![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17089 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x000000020954c840 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, lxml._elementpath, lxml.etree, chimerax.surface._surface, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast, chimerax.mlp._mlp (total: 61)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 1298,
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"build" : "24D70",
"releaseType" : "User"
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"captureTime" : "2025-03-13 11:07:31.8171 -0500",
"codeSigningMonitor" : 1,
"incident" : "69343086-CCD4-4610-BBE2-1E2B74C8EC06",
"pid" : 78433,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-12 22:17:53.1384 -0500",
"procStartAbsTime" : 7880780866538,
"procExitAbsTime" : 8128691747725,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3C03AB57-DF91-6538-731F-87145E7E925C",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "740CAC07-7A35-4E6E-9C78-D586F3D0754E",
"wakeTime" : 5426,
"sleepWakeUUID" : "697FDE6D-1F24-405B-95E5-1AE0A368F3C2",
"sip" : "enabled",
"vmRegionInfo" : "0x168 is not in any region. Bytes before following region: 4333092504\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10245c000-102460000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000168","rawCodes":[1,360],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000168"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":78433},
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/kompa012/Desktop/P53/Y220C mutation.cxs"
opened ChimeraX session
> select #23-26 /A :151,153,155,223,220,147
170 atoms, 159 bonds, 24 residues, 4 models selected
> ui tool show Contacts
> contacts sel restrict both ignoreHiddenModels true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
12 contacts
atom1 atom2 overlap distance
1uol #25/A TYR 220 CD2 1uol #25/A PRO 151 CG 0.038 3.602
1uol #25/A TYR 220 CE2 1uol #25/A PRO 151 CG 0.035 3.605
1uol #25/A PRO 151 CD 1uol #25/A TYR 220 CE2 0.026 3.614
1uol #25/A THR 155 OG1 1uol #25/A PRO 151 CB -0.144 3.484
1uol #25/A TYR 220 CB 1uol #25/A THR 155 O -0.159 3.459
1uol #25/A THR 155 CG2 1uol #25/A PRO 151 CB -0.190 3.950
1uol #25/A TYR 220 OH 1uol #25/A VAL 147 CG2 -0.199 3.539
1uol #25/A PRO 151 CG 1uol #25/A THR 155 CG2 -0.208 3.968
1uol #25/A TYR 220 N 1uol #25/A THR 155 O -0.225 2.885
1uol #25/A PRO 223 CD 1uol #25/A TYR 220 OH -0.294 3.634
1uol #25/A TYR 220 CB 1uol #25/A THR 155 CG2 -0.295 4.055
1uol #25/A THR 155 CB 1uol #25/A PRO 151 CB -0.322 4.082
12 contacts
> ui mousemode right select
> select clear
> select #25/A:151@CD
1 atom, 1 residue, 1 model selected
> select #25/A:220@OH
1 atom, 1 residue, 1 model selected
> select add #25/A:151@CD
2 atoms, 2 residues, 2 models selected
> ui tool show Contacts
> contacts sel restrict both ignoreHiddenModels true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
0 contacts
atom1 atom2 overlap distance
No contacts
> select #23-26 /A :151,153,155,223,220,147
170 atoms, 159 bonds, 12 pseudobonds, 24 residues, 5 models selected
> color (#!25 & sel) byelement
> style sel & #!25 ball
Changed 47 atom styles
> select clear
> hide #!25 atoms
> show #!25 atoms
> hide #!25 atoms
> select up
12 pseudobonds, 1 model selected
> select up
130556 atoms, 124515 bonds, 12 pseudobonds, 24333 residues, 27 models selected
> select #23-26 /A :151,153,155,223,220,147
170 atoms, 159 bonds, 12 pseudobonds, 24 residues, 5 models selected
> show sel & #!25 atoms
> hide sel & #!25 cartoons
> show sel & #!25 cartoons
> hide sel & #!25 cartoons
> ui mousemode right distance
> distance #25/A:153@CD #25/A:220@O
Distance between 1uol #25/A PRO 153 CD and TYR 220 O: 8.203Å
> distance #25/A:153@CA #25/A:220@O
Distance between 1uol #25/A PRO 153 CA and TYR 220 O: 6.286Å
> distance #25/A:153@CB #25/A:220@O
Distance between 1uol #25/A PRO 153 CB and TYR 220 O: 7.164Å
> hide #25.4 models
> select subtract #25.4
170 atoms, 159 bonds, 12 pseudobonds, 24 residues, 9 models selected
> select add #25.4
170 atoms, 159 bonds, 12 pseudobonds, 24 residues, 9 models selected
> show #25.4 models
> distance #25/A:223@CD #25/A:220@OH
Distance between 1uol #25/A PRO 223 CD and TYR 220 OH: 3.634Å
> close #25.4
> open "/Users/kompa012/Desktop/P53/Y220C mutation.cxs"
opened ChimeraX session
> style sel & #!25 ball
Changed 47 atom styles
> color (#!25 & sel) byelement
> distance #25/A:153@CA #25/A:220@CD2
Distance between 1uol #25/A PRO 153 CA and TYR 220 CD2: 6.945Å
> close #27
> hide sel & #!25 cartoons
> distance #25/A:223@CD #25/A:220@OH
Distance between 1uol #25/A PRO 223 CD and TYR 220 OH: 3.634Å
> distance #25/A:147@CG2 #25/A:220@OH
Distance between 1uol #25/A VAL 147 CG2 and TYR 220 OH: 3.539Å
> distance #25/A:151@CD #25/A:220@OH
Distance between 1uol #25/A PRO 151 CD and TYR 220 OH: 4.277Å
> distance #25/A:155@O #25/A:220@N
Distance between 1uol #25/A THR 155 O and TYR 220 N: 2.885Å
> ui mousemode right select
> select #25/A:153@CA
1 atom, 1 residue, 1 model selected
> select #23-26 /A :153
28 atoms, 28 bonds, 4 residues, 4 models selected
> show sel & #!25 cartoons
> hide sel & #!25 atoms
> color (#!25 & sel) dark gray
> select clear
> select #23-26 /A :155
28 atoms, 24 bonds, 4 residues, 4 models selected
> select #23-26 /A :222
28 atoms, 28 bonds, 4 residues, 4 models selected
> show sel & #!25 atoms
> style sel & #!25 ball
Changed 7 atom styles
> color (#!25 & sel) byelement
> hide #27.1 models
> show #27.1 models
> select #23-26 /A :22
Nothing selected
> select #23-26 /A :220
30 atoms, 27 bonds, 4 residues, 4 models selected
> style (#!25 & sel) ringFill thick
Changed 1 residue ring style
> select clear
> select #23-26 /A :220
30 atoms, 27 bonds, 4 residues, 4 models selected
> style (#!25 & sel) ringFill thin
Changed 1 residue ring style
> select clear
> select #23-26 /A :222, 153
56 atoms, 56 bonds, 8 residues, 4 models selected
> select #23-26 /A :222, 151
56 atoms, 56 bonds, 8 residues, 4 models selected
> style (#!25 & sel) ringFill thin
Changed 2 residue ring styles
> color (#!25 & sel) black
> color (#!25 & sel) byelement
> select clear
> select #23-26 /A :156-146
Nothing selected
> select #23-26 /A :146-156
340 atoms, 356 bonds, 44 residues, 4 models selected
> hide sel & #!25 cartoons
> show sel & #!25 atoms
> hide (#!25 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!25 & sel-residues)
> show (#!25 & sel-residues & backbone) target ab
> select #23-26 /A :219-224
179 atoms, 188 bonds, 1 pseudobond, 24 residues, 5 models selected
> select #23-26 /A :219-230
331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected
> hide sel & #!25 cartoons
> show sel & #!25 atoms
> hide (#!25 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!25 & sel-residues)
> show (#!25 & sel-residues & backbone) target ab
> select #23-26 /A :151,155,223,220,147
142 atoms, 131 bonds, 4 pseudobonds, 20 residues, 5 models selected
> select #23-26 /A :151,155,223,220,147,222
170 atoms, 163 bonds, 4 pseudobonds, 24 residues, 5 models selected
> show (#!25 & sel-residues & sidechain) target ab
> select clear
> select #25/A:145
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #25/A:230@C
1 atom, 1 residue, 1 model selected
> select #25/A:230@CA
1 atom, 1 residue, 1 model selected
> select #25/A:230@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #23-26 /A :220
30 atoms, 27 bonds, 4 residues, 4 models selected
> style sel & #!25 sphere
Changed 12 atom styles
> select clear
> select #23-26 /A :220
30 atoms, 27 bonds, 4 residues, 4 models selected
> style sel & #!25 ball
Changed 12 atom styles
> select clear
> hide #27.1 models
> hide #!27 models
> show #!26 models
> hide #!25 models
> show #!25 models
> show #!24 models
> hide #!25 models
> hide #!26 models
> show #!25 models
> hide #!25 models
> show #!23 models
> hide #!23 models
> hide #!24 models
> show #!24 models
> show #!26 models
> hide #!26 models
> show #!25 models
> show #!23 models
> select #23-26 /A :151,155,223,220,147,222
170 atoms, 163 bonds, 4 pseudobonds, 24 residues, 5 models selected
> style sel & #!23-25 ball
Changed 129 atom styles
> show sel & #!23-25 atoms
> color (#!23-25 & sel) byelement
> style (#!23-25 & sel) ringFill thin
Changed 18 residue ring styles
> hide #!25 models
> hide #!24 models
> show #!24 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> show #!25 models
> hide #!23 models
> show #!27 models
> select clear
> ui tool show "Side View"
> save "/Users/kompa012/Desktop/P53/1uol Y220 .png" width 3000 height 2320
> supersample 3 transparentBackground true
> hide #!25 models
> show #!24 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> select #23-26 /A :220,155
58 atoms, 51 bonds, 1 pseudobond, 8 residues, 5 models selected
> hide sel & #!24 cartoons
> ui mousemode right distance
> distance #24/A:220@N #24/A:155@O
Distance between 2j1x #24/A CYS 220 N and THR 155 O: 2.911Å
> select #23-26 /A :219-230
331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected
> hide sel & #!24 cartoons
> hide sel & #!24 atoms
> show sel & #!24 atoms
> hide sel & #!24 cartoons
> hide (#!24 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!24 & sel-residues)
> show (#!24 & sel-residues & backbone) target ab
> select up
707 atoms, 732 bonds, 1 pseudobond, 92 residues, 9 models selected
> select #23-26 /A :146-156
340 atoms, 356 bonds, 44 residues, 4 models selected
> hide (#!24 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!24 & sel-residues)
> show (#!24 & sel-residues & backbone) target ab
> hide sel & #!24 cartoons
> show sel & #!24 atoms
> hide (#!24 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!24 & sel-residues)
> show (#!24 & sel-residues & backbone) target ab
> select #23-26 /A :151,155,223,220,147,222
170 atoms, 163 bonds, 5 pseudobonds, 24 residues, 5 models selected
> show (#!24 & sel-residues & sidechain) target ab
> ui mousemode right select
> select clear
> select #23-26 /A :151,223,222
84 atoms, 88 bonds, 12 residues, 4 models selected
> color (#!24 & sel) black
> color (#!24 & sel) byelement
> select clear
> show #!23 models
> hide #!24 models
> select #23-26 /A :151,223,222
84 atoms, 88 bonds, 12 residues, 4 models selected
> color (#!23 & sel) black
> color (#!23 & sel) byelement
> select #23-26 /A :219-230
331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected
> hide sel & #!23 cartoons
> show sel & #!23 atoms
> hide (#!23 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!23 & sel-residues)
> show (#!23 & sel-residues & backbone) target ab
> select #23-26 /A :146-156
340 atoms, 356 bonds, 44 residues, 4 models selected
> hide sel & #!23 cartoons
> show sel & #!23 atoms
> hide (#!23 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!23 & sel-residues)
> show (#!23 & sel-residues & backbone) target ab
> select #23-26 /A :151,155,223,220,147,222
170 atoms, 163 bonds, 5 pseudobonds, 24 residues, 5 models selected
> show (#!23 & sel-residues & sidechain) target ab
> show #!24 models
> select clear
> save "/Users/kompa012/Desktop/P53/6shz_2j1x C220.png" width 3000 height 2320
> supersample 3 transparentBackground true
> hide #!24 models
> hide #!23 models
> show #!26 models
> show #!25 models
> hide #!25 models
> select add #26
3531 atoms, 3159 bonds, 8 pseudobonds, 842 residues, 2 models selected
> select solvent
19518 atoms, 19518 residues, 51 models selected
> hide sel & #!26 atoms
> select clear
> show #!24 models
> hide #!24 models
> hide #!26 models
> show #!26 models
> select #23-26 /A :219-230
331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected
> hide sel & #!26 cartoons
> show sel & #!26 cartoons
> style sel & #!26 ball
Changed 79 atom styles
> hide (#!26 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!26 & sel-residues)
> show (#!26 & sel-residues & backbone) target ab
> select #23-26 /A :146-156
340 atoms, 356 bonds, 44 residues, 4 models selected
> hide sel & #!26 cartoons
> show sel & #!26 atoms
> style sel & #!26 ball
Changed 85 atom styles
> hide (#!26 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!26 & sel-residues)
> show (#!26 & sel-residues & backbone) target ab
> select #23-26 /A :151,155,223,220,147,222
170 atoms, 163 bonds, 5 pseudobonds, 24 residues, 5 models selected
> color (#!26 & sel) black
> style (#!26 & sel) ringFill thin
Changed 6 residue ring styles
> show (#!26 & sel-residues & sidechain) target ab
> color (#!26 & sel) byelement
> select add #26.3
1690 atoms, 163 bonds, 5 pseudobonds, 223 residues, 9 models selected
> select subtract #26.2
1649 atoms, 124 bonds, 5 pseudobonds, 217 residues, 10 models selected
> select add #26.1
1649 atoms, 124 bonds, 13 pseudobonds, 217 residues, 10 models selected
> select add #26
3660 atoms, 3283 bonds, 13 pseudobonds, 860 residues, 10 models selected
> show sel & #!26 surfaces
> hide sel & #!26 surfaces
> select ligand
274 atoms, 218 bonds, 60 residues, 16 models selected
> style sel & #!26 ball
Changed 48 atom styles
> color (#!26 & sel) byelement
> style sel & #!26 stick
Changed 48 atom styles
> ui mousemode right distance
> distance #26/A:220@N #26/A:155@O
Distance between 8a32 #26/A CYS 220 N and THR 155 O: 2.934Å
> style (#!26 & sel) ringFill thin
Changed 4 residue ring styles
> color (#!26 & sel) black
> color (#!26 & sel) byelement
> distance #26/A:401@O #26/A:151@CD
Distance between 8a32 #26/A KVA 401 O and PRO 151 CD: 6.205Å
> distance #26/A:401@O1 #26/A:147@CG2
Distance between 8a32 #26/A KVA 401 O1 and VAL 147 CG2: 5.072Å
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> distance #26/A:401@O2 #26/A:147@CG2
Distance between 8a32 #26/A KVA 401 O2 and VAL 147 CG2: 3.735Å
> show #27.1 models
> hide #27.1 models
> ui mousemode right select
> hide #!26 atoms
> undo
> hide #!27 models
> show #!27 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> ui mousemode right "delete markers"
> ui mousemode right distance
> ~distance #26/A:401@O #26/A:151@CD
> ~distance #26/A:401@O1 #26/A:147@CG2
> save "/Users/kompa012/Desktop/P53/8a32 C220 woth cjc769.png" width 3000
> height 2320 supersample 3 transparentBackground true
> save "/Users/kompa012/Desktop/P53/Y220C mutation details.cxs"
> hide #!26 models
> show #!25 models
> show #!26 models
> show #!24 models
> show #!23 models
> hide #!23 models
> hide #!24 models
> hide #!25 models
> hide #!26 models
> show #!25 models
> hide #!27 models
> transparency #25 70
> select add #25
3465 atoms, 3144 bonds, 12 pseudobonds, 783 residues, 3 models selected
> show sel surfaces
> select add #25.3
3465 atoms, 3144 bonds, 12 pseudobonds, 783 residues, 6 models selected
> select subtract #25.3
1929 atoms, 1572 bonds, 8 pseudobonds, 588 residues, 5 models selected
> select subtract #25.2
393 atoms, 393 residues, 2 models selected
> select add #25.3
1929 atoms, 588 residues, 2 models selected
> hide sel surfaces
> select add #25
3465 atoms, 3144 bonds, 12 pseudobonds, 783 residues, 5 models selected
> select subtract #25.3
1929 atoms, 1572 bonds, 8 pseudobonds, 588 residues, 5 models selected
> hide #!25.3 models
> transparency (#!25 & sel) 90
> ui mousemode right select
> select clear
> select add #25.2
1536 atoms, 195 residues, 1 model selected
> mlp sel
Map values for surface "1uol_A SES surface": minimum -28.72, mean -5.719,
maximum 23.04
To also show corresponding color key, enter the above mlp command and add key
true
> transparency (#!25 & sel) 80
> ui mousemode right "color key"
> transparency (#!25 & sel) 0
> hide sel surfaces
> key pos 0.855729,0.814485 size 0,0
> ui mousemode right select
> select clear
> ui mousemode right select
> select clear
> ui tool show "Side View"
> select add #25.2
1536 atoms, 195 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide #!25 models
> show #!24 models
> select add #24
4995 atoms, 3133 bonds, 9 pseudobonds, 981 residues, 5 models selected
> select subtract #24.3
3462 atoms, 1565 bonds, 5 pseudobonds, 786 residues, 7 models selected
> mlp sel & #!24
Map values for surface "2j1x_A SES surface": minimum -27.43, mean -5.658,
maximum 22.9
To also show corresponding color key, enter the above mlp command and add key
true
> show #!25 models
> hide #!25 models
> show #!26 models
> hide #!24 models
> select add #26
6993 atoms, 4724 bonds, 15 pseudobonds, 1628 residues, 8 models selected
> select subtract #26.3
5473 atoms, 3169 bonds, 11 pseudobonds, 1429 residues, 10 models selected
> mlp sel & #!26
Map values for surface "8a32_A SES surface": minimum -30.19, mean -5.652,
maximum 22.73
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> hide #!26 models
> show #!25 models
> save "/Users/kompa012/Desktop/P53/1uol Y220 surface.png" width 3000 height
> 2320 supersample 3 transparentBackground true
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!24 models
> show #!23 models
> hide #!23 models
> save "/Users/kompa012/Desktop/P53/2j1x Y220 surface.png" width 3000 height
> 2320 supersample 3 transparentBackground true
> show #!26 models
> hide #!24 models
> save "/Users/kompa012/Desktop/P53/8a32 C220 woth cjc769 surface.png" width
> 3000 height 2320 supersample 3 transparentBackground true
> hide #!26 models
> hide #28 models
> show #!25 models
> transparency #25.1-2#!25 90
> save "/Users/kompa012/Desktop/P53/Transparrent surface 1uol.png" width 3000
> height 2320 supersample 3 transparentBackground true
> ui mousemode right "color key"
> key lipophilicity :min : :max
> show #!26 models
> show #!24 models
> show #!23 models
> hide #!26 models
> hide #!23 models
> key lipophilicity :min : :max
> help help:user/tools/colorkey.html
> ui mousemode right select
> select add #24
3459 atoms, 3133 bonds, 9 pseudobonds, 786 residues, 3 models selected
> select subtract #24
2 models selected
> select add #25
3465 atoms, 3144 bonds, 12 pseudobonds, 783 residues, 3 models selected
> ui mousemode right "color key"
> key lipophilicity :min : :max
> ui mousemode right select
> show #28 models
> select clear
> ui mousemode right "move label"
> ui mousemode right "color key"
> key labelSide left/top
> select add #28
1 model selected
> ui mousemode right "move label"
> ui mousemode right "color key"
> key pos 0.70206,0.0744216
> ui mousemode right "move label"
> select subtract #28
Nothing selected
> ui mousemode right "move label"
> ui mousemode right clip
> ui mousemode right "move label"
> ui mousemode right "color key"
> key pos 0.474902,0.105324 size 0.267526,0.0631905
> hide #!25 models
> show #!26 models
> hide #!24 models
> key pos 0.339284,0.0601194 size 0.39171,0.0330387
> ui mousemode right "move label"
> save "/Users/kompa012/Desktop/P53/8a32 C220 woth cjc769 surface.png" width
> 3000 height 2282 supersample 3 transparentBackground true
> show #!25 models
> hide #!26 models
> show #!24 models
> hide #!25 models
> save "/Users/kompa012/Desktop/P53/2j1x Y220 surface.png" width 3000 height
> 2282 supersample 3 transparentBackground true
> show #!25 models
> hide #!24 models
> transparency #28#25.1-2#!25 0
> save "/Users/kompa012/Desktop/P53/1uol Y220 surface.png" width 3000 height
> 2282 supersample 3 transparentBackground true
> hide #28 models
> transparency #25.1-2#!25 80
> select add #25
3465 atoms, 3144 bonds, 12 pseudobonds, 783 residues, 3 models selected
> ui mousemode right select
> select clear
> transparency #25.1-2#!25 90
> save "/Users/kompa012/Desktop/P53/Transparrent surface 1uol.png" width 3000
> height 2282 supersample 3 transparentBackground true
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/kompa012/Desktop/P53/Y220C mutation details.cxs"
Log from Thu Mar 13 10:36:24 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/kompa012/Desktop/P53/Y220C mutation.cxs"
Log from Wed Mar 12 17:13:32 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/kompa012/Desktop/P53/Y220C mutation.cxs"
Log from Wed Mar 12 16:42:08 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/kompa012/Desktop/New Folder/Experiment6.mrc" format mrc
Opened Experiment6.mrc as #1, grid size 336,336,336, pixel 0.66, shown at
level 1.18, step 2, values float32
> close
> toolshed show
> ui tool show Rotamers
Populating font family aliases took 164 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> open 1TUP fromDatabase pdb format mmcif
Summary of feedback from opening 1TUP fetched from pdb
---
note | Fetching compressed mmCIF 1tup from http://files.rcsb.org/download/1tup.cif
1tup title:
Tumor suppressor P53 complexed with DNA [more info...]
Chain information for 1tup #1
---
Chain | Description | UniProt
A B C | PROTEIN (P53 TUMOR SUPPRESSOR ) | P53_HUMAN 94-312
E | DNA (5'-D(*TP*TP*TP*CP*CP*TP*AP*GP*AP*CP*TP*TP*GP*CP*CP*CP*A P*AP*TP*TP*A)-3') |
F | DNA (5'-D(*AP*TP*AP*AP*TP*TP*GP*GP*GP*CP*AP*AP*GP*TP*CP*TP*A P*GP*GP*AP*A)-3') |
Non-standard residues in 1tup #1
---
ZN — zinc ion
> open 1TSR fromDatabase pdb format mmcif
Summary of feedback from opening 1TSR fetched from pdb
---
note | Fetching compressed mmCIF 1tsr from http://files.rcsb.org/download/1tsr.cif
1tsr title:
P53 core domain In complex with DNA [more info...]
Chain information for 1tsr #2
---
Chain | Description | UniProt
A B C | PROTEIN (P53 TUMOR SUPPRESSOR) | P53_HUMAN 94-312
E | DNA (5'-D(*TP*TP*TP*CP*CP*TP*AP*GP*AP*CP*TP*TP*GP*CP*CP*CP*A P*AP*TP*TP*A)-3') |
F | DNA (5'-D(*AP*TP*AP*AP*TP*TP*GP*GP*GP*CP*AP*AP*GP*TP*CP*TP*A P*GP*GP*AP*A)-3') |
Non-standard residues in 1tsr #2
---
ZN — zinc ion
> select add #1
5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected
> select add #2
11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected
> hide sel atoms
> show sel cartoons
> select subtract #2
5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #2
5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected
> select add #1
11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected
> select subtract #2
5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #2
11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected
> select subtract #2
5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected
> select add #2
11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected
> select subtract #1
5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected
> select add #1
11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected
> select subtract #1
5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected
> select add #1
11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected
> select subtract #1
5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected
> select add #1
11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected
> select subtract #1
5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected
> select add #1
11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected
> select subtract #1
5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected
> select add #1
11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected
> select subtract #1
5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected
> close #2
> select add #1
5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected
> select subtract #1
Nothing selected
> open 2ac0 fromDatabase pdb format mmcif
Summary of feedback from opening 2ac0 fetched from pdb
---
note | Fetching compressed mmCIF 2ac0 from http://files.rcsb.org/download/2ac0.cif
2ac0 title:
Structural Basis of DNA Recognition by p53 Tetramers (complex I) [more
info...]
Chain information for 2ac0 #2
---
Chain | Description | UniProt
A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293
E F G H | 5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3' |
Non-standard residues in 2ac0 #2
---
ZN — zinc ion
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1 models
> open 2ady fromDatabase pdb format mmcif
Summary of feedback from opening 2ady fetched from pdb
---
note | Fetching compressed mmCIF 2ady from http://files.rcsb.org/download/2ady.cif
2ady title:
Structural Basis of DNA Recognition by p53 Tetramers (complex IV) [more
info...]
Chain information for 2ady #3
---
Chain | Description | UniProt
A B | Cellular tumor antigen p53 | P53_HUMAN 94-293
E F | 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3' |
Non-standard residues in 2ady #3
---
ZN — zinc ion
2ady mmCIF Assemblies
---
1| author_defined_assembly
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2ahi fromDatabase pdb format mmcif
Summary of feedback from opening 2ahi fetched from pdb
---
note | Fetching compressed mmCIF 2ahi from http://files.rcsb.org/download/2ahi.cif
2ahi title:
Structural Basis of DNA Recognition by p53 Tetramers (complex III) [more
info...]
Chain information for 2ahi #4
---
Chain | Description | UniProt
A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293
E F G H | 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3' |
Non-standard residues in 2ahi #4
---
ZN — zinc ion
23 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2ata fromDatabase pdb format mmcif
Summary of feedback from opening 2ata fetched from pdb
---
note | Fetching compressed mmCIF 2ata from http://files.rcsb.org/download/2ata.cif
2ata title:
Structural Basis of DNA Recognition by p53 Tetramers (complex II) [more
info...]
Chain information for 2ata #5
---
Chain | Description | UniProt
A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293
E F G H | 5'-D(*AP*AP*GP*GP*CP*AP*TP*GP*CP*CP*TP*T)-3' |
Non-standard residues in 2ata #5
---
ZN — zinc ion
9 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #2
8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #2
8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected
> select add #4
16245 atoms, 14689 bonds, 152 pseudobonds, 3729 residues, 6 models selected
> select add #3
20034 atoms, 18391 bonds, 189 pseudobonds, 4364 residues, 9 models selected
> select add #5
27815 atoms, 25698 bonds, 259 pseudobonds, 5919 residues, 12 models selected
> hide sel atoms
> show sel cartoons
> hide #!2 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> show #!4 models
> show #!2 models
> ui tool show Matchmaker
> matchmaker #!3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2ac0, chain D (#2) with 2ady, chain A (#3), sequence alignment
score = 1041
RMSD between 194 pruned atom pairs is 0.457 angstroms; (across all 196 pairs:
0.530)
> hide #!5 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> show #!4 models
> show #!5 models
> style sel sphere
Changed 27815 atom styles
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 27815 atom styles
> hide #!4 models
> hide #!5 models
> hide #!2 models
> nucleotides sel & #!3 atoms
> style nucleic & sel & #!3 stick
Changed 486 atom styles
> show #!4 models
> show #!2 models
> show #!5 models
> show sel surfaces
> hide sel surfaces
> select subtract #2
19605 atoms, 18290 bonds, 181 pseudobonds, 4023 residues, 37 models selected
> select subtract #3
15816 atoms, 14588 bonds, 144 pseudobonds, 3388 residues, 26 models selected
> select subtract #4
7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 19 models selected
> select subtract #5
8 models selected
> show #!1 models
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2ac0, chain A (#2) with 1tup, chain A (#1), sequence alignment
score = 1024.8
RMSD between 191 pruned atom pairs is 0.546 angstroms; (across all 196 pairs:
1.132)
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #1
5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 5828 atom styles
> hide sel cartoons
> select subtract #1
Nothing selected
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> 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 #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> select add #1
5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.33546,-0.80914,-0.48246,77.205,0.20225,-0.43834,0.87576,-68.732,-0.92009,-0.39136,0.016605,93.096
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.33546,-0.80914,-0.48246,75.538,0.20225,-0.43834,0.87576,-81.654,-0.92009,-0.39136,0.016605,70.995
> select subtract #1
Nothing selected
> select add #2
8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected
> select add #1
14038 atoms, 13057 bonds, 133 pseudobonds, 2910 residues, 14 models selected
> show sel cartoons
> hide sel atoms
> select subtract #2
5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 11 models selected
> view matrix models
> #1,0.33546,-0.80914,-0.48246,83.959,0.20225,-0.43834,0.87576,-27.201,-0.92009,-0.39136,0.016605,56.212
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.47854,-0.70175,0.52777,0.92818,-0.3715,0.3828,0.84584,-5.1579,-0.7956,-0.60084,-0.077517,59.209
> view matrix models
> #1,0.66211,-0.70583,0.25184,10.847,0.14066,-0.21303,-0.96687,106.96,0.73609,0.67559,-0.04177,-47.372
> view matrix models
> #1,-0.22202,0.86187,0.45595,22.171,0.41802,-0.33833,0.84308,-38.3,0.88089,0.37778,-0.28516,-33.349
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.22202,0.86187,0.45595,17.518,0.41802,-0.33833,0.84308,-75.138,0.88089,0.37778,-0.28516,-18.673
> view matrix models
> #1,-0.22202,0.86187,0.45595,-30.27,0.41802,-0.33833,0.84308,-66.789,0.88089,0.37778,-0.28516,-17.681
> view matrix models
> #1,-0.22202,0.86187,0.45595,-32.908,0.41802,-0.33833,0.84308,-66.426,0.88089,0.37778,-0.28516,-19.539
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.58924,-0.80159,-0.10128,-13.083,0.17546,0.24931,-0.9524,69.057,0.78868,0.54342,0.28755,-58.505
> view matrix models
> #1,0.080048,-0.6908,0.7186,-46.019,-0.56887,0.56032,0.60202,-7.1708,-0.81852,-0.45698,-0.34813,91.867
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.080048,-0.6908,0.7186,-15.014,-0.56887,0.56032,0.60202,-25.742,-0.81852,-0.45698,-0.34813,109
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2ac0, chain A (#2) with 1tup, chain A (#1), sequence alignment
score = 1024.8
RMSD between 191 pruned atom pairs is 0.546 angstroms; (across all 196 pairs:
1.132)
> matchmaker #1/E to #2/E pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match 1tup #1/E to 2ac0 #2/E
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 2ac0, chain E (#2) with 1tup, chain E (#1), sequence alignment
score = 23.5
RMSD between 8 pruned atom pairs is 1.096 angstroms; (across all 12 pairs:
3.330)
> matchmaker #1/F to #2/F pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match 1tup #1/F to 2ac0 #2/F
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 2ac0, chain F (#2) with 1tup, chain F (#1), sequence alignment
score = 23.5
RMSD between 9 pruned atom pairs is 1.079 angstroms; (across all 12 pairs:
2.836)
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!1 models
> matchmaker #1/E to #2/E pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match 1tup #1/E to 2ac0 #2/E
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 2ac0, chain E (#2) with 1tup, chain E (#1), sequence alignment
score = 23.5
RMSD between 8 pruned atom pairs is 1.096 angstroms; (across all 12 pairs:
3.330)
> show #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> matchmaker #1/B to #2/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2ac0, chain B (#2) with 1tup, chain B (#1), sequence alignment
score = 1007.4
RMSD between 191 pruned atom pairs is 0.597 angstroms; (across all 194 pairs:
0.710)
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> show #!4 models
> hide #!4 models
> select add #3
9617 atoms, 9351 bonds, 92 pseudobonds, 1649 residues, 6 models selected
> select subtract #1
3789 atoms, 3702 bonds, 37 pseudobonds, 635 residues, 7 models selected
> close #3
> show #!4 models
> show #!5 models
> hide #!1 models
> hide #!5 models
> hide #!4 models
> open 5lgy fromDatabase pdb format mmcif
Summary of feedback from opening 5lgy fetched from pdb
---
note | Fetching compressed mmCIF 5lgy from http://files.rcsb.org/download/5lgy.cif
5lgy title:
Lysine 120-acetylated P53 DNA binding domain in a complex with the BAX
response element. [more info...]
Chain information for 5lgy #3
---
Chain | Description | UniProt
A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-291
E | DNA (5'-D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP*GP*CP*CP*T)-3') |
F | DNA (5'-D(*AP*GP*GP*CP*TP*TP*GP*TP*CP*TP*CP*TP*AP*AP*CP*TP*TP*GP*TP*GP*A)-3') |
Non-standard residues in 5lgy #3
---
ALY — N(6)-acetyllysine
ZN — zinc ion
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 5bua fromDatabase pdb format mmcif
Summary of feedback from opening 5bua fetched from pdb
---
note | Fetching compressed mmCIF 5bua from http://files.rcsb.org/download/5bua.cif
5bua title:
Lysine 120-acetylated P53 DNA binding domain in a complex with DNA. [more
info...]
Chain information for 5bua #6
---
Chain | Description | UniProt
A | Cellular tumor antigen p53 | P53_HUMAN 94-293
B | DNA (5'-D(P*GP*GP*AP*CP*AP*TP*GP*TP*CP*C)-3') |
Non-standard residues in 5bua #6
---
ALY — N(6)-acetyllysine
ZN — zinc ion
5bua mmCIF Assemblies
---
1| author_and_software_defined_assembly
58 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!6 models
> show #!3 models
> show #!6 models
> matchmaker #6/A to #2/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2ac0, chain B (#2) with 5bua, chain A (#6), sequence alignment
score = 1001.4
RMSD between 187 pruned atom pairs is 0.507 angstroms; (across all 198 pairs:
1.246)
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!3 models
> hide #!2 models
> select add #3
7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 3 models selected
> hide sel atoms
> style sel stick
Changed 7093 atom styles
> show sel atoms
> show sel cartoons
> hide sel atoms
> show #!2 models
> matchmaker #3/C to #2/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2ac0, chain B (#2) with 5lgy, chain C (#3), sequence alignment
score = 1018.3
RMSD between 196 pruned atom pairs is 0.474 angstroms; (across all 197 pairs:
0.534)
> matchmaker #3/D to #2/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2ac0, chain B (#2) with 5lgy, chain D (#3), sequence alignment
score = 1015.3
RMSD between 194 pruned atom pairs is 0.536 angstroms; (across all 197 pairs:
0.673)
> open 4mzr fromDatabase pdb format mmcif
Summary of feedback from opening 4mzr fetched from pdb
---
note | Fetching compressed mmCIF 4mzr from http://files.rcsb.org/download/4mzr.cif
4mzr title:
Crystal structure of a polypeptide p53 mutant bound to DNA [more info...]
Chain information for 4mzr #7
---
Chain | Description | UniProt
A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-358
K | consensus DNA sense strand |
L | consensus DNA anti-sense strand |
Non-standard residues in 4mzr #7
---
ZN — zinc ion
> matchmaker #7/A to #2/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2ac0, chain B (#2) with 4mzr, chain A (#7), sequence alignment
score = 948.8
RMSD between 186 pruned atom pairs is 0.543 angstroms; (across all 198 pairs:
2.117)
> select add #7
15686 atoms, 16125 bonds, 130 pseudobonds, 1916 residues, 6 models selected
> select subtract #3
8593 atoms, 8812 bonds, 73 pseudobonds, 1061 residues, 3 models selected
> style sel stick
Changed 8593 atom styles
> show sel cartoons
> hide sel atoms
[deleted to fit within ticket limits]
> select subtract #12
48227 atoms, 46476 bonds, 364 pseudobonds, 8577 residues, 70 models selected
> select subtract #13
40640 atoms, 39178 bonds, 300 pseudobonds, 7212 residues, 61 models selected
> select subtract #11
32665 atoms, 31792 bonds, 237 pseudobonds, 5534 residues, 52 models selected
> select subtract #14
30572 atoms, 29978 bonds, 232 pseudobonds, 4987 residues, 43 models selected
> select subtract #15
28463 atoms, 28151 bonds, 227 pseudobonds, 4436 residues, 38 models selected
> select subtract #16
24766 atoms, 24652 bonds, 217 pseudobonds, 3711 residues, 33 models selected
> select subtract #17
16089 atoms, 15852 bonds, 140 pseudobonds, 2558 residues, 27 models selected
> select subtract #18
7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 18 models selected
> select subtract #19
8 models selected
> select add #1.7
435 atoms, 21 residues, 1 model selected
> select add #1.6
855 atoms, 42 residues, 2 models selected
> show sel cartoons
> hide #!19 models
> hide #!18 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> hide #!11 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> color (#!1 & sel) blue
> select subtract #1.6
435 atoms, 21 residues, 3 models selected
> select subtract #1.7
1 model selected
> select add #1.4
1522 atoms, 194 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select #1-19 /A :282
209 atoms, 190 bonds, 19 residues, 19 models selected
> show sel & #!1 atoms
> select subtract #1.3
198 atoms, 180 bonds, 18 residues, 35 models selected
> select add #1.3
1733 atoms, 180 bonds, 214 residues, 35 models selected
> hide sel & #!1 atoms
> select clear
> show #!2 models
> select add #2
8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected
> hide sel atoms
> select subtract #2
8 models selected
> select add #2.10
243 atoms, 12 residues, 1 model selected
> select subtract #2.10
1 model selected
> select add #2.10
243 atoms, 12 residues, 1 model selected
> select add #2.9
486 atoms, 24 residues, 2 models selected
> select subtract #2.10
243 atoms, 12 residues, 3 models selected
> select subtract #2.9
1 model selected
> select add #2.8
243 atoms, 12 residues, 1 model selected
> select add #2.7
486 atoms, 24 residues, 2 models selected
> show sel cartoons
> select subtract #2.7
243 atoms, 12 residues, 3 models selected
> select subtract #2.8
1 model selected
> select add #2.3
1552 atoms, 199 residues, 1 model selected
> show sel cartoons
> select add #2.8
1795 atoms, 211 residues, 2 models selected
> select add #2.7
2038 atoms, 223 residues, 3 models selected
> select subtract #2.3
486 atoms, 24 residues, 4 models selected
> color (#!2 & sel) blue
> select add #2
8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 5 models selected
> select subtract #2
8 models selected
> show #!3 models
> select add #3.8
427 atoms, 21 residues, 1 model selected
> select add #3.7
855 atoms, 42 residues, 2 models selected
> show sel cartoons
> color (#!3 & sel) blue
> select subtract #3.7
427 atoms, 21 residues, 3 models selected
> select subtract #3.8
1 model selected
> select add #3.3
1552 atoms, 197 residues, 1 model selected
> show sel cartoons
> hide sel atoms
Cell requested for row 8 is out of bounds for table with 27 rows! Resizing
table model.
> select add #3
7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 4 models selected
> select subtract #3
6 models selected
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> show #!4 models
> select add #4.10
243 atoms, 12 residues, 1 model selected
> select subtract #4.10
1 model selected
> select add #4.8
224 atoms, 11 residues, 1 model selected
> select add #4.7
426 atoms, 21 residues, 2 models selected
> select add #4.3
1977 atoms, 220 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> show sel atoms
> select subtract #4.7
1775 atoms, 210 residues, 4 models selected
> select subtract #4.8
1551 atoms, 199 residues, 3 models selected
> hide sel atoms
> select subtract #4.3
1 model selected
> select add #4.8
224 atoms, 11 residues, 1 model selected
> select add #4.7
426 atoms, 21 residues, 2 models selected
> color (#!4 & sel) blue
> show #!5 models
> select add #4
8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 5 models selected
> select subtract #4
8 models selected
> select add #5.8
222 atoms, 11 residues, 1 model selected
> select add #5.7
425 atoms, 21 residues, 2 models selected
> show sel cartoons
> color (#!5 & sel) blue
> select subtract #5.8
203 atoms, 10 residues, 3 models selected
> select subtract #5.7
1 model selected
> select add #5.3
1546 atoms, 197 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select add #5
7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 4 models selected
> select subtract #5
8 models selected
> show #!6 models
> select add #6
1932 atoms, 1835 bonds, 4 pseudobonds, 366 residues, 2 models selected
> select subtract #6
2 models selected
> select add #6.3
205 atoms, 10 residues, 1 model selected
> show sel cartoons
> color (#!6 & sel) blue
> select subtract #6.3
1 model selected
> select add #6.2
1571 atoms, 200 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select add #6
1932 atoms, 1835 bonds, 4 pseudobonds, 366 residues, 3 models selected
> select subtract #6
2 models selected
> hide #!6 models
> select add #5
7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 3 models selected
> select subtract #5
8 models selected
> select add #5.3
1546 atoms, 197 residues, 1 model selected
> show sel cartoons
> select add #5
7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 4 models selected
> select subtract #5
8 models selected
> show #!6 models
> show #!7 models
> select add #7.8
535 atoms, 26 residues, 1 model selected
> select add #7.7
1060 atoms, 52 residues, 2 models selected
> show sel cartoons
> color (#!7 & sel) blue
> select subtract #7.7
535 atoms, 26 residues, 3 models selected
> select subtract #7.8
1 model selected
> select add #7.3
1865 atoms, 234 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select subtract #7.3
1 model selected
> show #!8 models
> select add #8.8
227 atoms, 11 residues, 1 model selected
> select add #8.7
448 atoms, 22 residues, 2 models selected
> show sel cartoons
> color (#!8 & sel) blue
> select subtract #8.7
227 atoms, 11 residues, 3 models selected
> select subtract #8.8
1 model selected
> select add #8.3
1545 atoms, 197 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
> select subtract #8.3
1 model selected
> show #!9 models
> select add #9.2
1 pseudobond, 1 model selected
> select subtract #9.2
Nothing selected
> select add #9
1949 atoms, 1837 bonds, 5 pseudobonds, 380 residues, 3 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #9
2 models selected
> select add #9.4
221 atoms, 11 residues, 1 model selected
> nucleotides sel tube/slab shape box
> show sel cartoons
> color (#!9 & sel) blue
> select subtract #9.4
1 model selected
> select add #9.3
1535 atoms, 197 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select add #9
1949 atoms, 1837 bonds, 5 pseudobonds, 380 residues, 4 models selected
> select subtract #9
2 models selected
> show #!10 models
> select add #10
2172 atoms, 1880 bonds, 5 pseudobonds, 562 residues, 3 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #10.4
1947 atoms, 1629 bonds, 5 pseudobonds, 550 residues, 5 models selected
> select subtract #10.3
404 atoms, 51 bonds, 353 residues, 2 models selected
> select add #10.3
1947 atoms, 51 bonds, 550 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select add #10.4
2172 atoms, 51 bonds, 562 residues, 2 models selected
> select subtract #10.3
629 atoms, 51 bonds, 365 residues, 3 models selected
> show sel cartoons
> color (#!10 & sel) blue
> select add #10
2172 atoms, 1880 bonds, 5 pseudobonds, 562 residues, 4 models selected
> select subtract #10
2 models selected
> show #!11 models
> hide #!10 models
> hide #!11 models
> show #!10 models
> show #!11 models
> select add #11.3
1571 atoms, 200 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select add #11.7
1999 atoms, 221 residues, 2 models selected
> select add #11.8
2426 atoms, 242 residues, 3 models selected
> select subtract #11.3
855 atoms, 42 residues, 4 models selected
> show sel cartoons
> color (#!11 & sel) blue
> select add #11
7975 atoms, 7386 bonds, 63 pseudobonds, 1678 residues, 5 models selected
> select subtract #11
6 models selected
> show #!12 models
> select add #12.8
526 atoms, 26 residues, 1 model selected
> select add #12.7
1060 atoms, 52 residues, 2 models selected
> show sel cartoons
> color (#!12 & sel) blue
> select subtract #12.7
526 atoms, 26 residues, 3 models selected
> select subtract #12.8
1 model selected
> select add #12.4
1863 atoms, 234 residues, 1 model selected
> select subtract #12.4
1 model selected
> select add #12.3
1863 atoms, 234 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> show #!13 models
> select add #12
8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 4 models selected
> select subtract #12
6 models selected
> select add #13.3
1571 atoms, 200 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select subtract #13.3
1 model selected
> select add #13.8
388 atoms, 19 residues, 1 model selected
> select add #13.7
776 atoms, 38 residues, 2 models selected
> show sel cartoons
> color (#!13 & sel) blue
> select add #13
7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 5 models selected
> select subtract #13
6 models selected
> show #!14 models
> select add #14.4
225 atoms, 12 residues, 1 model selected
> show sel cartoons
> color (#!14 & sel) blue
> select add #14.3
1755 atoms, 209 residues, 2 models selected
> select subtract #14.4
1530 atoms, 197 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> select add #14
2093 atoms, 1814 bonds, 5 pseudobonds, 547 residues, 4 models selected
> select subtract #14
2 models selected
> show #!15 models
> select add #15.4
225 atoms, 12 residues, 1 model selected
> show sel cartoons
> color (#!15 & sel) blue
> select add #15.3
1764 atoms, 209 residues, 2 models selected
> select subtract #15.4
1539 atoms, 197 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select add #15
2109 atoms, 1827 bonds, 5 pseudobonds, 551 residues, 4 models selected
> select subtract #15
2 models selected
> show #!16 models
> select add #16.5
410 atoms, 20 residues, 1 model selected
> color (#!16 & sel) blue
> show sel cartoons
> select add #16.4
1896 atoms, 215 residues, 2 models selected
> select subtract #16.5
1486 atoms, 195 residues, 3 models selected
> select add #16.5
1896 atoms, 215 residues, 2 models selected
> select subtract #16.5
1486 atoms, 195 residues, 3 models selected
> select add #16.3
2972 atoms, 390 residues, 2 models selected
> select subtract #16.4
1486 atoms, 195 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> select add #16.4
2972 atoms, 390 residues, 2 models selected
> select subtract #16.4
1486 atoms, 195 residues, 3 models selected
> select subtract #16.3
1 model selected
> show #!17 models
> select add #17.8
533 atoms, 26 residues, 1 model selected
> select add #17.7
1060 atoms, 52 residues, 2 models selected
> show sel cartoons
> color (#!17 & sel) blue
> select subtract #17.7
533 atoms, 26 residues, 3 models selected
> select subtract #17.8
1 model selected
> select add #17.3
1863 atoms, 234 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select add #17
8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 4 models selected
> select subtract #17
6 models selected
> show #!18 models
> select add #18.8
533 atoms, 26 residues, 1 model selected
> select add #18.7
1060 atoms, 52 residues, 2 models selected
> color (#!18 & sel) blue
> show sel cartoons
> select subtract #18.7
533 atoms, 26 residues, 3 models selected
> select subtract #18.8
1 model selected
> select add #18.3
1848 atoms, 231 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select add #18
8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 4 models selected
> select subtract #18
6 models selected
> show #!19 models
> select add #19.11
227 atoms, 12 residues, 1 model selected
> select subtract #19.11
1 model selected
> select add #19.9
216 atoms, 11 residues, 1 model selected
> select add #19.8
429 atoms, 23 residues, 2 models selected
> show sel cartoons
> color (#!19 & sel) blue
> select subtract #19.8
216 atoms, 11 residues, 3 models selected
> select subtract #19.9
1 model selected
> select add #19.4
1514 atoms, 196 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select add #19
7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 5 models selected
> select subtract #19
8 models selected
> select #1-19 /A :282
209 atoms, 190 bonds, 19 residues, 19 models selected
> show sel atoms
> select #1-19 /A :248
207 atoms, 188 bonds, 19 residues, 19 models selected
> show sel atoms
> select #1-19 /A :220
228 atoms, 228 bonds, 19 residues, 19 models selected
> show sel atoms
Drag select of 23 atoms
> hide sel atoms
Drag select of 11 atoms, 10 bonds
> hide sel atoms
> select #!1/B:220
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #!1/B:220
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #!1/B:248
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #!1/B:248
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #!1/B:282
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #!1/B:282
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
Drag select of 123 residues, 341 shapes, 1 atoms
> hide sel cartoons
> hide sel atoms
> select clear
> save "/Users/kompa012/Desktop/P53/Superposition of P53.png" width 3000
> height 2520 supersample 3 transparentBackground true
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> save /Users/kompa012/Desktop/P53/1tup.png width 3000 height 2520 supersample
> 3 transparentBackground true
> show #!2 models
> hide #!1 models
> select add #2.8
243 atoms, 12 residues, 1 model selected
> select add #2.7
486 atoms, 24 residues, 2 models selected
> show sel atoms
> select subtract #2.7
243 atoms, 12 residues, 3 models selected
> select subtract #2.8
1 model selected
Drag select of 7 residues, 7 shapes
> select subtract #2.8
81 atoms, 6 residues, 4 models selected
> select subtract #2.7
21 atoms, 3 residues, 3 models selected
> select add #2.9
264 atoms, 15 residues, 2 models selected
> select add #2.10
507 atoms, 27 residues, 3 models selected
> show sel cartoons
> hide sel cartoons
> save /Users/kompa012/Desktop/P53/2ac0.png width 3000 height 2520 supersample
> 3 transparentBackground true
Cell requested for row 11 is out of bounds for table with 29 rows! Resizing
table model.
> show #!4 models
> hide #!2 models
> show #!2 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> show #!5 models
> select add #2
8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 6 models selected
> select subtract #2
8 models selected
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!4 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 #!2 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> show #!5 models
> show #!2 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> hide #!2 models
> save /Users/kompa012/Desktop/P53/2ahi.png width 3000 height 2520 supersample
> 3 transparentBackground true
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!6 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!6 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!16 models
> show #!15 models
> show #!14 models
> hide #!15 models
> hide #!16 models
> show #!19 models
> hide #!14 models
> save /Users/kompa012/Desktop/P53/3d0a.png width 3000 height 2520 supersample
> 3 transparentBackground true
> hide #!19 models
> show #!18 models
> show #!17 models
> hide #!17 models
> hide #!18 models
> show #!18 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> hide #!17 models
> show #!17 models
> show #!18 models
> hide #!17 models
> save /Users/kompa012/Desktop/P53/3q06.png width 3000 height 2520 supersample
> 3 transparentBackground true
> show #!17 models
> hide #!18 models
> save /Users/kompa012/Desktop/P53/3q05.png width 3000 height 2520 supersample
> 3 transparentBackground true
> hide #!17 models
> show #!16 models
> select add #16.5
410 atoms, 20 residues, 1 model selected
> select subtract #16.5
1 model selected
> select add #16.4
1486 atoms, 195 residues, 1 model selected
> select subtract #16.4
1 model selected
> select add #16.3
1486 atoms, 195 residues, 1 model selected
> select subtract #16.3
1 model selected
> show #!15 models
> hide #!15 models
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> open /Users/kompa012/Desktop/P53/3kz8.pdb1
3kz8.pdb1 title:
Diversity In DNA recognition by P53 revealed by crystal structures with
hoogsteen base pairs (P53-DNA complex 3) [more info...]
87 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for 3kz8.pdb1
---
Chain | Description
20.1/A 20.1/B | No description available
20.2/A 20.2/B | No description available
20.1/C | No description available
20.2/C | No description available
87 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #20.1/A to #12/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3ts8, chain A (#12) with 3kz8.pdb1, chain A (#20.1), sequence
alignment score = 948.3
RMSD between 180 pruned atom pairs is 0.603 angstroms; (across all 195 pairs:
2.497)
> matchmaker #20.2/A to #12/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3ts8, chain B (#12) with 3kz8.pdb1, chain A (#20.2), sequence
alignment score = 882.9
RMSD between 180 pruned atom pairs is 0.876 angstroms; (across all 195 pairs:
1.248)
> matchmaker #20.2/B to #12/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3ts8, chain B (#12) with 3kz8.pdb1, chain B (#20.2), sequence
alignment score = 891.9
RMSD between 180 pruned atom pairs is 0.881 angstroms; (across all 195 pairs:
1.263)
> show #!12 models
> matchmaker #20.1/C to #12/K pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match 3kz8.pdb1 #20.1/C to 3ts8
#12/K
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 3ts8, chain K (#12) with 3kz8.pdb1, chain C (#20.1), sequence
alignment score = 33.8
RMSD between 16 pruned atom pairs is 1.144 angstroms; (across all 20 pairs:
1.781)
> matchmaker #20.2/C to #12/K pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match 3kz8.pdb1 #20.2/C to 3ts8
#12/K
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 3ts8, chain K (#12) with 3kz8.pdb1, chain C (#20.2), sequence
alignment score = 35.9
RMSD between 16 pruned atom pairs is 1.144 angstroms; (across all 20 pairs:
1.781)
> matchmaker #20.1/C to #12/L pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match 3kz8.pdb1 #20.1/C to 3ts8
#12/L
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 3ts8, chain L (#12) with 3kz8.pdb1, chain C (#20.1), sequence
alignment score = 38.7
RMSD between 17 pruned atom pairs is 1.147 angstroms; (across all 20 pairs:
1.783)
> hide #!12 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!12 models
> hide #!16 models
> hide #!20.1 models
> show #!20.1 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!12 models
> ui tool show "Crystal Contacts"
> show #!16 models
> hide #!20 models
> crystalcontacts #20.1 distance 8
11 pairs of asymmetric units of 3kz8.pdb1 contact at distance 8.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
961 0 1 0 0 1 0 1
437 0 3 0 0 1 0 1
298 0 3 0 -1 1 0 1
222 0 0 0 0 -1 0 1
172 0 0 0 0 1 0 1
59 0 0 0 1 0 0 1
56 0 0 0 -1 0 0 1
35 0 1 0 0 2 0 1
34 0 1 0 0 0 0 1
9 0 3 0 -1 0 0 1
7 0 3 0 0 0 0 1
> select add #21
40667 atoms, 38489 bonds, 110 pseudobonds, 7975 residues, 34 models selected
> show sel atoms
> show sel cartoons
> show sel surfaces
> crystalcontacts #20.1 distance 4
9 pairs of asymmetric units of 3kz8.pdb1 contact at distance 4.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
321 0 1 0 0 1 0 1
67 0 3 0 0 1 0 1
66 0 3 0 -1 1 0 1
43 0 0 0 0 -1 0 1
41 0 0 0 0 1 0 1
18 0 0 0 1 0 0 1
11 0 0 0 -1 0 0 1
3 0 1 0 0 2 0 1
3 0 1 0 0 0 0 1
> select clear
> select add #20
7394 atoms, 6998 bonds, 12 pseudobonds, 1450 residues, 6 models selected
> show #!20 models
> close #20
> select add #21.9
3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 3 models selected
> select add #21.8
7394 atoms, 6998 bonds, 20 pseudobonds, 1450 residues, 6 models selected
> select add #21.7
11091 atoms, 10497 bonds, 30 pseudobonds, 2175 residues, 9 models selected
> select add #21.6
14788 atoms, 13996 bonds, 40 pseudobonds, 2900 residues, 12 models selected
> select add #21.5
18485 atoms, 17495 bonds, 50 pseudobonds, 3625 residues, 15 models selected
> select add #21.4
22182 atoms, 20994 bonds, 60 pseudobonds, 4350 residues, 18 models selected
> select add #21.3
25879 atoms, 24493 bonds, 70 pseudobonds, 5075 residues, 21 models selected
> hide sel atoms
> hide sel cartoons
> select add #21.2
29576 atoms, 27992 bonds, 80 pseudobonds, 5800 residues, 24 models selected
> hide sel atoms
> hide sel cartoons
> select add #21.1
33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 27 models selected
> select add #21
33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 28 models selected
> select subtract #21
Nothing selected
> select add #21.1
3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 3 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #21.1.5
3287 atoms, 3040 bonds, 10 pseudobonds, 705 residues, 6 models selected
> hide sel cartoons
> hide sel atoms
Drag select of 92 atoms, 101 bonds, 7 residues
> hide sel atoms
> hide sel cartoons
> select subtract #21.1.5
1 model selected
> select add #21.1.5
410 atoms, 20 residues, 1 model selected
> nucleotides sel tube/slab shape box
Drag select of 27 atoms, 221 residues, 1 pseudobonds, 78 shapes
> show #!15 models
> show #!14 models
> show #!2 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> select add #16
3959 atoms, 3499 bonds, 10 pseudobonds, 738 residues, 7 models selected
> select subtract #16
262 atoms, 13 residues, 5 models selected
> select add #21
33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 29 models selected
> select subtract #21
3 models selected
> select add #21.1.3
1486 atoms, 195 residues, 1 model selected
> select add #21.1.5
1896 atoms, 215 residues, 2 models selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!16 models
> select add #21
33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 30 models selected
> show #!15 models
> hide #!21 models
> hide #!16 models
> show #!14 models
> hide #!14 models
> hide #!15 models
> select subtract #21
3 models selected
> show #!15 models
> show #!14 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!14 models
> hide #!15 models
> hide #!11 models
> show #!11 models
> show #!21 models
> show #!16 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> select add #21
33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 28 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.98958,0.012409,-0.14344,0.91941,-0.039208,0.98185,-0.18555,1.6593,0.13854,0.18924,0.97211,-2.389
> hide #!11 models
> view matrix models
> #21,0.98313,0.082637,-0.16316,0.71163,-0.11628,0.97101,-0.20883,2.6873,0.14117,0.22428,0.96425,-2.5673
> view matrix models
> #21,0.98538,0.07809,-0.15144,0.64248,-0.10827,0.97326,-0.20261,2.5513,0.13157,0.21604,0.96748,-2.4375
> show #!2 models
> hide #!16 models
> hide #!21 models
> ui mousemode right select
> select clear
> show #!19 models
> hide #!19 models
> hide #!2 models
> show #!21 models
> show #!16 models
> show #!15 models
> show #!14 models
> hide #!21 models
> hide #!16 models
> ui tool show "Crystal Contacts"
> crystalcontacts #15 distance 4
10 pairs of asymmetric units of 3igl contact at distance 4.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
201 0 1 0 0 2 0 1
99 0 0 0 0 1 0 1
86 0 0 0 0 -1 0 1
80 0 3 0 0 2 0 1
65 0 3 0 -1 2 0 1
21 0 1 0 0 1 0 1
12 0 0 0 1 0 0 1
9 0 0 0 -1 0 0 1
1 0 3 0 0 1 0 1
1 0 3 0 -1 1 0 1
> crystalcontacts #14 distance 4
10 pairs of asymmetric units of 3igk contact at distance 4.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
174 0 1 0 0 2 0 1
101 0 0 0 0 -1 0 1
86 0 0 0 0 1 0 1
72 0 3 0 -1 2 0 1
64 0 3 0 0 2 0 1
22 0 1 0 0 1 0 1
12 0 0 0 1 0 0 1
9 0 0 0 -1 0 0 1
3 0 3 0 0 1 0 1
1 0 3 0 -1 1 0 1
> hide #!22 models
> hide #!20 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> show #!14 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!15 models
> hide #!14 models
> show #!13 models
> hide #!16 models
> show #!7 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!7 models
> show #!10 models
> show #!9 models
> show #!8 models
> hide #!9 models
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!9 models
> hide #!10 models
> show #!9 models
> hide #!8 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> show #!8 models
> show #!11 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!6 models
> show #!3 models
> hide #!11 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> ui tool show Matchmaker
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!2 models
> save /Users/kompa012/Desktop/P53/5lgy.png width 3000 height 2520 supersample
> 3 transparentBackground true
[Repeated 1 time(s)]
> show #!18 models
> hide #!3 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> hide #!17 models
> show #!16 models
> show #!21 models
> save /Users/kompa012/Desktop/P53/3kz8.png width 3000 height 2520 supersample
> 3 transparentBackground true
> hide #!16 models
> hide #!21 models
> show #!13 models
Drag select of 11 atoms, 11 bonds
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
> save /Users/kompa012/Desktop/P53/3kmd.png width 3000 height 2520 supersample
> 3 transparentBackground true
> hide #!13 models
> select add #13
7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 3 models selected
> select subtract #13
6 models selected
> show #!12 models
> save /Users/kompa012/Desktop/P53/3ts8.png width 3000 height 2520 supersample
> 3 transparentBackground true
> show #!7 models
> hide #!12 models
> save /Users/kompa012/Desktop/P53/4mzr.png width 3000 height 2520 supersample
> 3 transparentBackground true
> hide #!7 models
> show #!8 models
> save /Users/kompa012/Desktop/P53/4ibu.png width 3000 height 2520 supersample
> 3 transparentBackground true
> save "/Users/kompa012/Desktop/P53/Before mutation.cxs"
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> show #!13 models
> hide #!12 models
> hide #!13 models
> show #!14 models
> show #!13 models
> show #!12 models
> show #!15 models
> show #!16 models
> show #!17 models
> show #!18 models
> show #!19 models
> open 6shz fromDatabase pdb format mmcif
Summary of feedback from opening 6shz fetched from pdb
---
note | Fetching compressed mmCIF 6shz from http://files.rcsb.org/download/6shz.cif
6shz title:
p53 cancer mutant Y220C [more info...]
Chain information for 6shz #23
---
Chain | Description | UniProt
A B | Cellular tumor antigen p53 | P53_HUMAN 94-311
Non-standard residues in 6shz #23
---
EDO — 1,2-ethanediol (ethylene glycol)
GOL — glycerol (glycerin; propane-1,2,3-triol)
ZN — zinc ion
6shz mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
134 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2J1x fromDatabase pdb format mmcif
Summary of feedback from opening 2J1x fetched from pdb
---
note | Fetching compressed mmCIF 2j1x from http://files.rcsb.org/download/2j1x.cif
2j1x title:
Human p53 core domain mutant M133L-V203A-Y220C-N239Y-N268D [more info...]
Chain information for 2j1x #24
---
Chain | Description | UniProt
A B | CELLULAR TUMOR ANTIGEN P53 | P53_HUMAN 94-312
Non-standard residues in 2j1x #24
---
ZN — zinc ion
2j1x mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
35 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 1uol fromDatabase pdb format mmcif
Summary of feedback from opening 1uol fetched from pdb
---
note | Fetching compressed mmCIF 1uol from http://files.rcsb.org/download/1uol.cif
1uol title:
Crystal structure of the human p53 core domain mutant M133L/V203A/N239Y/N268D
at 1.9 A resolution. [more info...]
Chain information for 1uol #25
---
Chain | Description | UniProt
A B | CELLULAR TUMOR ANTIGEN P53 | P53_HUMAN 94-312
Non-standard residues in 1uol #25
---
ZN — zinc ion
1uol mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> open 8a32 fromDatabase pdb format mmcif
Summary of feedback from opening 8a32 fetched from pdb
---
note | Fetching compressed mmCIF 8a32 from http://files.rcsb.org/download/8a32.cif
8a32 title:
p53 cancer mutant Y220C in complex with iodophenol-based small-molecule
stabilizer JC769 [more info...]
Chain information for 8a32 #26
---
Chain | Description | UniProt
A B | Cellular tumor antigen p53 | P53_HUMAN 94-312
Non-standard residues in 8a32 #26
---
EDO — 1,2-ethanediol (ethylene glycol)
GOL — glycerol (glycerin; propane-1,2,3-triol)
KVA — 4-[3,4-bis(fluoranyl)pyrrol-1-yl]-3,5-bis(iodanyl)-2-oxidanyl-benzoic
acid
ZN — zinc ion
8a32 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
102 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #25/A to #12/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3ts8, chain A (#12) with 1uol, chain A (#25), sequence alignment
score = 927.9
RMSD between 187 pruned atom pairs is 0.575 angstroms; (across all 195 pairs:
2.313)
> matchmaker #25/B to #12/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3ts8, chain A (#12) with 1uol, chain B (#25), sequence alignment
score = 927.9
RMSD between 186 pruned atom pairs is 0.585 angstroms; (across all 195 pairs:
2.289)
> matchmaker #25/A to #12/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3ts8, chain A (#12) with 1uol, chain A (#25), sequence alignment
score = 927.9
RMSD between 187 pruned atom pairs is 0.575 angstroms; (across all 195 pairs:
2.313)
> matchmaker #24/A to #12/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3ts8, chain A (#12) with 2j1x, chain A (#24), sequence alignment
score = 909.6
RMSD between 187 pruned atom pairs is 0.557 angstroms; (across all 195 pairs:
2.329)
> matchmaker #23/A to #12/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3ts8, chain A (#12) with 6shz, chain A (#23), sequence alignment
score = 916.9
RMSD between 189 pruned atom pairs is 0.550 angstroms; (across all 197 pairs:
2.279)
> matchmaker #26/A to #12/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3ts8, chain A (#12) with 8a32, chain A (#26), sequence alignment
score = 916.2
RMSD between 189 pruned atom pairs is 0.590 angstroms; (across all 197 pairs:
2.303)
> hide #!12 models
> matchmaker #25/A to #24/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2j1x, chain A (#24) with 1uol, chain A (#25), sequence alignment
score = 1098.9
RMSD between 195 pruned atom pairs is 0.170 angstroms; (across all 195 pairs:
0.170)
> hide #!23 models
> hide #!26 models
> ui tool show "Show Sequence Viewer"
> sequence chain #24/A
Alignment identifier is 24/A
> sequence chain #25/A
Alignment identifier is 25/A
> sequence chain #26/A
Alignment identifier is 26/A
> sequence chain #23/A
Alignment identifier is 23/A
> select #25/A:220
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #25/A:220-221
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #25/A:220
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #25/A:220
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #25
3465 atoms, 3144 bonds, 8 pseudobonds, 783 residues, 2 models selected
> color (#!25 & sel) dark gray
> select subtract #25
Nothing selected
> select add #24
3459 atoms, 3133 bonds, 8 pseudobonds, 786 residues, 2 models selected
> color (#!24 & sel) yellow
> select add #26
6990 atoms, 6292 bonds, 16 pseudobonds, 1628 residues, 4 models selected
> select subtract #24
3531 atoms, 3159 bonds, 8 pseudobonds, 842 residues, 2 models selected
> show #!26 models
> color (#!26 & sel) orange
> color (#!26 & sel) red
> select add #23
7103 atoms, 6283 bonds, 16 pseudobonds, 1755 residues, 4 models selected
> select subtract #26
3572 atoms, 3124 bonds, 8 pseudobonds, 913 residues, 2 models selected
> show #!23 models
> color (#!23 & sel) forest green
> select add #24
7031 atoms, 6257 bonds, 16 pseudobonds, 1699 residues, 4 models selected
> select add #26
10562 atoms, 9416 bonds, 24 pseudobonds, 2541 residues, 6 models selected
> select add #25
14027 atoms, 12560 bonds, 32 pseudobonds, 3324 residues, 8 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #23
10455 atoms, 9436 bonds, 24 pseudobonds, 2411 residues, 14 models selected
> select add #23.3
11975 atoms, 9436 bonds, 24 pseudobonds, 2609 residues, 13 models selected
> hide sel cartoons
> select subtract #23.3
10455 atoms, 9436 bonds, 24 pseudobonds, 2411 residues, 13 models selected
> select add #23.2
11978 atoms, 9436 bonds, 24 pseudobonds, 2608 residues, 13 models selected
> select subtract #23.2
10455 atoms, 9436 bonds, 24 pseudobonds, 2411 residues, 13 models selected
> select subtract #24.3
8922 atoms, 7868 bonds, 20 pseudobonds, 2216 residues, 12 models selected
> select add #24.3
10455 atoms, 7868 bonds, 20 pseudobonds, 2411 residues, 11 models selected
> select subtract #24.2
8925 atoms, 6303 bonds, 16 pseudobonds, 2216 residues, 11 models selected
> select subtract #24.3
7392 atoms, 6303 bonds, 16 pseudobonds, 2021 residues, 10 models selected
> select add #24.3
8925 atoms, 6303 bonds, 16 pseudobonds, 2216 residues, 9 models selected
> select subtract #25
5460 atoms, 3159 bonds, 8 pseudobonds, 1433 residues, 8 models selected
> select subtract #26
1929 atoms, 591 residues, 4 models selected
> select subtract #24.3
396 atoms, 396 residues, 2 models selected
> select add #24.3
1929 atoms, 591 residues, 1 model selected
> select subtract #24.3
396 atoms, 396 residues, 2 models selected
> select add #24.2
1926 atoms, 591 residues, 1 model selected
> show sel cartoons
> select subtract #24.2
396 atoms, 396 residues, 2 models selected
> select add #24.2
1926 atoms, 591 residues, 1 model selected
> select subtract #24.2
396 atoms, 396 residues, 2 models selected
> select add #24
3459 atoms, 3133 bonds, 8 pseudobonds, 786 residues, 2 models selected
> select subtract #24
2 models selected
> select add #25.2
1536 atoms, 195 residues, 1 model selected
> show sel cartoons
> select add #25
3465 atoms, 3144 bonds, 8 pseudobonds, 783 residues, 3 models selected
> select subtract #25
2 models selected
> select add #26.2
1521 atoms, 197 residues, 1 model selected
> show sel cartoons
> select add #26
3531 atoms, 3159 bonds, 8 pseudobonds, 842 residues, 3 models selected
> select subtract #26
2 models selected
Drag select of 277 atoms, 16 pseudobonds, 244 bonds
> hide sel atoms
> select #25/A:220
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #25/A:220
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #23-26 /A :220
30 atoms, 27 bonds, 4 residues, 4 models selected
> show sel atoms
> hide #!25 models
> hide #!24 models
> hide #!23 models
> show #!11 models
> hide #!26 models
> select add #23
3596 atoms, 3146 bonds, 8 pseudobonds, 916 residues, 9 models selected
> select subtract #23
24 atoms, 22 bonds, 3 residues, 8 models selected
> select add #23
3596 atoms, 3146 bonds, 8 pseudobonds, 916 residues, 8 models selected
> select subtract #23
24 atoms, 22 bonds, 3 residues, 8 models selected
> select add #24
3477 atoms, 3150 bonds, 8 pseudobonds, 788 residues, 7 models selected
> select subtract #24
18 atoms, 17 bonds, 2 residues, 6 models selected
> select add #25
3471 atoms, 3149 bonds, 8 pseudobonds, 784 residues, 5 models selected
> select subtract #25
6 atoms, 5 bonds, 1 residue, 4 models selected
> select add #26
3531 atoms, 3159 bonds, 8 pseudobonds, 842 residues, 3 models selected
> select subtract #26
2 models selected
> save "/Users/kompa012/Desktop/P53/Y220C mutation.cxs"
——— End of log from Wed Mar 12 16:42:08 2025 ———
opened ChimeraX session
> hide #!11 models
> show #!25 models
> show #!24 models
> show #!26 models
> hide #!26 models
> show #!23 models
> show #!26 models
> hide #!25 models
> hide #!26 models
> show #!25 models
> hide #!23 models
> show #!26 models
> hide #!24 models
> hide #!26 models
> select #23-26 /A :151
28 atoms, 28 bonds, 4 residues, 4 models selected
> show sel & #!25 atoms
> select #23-26 /A :153
28 atoms, 28 bonds, 4 residues, 4 models selected
> show sel & #!25 atoms
> hide sel & #!25 atoms
> select #23-26 /A :155
28 atoms, 24 bonds, 4 residues, 4 models selected
> show sel & #!25 atoms
> select #23-26 /A :222
28 atoms, 28 bonds, 4 residues, 4 models selected
> show sel & #!25 atoms
> select #23-26 /A :220, 222, 153
86 atoms, 83 bonds, 12 residues, 4 models selected
> select #23-26 /A :220, 222, 151
86 atoms, 83 bonds, 12 residues, 4 models selected
> color (#!25 & sel) black
> select #23-26 /A :223
28 atoms, 28 bonds, 4 residues, 4 models selected
> show sel & #!25 atoms
> hide sel & #!25 cartoons
> show sel & #!25 cartoons
> hide sel & #!25 atoms
> select #23-26 /A :145
32 atoms, 28 bonds, 4 residues, 4 models selected
> show sel & #!25 atoms
> select #23-26 /A :223
28 atoms, 28 bonds, 4 residues, 4 models selected
> show sel & #!25 atoms
> select #23-26 /A :147
28 atoms, 24 bonds, 4 residues, 4 models selected
> show sel & #!25 atoms
> select ~sel & ##selected
13999 atoms, 12536 bonds, 32 pseudobonds, 3320 residues, 8 models selected
> select #23-26 /A :151,153,155
84 atoms, 80 bonds, 12 residues, 4 models selected
> show sel & #!25 atoms
> select #23-26 /A :151,153,155,223,220,147
170 atoms, 159 bonds, 24 residues, 4 models selected
> show sel & #!25 cartoons
> show sel & #!25 atoms
> select #23-26 /A :222
28 atoms, 28 bonds, 4 residues, 4 models selected
> hide sel & #!25 atoms
> color (#!25 & sel) light gray
> color (#!25 & sel) dark gray
> select #23-26 /A :151,153,155,223,220,147
170 atoms, 159 bonds, 24 residues, 4 models selected
> color (#!25 & sel) black
> ui tool show H-Bonds
> save "/Users/kompa012/Desktop/P53/Y220C mutation.cxs"
——— End of log from Wed Mar 12 17:13:32 2025 ———
opened ChimeraX session
> style sel & #!25 ball
Changed 47 atom styles
> color (#!25 & sel) byelement
> distance #25/A:153@CA #25/A:220@CD2
Distance between 1uol #25/A PRO 153 CA and TYR 220 CD2: 6.945Å
> close #27
> hide sel & #!25 cartoons
> distance #25/A:223@CD #25/A:220@OH
Distance between 1uol #25/A PRO 223 CD and TYR 220 OH: 3.634Å
> distance #25/A:147@CG2 #25/A:220@OH
Distance between 1uol #25/A VAL 147 CG2 and TYR 220 OH: 3.539Å
> distance #25/A:151@CD #25/A:220@OH
Distance between 1uol #25/A PRO 151 CD and TYR 220 OH: 4.277Å
> distance #25/A:155@O #25/A:220@N
Distance between 1uol #25/A THR 155 O and TYR 220 N: 2.885Å
> ui mousemode right select
> select #25/A:153@CA
1 atom, 1 residue, 1 model selected
> select #23-26 /A :153
28 atoms, 28 bonds, 4 residues, 4 models selected
> show sel & #!25 cartoons
> hide sel & #!25 atoms
> color (#!25 & sel) dark gray
> select clear
> select #23-26 /A :155
28 atoms, 24 bonds, 4 residues, 4 models selected
> select #23-26 /A :222
28 atoms, 28 bonds, 4 residues, 4 models selected
> show sel & #!25 atoms
> style sel & #!25 ball
Changed 7 atom styles
> color (#!25 & sel) byelement
> hide #27.1 models
> show #27.1 models
> select #23-26 /A :22
Nothing selected
> select #23-26 /A :220
30 atoms, 27 bonds, 4 residues, 4 models selected
> style (#!25 & sel) ringFill thick
Changed 1 residue ring style
> select clear
> select #23-26 /A :220
30 atoms, 27 bonds, 4 residues, 4 models selected
> style (#!25 & sel) ringFill thin
Changed 1 residue ring style
> select clear
> select #23-26 /A :222, 153
56 atoms, 56 bonds, 8 residues, 4 models selected
> select #23-26 /A :222, 151
56 atoms, 56 bonds, 8 residues, 4 models selected
> style (#!25 & sel) ringFill thin
Changed 2 residue ring styles
> color (#!25 & sel) black
> color (#!25 & sel) byelement
> select clear
> select #23-26 /A :156-146
Nothing selected
> select #23-26 /A :146-156
340 atoms, 356 bonds, 44 residues, 4 models selected
> hide sel & #!25 cartoons
> show sel & #!25 atoms
> hide (#!25 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!25 & sel-residues)
> show (#!25 & sel-residues & backbone) target ab
> select #23-26 /A :219-224
179 atoms, 188 bonds, 1 pseudobond, 24 residues, 5 models selected
> select #23-26 /A :219-230
331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected
> hide sel & #!25 cartoons
> show sel & #!25 atoms
> hide (#!25 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!25 & sel-residues)
> show (#!25 & sel-residues & backbone) target ab
> select #23-26 /A :151,155,223,220,147
142 atoms, 131 bonds, 4 pseudobonds, 20 residues, 5 models selected
> select #23-26 /A :151,155,223,220,147,222
170 atoms, 163 bonds, 4 pseudobonds, 24 residues, 5 models selected
> show (#!25 & sel-residues & sidechain) target ab
> select clear
> select #25/A:145
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #25/A:230@C
1 atom, 1 residue, 1 model selected
> select #25/A:230@CA
1 atom, 1 residue, 1 model selected
> select #25/A:230@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #23-26 /A :220
30 atoms, 27 bonds, 4 residues, 4 models selected
> style sel & #!25 sphere
Changed 12 atom styles
> select clear
> select #23-26 /A :220
30 atoms, 27 bonds, 4 residues, 4 models selected
> style sel & #!25 ball
Changed 12 atom styles
> select clear
> hide #27.1 models
> hide #!27 models
> show #!26 models
> hide #!25 models
> show #!25 models
> show #!24 models
> hide #!25 models
> hide #!26 models
> show #!25 models
> hide #!25 models
> show #!23 models
> hide #!23 models
> hide #!24 models
> show #!24 models
> show #!26 models
> hide #!26 models
> show #!25 models
> show #!23 models
> select #23-26 /A :151,155,223,220,147,222
170 atoms, 163 bonds, 4 pseudobonds, 24 residues, 5 models selected
> style sel & #!23-25 ball
Changed 129 atom styles
> show sel & #!23-25 atoms
> color (#!23-25 & sel) byelement
> style (#!23-25 & sel) ringFill thin
Changed 18 residue ring styles
> hide #!25 models
> hide #!24 models
> show #!24 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> show #!25 models
> hide #!23 models
> show #!27 models
> select clear
[Repeated 1 time(s)]
> ui tool show "Side View"
> save "/Users/kompa012/Desktop/P53/1uol Y220 .png" width 3000 height 2320
> supersample 3 transparentBackground true
> hide #!25 models
> show #!24 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> select #23-26 /A :220,155
58 atoms, 51 bonds, 1 pseudobond, 8 residues, 5 models selected
> hide sel & #!24 cartoons
> ui mousemode right distance
> distance #24/A:220@N #24/A:155@O
Distance between 2j1x #24/A CYS 220 N and THR 155 O: 2.911Å
> select #23-26 /A :219-230
331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected
> hide sel & #!24 cartoons
> hide sel & #!24 atoms
> show sel & #!24 atoms
> hide sel & #!24 cartoons
> hide (#!24 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!24 & sel-residues)
> show (#!24 & sel-residues & backbone) target ab
> select up
707 atoms, 732 bonds, 1 pseudobond, 92 residues, 9 models selected
> select #23-26 /A :146-156
340 atoms, 356 bonds, 44 residues, 4 models selected
> hide (#!24 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!24 & sel-residues)
> show (#!24 & sel-residues & backbone) target ab
> hide sel & #!24 cartoons
[Repeated 1 time(s)]
> show sel & #!24 atoms
> hide (#!24 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!24 & sel-residues)
> show (#!24 & sel-residues & backbone) target ab
> select #23-26 /A :151,155,223,220,147,222
170 atoms, 163 bonds, 5 pseudobonds, 24 residues, 5 models selected
> show (#!24 & sel-residues & sidechain) target ab
> ui mousemode right select
> select clear
> select #23-26 /A :151,223,222
84 atoms, 88 bonds, 12 residues, 4 models selected
> color (#!24 & sel) black
> color (#!24 & sel) byelement
> select clear
> show #!23 models
> hide #!24 models
> select #23-26 /A :151,223,222
84 atoms, 88 bonds, 12 residues, 4 models selected
> color (#!23 & sel) black
> color (#!23 & sel) byelement
> select #23-26 /A :219-230
331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected
> hide sel & #!23 cartoons
> show sel & #!23 atoms
> hide (#!23 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!23 & sel-residues)
> show (#!23 & sel-residues & backbone) target ab
> select #23-26 /A :146-156
340 atoms, 356 bonds, 44 residues, 4 models selected
> hide sel & #!23 cartoons
> show sel & #!23 atoms
> hide (#!23 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!23 & sel-residues)
> show (#!23 & sel-residues & backbone) target ab
> select #23-26 /A :151,155,223,220,147,222
170 atoms, 163 bonds, 5 pseudobonds, 24 residues, 5 models selected
> show (#!23 & sel-residues & sidechain) target ab
> show #!24 models
> select clear
> save "/Users/kompa012/Desktop/P53/6shz_2j1x C220.png" width 3000 height 2320
> supersample 3 transparentBackground true
> hide #!24 models
> hide #!23 models
> show #!26 models
> show #!25 models
> hide #!25 models
> select add #26
3531 atoms, 3159 bonds, 8 pseudobonds, 842 residues, 2 models selected
> select solvent
19518 atoms, 19518 residues, 51 models selected
> hide sel & #!26 atoms
> select clear
> show #!24 models
> hide #!24 models
> hide #!26 models
> show #!26 models
> select #23-26 /A :219-230
331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected
> hide sel & #!26 cartoons
> show sel & #!26 cartoons
> style sel & #!26 ball
Changed 79 atom styles
> hide (#!26 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!26 & sel-residues)
> show (#!26 & sel-residues & backbone) target ab
> select #23-26 /A :146-156
340 atoms, 356 bonds, 44 residues, 4 models selected
> hide sel & #!26 cartoons
> show sel & #!26 atoms
> style sel & #!26 ball
Changed 85 atom styles
> hide (#!26 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!26 & sel-residues)
> show (#!26 & sel-residues & backbone) target ab
> select #23-26 /A :151,155,223,220,147,222
170 atoms, 163 bonds, 5 pseudobonds, 24 residues, 5 models selected
> color (#!26 & sel) black
> style (#!26 & sel) ringFill thin
Changed 6 residue ring styles
> show (#!26 & sel-residues & sidechain) target ab
> color (#!26 & sel) byelement
> select add #26.3
1690 atoms, 163 bonds, 5 pseudobonds, 223 residues, 9 models selected
> select subtract #26.2
1649 atoms, 124 bonds, 5 pseudobonds, 217 residues, 10 models selected
> select add #26.1
1649 atoms, 124 bonds, 13 pseudobonds, 217 residues, 10 models selected
> select add #26
3660 atoms, 3283 bonds, 13 pseudobonds, 860 residues, 10 models selected
> show sel & #!26 surfaces
> hide sel & #!26 surfaces
> select ligand
274 atoms, 218 bonds, 60 residues, 16 models selected
> style sel & #!26 ball
Changed 48 atom styles
> color (#!26 & sel) byelement
> style sel & #!26 stick
Changed 48 atom styles
> ui mousemode right distance
> distance #26/A:220@N #26/A:155@O
Distance between 8a32 #26/A CYS 220 N and THR 155 O: 2.934Å
> style (#!26 & sel) ringFill thin
Changed 4 residue ring styles
> color (#!26 & sel) black
> color (#!26 & sel) byelement
> distance #26/A:401@O #26/A:151@CD
Distance between 8a32 #26/A KVA 401 O and PRO 151 CD: 6.205Å
> distance #26/A:401@O1 #26/A:147@CG2
Distance between 8a32 #26/A KVA 401 O1 and VAL 147 CG2: 5.072Å
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> distance #26/A:401@O2 #26/A:147@CG2
Distance between 8a32 #26/A KVA 401 O2 and VAL 147 CG2: 3.735Å
> show #27.1 models
> hide #27.1 models
> ui mousemode right select
> hide #!26 atoms
> undo
[Repeated 1 time(s)]
> hide #!27 models
> show #!27 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> ui mousemode right "delete markers"
[Repeated 1 time(s)]
> ui mousemode right distance
> ~distance #26/A:401@O #26/A:151@CD
> ~distance #26/A:401@O1 #26/A:147@CG2
> save "/Users/kompa012/Desktop/P53/8a32 C220 woth cjc769.png" width 3000
> height 2320 supersample 3 transparentBackground true
> save "/Users/kompa012/Desktop/P53/Y220C mutation details.cxs"
——— End of log from Thu Mar 13 10:36:24 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16S0005DLL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 13 days, 23 hours, 45 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PHL 272P7VU:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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