![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Closed 16 months ago
#15587 closed defect (can't reproduce)
Crash either moving window or changing display
| 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
The following bug report has been submitted:
Platform: macOS-15.0-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000202a8f200 (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, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 66)
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{
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"procRole" : "Foreground",
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"modelCode" : "Mac14,9",
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"codeSigningMonitor" : 1,
"incident" : "AC3A330F-541B-4E09-A7EE-F0DE2C12FD7A",
"pid" : 22929,
"translated" : true,
"cpuType" : "X86-64",
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"procLaunch" : "2024-07-09 11:28:14.4459 +0100",
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"procExitAbsTime" : 9947116596897,
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"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" : "743502C5-F125-8AEC-9987-47D4FCAF21E5",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
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"bootSessionUUID" : "A89A1D1C-2F83-4284-A0F0-59E1A4124262",
"wakeTime" : 4760,
"sleepWakeUUID" : "A17AE858-1282-4775-95D0-3971798D1524",
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"vmRegionInfo" : "0x1575470c8f8 is not in any region. Bytes after previous region: 993554123001 Bytes before following region: 104078525806344\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":22929},
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
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},
"legacyInfo" : {
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},
"logWritingSignature" : "a322743e29d8d9df74dd71acc1436e7b91892565",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "64c17a9925d75a7281053d4c",
"factorPackIds" : {
"SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC" : "64d29746ad29a465b3bbeace"
},
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},
{
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}
],
"experiments" : [
{
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},
{
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"deploymentId" : 400000015
}
]
},
"reportNotes" : [
"PC register does not match crashing frame (0x0 vs 0x7FF8A4072A7C)"
]
}
===== 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/niltonarandaneto/Downloads/6q3v.cif
6q3v.cif title:
Crystal structure of Human N4BP1 KH domains [more info...]
Chain information for 6q3v.cif #1
---
Chain | Description | UniProt
A | NEDD4-binding protein 1 | N4BP1_HUMAN 1-186
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "/Users/niltonarandaneto/Documents/untitled folder/n4bp1_human.pdb"
Chain information for n4bp1_human.pdb #2
---
Chain | Description
A | No description available
> ui tool show Matchmaker
No reference and/or match structure/chain chosen
> ui tool show Matchmaker
> 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 n4bp1_human.pdb, chain A (#2) with 6q3v.cif, chain A (#1), sequence
alignment score = 939.7
RMSD between 166 pruned atom pairs is 0.914 angstroms; (across all 188 pairs:
1.810)
> open "/Users/niltonarandaneto/Documents/untitled folder/AF-colour-N4BP1.cxs"
> format session
opened ChimeraX session
> open "/Users/niltonarandaneto/Downloads/Aligned Kh.pdb"
Chain information for Aligned Kh.pdb #3
---
Chain | Description
A | No description available
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #3 to #1
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 n4bp1_human.pdb, chain A (#1) with Aligned Kh.pdb, chain A (#3),
sequence alignment score = 939.7
RMSD between 166 pruned atom pairs is 0.914 angstroms; (across all 188 pairs:
1.810)
> matchmaker #3 to #1
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 n4bp1_human.pdb, chain A (#1) with Aligned Kh.pdb, chain A (#3),
sequence alignment score = 939.7
RMSD between 166 pruned atom pairs is 0.914 angstroms; (across all 188 pairs:
1.810)
> save "/Users/niltonarandaneto/Documents/untitled folder/AF-colour-N4BP1.cxs"
> hide #2 models
> hide #3 models
> open /Users/niltonarandaneto/Downloads/AF-O75113-F1-model_v4.pdb
AF-O75113-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for NEDD4-binding protein 1 (O75113) [more
info...]
Chain information for AF-O75113-F1-model_v4.pdb #4
---
Chain | Description | UniProt
A | NEDD4-binding protein 1 | N4BP1_HUMAN 1-896
> select #4/A:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> ui tool show "Render/Select by Attribute"
> color bfactor sel
7052 atoms, 896 residues, atom bfactor range 26.4 to 98.8
> show #2 models
> hide #2 models
> hide #1 models
> show #1 models
> show #2 models
> hide #2 models
> hide #4 models
> show #3 models
> hide #1 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #3 models
> show #4 models
> show #1 models
> ui tool show "Render/Select by Attribute"
> toolshed show
> palette list
No custom palettes.
315 builtin palettes: Accent, Accent-3, Accent-4, Accent-5, Accent-6,
Accent-7, Accent-8, alphafold, blue-white-red, bluered, Blues, Blues-3,
Blues-4, Blues-5, Blues-6, Blues-7, Blues-8, Blues-9, BrBG, BrBG-10, BrBG-11,
BrBG-3, BrBG-4, BrBG-5, BrBG-6, BrBG-7, BrBG-8, BrBG-9, BuGn, BuGn-3, BuGn-4,
BuGn-5, BuGn-6, BuGn-7, BuGn-8, BuGn-9, BuPu, BuPu-3, BuPu-4, BuPu-5, BuPu-6,
BuPu-7, BuPu-8, BuPu-9, cyan-gray-maroon, cyan-white-maroon, cyanmaroon,
Dark2, Dark2-3, Dark2-4, Dark2-5, Dark2-6, Dark2-7, Dark2-8, esmfold, GnBu,
GnBu-3, GnBu-4, GnBu-5, GnBu-6, GnBu-7, GnBu-8, GnBu-9, gray, grayscale,
Greens, Greens-3, Greens-4, Greens-5, Greens-6, Greens-7, Greens-8, Greens-9,
Greys, Greys-3, Greys-4, Greys-5, Greys-6, Greys-7, Greys-8, Greys-9,
lipophilicity, Oranges, Oranges-3, Oranges-4, Oranges-5, Oranges-6, Oranges-7,
Oranges-8, Oranges-9, OrRd, OrRd-3, OrRd-4, OrRd-5, OrRd-6, OrRd-7, OrRd-8,
OrRd-9, pae, paecontacts, paegreen, Paired, Paired-10, Paired-11, Paired-12,
Paired-3, Paired-4, Paired-5, Paired-6, Paired-7, Paired-8, Paired-9, Pastel1,
Pastel1-3, Pastel1-4, Pastel1-5, Pastel1-6, Pastel1-7, Pastel1-8, Pastel1-9,
Pastel2, Pastel2-3, Pastel2-4, Pastel2-5, Pastel2-6, Pastel2-7, Pastel2-8,
PiYG, PiYG-10, PiYG-11, PiYG-3, PiYG-4, PiYG-5, PiYG-6, PiYG-7, PiYG-8,
PiYG-9, PRGn, PRGn-10, PRGn-11, PRGn-3, PRGn-4, PRGn-5, PRGn-6, PRGn-7,
PRGn-8, PRGn-9, PuBu, PuBu-3, PuBu-4, PuBu-5, PuBu-6, PuBu-7, PuBu-8, PuBu-9,
PuBuGn, PuBuGn-3, PuBuGn-4, PuBuGn-5, PuBuGn-6, PuBuGn-7, PuBuGn-8, PuBuGn-9,
PuOr, PuOr-10, PuOr-11, PuOr-3, PuOr-4, PuOr-5, PuOr-6, PuOr-7, PuOr-8,
PuOr-9, PuRd, PuRd-3, PuRd-4, PuRd-5, PuRd-6, PuRd-7, PuRd-8, PuRd-9, Purples,
Purples-3, Purples-4, Purples-5, Purples-6, Purples-7, Purples-8, Purples-9,
rainbow, RdBu, RdBu-10, RdBu-11, RdBu-3, RdBu-4, RdBu-5, RdBu-6, RdBu-7,
RdBu-8, RdBu-9, RdGy, RdGy-10, RdGy-11, RdGy-3, RdGy-4, RdGy-5, RdGy-6,
RdGy-7, RdGy-8, RdGy-9, RdPu, RdPu-3, RdPu-4, RdPu-5, RdPu-6, RdPu-7, RdPu-8,
RdPu-9, RdYlBu, RdYlBu-10, RdYlBu-11, RdYlBu-3, RdYlBu-4, RdYlBu-5, RdYlBu-6,
RdYlBu-7, RdYlBu-8, RdYlBu-9, RdYlGn, RdYlGn-10, RdYlGn-11, RdYlGn-3,
RdYlGn-4, RdYlGn-5, RdYlGn-6, RdYlGn-7, RdYlGn-8, RdYlGn-9, red-white-blue,
redblue, Reds, Reds-3, Reds-4, Reds-5, Reds-6, Reds-7, Reds-8, Reds-9, Set1,
Set1-3, Set1-4, Set1-5, Set1-6, Set1-7, Set1-8, Set1-9, Set2, Set2-3, Set2-4,
Set2-5, Set2-6, Set2-7, Set2-8, Set3, Set3-10, Set3-11, Set3-12, Set3-3,
Set3-4, Set3-5, Set3-6, Set3-7, Set3-8, Set3-9, Spectral, Spectral-10,
Spectral-11, Spectral-3, Spectral-4, Spectral-5, Spectral-6, Spectral-7,
Spectral-8, Spectral-9, YlGn, YlGn-3, YlGn-4, YlGn-5, YlGn-6, YlGn-7, YlGn-8,
YlGn-9, YlGnBu, YlGnBu-3, YlGnBu-4, YlGnBu-5, YlGnBu-6, YlGnBu-7, YlGnBu-8,
YlGnBu-9, YlOrBr, YlOrBr-3, YlOrBr-4, YlOrBr-5, YlOrBr-6, YlOrBr-7, YlOrBr-8,
YlOrBr-9, YlOrRd, YlOrRd-3, YlOrRd-4, YlOrRd-5, YlOrRd-6, YlOrRd-7, and
YlOrRd-8.
> ui tool show "Render/Select by Attribute"
> key ylgn-3 :6.1 :52.5 :98.8 showTool true
> ui mousemode right "color key"
> key colorTreatment distinct
> key ylgn-3 :6.1 :52.5 :98.8 white:
> ui mousemode right translate
> key greys-3 :6.1 :52.5 :98.8 showTool true
> ui mousemode right "color key"
> key greys-3 :6.1 :52.5 :98.8
> key greys-3 :6.1 :52.5 :98.8 white:
Fetching compressed palette custom from
https://www.colourlovers.com/api/palettes?keywords=custom&format=json&numResults=100
Could not find palette custom at COLOURlovers.com using keyword search
> key #f0f0f0:6.1 #bdbdbd:52.5 #636363:98.8 #0000f5:
> key #f0f0f0:6.1 #bdbdbd:52.5 #326bf6:98.8 #0000f5:
> key #f0f0f0:6.1 #5fcced:52.5 #326bf6:98.8 #0000f5:
> key #f0f0f0:6.1 #5fcced:52.5 #326bf6:98.8 #0000f5: white:
> key #f0f0f0:6.1 #5fcced:52.5 #326bf6:98.8 #0000f5: #0000f5:
> key #f0f0f0:6.1 #5fcced:52.5 #326bf6:98.8 #326bf6: #0000f5:
> key #f0f0f0:6.1 #5fcced:52.5 #f4ed51:98.8 #326bf6: #0000f5:
> key #f0f0f0:6.1 #5fcced:52.5 #5fcced:98.8 #326bf6: #0000f5:
> key #f0f0f0:6.1 #f4ed51:52.5 #5fcced:98.8 #326bf6: #0000f5:
> key #e1883a:6.1 #f4ed51:52.5 #5fcced:98.8 #326bf6: #0000f5:
> key #e1883a:6.1 #f4ed51:52.5 #5fcced:98.8 #326bf6: #0000f5: white:
> key white: #0000f5: #326bf6: #5fcced:98.8 #f4ed51:52.5 #e1883a:6.1
> key #e1883a:6.1 #f4ed51:52.5 #5fcced:98.8 #326bf6: #0000f5: white:
> key #e1883a:6.1 #f4ed51:52.5 #5fcced:98.8 #326bf6: #0000f5: #0000f5:
> key #e1883a:6.1 #f4ed51:52.5 #5fcced:98.8 #326bf6: #326bf6: #0000f5:
> key #e1883a:6.1 #f4ed51:52.5 #5fcced:98.8 #5fcced: #326bf6: #0000f5:
> key #e1883a:6.1 #f4ed51:52.5 #f4ed51:98.8 #5fcced: #326bf6: #0000f5:
> key #e1883a:6.1 #f4ed51:52.5 #e1883a:98.8 #5fcced: #326bf6: #0000f5:
> key #e1883a:6.1 #f4ed51:52.5 #f4ed51:98.8 #5fcced: #326bf6: #0000f5:
> key #e1883a:6.1 #e1883a:52.5 #f4ed51:98.8 #5fcced: #326bf6: #0000f5:
> key #ea3323:6.1 #e1883a:52.5 #f4ed51:98.8 #5fcced: #326bf6: #0000f5:
> key #ea3323: #e1883a:52.5 #f4ed51:98.8 #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a:52.5 #f4ed51:98.8 #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a:52. #f4ed51:98.8 #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a:52 #f4ed51:98.8 #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a:5 #f4ed51:98.8 #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a: #f4ed51:98.8 #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a:5 #f4ed51:98.8 #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a:50 #f4ed51:98.8 #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a:50 #f4ed51:98. #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a:50 #f4ed51:98 #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a:50 #f4ed51:9 #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a:50 #f4ed51: #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a:50 #f4ed51:7 #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced: #326bf6: #0000f5:
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced:9 #326bf6: #0000f5:
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced:90 #326bf6: #0000f5:
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced:90 #326bf6:9 #0000f5:
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced:90 #326bf6:99 #0000f5:
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced:90 #326bf6:99 #0000f5:1
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced:90 #326bf6:99 #0000f5:10
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced:90 #326bf6:99 #0000f5:100
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced:90 #326bf6:9 #0000f5:100
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced:90 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced:9 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced: #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced:7 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:50 #f4ed51:70 #5fcced:70 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:50 #f4ed51: #5fcced:70 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:50 #f4ed51:6 #5fcced:70 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:50 #f4ed51:60 #5fcced:70 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:50 #f4ed51:6 #5fcced:70 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:50 #f4ed51: #5fcced:70 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:50 #f4ed51:5 #5fcced:70 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:50 #f4ed51:50 #5fcced:70 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:5 #f4ed51:50 #5fcced:70 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a: #f4ed51:50 #5fcced:70 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:1 #f4ed51:50 #5fcced:70 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:1 #f4ed51:50 #5fcced:70 #326bf6:90 #0000f5:100 white:
> key #ea3323:0 #e1883a:1 #f4ed51:50 #5fcced:70 #326bf6:90 #0000f5:100
> key #ea3323:0 #e1883a:1 #f4ed51:50 #5fcced:70 #326bf6:90
> key #ea3323:0 #e1883a:1 #f4ed51:50 #5fcced:70 #326bf6:90 white:
> key #ea3323:0 #e1883a:1 #f4ed51:50 #5fcced:70 #326bf6:90
> key #ea3323:0 #e1883a:1 #f4ed51:50 #5fcced:70
> key #ea3323:0 #e1883a:1 #f4ed51:50 #326bf6:70
> key #ea3323:0 #e1883a:1 #5fcced:50 #326bf6:70
> key #ea3323:0 #f4ed51:1 #5fcced:50 #326bf6:70
> key #e1883a:0 #f4ed51:1 #5fcced:50 #326bf6:70
> key #e1883a:0 #f4ed51:1 #5fcced:50 #326bf6:
> key #e1883a:0 #f4ed51:1 #5fcced:50 #326bf6:9
> key #e1883a:0 #f4ed51:1 #5fcced:50 #326bf6:99
> key #e1883a:0 #f4ed51:1 #5fcced:50 #326bf6:990
> key #e1883a:0 #f4ed51:1 #5fcced:50 #326bf6:99
> key #e1883a:0 #f4ed51:1 #5fcced:50 #326bf6:9
> key #e1883a:0 #f4ed51:1 #5fcced:50 #326bf6:90
> key #e1883a:0 #f4ed51:1 #5fcced: #326bf6:90
> key #e1883a:0 #f4ed51:1 #5fcced:7 #326bf6:90
> key #e1883a:0 #f4ed51:1 #5fcced:70 #326bf6:90
> key #e1883a:0 #f4ed51:15 #5fcced:70 #326bf6:90
> key #e1883a:0 #f4ed51:1 #5fcced:70 #326bf6:90
> key #e1883a:0 #f4ed51: #5fcced:70 #326bf6:90
> key #e1883a:0 #f4ed51:5 #5fcced:70 #326bf6:90
> key #e1883a:0 #f4ed51:50 #5fcced:70 #326bf6:90
> key colorTreatment blended
> key greys-4 :0 :50 :70 :90
> key #f7f7f7:0 #cccccc:50 #969696:70 #326bf6:90
> ui mousemode right translate
> show #2 models
> hide #2 models
> show #2 models
> ui tool show "Render/Select by Attribute"
> key #e1883a:0.0 #f4ed51:46.8 #5fcced:68.1 #326bf6:89.4 showTool true
> ui mousemode right "color key"
Window position QRect(605,1057 100x30) outside any known screen, using primary
screen
> ui mousemode right translate
> color byattribute a:bfactor #1,4 target abcs palette
> 0,#e1883a:46.7779,#f4ed51:68.0987,#5fcced:89.4195,#326bf6
14104 atoms, 1792 residues, atom bfactor range 6.12 to 98.8
> show #3 models
> hide #3 models
> help help:user/tools/render.html
Window position QRect(769,1326 100x30) outside any known screen, using primary
screen
> key #e1883a:0 #f4ed51:50 #5fcced:70 #326bf6:90 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> palette list
No custom palettes.
315 builtin palettes: Accent, Accent-3, Accent-4, Accent-5, Accent-6,
Accent-7, Accent-8, alphafold, blue-white-red, bluered, Blues, Blues-3,
Blues-4, Blues-5, Blues-6, Blues-7, Blues-8, Blues-9, BrBG, BrBG-10, BrBG-11,
BrBG-3, BrBG-4, BrBG-5, BrBG-6, BrBG-7, BrBG-8, BrBG-9, BuGn, BuGn-3, BuGn-4,
BuGn-5, BuGn-6, BuGn-7, BuGn-8, BuGn-9, BuPu, BuPu-3, BuPu-4, BuPu-5, BuPu-6,
BuPu-7, BuPu-8, BuPu-9, cyan-gray-maroon, cyan-white-maroon, cyanmaroon,
Dark2, Dark2-3, Dark2-4, Dark2-5, Dark2-6, Dark2-7, Dark2-8, esmfold, GnBu,
GnBu-3, GnBu-4, GnBu-5, GnBu-6, GnBu-7, GnBu-8, GnBu-9, gray, grayscale,
Greens, Greens-3, Greens-4, Greens-5, Greens-6, Greens-7, Greens-8, Greens-9,
Greys, Greys-3, Greys-4, Greys-5, Greys-6, Greys-7, Greys-8, Greys-9,
lipophilicity, Oranges, Oranges-3, Oranges-4, Oranges-5, Oranges-6, Oranges-7,
Oranges-8, Oranges-9, OrRd, OrRd-3, OrRd-4, OrRd-5, OrRd-6, OrRd-7, OrRd-8,
OrRd-9, pae, paecontacts, paegreen, Paired, Paired-10, Paired-11, Paired-12,
Paired-3, Paired-4, Paired-5, Paired-6, Paired-7, Paired-8, Paired-9, Pastel1,
Pastel1-3, Pastel1-4, Pastel1-5, Pastel1-6, Pastel1-7, Pastel1-8, Pastel1-9,
Pastel2, Pastel2-3, Pastel2-4, Pastel2-5, Pastel2-6, Pastel2-7, Pastel2-8,
PiYG, PiYG-10, PiYG-11, PiYG-3, PiYG-4, PiYG-5, PiYG-6, PiYG-7, PiYG-8,
PiYG-9, PRGn, PRGn-10, PRGn-11, PRGn-3, PRGn-4, PRGn-5, PRGn-6, PRGn-7,
PRGn-8, PRGn-9, PuBu, PuBu-3, PuBu-4, PuBu-5, PuBu-6, PuBu-7, PuBu-8, PuBu-9,
PuBuGn, PuBuGn-3, PuBuGn-4, PuBuGn-5, PuBuGn-6, PuBuGn-7, PuBuGn-8, PuBuGn-9,
PuOr, PuOr-10, PuOr-11, PuOr-3, PuOr-4, PuOr-5, PuOr-6, PuOr-7, PuOr-8,
PuOr-9, PuRd, PuRd-3, PuRd-4, PuRd-5, PuRd-6, PuRd-7, PuRd-8, PuRd-9, Purples,
Purples-3, Purples-4, Purples-5, Purples-6, Purples-7, Purples-8, Purples-9,
rainbow, RdBu, RdBu-10, RdBu-11, RdBu-3, RdBu-4, RdBu-5, RdBu-6, RdBu-7,
RdBu-8, RdBu-9, RdGy, RdGy-10, RdGy-11, RdGy-3, RdGy-4, RdGy-5, RdGy-6,
RdGy-7, RdGy-8, RdGy-9, RdPu, RdPu-3, RdPu-4, RdPu-5, RdPu-6, RdPu-7, RdPu-8,
RdPu-9, RdYlBu, RdYlBu-10, RdYlBu-11, RdYlBu-3, RdYlBu-4, RdYlBu-5, RdYlBu-6,
RdYlBu-7, RdYlBu-8, RdYlBu-9, RdYlGn, RdYlGn-10, RdYlGn-11, RdYlGn-3,
RdYlGn-4, RdYlGn-5, RdYlGn-6, RdYlGn-7, RdYlGn-8, RdYlGn-9, red-white-blue,
redblue, Reds, Reds-3, Reds-4, Reds-5, Reds-6, Reds-7, Reds-8, Reds-9, Set1,
Set1-3, Set1-4, Set1-5, Set1-6, Set1-7, Set1-8, Set1-9, Set2, Set2-3, Set2-4,
Set2-5, Set2-6, Set2-7, Set2-8, Set3, Set3-10, Set3-11, Set3-12, Set3-3,
Set3-4, Set3-5, Set3-6, Set3-7, Set3-8, Set3-9, Spectral, Spectral-10,
Spectral-11, Spectral-3, Spectral-4, Spectral-5, Spectral-6, Spectral-7,
Spectral-8, Spectral-9, YlGn, YlGn-3, YlGn-4, YlGn-5, YlGn-6, YlGn-7, YlGn-8,
YlGn-9, YlGnBu, YlGnBu-3, YlGnBu-4, YlGnBu-5, YlGnBu-6, YlGnBu-7, YlGnBu-8,
YlGnBu-9, YlOrBr, YlOrBr-3, YlOrBr-4, YlOrBr-5, YlOrBr-6, YlOrBr-7, YlOrBr-8,
YlOrBr-9, YlOrRd, YlOrRd-3, YlOrRd-4, YlOrRd-5, YlOrRd-6, YlOrRd-7, and
YlOrRd-8.
> key #e1883a:0 #f4ed51:51 #5fcced:71 #326bf6:91 #0000f5:100 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> color byattribute a:bfactor #1,4 target abcs palette
> 0,#e1883a:50.6124,#f4ed51:70.8574,#5fcced:91.1023,#326bf6:100,#0000f5
14104 atoms, 1792 residues, atom bfactor range 6.12 to 98.8
> ui tool show "Render/Select by Attribute"
> key #e1883a:0.0 #f4ed51:50.0 #5fcced:68.0 #326bf6:89.3 showTool true
> ui mousemode right "color key"
Window position QRect(935,1054 100x30) outside any known screen, using primary
screen
> key #e1883a:0.0 #f4ed51:50.0 #5fcced:68.0 #326bf6:
> key #e1883a:0.0 #f4ed51:50.0 #5fcced:68.0 #326bf6:9
> key #e1883a:0.0 #f4ed51:50.0 #5fcced:68.0 #326bf6:90
> key #e1883a:0.0 #f4ed51:50.0 #5fcced: #326bf6:90
> key #e1883a:0.0 #f4ed51:50.0 #5fcced:7 #326bf6:90
> key #e1883a:0.0 #f4ed51:50.0 #5fcced:70 #326bf6:90
> key #e1883a:0.0 #f4ed51:50. #5fcced:70 #326bf6:90
> key #e1883a:0.0 #f4ed51:50 #5fcced:70 #326bf6:90
> key #e1883a:0. #f4ed51:50 #5fcced:70 #326bf6:90
> key #e1883a:0 #f4ed51:50 #5fcced:70 #326bf6:90
> key #e1883a: #f4ed51:50 #5fcced:70 #326bf6:90
> ui mousemode right translate
> hide #2 models
> hide #1 models
> show #3 models
> ui tool show Matchmaker
No reference and/or match structure/chain chosen
> ui tool show Matchmaker
> matchmaker #4 to #3
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 Aligned Kh.pdb, chain A (#3) with AF-O75113-F1-model_v4.pdb, chain
A (#4), sequence alignment score = 949.3
RMSD between 173 pruned atom pairs is 0.557 angstroms; (across all 188 pairs:
1.458)
> matchmaker #4 to #3
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 Aligned Kh.pdb, chain A (#3) with AF-O75113-F1-model_v4.pdb, chain
A (#4), sequence alignment score = 949.3
RMSD between 173 pruned atom pairs is 0.557 angstroms; (across all 188 pairs:
1.458)
> hide #4 models
> show #1 models
> hide #1 models
> hide #3 models
> show #4 models
> show #1 models
> select clear
> show #3 models
> hide #3 models
> hide #4 models
> hide #1 models
> show #1 models
> show #3 models
> show #4 models
> save "/Users/niltonarandaneto/Documents/untitled folder/AF-colour-N4BP1.cxs"
> open "/Users/niltonarandaneto/Documents/untitled folder/Coloured N4BP1.cxs"
opened ChimeraX session
> hide #2 models
> show #2 models
> hide #2 models
> open "/Users/niltonarandaneto/Documents/untitled folder/AF-colour-N4BP1.cxs"
opened ChimeraX session
> select #1/A#3/A
8592 atoms, 8654 bonds, 1190 residues, 2 models selected
> select subtract #1
1540 atoms, 1457 bonds, 294 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #1
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select subtract #1
Nothing selected
> combine
Remapping chain ID 'A' in Aligned Kh.pdb #3 to 'B'
Remapping chain ID 'A' in AF-O75113-F1-model_v4.pdb #4 to 'C'
> hide #4 models
> hide #3 models
> hide #1 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> close #5
> show #4 models
> hide #4 models
> select add #1
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> show #1 models
> hide #1 models
> combine
Remapping chain ID 'A' in Aligned Kh.pdb #3 to 'B'
Remapping chain ID 'A' in AF-O75113-F1-model_v4.pdb #4 to 'C'
> combine refspec 1
Expected a keyword
> combine refspec #1
Expected a keyword
> combine #1
> hide #5 models
> hide #6 models
> show #6 models
> hide #6 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #6 models
> close #5, #6
Expected a models specifier or a keyword
> close #5
> close #6
> show #2 models
> show #1 models
> hide #2 models
> hide #1 models
> select subtract #1
Nothing selected
> show #2 models
> show #1 models
> hide #2 models
> hide #1 models
> show #4 models
> hide #4 models
> show #1 models
> show #2 models
> save "/Users/niltonarandaneto/Documents/untitled folder/Working Session.cxs"
> hide #2 models
> hide #1 models
> show #1 models
> show #2 models
> hide #2 models
> show #2 models
> combine #1 name Coloured N4BP1 Monomer
Expected a keyword
> combine #1
> hide #2 models
> hide #1 models
> select add #5
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> color sel light gray
> open "/Users/niltonarandaneto/Documents/untitled
> folder/fold_n4bp1_human_full_dimer/fold_n4bp1_human_full_dimer_model_0.cif"
Chain information for fold_n4bp1_human_full_dimer_model_0.cif #6
---
Chain | Description
A B | .
> hide #5 models
> select add #6
21156 atoms, 21591 bonds, 2688 residues, 2 models selected
> color (#6 & sel) dark gray
> select subtract #5
14104 atoms, 14394 bonds, 1792 residues, 1 model selected
> hide #6 models
> select subtract #6
Nothing selected
> select add #5
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select add #6
21156 atoms, 21591 bonds, 2688 residues, 2 models selected
> select subtract #6
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select subtract #5
Nothing selected
> show #5 models
> show #6 models
> hide #6 models
> select add #5
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> hide #5 models
No visible atoms, bonds, or surfaces selected
> show #5 models
> color sel dark gray
> hide #5 models
> select add #6
21156 atoms, 21591 bonds, 2688 residues, 2 models selected
> show #6 models
> show #5 models
> select subtract #6
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select subtract #5
Nothing selected
> log metadata #5
The model has no metadata
> log chains #5
Chain information for copy of n4bp1_human.pdb #5
---
Chain | Description
A | No description available
> log metadata #6
The model has no metadata
> log chains #6
Chain information for fold_n4bp1_human_full_dimer_model_0.cif #6
---
Chain | Description
A B | .
> select #6/A:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> show #1 models
> show #3 models
> show #4 models
> color /a:1-800 firebrick
> ui tool show "Change Chain IDs"
> select #6/A:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> log metadata #1
The model has no metadata
> log chains #1
Chain information for n4bp1_human.pdb #1
---
Chain | Description
A | No description available
> select #1/A:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel ZZZ
Chain IDs of 896 residues changed
> changechains sel ZZZ
Chain IDs of 0 residues changed
> log metadata #1
The model has no metadata
> log chains #1
Chain information for n4bp1_human.pdb #1
---
Chain | Description
ZZZ | No description available
> ui tool show "Change Chain IDs"
> changechains sel AF3
Chain IDs of 896 residues changed
> select subtract #1
Nothing selected
> select add #4
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> changechains sel AF2
Chain IDs of 896 residues changed
> log metadata #1
The model has no metadata
> log chains #1
Chain information for n4bp1_human.pdb #1
---
Chain | Description
AF3 | No description available
> log metadata #4
The model has no metadata
> log chains #4
Chain information for AF-O75113-F1-model_v4.pdb #4
---
Chain | Description
AF2 | NEDD4-binding protein 1
> select subtract #4
Nothing selected
> select add #3
1540 atoms, 1457 bonds, 294 residues, 1 model selected
> changechains sel Kh
Chain IDs of 294 residues changed
> select subtract #3
Nothing selected
> log metadata #3
The model has no metadata
> log chains #3
Chain information for Aligned Kh.pdb #3
---
Chain | Description
Kh | No description available
> log metadata #3
The model has no metadata
> log chains #3
Chain information for Aligned Kh.pdb #3
---
Chain | Description
Kh | No description available
> log metadata #5
The model has no metadata
> log chains #5
Chain information for copy of n4bp1_human.pdb #5
---
Chain | Description
A | No description available
> log metadata #5
The model has no metadata
> log chains #5
Chain information for copy of n4bp1_human.pdb #5
---
Chain | Description
A | No description available
> select add #5
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> changechains sel AF3C
Chain IDs of 896 residues changed
> select subtract #5
Nothing selected
> select add #6
14104 atoms, 14394 bonds, 1792 residues, 1 model selected
> changechains sel AF3Di
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (AF3Di/1/)
> log metadata #6
The model has no metadata
> log chains #6
Chain information for fold_n4bp1_human_full_dimer_model_0.cif #6
---
Chain | Description
A B | .
> select #6/A:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> changechains sel DiA
Chain IDs of 896 residues changed
> log metadata #6
The model has no metadata
> log chains #6
Chain information for fold_n4bp1_human_full_dimer_model_0.cif #6
---
Chain | Description
B DiA | .
> select #6/B:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel DiB
Chain IDs of 896 residues changed
> select add #6
14104 atoms, 14394 bonds, 1792 residues, 1 model selected
> log metadata #6
The model has no metadata
> log chains #6
Chain information for fold_n4bp1_human_full_dimer_model_0.cif #6
---
Chain | Description
DiA DiB | .
> hide #5 models
> hide #6 models
> hide #4 models
> hide #3 models
> select subtract #6
Nothing selected
> show #6 models
> hide #1 models
> show #5 models
> log metadata #5
The model has no metadata
> log chains #5
Chain information for copy of n4bp1_human.pdb #5
---
Chain | Description
AF3C | No description available
> color /AF3C:6-143,DiA:6-143,DiB:6-143 firebrick
> log metadata #6
The model has no metadata
> log chains #6
Chain information for fold_n4bp1_human_full_dimer_model_0.cif #6
---
Chain | Description
DiA DiB | .
> log metadata #6
The model has no metadata
> log chains #6
Chain information for fold_n4bp1_human_full_dimer_model_0.cif #6
---
Chain | Description
DiA DiB | .
> hide #5 models
> select #6/DiA:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select add #6
14104 atoms, 14394 bonds, 1792 residues, 1 model selected
> select subtract #6
Nothing selected
> color /DiB:6-143 firebrick
> color /AF3C:6-143,DiA:6-143,DiB:6-143 firebrick
> color /AF3C:6-143, DiA:6-143, DiB:6-143 firebrick
> color /DiB:6-143 firebrick
> color /DiA:6-143 firebrick
> show #5 models
> color /AF3C:155-195 yellow
> color /DiB:155-195 yellow
> color /DiA:155-195 yellow
> color /AF3C:343-398 firebrick
> color /AF3C:6-143, DiA:6-143, DiB:6-143 cornflower blue
> show #5 models
> color /DiA:6-143 cornflower blue
> color /DiB:6-143 cornflower blue
> color /DiA:155-195 yellow
> color /DiB:155-195 yellow
> color /DiA:155-195 yellow
> color /DiB:155-195 yellow
> color /AF3C:155-195 yellow
> color /AF3C:343-398 firebrick
> color /DiB:343-398 firebrick
> color /DiA:343-398 firebrick
> color /DiA:591-773 orange
> color /DiB:591-773 orange
> color /AF3C:591-773 orange
> color /AF3C:850-893 FOREST green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /AF3C:850-893 forest green
> color /DiA:850-893 forest green
> color /DiB:850-893 forest green
> ui tool show Matchmaker
> matchmaker #6 to #5
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 copy of n4bp1_human.pdb, chain AF3C (#5) with
fold_n4bp1_human_full_dimer_model_0.cif, chain DiB (#6), sequence alignment
score = 4382
RMSD between 5 pruned atom pairs is 1.101 angstroms; (across all 896 pairs:
55.643)
> matchmaker #6 to #5
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 copy of n4bp1_human.pdb, chain AF3C (#5) with
fold_n4bp1_human_full_dimer_model_0.cif, chain DiB (#6), sequence alignment
score = 4382
RMSD between 5 pruned atom pairs is 1.101 angstroms; (across all 896 pairs:
55.643)
> undo
> redo
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #6 models
> show #6 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> ui tool show Matchmaker
> matchmaker #5 to #6
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 fold_n4bp1_human_full_dimer_model_0.cif, chain DiB (#6) with copy
of n4bp1_human.pdb, chain AF3C (#5), sequence alignment score = 4382
RMSD between 5 pruned atom pairs is 1.101 angstroms; (across all 896 pairs:
55.643)
> matchmaker #5 to #6
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 fold_n4bp1_human_full_dimer_model_0.cif, chain DiB (#6) with copy
of n4bp1_human.pdb, chain AF3C (#5), sequence alignment score = 4382
RMSD between 5 pruned atom pairs is 1.101 angstroms; (across all 896 pairs:
55.643)
> hide #6 models
> hide #5 models
> show #6 models
> show #5 models
> hide #5 models
> hide #6 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #1 models
> hide #1 models
> show #5 models
> show #6 models
> hide #5 models
> hide #6 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #1 models
> show #4 models
> hide #4 models
> hide #1 models
> combine #4
> color #7 dark gray
> hide #7 models
> show #7 models
> log metadata #1
The model has no metadata
> log chains #1
Chain information for n4bp1_human.pdb #1
---
Chain | Description
AF3 | No description available
> log metadata #3
The model has no metadata
> log chains #3
Chain information for Aligned Kh.pdb #3
---
Chain | Description
Kh | No description available
> log metadata #4
The model has no metadata
> log chains #4
Chain information for AF-O75113-F1-model_v4.pdb #4
---
Chain | Description
AF2 | NEDD4-binding protein 1
> log metadata #5
The model has no metadata
> log chains #5
Chain information for copy of n4bp1_human.pdb #5
---
Chain | Description
AF3C | No description available
> log metadata #6
The model has no metadata
> log chains #6
Chain information for fold_n4bp1_human_full_dimer_model_0.cif #6
---
Chain | Description
DiA DiB | .
> log metadata #7
The model has no metadata
> log chains #7
Chain information for copy of AF-O75113-F1-model_v4.pdb #7
---
Chain | Description
AF2 | No description available
> select #7/AF2:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel AF2C
Chain IDs of 896 residues changed
> select up
43852 atoms, 44639 bonds, 5670 residues, 6 models selected
> select up
43852 atoms, 44639 bonds, 5670 residues, 6 models selected
> select down
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select down
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> color /AF2:850-893 forest green
> hide #7 models
> undo
> show #4 models
> hide #4 models
> show #4 models
> hide #7 models
> select subtract #7
Nothing selected
> undo
> hide #7 models
> select subtract #7
Nothing selected
> undo
> hide #7 models
> select subtract #7
Nothing selected
> select add #7
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> show #4 models
> select subtract #7
Nothing selected
> hide #4 models
> show #5 models
> show #6 models
> hide #6 models
> hide #5 models
> show #7 models
> color /AF2C:850-893 forest green
> color /AF2C:591-773 orange
> color /AF2C:343-398 firebrick
> color /AF2C:155-195 yellow
> color /AF2C:6-143 cornflower blue
> show #5 models
> hide #5 models
> show #5 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> hide #5 models
> show #6 models
> show #5 models
> hide #5 models
> hide #6 models
> show #6 models
> hide #6 models
> show #7 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #7 models
> show #5 models
> show #6 models
> hide #6 models
> hide #5 models
> show #5 models
> show #6 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #6 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #5 models
> log metadata #5
The model has no metadata
> log chains #5
Chain information for copy of n4bp1_human.pdb #5
---
Chain | Description
AF3C | No description available
> ui tool show "Change Chain IDs"
> select #5/AF3C:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> changechains sel AF3C_0
Chain IDs of 896 residues changed
> log metadata #1
The model has no metadata
> log chains #1
Chain information for n4bp1_human.pdb #1
---
Chain | Description
AF3 | No description available
> log metadata #3
The model has no metadata
> log chains #3
Chain information for Aligned Kh.pdb #3
---
Chain | Description
Kh | No description available
> log metadata #4
The model has no metadata
> log chains #4
Chain information for AF-O75113-F1-model_v4.pdb #4
---
Chain | Description
AF2 | NEDD4-binding protein 1
> log metadata #5
The model has no metadata
> log chains #5
Chain information for copy of n4bp1_human.pdb #5
---
Chain | Description
AF3C_0 | No description available
> log metadata #6
The model has no metadata
> log chains #6
Chain information for fold_n4bp1_human_full_dimer_model_0.cif #6
---
Chain | Description
DiA DiB | .
> log metadata #7
The model has no metadata
> log chains #7
Chain information for copy of AF-O75113-F1-model_v4.pdb #7
---
Chain | Description
AF2C | No description available
> log metadata #5
The model has no metadata
> log chains #5
Chain information for copy of n4bp1_human.pdb #5
---
Chain | Description
AF3C_0 | No description available
> log metadata #5
The model has no metadata
> log chains #5
Chain information for copy of n4bp1_human.pdb #5
---
Chain | Description
AF3C_0 | No description available
> open "/Users/niltonarandaneto/Documents/untitled
> folder/fold_n4bp1_human_full_dimer/fold_n4bp1_human_full_dimer_model_1.cif"
Chain information for fold_n4bp1_human_full_dimer_model_1.cif #8
---
Chain | Description
A B | .
> open "/Users/niltonarandaneto/Documents/untitled
> folder/fold_n4bp1_human_full_dimer/fold_n4bp1_human_full_dimer_model_2.cif"
Chain information for fold_n4bp1_human_full_dimer_model_2.cif #9
---
Chain | Description
A B | .
> open "/Users/niltonarandaneto/Documents/untitled
> folder/fold_n4bp1_human_full_dimer/fold_n4bp1_human_full_dimer_model_3.cif"
Chain information for fold_n4bp1_human_full_dimer_model_3.cif #10
---
Chain | Description
A B | .
> open "/Users/niltonarandaneto/Documents/untitled
> folder/fold_n4bp1_human_full_dimer/fold_n4bp1_human_full_dimer_model_4.cif"
Chain information for fold_n4bp1_human_full_dimer_model_4.cif #11
---
Chain | Description
A B | .
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #5 models
> select subtract #5
Nothing selected
> select add #8
14104 atoms, 14394 bonds, 1792 residues, 1 model selected
> select add #9
28208 atoms, 28788 bonds, 3584 residues, 2 models selected
> select add #10
42312 atoms, 43182 bonds, 5376 residues, 3 models selected
> select add #11
56416 atoms, 57576 bonds, 7168 residues, 4 models selected
> combine #5,#8,#9,#10,#11
Expected a keyword
> combine #5, #8, #9 #10, #11
Expected a keyword
> combine #5, #8, #9 #10, #11
Expected a keyword
> combine #5
> close #12
> select add #11
56416 atoms, 57576 bonds, 7168 residues, 4 models selected
> show #11 models
> show #10 models
> show #9 models
> show #8 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> close #11
> close #10
> close #9
> close #8
> open "/Users/niltonarandaneto/Documents/untitled
> folder/fold_n4bp1_human_full/fold_n4bp1_human_full_model_1.cif"
Chain information for fold_n4bp1_human_full_model_1.cif #8
---
Chain | Description
A | .
> open "/Users/niltonarandaneto/Documents/untitled
> folder/fold_n4bp1_human_full/fold_n4bp1_human_full_model_4.cif"
Chain information for fold_n4bp1_human_full_model_4.cif #9
---
Chain | Description
A | .
> open "/Users/niltonarandaneto/Documents/untitled
> folder/fold_n4bp1_human_full/fold_n4bp1_human_full_model_3.cif"
Chain information for fold_n4bp1_human_full_model_3.cif #10
---
Chain | Description
A | .
> open "/Users/niltonarandaneto/Documents/untitled
> folder/fold_n4bp1_human_full/fold_n4bp1_human_full_model_2.cif"
Chain information for fold_n4bp1_human_full_model_2.cif #11
---
Chain | Description
A | .
> hide #11 models
> hide #10 models
> hide #9 models
> hide #8 models
> show #8 models
> hide #8 models
> select add #11
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select add #10
14104 atoms, 14394 bonds, 1792 residues, 2 models selected
> select add #9
21156 atoms, 21591 bonds, 2688 residues, 3 models selected
> select add #8
28208 atoms, 28788 bonds, 3584 residues, 4 models selected
> select add #5
35260 atoms, 35985 bonds, 4480 residues, 5 models selected
> combine
Remapping chain ID 'A' in fold_n4bp1_human_full_model_4.cif #9 to 'B'
Remapping chain ID 'A' in fold_n4bp1_human_full_model_3.cif #10 to 'C'
Remapping chain ID 'A' in fold_n4bp1_human_full_model_2.cif #11 to 'D'
> show #11 models
> hide #11 models
> select subtract #11
28208 atoms, 28788 bonds, 3584 residues, 4 models selected
> select subtract #10
21156 atoms, 21591 bonds, 2688 residues, 3 models selected
> select subtract #9
14104 atoms, 14394 bonds, 1792 residues, 2 models selected
> select subtract #8
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select subtract #5
Nothing selected
> log metadata #12
The model has no metadata
> log chains #12
Chain information for combination #12
---
Chain | Description | UniProt
A B C D DiA DiB | . | N4BP1_HUMAN 1-896
AF2 | NEDD4-binding protein 1 |
AF2C AF3 AF3C_0 | No description available |
Kh | No description available |
> select #12/A:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select #12/AF2:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> hide #12 models
> show #1 models
> hide #1 models
> show #12 models
> select #12/A:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> delete
Missing or invalid "atoms" argument: empty atom specifier
> select #12/A:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select #12/A:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> log metadata #12
The model has no metadata
> log chains #12
Chain information for combination #12
---
Chain | Description
AF2 | NEDD4-binding protein 1
AF2C AF3 AF3C_0 | No description available
B C D DiA DiB | .
Kh | No description available
> clear #12
Unknown command: clear #12
> close #12
> combine #11 & #8
No structures specified
> combine #11 & 8
Expected a keyword
> combine #11 & #8
No structures specified
> show #11 models
> show #9 models
> combine #11 & #8
No structures specified
> select add #11
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select add #9
14104 atoms, 14394 bonds, 1792 residues, 2 models selected
> combine #11 & #8
No structures specified
> select subtract #11
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> hide #11 models
> show #8 models
> hide #9 models
> hide #8 models
> select subtract #9
Nothing selected
> combine #8-11
Remapping chain ID 'A' in fold_n4bp1_human_full_model_4.cif #9 to 'B'
Remapping chain ID 'A' in fold_n4bp1_human_full_model_3.cif #10 to 'C'
Remapping chain ID 'A' in fold_n4bp1_human_full_model_2.cif #11 to 'D'
> log metadata #1
The model has no metadata
> log chains #1
Chain information for n4bp1_human.pdb #1
---
Chain | Description
AF3 | No description available
> log metadata #3
The model has no metadata
> log chains #3
Chain information for Aligned Kh.pdb #3
---
Chain | Description
Kh | No description available
> log metadata #4
The model has no metadata
> log chains #4
Chain information for AF-O75113-F1-model_v4.pdb #4
---
Chain | Description
AF2 | NEDD4-binding protein 1
> log metadata #5
The model has no metadata
> log chains #5
Chain information for copy of n4bp1_human.pdb #5
---
Chain | Description
AF3C_0 | No description available
> log metadata #6
The model has no metadata
> log chains #6
Chain information for fold_n4bp1_human_full_dimer_model_0.cif #6
---
Chain | Description
DiA DiB | .
> log metadata #7
The model has no metadata
> log chains #7
Chain information for copy of AF-O75113-F1-model_v4.pdb #7
---
Chain | Description
AF2C | No description available
> log metadata #8
The model has no metadata
> log chains #8
Chain information for fold_n4bp1_human_full_model_1.cif #8
---
Chain | Description
A | .
> log metadata #9
The model has no metadata
> log chains #9
Chain information for fold_n4bp1_human_full_model_4.cif #9
---
Chain | Description
A | .
> log metadata #10
The model has no metadata
> log chains #10
Chain information for fold_n4bp1_human_full_model_3.cif #10
---
Chain | Description
A | .
> log metadata #11
The model has no metadata
> log chains #11
Chain information for fold_n4bp1_human_full_model_2.cif #11
---
Chain | Description
A | .
> log metadata #12
The model has no metadata
> log chains #12
Chain information for combination #12
---
Chain | Description
A B C D | .
> combine #12,#11
Expected a keyword
> combine #12,#11
Expected a keyword
> combine #12,#11
Expected a keyword
> combine #12,#11
Expected a keyword
> combine #12,#6
Expected a keyword
> combine #12, #6
Expected a keyword
> combine #12&6
Expected a keyword
> combine #12,6
> hide #12 models
> log metadata #1
The model has no metadata
> log chains #1
Chain information for n4bp1_human.pdb #1
---
Chain | Description
AF3 | No description available
> log metadata #3
The model has no metadata
> log chains #3
Chain information for Aligned Kh.pdb #3
---
Chain | Description
Kh | No description available
> log metadata #4
The model has no metadata
> log chains #4
Chain information for AF-O75113-F1-model_v4.pdb #4
---
Chain | Description
AF2 | NEDD4-binding protein 1
> log metadata #5
The model has no metadata
> log chains #5
Chain information for copy of n4bp1_human.pdb #5
---
Chain | Description
AF3C_0 | No description available
> log metadata #6
The model has no metadata
> log chains #6
Chain information for fold_n4bp1_human_full_dimer_model_0.cif #6
---
Chain | Description
DiA DiB | .
> log metadata #7
The model has no metadata
> log chains #7
Chain information for copy of AF-O75113-F1-model_v4.pdb #7
---
Chain | Description
AF2C | No description available
> log metadata #8
The model has no metadata
> log chains #8
Chain information for fold_n4bp1_human_full_model_1.cif #8
---
Chain | Description
A | .
> log metadata #9
The model has no metadata
> log chains #9
Chain information for fold_n4bp1_human_full_model_4.cif #9
---
Chain | Description
A | .
> log metadata #10
The model has no metadata
> log chains #10
Chain information for fold_n4bp1_human_full_model_3.cif #10
---
Chain | Description
A | .
> log metadata #11
The model has no metadata
> log chains #11
Chain information for fold_n4bp1_human_full_model_2.cif #11
---
Chain | Description
A | .
> log metadata #12
The model has no metadata
> log chains #12
Chain information for combination #12
---
Chain | Description
A B C D | .
> log metadata #13
The model has no metadata
> log chains #13
Chain information for combination #13
---
Chain | Description
A B C D DiA DiB | .
> hide #13 models
> close #13
> combine #5&8-11
Expected a keyword
> combine #5,8-11
Remapping chain ID 'A' in fold_n4bp1_human_full_model_4.cif #9 to 'B'
Remapping chain ID 'A' in fold_n4bp1_human_full_model_3.cif #10 to 'C'
Remapping chain ID 'A' in fold_n4bp1_human_full_model_2.cif #11 to 'D'
> log metadata #1
The model has no metadata
> log chains #1
Chain information for n4bp1_human.pdb #1
---
Chain | Description
AF3 | No description available
> log metadata #3
The model has no metadata
> log chains #3
Chain information for Aligned Kh.pdb #3
---
Chain | Description
Kh | No description available
> log metadata #4
The model has no metadata
> log chains #4
Chain information for AF-O75113-F1-model_v4.pdb #4
---
Chain | Description
AF2 | NEDD4-binding protein 1
> log metadata #5
The model has no metadata
> log chains #5
Chain information for copy of n4bp1_human.pdb #5
---
Chain | Description
AF3C_0 | No description available
> log metadata #6
The model has no metadata
> log chains #6
Chain information for fold_n4bp1_human_full_dimer_model_0.cif #6
---
Chain | Description
DiA DiB | .
> log metadata #7
The model has no metadata
> log chains #7
Chain information for copy of AF-O75113-F1-model_v4.pdb #7
---
Chain | Description
AF2C | No description available
> log metadata #8
The model has no metadata
> log chains #8
Chain information for fold_n4bp1_human_full_model_1.cif #8
---
Chain | Description
A | .
> log metadata #9
The model has no metadata
> log chains #9
Chain information for fold_n4bp1_human_full_model_4.cif #9
---
Chain | Description
A | .
> log metadata #10
The model has no metadata
> log chains #10
Chain information for fold_n4bp1_human_full_model_3.cif #10
---
Chain | Description
A | .
> log metadata #11
The model has no metadata
> log chains #11
Chain information for fold_n4bp1_human_full_model_2.cif #11
---
Chain | Description
A | .
> log metadata #12
The model has no metadata
> log chains #12
Chain information for combination #12
---
Chain | Description
A B C D | .
> log metadata #13
The model has no metadata
> log chains #13
Chain information for combination #13
---
Chain | Description
A B C D | .
AF3C_0 | No description available
> close #12-13
> combine #5,8-11
Remapping chain ID 'A' in fold_n4bp1_human_full_model_4.cif #9 to 'B'
Remapping chain ID 'A' in fold_n4bp1_human_full_model_3.cif #10 to 'C'
Remapping chain ID 'A' in fold_n4bp1_human_full_model_2.cif #11 to 'D'
> split #12
Split combination (#12) into 5 models
Chain information for combination A #12.1
---
Chain | Description
A | No description available
Chain information for combination AF3C_0 #12.2
---
Chain | Description
AF3C_0 | No description available
Chain information for combination B #12.3
---
Chain | Description
B | No description available
Chain information for combination C #12.4
---
Chain | Description
C | No description available
Chain information for combination D #12.5
---
Chain | Description
D | No description available
> hide #!12 models
> hide #12.1 models
> show #12.1 models
> hide #12.1 models
> hide #12.2 models
> hide #12.3 models
> hide #12.4 models
> show #12.4 models
> hide #12.5 models
> hide #12.4 models
> show #12.2 models
> hide #12.2 models
> show #12.2 models
> mcopy #12.2 #12.1
Missing required "to_atoms" argument
> mcopy #12.2 #12.1
Missing required "to_atoms" argument
> hide #12.2 models
> show #12.1 models
> show #12.3 models
> mcopy /a /b
Missing required "to_atoms" argument
> mcopy /a:1-896 /b:1-896
Missing required "to_atoms" argument
> mcopy
Missing or invalid "fromAtoms" argument: empty atom specifier
> select add #12.1
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> mcopy
Missing or invalid "fromAtoms" argument: empty atom specifier
> mcopy #12.1 toAtoms #12.3
> mcopy #12.1 toAtoms #12.3 setttings c
Expected a keyword
> mcopy #12.1 toAtoms #12.3 setttingsc
Expected a keyword
> mcopy #12.1 toAtoms #12.3 setttings [c]
Expected a keyword
> mcopy #12.1 toAtoms #12.3 [c]
Expected a keyword
> mcopy #12.1 toAtoms #12.3 c
Expected a keyword
> mcopy #12.1 toAtoms #12.3 settings csvc
> mcopy #12.1 toAtoms #12.3 settings csvc matchResidues true
> select subtract #12.1
Nothing selected
> mcopy #12.1 toAtoms #12.3 settings csvc matchResidues true
> mcopy #12.2 toAtoms #12.1 settings csvc matchResidues true
> hide #12.3 models
> show #12.2 models
> show #12.1 models
> hide #12.1 models
> hide #12.2 models
> hide #12.1 models
> show #12.3 models
> color /A:155-195&B:155-195&C:155-195&D:155-195 yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /A:155-195yellow
> color /A:155-195 yellow
> hide #12.3 models
> show #1 models
> show #2 models
> show #4 models
> hide #!12 models
> show #!12 models
> hide #4 models
> hide #2 models
> hide #1 models
> show #12.1 models
> show #12.2 models
> show #12.3 models
> show #12.4 models
> show #12.5 models
> hide #12.3 models
> hide #12.4 models
> hide #12.5 models
> hide #12.1 models
> hide #12.2 models
> show #6 models
> show #12.2 models
> hide #!12 models
> hide #12.2 models
> show #5 models
> hide #6 models
> hide #5 models
> show #6 models
> show #7 models
> hide #6 models
> hide #7 models
> show #7 models
> hide #7 models
> show #6 models
> show #6 atoms
> log metadata #6
The model has no metadata
> log chains #6
Chain information for fold_n4bp1_human_full_dimer_model_0.cif #6
---
Chain | Description
DiA DiB | .
> select #6/DiB:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select #6/DiB:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select clear
> color #6 byhetero
> coulombic #6
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_n4bp1_human_full_dimer_model_0.cif_DiA SES surface
#6.1: minimum, -22.02, mean -2.71, maximum 14.11
Coulombic values for fold_n4bp1_human_full_dimer_model_0.cif_DiB SES surface
#6.2: minimum, -30.22, mean -2.67, maximum 14.57
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> coulombic #!6
Coulombic values for fold_n4bp1_human_full_dimer_model_0.cif_DiA SES surface
#6.1: minimum, -22.02, mean -2.71, maximum 14.11
Coulombic values for fold_n4bp1_human_full_dimer_model_0.cif_DiB SES surface
#6.2: minimum, -30.22, mean -2.67, maximum 14.57
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!6 surfaces
> hbonds #!6 reveal true
2291 hydrogen bonds found
> mlp #!6
Map values for surface "fold_n4bp1_human_full_dimer_model_0.cif_DiA SES
surface": minimum -29.59, mean -5.271, maximum 23.26
Map values for surface "fold_n4bp1_human_full_dimer_model_0.cif_DiB SES
surface": minimum -29.9, mean -5.253, maximum 22.53
To also show corresponding color key, enter the above mlp command and add key
true
> ui tool show "Side View"
> hide #!6 surfaces
> hide #13 models
> ui tool show "Render/Select by Attribute"
> hide #!6 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #1 models
> show #4 models
> ui tool show Matchmaker
> hide #4 models
> hide #1 models
> show #3 models
> hide #3 models
> show #3 models
> show #1 models
> show #4 models
> show #2 models
> show #5 models
> show #!6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #!12 models
> show #13 models
> hide #1,3-5,7-11#!6 atoms
> hide #1 models
> hide #2 models
> hide #4 models
> hide #3 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
> show #10 models
> hide #10 models
> show #9 models
> color #9 /DiB:850-893 forest green
> hide #6.2 models
> hide #6.1 models
> show #6.2 models
> hide #6.2 models
> hide #9 models
> hide #!6 models
> show #6.1 models
> undo
> hide #9 models
> show #12.1 models
> show #12.3 models
> show #12.4 models
> show #12.5 models
> color #12.1 #12.3 dark gray
> color #12.1 #12.3 /A,B:1-200 dark gray
> color #12.1 #12.3 /A,B:1-200 green
> hide #12.3 models
> hide #12.4 models
> hide #12.5 models
> show #12.3 models
> hide #12.3 models
> color #12.1 #12.3 /A,B:1-200 gray
> color /A,B:1-200 gray
> log metadata #12.1
The model has no metadata
> log chains #12.1
Chain information for combination A #12.1
---
Chain | Description
A | No description available
> log metadata #12.3
The model has no metadata
> log chains #12.3
Chain information for combination B #12.3
---
Chain | Description
B | No description available
> show #12.3 models
> color /A,B:1-200 green
> hide #12.3 models
> hide #12.1 models
> hide #!12 models
> show #7 models
> hide #7 models
> show #!6 models
> ui tool show "Scale Bar"
> scalebar
> scalebar off
> toolshed show
> ui tool show "Side View"
> show #12.1 models
> hide #!6 models
> select add #12.1
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> color sel dark gray
> ui tool show "Change Chain IDs"
> log metadata #12.1
The model has no metadata
> log chains #12.1
Chain information for combination A #12.1
---
Chain | Description
A | No description available
> select #12.1/A:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> changechains sel A1
Chain IDs of 896 residues changed
> log metadata #12.2
The model has no metadata
> log chains #12.2
Chain information for combination AF3C_0 #12.2
---
Chain | Description
AF3C_0 | No description available
> select #12.2//chain_id='AF3C_0':1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select #12.2//chain_id='AF3C_0':1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select #12.2//chain_id='AF3C_0':1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> hide #12.1 models
> show #12.2 models
> show #12.1 models
> hide #12.2 models
> select subtract #12.2
Nothing selected
> show #12.3 models
> hide #12.1 models
> show #12.4 models
> show #12.5 models
> select add #12.3
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select add #12.4
14104 atoms, 14394 bonds, 1792 residues, 2 models selected
> select subtract #12.4
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select add #12.4
14104 atoms, 14394 bonds, 1792 residues, 2 models selected
> select add #12.5
21156 atoms, 21591 bonds, 2688 residues, 3 models selected
> color sel dark gray
> select add #1
28208 atoms, 28788 bonds, 3584 residues, 4 models selected
> select add #2
28208 atoms, 28788 bonds, 3584 residues, 5 models selected
> select add #3
29748 atoms, 30245 bonds, 3878 residues, 6 models selected
> select add #4
36800 atoms, 37442 bonds, 4774 residues, 7 models selected
> select add #5
43852 atoms, 44639 bonds, 5670 residues, 8 models selected
> select add #6
57956 atoms, 59033 bonds, 1017 pseudobonds, 7462 residues, 10 models selected
> select add #7
65008 atoms, 66230 bonds, 1017 pseudobonds, 8358 residues, 13 models selected
> select add #8
72060 atoms, 73427 bonds, 1017 pseudobonds, 9254 residues, 14 models selected
> select add #9
79112 atoms, 80624 bonds, 1017 pseudobonds, 10150 residues, 15 models selected
> select add #10
86164 atoms, 87821 bonds, 1017 pseudobonds, 11046 residues, 16 models selected
> select add #11
93216 atoms, 95018 bonds, 1017 pseudobonds, 11942 residues, 17 models selected
> select add #12.1
100268 atoms, 102215 bonds, 1017 pseudobonds, 12838 residues, 18 models
selected
> select add #12.2
107320 atoms, 109412 bonds, 1017 pseudobonds, 13734 residues, 19 models
selected
> select add #12
107320 atoms, 109412 bonds, 1017 pseudobonds, 13734 residues, 20 models
selected
> select add #13
107320 atoms, 109412 bonds, 2291 pseudobonds, 13734 residues, 20 models
selected
> select subtract #13
107320 atoms, 109412 bonds, 13734 residues, 19 models selected
> hide sel & #12.3-5 atoms
> select clear
> hide #12.5 models
> hide #12.4 models
> hide #12.3 models
> show #11 models
> hide #!12 models
> hide #11 models
> show #!12 models
> close #8-11
> show #12.2 models
> hide #12.2 models
> show #12.1 models
> log metadata #12.2
The model has no metadata
> log chains #12.2
Chain information for combination AF3C_0 #12.2
---
Chain | Description
AF3C_0 | No description available
> log metadata #12.1
The model has no metadata
> log chains #12.1
Chain information for combination A #12.1
---
Chain | Description
A1 | No description available
> select #12.1/A1:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel AF3C_1
Chain IDs of 896 residues changed
> log metadata #12.1
The model has no metadata
> log chains #12.1
Chain information for combination A #12.1
---
Chain | Description
AF3C_1 | No description available
> ui tool show "Change Chain IDs"
> changechains sel AF3C_2
Chain IDs of 896 residues changed
> select subtract #12.1
Nothing selected
> log metadata #12.1
The model has no metadata
> log chains #12.1
Chain information for combination A #12.1
---
Chain | Description
AF3C_2 | No description available
> log metadata #12.3
The model has no metadata
> log chains #12.3
Chain information for combination B #12.3
---
Chain | Description
B | No description available
> log metadata #12.1
The model has no metadata
> log chains #12.1
Chain information for combination A #12.1
---
Chain | Description
AF3C_2 | No description available
> select #12.1//chain_id='AF3C_2':1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> select subtract #12.1
Nothing selected
> log metadata #12.3
The model has no metadata
> log chains #12.3
Chain information for combination B #12.3
---
Chain | Description
B | No description available
> select #12.3/B:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> changechains sel AF3C_2
Chain IDs of 896 residues changed
> log metadata #12.1
The model has no metadata
> log chains #12.1
Chain information for combination A #12.1
---
Chain | Description
AF3C_2 | No description available
> log metadata #12.3
The model has no metadata
> log chains #12.3
Chain information for combination B #12.3
---
Chain | Description
AF3C_2 | No description available
> log metadata #12.1
The model has no metadata
> log chains #12.1
Chain information for combination A #12.1
---
Chain | Description
AF3C_2 | No description available
> select #12.1//chain_id='AF3C_2':1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel AF3C_1
Chain IDs of 896 residues changed
> select subtract #12.1
Nothing selected
> show #12.4 models
> hide #12.1 models
> log metadata #12.4
The model has no metadata
> log chains #12.4
Chain information for combination C #12.4
---
Chain | Description
C | No description available
> select #12.4/C:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel AF3C_3
Chain IDs of 896 residues changed
> log metadata #12.4
The model has no metadata
> log chains #12.4
Chain information for combination C #12.4
---
Chain | Description
AF3C_3 | No description available
> log metadata #12.5
The model has no metadata
> log chains #12.5
Chain information for combination D #12.5
---
Chain | Description
D | No description available
> select #12.5/D:1-896
7052 atoms, 7197 bonds, 896 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel AF3C_4
Chain IDs of 896 residues changed
> changechains sel AF3C_4
Chain IDs of 0 residues changed
> log metadata #12.5
The model has no metadata
> log chains #12.5
Chain information for combination D #12.5
---
Chain | Description
AF3C_4 | No description available
> select subtract #12.5
Nothing selected
> show #12.5 models
> show #12.3 models
> show #12.2 models
> show #12.1 models
> ui tool show Matchmaker
> matchmaker #12.1,3-5 to #12.2
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 combination AF3C_0, chain AF3C_0 (#12.2) with combination A, chain
AF3C_1 (#12.1), sequence alignment score = 4484
RMSD between 206 pruned atom pairs is 0.821 angstroms; (across all 896 pairs:
45.990)
Matchmaker combination AF3C_0, chain AF3C_0 (#12.2) with combination B, chain
AF3C_2 (#12.3), sequence alignment score = 4487.6
RMSD between 181 pruned atom pairs is 0.161 angstroms; (across all 896 pairs:
58.759)
Matchmaker combination AF3C_0, chain AF3C_0 (#12.2) with combination C, chain
AF3C_3 (#12.4), sequence alignment score = 4472
RMSD between 26 pruned atom pairs is 1.300 angstroms; (across all 896 pairs:
46.319)
Matchmaker combination AF3C_0, chain AF3C_0 (#12.2) with combination D, chain
AF3C_4 (#12.5), sequence alignment score = 4449.2
RMSD between 189 pruned atom pairs is 0.308 angstroms; (across all 896 pairs:
50.568)
> matchmaker #12.1,3-5 to #12.2
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 combination AF3C_0, chain AF3C_0 (#12.2) with combination A, chain
AF3C_1 (#12.1), sequence alignment score = 4484
RMSD between 206 pruned atom pairs is 0.821 angstroms; (across all 896 pairs:
45.990)
Matchmaker combination AF3C_0, chain AF3C_0 (#12.2) with combination B, chain
AF3C_2 (#12.3), sequence alignment score = 4487.6
RMSD between 181 pruned atom pairs is 0.161 angstroms; (across all 896 pairs:
58.759)
Matchmaker combination AF3C_0, chain AF3C_0 (#12.2) with combination C, chain
AF3C_3 (#12.4), sequence alignment score = 4472
RMSD between 26 pruned atom pairs is 1.300 angstroms; (across all 896 pairs:
46.319)
Matchmaker combination AF3C_0, chain AF3C_0 (#12.2) with combination D, chain
AF3C_4 (#12.5), sequence alignment score = 4449.2
RMSD between 189 pruned atom pairs is 0.308 angstroms; (across all 896 pairs:
50.568)
> hide #12.3 models
> hide #12.4 models
> hide #12.5 models
> show #12.3 models
> hide #12.3 models
> hide #12.2 models
> log metadata #12.1
The model has no metadata
> log chains #12.1
Chain information for combination A #12.1
---
Chain | Description
AF3C_1 | No description available
> color /AFC_1:850-893 forest green
> color /AFC_1:591-773 orange
> color /AFC_1:343-398 firebrick
> color /AFC_1:155-195 yellow
> color /AFC_1:6-143 cornflower blue
> log metadata #12.1
The model has no metadata
> log chains #12.1
Chain information for combination A #12.1
---
Chain | Description
AF3C_1 | No description available
> color /AF3C_1:850-893 forest green
> color /AF3C_1:591-773 orange
> color /AF3C_1:343-398 firebrick
> color /AF3C_1:155-195 yellow
> color /AF3C_1:6-143 cornflower blue
> color /AF3C_2:850-893 forest green
> color /AF3C_2:591-773 orange
> color /AF3C_2:343-398 firebrick
> color /AF3C_2:155-195 yellow
> color /AF3C_2:6-143 cornflower blue
> show #12.3 models
> hide #12.3 models
> show #12.2 models
> show #12.3 models
> hide #12.1 models
> hide #12.2 models
> show #12.2 models
> hide #12.2 models
> hide #12.3 models
> show #12.5 models
> show #12.4 models
> hide #12.4 models
> hide #12.5 models
> show #12.1 models
> show #12.2 models
> show #12.3 models
> hide #12.3 models
> hide #12.2 models
> hide #12.1 models
> hide #!12 models
> show #1 models
> show #3 models
> show #4 models
> hide #4 models
> hide #3 models
> hide #1 models
> show #5 models
> show #4 models
> show #1 models
> show #3 models
> hide #3 models
> hide #1 models
> hide #4 models
> hide #5 models
> show #7 models
> hide #7 models
> show #12.1 models
> show #12.2 models
> hide #12.1 models
> hide #12.2 models
> show #12.2 models
> show #12.3 models
> ui tool show Matchmaker
> matchmaker #12.3 to #12.2
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 combination AF3C_0, chain AF3C_0 (#12.2) with combination B, chain
AF3C_2 (#12.3), sequence alignment score = 4487.6
RMSD between 181 pruned atom pairs is 0.161 angstroms; (across all 896 pairs:
58.759)
> matchmaker #12.3 to #12.2
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 combination AF3C_0, chain AF3C_0 (#12.2) with combination B, chain
AF3C_2 (#12.3), sequence alignment score = 4487.6
RMSD between 181 pruned atom pairs is 0.161 angstroms; (across all 896 pairs:
58.759)
> matchmaker #12.3 to #12.2
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 combination AF3C_0, chain AF3C_0 (#12.2) with combination B, chain
AF3C_2 (#12.3), sequence alignment score = 4487.6
RMSD between 181 pruned atom pairs is 0.161 angstroms; (across all 896 pairs:
58.759)
> matchmaker #12.3 to #12.2//chain_id='AF3C_0' pairing bs
Parameters
---
Chain pairing | bs
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 combination AF3C_0, chain AF3C_0 (#12.2) with combination B, chain
AF3C_2 (#12.3), sequence alignment score = 4487.6
RMSD between 181 pruned atom pairs is 0.161 angstroms; (across all 896 pairs:
58.759)
> matchmaker #12.3 to #12.2//chain_id='AF3C_0' pairing bs ssFraction 0.8088
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.8088
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 combination AF3C_0, chain AF3C_0 (#12.2) with combination B, chain
AF3C_2 (#12.3), sequence alignment score = 4218.95
RMSD between 181 pruned atom pairs is 0.161 angstroms; (across all 896 pairs:
58.759)
> matchmaker #12.3 to #12.2//chain_id='AF3C_0' pairing bs ssFraction 0.8088
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.8088
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 combination AF3C_0, chain AF3C_0 (#12.2) with combination B, chain
AF3C_2 (#12.3), sequence alignment score = 4218.95
RMSD between 181 pruned atom pairs is 0.161 angstroms; (across all 896 pairs:
58.759)
> matchmaker #12.3 to #12.2 ssFraction 1.0
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 1
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 combination AF3C_0, chain AF3C_0 (#12.2) with combination B, chain
AF3C_2 (#12.3), sequence alignment score = 4122
RMSD between 177 pruned atom pairs is 0.166 angstroms; (across all 892 pairs:
58.895)
> matchmaker #12.3 to #12.2 ssFraction 1.0
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 1
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 combination AF3C_0, chain AF3C_0 (#12.2) with combination B, chain
AF3C_2 (#12.3), sequence alignment score = 4122
RMSD between 177 pruned atom pairs is 0.166 angstroms; (across all 892 pairs:
58.895)
> show #12.4 models
> hide #12.3 models
> color /AF3C_3:850-893 forest green
> color /AF3C_3:591-773 orange
> color /AF3C_3:343-398 firebrick
> color /AF3C_3:155-195 yellow
> color /AF3C_3:6-143 cornflower blue
> color /AF3C_4:850-893 forest green
> color /AF3C_4:591-773 orange
> color /AF3C_4:343-398 firebrick
> color /AF3C_4:155-195 yellow
> color /AF3C_4:6-143 cornflower blue
> ui tool show Matchmaker
> matchmaker #12.4 to #12.2 ssFraction 1.0
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 1
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 combination AF3C_0, chain AF3C_0 (#12.2) with combination C, chain
AF3C_3 (#12.4), sequence alignment score = 4126
RMSD between 26 pruned atom pairs is 1.300 angstroms; (across all 892 pairs:
46.410)
> matchmaker #12.4 to #12.2 ssFraction 1.0
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 1
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 combination AF3C_0, chain AF3C_0 (#12.2) with combination C, chain
AF3C_3 (#12.4), sequence alignment score = 4126
RMSD between 26 pruned atom pairs is 1.300 angstroms; (across all 892 pairs:
46.410)
> matchmaker #12.4 to #12.2//chain_id='AF3C_0' pairing bs ssFraction 1.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 1
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 combination AF3C_0, chain AF3C_0 (#12.2) with combination C, chain
AF3C_3 (#12.4), sequence alignment score = 4126
RMSD between 26 pruned atom pairs is 1.300 angstroms; (across all 892 pairs:
46.410)
> matchmaker #12.4 to #12.2//chain_id='AF3C_0' pairing bs ssFraction 1.0 hgap
> 22 sgap 22
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 1
Gap open (HH/SS/other) | 22/22/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker combination AF3C_0, chain AF3C_0 (#12.2) with combination C, chain
AF3C_3 (#12.4), sequence alignment score = 4126
RMSD between 26 pruned atom pairs is 1.300 angstroms; (across all 892 pairs:
46.410)
> matchmaker #12.4 to #12.2//chain_id='AF3C_0' pairing bs ssFraction 1.0 hgap
> 22 sgap 22
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 1
Gap open (HH/SS/other) | 22/22/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker combination AF3C_0, chain AF3C_0 (#12.2) with combination C, chain
AF3C_3 (#12.4), sequence alignment score = 4126
RMSD between 26 pruned atom pairs is 1.300 angstroms; (across all 892 pairs:
46.410)
> show #12.3 models
> hide #12.4 models
> hide #12.2 models
> show #12.2 models
> hide #12.2 models
> show #12.2 models
> hide #12.2 models
> show #12.2 models
> show #12.4 models
> hide #12.4 models
> show #12.4 models
> hide #12.4 models
> show #12.4 models
> hide #12.4 models
> show #12.4 models
> hide #12.4 models
> show #12.5 models
> hide #12.5 models
> show #12.1 models
> hide #12.3 models
> show #1 models
> hide #1 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> hide #12.2 models
> hide #12.1 models
> show #7 models
> show #!6 models
> hide #7 models
> hide #!12 models
> show #12.2 models
> hide #!6 models
> color /AF3C_4:6-143 cornflower blue
===== Log before crash end =====
Log:
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
OpenGL version: 4.1 Metal - 89
OpenGL renderer: Apple M2 Pro
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: Mac
Model Identifier: Mac14,9
Model Number: MPHE3B/A
Chip: Unknown
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.0.80.0.2
OS Loader Version: 11881.0.80.0.2
Software:
System Software Overview:
System Version: macOS 15.0 (24A5264n)
Kernel Version: Darwin 24.0.0
Time since boot: 19 days, 10 hours, 20 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL P2715Q:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Mirror: Off
Online: Yes
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 (3)
comment:1 by , 16 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash either moving window or changing display |
comment:2 by , 16 months ago
comment:3 by , 16 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
The [NSWindow _windowMovedToRect:dueToMoveEvent] entry in the stack trace may be was because the an external display was plugged in and laptop screen closed or unplugged, and ChimeraX moved on its own to a different display. We know the plugging in and unplugging of displays on Mac causes crashes in Qt 6.6. Hopefully it gets fixed in Qt 6.7 which we use in the daily build, but I don't think it is likely.
{"imageOffset":427590,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":394,"imageIndex":175},{"imageOffset":13942027,"symbol":"-[NSWindow _postWindowDidChangeBackingPropertiesAndDisplayWindowForPreviousBackingScaleFactor:previousColorSpace:]","symbolLocation":222,"imageIndex":175},{"imageOffset":2414576,"symbol":"__67-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]_block_invoke","symbolLocation":522,"imageIndex":175},{"imageOffset":576772,"symbol":"NSPerformVisuallyAtomicChange","symbolLocation":134,"imageIndex":175},{"imageOffset":2414048,"symbol":"-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]","symbolLocation":69,"imageIndex":175},{"imageOffset":583354,"symbol":"-[NSWindow _setFrameCommon:display:fromServer:]","symbolLocation":1905,"imageIndex":175},{"imageOffset":13951507,"symbol":"-[NSWindow _windowMovedToRect:dueToMoveEvent:]","symbolLocation":133,"imageIndex":175},{"imageOffset":1681802,"symbol":"-[NSWindow _windowMoved:]","symbolLocation":1017,"imageIndex":175},{"imageOffset":1680743,"symbol":"-[NSWindow _internalHandleAppKitDefinedEvent:]","symbolLocation":160,"imageIndex":175},{"imageOffset":1679809,"symbol":"-[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:]","symbolLocation":533,"imageIndex":175},{"imageOffset":1678737,"symbol":"-[NSWindow(NSEventRouting) sendEvent:]","symbolLocation":339,"imageIndex":175},{"imageOffset":453268,"imageIndex":98},
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Maybe moving window onto a different display?