![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 21 months ago
Closed 21 months ago
#14456 closed defect (can't reproduce)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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-14.2.1-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
Current thread 0x00007ff848b9eb80 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/logger.py", line 580 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/logger.py", line 580 in summarize_msgs
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/logger.py", line 569 in log_summary
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/logger.py", line 682 in __exit__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 482 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 195 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/core/commands/run.py", line 38 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 162 in _qt_safe
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.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 64)
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{
"uptime" : 1300000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 505,
"deployVersion" : 210,
"modelCode" : "iMac19,1",
"coalitionID" : 3492,
"osVersion" : {
"train" : "macOS 14.2.1",
"build" : "23C71",
"releaseType" : "User"
},
"captureTime" : "2024-01-23 14:44:47.4677 +0100",
"codeSigningMonitor" : 0,
"incident" : "37F957D8-E13A-42C2-AFF2-3D2E14D739E6",
"pid" : 35118,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-01-23 09:27:24.3046 +0100",
"procStartAbsTime" : 1291441629275301,
"procExitAbsTime" : 1310483968260274,
"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"},
"storeInfo" : {"deviceIdentifierForVendor":"2BF767B5-E5D0-550C-9BFF-13147159001D","thirdParty":true},
"parentProc" : "launchd",
"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: 140737486954327\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffeaa000-7fffffeab000 [ 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":35118},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737486954327\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffeaa000-7fffffeab000 [ 4K] r-x\/r-x SM=SHM ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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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
> 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
> open /Users/Haaris/Desktop/Temporary_Processing/Edeine/run_class001.mrc
Opened run_class001.mrc as #1, grid size 400,400,400, pixel 0.832, shown at
level 0.00588, step 2, values float32
> set bgColor white
> volume #1 step 1
> volume #1 level 0.003733
> volume #1 level 0.004176
> open
> /Users/Haaris/Desktop/Temporary_Processing/Edeine/run_class001_class3.mrc
Opened run_class001_class3.mrc as #2, grid size 400,400,400, pixel 0.832,
shown at level 0.00811, step 2, values float32
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #2 step 1
> volume #2 level 0.004326
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> open /Users/Haaris/Desktop/Edeine/Edeine_Comparsion_maps.cxs
Opened run_it100_class001.mrc as #1.1, grid size 200,200,200, pixel 1.66,
shown at level 0.0136, step 1, values float32
Opened run_it100_class002.mrc as #1.2, grid size 200,200,200, pixel 1.66,
shown at level 0.0181, step 1, values float32
Opened run_it100_class003.mrc as #1.3, grid size 200,200,200, pixel 1.66,
shown at level 0.017, step 1, values float32
Opened run_it100_class004.mrc as #1.4, grid size 200,200,200, pixel 1.66,
shown at level 0.0256, step 1, values float32
Opened run_it100_class005.mrc as #1.5, grid size 200,200,200, pixel 1.66,
shown at level 0.0165, step 1, values float32
opened ChimeraX session
> hide #!1.4 models
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1.3 models
> hide #!4 models
> hide #!4.1 models
> hide #!2 models
> volume #1.3 level 0.01056
> volume #1.3 level 0.01099
> show #!4 models
> hide #!4 models
> show #!4.1 models
> volume #1.3 level 0.02218
> volume #1.3 level 0.02261
> show #!1.2 models
> hide #!1.3 models
> color #1.2 #b2b2b2b1 models
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.4 models
> hide #!1.1 models
> show #!1.3 models
> hide #!1.4 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> hide #!1.3 models
> show #!1.4 models
> show #!1.3 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!4 models
> hide #!4.1 models
> show #!1.2 models
> volume #1.2 level 0.01525
> hide #!1.2 models
> close #1.2
> close
> open /Users/Haaris/Desktop/Temporary_Processing/Edeine/run_class001.mrc
Opened run_class001.mrc as #1, grid size 400,400,400, pixel 0.832, shown at
level 0.00588, step 2, values float32
> open
> /Users/Haaris/Desktop/Temporary_Processing/Edeine/run_class001_class3.mrc
Opened run_class001_class3.mrc as #2, grid size 400,400,400, pixel 0.832,
shown at level 0.00811, step 2, values float32
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> fitmap #1 inMap #2
Fit map run_class001.mrc in map run_class001_class3.mrc using 79930 points
correlation = 0.9679, correlation about mean = 0.8419, overlap = 13.53
steps = 56, shift = 0.903, angle = 1.12 degrees
Position of run_class001.mrc (#1) relative to run_class001_class3.mrc (#2)
coordinates:
Matrix rotation and translation
0.99981252 -0.00322003 0.01909326 -3.36117137
0.00317458 0.99999206 0.00241019 -0.38362619
-0.01910087 -0.00234912 0.99981480 2.78245839
Axis -0.12198018 0.97890759 0.16389257
Axis point 139.77349753 0.00000000 174.27857876
Rotation angle (degrees) 1.11782834
Shift along axis 0.49048597
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> select ~sel & ##selected
Nothing selected
> open 4u4n
Summary of feedback from opening 4u4n fetched from pdb
---
warnings | Atom OP1 has no neighbors to form bonds with according to residue
template for G /5:420
Atom OP2 has no neighbors to form bonds with according to residue template for
G /5:420
4u4n title:
Crystal structure of Edeine bound to the yeast 80S ribosome [more info...]
Chain information for 4u4n #3
---
Chain | Description | UniProt
1 5 | 25S ribosomal RNA |
2 6 | 18S ribosomal RNA |
3 7 | 5S ribosomal RNA |
4 8 | 5.8S ribosomal RNA |
C0 c0 | 40S ribosomal protein S10-A | RS10A_YEAST 1-105
C1 c1 | 40S ribosomal protein S11-A | RS11A_YEAST 2-156
C2 c2 | 40S ribosomal protein S12 | RS12_YEAST 2-143
C3 c3 | 40S ribosomal protein S13 | RS13_YEAST 2-151
C4 c4 | 40S ribosomal protein S14-A | RS14A_YEAST 2-137
C5 c5 | 40S ribosomal protein S15 | RS15_YEAST 2-142
C6 c6 | 40S ribosomal protein S16-A | RS16A_YEAST 2-143
C7 c7 | 40S ribosomal protein S17-A | RS17A_YEAST 1-136
C8 c8 | 40S ribosomal protein S18-A | RS18A_YEAST 2-146
C9 c9 | 40S ribosomal protein S19-A | RS19A_YEAST 2-144
D0 d0 | 40S ribosomal protein S20 | RS20_YEAST 2-121
D1 d1 | 40S ribosomal protein S21-A | RS21A_YEAST 1-87
D2 d2 | 40S ribosomal protein S22-A | RS22A_YEAST 2-130
D3 d3 | 40S ribosomal protein S23-A | RS23A_YEAST 2-145
D4 d4 | 40S ribosomal protein S24-A | RS24A_YEAST 2-135
D5 d5 | 40S ribosomal protein S25-A | RS25A_YEAST 2-108
D6 d6 | 40S ribosomal protein S26-B | RS26B_YEAST 2-98
D7 d7 | 40S ribosomal protein S27-A | RS27_YEAST 2-82
D8 d8 | 40S ribosomal protein S28-A | RS28A_YEAST 2-67
D9 d9 | 40S ribosomal protein S29-A | RS29A_YEAST 2-56
E0 | 40S ribosomal protein S30-A | RS30A_YEAST 2-61
E1 e1 | Ubiquitin-40S ribosomal protein S31 | RS27A_YEAST 77-152
L2 l2 | 60S ribosomal protein L2-A | RL2A_YEAST 2-254
L3 l3 | 60S ribosomal protein L3 | RL3_YEAST 2-387
L4 l4 | 60S ribosomal protein L4-A | RL4A_YEAST 2-362
L5 l5 | 60S ribosomal protein L5 | RL5_YEAST 2-297
L6 l6 | 60S ribosomal protein L6-A | RL6A_YEAST 2-176
L7 l7 | 60S ribosomal protein L7-A | RL7A_YEAST 2-244
L8 l8 | 60S ribosomal protein L8-A | RL8A_YEAST 2-256
L9 l9 | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
M0 m0 | 60S ribosomal protein L10 | RL10_YEAST 2-221
M1 m1 | 60S ribosomal protein L11-B | RL11B_YEAST 2-174
M3 m3 | 60S ribosomal protein L13-A | RL13A_YEAST 2-199
M4 m4 | 60S ribosomal protein L14-A | RL14A_YEAST 2-138
M5 m5 | 60S ribosomal protein L15-A | RL15A_YEAST 2-204
M6 m6 | 60S ribosomal protein L16-A | RL16A_YEAST 2-199
M7 m7 | 60S ribosomal protein L17-A | RL17A_YEAST 2-184
M8 m8 | 60S ribosomal protein L18-A | RL18A_YEAST 2-186
M9 m9 | 60S ribosomal protein L19-A | RL19A_YEAST 2-189
N0 n0 | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
N1 n1 | 60S ribosomal protein L21-A | RL21A_YEAST 2-160
N2 n2 | 60S ribosomal protein L22-A | RL22A_YEAST 2-121
N3 n3 | 60S ribosomal protein L23-A | RL23A_YEAST 2-137
N4 n4 | 60S ribosomal protein L24-A | RL24A_YEAST 1-155
N5 n5 | 60S ribosomal protein L25 | RL25_YEAST 2-142
N6 n6 | 60S ribosomal protein L26-A | RL26A_YEAST 2-127
N7 n7 | 60S ribosomal protein L27-A | RL27A_YEAST 2-136
N8 n8 | 60S ribosomal protein L28 | RL28_YEAST 2-149
N9 n9 | 60S ribosomal protein L29 | RL29_YEAST 2-59
O0 o0 | 60S ribosomal protein L30 | RL30_YEAST 2-105
O1 o1 | 60S ribosomal protein L31-A | RL31A_YEAST 2-113
O2 o2 | 60S ribosomal protein L32 | RL32_YEAST 2-130
O3 o3 | 60S ribosomal protein L33-A | RL33A_YEAST 2-107
O4 o4 | 60S ribosomal protein L34-A | RL34A_YEAST 2-120
O5 o5 | 60S ribosomal protein L35-A | RL35A_YEAST 2-120
O6 o6 | 60S ribosomal protein L36-A | RL36A_YEAST 2-100
O7 o7 | 60S ribosomal protein L37-A | RL37A_YEAST 2-88
O8 o8 | 60S ribosomal protein L38 | RL38_YEAST 2-78
O9 o9 | 60S ribosomal protein L39 | RL39_YEAST 2-51
Q0 q0 | Ubiquitin-60S ribosomal protein L40 | RL401_YEAST 77-128
Q1 q1 | 60S ribosomal protein L41-A | RL41A_YEAST 1-25
Q2 q2 | 60S ribosomal protein L42-A | RL44A_YEAST 2-106
Q3 q3 | 60S ribosomal protein L43-A | RL43A_YEAST 2-92
S0 s0 | 40S ribosomal protein S0-A | RSSA1_YEAST 2-252
S1 s1 | 40S ribosomal protein S1-A | RS3A1_YEAST 2-255
S2 s2 | 40S ribosomal protein S2 | RS2_YEAST 2-254
S3 s3 | 40S ribosomal protein S3 | RS3_YEAST 2-240
S4 s4 | 40S ribosomal protein S4-A | RS4A_YEAST 2-261
S5 s5 | 40S ribosomal protein S5 | RS5_YEAST 2-225
S6 s6 | 40S ribosomal protein S6-A | RS6A_YEAST 1-236
S7 s7 | 40S ribosomal protein S7-A | RS7A_YEAST 2-190
S8 s8 | 40S ribosomal protein S8-A | RS8A_YEAST 1-200
S9 s9 | 40S ribosomal protein S9-A | RS9A_YEAST 2-197
SM sM | Suppressor protein STM1 | STM1_YEAST 1-273
SR sR | Guanine nucleotide-binding protein subunit beta-like protein |
GBLP_YEAST 2-319
e0 | 40S ribosomal protein S30-A | RS30A_YEAST 2-63
m2 | Unknown protein m2 |
p0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 2-312
p1 | Unknown protein p1 |
p2 | Unknown protein p2 |
Non-standard residues in 4u4n #3
---
EDE — edeine B
MG — magnesium ion
OHX — osmium (III) hexammine (osmium(6+) hexaazanide)
ZN — zinc ion
4u4n mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
> sym #3 assembly 2
Made 1 copies for 4u4n assembly 2
> view
> close #3
> select add #4.1
207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 4 models
selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> select subtract #4.1
Nothing selected
> select add #4
207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 5 models
selected
> open 1I96
1i96 title:
Crystal structure of the 30S ribosomal subunit from thermus thermophilus In
complex with the translation initiation factor IF3 (C-terminal domain) [more
info...]
Chain information for 1i96 #3
---
Chain | Description | UniProt
A | 16S RRNA |
B | 30S RIBOSOMAL PROTEIN S2 |
C | 30S RIBOSOMAL PROTEIN S3 |
D | 30S RIBOSOMAL PROTEIN S4 | RS4_THETH 2-209
E | 30S RIBOSOMAL PROTEIN S5 | RS5_THETH 2-162
F | 30S RIBOSOMAL PROTEIN S6 | RS6_THETH 1-101
G | 30S RIBOSOMAL PROTEIN S7 | P17291 2-156
H | 30S RIBOSOMAL PROTEIN S8 | RS8_THETH 1-138
I | 30S RIBOSOMAL PROTEIN S9 |
J | 30S RIBOSOMAL PROTEIN S10 | RS10_THETH 2-105
K | 30S RIBOSOMAL PROTEIN S11 |
L | 30S RIBOSOMAL PROTEIN S12 | RS12_THETH 5-135
M | 30S RIBOSOMAL PROTEIN S13 |
N | 30S RIBOSOMAL PROTEIN S14 | RS14_THETH 2-61
O | 30S RIBOSOMAL PROTEIN S15 | RS15_THETH 2-89
P | 30S RIBOSOMAL PROTEIN S16 |
Q | 30S RIBOSOMAL PROTEIN S17 | RS17_THETH 2-105
R | 30S RIBOSOMAL PROTEIN S18 |
S | 30S RIBOSOMAL PROTEIN S19 | RS19_THETH 2-93
T | 30S RIBOSOMAL PROTEIN S20 |
U | 30S RIBOSOMAL PROTEIN THX |
V | TRANSLATION INITIATION FACTOR IF3 |
Non-standard residues in 1i96 #3
---
MG — magnesium ion
WO2 — octadecatungstenyl diphosphate
ZN — zinc ion
> select add #3
243351 atoms, 253813 bonds, 13856 pseudobonds, 22262 residues, 9 models
selected
> select subtract #4
36091 atoms, 36513 bonds, 5230 pseudobonds, 4099 residues, 4 models selected
> select subtract #4.1
36091 atoms, 36513 bonds, 5230 pseudobonds, 4099 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> select add #4.1
243351 atoms, 253813 bonds, 13856 pseudobonds, 22262 residues, 8 models
selected
> view matrix models
> #4.1,0.99984,-0.0040773,-0.017182,3.9991,0.0032659,0.99889,-0.046989,9.8597,0.017354,0.046926,0.99875,-4.7723,#3,0.99984,-0.0040773,-0.017182,3.9991,0.0032659,0.99889,-0.046989,9.8597,0.017354,0.046926,0.99875,-4.7723
> select subtract #3
207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 4 models
selected
> select add #4
207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 5 models
selected
> select subtract #4.1
1 model selected
> select add #4
207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 5 models
selected
> ui mousemode right "translate selected models"
> select subtract #4
Nothing selected
> select add #4.1
207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 4 models
selected
> select add #3
243351 atoms, 253813 bonds, 13856 pseudobonds, 22262 residues, 8 models
selected
> select add #4
243351 atoms, 253813 bonds, 13856 pseudobonds, 22262 residues, 9 models
selected
> select subtract #4.1
36091 atoms, 36513 bonds, 5230 pseudobonds, 4099 residues, 5 models selected
> select add #4
243351 atoms, 253813 bonds, 13856 pseudobonds, 22262 residues, 9 models
selected
> view matrix models
> #4,0.99927,-0.012456,-0.036246,8.8285,0.011052,0.99919,-0.038695,6.9474,0.036698,0.038266,0.99859,-7.0206,#3,0.99844,-0.018218,-0.052784,12.875,0.013642,0.99622,-0.085788,17.028,0.054147,0.084934,0.99491,-11.262
> view matrix models
> #4,0.99927,-0.012456,-0.036246,58.641,0.011052,0.99919,-0.038695,-70.422,0.036698,0.038266,0.99859,12.52,#3,0.99844,-0.018218,-0.052784,62.687,0.013642,0.99622,-0.085788,-60.341,0.054147,0.084934,0.99491,8.2785
> select subtract #4.1
36091 atoms, 36513 bonds, 5230 pseudobonds, 4099 residues, 5 models selected
> view matrix models
> #4,0.99927,-0.012456,-0.036246,90.05,0.011052,0.99919,-0.038695,-129.17,0.036698,0.038266,0.99859,-219.51,#3,0.99844,-0.018218,-0.052784,94.096,0.013642,0.99622,-0.085788,-119.09,0.054147,0.084934,0.99491,-223.75
> view matrix models
> #4,0.99493,0.018263,0.098867,58.862,-0.013864,0.99889,-0.044996,-124.47,-0.099579,0.043397,0.99408,-199.59,#3,0.99655,0.018826,0.080791,62.549,-0.011381,0.99573,-0.091638,-114.46,-0.082171,0.090403,0.99251,-204.3
> view matrix models
> #4,0.92117,-0.21364,-0.32527,176.78,-0.040083,0.7793,-0.62537,23.663,0.38709,0.58911,0.70931,-238.4,#3,0.91468,-0.23242,-0.33065,179.91,-0.048385,0.74925,-0.66051,34.171,0.40126,0.62016,0.67408,-234.43
> view matrix models
> #4,0.92789,-0.20155,-0.31369,172.34,-0.047071,0.77126,-0.63478,27.433,0.36987,0.60377,0.70616,-235.86,#3,0.92164,-0.21983,-0.31977,175.56,-0.05556,0.74081,-0.66941,37.878,0.38404,0.63473,0.67055,-231.8
> view matrix models
> #4,0.92789,-0.20155,-0.31369,168.76,-0.047071,0.77126,-0.63478,-27.963,0.36987,0.60377,0.70616,-228.28,#3,0.92164,-0.21983,-0.31977,171.98,-0.05556,0.74081,-0.66941,-17.518,0.38404,0.63473,0.67055,-224.22
> view matrix models
> #4,0.95711,-0.12838,-0.25972,147.38,-0.034838,0.83896,-0.54308,-54.877,0.28761,0.52884,0.7985,-231.48,#3,0.95204,-0.14433,-0.2698,151.18,-0.041518,0.81268,-0.58123,-44.153,0.30315,0.56455,0.76771,-228.93
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99902,0.043649,0.0071443,70.54,-0.041425,0.97999,-0.19469,-141.47,-0.015499,0.19421,0.98084,-207.82,#3,0.99913,0.039862,-0.01208,74.932,-0.041596,0.96993,-0.23979,-131.04,0.0021588,0.24008,0.97075,-210.65
> select add #4
243351 atoms, 253813 bonds, 13856 pseudobonds, 22262 residues, 9 models
selected
> select subtract #4
36091 atoms, 36513 bonds, 5230 pseudobonds, 4099 residues, 4 models selected
> view matrix models
> #3,0.49949,-0.76092,0.41415,129.97,0.83266,0.55363,0.012952,-156.92,-0.23914,0.33837,0.91012,-202.87
> view matrix models
> #3,0.49949,-0.76092,0.41415,321.42,0.83266,0.55363,0.012952,-151.96,-0.23914,0.33837,0.91012,-187.39
> view matrix models
> #3,0.57947,-0.76901,0.26988,339.6,0.58014,0.62179,0.52613,-222.68,-0.57241,-0.14831,0.80644,-100.46
> view matrix models
> #3,0.57947,-0.76901,0.26988,336.68,0.58014,0.62179,0.52613,-111.19,-0.57241,-0.14831,0.80644,-50.458
> view matrix models
> #3,0.40934,-0.73922,0.53479,302.56,0.74155,0.61104,0.27701,-81.204,-0.53155,0.28319,0.79829,-101.91
> view matrix models
> #3,0.40934,-0.73922,0.53479,290.78,0.74155,0.61104,0.27701,-229.15,-0.53155,0.28319,0.79829,-169.97
> view matrix models
> #3,0.18431,-0.67499,0.71443,267.29,0.89453,0.41638,0.16262,-196.52,-0.40724,0.60911,0.68054,-196.9
> view matrix models
> #3,0.18431,-0.67499,0.71443,260.91,0.89453,0.41638,0.16262,-209.99,-0.40724,0.60911,0.68054,-121.09
> view matrix models
> #3,0.36953,-0.68929,0.62316,267.55,0.86579,0.49893,0.038469,-200.59,-0.33743,0.52531,0.78115,-128.77
> view matrix models
> #3,0.36953,-0.68929,0.62316,286.36,0.86579,0.49893,0.038469,-284.22,-0.33743,0.52531,0.78115,-136.29
> view matrix models
> #3,0.54465,-0.7064,0.45205,305.27,0.81273,0.57757,-0.076676,-274.58,-0.20693,0.40916,0.88869,-143.83
> view matrix models
> #3,0.58673,-0.67071,0.45376,298.96,0.77004,0.6355,-0.056346,-282.45,-0.25057,0.38247,0.88934,-138.86
> view matrix models
> #3,0.58673,-0.67071,0.45376,295.12,0.77004,0.6355,-0.056346,-291.27,-0.25057,0.38247,0.88934,-180.58
> view matrix models
> #3,0.59749,-0.67806,0.42807,299.21,0.79979,0.54236,-0.25725,-252.71,-0.057739,0.49607,0.86636,-199.16
> view matrix models
> #3,0.59749,-0.67806,0.42807,296.73,0.79979,0.54236,-0.25725,-235.32,-0.057739,0.49607,0.86636,-189.38
> view matrix models
> #3,0.59749,-0.67806,0.42807,306.98,0.79979,0.54236,-0.25725,-244.29,-0.057739,0.49607,0.86636,-184.39
> view matrix models
> #3,0.62547,-0.66361,0.41038,306.58,0.76412,0.62736,-0.15015,-268.14,-0.15782,0.4075,0.89947,-174.31
> view matrix models
> #3,0.62547,-0.66361,0.41038,303.23,0.76412,0.62736,-0.15015,-266.11,-0.15782,0.4075,0.89947,-174.68
> select subtract #3
Nothing selected
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> hide #!3 models
> hide #!4 models
> hide #!4.1 models
> show #!3 models
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #3
36091 atoms, 36513 bonds, 5230 pseudobonds, 4099 residues, 4 models selected
> view matrix models
> #3,0.49356,-0.65638,0.57059,285.15,0.68357,-0.11285,-0.72111,-93.241,0.53771,0.74595,0.39298,-172.35
> view matrix models
> #3,0.49356,-0.65638,0.57059,224.17,0.68357,-0.11285,-0.72111,99.994,0.53771,0.74595,0.39298,-71.436
> view matrix models
> #3,-0.72314,-0.060264,0.68806,190.7,0.4624,-0.78225,0.41746,24.8,0.51308,0.62004,0.59355,-84.373
> view matrix models
> #3,-0.72314,-0.060264,0.68806,116.52,0.4624,-0.78225,0.41746,158.4,0.51308,0.62004,0.59355,-0.99605
> view matrix models
> #3,-0.80887,-0.41837,0.41316,202.03,0.54148,-0.80389,0.24607,182.12,0.22919,0.42276,0.87678,-5.9877
> view matrix models
> #3,-0.80887,-0.41837,0.41316,204.44,0.54148,-0.80389,0.24607,179.83,0.22919,0.42276,0.87678,-9.8855
> view matrix models
> #3,-0.80887,-0.41837,0.41316,202.15,0.54148,-0.80389,0.24607,177.86,0.22919,0.42276,0.87678,-16.656
> view matrix models
> #3,-0.77858,-0.2824,0.56042,163.62,0.47968,-0.84362,0.24129,185.95,0.40464,0.45668,0.79228,-16.231
> view matrix models
> #3,-0.77858,-0.2824,0.56042,166.65,0.47968,-0.84362,0.24129,191,0.40464,0.45668,0.79228,-22.107
> view matrix models
> #3,-0.77858,-0.2824,0.56042,156.6,0.47968,-0.84362,0.24129,197.86,0.40464,0.45668,0.79228,-33.091
> view matrix models
> #3,-0.77814,-0.276,0.5642,148.74,0.47493,-0.84639,0.24097,199.23,0.41102,0.45546,0.78969,-23.721
> hide #!1 models
> fitmap #3 inMap #2
Fit molecule 1i96 (#3) to map run_class001_class3.mrc (#2) using 36091 atoms
average map value = 0.01358, steps = 172
shifted from previous position = 7.93
rotated from previous position = 12 degrees
atoms outside contour = 14241, contour level = 0.0081123
Position of 1i96 (#3) relative to run_class001_class3.mrc (#2) coordinates:
Matrix rotation and translation
-0.70372535 -0.40050105 0.58683008 162.16578436
0.51726758 -0.85503386 0.03676081 225.72965937
0.48703685 0.32941769 0.80887521 -11.83435366
Axis 0.30218930 0.10304370 0.94766219
Axis point 53.06833400 133.09158106 0.00000000
Rotation angle (degrees) 151.03811207
Shift along axis 61.04981461
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!4.1 models
> select subtract #3
Nothing selected
> select add #4.1
207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 4 models
selected
> view matrix models
> #4.1,0.99984,-0.0040773,-0.017182,-16.266,0.0032659,0.99889,-0.046989,84.29,0.017354,0.046926,0.99875,76.79
> view matrix models
> #4.1,0.38264,-0.42533,0.82017,-100.11,0.85941,-0.16198,-0.48494,59.055,0.33911,0.89043,0.30356,171.1
> view matrix models
> #4.1,0.38264,-0.42533,0.82017,-100.79,0.85941,-0.16198,-0.48494,93.958,0.33911,0.89043,0.30356,200.45
> view matrix models
> #4.1,0.63319,-0.57684,0.51607,-68.571,0.68103,0.098393,-0.72561,181.31,0.36779,0.81091,0.45515,159.17
> view matrix models
> #4.1,0.63319,-0.57684,0.51607,-59.917,0.68103,0.098393,-0.72561,235.27,0.36779,0.81091,0.45515,78.598
> view matrix models
> #4.1,0.6069,-0.22179,0.7632,-124.24,0.75247,-0.14877,-0.6416,206.5,0.25584,0.96368,0.076607,190.2
> view matrix models
> #4.1,0.6069,-0.22179,0.7632,-145.58,0.75247,-0.14877,-0.6416,281.47,0.25584,0.96368,0.076607,143.55
> view matrix models
> #4.1,0.36001,0.061262,0.93094,-147.46,0.78979,-0.55117,-0.26915,190.78,0.49661,0.83214,-0.24681,181.95
> view matrix models
> #4.1,0.36001,0.061262,0.93094,-210.89,0.78979,-0.55117,-0.26915,244.14,0.49661,0.83214,-0.24681,188.4
> view matrix models
> #4.1,0.38033,-0.74051,0.55407,-103.41,0.89454,0.14244,-0.42368,247.8,0.23482,0.65678,0.71659,1.5881
> view matrix models
> #4.1,0.38033,-0.74051,0.55407,-144.85,0.89454,0.14244,-0.42368,266.8,0.23482,0.65678,0.71659,43.895
> view matrix models
> #4.1,0.33227,-0.48767,0.80733,-204.39,0.91126,-0.054842,-0.40817,264.17,0.24333,0.87131,0.42617,109.79
> view matrix models
> #4.1,0.33227,-0.48767,0.80733,-189.71,0.91126,-0.054842,-0.40817,263.39,0.24333,0.87131,0.42617,106.66
> view matrix models
> #4.1,0.41421,-0.23318,0.8798,-228.58,0.83733,-0.28131,-0.46877,297.21,0.3568,0.93086,0.07873,170.56
> view matrix models
> #4.1,0.41421,-0.23318,0.8798,-240.32,0.83733,-0.28131,-0.46877,293.11,0.3568,0.93086,0.07873,186.83
> view matrix models
> #4.1,0.5362,-0.70048,0.47098,-151.18,0.72059,0.089296,-0.68758,361.12,0.43958,0.70807,0.55264,58.501
> ui tool show Matchmaker
> matchmaker #4.1/6 to #3/A pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match 4u4n #4.1/6 to 1i96 #3/A
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 1i96, chain A (#3) with 4u4n, chain 6 (#4.1), sequence alignment
score = 2337.6
RMSD between 415 pruned atom pairs is 1.120 angstroms; (across all 1462 pairs:
27.040)
> hide #!3 models
> hide #!4 models
> show #!4 models
> select add #4
207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 5 models
selected
> select subtract #4
Nothing selected
> select add #4.1
207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 4 models
selected
> select subtract #4.1
Nothing selected
> select ::name="EDE"
55 atoms, 55 bonds, 1 residue, 1 model selected
> show sel atoms
> color #2 #ffffb28a models
> volume #2 step 1
> volume #2 level 0.008845
> show #!3 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!4.1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!2 models
> hide #!3 models
> show #!4.1 models
> volume #1 step 1
> save "/Users/Haaris/Desktop/Temporary_Processing/Edeine/chimerax_maps_class3
> and withouttrna.cxs" includeMaps true
> open
> /Users/Haaris/Desktop/Temporary_Processing/Edeine/run_class001_firstrefine.mrc
Opened run_class001_firstrefine.mrc as #5, grid size 200,200,200, pixel 1.66,
shown at level 0.0231, step 1, values float32
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> color #5 #b2ffff60 models
> hide #!4 models
> color #5 #b2ffff61 models
> show #!4 models
> hide #!2 models
> show #!4.1 models
> volume #5 level 0.02354
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4.1 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!3 models
> show #!5 models
> hide #!5 models
> show #!4.1 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> hide #!4 models
> hide #!4.1 models
> hide #!5 models
> show #!5 models
> volume #5 level 0.009282
> volume #5 level 0.02116
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> show #!2 models
> show #!5 models
> hide #!2 models
> volume #5 level 0.01522
> open /Users/Haaris/Desktop/Modelling_Ksg/run_class001_body.mrc
Opened run_class001_body.mrc as #6, grid size 400,400,400, pixel 0.832, shown
at level 0.00496, step 2, values float32
> hide #!5 models
> volume #6 step 1
> volume #6 level 0.007256
> volume #6 level 0.007796
> close #6
> show #!5 models
> show #!4.1 models
> hide #!4.1 models
> hide #!5 models
> show #!2 models
> show #!4.1 models
> save "/Users/Haaris/Desktop/Temporary_Processing/Edeine/chimerax_maps_class3
> and withouttrna.cxs" includeMaps true
> open /Users/Haaris/Desktop/Modelling_Ksg/run_class001_body.mrc
Opened run_class001_body.mrc as #6, grid size 400,400,400, pixel 0.832, shown
at level 0.00496, step 2, values float32
> hide #!4.1 models
> hide #!4 models
> hide #!2 models
> volume #5 level 0.01839
> hide #!5 models
> volume #6 step 1
> volume #6 level 0.006851
> open /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot12.pdb
Chain information for Haaris_Kasugamycin_Coot12.pdb #7
---
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 #!7 cartoons
> hide #!7 atoms
> close
> open /Users/Haaris/Desktop/Modelling_Ksg/run_class001_body.mrc
Opened run_class001_body.mrc as #1, grid size 400,400,400, pixel 0.832, shown
at level 0.00496, step 2, values float32
> volume #1 step 1
> volume #1 level 0.006535
> open /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot12.pdb
Chain information for Haaris_Kasugamycin_Coot12.pdb #2
---
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 cartoons
> hide atoms
> select add #2
35059 atoms, 37996 bonds, 5 pseudobonds, 2591 residues, 2 models selected
> view matrix models #2,1,0,0,20.863,0,1,0,15.292,0,0,1,-5.5963
> fitmap #2 inMap #1
Fit molecule Haaris_Kasugamycin_Coot12.pdb (#2) to map run_class001_body.mrc
(#1) using 35059 atoms
average map value = 0.006915, steps = 92
shifted from previous position = 5.33
rotated from previous position = 1.75 degrees
atoms outside contour = 21787, contour level = 0.0065348
Position of Haaris_Kasugamycin_Coot12.pdb (#2) relative to
run_class001_body.mrc (#1) coordinates:
Matrix rotation and translation
0.99967811 0.02520518 -0.00289489 21.20704341
-0.02525112 0.99953466 -0.01711247 18.95538469
0.00246222 0.01718006 0.99984938 -6.15013976
Axis 0.55995627 -0.08747533 -0.82389140
Axis point 812.67860126 -491.45110025 0.00000000
Rotation angle (degrees) 1.75471226
Shift along axis 15.28393578
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99968,0.025205,-0.0028949,23.445,-0.025251,0.99953,-0.017112,18.896,0.0024622,0.01718,0.99985,-9.369
> fitmap #2 inMap #1
Fit molecule Haaris_Kasugamycin_Coot12.pdb (#2) to map run_class001_body.mrc
(#1) using 35059 atoms
average map value = 0.01826, steps = 56
shifted from previous position = 0.928
rotated from previous position = 1.2 degrees
atoms outside contour = 2861, contour level = 0.0065348
Position of Haaris_Kasugamycin_Coot12.pdb (#2) relative to
run_class001_body.mrc (#1) coordinates:
Matrix rotation and translation
0.99994116 0.01043734 0.00295644 24.10229484
-0.01042697 0.99993951 -0.00349995 13.69397562
-0.00299279 0.00346892 0.99998950 -6.69780310
Axis 0.30581760 0.26107201 -0.91559653
Axis point 896.17225323 -1803.77974033 0.00000000
Rotation angle (degrees) 0.65283266
Shift along axis 17.07850489
> volume #1 level 0.004305
> volume #1 level 0.00483
> volume #1 level 0.005486
> save /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot13.pdb
> relModel #1
> hide #!1 models
> select subtract #2
Nothing selected
> select /B
564 atoms, 633 bonds, 26 residues, 1 model selected
> select add #2
35059 atoms, 37996 bonds, 5 pseudobonds, 2591 residues, 2 models selected
> select subtract #2
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 2/B
> show #!1 models
> hide #!2 models
> volume #1 level 0.006797
> volume #1 level 0.007059
> show #!2 models
> open "/Users/Haaris/Desktop/Modelling_Ksg/5lmv_aligned_AndreaAUGmap-coot-1
> (1).pdb"
Chain information for 5lmv_aligned_AndreaAUGmap-coot-1 (1).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
Z | No description available
a | No description available
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!3 cartoons
> hide #!3 atoms
> close #3
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> open /Users/Haaris/Desktop/Modelling_Ksg/6vwm_aligned.pdb
Chain information for 6vwm_aligned.pdb #3
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
A | No description available
AA | No description available
AB | No description available
AC | No description available
B | No description available
C | No description available
D | No description available
E | 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
> select add #3
140044 atoms, 152352 bonds, 74 pseudobonds, 9975 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> view matrix models
> #3,0.92864,-0.17248,0.32844,-16.243,0.16405,0.985,0.053435,-32.583,-0.33273,0.0042566,0.94301,61.642
> view matrix models
> #3,0.92864,-0.17248,0.32844,7.5618,0.16405,0.985,0.053435,-26.046,-0.33273,0.0042566,0.94301,47.096
> view matrix models
> #3,0.9918,0.12535,-0.024996,14.511,-0.12484,0.99195,0.021003,24.645,0.027428,-0.01771,0.99947,-16.902
> view matrix models
> #3,0.99137,-0.065524,0.11356,16.259,0.060068,0.9969,0.050816,-10.173,-0.11653,-0.043556,0.99223,10.398
> view matrix models
> #3,0.99137,-0.065524,0.11356,14.086,0.060068,0.9969,0.050816,-7.8441,-0.11653,-0.043556,0.99223,14.225
> view matrix models
> #3,0.9854,-0.065548,0.15713,8.7703,0.047105,0.99185,0.11835,-14.914,-0.16361,-0.10922,0.98046,31.003
> fitmap #3 inMap #1
Fit molecule 6vwm_aligned.pdb (#3) to map run_class001_body.mrc (#1) using
140044 atoms
average map value = 0.003391, steps = 304
shifted from previous position = 6.27
rotated from previous position = 12 degrees
atoms outside contour = 115070, contour level = 0.0070593
Position of 6vwm_aligned.pdb (#3) relative to run_class001_body.mrc (#1)
coordinates:
Matrix rotation and translation
0.99993638 0.01097084 0.00262103 24.09129339
-0.01096138 0.99993346 -0.00359628 13.77834458
-0.00266031 0.00356732 0.99999010 -6.76724154
Axis 0.30265489 0.22313070 -0.92661357
Axis point 928.85137536 -1731.60218196 0.00000000
Rotation angle (degrees) 0.67808919
Shift along axis 16.63633736
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save /Users/Haaris/Desktop/Modelling_Ksg/6vwm_aligned.pdb models #3 relModel
> #1
> 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
> select add #3
146883 atoms, 159526 bonds, 10662 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> hide #!1 models
> show #!1 models
> view matrix models
> #3,0.95304,-0.11333,0.28086,-21.011,0.10609,0.99352,0.040896,-22.544,-0.28367,-0.0091798,0.95888,53.208
> view matrix models
> #3,0.95304,-0.11333,0.28086,-11.174,0.10609,0.99352,0.040896,-20.315,-0.28367,-0.0091798,0.95888,46.249
> view matrix models
> #3,0.94898,0.26305,0.1739,-37.161,-0.25673,0.96472,-0.058305,56.533,-0.1831,0.010684,0.98304,24.102
> view matrix models
> #3,0.94898,0.26305,0.1739,-35.242,-0.25673,0.96472,-0.058305,57.7,-0.1831,0.010684,0.98304,11.757
> view matrix models
> #3,0.93908,0.31552,0.13627,-33.997,-0.31176,0.94891,-0.048673,67.007,-0.14466,0.0032251,0.98948,5.3991
> fitmap #3 inMap #1
Fit molecule 5np6_aligned.pdb (#3) to map run_class001_body.mrc (#1) using
146883 atoms
average map value = 0.003255, steps = 728
shifted from previous position = 20.9
rotated from previous position = 19.4 degrees
atoms outside contour = 121667, contour level = 0.0070593
Position of 5np6_aligned.pdb (#3) relative to run_class001_body.mrc (#1)
coordinates:
Matrix rotation and translation
0.99991637 0.01257933 0.00300382 23.76375413
-0.01256970 0.99991587 -0.00320224 13.95056368
-0.00304385 0.00316422 0.99999036 -6.66117709
Axis 0.23899962 0.22703247 -0.94410563
Axis point 847.16032451 -1595.91193628 0.00000000
Rotation angle (degrees) 0.76314323
Shift along axis 15.13561390
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> fitmap #3 inMap #1
Fit molecule 5np6_aligned.pdb (#3) to map run_class001_body.mrc (#1) using
146883 atoms
average map value = 0.003255, steps = 1580
shifted from previous position = 0.0152
rotated from previous position = 0.00125 degrees
atoms outside contour = 121656, contour level = 0.0070593
Position of 5np6_aligned.pdb (#3) relative to run_class001_body.mrc (#1)
coordinates:
Matrix rotation and translation
0.99991662 0.01256063 0.00299769 23.76788665
-0.01255100 0.99991608 -0.00321174 13.93475803
-0.00303778 0.00317385 0.99999035 -6.66858997
Axis 0.24001943 0.22685983 -0.94388839
Axis point 846.90457993 -1596.93260426 0.00000000
Rotation angle (degrees) 0.76218367
Shift along axis 15.16039622
> hide #!1 models
> show #!1 models
> select subtract #3
Nothing selected
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> ui tool show H-Bonds
> hbonds sel restrict both saltOnly true select true reveal true log true
Atom specifier selects no atoms
> select #3/A:14
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
621 atoms, 694 bonds, 29 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict both saltOnly true select true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
3 5np6_aligned.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select #3/A:17
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
621 atoms, 694 bonds, 29 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel saltOnly true select true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 Haaris_Kasugamycin_Coot12.pdb
3 5np6_aligned.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
Haaris_Kasugamycin_Coot12.pdb #2/W HIS 43 ND1 5np6_aligned.pdb #3/A U 19 OP1 no hydrogen 1.574 N/A
1 hydrogen bonds found
> select add #2
35060 atoms, 37996 bonds, 5 pseudobonds, 2592 residues, 3 models selected
> select subtract #2
1 atom, 1 residue, 1 model selected
> select add #3
146883 atoms, 159526 bonds, 10662 residues, 1 model selected
> hide #3 models
> select add #4
146883 atoms, 159526 bonds, 1 pseudobond, 10662 residues, 2 models selected
> show #3 models
> close #4
> select subtract #3
Nothing selected
> hide #3 models
> show #3 models
> 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
> show #!1 models
> select add #3
146883 atoms, 159526 bonds, 10662 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> fitmap #3 inMap #1
Fit molecule 5np6_aligned.pdb (#3) to map run_class001_body.mrc (#1) using
146883 atoms
average map value = 0.001179, steps = 288
shifted from previous position = 9.77
rotated from previous position = 4.86 degrees
atoms outside contour = 138826, contour level = 0.0070593
Position of 5np6_aligned.pdb (#3) relative to run_class001_body.mrc (#1)
coordinates:
Matrix rotation and translation
0.99835362 -0.03346963 0.04658153 3.92921316
0.03631751 0.99743392 -0.06169771 9.89237255
-0.04439700 0.06328785 0.99700730 3.12901804
Axis 0.73688466 0.53638744 0.41144807
Axis point 0.00000000 15.89828662 77.17990237
Rotation angle (degrees) 4.86491126
Shift along axis 9.48894971
> view matrix models
> #3,0.98925,-0.10448,0.10227,5.1999,0.097652,0.99278,0.069687,-18.928,-0.10881,-0.058952,0.99231,28.068
> view matrix models
> #3,0.98925,-0.10448,0.10227,24.037,0.097652,0.99278,0.069687,-16.564,-0.10881,-0.058952,0.99231,16.159
> view matrix models
> #3,0.98048,-0.051195,0.18981,6.5461,0.087367,0.97839,-0.18741,24.644,-0.17612,0.20034,0.96377,2.0857
> view matrix models
> #3,0.98048,-0.051195,0.18981,3.2016,0.087367,0.97839,-0.18741,22.35,-0.17612,0.20034,0.96377,-6.2266
> view matrix models
> #3,0.98619,-0.025903,0.16355,3.2954,0.058291,0.97878,-0.19646,28.366,-0.15499,0.20329,0.96677,-10.435
> view matrix models
> #3,0.98619,-0.025903,0.16355,-3.3241,0.058291,0.97878,-0.19646,36.689,-0.15499,0.20329,0.96677,-6.7037
> fitmap #3 inMap #1
Fit molecule 5np6_aligned.pdb (#3) to map run_class001_body.mrc (#1) using
146883 atoms
average map value = 0.001115, steps = 280
shifted from previous position = 4.63
rotated from previous position = 7.67 degrees
atoms outside contour = 139449, contour level = 0.0070593
Position of 5np6_aligned.pdb (#3) relative to run_class001_body.mrc (#1)
coordinates:
Matrix rotation and translation
0.99468237 0.07143553 0.07418866 14.14805644
-0.05271842 0.97197739 -0.22908670 75.80680390
-0.08847463 0.22395739 0.97057474 -30.96473780
Axis 0.91134818 0.32721515 -0.24974938
Axis point 0.00000000 120.60995147 251.26225221
Rotation angle (degrees) 14.39214450
Shift along axis 45.43236381
> view matrix models
> #3,0.99694,0.06522,0.043178,19.055,-0.040567,0.90311,-0.4275,110.85,-0.066875,0.42444,0.90298,-47.103
> view matrix models
> #3,0.99694,0.06522,0.043178,8.961,-0.040567,0.90311,-0.4275,109.35,-0.066875,0.42444,0.90298,-44.842
> view matrix models
> #3,0.96419,0.25283,-0.080128,11.324,-0.26512,0.9104,-0.31763,128.83,-0.0073582,0.3275,0.94482,-49.76
> view matrix models
> #3,0.96419,0.25283,-0.080128,16.466,-0.26512,0.9104,-0.31763,128.88,-0.0073582,0.3275,0.94482,-47.339
> view matrix models
> #3,0.99424,-0.046685,-0.096454,47.744,0.049878,0.99828,0.030966,16.363,0.094842,-0.035599,0.99486,-30.407
> fitmap #3 inMap #1
Fit molecule 5np6_aligned.pdb (#3) to map run_class001_body.mrc (#1) using
146883 atoms
average map value = 0.003255, steps = 992
shifted from previous position = 21.6
rotated from previous position = 6.98 degrees
atoms outside contour = 121658, contour level = 0.0070593
Position of 5np6_aligned.pdb (#3) relative to run_class001_body.mrc (#1)
coordinates:
Matrix rotation and translation
0.99991627 0.01258777 0.00299901 23.76470096
-0.01257841 0.99991602 -0.00312051 13.92817034
-0.00303804 0.00308253 0.99999063 -6.65277166
Axis 0.23308158 0.22684448 -0.94562919
Axis point 847.69121731 -1604.72460587 0.00000000
Rotation angle (degrees) 0.76243328
Shift along axis 14.98969771
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> save /Users/Haaris/Desktop/Modelling_Ksg/5np6_aligned.pdb models #3 relModel
> #1
> close #2
> close #3
> close
> open /Users/Haaris/Desktop/Modelling_Ksg/30S_IF2_flipped.mrc
Opened 30S_IF2_flipped.mrc as #1, grid size 440,440,440, pixel 0.8, shown at
level 0.0586, step 2, values float32
> volume #1 step 1
> volume #1 level 0.07981
> open "/Users/Haaris/Desktop/Modelling_Ksg/5lmv_aligned_AndreaAUGmap-coot-1
> (1).pdb"
Chain information for 5lmv_aligned_AndreaAUGmap-coot-1 (1).pdb #2
---
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
Z | No description available
a | No description available
> select add #2
59485 atoms, 63983 bonds, 20 pseudobonds, 4744 residues, 3 models selected
> view matrix models
> #2,0.54298,-0.81951,0.18326,173.26,0.30385,-0.011715,-0.95265,267.45,0.78285,0.57295,0.24264,-92.547
> show sel cartoons
> hide sel atoms
> view matrix models
> #2,0.43492,-0.90045,0.0063817,233.38,-0.525,-0.25932,-0.81063,419.81,0.73158,0.34921,-0.58552,89.333
> view matrix models
> #2,0.43492,-0.90045,0.0063817,250.43,-0.525,-0.25932,-0.81063,424.56,0.73158,0.34921,-0.58552,101.68
> view matrix models
> #2,0.33941,-0.93655,-0.08757,287.61,-0.61993,-0.1527,-0.76965,416.78,0.70745,0.31552,-0.63243,118.78
> view matrix models
> #2,0.33941,-0.93655,-0.08757,292.74,-0.61993,-0.1527,-0.76965,429.41,0.70745,0.31552,-0.63243,120.26
> view matrix models
> #2,0.26779,-0.87968,-0.393,346.75,-0.81017,0.015169,-0.58599,404,0.52145,0.47532,-0.70863,138.83
> view matrix models
> #2,0.26779,-0.87968,-0.393,342.02,-0.81017,0.015169,-0.58599,402.27,0.52145,0.47532,-0.70863,136.96
> fitmap #2 inMap #1
Fit molecule 5lmv_aligned_AndreaAUGmap-coot-1 (1).pdb (#2) to map
30S_IF2_flipped.mrc (#1) using 59485 atoms
average map value = 0.1923, steps = 220
shifted from previous position = 2.34
rotated from previous position = 15 degrees
atoms outside contour = 13557, contour level = 0.079807
Position of 5lmv_aligned_AndreaAUGmap-coot-1 (1).pdb (#2) relative to
30S_IF2_flipped.mrc (#1) coordinates:
Matrix rotation and translation
0.16141245 -0.95085759 -0.26422692 348.03537918
-0.69255635 0.08160319 -0.71673330 392.99161741
0.70307306 0.29868171 -0.64535069 122.88646307
Axis 0.71207566 -0.67833425 0.18113779
Axis point 0.00000000 326.28972187 133.53259185
Rotation angle (degrees) 134.52074992
Shift along axis 3.50723285
> select subtract #2
Nothing selected
> volume #1 level 0.05152
> volume #1 level 0.08216
> volume #1 level 0.06331
> save "/Users/Haaris/Desktop/Modelling_Ksg/5lmv_aligned_AndreaAUGmap-coot-1
> (1).pdb" relModel #1
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain /Y
Alignment identifier is 2/Y
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.07509
> ui tool show "Show Sequence Viewer"
> sequence chain /Y
Destroying pre-existing alignment with identifier 2/Y
Alignment identifier is 2/Y
> hide #!1 models
> open /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot13.pdb
Chain information for Haaris_Kasugamycin_Coot13.pdb #3
---
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
> hide #!2 models
> select add #3
35059 atoms, 37996 bonds, 5 pseudobonds, 2591 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select subtract #3
Nothing selected
> open /Users/Haaris/Desktop/Modelling_Ksg/run_class001_body.mrc
Opened run_class001_body.mrc as #4, grid size 400,400,400, pixel 0.832, shown
at level 0.00496, step 2, values float32
> volume #4 step 1
> volume #4 level 0.007584
> open 5lmn
5lmn title:
Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex
(state-1A) [more info...]
Chain information for 5lmn #5
---
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 #5
---
MG — magnesium ion
ZN — zinc ion
> hide #!4 models
> select add #5
54149 atoms, 58290 bonds, 1844 pseudobonds, 4286 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> hide #!3 models
> select subtract #5
Nothing selected
> close #5
> open /Users/Haaris/Desktop/Modelling_Ksg/6vwm_aligned.pdb
Chain information for 6vwm_aligned.pdb #5
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
A | No description available
AA | No description available
AB | No description available
AC | No description available
B | No description available
C | No description available
D | No description available
E | 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
> show #!5 cartoons
> hide #!5 atoms
> show #!3 models
> hide #!3 models
> show #!4 models
> volume #4 level 0.002469
> volume #4 level 0.006535
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!2 models
> show #!1 models
> close #5
> hide #!1 models
> show #!1 models
> color #1 #b2b2b29a models
> color #1 #b2b2b299 models
> volume #1 level 0.05388
> volume #1 level 0.08216
> volume #1 level 0.06566
> show #!4 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> volume #4 level 0.005092
> close #1
> close #2
> hide #!3 models
> show #!3 models
> hide #!4 models
> select ::name="KSG"
26 atoms, 27 bonds, 1 residue, 1 model selected
> open /Users/Haaris/Desktop/Modelling_Ksg/run_class001_body.mrc
Opened run_class001_body.mrc as #1, grid size 400,400,400, pixel 0.832, shown
at level 0.00496, step 2, values float32
> volume #1 step 1
> volume #1 level 0.007059
> volume #1 level 0.007453
> open /Users/Haaris/Desktop/Modelling_Ksg/30S_IF2_flipped.mrc
Opened 30S_IF2_flipped.mrc as #2, grid size 440,440,440, pixel 0.8, shown at
level 0.0586, step 2, values float32
> close #3
> close #1
> close #4
> volume #2 step 1
> volume #2 level 0.04916
> volume #2 level 0.05388
> close
> open /Users/Haaris/Desktop/Modelling_Ksg/run_class001.mrc
Opened run_class001.mrc as #1, grid size 400,400,400, pixel 0.832, shown at
level 0.00636, step 2, values float32
> volume #1 step 1
> volume #1 level 0.004792
> open /Users/Haaris/Desktop/Modelling_Ksg/30S_IF2_flipped.mrc
Opened 30S_IF2_flipped.mrc as #2, grid size 440,440,440, pixel 0.8, shown at
level 0.0586, step 2, values float32
> select add #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.23487,-0.59138,0.77143,101.3,-0.96393,-0.24394,0.10648,368.37,0.12521,-0.76861,-0.62735,401.01
> view matrix models
> #2,0.23487,-0.59138,0.77143,91.476,-0.96393,-0.24394,0.10648,351,0.12521,-0.76861,-0.62735,389.59
> view matrix models
> #2,0.35134,-0.63089,0.69176,92.186,-0.93607,-0.2225,0.27251,313.03,-0.018006,-0.74328,-0.66873,417.44
> fitmap #2 inMap #1
Fit map 30S_IF2_flipped.mrc in map run_class001.mrc using 106331 points
correlation = 0.912, correlation about mean = 0.7422, overlap = 196
steps = 312, shift = 5.88, angle = 18 degrees
Position of 30S_IF2_flipped.mrc (#2) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.16229209 -0.69262641 0.70280149 129.51610375
-0.95060331 0.08124797 0.29958658 262.04742830
-0.26460277 -0.71670596 -0.64522705 452.97789476
Axis -0.71237281 0.67810445 -0.18082956
Axis point 0.00000000 326.19283390 133.61685565
Rotation angle (degrees) 134.49471673
Shift along axis 3.51998480
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #2 step 1
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #1 level 0.003339
> volume #1 level 0.006134
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> open /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot13.pdb
Chain information for Haaris_Kasugamycin_Coot13.pdb #3
---
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
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> select add #3
35059 atoms, 37996 bonds, 5 pseudobonds, 2591 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> view matrix models
> #3,0.99827,-0.045892,-0.03688,13.731,0.045318,0.99884,-0.016241,-4.6294,0.037583,0.014542,0.99919,-8.4134
> view matrix models
> #3,0.98299,0.0014204,-0.18368,32.081,-0.00071018,0.99999,0.0039324,-0.51434,0.18368,-0.003735,0.98298,-26.767
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98299,0.0014204,-0.18368,11.364,-0.00071018,0.99999,0.0039324,-12.761,0.18368,-0.003735,0.98298,-15.25
> view matrix models
> #3,0.98299,0.0014204,-0.18368,10.912,-0.00071018,0.99999,0.0039324,-12.66,0.18368,-0.003735,0.98298,-15.791
> fitmap #3 inMap #1
Fit molecule Haaris_Kasugamycin_Coot13.pdb (#3) to map run_class001.mrc (#1)
using 35059 atoms
average map value = 0.01616, steps = 144
shifted from previous position = 6.18
rotated from previous position = 10.4 degrees
atoms outside contour = 2870, contour level = 0.0061341
Position of Haaris_Kasugamycin_Coot13.pdb (#3) relative to run_class001.mrc
(#1) coordinates:
Matrix rotation and translation
0.99994195 -0.01035860 -0.00296606 -23.99666021
0.01036889 0.99994021 0.00347345 -13.91681403
0.00292991 -0.00350400 0.99998957 6.67826541
Axis -0.30803884 -0.26029409 0.91507325
Axis point 901.81225901 -1812.37751700 0.00000000
Rotation angle (degrees) 0.64892251
Shift along axis 17.12546993
> select subtract #3
Nothing selected
> open /Users/Haaris/Desktop/Modelling_Ksg/1vy4_aligned.pdb
===== 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-5.2.4
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: 580~1053
SMC Version (system): 2.46f13
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 15 days, 4 hours, 3 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 (2)
comment:1 by , 21 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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Hi Haaris,
--Eric