![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 19 months ago
Closed 19 months ago
#15070 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.4.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff85f1a5100 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 81 in msgpack_deserialize
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 721 in restore
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 1017 in open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 334 in _qt_safe
File "/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, 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, PIL._webp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 66)
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{
"uptime" : 2700000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 505,
"deployVersion" : 210,
"modelCode" : "iMac19,1",
"coalitionID" : 125809,
"osVersion" : {
"train" : "macOS 14.4.1",
"build" : "23E224",
"releaseType" : "User"
},
"captureTime" : "2024-04-30 12:19:08.0411 +0200",
"codeSigningMonitor" : 0,
"incident" : "E7AF587D-B0D3-4B92-8630-D663C0D3A587",
"pid" : 57168,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-04-30 10:07:55.9873 +0200",
"procStartAbsTime" : 2748219983899973,
"procExitAbsTime" : 2756091665459921,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","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,
"wakeTime" : 1270810,
"sleepWakeUUID" : "C5AE1E21-2569-4D4B-8C96-044A213A4EF2",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4398915415\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 106322000-106326000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"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":57168},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 4398915415\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 106322000-106326000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs
Log from Mon Apr 29 15:45:41 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
> mousemode shift leftMode "translate selected models"
> mousemode shift middleMode "rotate selected models"
> mousemode rightMode zoom
> mousemode control wheelMode "contour level"
> mousemode setting "contour level" speed 0.1
> mousemode shift wheelMode "rotate selected models"
> camera ortho
> set bgColor grey
> lighting shadows false
> lighting depthCue false
> graphics silhouettes true
> lighting simple
> functionkey F1 cofr sel
> functionkey F2 mousemode rightMode 'mark surface'
> functionkey F3 mousemode rightMode 'move markers'
> functionkey F4 mk 3 1
> functionkey F5 view
> functionkey F6 view sel pad 0.92 clip false
> functionkey F7 mousemode rightMode 'delete markers'
> functionkey F8 mousemode rightMode zoom
> functionkey F9 sequence chain sel
> functionkey F10 transparency sel 65
> functionkey F11 transparency sel 0
> functionkey F12 tool show 'Fit in Map'
> color name f01graublau #BADBED
Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed
> color name f02silber #F6FAFC
Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc
> color name f03muschel #FFFFE5
Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5
> color name f04beige #F3F3A9
Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9
> color name f05gelb #f2b701
Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701
> color name f06orange #e68310
Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310
> color name f07rotorange #FF6A25
Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25
> color name f08rot #dd3d2d
Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d
> color name f09lachs #f97b72
Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72
> color name f10flieder #D57AD5
Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5
> color name f11violett #cf1c90
Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90
> color name f12lila #4b148f
Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f
> color name f13dunkelblau #2E2EF7
Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7
> color name f14blau #00AAFF
Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff
> color name f15cyan #60e2d6
Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6
> color name f16blaugrün #30ffa6
Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6
> color name f17grün #00FF00
Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00
> color name f18dunkelgrün #228B22
Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22
> color name f19hellgrau #DCDCDC
Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc
> color name f20grau #B2B2B2
Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2
> color name f21anthrazit #323F45
Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45
> alias localres color sample #$1 map #$2 offset 0.0 update true palette
> "#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"
> range $3,$4
> alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1
> $2'
> alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4
> 'quickmk $1 $2'
> alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3
> alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep
> $3
> alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep
> $3
> alias consurf color byattr seq_conservation protein palette cyanmaroon
> novalue yellow
> alias chaininfo preset custom chaininfo
> alias foto save browse format tiff height 4000 width 5500 supersample 4
> transparentBackground false
> alias durch save browse format tiff height 4000 width 5500 supersample 4
> transparentBackground true
> alias session save browse format session includeMaps true compress lz4
> alias nomapsession save browse format session includeMaps false compress lz4
> alias splitup color zone #$1 near sel sharpEdges true distance $2
> alias quicksplitup color zone #$1 near sel sharpEdges false distance $2
> alias spalt volume splitbyzone #$1
> alias undust surface undust #$1
> alias dust surface dust #$2 size $1
> alias dust1 surface dust #$1 size 1
> alias dust2 surface dust #$1 size 2
> alias dust3 surface dust #$1 size 3
> alias dust4 surface dust #$1 size 4
> alias dust5 surface dust #$1 size 5
> alias dust6 surface dust #$1 size 6
> alias dust7 surface dust #$1 size 7
> alias dust8 surface dust #$1 size 8
> alias dust9 surface dust #$1 size 9
> alias dust10 surface dust #$1 size 10
> alias dust11 surface dust #$1 size 11
> alias dust12 surface dust #$1 size 12
> alias dust13 surface dust #$1 size 13
> alias dust14 surface dust #$1 size 14
> alias dust15 surface dust #$1 size 15
> alias dust20 surface dust #$1 size 20
> alias dust25 surface dust #$1 size 25
> alias dust30 surface dust #$1 size 30
> alias dust35 surface dust #$1 size 35
> alias dust40 surface dust #$1 size 40
> alias dust45 surface dust #$1 size 45
> alias dust50 surface dust #$1 size 50
> alias sunset color sample #$1 map #$2 offset 0.1 update true palette
> "#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026"
> range $3,$4
> alias nicemap volume #$1 subdivideSurface true surfacesmoothing true
> smoothLines true squareMesh false meshLighting true
> alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false
> smoothLines false squareMesh true meshLighting true
> alias figure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ;
> camera ortho
> alias tryfigure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.01 ; set bgColor white ;
> camera ortho; cartoon style width 2.4 thickness 0.4; lighting
> ambientintensity 1.2 fillIntensity 0.4
> alias abbild sel zone sel 1 #$1 residues true extend true
> alias abbild+ sel zone sel 1 #$1 residues true extend true; show sel; sel
> intersect #$1; style sel stick; sel compound; sel zone sel 7 #$1 residues
> true extend true; sel intersect :HOH:MG:K:ZN:SPD:SPM; show sel; sel
> intersect :MG; style sel ball; size sel ballscale 0.5
> alias network sel zone sel $1 #$2 residues true extend true
> alias network34 sel zone sel 3.4 #$1 residues true extend true
> alias network4 sel zone sel 4 #$1 residues true extend true
> alias network10 sel zone sel 10 #$1 residues true extend true
> alias wasser sel zone #$1 3.4 #$2 residues true extend true; sel intersect
> #$2:HOH; sel add #$1; sel zone sel 3.4 #$2 residues true extend true
> alias 1st-wasser sel zone #$1 3.4 #$2 residues true extend true; sel
> intersect #$2:HOH
> alias farben color sel f14; sel #$1 & nucleic; color sel f20; sel #$1 &
> protein; color sel f07; sel #$1:HOH; color sel red; sel #$1:MG; color sel
> f17; sel #$1:K; color sel f15
> alias magnesiumcluster sel zone sel 2.7 #$1 extend true; sel intersect
> #$1@o*:HOH:MG
> alias magnesiumcluster4 sel zone sel 4 #$1 extend true; sel intersect
> #$1@o*:HOH:MG
> alias upsplit color zone #$1 near #$3 sharpEdges true distance $2
> alias weihwasser sel zone #$1 3.4 #$2 residues true extend true; sel
> intersect #$2:HOH; sel add #$1; sel subtract badwaters; sel zone sel 3.4 #$2
> residues true extend true; sel subtract badwaters
> alias fixall size pseudobondRadius 0.075; sel :MG; style sel ball; size sel
> ballscale 0.5
> alias fix size pseudobondRadius 0.075; da $1; sel intersect :MG; style sel
> ball; color sel f17; size sel ballscale 0.5; da $1; sel intersect
> ##name="K"; color sel blueviolet
> alias pixel zoom pixelsize 0.04
> alias da sel #$1 @@display
> alias neu hide #$1; da $2; sel intersect ligand; mm #$1 to #$2 matrix
> Nucleic; network10 $1,$2; mm #!$1 & sel to #$2 & sel matrix Nucleic; da $2;
> abbild+ $1
> alias neu2 da $1; sel intersect ligand; farben $1; da $1; color sel byhet;
> hbonds sel color f05 restrict both interModel false intraMol false intraRes
> false; sel intersect :HOH; style sel stick; combine #$1; da $1; sel
> intersect :HOH; name frozen temp sel; hide sel; da $1; sel intersect
> ##name="hydrogen bonds"; del pbonds sel; sel temp; show sel; da $2; sel
> intersect :HOH; hide sel; da $2; sel intersect nucleic; sel intersect
> ##name="hydrogen bonds"; hide sel; da $2; sel intersect protein; sel
> intersect ##name="hydrogen bonds"; hide sel; da $1; sel intersect
> ##name="hydrogen bonds"; color sel f15
> alias kalium da $1; sel intersect :K; style sel ball; size sel ballscale
> 0.3; name frozen temp sel; sel zone sel 3.5 #$1 extend true; sel intersect
> @o*,n*:K; contacts sel restrict temp overlapCutoff -3.0 color #8A2BE2 name K
> log true
> alias magnesium da $1; sel intersect :MG; style sel ball; size sel ballscale
> 0.5; name frozen temp sel; magnesiumcluster $1; contacts sel restrict temp
> overlapCutoff -0.8 color #00FF00 name Mg log true
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/refined_Ede_Round5-coot-1_withW.pdb
Chain information for refined_Ede_Round5-coot-1_withW.pdb #1
---
Chain | Description
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | 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
> set bgColor white
> show cartoons
> hide atoms
> open 5lmv
5lmv title:
Structure of bacterial 30S-IF1-IF2-IF3-mRNA-tRNA translation pre-initiation
complex(state-III) [more info...]
Chain information for 5lmv #2
---
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 |
a | Translation initiation factor IF-2 | IF2_THET8 1-571
Non-standard residues in 5lmv #2
---
FME — N-formylmethionine
MG — magnesium ion
ZN — zinc ion
> hide #!1 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #2/A to #1/B pairing ss matrix Nucleic
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 refined_Ede_Round5-coot-1_withW.pdb, chain B (#1) with 5lmv, chain
A (#2), sequence alignment score = 2553.7
RMSD between 463 pruned atom pairs is 1.372 angstroms; (across all 1023 pairs:
39.083)
> hide #!2 models
> select add #1
36142 atoms, 37014 bonds, 4 pseudobonds, 4357 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> show #!2 models
> show #!2 cartoons
> hide #!2 atoms
> show #!1 models
> hide #!2 models
> open 1i95
1i95 title:
Crystal structure of the 30S ribosomal subunit from thermus thermophilus In
complex with edeine [more info...]
Chain information for 1i95 #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 |
Non-standard residues in 1i95 #3
---
EDE — edeine B
MG — magnesium ion
WO2 — octadecatungstenyl diphosphate
ZN — zinc ion
> select add #3
36224 atoms, 36584 bonds, 5311 pseudobonds, 4016 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> select subtract #3
Nothing selected
> ui tool show Matchmaker
> matchmaker #3/A to #1/B pairing ss matrix Nucleic
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 refined_Ede_Round5-coot-1_withW.pdb, chain B (#1) with 1i95, chain
A (#3), sequence alignment score = 2559.4
RMSD between 662 pruned atom pairs is 1.173 angstroms; (across all 1026 pairs:
39.583)
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> open /Users/Haaris/Desktop/Figures_Ksg_Edeine/4u4n_model.pdb
Summary of feedback from opening
/Users/Haaris/Desktop/Figures_Ksg_Edeine/4u4n_model.pdb
---
warnings | Cannot find LINK/SSBOND residue ZN (500 )
Cannot find LINK/SSBOND residue ZN (500 )
Cannot find LINK/SSBOND residue ZN (500 )
Cannot find LINK/SSBOND residue ZN (500 )
Cannot find LINK/SSBOND residue ZN (101 )
33 messages similar to the above omitted
Chain information for 4u4n_model.pdb #4
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
C0 | No description available
C1 | No description available
C2 | No description available
C3 | No description available
C4 | No description available
C5 | No description available
C6 | No description available
C7 | No description available
C8 | No description available
C9 | No description available
D0 | No description available
D1 | No description available
D2 | No description available
D3 | No description available
D4 | No description available
D5 | No description available
D6 | No description available
D7 | No description available
D8 | No description available
D9 | No description available
E0 | No description available
E1 | No description available
L2 | No description available
L3 | No description available
L4 | No description available
L5 | No description available
L6 | No description available
L7 | No description available
L8 | No description available
L9 | No description available
M0 | No description available
M1 | No description available
M3 | No description available
M4 | No description available
M5 | No description available
M6 | No description available
M7 | No description available
M8 | No description available
M9 | No description available
N0 | No description available
N1 | No description available
N2 | No description available
N3 | No description available
N4 | No description available
N5 | No description available
N6 | No description available
N7 | No description available
N8 | No description available
N9 | No description available
O0 | No description available
O1 | No description available
O2 | No description available
O3 | No description available
O4 | No description available
O5 | No description available
O6 | No description available
O7 | No description available
O8 | No description available
O9 | No description available
Q0 | No description available
Q1 | No description available
Q2 | No description available
Q3 | No description available
S0 | No description available
S1 | No description available
S2 | No description available
S3 | No description available
S4 | No description available
S5 | No description available
S6 | No description available
S7 | No description available
S8 | No description available
S9 | No description available
SM | No description available
SR | No description available
> select add #4
203998 atoms, 214099 bonds, 3903 pseudobonds, 17698 residues, 3 models
selected
> hide #!3 models
> hide #!1 models
> show sel cartoons
> hide sel atoms
> select subtract #4
Nothing selected
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #4/2 to #1/B pairing ss matrix Nucleic
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 refined_Ede_Round5-coot-1_withW.pdb, chain B (#1) with
4u4n_model.pdb, chain 2 (#4), sequence alignment score = 1453
RMSD between 241 pruned atom pairs is 1.093 angstroms; (across all 1014 pairs:
52.158)
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs
> includeMaps true
> hide #!4 models
> select ::name="EDE"
165 atoms, 165 bonds, 3 residues, 3 models selected
> show sel & #!1 atoms
> select add #3
36334 atoms, 36694 bonds, 5311 pseudobonds, 4018 residues, 6 models selected
> select add #4
240277 atoms, 250738 bonds, 9214 pseudobonds, 21715 residues, 8 models
selected
> select subtract #3
204053 atoms, 214154 bonds, 3903 pseudobonds, 17699 residues, 4 models
selected
> select subtract #4
55 atoms, 55 bonds, 1 residue, 1 model selected
> select add #1
36142 atoms, 37014 bonds, 4 pseudobonds, 4357 residues, 2 models selected
> select subtract #1
Nothing selected
> select #1/B:770
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
22602 atoms, 25313 bonds, 1051 residues, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
36087 atoms, 36959 bonds, 4 pseudobonds, 4356 residues, 2 models selected
> delete sel
> ui mousemode right distance
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 1 residue, 1 model selected
> color sel byhetero
> style sel sphere
Changed 55 atom styles
> style sel stick
Changed 55 atom styles
> ui tool show Clashes
> clashes sel restrict both interModel false intraMol false select true reveal
> true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: False
0 clashes
atom1 atom2 overlap distance
No clashes
> select add #1
55 atoms, 55 bonds, 1 residue, 1 model selected
> ui tool show Clashes
> clashes sel restrict both interModel false intraRes true intraMol false
> select true reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: False
0 clashes
atom1 atom2 overlap distance
No clashes
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2 /Y /Z
2095 atoms, 2340 bonds, 83 pseudobonds, 99 residues, 3 models selected
> select ~sel & ##selected
57375 atoms, 61640 bonds, 1741 pseudobonds, 4641 residues, 4 models selected
> delete sel
> show #!1 models
> hide #!1 models
> show #!1 models
> lighting soft
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> select ::name="EDE"
165 atoms, 165 bonds, 3 residues, 3 models selected
> select subtract #1
110 atoms, 110 bonds, 2 residues, 2 models selected
> select add #4
204053 atoms, 214154 bonds, 3903 pseudobonds, 17699 residues, 4 models
selected
> select subtract #4
55 atoms, 55 bonds, 1 residue, 1 model selected
> show sel atoms
> select ~sel & ##selected
36169 atoms, 36529 bonds, 5311 pseudobonds, 4015 residues, 4 models selected
> delete sel
> show #!4 models
> hide #!3 models
> select ::name="EDE"
165 atoms, 165 bonds, 3 residues, 3 models selected
> select subtract #3
110 atoms, 110 bonds, 2 residues, 2 models selected
> select subtract #1
55 atoms, 55 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
203943 atoms, 214044 bonds, 3903 pseudobonds, 17697 residues, 3 models
selected
> delete sel
> show #!3 models
> show #!2 models
> show #!1 models
> select #2/Y:34
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
439 atoms, 494 bonds, 20 residues, 1 model selected
> color sel saömon
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel salmon
> select add #2
2095 atoms, 2340 bonds, 83 pseudobonds, 99 residues, 3 models selected
> select subtract #2
Nothing selected
> select #2/Z:26
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1646 atoms, 1838 bonds, 77 residues, 1 model selected
> color sel orange
> select add #2
2095 atoms, 2340 bonds, 83 pseudobonds, 99 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #3
55 atoms, 55 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select subtract #3
Nothing selected
> color #3 #e9e84cff
> color #3 #e5e34bff
> color #3 #e0e55fff
> color #3 #e4e500ff
> color #3 #d8d900ff
> color #3 #e8e800ff
> color #3 #e3e848ff
> color #3 #e2e841ff
> color byhetero
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> durch
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_1
> format tiff height 4000 width 5500 supersample 4 transparentBackground true
> select #1/6:2202@C35
1 atom, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 1 residue, 1 model selected
> color sel f14blau
> color sel byhetero
> select subtract #1
Nothing selected
> foto
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_1
> format tiff height 4000 width 5500 supersample 4 transparentBackground false
> show #!3 models
> foto
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_2
> format tiff height 4000 width 5500 supersample 4 transparentBackground false
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> select ::name="EDE"
165 atoms, 165 bonds, 3 residues, 3 models selected
> show sel & #!4 atoms
> 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
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> view name 1
> select subtract #4
110 atoms, 110 bonds, 2 residues, 2 models selected
> select add #4
165 atoms, 165 bonds, 3 residues, 3 models selected
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 1 residue, 1 model selected
> color sel brown
> color #4 #ca544bff
> color #4 #a8463eff
> color sel byhetero
> select subtract #4
Nothing selected
> select add #4
55 atoms, 55 bonds, 1 residue, 1 model selected
> select subtract #4
Nothing selected
> show #!1 models
> hide #!1 models
> show #!1 models
> foto
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_3
> format tiff height 4000 width 5500 supersample 4 transparentBackground false
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs
> includeMaps true
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> hide #!1 models
> open 5lmv
5lmv title:
Structure of bacterial 30S-IF1-IF2-IF3-mRNA-tRNA translation pre-initiation
complex(state-III) [more info...]
Chain information for 5lmv #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 |
Z | tRNAi |
a | Translation initiation factor IF-2 | IF2_THET8 1-571
Non-standard residues in 5lmv #5
---
FME — N-formylmethionine
MG — magnesium ion
ZN — zinc ion
> select add #5
59470 atoms, 63980 bonds, 1824 pseudobonds, 4740 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> hide #!2 models
> select subtract #5
Nothing selected
> select #5/Y:36
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
439 atoms, 494 bonds, 20 residues, 1 model selected
> select add #5/Z:11
461 atoms, 518 bonds, 21 residues, 1 model selected
> select up
2085 atoms, 2332 bonds, 97 residues, 1 model selected
> delete sel
> close #5
> open 5lmv
5lmv title:
Structure of bacterial 30S-IF1-IF2-IF3-mRNA-tRNA translation pre-initiation
complex(state-III) [more info...]
Chain information for 5lmv #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 |
Z | tRNAi |
a | Translation initiation factor IF-2 | IF2_THET8 1-571
Non-standard residues in 5lmv #5
---
FME — N-formylmethionine
MG — magnesium ion
ZN — zinc ion
> select add #5
59470 atoms, 63980 bonds, 1824 pseudobonds, 4740 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> select subtract #5
Nothing selected
> ui tool show Matchmaker
> matchmaker #5/Y to #2/Y pairing ss matrix Nucleic
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 5lmv, chain Y (#2) with 5lmv, chain Y (#5), sequence alignment
score = 141.6
RMSD between 20 pruned atom pairs is 0.000 angstroms; (across all 20 pairs:
0.000)
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> color #5 silver
> select #5/a:562
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
40 atoms, 40 bonds, 5 residues, 1 model selected
> select up
692 atoms, 701 bonds, 88 residues, 1 model selected
> select up
724 atoms, 732 bonds, 93 residues, 1 model selected
> select up
2356 atoms, 2384 bonds, 316 residues, 1 model selected
> select up
2384 atoms, 2412 bonds, 319 residues, 1 model selected
> delete sel
> select #5/X:104
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
163 atoms, 166 bonds, 19 residues, 1 model selected
> select up
719 atoms, 729 bonds, 88 residues, 1 model selected
> select up
1336 atoms, 1354 bonds, 164 residues, 1 model selected
> delete sel
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> show #!5 models
> select #5 /Y /Z
2095 atoms, 2340 bonds, 83 pseudobonds, 99 residues, 3 models selected
> delete sel
> select add #5
53655 atoms, 57873 bonds, 1716 pseudobonds, 4158 residues, 4 models selected
> select subtract #5
Nothing selected
> show #!2 models
> view list
Named views: 1
> view 1
> view list
Named views: 1
> view 1
> ui tool show "Side View"
> view list
Named views: 1
> view 1
> 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 #!2 models
> show #!2 models
> show #!1 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 #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> lighting soft
> foto
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_1_back
> format tiff height 4000 width 5500 supersample 4 transparentBackground false
> show #!2 models
> hide #!5 models
> show #!1 models
> lighting soft
> durch
Command cancelled by user
> durch
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_1
> format tiff height 4000 width 5500 supersample 4 transparentBackground true
> show #!3 models
> durch
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_2
> format tiff height 4000 width 5500 supersample 4 transparentBackground true
> hide #!3 models
> show #!4 models
> durch
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_3
> format tiff height 4000 width 5500 supersample 4 transparentBackground true
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> durch
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_1
> format tiff height 4000 width 5500 supersample 4 transparentBackground true
> view name 2
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs
> includeMaps true
> show #!3 models
> durch
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_2
> format tiff height 4000 width 5500 supersample 4 transparentBackground true
> hide #!3 models
> show #!4 models
> durch
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_3
> format tiff height 4000 width 5500 supersample 4 transparentBackground true
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs
> includeMaps true
——— End of log from Mon Apr 29 15:45:41 2024 ———
opened ChimeraX session
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!3 to #1
No matrix compatible with both reference structure and all match structures
> align #3 toAtoms #1
RMSD between 55 atom pairs is 5.926 angstroms
Drag select of 7 atoms, 7 bonds
> align #3:sel toAtoms #1:sel
No atoms paired for alignment
> align sel
Missing required "to_atoms" argument
> ui tool show Matchmaker
No reference and/or match structure/chain chosen
> matchmaker #!3 & sel to #1 & sel
No matrix compatible with both reference structure and all match structures
> matchmaker #!3 & sel to #1 & sel
No matrix compatible with both reference structure and all match structures
> select add #1
62 atoms, 62 bonds, 2 residues, 2 models selected
> select add #3
110 atoms, 110 bonds, 2 residues, 2 models selected
> select subtract #3
55 atoms, 55 bonds, 1 residue, 1 model selected
> select add #3
110 atoms, 110 bonds, 2 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.93896,0.24644,-0.24005,1.5335,-0.23785,0.96915,0.064567,46.238,0.24855,-0.0035302,0.96861,-46.865,#3,-0.12274,-0.79378,0.5957,217.67,-0.36837,-0.52092,-0.77003,328.04,0.92154,-0.31395,-0.22846,168.04
> select subtract #1
55 atoms, 55 bonds, 1 residue, 1 model selected
> view matrix models
> #3,0.61519,0.047618,0.78694,87.36,0.78051,-0.17753,-0.59941,245.77,0.11116,0.98296,-0.14638,34.031
> view matrix models
> #3,0.61519,0.047618,0.78694,86.055,0.78051,-0.17753,-0.59941,245.62,0.11116,0.98296,-0.14638,32.991
> view matrix models
> #3,0.45792,-0.22054,0.8612,108.56,0.88878,0.092631,-0.44887,194.88,0.019219,0.97097,0.23843,-13.508
> view matrix models
> #3,0.45792,-0.22054,0.8612,104.74,0.88878,0.092631,-0.44887,191.45,0.019219,0.97097,0.23843,-11.289
> view matrix models
> #3,-0.24583,-0.63934,0.72857,181.24,0.9182,-0.39446,-0.036338,190.13,0.31062,0.66004,0.68401,-41.156
> view matrix models
> #3,-0.24583,-0.63934,0.72857,185.03,0.9182,-0.39446,-0.036338,189.54,0.31062,0.66004,0.68401,-38.528
> view matrix models
> #3,0.093225,-0.5029,0.8593,146.6,0.91024,-0.30667,-0.27823,211.45,0.40344,0.80811,0.42917,-23.487
> view matrix models
> #3,0.093225,-0.5029,0.8593,146.31,0.91024,-0.30667,-0.27823,208.81,0.40344,0.80811,0.42917,-25.131
> view matrix models
> #3,0.095368,0.1061,-0.98977,319.2,-0.87419,-0.46665,-0.13425,243.57,-0.47613,0.87805,0.048245,34.27
> view matrix models
> #3,0.095368,0.1061,-0.98977,320.17,-0.87419,-0.46665,-0.13425,251.42,-0.47613,0.87805,0.048245,38.376
> view matrix models
> #3,0.29208,-0.015669,-0.95627,325,-0.81297,-0.53072,-0.23961,270.68,-0.50375,0.8474,-0.16775,70.109
> view matrix models
> #3,0.29208,-0.015669,-0.95627,320.82,-0.81297,-0.53072,-0.23961,269.41,-0.50375,0.8474,-0.16775,68.83
> view matrix models
> #3,0.29208,-0.015669,-0.95627,321.08,-0.81297,-0.53072,-0.23961,270.62,-0.50375,0.8474,-0.16775,69.133
> view matrix models
> #3,0.29208,-0.015669,-0.95627,320.38,-0.81297,-0.53072,-0.23961,270.56,-0.50375,0.8474,-0.16775,69.12
> view matrix models
> #3,0.19915,-0.0092373,-0.97993,324.62,-0.83064,-0.53218,-0.16379,261.29,-0.51998,0.84658,-0.11366,62.557
> view matrix models
> #3,0.19915,-0.0092373,-0.97993,325.17,-0.83064,-0.53218,-0.16379,261.27,-0.51998,0.84658,-0.11366,62.657
> view matrix models
> #3,-0.14466,-0.085148,-0.98581,341.06,-0.86504,-0.47281,0.16778,212.78,-0.48039,0.87704,-0.0052584,44.586
> view matrix models
> #3,-0.14466,-0.085148,-0.98581,341.56,-0.86504,-0.47281,0.16778,214.25,-0.48039,0.87704,-0.0052584,45.314
> view matrix models
> #3,0.14651,-0.12901,-0.98076,339.75,-0.83908,-0.54132,-0.054134,249.74,-0.52392,0.83086,-0.18756,74.695
> view matrix models
> #3,0.14651,-0.12901,-0.98076,339.31,-0.83908,-0.54132,-0.054134,248.85,-0.52392,0.83086,-0.18756,73.792
> view matrix models
> #3,0.017885,-0.15035,-0.98847,345.21,-0.83519,-0.54575,0.067899,233.5,-0.54967,0.82435,-0.13533,68.276
> view matrix models
> #3,0.017885,-0.15035,-0.98847,345.32,-0.83519,-0.54575,0.067899,233.95,-0.54967,0.82435,-0.13533,68.574
> view matrix models
> #3,0.056714,-0.14911,-0.98719,344.23,-0.80839,-0.58713,0.04224,241.18,-0.58591,0.79564,-0.15383,74.79
> view matrix models
> #3,0.056714,-0.14911,-0.98719,344.29,-0.80839,-0.58713,0.04224,241.09,-0.58591,0.79564,-0.15383,75.003
> view matrix models
> #3,0.056714,-0.14911,-0.98719,344.25,-0.80839,-0.58713,0.04224,240.72,-0.58591,0.79564,-0.15383,74.866
> view matrix models
> #3,0.056714,-0.14911,-0.98719,351.37,-0.80839,-0.58713,0.04224,238.87,-0.58591,0.79564,-0.15383,78.146
> view matrix models
> #3,0.056714,-0.14911,-0.98719,344.4,-0.80839,-0.58713,0.04224,240.67,-0.58591,0.79564,-0.15383,74.717
> view matrix models
> #3,0.056714,-0.14911,-0.98719,344.95,-0.80839,-0.58713,0.04224,240.87,-0.58591,0.79564,-0.15383,75.034
> view matrix models
> #3,0.056714,-0.14911,-0.98719,344.34,-0.80839,-0.58713,0.04224,240.63,-0.58591,0.79564,-0.15383,74.857
> view matrix models
> #3,0.056714,-0.14911,-0.98719,344.17,-0.80839,-0.58713,0.04224,240.72,-0.58591,0.79564,-0.15383,74.923
> view matrix models
> #3,0.056714,-0.14911,-0.98719,344.2,-0.80839,-0.58713,0.04224,240.75,-0.58591,0.79564,-0.15383,74.943
> select subtract #3
Nothing selected
> select add #3
55 atoms, 55 bonds, 1 residue, 1 model selected
> color sel #FAFF95
> select subtract #3
Nothing selected
> select add #3
55 atoms, 55 bonds, 1 residue, 1 model selected
> select subtract #3
Nothing selected
> select add #3
55 atoms, 55 bonds, 1 residue, 1 model selected
> color sel byhetero
> select subtract #3
Nothing selected
> lighting soft
> foto
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparsion_Sup_Edeine-
> My_Ada format tiff height 4000 width 5500 supersample 4
> transparentBackground false
> close #3
> close
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/My_edeine_in_Thermus_ribosome.cxs
opened ChimeraX session
> close #2
> close #1
> select ::name="EDE"
55 atoms, 55 bonds, 1 residue, 1 model selected
> show sel atoms
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/postprocess_masked_Edeine_onlybody.mrc
Opened postprocess_masked_Edeine_onlybody.mrc as #1, grid size 400,400,400,
pixel 0.832, shown at level 0.00533, step 2, values float32
> volume #1 step 1
> volume #1 level 0.0132
> fitmap #3 inMap #1
Fit molecule combination (#3) to map postprocess_masked_Edeine_onlybody.mrc
(#1) using 36224 atoms
average map value = 0.01075, steps = 84
shifted from previous position = 0.107
rotated from previous position = 0.185 degrees
atoms outside contour = 24435, contour level = 0.013202
Position of combination (#3) relative to
postprocess_masked_Edeine_onlybody.mrc (#1) coordinates:
Matrix rotation and translation
0.99999736 -0.00227813 0.00029255 0.43643518
0.00227747 0.99999485 0.00226047 -0.79087533
-0.00029769 -0.00225979 0.99999740 0.50138987
Axis -0.70138787 0.09158511 0.70687143
Axis point 346.70631245 183.74693902 0.00000000
Rotation angle (degrees) 0.18462838
Shift along axis -0.02412457
> select add #3
36224 atoms, 36584 bonds, 5311 pseudobonds, 4016 residues, 4 models selected
> select subtract #3
Nothing selected
> hide #!1 models
> color #2 f02silber
> select #1
2 models selected
> farben 1
Nothing selected
> hide #1
> wasser 1/6:2202 1
No atoms or surfaces specified
> close #3
> close
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/My_edeine_in_Thermus_ribosome.pdb
Summary of feedback from opening
/Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/My_edeine_in_Thermus_ribosome.pdb
---
warnings | Cannot find LINK/SSBOND residue IAS (119 )
Cannot find LINK/SSBOND residue IAS (119 )
Chain information for My_edeine_in_Thermus_ribosome.pdb #1
---
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
U | No description available
> show cartoons
> show atoms
> select add #1
36224 atoms, 36584 bonds, 3909 pseudobonds, 4016 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> select subtract #1
Nothing selected
> lighting soft
> select ::name="EDE"
55 atoms, 55 bonds, 1 residue, 1 model selected
> show sel atoms
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/postprocess_masked_Edeine_onlybody.mrc
Opened postprocess_masked_Edeine_onlybody.mrc as #2, grid size 400,400,400,
pixel 0.832, shown at level 0.00533, step 2, values float32
> volume #2 step 1
> volume #2 level 0.01283
> surface dust #2 size 8.32
> fitmap #1 inMap #2
Fit molecule My_edeine_in_Thermus_ribosome.pdb (#1) to map
postprocess_masked_Edeine_onlybody.mrc (#2) using 36224 atoms
average map value = 0.01075, steps = 84
shifted from previous position = 0.105
rotated from previous position = 0.185 degrees
atoms outside contour = 24230, contour level = 0.012827
Position of My_edeine_in_Thermus_ribosome.pdb (#1) relative to
postprocess_masked_Edeine_onlybody.mrc (#2) coordinates:
Matrix rotation and translation
0.99999733 -0.00229160 0.00028743 0.43546268
0.00229094 0.99999483 0.00225797 -0.79294388
-0.00029260 -0.00225730 0.99999741 0.50353530
Axis -0.69902318 0.08979590 0.70943871
Axis point 345.81629974 184.01838732 0.00000000
Rotation angle (degrees) 0.18504831
Shift along axis -0.01837418
> color #2 f02silber
> select #1
36224 atoms, 36584 bonds, 3909 pseudobonds, 4016 residues, 3 models selected
> farben 1
32534 atoms, 36417 bonds, 1514 residues, 1 model selected
2410 atoms, 2390 pseudobonds, 2410 residues, 2 models selected
Nothing selected
75 atoms, 75 residues, 1 model selected
Nothing selected
> hide #1
> wasser 1/6:2202 1
Selected 184 atoms
Nothing selected
55 atoms, 55 bonds, 1 residue, 1 model selected
Selected 184 atoms
> show sel
> style sel stick
Changed 184 atom styles
> select #1:MG
75 atoms, 75 residues, 1 model selected
> style sel ball
Changed 75 atom styles
> select #1:MG
75 atoms, 75 residues, 1 model selected
> size sel ballScale 0.5
Changed 1 ball scales
> hide #!2 models
> da 1
184 atoms, 194 bonds, 7 residues, 1 model selected
> name frozen netzwerk sel
> select ~ sel
36040 atoms, 36380 bonds, 3909 pseudobonds, 4009 residues, 5 models selected
> select intersect #1
36040 atoms, 36380 bonds, 3909 pseudobonds, 4009 residues, 3 models selected
> color sel f02silber
> upsplit 2 2 1
> spalt 2
Opened postprocess_masked_Edeine_onlybody.mrc 0 as #3.1, grid size
400,400,400, pixel 0.832, shown at level 0.0128, step 1, values float32
Opened postprocess_masked_Edeine_onlybody.mrc 1 as #3.2, grid size
400,400,400, pixel 0.832, shown at level 0.0128, step 1, values float32
Opened postprocess_masked_Edeine_onlybody.mrc 2 as #3.3, grid size
400,400,400, pixel 0.832, shown at level 0.0128, step 1, values float32
Opened postprocess_masked_Edeine_onlybody.mrc 3 as #3.4, grid size
400,400,400, pixel 0.832, shown at level 0.0128, step 1, values float32
> nicemap 3
> volume step 1
> select netzwerk
184 atoms, 194 bonds, 7 residues, 1 model selected
> color sel byhetero
> hide #!3.1 models
> hide #!3.2 models
> hide #!3.3 models
> hide #!3.4 models
> select ~sel & ##selected
36040 atoms, 36390 bonds, 3909 pseudobonds, 4009 residues, 3 models selected
> delete sel
> close #1.1
> close #1.2
> select add #1
184 atoms, 194 bonds, 7 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select subtract #1
Nothing selected
> select add #1
184 atoms, 194 bonds, 7 residues, 1 model selected
> close #3
> color #1 silver
> select subtract #1
Nothing selected
> select /6:2202@N24
1 atom, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 1 residue, 1 model selected
> color sel f14blau
> color sel byhetero
> select add #1
184 atoms, 194 bonds, 7 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
184 atoms, 194 bonds, 7 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #3afaf9 restrict both interModel false intraMol false
> intraRes false log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 My_edeine_in_Thermus_ribosome.pdb
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/6 EDE 2202 N46 /A G 1482 OP2 no hydrogen 2.994 N/A
/6 EDE 2202 N50 /A U 1483 OP2 no hydrogen 3.213 N/A
/6 EDE 2202 O51 /A U 771 O2 no hydrogen 3.551 N/A
/A G 676 N1 /A C 778 N3 no hydrogen 3.298 N/A
/A G 676 N1 /A C 778 O2 no hydrogen 3.314 N/A
/A G 676 N2 /A C 778 O2 no hydrogen 3.059 N/A
/A C 778 N4 /A G 676 O6 no hydrogen 3.436 N/A
/A G 903 N2 /6 EDE 2202 O44 no hydrogen 3.159 N/A
8 hydrogen bonds found
> select add #1.1
184 atoms, 194 bonds, 8 pseudobonds, 7 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1.1
8 pseudobonds, 1 model selected
> color sel orange
> select add #1
184 atoms, 194 bonds, 8 pseudobonds, 7 residues, 2 models selected
> select subtract #1
Nothing selected
> view namw 1
Expected an objects specifier or a view name or a keyword
> view name 1
> hide sel pbonds
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/My_edeine_in_Thermus_ribosome.cxs
> includeMaps true
> view name 1
> view list+
Expected an objects specifier or a view name or a keyword
> view list
Named views: 1
> view 1
> select /A:903@N2
1 atom, 1 residue, 1 model selected
> select add /A:1482@OP2
2 atoms, 2 residues, 1 model selected
> select add /A:1483@OP2
3 atoms, 3 residues, 1 model selected
> select add /A:676@O6
4 atoms, 4 residues, 1 model selected
> select add /A:771@O2
5 atoms, 5 residues, 1 model selected
> select add /A:778@N4
6 atoms, 6 residues, 1 model selected
> color sel byhetero
> select add #1
184 atoms, 194 bonds, 8 pseudobonds, 7 residues, 2 models selected
> select subtract #1
Nothing selected
> foto
Command cancelled by user
> foto
> save /Users/Haaris/Desktop/Figures_Ksg_Edeine/Ksg_Main_Figures/My_Edeine_On-
> Thermus_aligned_16s format tiff height 4000 width 5500 supersample 4
> transparentBackground false
> close
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/refined_Ede_Round5-coot-1_withW.pdb
Chain information for refined_Ede_Round5-coot-1_withW.pdb #1
---
Chain | Description
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | 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
> show cartoons
> hide atoms
> color #1 silver
> open 5lmn
5lmn title:
Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex
(state-1A) [more info...]
Chain information for 5lmn #2
---
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 #2
---
MG — magnesium ion
ZN — zinc ion
> hide #!1 models
> select add #2
54149 atoms, 58290 bonds, 1844 pseudobonds, 4286 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> show #!1 models
> select add #1
90291 atoms, 95304 bonds, 1848 pseudobonds, 8643 residues, 6 models selected
> select subtract #1
54149 atoms, 58290 bonds, 1844 pseudobonds, 4286 residues, 4 models selected
> select add #1
90291 atoms, 95304 bonds, 1848 pseudobonds, 8643 residues, 6 models selected
> select subtract #1
54149 atoms, 58290 bonds, 1844 pseudobonds, 4286 residues, 4 models selected
> hide #!1 models
> select subtract #2
Nothing selected
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> ui tool show Matchmaker
> matchmaker #2/A to #1/B pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match 5lmn #2/A to
refined_Ede_Round5-coot-1_withW.pdb #1/B
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 refined_Ede_Round5-coot-1_withW.pdb, chain B (#1) with 5lmn, chain
A (#2), sequence alignment score = 2553.7
RMSD between 432 pruned atom pairs is 1.387 angstroms; (across all 1023 pairs:
39.110)
> show #!1 models
> hide #!2 models
> select ::name="EDE"
55 atoms, 55 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!1 models
> show #!1 models
> select add #1
36142 atoms, 37014 bonds, 4 pseudobonds, 4357 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!2 models
> select #1 /B:790
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> select #2 /A:790
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/My_edeine_in_Thermus_ribosome_5lmn.cxs
> includeMaps true
> select add #2
54149 atoms, 58290 bonds, 1844 pseudobonds, 4286 residues, 4 models selected
> select subtract #2
Nothing selected
> close
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/My_edeine_in_Thermus_ribosome.cxs
> format session
Opened postprocess_masked_Edeine_onlybody.mrc as #2, grid size 400,400,400,
pixel 0.832, shown at level 0.0128, step 1, values float32
opened ChimeraX session
> close
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/refined_Ede_Round5-coot-1_withW.pdb
Chain information for refined_Ede_Round5-coot-1_withW.pdb #1
---
Chain | Description
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | 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
> show cartoons
> hide atoms
> lighting soft
> oopen 1i95
Unknown command: oopen 1i95
> oopen i195
Unknown command: oopen i195
> oopen 1i95
Unknown command: oopen 1i95
> oopen 1I95
Unknown command: oopen 1I95
> open 1I95
1i95 title:
Crystal structure of the 30S ribosomal subunit from thermus thermophilus In
complex with edeine [more info...]
Chain information for 1i95 #2
---
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 |
Non-standard residues in 1i95 #2
---
EDE — edeine B
MG — magnesium ion
WO2 — octadecatungstenyl diphosphate
ZN — zinc ion
> select add #2
36224 atoms, 36584 bonds, 5311 pseudobonds, 4016 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> select subtract #2
Nothing selected
> ui tool show Matchmaker
> matchmaker #2/A to #1/B pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match 1i95 #2/A to
refined_Ede_Round5-coot-1_withW.pdb #1/B
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 refined_Ede_Round5-coot-1_withW.pdb, chain B (#1) with 1i95, chain
A (#2), sequence alignment score = 2563.6
RMSD between 662 pruned atom pairs is 1.173 angstroms; (across all 1026 pairs:
39.583)
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1 /B:790
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> show #!2 models
> hide #!1 models
> select add #1
36142 atoms, 37014 bonds, 4 pseudobonds, 4357 residues, 2 models selected
> select add #2
72366 atoms, 73598 bonds, 5315 pseudobonds, 8373 residues, 6 models selected
> select subtract #1
36224 atoms, 36584 bonds, 5311 pseudobonds, 4016 residues, 4 models selected
> select #1 /A:790
Nothing selected
> show #!1 models
> select #2 /A:790
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> style sel stick
Changed 22 atom styles
> show sel atoms
> show sel cartoons
> close
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/My_edeine_in_Thermus_ribosome_5lmn.cxs
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
> mousemode shift leftMode "translate selected models"
> mousemode shift middleMode "rotate selected models"
> mousemode rightMode zoom
> mousemode control wheelMode "contour level"
> mousemode setting "contour level" speed 0.1
> mousemode shift wheelMode "rotate selected models"
> camera ortho
> set bgColor grey
> lighting shadows false
> lighting depthCue false
> graphics silhouettes true
> lighting simple
> functionkey F1 cofr sel
> functionkey F2 mousemode rightMode 'mark surface'
> functionkey F3 mousemode rightMode 'move markers'
> functionkey F4 mk 3 1
> functionkey F5 view
> functionkey F6 view sel pad 0.92 clip false
> functionkey F7 mousemode rightMode 'delete markers'
> functionkey F8 mousemode rightMode zoom
> functionkey F9 sequence chain sel
> functionkey F10 transparency sel 65
> functionkey F11 transparency sel 0
> functionkey F12 tool show 'Fit in Map'
> color name f01graublau #BADBED
Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed
> color name f02silber #F6FAFC
Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc
> color name f03muschel #FFFFE5
Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5
> color name f04beige #F3F3A9
Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9
> color name f05gelb #f2b701
Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701
> color name f06orange #e68310
Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310
> color name f07rotorange #FF6A25
Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25
> color name f08rot #dd3d2d
Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d
> color name f09lachs #f97b72
Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72
> color name f10flieder #D57AD5
Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5
> color name f11violett #cf1c90
Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90
> color name f12lila #4b148f
Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f
> color name f13dunkelblau #2E2EF7
Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7
> color name f14blau #00AAFF
Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff
> color name f15cyan #60e2d6
Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6
> color name f16blaugrün #30ffa6
Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6
> color name f17grün #00FF00
Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00
> color name f18dunkelgrün #228B22
Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22
> color name f19hellgrau #DCDCDC
Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc
> color name f20grau #B2B2B2
Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2
> color name f21anthrazit #323F45
Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45
> alias localres color sample #$1 map #$2 offset 0.0 update true palette
> "#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"
> range $3,$4
> alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1
> $2'
> alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4
> 'quickmk $1 $2'
> alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3
> alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep
> $3
> alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep
> $3
> alias consurf color byattr seq_conservation protein palette cyanmaroon
> novalue yellow
> alias chaininfo preset custom chaininfo
> alias foto save browse format tiff height 4000 width 5500 supersample 4
> transparentBackground false
> alias durch save browse format tiff height 4000 width 5500 supersample 4
> transparentBackground true
> alias session save browse format session includeMaps true compress lz4
> alias nomapsession save browse format session includeMaps false compress lz4
> alias splitup color zone #$1 near sel sharpEdges true distance $2
> alias quicksplitup color zone #$1 near sel sharpEdges false distance $2
> alias spalt volume splitbyzone #$1
> alias undust surface undust #$1
> alias dust surface dust #$2 size $1
> alias dust1 surface dust #$1 size 1
> alias dust2 surface dust #$1 size 2
> alias dust3 surface dust #$1 size 3
> alias dust4 surface dust #$1 size 4
> alias dust5 surface dust #$1 size 5
> alias dust6 surface dust #$1 size 6
> alias dust7 surface dust #$1 size 7
> alias dust8 surface dust #$1 size 8
> alias dust9 surface dust #$1 size 9
> alias dust10 surface dust #$1 size 10
> alias dust11 surface dust #$1 size 11
> alias dust12 surface dust #$1 size 12
> alias dust13 surface dust #$1 size 13
> alias dust14 surface dust #$1 size 14
> alias dust15 surface dust #$1 size 15
> alias dust20 surface dust #$1 size 20
> alias dust25 surface dust #$1 size 25
> alias dust30 surface dust #$1 size 30
> alias dust35 surface dust #$1 size 35
> alias dust40 surface dust #$1 size 40
> alias dust45 surface dust #$1 size 45
> alias dust50 surface dust #$1 size 50
> alias sunset color sample #$1 map #$2 offset 0.1 update true palette
> "#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026"
> range $3,$4
> alias nicemap volume #$1 subdivideSurface true surfacesmoothing true
> smoothLines true squareMesh false meshLighting true
> alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false
> smoothLines false squareMesh true meshLighting true
> alias figure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ;
> camera ortho
> alias tryfigure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.01 ; set bgColor white ;
> camera ortho; cartoon style width 2.4 thickness 0.4; lighting
> ambientintensity 1.2 fillIntensity 0.4
> alias abbild sel zone sel 1 #$1 residues true extend true
> alias abbild+ sel zone sel 1 #$1 residues true extend true; show sel; sel
> intersect #$1; style sel stick; sel compound; sel zone sel 7 #$1 residues
> true extend true; sel intersect :HOH:MG:K:ZN:SPD:SPM; show sel; sel
> intersect :MG; style sel ball; size sel ballscale 0.5
> alias network sel zone sel $1 #$2 residues true extend true
> alias network34 sel zone sel 3.4 #$1 residues true extend true
> alias network4 sel zone sel 4 #$1 residues true extend true
> alias network10 sel zone sel 10 #$1 residues true extend true
> alias wasser sel zone #$1 3.4 #$2 residues true extend true; sel intersect
> #$2:HOH; sel add #$1; sel zone sel 3.4 #$2 residues true extend true
> alias 1st-wasser sel zone #$1 3.4 #$2 residues true extend true; sel
> intersect #$2:HOH
> alias farben color sel f14; sel #$1 & nucleic; color sel f20; sel #$1 &
> protein; color sel f07; sel #$1:HOH; color sel red; sel #$1:MG; color sel
> f17; sel #$1:K; color sel f15
> alias magnesiumcluster sel zone sel 2.7 #$1 extend true; sel intersect
> #$1@o*:HOH:MG
> alias magnesiumcluster4 sel zone sel 4 #$1 extend true; sel intersect
> #$1@o*:HOH:MG
> alias upsplit color zone #$1 near #$3 sharpEdges true distance $2
> alias weihwasser sel zone #$1 3.4 #$2 residues true extend true; sel
> intersect #$2:HOH; sel add #$1; sel subtract badwaters; sel zone sel 3.4 #$2
> residues true extend true; sel subtract badwaters
> alias fixall size pseudobondRadius 0.075; sel :MG; style sel ball; size sel
> ballscale 0.5
> alias fix size pseudobondRadius 0.075; da $1; sel intersect :MG; style sel
> ball; color sel f17; size sel ballscale 0.5; da $1; sel intersect
> ##name="K"; color sel blueviolet
> alias pixel zoom pixelsize 0.04
> alias da sel #$1 @@display
> alias neu hide #$1; da $2; sel intersect ligand; mm #$1 to #$2 matrix
> Nucleic; network10 $1,$2; mm #!$1 & sel to #$2 & sel matrix Nucleic; da $2;
> abbild+ $1
> alias neu2 da $1; sel intersect ligand; farben $1; da $1; color sel byhet;
> hbonds sel color f05 restrict both interModel false intraMol false intraRes
> false; sel intersect :HOH; style sel stick; combine #$1; da $1; sel
> intersect :HOH; name frozen temp sel; hide sel; da $1; sel intersect
> ##name="hydrogen bonds"; del pbonds sel; sel temp; show sel; da $2; sel
> intersect :HOH; hide sel; da $2; sel intersect nucleic; sel intersect
> ##name="hydrogen bonds"; hide sel; da $2; sel intersect protein; sel
> intersect ##name="hydrogen bonds"; hide sel; da $1; sel intersect
> ##name="hydrogen bonds"; color sel f15
> alias kalium da $1; sel intersect :K; style sel ball; size sel ballscale
> 0.3; name frozen temp sel; sel zone sel 3.5 #$1 extend true; sel intersect
> @o*,n*:K; contacts sel restrict temp overlapCutoff -3.0 color #8A2BE2 name K
> log true
> alias magnesium da $1; sel intersect :MG; style sel ball; size sel ballscale
> 0.5; name frozen temp sel; magnesiumcluster $1; contacts sel restrict temp
> overlapCutoff -0.8 color #00FF00 name Mg log true
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.5.17
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: 2020.80.5.0.0
OS Loader Version: 580~1678
SMC Version (system): 2.46f13
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 33 days, 48 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: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
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: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 2.10.5
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: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
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: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
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: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
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-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
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: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
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.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
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: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 19 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 , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Haaris,
--Eric