, shown at
level 0.948, step 1, values float32
> close #3
> open "/Users/Haaris/Desktop/Modelling_Ksg/cryosparc_P18_J36_007_volume_map
> (1).mrc"
Opened cryosparc_P18_J36_007_volume_map (1).mrc as #3, grid size 420,420,420,
pixel 0.8, shown at level 0.0551, step 2, values float32
> volume #3 step 1
> select add #3
2 models selected
> view matrix models
> #3,-0.17708,-0.65534,0.73428,169.84,-0.85404,0.47311,0.21628,182.61,-0.48913,-0.58881,-0.64347,436.19
> view matrix models
> #3,-0.17708,-0.65534,0.73428,172.46,-0.85404,0.47311,0.21628,197.46,-0.48913,-0.58881,-0.64347,451.55
> view matrix models
> #3,-0.03201,-0.75958,0.64963,178.48,-0.89725,0.30821,0.31615,213.05,-0.44036,-0.57276,-0.69139,449.04
> view matrix models
> #3,-0.03201,-0.75958,0.64963,184.48,-0.89725,0.30821,0.31615,214.97,-0.44036,-0.57276,-0.69139,451.36
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!1.2 models
> hide #!1 models
> hide #!2 models
> show #!1.2 models
> fitmap #3 inMap #1.2
Fit map cryosparc_P18_J36_007_volume_map (1).mrc in map run_class001.mrc using
739407 points
correlation = 0.9474, correlation about mean = 0.8298, overlap = 1512
steps = 276, shift = 6.9, angle = 16.1 degrees
Position of cryosparc_P18_J36_007_volume_map (1).mrc (#3) relative to
run_class001.mrc (#1.2) coordinates:
Matrix rotation and translation
0.17069831 -0.69465086 0.69880060 130.53409619
-0.94857678 0.07602228 0.30728279 257.03875485
-0.26657867 -0.71531867 -0.64595279 440.20267930
Axis -0.71558737 0.67554491 -0.17769013
Axis point 0.00000000 319.54658078 128.79028775
Rotation angle (degrees) 134.39621182
Shift along axis 2.01300185
> hide #!1.2 models
> select subtract #3
Nothing selected
> show #!1.2 models
> volume resample #3 onGrid #1.2
Opened cryosparc_P18_J36_007_volume_map (1).mrc resampled as #4, grid size
400,400,400, pixel 0.832, shown at step 1, values float32
> close #3
> save "/Users/Haaris/Desktop/Modelling_Ksg/cryosparc_P18_J36_007_volume_map
> (1).mrc" models #4
> hide #!1.2 models
> show #!1.2 models
> hide #!4 models
> show #!2 models
> color #1.2 #b2b2b276 models
> volume #4 level 0.07887
> volume #4 level 0.08536
> volume #4 level 0.06588
> volume #4 level 0.0464
> volume #1.2 level 0.006608
> volume #1.2 level 0.00845
> hide #!2 models
> hide #!1.2 models
> hide #!4 models
> show #!2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> open /Users/Haaris/Desktop/Modelling_Ksg/5lmn_aligned.pdb
Chain information for 5lmn_aligned.pdb #3
---
Chain | Description
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
V | No description available
W | No description available
X | No description available
Y | No description available
> close #3
> open /Users/Haaris/Desktop/Modelling_Ksg/5np6_aligned.pdb
Chain information for 5np6_aligned.pdb #3
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | 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
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
> hide #!2 models
> show #3 cartoons
> hide #3 atoms
> select #3/B:22
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1623 atoms, 1812 bonds, 76 residues, 1 model selected
> select up
146883 atoms, 159526 bonds, 10662 residues, 1 model selected
> select down
1623 atoms, 1812 bonds, 76 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B
Alignment identifier is 3/B
> select #3/B:33
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/B:33
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/B:70
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/B:70
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/B:53
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #3/B:53
23 atoms, 25 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> select #3/B:24
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #3/B:24
23 atoms, 25 bonds, 1 residue, 1 model selected
> hide #3 models
> show #!1.2 models
> open /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot12.pdb
Chain information for Haaris_Kasugamycin_Coot12.pdb #5
---
Chain | Description
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
K | No description available
L | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
T | No description available
U | No description available
W | No description available
X | No description available
> show #!5 cartoons
> hide #!5 atoms
> volume #1.2 level 0.004075
> volume #1.2 level 0.006493
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select add #1.2
23 atoms, 25 bonds, 1 residue, 3 models selected
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> hide #!5 models
> hide #!1.2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> open 5lmo
Summary of feedback from opening 5lmo fetched from pdb
---
note | Fetching compressed mmCIF 5lmo from
http://files.rcsb.org/download/5lmo.cif
5lmo title:
Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex
(state-1B) [more info...]
Chain information for 5lmo #6
---
Chain | Description | UniProt
A | 16S rRNA |
B | 30S ribosomal protein S2 | RS2_THET8 1-256
C | 30S ribosomal protein S3 | RS3_THET8 1-239
D | 30S ribosomal protein S4 | RS4_THET8 1-209
E | 30S ribosomal protein S5 | RS5_THET8 1-162
F | 30S ribosomal protein S6 | RS6_THET8 1-101
G | 30S ribosomal protein S7 | RS7_THET8 1-156
H | 30S ribosomal protein S8 | RS8_THET8 1-138
I | 30S ribosomal protein S9 | RS9_THET8 1-128
J | 30S ribosomal protein S10 | RS10_THET8 1-105
K | 30S ribosomal protein S11 | RS11_THET8 1-129
L | 30S ribosomal protein S12 | RS12_THET8 4-135
M | 30S ribosomal protein S13 | RS13_THET8 1-126
N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61
O | 30S ribosomal protein S15 | RS15_THET8 1-89
P | 30S ribosomal protein S16 | RS16_THET8 1-88
Q | 30S ribosomal protein S17 | RS17_THET8 1-105
R | 30S ribosomal protein S18 | RS18_THET8 1-88
S | 30S ribosomal protein S19 | RS19_THET8 1-93
T | 30S ribosomal protein S20 | RS20_THET8 1-106
V | 30S ribosomal protein Thx | RSHX_THET8 1-27
W | Translation initiation factor IF-1 | IF1_THET8 0-71
X | Translation initiation factor IF-3 | IF3_THET8 2-172
Y | mRNA |
Non-standard residues in 5lmo #6
---
A — adenosine-5'-monophosphate
G — guanosine-5'-monophosphate
MG — magnesium ion
U — uridine-5'-monophosphate
ZN — zinc ion
> show #!6 cartoons
> hide #!6 atoms
> open 5lmp
Summary of feedback from opening 5lmp fetched from pdb
---
note | Fetching compressed mmCIF 5lmp from
http://files.rcsb.org/download/5lmp.cif
5lmp title:
Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex
(state-1C) [more info...]
Chain information for 5lmp #7
---
Chain | Description | UniProt
A | 16S rRNA |
B | 30S ribosomal protein S2 | RS2_THET8 1-256
C | 30S ribosomal protein S3 | RS3_THET8 1-239
D | 30S ribosomal protein S4 | RS4_THET8 1-209
E | 30S ribosomal protein S5 | RS5_THET8 1-162
F | 30S ribosomal protein S6 | RS6_THET8 1-101
G | 30S ribosomal protein S7 | RS7_THET8 1-156
H | 30S ribosomal protein S8 | RS8_THET8 1-138
I | 30S ribosomal protein S9 | RS9_THET8 1-128
J | 30S ribosomal protein S10 | RS10_THET8 1-105
K | 30S ribosomal protein S11 | RS11_THET8 1-129
L | 30S ribosomal protein S12 | RS12_THET8 4-135
M | 30S ribosomal protein S13 | RS13_THET8 1-126
N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61
O | 30S ribosomal protein S15 | RS15_THET8 1-89
P | 30S ribosomal protein S16 | RS16_THET8 1-88
Q | 30S ribosomal protein S17 | RS17_THET8 1-105
R | 30S ribosomal protein S18 | RS18_THET8 1-88
S | 30S ribosomal protein S19 | RS19_THET8 1-93
T | 30S ribosomal protein S20 | RS20_THET8 1-106
V | 30S ribosomal protein Thx | RSHX_THET8 1-27
W | Translation initiation factor IF-1 | IF1_THET8 0-71
X | Translation initiation factor IF-3 | IF3_THET8 2-172
Y | mRNA |
Non-standard residues in 5lmp #7
---
MG — magnesium ion
ZN — zinc ion
> close #6
> select add #7
54155 atoms, 58316 bonds, 1819 pseudobonds, 4267 residues, 7 models selected
> close #7
> close
> open 5lmn
5lmn title:
Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex
(state-1A) [more info...]
Chain information for 5lmn #1
---
Chain | Description | UniProt
A | 16S ribosomal RNA |
B | 30S ribosomal protein S2 | RS2_THET8 1-256
C | 30S ribosomal protein S3 | RS3_THET8 1-239
D | 30S ribosomal protein S4 | RS4_THET8 1-209
E | 30S ribosomal protein S5 | RS5_THET8 1-162
F | 30S ribosomal protein S6 | RS6_THET8 1-101
G | 30S ribosomal protein S7 | RS7_THET8 1-156
H | 30S ribosomal protein S8 | RS8_THET8 1-138
I | 30S ribosomal protein S9 | RS9_THET8 1-128
J | 30S ribosomal protein S10 | RS10_THET8 1-105
K | 30S ribosomal protein S11 | RS11_THET8 1-129
L | 30S ribosomal protein S12 | RS12_THET8 4-135
M | 30S ribosomal protein S13 | RS13_THET8 1-126
N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61
O | 30S ribosomal protein S15 | RS15_THET8 1-89
P | 30S ribosomal protein S16 | RS16_THET8 1-88
Q | 30S ribosomal protein S17 | RS17_THET8 1-105
R | 30S ribosomal protein S18 | RS18_THET8 1-88
S | 30S ribosomal protein S19 | RS19_THET8 1-93
T | 30S ribosomal protein S20 | RS20_THET8 1-106
V | 30S ribosomal protein Thx | RSHX_THET8 1-27
W | Translation initiation factor IF-1 | IF1_THET8 0-71
X | Translation initiation factor IF-3 | IF3_THET8 2-172
Y | mRNA |
Non-standard residues in 5lmn #1
---
MG — magnesium ion
ZN — zinc ion
> open 5lmo
5lmo title:
Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex
(state-1B) [more info...]
Chain information for 5lmo #2
---
Chain | Description | UniProt
A | 16S rRNA |
B | 30S ribosomal protein S2 | RS2_THET8 1-256
C | 30S ribosomal protein S3 | RS3_THET8 1-239
D | 30S ribosomal protein S4 | RS4_THET8 1-209
E | 30S ribosomal protein S5 | RS5_THET8 1-162
F | 30S ribosomal protein S6 | RS6_THET8 1-101
G | 30S ribosomal protein S7 | RS7_THET8 1-156
H | 30S ribosomal protein S8 | RS8_THET8 1-138
I | 30S ribosomal protein S9 | RS9_THET8 1-128
J | 30S ribosomal protein S10 | RS10_THET8 1-105
K | 30S ribosomal protein S11 | RS11_THET8 1-129
L | 30S ribosomal protein S12 | RS12_THET8 4-135
M | 30S ribosomal protein S13 | RS13_THET8 1-126
N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61
O | 30S ribosomal protein S15 | RS15_THET8 1-89
P | 30S ribosomal protein S16 | RS16_THET8 1-88
Q | 30S ribosomal protein S17 | RS17_THET8 1-105
R | 30S ribosomal protein S18 | RS18_THET8 1-88
S | 30S ribosomal protein S19 | RS19_THET8 1-93
T | 30S ribosomal protein S20 | RS20_THET8 1-106
V | 30S ribosomal protein Thx | RSHX_THET8 1-27
W | Translation initiation factor IF-1 | IF1_THET8 0-71
X | Translation initiation factor IF-3 | IF3_THET8 2-172
Y | mRNA |
Non-standard residues in 5lmo #2
---
A — adenosine-5'-monophosphate
G — guanosine-5'-monophosphate
MG — magnesium ion
U — uridine-5'-monophosphate
ZN — zinc ion
> open 5lmp
5lmp title:
Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex
(state-1C) [more info...]
Chain information for 5lmp #3
---
Chain | Description | UniProt
A | 16S rRNA |
B | 30S ribosomal protein S2 | RS2_THET8 1-256
C | 30S ribosomal protein S3 | RS3_THET8 1-239
D | 30S ribosomal protein S4 | RS4_THET8 1-209
E | 30S ribosomal protein S5 | RS5_THET8 1-162
F | 30S ribosomal protein S6 | RS6_THET8 1-101
G | 30S ribosomal protein S7 | RS7_THET8 1-156
H | 30S ribosomal protein S8 | RS8_THET8 1-138
I | 30S ribosomal protein S9 | RS9_THET8 1-128
J | 30S ribosomal protein S10 | RS10_THET8 1-105
K | 30S ribosomal protein S11 | RS11_THET8 1-129
L | 30S ribosomal protein S12 | RS12_THET8 4-135
M | 30S ribosomal protein S13 | RS13_THET8 1-126
N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61
O | 30S ribosomal protein S15 | RS15_THET8 1-89
P | 30S ribosomal protein S16 | RS16_THET8 1-88
Q | 30S ribosomal protein S17 | RS17_THET8 1-105
R | 30S ribosomal protein S18 | RS18_THET8 1-88
S | 30S ribosomal protein S19 | RS19_THET8 1-93
T | 30S ribosomal protein S20 | RS20_THET8 1-106
V | 30S ribosomal protein Thx | RSHX_THET8 1-27
W | Translation initiation factor IF-1 | IF1_THET8 0-71
X | Translation initiation factor IF-3 | IF3_THET8 2-172
Y | mRNA |
Non-standard residues in 5lmp #3
---
MG — magnesium ion
ZN — zinc ion
> open 5lmq
Summary of feedback from opening 5lmq fetched from pdb
---
note | Fetching compressed mmCIF 5lmq from
http://files.rcsb.org/download/5lmq.cif
5lmq title:
Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation
complex, open form (state-2A) [more info...]
Chain information for 5lmq #4
---
Chain | Description | UniProt
A | 16S rRNA |
B | 30S ribosomal protein S2 | RS2_THET8 1-256
C | 30S ribosomal protein S3 | RS3_THET8 1-239
D | 30S ribosomal protein S4 | RS4_THET8 1-209
E | 30S ribosomal protein S5 | RS5_THET8 1-162
F | 30S ribosomal protein S6 | RS6_THET8 1-101
G | 30S ribosomal protein S7 | RS7_THET8 1-156
H | 30S ribosomal protein S8 | RS8_THET8 1-138
I | 30S ribosomal protein S9 | RS9_THET8 1-128
J | 30S ribosomal protein S10 | RS10_THET8 1-105
K | 30S ribosomal protein S11 | RS11_THET8 1-129
L | 30S ribosomal protein S12 | RS12_THET8 4-135
M | 30S ribosomal protein S13 | RS13_THET8 1-126
N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61
O | 30S ribosomal protein S15 | RS15_THET8 1-89
P | 30S ribosomal protein S16 | RS16_THET8 1-88
Q | 30S ribosomal protein S17 | RS17_THET8 1-105
R | 30S ribosomal protein S18 | RS18_THET8 1-88
S | 30S ribosomal protein S19 | RS19_THET8 1-93
T | 30S ribosomal protein S20 | RS20_THET8 1-106
V | 30S ribosomal protein Thx | RSHX_THET8 1-27
W | Translation initiation factor IF-1 | IF1_THET8 0-71
X | Translation initiation factor IF-3 | IF3_THET8 2-172
Y | mRNA |
Z | tRNA |
Non-standard residues in 5lmq #4
---
MG — magnesium ion
ZN — zinc ion
> open 5lmr
Summary of feedback from opening 5lmr fetched from pdb
---
note | Fetching compressed mmCIF 5lmr from
http://files.rcsb.org/download/5lmr.cif
5lmr title:
Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation
complex(state-2B) [more info...]
Chain information for 5lmr #5
---
Chain | Description | UniProt
A | 16S rRNA |
B | 30S ribosomal protein S2 | RS2_THET8 1-256
C | 30S ribosomal protein S3 | RS3_THET8 1-239
D | 30S ribosomal protein S4 | RS4_THET8 1-209
E | 30S ribosomal protein S5 | RS5_THET8 1-162
F | 30S ribosomal protein S6 | RS6_THET8 1-101
G | 30S ribosomal protein S7 | RS7_THET8 1-156
H | 30S ribosomal protein S8 | RS8_THET8 1-138
I | 30S ribosomal protein S9 | RS9_THET8 1-128
J | 30S ribosomal protein S10 | RS10_THET8 1-105
K | 30S ribosomal protein S11 | RS11_THET8 1-129
L | 30S ribosomal protein S12 | RS12_THET8 4-135
M | 30S ribosomal protein S13 | RS13_THET8 1-126
N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61
O | 30S ribosomal protein S15 | RS15_THET8 1-89
P | 30S ribosomal protein S16 | RS16_THET8 1-88
Q | 30S ribosomal protein S17 | RS17_THET8 1-105
R | 30S ribosomal protein S18 | RS18_THET8 1-88
S | 30S ribosomal protein S19 | RS19_THET8 1-93
T | 30S ribosomal protein S20 | RS20_THET8 1-106
V | 30S ribosomal protein Thx | RSHX_THET8 1-27
W | Translation initiation factor IF-1 | IF1_THET8 0-71
X | Translation initiation factor IF-3 | IF3_THET8 2-172
Y | mRNA |
Z | tRNAi |
Non-standard residues in 5lmr #5
---
MG — magnesium ion
ZN — zinc ion
> open 5lms
Summary of feedback from opening 5lms fetched from pdb
---
note | Fetching compressed mmCIF 5lms from
http://files.rcsb.org/download/5lms.cif
5lms title:
Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation
complex(state-2C) [more info...]
Chain information for 5lms #6
---
Chain | Description | UniProt
A | 16S rRNA |
B | 30S ribosomal protein S2 | RS2_THET8 1-256
C | 30S ribosomal protein S3 | RS3_THET8 1-239
D | 30S ribosomal protein S4 | RS4_THET8 1-209
E | 30S ribosomal protein S5 | RS5_THET8 1-162
F | 30S ribosomal protein S6 | RS6_THET8 1-101
G | 30S ribosomal protein S7 | RS7_THET8 1-156
H | 30S ribosomal protein S8 | RS8_THET8 1-138
I | 30S ribosomal protein S9 | RS9_THET8 1-128
J | 30S ribosomal protein S10 | RS10_THET8 1-105
K | 30S ribosomal protein S11 | RS11_THET8 1-129
L | 30S ribosomal protein S12 | RS12_THET8 4-135
M | 30S ribosomal protein S13 | RS13_THET8 1-126
N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61
O | 30S ribosomal protein S15 | RS15_THET8 1-89
P | 30S ribosomal protein S16 | RS16_THET8 1-88
Q | 30S ribosomal protein S17 | RS17_THET8 1-105
R | 30S ribosomal protein S18 | RS18_THET8 1-88
S | 30S ribosomal protein S19 | RS19_THET8 1-93
T | 30S ribosomal protein S20 | RS20_THET8 1-106
V | 30S ribosomal protein Thx | RSHX_THET8 1-27
W | Translation initiation factor IF-1 | IF1_THET8 0-71
X | Translation initiation factor IF-3 | IF3_THET8 2-172
Y | mRNA |
Z | tRNAi |
Non-standard residues in 5lms #6
---
MG — magnesium ion
ZN — zinc ion
> open 5lmt
Summary of feedback from opening 5lmt fetched from pdb
---
note | Fetching compressed mmCIF 5lmt from
http://files.rcsb.org/download/5lmt.cif
5lmt title:
Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation
complex(state-3) [more info...]
Chain information for 5lmt #7
---
Chain | Description | UniProt
A | 16S ribosomal RNA |
B | 30S ribosomal protein S2 | RS2_THET8 1-256
C | 30S ribosomal protein S3 | RS3_THET8 1-239
D | 30S ribosomal protein S4 | RS4_THET8 1-209
E | 30S ribosomal protein S5 | RS5_THET8 1-162
F | 30S ribosomal protein S6 | RS6_THET8 1-101
G | 30S ribosomal protein S7 | RS7_THET8 1-156
H | 30S ribosomal protein S8 | RS8_THET8 1-138
I | 30S ribosomal protein S9 | RS9_THET8 1-128
J | 30S ribosomal protein S10 | RS10_THET8 1-105
K | 30S ribosomal protein S11 | RS11_THET8 1-129
L | 30S ribosomal protein S12 | RS12_THET8 4-135
M | 30S ribosomal protein S13 | RS13_THET8 1-126
N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61
O | 30S ribosomal protein S15 | RS15_THET8 1-89
P | 30S ribosomal protein S16 | RS16_THET8 1-88
Q | 30S ribosomal protein S17 | RS17_THET8 1-105
R | 30S ribosomal protein S18 | RS18_THET8 1-88
S | 30S ribosomal protein S19 | RS19_THET8 1-93
T | 30S ribosomal protein S20 | RS20_THET8 1-106
V | 30S ribosomal protein Thx | RSHX_THET8 1-27
W | Translation initiation factor IF-1 | IF1_THET8 0-71
X | Translation initiation factor IF-3 | IF3_THET8 2-172
Y | mRNA |
Z | tRNAi |
Non-standard residues in 5lmt #7
---
MG — magnesium ion
ZN — zinc ion
> open 5lmu
Summary of feedback from opening 5lmu fetched from pdb
---
note | Fetching compressed mmCIF 5lmu from
http://files.rcsb.org/download/5lmu.cif
5lmu title:
Structure of bacterial 30S-IF3-mRNA-tRNA translation pre-initiation complex,
closed form (state-4) [more info...]
Chain information for 5lmu #8
---
Chain | Description | UniProt
A | 16S ribosomal RNA |
B | 30S ribosomal protein S2 | RS2_THET8 1-256
C | 30S ribosomal protein S3 | RS3_THET8 1-239
D | 30S ribosomal protein S4 | RS4_THET8 1-209
E | 30S ribosomal protein S5 | RS5_THET8 1-162
F | 30S ribosomal protein S6 | RS6_THET8 1-101
G | 30S ribosomal protein S7 | RS7_THET8 1-156
H | 30S ribosomal protein S8 | RS8_THET8 1-138
I | 30S ribosomal protein S9 | RS9_THET8 1-128
J | 30S ribosomal protein S10 | RS10_THET8 1-105
K | 30S ribosomal protein S11 | RS11_THET8 1-129
L | 30S ribosomal protein S12 | RS12_THET8 4-135
M | 30S ribosomal protein S13 | RS13_THET8 1-126
N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61
O | 30S ribosomal protein S15 | RS15_THET8 1-89
P | 30S ribosomal protein S16 | RS16_THET8 1-88
Q | 30S ribosomal protein S17 | RS17_THET8 1-105
R | 30S ribosomal protein S18 | RS18_THET8 1-88
S | 30S ribosomal protein S19 | RS19_THET8 1-93
T | 30S ribosomal protein S20 | RS20_THET8 1-106
V | 30S ribosomal protein Thx | RSHX_THET8 1-27
X | Translation initiation factor IF-3 | IF3_THET8 2-172
Y | mRNA |
Z | tRNAi |
Non-standard residues in 5lmu #8
---
MG — magnesium ion
ZN — zinc ion
> open 5lmv
===== Log before crash end =====
Log:
> 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 0.1 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 supersample 4
> transparentBackground false
> alias durch save browse format tiff height 4000 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 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
UCSF ChimeraX version: 1.7.dev202307312254 (2023-07-31)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.1.35
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
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: 2020.40.3.0.0
OS Loader Version: 580~743
SMC Version (system): 2.46f13
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 3 days, 2 hours, 39 minutes
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: 0FFXD31242JL
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.46.1
ChimeraX-AtomicLibrary: 10.0.8
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.4
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202307312254
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
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: 1.2.1
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: 1.1.8
ChimeraX-ListInfo: 1.2
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.1.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.9
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-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: 1.31.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.41.1
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.0
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.8
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.7
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.10.0
prompt-toolkit: 3.0.39
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.1.0
qtconsole: 5.4.3
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.2
traitlets: 5.9.0
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 2.0.4
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.8
Change History (3)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in garbage collection while fetching mmCIF |
comment:2 by , 2 years ago
comment:3 by , 6 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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