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Opened 5 months ago
Closed 5 months ago
#17763 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.7.1-arm64-arm-64bit
ChimeraX Version: 1.8rc202405250712 (2024-05-25 07:12:25 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000003f780f000 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000002021fcf40 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 91 in cmd_coulombic
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 535 in run
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 592 in run_expanded_command
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 72 in func_plus_tip
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 338 in run
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 419 in run_shortcut
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 401 in try_shortcut
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1386 in run_provider
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1306 in run_provider
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
File "/Applications/ChimeraX-1.8-rc2024.05.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 307 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.05.25.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-rc2024.05.25.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, 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, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath (total: 65)
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"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":61486},
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"path" : "\/Applications\/ChimeraX-1.8-rc2024.05.25.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
"name" : "Python",
"CFBundleVersion" : "3.11.4"
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"size" : 16384,
"uuid" : "17982d98-65bc-3327-8526-577ec996453c",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.05.25.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
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"source" : "P",
"arch" : "arm64e",
"base" : 6882455552,
"size" : 53248,
"uuid" : "57cf0002-c127-3580-a0b7-fd447cc0f745",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
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"size" : 520184,
"uuid" : "6b8ba6ce-63d9-3d2f-b380-c78392e7b8ec",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
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"arch" : "arm64e",
"base" : 6882664448,
"size" : 32744,
"uuid" : "db02da28-4c07-365e-82d0-b474e56ae2fa",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
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"arch" : "arm64e",
"base" : 6882881536,
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"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5083136,
"uuid" : "541c3d67-9162-32dc-bd2c-894dd0f013aa",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
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},
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"base" : 7058993152,
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"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2899968,
"uuid" : "5b90a7da-19ee-3b7b-bc3f-76302604a8b6",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
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"name" : "AppKit",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=5.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.9G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 928K 50 \nColorSync 608K 31 \nCoreAnimation 2528K 113 \nCoreGraphics 48K 3 \nCoreUI image data 4016K 28 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 4.8G 140 \nMALLOC guard page 192K 12 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.9M 58 \nStack 196.0M 58 \nVM_ALLOCATE 648.6M 448 \nVM_ALLOCATE (reserved) 320.0M 4 reserved VM address space (unallocated)\n__AUTH 2203K 404 \n__AUTH_CONST 31.8M 622 \n__CTF 824 1 \n__DATA 22.2M 780 \n__DATA_CONST 42.5M 789 \n__DATA_DIRTY 2024K 232 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 555.5M 162 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2200K 1 \n__TEXT 941.3M 806 \ndyld private memory 320K 4 \nmapped file 522.5M 83 \nshared memory 3264K 30 \n=========== ======= ======= \nTOTAL 8.1G 4875 \nTOTAL, minus reserved VM space 7.8G 4875 \n",
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.8rc202405250712 (2024-05-25)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/angelas/Desktop/KlebG + OmpK35/model OmpK35-KlebG.cxs"
Log from Mon Jan 20 10:44:56 2025UCSF ChimeraX version: 1.8rc202405250712
(2024-05-25)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/angelas/Desktop/KlebG + OmpK35/model OmpK35-KlebG.cxs"
Log from Fri Nov 29 17:26:52 2024UCSF ChimeraX version: 1.8rc202405250712
(2024-05-25)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/angelas/Desktop/KlebG + OmpK35/model OmpK35-KlebG.cxs"
Log from Tue Jun 25 18:30:32 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202405250712 (2024-05-25)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/Users/angelas/Library/Containers/com.microsoft.Outlook/Data/tmp/Outlook
> Temp/OmpK35-KlebG_model .pdb"
Chain information for OmpK35-KlebG_model .pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> set bgColor white
> save "/Users/angelas/Desktop/KlebG + OmpK35/model OmpK35-KlebG.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain /D
Alignment identifier is 1/D
> select /D:250
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /D:250-268
323 atoms, 332 bonds, 19 residues, 1 model selected
> select /D:244
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /D:244-268
417 atoms, 427 bonds, 25 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> sequence chain /B
Alignment identifier is 1/B
> sequence chain /C
Alignment identifier is 1/C
> select /B:120
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /B:35-120
1259 atoms, 1273 bonds, 1 pseudobond, 84 residues, 2 models selected
> select /A:125
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:125-148
352 atoms, 357 bonds, 24 residues, 1 model selected
> select /D:102-103
38 atoms, 37 bonds, 2 residues, 1 model selected
> select /D:102-128
371 atoms, 373 bonds, 27 residues, 1 model selected
> select /C:243
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /C:243-263
314 atoms, 318 bonds, 21 residues, 1 model selected
> select /A:126-127
24 atoms, 23 bonds, 2 residues, 1 model selected
> select /A:126-141
233 atoms, 237 bonds, 16 residues, 1 model selected
> select /C:184-185
39 atoms, 39 bonds, 2 residues, 1 model selected
> select /C:184-200
238 atoms, 241 bonds, 17 residues, 1 model selected
> measure buriedarea 1/D with 1/C
Missing or invalid "atoms1" argument: invalid atoms specifier
> measure buriedarea /D withAtoms2 /C
Buried area between /D and /C = 664.14
area /D = 11469, area /C = 16967, area both = 27108
> select /D:244-245
36 atoms, 36 bonds, 2 residues, 1 model selected
> select /D:244-268
417 atoms, 427 bonds, 25 residues, 1 model selected
> measure buriedarea /D:244-268 withAtoms2 /C
Buried area between /D:244-268 and /C = 138.13
area /D:244-268 = 2574, area /C = 16967, area both = 19265
> select /D:221
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /D:219-221
40 atoms, 40 bonds, 3 residues, 1 model selected
> select /D:263-264
28 atoms, 28 bonds, 2 residues, 1 model selected
> select /D:263-274
190 atoms, 193 bonds, 12 residues, 1 model selected
> select /D:2-3
20 atoms, 19 bonds, 2 residues, 1 model selected
> select /D:2-105
140 atoms, 140 bonds, 1 pseudobond, 10 residues, 2 models selected
> select /D:101-102
29 atoms, 28 bonds, 2 residues, 1 model selected
> select /D:101-105
77 atoms, 76 bonds, 5 residues, 1 model selected
> select /D:4
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /D:3-4
20 atoms, 19 bonds, 2 residues, 1 model selected
> select clear
> select /D:100
23 atoms, 24 bonds, 1 residue, 1 model selected
> select /D:101
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /D:101
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /D:100
23 atoms, 24 bonds, 1 residue, 1 model selected
> select /D:100-121
308 atoms, 311 bonds, 22 residues, 1 model selected
> select /C:283
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /C:136-137
19 atoms, 18 bonds, 2 residues, 1 model selected
> select /C:136-198
937 atoms, 949 bonds, 63 residues, 1 model selected
> select /B:317
24 atoms, 25 bonds, 1 residue, 1 model selected
> measure buriedarea /D:100-121 withAtoms2 /C
Buried area between /D:100-121 and /C = 524.34
area /D:100-121 = 2160.5, area /C = 16967, area both = 18079
> select /A:168-169
31 atoms, 31 bonds, 2 residues, 1 model selected
> select /A:168-237
997 atoms, 1007 bonds, 70 residues, 1 model selected
> select /C:35
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /C:35-262
3314 atoms, 3355 bonds, 1 pseudobond, 226 residues, 2 models selected
> select /D:250
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /D:250
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /D:250-251
39 atoms, 40 bonds, 2 residues, 1 model selected
> select /D:250-268
323 atoms, 332 bonds, 19 residues, 1 model selected
> select /D:244-245
36 atoms, 36 bonds, 2 residues, 1 model selected
> select /D:244-268
417 atoms, 427 bonds, 25 residues, 1 model selected
> measure buriedarea /D:244-268 withAtoms2 /B
Buried area between /D:244-268 and /B = 737.13
area /D:244-268 = 2574, area /B = 16708, area both = 17807
> save "/Users/angelas/Desktop/KlebG + OmpK35/model OmpK35-KlebG.cxs"
——— End of log from Tue Jun 25 18:30:32 2024 ———
opened ChimeraX session
> select /D:1
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /D
2160 atoms, 2176 bonds, 2 pseudobonds, 143 residues, 2 models selected
> ui tool show "Color Actions"
> color sel sea green
> select #1/A-C
14887 atoms, 15063 bonds, 7 pseudobonds, 997 residues, 2 models selected
> ui tool show "Color Actions"
> color sel silver
> select /D:101
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /D:101-107
94 atoms, 93 bonds, 7 residues, 1 model selected
> select /D:100
23 atoms, 24 bonds, 1 residue, 1 model selected
> select /D:100-119
285 atoms, 288 bonds, 20 residues, 1 model selected
> color sel cornflower blue
> select /D:244
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /D:244-268
417 atoms, 427 bonds, 25 residues, 1 model selected
> color sel violet
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select add #1
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 2 models selected
> select subtract #1
Nothing selected
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting shadows true
> lighting flat
> graphics silhouettes false
> lighting simple
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save /Users/angelas/Desktop/Figures/KlebGOmpK35cartoon.png
> transparentBackground true
> select /D:1
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /D
2160 atoms, 2176 bonds, 2 pseudobonds, 143 residues, 2 models selected
> hide sel cartoons
> select /D:1
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /D:1-5
52 atoms, 51 bonds, 5 residues, 1 model selected
> show sel cartoons
> select /D:100
23 atoms, 24 bonds, 1 residue, 1 model selected
> select /D:100-119
285 atoms, 288 bonds, 20 residues, 1 model selected
> show sel cartoons
> select /D:244
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /D:244-268
417 atoms, 427 bonds, 25 residues, 1 model selected
> show sel cartoons
> select add #1
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 2 models selected
> select subtract #1
Nothing selected
> select /D:1
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /D
2160 atoms, 2176 bonds, 2 pseudobonds, 143 residues, 2 models selected
> show sel cartoons
> show sel surfaces
> ui tool show "Color Actions"
> color sel sea green
> select /D:100
23 atoms, 24 bonds, 1 residue, 1 model selected
> select /D:100-119
285 atoms, 288 bonds, 20 residues, 1 model selected
> color sel cornflower blue
> select /D:244
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /D:243-244
22 atoms, 21 bonds, 2 residues, 1 model selected
> select /D:244-268
417 atoms, 427 bonds, 25 residues, 1 model selected
> color sel violet
> select add #1
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 3 models selected
> select subtract #1
1 model selected
> select #1/A-C
14887 atoms, 15063 bonds, 7 pseudobonds, 997 residues, 2 models selected
> show sel surfaces
> color sel silver
[Repeated 1 time(s)]
> select add #1
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 5 models selected
> select subtract #1
4 models selected
> select #1.2.1
1 model selected
> select #1.2.1
1 model selected
> color sel cornflower blue
> select clear
> select #1.2.1
1 model selected
> select /D:1-2
22 atoms, 21 bonds, 2 residues, 1 model selected
> select /D
2160 atoms, 2176 bonds, 2 pseudobonds, 143 residues, 2 models selected
> select /D:295
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /D:295
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /D:295
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2.1
1 model selected
> select /D:1-2
22 atoms, 21 bonds, 2 residues, 1 model selected
> select /D
2160 atoms, 2176 bonds, 2 pseudobonds, 143 residues, 2 models selected
> color sel sea green
> select clear
> select #1.2.1
1 model selected
> color sel sea green
> select add #1
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 6 models selected
> select subtract #1
4 models selected
> save /Users/angelas/Desktop/Figures/KlebGOmpK35surfacetopcut.png
> transparentBackground true
Drag select of OmpK35-KlebG_model .pdb_D SES surface, OmpK35-KlebG_model
.pdb_A SES surface, OmpK35-KlebG_model .pdb_B SES surface, OmpK35-KlebG_model
.pdb_C SES surface, 1140 residues, 9 pseudobonds
> hide sel surfaces
> select add #1
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 10 models selected
> select subtract #1
4 models selected
> save /Users/angelas/Desktop/Figures/KlebGOmpK35cartoon.png
> transparentBackground true
Drag select of 1140 residues, 9 pseudobonds
> show sel surfaces
> select add #1
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 10 models selected
> select subtract #1
4 models selected
> save /Users/angelas/Desktop/Figures/KlebGOmpK35surfacesidecut.png
> transparentBackground true
> save /Users/angelas/Desktop/Figures/KlebGOmpK35surfacetopcut.png
> transparentBackground true
Drag select of OmpK35-KlebG_model .pdb_D SES surface, OmpK35-KlebG_model
.pdb_A SES surface, OmpK35-KlebG_model .pdb_B SES surface, OmpK35-KlebG_model
.pdb_C SES surface, 1140 residues, 9 pseudobonds
> hide sel surfaces
> select add #1
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 10 models selected
> select subtract #1
4 models selected
> save "/Users/angelas/Desktop/KlebG + OmpK35/model OmpK35-KlebG.cxs"
——— End of log from Fri Nov 29 17:26:52 2024 ———
opened ChimeraX session
> select #1/a-c
14887 atoms, 15063 bonds, 7 pseudobonds, 997 residues, 2 models selected
> ui tool show "Color Actions"
> transparency sel 70 cartoons
> transparency sel 50 cartoons
> select add #1
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 9 models selected
> select subtract #1
4 models selected
> save /Users/angelas/Desktop/Figures/test.png transparentBackground true
> lighting flat
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting flat
> graphics silhouettes false
> lighting soft
> lighting full
> save /Users/angelas/Desktop/Figures/test.png transparentBackground true
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save /Users/angelas/Desktop/Figures/test.png transparentBackground true
[Repeated 1 time(s)]
> save /Users/angelas/Desktop/Figures/KlebGOmpK35cartoon.png
> transparentBackground true
> save "/Users/angelas/Desktop/KlebG + OmpK35/model OmpK35-KlebG.cxs"
——— End of log from Mon Jan 20 10:44:56 2025 ———
opened ChimeraX session
> open 6rd3 fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 6rd3 fetched from pdbe_bio
---
warnings | Missing or incomplete sequence information. Inferred polymer connectivity.
Missing or incomplete sequence information. Inferred polymer connectivity.
6rd3 bioassembly 1 title:
Crystal structure of the wild type OmpK36 from Klebsiella pneumonia [more
info...]
Chain information for 6rd3 bioassembly 1 #2.1
---
Chain | Description
A | OmpK36
B | OmpK36
C | OmpK36
Non-standard residues in 6rd3 bioassembly 1 #2.1
---
C8E — (C8E)
MG — (MG)
6rd3 bioassembly 1 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
6rd3 bioassembly 2 title:
Crystal structure of the wild type OmpK36 from Klebsiella pneumonia [more
info...]
Chain information for 6rd3 bioassembly 2 #2.2
---
Chain | Description
D E F | OmpK36
Non-standard residues in 6rd3 bioassembly 2 #2.2
---
C8E — (C8E)
MG — (MG)
6rd3 bioassembly 2 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Opened 2 biological assemblies for 6rd3
Drag select of 363 atoms, 1029 residues, 2 pseudobonds, 320 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 308 atoms, 1035 residues, 268 bonds
> hide sel atoms
> select add #2
17283 atoms, 16720 bonds, 2 pseudobonds, 2981 residues, 4 models selected
> select subtract #2
Nothing selected
> select #1/d
2160 atoms, 2176 bonds, 2 pseudobonds, 143 residues, 2 models selected
> hide sel cartoons
Drag select of 1035 residues
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6rd3 bioassembly 2_D SES surface #2.2.1: minimum, -17.66,
mean -3.42, maximum 9.33
Coulombic values for 6rd3 bioassembly 2_E SES surface #2.2.2: minimum, -21.52,
mean -3.42, maximum 9.40
Coulombic values for 6rd3 bioassembly 2_F SES surface #2.2.3: minimum, -18.27,
mean -3.41, maximum 8.87
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
Drag select of 997 residues, 7 pseudobonds
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
OmpK35-KlebG_model .pdb #1/B PHE 160
OmpK35-KlebG_model .pdb #1/C THR 47
OmpK35-KlebG_model .pdb #1/C LYS 50
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for OmpK35-KlebG_model .pdb_A SES surface #1.3: minimum,
-18.49, mean -1.63, maximum 21.64
Coulombic values for OmpK35-KlebG_model .pdb_B SES surface #1.4: minimum,
-28.61, mean -2.51, maximum 16.29
Coulombic values for OmpK35-KlebG_model .pdb_C SES surface #1.5: minimum,
-19.53, mean -2.28, maximum 17.37
To also show corresponding color key, enter the above coulombic command and
add key true
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> view orient
> ui tool show "Side View"
> ui mousemode right "move picked models"
> view matrix models #1,1,0,0,-52.515,0,1,0,-7.6761,0,0,1,-31.98
> view matrix models #1,1,0,0,-39.493,0,1,0,-7.6434,0,0,1,-24.061
> view matrix models #1,1,0,0,-140.91,0,1,0,-5.8116,0,0,1,-46.619
> view matrix models #1,1,0,0,-140.56,0,1,0,-10.376,0,0,1,-21.777
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.99808,-0.04908,0.03783,108.59,0.060299,-0.90993,0.41036,163.94,0.014283,0.41185,0.91114,-62.799
> view matrix models
> #1,-0.9575,-0.25192,0.14049,115.63,0.28503,-0.90104,0.32692,144.8,0.044227,0.35307,0.93455,-62.077
> view matrix models
> #1,-0.92524,-0.34017,0.16795,119,0.37718,-0.87243,0.31081,131.76,0.0408,0.35092,0.93552,-61.492
> view matrix models
> #1,-0.96517,-0.22976,0.12512,115.76,0.25879,-0.90861,0.3278,148.88,0.038371,0.34876,0.93643,-61.038
> view matrix models
> #1,-0.87225,-0.43479,0.22391,117.02,0.4818,-0.84252,0.24088,123.48,0.083916,0.31799,0.94437,-63.864
> view matrix models
> #1,-0.98664,-0.028082,0.16049,89.59,0.074117,-0.95457,0.28863,182.18,0.14509,0.29667,0.9439,-68.846
> view matrix models
> #1,-0.95385,-0.18774,0.23437,95.757,0.22696,-0.96177,0.15324,180.55,0.19664,0.19935,0.95999,-65.157
> view matrix models
> #1,-0.98681,-0.15963,-0.027014,127.44,0.14704,-0.81383,-0.5622,257.2,0.067758,-0.55875,0.82656,60.549
> view matrix models
> #1,-0.98075,-0.132,-0.1439,137.43,0.19003,-0.81471,-0.54784,250.26,-0.044919,-0.56464,0.82411,75.505
> view matrix models
> #1,-0.99477,-0.074699,-0.069717,123.05,0.10061,-0.83525,-0.54059,262.96,-0.01785,-0.54477,0.83839,67.968
> view matrix models
> #1,-0.99865,-0.031165,-0.041536,114.7,0.04963,-0.80812,-0.58692,271.51,-0.015275,-0.58819,0.80858,76.663
> view matrix models
> #1,-0.99378,0.043302,-0.10255,112.24,0.022627,-0.82344,-0.56695,274.34,-0.109,-0.56574,0.81735,84.44
> view matrix models
> #1,-0.9808,-0.039623,-0.19093,131.66,0.13648,-0.83881,-0.52705,257.31,-0.13927,-0.54299,0.82811,84.069
> view matrix models
> #1,-0.97633,-0.032982,-0.21375,133.04,0.14299,-0.83994,-0.52351,256.22,-0.16227,-0.54168,0.82477,87.145
> ui mousemode right "move picked models"
> view matrix models
> #1,-0.97633,-0.032982,-0.21375,137.25,0.14299,-0.83994,-0.52351,272.44,-0.16227,-0.54168,0.82477,83.513
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.96652,-0.047491,-0.25216,142.49,0.17654,-0.83623,-0.51918,267.33,-0.18621,-0.54632,0.81662,88.023
> view matrix models
> #1,-0.97738,0.009417,-0.21129,131.81,0.10492,-0.84583,-0.52304,277.81,-0.18364,-0.53337,0.82571,84.998
> view matrix models
> #1,-0.96885,0.044936,-0.24356,130.24,0.091072,-0.84986,-0.51908,279.54,-0.23031,-0.52509,0.81929,90.513
> view matrix models
> #1,-0.95378,-0.023839,-0.29955,143.71,0.18131,-0.8406,-0.51041,266.2,-0.23963,-0.54114,0.80607,95.252
> view matrix models
> #1,-0.98484,-0.084738,-0.15136,137.19,0.15238,-0.83958,-0.52142,270.99,-0.082893,-0.53658,0.83977,71.346
> view matrix models
> #1,-0.99765,-0.043029,-0.053402,121.73,0.064564,-0.85183,-0.51982,283.14,-0.023123,-0.52204,0.85261,60.615
> view matrix models
> #1,-0.99924,-0.019248,-0.033943,116.61,0.034009,-0.85608,-0.51573,286.96,-0.019131,-0.51649,0.85608,59.009
> view matrix models
> #1,-0.99349,0.055986,-0.099177,114.42,0.001442,-0.86457,-0.50251,290.47,-0.11388,-0.49938,0.85887,68.313
> view matrix models
> #1,-0.99044,0.12057,-0.067035,102.1,-0.073299,-0.87159,-0.48473,298.52,-0.11687,-0.47518,0.87209,64.073
> view matrix models
> #1,-0.9782,0.15932,-0.13319,103.75,-0.076461,-0.87266,-0.48231,298.75,-0.19307,-0.46161,0.86582,72.676
> view matrix models
> #1,-0.98165,-0.04719,-0.18475,136.24,0.14306,-0.82284,-0.54997,273.14,-0.12606,-0.56631,0.81449,82.909
> view matrix models
> #1,-0.9736,-0.073151,-0.21623,142.29,0.18255,-0.81824,-0.54513,267.13,-0.13705,-0.57021,0.80999,85.289
> ui mousemode right "translate selected atoms"
> ui mousemode right "move picked models"
> view matrix models
> #1,-0.9736,-0.073151,-0.21623,142.31,0.18255,-0.81824,-0.54513,267.53,-0.13705,-0.57021,0.80999,85.267
> view matrix models
> #1,-0.9736,-0.073151,-0.21623,142.19,0.18255,-0.81824,-0.54513,265.71,-0.13705,-0.57021,0.80999,85.544
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.9736,-0.073151,-0.21623,141.94,0.18255,-0.81824,-0.54513,262.62,-0.13705,-0.57021,0.80999,86.307
> view matrix models
> #1,-0.9736,-0.073151,-0.21623,141.59,0.18255,-0.81824,-0.54513,257.52,-0.13705,-0.57021,0.80999,87.249
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.96659,-0.16667,-0.19473,149.74,0.2478,-0.80181,-0.54378,247.29,-0.065502,-0.57387,0.81633,78.127
> view matrix models
> #1,-0.99296,-0.096721,-0.068397,129.01,0.11837,-0.83299,-0.54047,266.74,-0.0046991,-0.54476,0.83858,64.311
> view matrix models
> #1,-0.98817,-0.023788,-0.15149,129.41,0.10252,-0.83714,-0.5373,268.82,-0.11404,-0.54647,0.82968,79.084
> view matrix models
> #1,-0.92765,0.23612,-0.28932,106.28,-0.023084,-0.80951,-0.58665,287.01,-0.37273,-0.53753,0.7564,118.37
> view matrix models
> #1,-0.9881,0.034117,-0.14998,121.95,0.062567,-0.80161,-0.59456,276.3,-0.14051,-0.59687,0.78994,92.688
> view matrix models
> #1,-0.99944,0.029723,-0.015107,107.54,-0.015086,-0.8072,-0.59008,286.1,-0.029733,-0.58953,0.8072,75.925
> view matrix models
> #1,-0.99981,0.014631,-0.013116,109.23,-0.0079141,-0.91081,-0.41275,276.63,-0.017985,-0.41257,0.91075,39.891
> ui mousemode right select
> ui mousemode right "move picked models"
> view matrix models
> #1,-0.99981,0.014631,-0.013116,110.24,-0.0079141,-0.91081,-0.41275,114.7,-0.017985,-0.41257,0.91075,-36.395
> view matrix models
> #1,-0.99981,0.014631,-0.013116,92.959,-0.0079141,-0.91081,-0.41275,217.54,-0.017985,-0.41257,0.91075,87.841
> lighting soft
> lighting simple
> view matrix models
> #1,-0.99333,0.051075,-0.10339,98.255,-0.0041344,-0.91177,-0.41069,216.95,-0.11524,-0.40752,0.90589,99.825
> view matrix models
> #1,-0.99333,0.051075,-0.10339,114.36,-0.0041344,-0.91177,-0.41069,225.67,-0.11524,-0.40752,0.90589,60.353
> ui mousemode right "rotate selected models"
> ui mousemode right select
> select add #1
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 5 models selected
> select subtract #1
4 models selected
> select clear
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> select add #1
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 2 models selected
> view matrix models
> #1,-0.99731,-0.031557,-0.066188,120.68,0.05618,-0.90893,-0.41314,218.11,-0.047123,-0.41575,0.90826,52.659
> view matrix models
> #1,-0.98168,0.0031541,-0.19052,129.56,-0.025413,-0.9931,0.1145,176.18,-0.18885,0.11725,0.97498,-3.7285
> view matrix models
> #1,-0.97916,-0.17136,-0.109,140.62,0.15036,-0.97246,0.17809,144.31,-0.13651,0.15799,0.97796,-15.494
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.97916,-0.17136,-0.109,141.11,0.15036,-0.97246,0.17809,132.56,-0.13651,0.15799,0.97796,-22.241
> view matrix models
> #1,-0.97916,-0.17136,-0.109,135.8,0.15036,-0.97246,0.17809,133.78,-0.13651,0.15799,0.97796,-26.178
> view matrix models
> #1,-0.97916,-0.17136,-0.109,136.71,0.15036,-0.97246,0.17809,134.05,-0.13651,0.15799,0.97796,-30.644
> select subtract #1
4 models selected
> select add #1
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 2 models selected
> select subtract #1
4 models selected
> open
> /Users/angelas/Downloads/fold_wt_klebg_imkg_70/fold_wt_klebg_imkg_70_model_0.cif
Chain information for fold_wt_klebg_imkg_70_model_0.cif #3
---
Chain | Description
A | .
> select #3
5269 atoms, 5357 bonds, 710 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_wt_klebg_imkg_70_model_0.cif_A SES surface #3.1:
minimum, -18.22, mean -1.06, maximum 11.64
To also show corresponding color key, enter the above coulombic command and
add key true
> open "/Users/angelas/Downloads/OmpK35-KlebG_model .pdb"
Chain information for OmpK35-KlebG_model .pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> select #4/a-c
14887 atoms, 15063 bonds, 7 pseudobonds, 997 residues, 2 models selected
> hide sel cartoons
> select #4/d
2160 atoms, 2176 bonds, 2 pseudobonds, 143 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for OmpK35-KlebG_model .pdb_D SES surface #4.2: minimum,
-11.64, mean 1.23, maximum 15.42
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show Matchmaker
> matchmaker #4/D to #3/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 fold_wt_klebg_imkg_70_model_0.cif, chain A (#3) with
OmpK35-KlebG_model .pdb, chain D (#4), sequence alignment score = 432.8
RMSD between 60 pruned atom pairs is 1.242 angstroms; (across all 143 pairs:
8.913)
> select add #4
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 3 models selected
> select subtract #4
1 model selected
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select add #4
17047 atoms, 17239 bonds, 9 pseudobonds, 1140 residues, 2 models selected
> view matrix models
> #4,-0.94347,-0.32213,0.078128,94.237,-0.32764,0.94202,-0.072477,65.717,-0.050251,-0.093978,-0.99431,303.01
> view matrix models
> #4,-0.94347,-0.32213,0.078128,133.27,-0.32764,0.94202,-0.072477,124.55,-0.050251,-0.093978,-0.99431,243.45
> view matrix models
> #4,-0.94347,-0.32213,0.078128,249.05,-0.32764,0.94202,-0.072477,38.282,-0.050251,-0.093978,-0.99431,185.2
> view matrix models
> #4,-0.94347,-0.32213,0.078128,230.13,-0.32764,0.94202,-0.072477,32.827,-0.050251,-0.093978,-0.99431,218.52
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.97982,0.088677,0.17912,171.93,-0.13879,0.34303,-0.92902,192.51,-0.14382,-0.93513,-0.3238,245.14
> ui mousemode right "move picked models"
> view matrix models
> #4,-0.97982,0.088677,0.17912,143.36,-0.13879,0.34303,-0.92902,189.48,-0.14382,-0.93513,-0.3238,235.29
> view matrix models
> #4,-0.97982,0.088677,0.17912,145.74,-0.13879,0.34303,-0.92902,163.61,-0.14382,-0.93513,-0.3238,241.19
> ui mousemode right select
> select clear
> hide #!4 models
> open 6v78 fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 6v78 fetched from pdbe_bio
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
6v78 bioassembly 1 title:
OmpK37 porin [more info...]
Chain information for 6v78 bioassembly 1 #5
---
Chain | Description
A B C | OmpK37
Opened 1 biological assemblies for 6v78
> ui mousemode right "move picked models"
> view matrix models #5,1,0,0,-19.363,0,1,0,38.462,0,0,1,-51.738
> view matrix models #5,1,0,0,-101.31,0,1,0,110.51,0,0,1,-104.54
> ui mousemode right "rotate selected models"
> select add #5
8455 atoms, 8565 bonds, 1132 residues, 1 model selected
> view matrix models
> #5,0.9798,0.14588,0.13678,-106.38,-0.13231,0.98578,-0.10356,131.37,-0.14995,0.083368,0.98517,-86.447
> view matrix models
> #5,0.94333,0.30794,0.12368,-106.9,-0.32925,0.82197,0.46471,153.69,0.041445,-0.47909,0.87679,-90.692
> view matrix models
> #5,0.77378,0.41153,0.48157,-93.954,-0.52684,-0.0040295,0.84995,203.44,0.35173,-0.91139,0.2137,-105.49
> view matrix models
> #5,0.72146,0.26692,0.63894,-84.509,-0.67768,0.082581,0.7307,223.54,0.14228,-0.96017,0.24047,-75.18
> view matrix models
> #5,0.79504,0.13806,0.59064,-89.157,-0.60235,0.065101,0.79558,212.48,0.071384,-0.98828,0.13492,-62.309
> view matrix models
> #5,0.88253,0.17005,0.43844,-99.531,-0.44471,-0.0013616,0.89567,191.07,0.15291,-0.98543,0.074423,-72.564
> view matrix models
> #5,0.80601,0.34171,0.48331,-95.948,-0.48629,-0.083219,0.86982,200.28,0.33745,-0.93611,0.099096,-100.42
> view matrix models
> #5,0.70796,0.29224,0.64295,-83.624,-0.65812,-0.057314,0.75072,225.48,0.25624,-0.95463,0.15176,-89.494
> view matrix models
> #5,0.75986,0.31525,0.56853,-90.227,-0.57934,-0.068362,0.81222,213.77,0.29492,-0.94654,0.13069,-94.747
> view matrix models
> #5,0.7949,0.32395,0.51302,-94.338,-0.49789,-0.13496,0.85668,204.01,0.34676,-0.9364,0.054015,-100.84
> view matrix models
> #5,0.76334,0.30289,0.57058,-90.304,-0.56218,-0.12363,0.81772,213.27,0.31822,-0.94497,0.075903,-96.987
> ui mousemode right "move picked models"
> view matrix models
> #5,0.76334,0.30289,0.57058,-85.534,-0.56218,-0.12363,0.81772,212.21,0.31822,-0.94497,0.075903,-96.348
> view matrix models
> #5,0.76334,0.30289,0.57058,-82.617,-0.56218,-0.12363,0.81772,210.48,0.31822,-0.94497,0.075903,-95.203
> ui mousemode right select
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6v78 bioassembly 1_A SES surface #5.1: minimum, -23.41,
mean -4.34, maximum 9.12
Coulombic values for 6v78 bioassembly 1_B SES surface #5.2: minimum, -21.66,
mean -4.38, maximum 11.38
Coulombic values for 6v78 bioassembly 1_C SES surface #5.3: minimum, -20.63,
mean -4.41, maximum 8.26
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #5
3 models selected
> select add #5
8455 atoms, 8565 bonds, 1132 residues, 1 model selected
> select subtract #5
3 models selected
> show #!4 models
> hide #!4 models
> show #!3 models
> toolshed show
> select clear
Drag select of OmpK35-KlebG_model .pdb_A SES surface, OmpK35-KlebG_model
.pdb_B SES surface, OmpK35-KlebG_model .pdb_C SES surface, 6rd3 bioassembly
2_D SES surface, 6rd3 bioassembly 2_E SES surface, 6rd3 bioassembly 2_F SES
surface, fold_wt_klebg_imkg_70_model_0.cif_A SES surface, 6v78 bioassembly 1_A
SES surface, 6v78 bioassembly 1_B SES surface, 6v78 bioassembly 1_C SES
surface, 3801 residues, 7 pseudobonds
> coulombic sel key true
Coulombic values for OmpK35-KlebG_model .pdb_A SES surface #1.3: minimum,
-18.49, mean -1.63, maximum 21.64
Coulombic values for OmpK35-KlebG_model .pdb_B SES surface #1.4: minimum,
-28.61, mean -2.51, maximum 16.29
Coulombic values for OmpK35-KlebG_model .pdb_C SES surface #1.5: minimum,
-19.53, mean -2.28, maximum 17.37
Coulombic values for 6rd3 bioassembly 2_D SES surface #2.2.1: minimum, -17.66,
mean -3.42, maximum 9.33
Coulombic values for 6rd3 bioassembly 2_E SES surface #2.2.2: minimum, -21.52,
mean -3.42, maximum 9.40
Coulombic values for 6rd3 bioassembly 2_F SES surface #2.2.3: minimum, -18.27,
mean -3.41, maximum 8.87
Coulombic values for fold_wt_klebg_imkg_70_model_0.cif_A SES surface #3.1:
minimum, -18.22, mean -1.06, maximum 11.64
Coulombic values for 6v78 bioassembly 1_A SES surface #5.1: minimum, -23.41,
mean -4.34, maximum 9.12
Coulombic values for 6v78 bioassembly 1_B SES surface #5.2: minimum, -21.66,
mean -4.38, maximum 11.38
Coulombic values for 6v78 bioassembly 1_C SES surface #5.3: minimum, -20.63,
mean -4.41, maximum 8.26
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> help help:user/tools/colorkey.html
> ui mousemode right select
> ui tool show "Volume Viewer"
> select add #1
38783 atoms, 17239 bonds, 9 pseudobonds, 3944 residues, 15 models selected
> select subtract #1
21736 atoms, 2804 residues, 14 models selected
> select add #2
30934 atoms, 16720 bonds, 2 pseudobonds, 4750 residues, 13 models selected
> select add #3
30934 atoms, 22077 bonds, 2 pseudobonds, 4750 residues, 13 models selected
> select subtract #2
13651 atoms, 5357 bonds, 1769 residues, 9 models selected
> select subtract #3
8382 atoms, 1059 residues, 5 models selected
> select add #5
8455 atoms, 8565 bonds, 1132 residues, 4 models selected
> select subtract #5
3 models selected
> select add #5
8455 atoms, 8565 bonds, 1132 residues, 1 model selected
> open 2omf fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 2omf fetched from pdbe_bio
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
note | Fetching compressed 2omf bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/2omf-assembly-1.cif.gz
2omf bioassembly 1 title:
OMPF porin [more info...]
Chain information for 2omf bioassembly 1 #7
---
Chain | Description
A AA AB | MATRIX PORIN OUTER MEMBRANE PROTEIN F
Non-standard residues in 2omf bioassembly 1 #7
---
C8E — (C8E)
2omf bioassembly 1 mmCIF Assemblies
---
1| author_and_software_defined_assembly
Opened 1 biological assemblies for 2omf
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!5 models
Drag select of 285 atoms, 1020 residues, 240 bonds
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 2omf bioassembly 1_A SES surface #7.1: minimum, -15.19,
mean -2.85, maximum 13.37
Coulombic values for 2omf bioassembly 1_AA SES surface #7.2: minimum, -14.94,
mean -2.86, maximum 12.99
Coulombic values for 2omf bioassembly 1_AB SES surface #7.3: minimum, -15.10,
mean -2.87, maximum 12.80
To also show corresponding color key, enter the above coulombic command and
add key true
> open 2omf
Summary of feedback from opening 2omf fetched from pdb
---
note | Fetching compressed mmCIF 2omf from http://files.rcsb.org/download/2omf.cif
2omf title:
OMPF porin [more info...]
Chain information for 2omf #8
---
Chain | Description | UniProt
A | MATRIX PORIN OUTER MEMBRANE PROTEIN F | OMPF_ECOLI 1-340
Non-standard residues in 2omf #8
---
C8E — (hydroxyethyloxy)tri(ethyloxy)octane
2omf mmCIF Assemblies
---
1| author_and_software_defined_assembly
> hide #!7 models
> hide #6 models
> help help:user/fetch.html
> open 2omf fromDatabase pdb format mmcif
2omf title:
OMPF porin [more info...]
Chain information for 2omf #9
---
Chain | Description | UniProt
A | MATRIX PORIN OUTER MEMBRANE PROTEIN F | OMPF_ECOLI 1-340
Non-standard residues in 2omf #9
---
C8E — (hydroxyethyloxy)tri(ethyloxy)octane
2omf mmCIF Assemblies
---
1| author_and_software_defined_assembly
> close #8
> close #9
> show #!7 models
> close #7
> show #!5 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!2 models
> show #!3 models
> open
> /Users/angelas/Downloads/fold_ompk35_wt_klebg/fold_ompk35_wt_klebg_model_0.cif
Chain information for fold_ompk35_wt_klebg_model_0.cif #7
---
Chain | Description
A | .
B | .
C D E | .
> close #7
> open
> /Users/angelas/Downloads/fold_ompk35_wt_klebg/fold_ompk35_wt_klebg_model_1.cif
Chain information for fold_ompk35_wt_klebg_model_1.cif #7
---
Chain | Description
A | .
B | .
C D E | .
> open
> /Users/angelas/Downloads/fold_ompk35_wt_klebg/fold_ompk35_wt_klebg_model_2.cif
Chain information for fold_ompk35_wt_klebg_model_2.cif #8
---
Chain | Description
A | .
B | .
C D E | .
> hide #7 target m
> select add #8
14400 atoms, 14700 bonds, 1882 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_ompk35_wt_klebg_model_2.cif_A SES surface #8.1:
minimum, -23.23, mean -0.87, maximum 9.94
Coulombic values for fold_ompk35_wt_klebg_model_2.cif_B SES surface #8.2:
minimum, -11.23, mean -0.56, maximum 11.62
Coulombic values for fold_ompk35_wt_klebg_model_2.cif_C SES surface #8.3:
minimum, -19.30, mean -2.88, maximum 14.97
Coulombic values for fold_ompk35_wt_klebg_model_2.cif_D SES surface #8.4:
minimum, -19.68, mean -3.07, maximum 13.92
Coulombic values for fold_ompk35_wt_klebg_model_2.cif_E SES surface #8.5:
minimum, -20.22, mean -3.08, maximum 13.00
To also show corresponding color key, enter the above coulombic command and
add key true
> select #8/d
2640 atoms, 2702 bonds, 338 residues, 1 model selected
> select #8/a
5760 atoms, 5859 bonds, 780 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> select add #8
14400 atoms, 14700 bonds, 1882 residues, 2 models selected
> select subtract #8
5 models selected
> select add #8
14400 atoms, 14700 bonds, 1882 residues, 1 model selected
Drag select of 6rd3 bioassembly 2_D SES surface, 37014 of 299598 triangles,
6rd3 bioassembly 2_E SES surface, 70081 of 303920 triangles, 6rd3 bioassembly
2_F SES surface, 2698 of 300612 triangles, fold_ompk35_wt_klebg_model_2.cif_C
SES surface, 64703 of 293048 triangles, fold_ompk35_wt_klebg_model_2.cif_D SES
surface, 83492 of 293770 triangles, 344 residues
Drag select of 6rd3 bioassembly 2_D SES surface, 30666 of 299598 triangles,
6rd3 bioassembly 2_E SES surface, 41121 of 303920 triangles, 6rd3 bioassembly
2_F SES surface, 11417 of 300612 triangles, fold_ompk35_wt_klebg_model_2.cif_C
SES surface, 31707 of 293048 triangles, fold_ompk35_wt_klebg_model_2.cif_D SES
surface, 26862 of 293770 triangles, fold_ompk35_wt_klebg_model_2.cif_E SES
surface, 19207 of 293056 triangles, 277 residues
> select add #8
15617 atoms, 14700 bonds, 2030 residues, 8 models selected
> select subtract #8
1217 atoms, 148 residues, 9 models selected
> select add #8
15617 atoms, 14700 bonds, 2030 residues, 5 models selected
> ui mousemode right "move picked models"
> view matrix models #8,1,0,0,109.72,0,1,0,52.794,0,0,1,24.236
> ui mousemode right "rotate selected models"
> view matrix models
> #2.2,0.95125,0.27803,-0.13354,-0.4873,-0.28171,0.95946,-0.0091318,25.873,0.12558,0.046305,0.991,-12.75,#8,0.95125,0.27803,-0.13354,115.33,-0.28171,0.95946,-0.0091318,45.395,0.12558,0.046305,0.991,27.492
> undo
> select add #2
31683 atoms, 31420 bonds, 2 pseudobonds, 4863 residues, 13 models selected
> select subtract #2
14400 atoms, 14700 bonds, 1882 residues, 9 models selected
> ui mousemode right "move picked models"
> view matrix models #8,1,0,0,108.82,0,1,0,144.32,0,0,1,83.286
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.48342,-0.6295,0.60831,80.373,0.59373,0.27487,0.75626,126.55,-0.64327,0.72676,0.24088,101.04
> view matrix models
> #8,-0.46812,-0.48875,0.7362,80.156,0.52687,0.51447,0.67656,132.32,-0.70942,0.70459,0.016679,104.04
> ui mousemode right "move picked models"
> view matrix models
> #8,-0.46812,-0.48875,0.7362,99.01,0.52687,0.51447,0.67656,16.924,-0.70942,0.70459,0.016679,-102.65
> view matrix models
> #8,-0.46812,-0.48875,0.7362,100.18,0.52687,0.51447,0.67656,8.2742,-0.70942,0.70459,0.016679,-110.42
> hide #!3 models
> select subtract #8
5 models selected
> hide #!4 models
Drag select of fold_ompk35_wt_klebg_model_2.cif_B SES surface, 88 residues
> hide sel surfaces
> hide sel cartoons
> view matrix models
> #8,-0.46812,-0.48875,0.7362,73.426,0.52687,0.51447,0.67656,-44.312,-0.70942,0.70459,0.016679,-14.964
> view matrix models
> #8,-0.46812,-0.48875,0.7362,48.054,0.52687,0.51447,0.67656,-67.009,-0.70942,0.70459,0.016679,61.759
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.19629,-0.93417,0.29799,51.318,0.3527,0.21629,0.91039,-39.512,-0.91492,0.2838,0.28703,97.708
> select add #8
14400 atoms, 14700 bonds, 1882 residues, 2 models selected
> select subtract #8
5 models selected
> show #7 models
> hide #7 models
> show #7 models
> close #7
> show #!3 models
> hide #!8 target m
> hide #!3 models
> open 2zfg fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 2zfg fetched from pdbe_bio
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
note | Fetching compressed 2zfg bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/2zfg-assembly-1.cif.gz
2zfg bioassembly 1 title:
Structure of OMPF PORIN [more info...]
Chain information for 2zfg bioassembly 1 #7
---
Chain | Description
A AA AB | Outer membrane protein F
Non-standard residues in 2zfg bioassembly 1 #7
---
C8E — (C8E)
MG — (MG)
2zfg bioassembly 1 mmCIF Assemblies
---
1| author_and_software_defined_assembly
66 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Opened 1 biological assemblies for 2zfg
> select add #7
8952 atoms, 8142 bonds, 3 pseudobonds, 1992 residues, 2 models selected
> view matrix models
> #7,0.98048,-0.11937,-0.15625,6.2245,0.11642,0.99281,-0.027966,-0.081413,0.15847,0.0092297,0.98732,-0.79852
> ui mousemode right "move picked models"
> view matrix models
> #7,0.98048,-0.11937,-0.15625,-0.62457,0.11642,0.99281,-0.027966,45.553,0.15847,0.0092297,0.98732,82.795
> view matrix models
> #7,0.98048,-0.11937,-0.15625,-27.658,0.11642,0.99281,-0.027966,-26.535,0.15847,0.0092297,0.98732,191.83
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.072064,-0.37013,-0.92618,-17.836,-0.44698,0.84211,-0.30176,-18.762,0.89163,0.39224,-0.22613,153.18
> view matrix models
> #7,0.27279,-0.37944,-0.88408,-17.3,-0.83093,0.37025,-0.4153,11.57,0.48491,0.8479,-0.21429,124.03
> hide sel atoms
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 2zfg bioassembly 1_A SES surface #7.2: minimum, -17.31,
mean -2.87, maximum 13.57
Coulombic values for 2zfg bioassembly 1_AA SES surface #7.3: minimum, -17.45,
mean -2.87, maximum 13.65
Coulombic values for 2zfg bioassembly 1_AB SES surface #7.4: minimum, -17.37,
mean -2.87, maximum 13.49
To also show corresponding color key, enter the above coulombic command and
add key true
> view matrix models
> #7,-0.051178,0.090934,-0.99454,-50.875,-0.85788,0.50584,0.090396,7.2638,0.5113,0.85782,0.052122,126
> view matrix models
> #7,-0.060351,-0.13912,-0.98844,-35.075,-0.83585,0.54833,-0.02614,3.1968,0.54563,0.82461,-0.14937,126.27
> view matrix models
> #7,-0.0073733,-0.18629,-0.98247,-31.751,-0.93294,0.35495,-0.060303,15.836,0.35996,0.91613,-0.17641,119.56
> hide #!7 models
> view matrix models
> #7,-0.0073733,-0.18629,-0.98247,-31.751,-0.93294,0.35495,-0.060303,15.836,0.35996,0.91613,-0.17641,119.56
> show #6 models
> hide #6 models
> hide #6 target m
> close #6
> open 3k19 fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 3k19 fetched from pdbe_bio
---
warnings | Missing or incomplete sequence information. Inferred polymer connectivity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Missing or incomplete sequence information. Inferred polymer connectivity.
3k19 bioassembly 1 title:
OmpF porin [more info...]
Chain information for 3k19 bioassembly 1 #6.1
---
Chain | Description
A B C | Outer membrane protein F
3k19 bioassembly 1 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
3k19 bioassembly 2 title:
OmpF porin [more info...]
Chain information for 3k19 bioassembly 2 #6.2
---
Chain | Description
D E F | Outer membrane protein F
3k19 bioassembly 2 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
3k19 bioassembly 3 title:
OmpF porin [more info...]
Chain information for 3k19 bioassembly 3 #6.3
---
Chain | Description
G H I | Outer membrane protein F
3k19 bioassembly 3 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
3k19 bioassembly 4 title:
OmpF porin [more info...]
Chain information for 3k19 bioassembly 4 #6.4
---
Chain | Description
J K L | Outer membrane protein F
3k19 bioassembly 4 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
Opened 4 biological assemblies for 3k19
> close #6
> close #7
> open 3k19 fromDatabase pdb format mmcif
Summary of feedback from opening 3k19 fetched from pdb
---
note | Fetching compressed mmCIF 3k19 from http://files.rcsb.org/download/3k19.cif
3k19 title:
OmpF porin [more info...]
Chain information for 3k19 #6
---
Chain | Description | UniProt
A B C D E F G H I J K L | Outer membrane protein F | OMPF_ECOLI 1-340
3k19 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
> close #6
> open 3k19 fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 3k19 fetched from pdbe_bio
---
warnings | Missing or incomplete sequence information. Inferred polymer connectivity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Missing or incomplete sequence information. Inferred polymer connectivity.
3k19 bioassembly 1 title:
OmpF porin [more info...]
Chain information for 3k19 bioassembly 1 #6.1
---
Chain | Description
A B C | Outer membrane protein F
3k19 bioassembly 1 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
3k19 bioassembly 2 title:
OmpF porin [more info...]
Chain information for 3k19 bioassembly 2 #6.2
---
Chain | Description
D E F | Outer membrane protein F
3k19 bioassembly 2 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
3k19 bioassembly 3 title:
OmpF porin [more info...]
Chain information for 3k19 bioassembly 3 #6.3
---
Chain | Description
G H I | Outer membrane protein F
3k19 bioassembly 3 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
3k19 bioassembly 4 title:
OmpF porin [more info...]
Chain information for 3k19 bioassembly 4 #6.4
---
Chain | Description
J K L | Outer membrane protein F
3k19 bioassembly 4 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
Opened 4 biological assemblies for 3k19
> open 2j1n fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 2j1n fetched from pdbe_bio
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
notes | Fetching compressed 2j1n bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/2j1n-assembly-1.cif.gz
Fetching CCD D12 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/D12/D12.cif
2j1n bioassembly 1 title:
osmoporin OmpC [more info...]
Chain information for 2j1n bioassembly 1 #7
---
Chain | Description
A B C | OUTER MEMBRANE PROTEIN C
Non-standard residues in 2j1n bioassembly 1 #7
---
CL — (CL)
D12 — (D12)
MG — (MG)
Opened 1 biological assemblies for 2j1n
> close #6.4
> close #6.3
> close #6.2
Drag select of OmpK35-KlebG_model .pdb_A SES surface, 2964 of 389238
triangles, 6rd3 bioassembly 2_D SES surface, 42 of 299598 triangles, 6rd3
bioassembly 2_F SES surface, 80454 of 300612 triangles, 2164 residues, 196
atoms, 156 bonds
> hide sel atoms
> select add #7
17508 atoms, 8397 bonds, 2746 residues, 5 models selected
> select add #6.1
17508 atoms, 16446 bonds, 2746 residues, 5 models selected
> select add #6
17508 atoms, 16446 bonds, 2746 residues, 6 models selected
> select subtract #6
9627 atoms, 8397 bonds, 1726 residues, 4 models selected
> select add #6.1
17508 atoms, 16446 bonds, 2746 residues, 5 models selected
> select subtract #7
8706 atoms, 8049 bonds, 1126 residues, 4 models selected
> select subtract #6.1
825 atoms, 106 residues, 3 models selected
> select add #6
8706 atoms, 8049 bonds, 1126 residues, 5 models selected
> select subtract #6
825 atoms, 106 residues, 3 models selected
> select add #2
17283 atoms, 16720 bonds, 2 pseudobonds, 2981 residues, 6 models selected
> select add #1
34330 atoms, 33959 bonds, 11 pseudobonds, 4121 residues, 10 models selected
> select subtract #1
17283 atoms, 16720 bonds, 2 pseudobonds, 2981 residues, 11 models selected
> select subtract #2
3 models selected
> select add #6.1
7881 atoms, 8049 bonds, 1020 residues, 1 model selected
> view matrix models
> #6.1,0.39306,-0.88059,0.26469,2.5266,-0.010598,0.2835,0.95891,-14.026,-0.91945,-0.37972,0.1021,22.979
> ui mousemode right "move picked models"
> view matrix models #7,1,0,0,52.56,0,1,0,-116,0,0,1,37.789
> view matrix models
> #6.1,0.39306,-0.88059,0.26469,45.749,-0.010598,0.2835,0.95891,-118.44,-0.91945,-0.37972,0.1021,123.72
> view matrix models #7,1,0,0,48.276,0,1,0,-106.77,0,0,1,36.455
> ui mousemode right "rotate selected models"
> view matrix models
> #6.1,0.3215,-0.94343,-0.081065,51.42,0.09425,-0.053302,0.99412,-120.4,-0.94221,-0.32725,0.071782,124.45
> view matrix models
> #6.1,0.25267,-0.88979,-0.38005,56.488,0.15031,-0.35192,0.92388,-120.29,-0.9558,-0.29057,0.044821,125.02
> view matrix models
> #6.1,0.33851,-0.93288,-0.1231,51.828,0.10814,-0.091385,0.98993,-120.54,-0.93473,-0.34841,0.069948,124.37
> select subtract #6.1
Nothing selected
> select add #6.1
7881 atoms, 8049 bonds, 1020 residues, 1 model selected
> select subtract #6.1
Nothing selected
> select add #7
8802 atoms, 8397 bonds, 1620 residues, 1 model selected
> view matrix models
> #7,0.96038,-0.2779,0.021039,50.74,0.27705,0.96018,0.036133,-114.89,-0.030243,-0.028873,0.99913,37.494
> view matrix models
> #7,0.96504,-0.2596,0.036199,50.43,0.25811,0.96524,0.04098,-114.39,-0.045579,-0.030204,0.9985,37.954
> select add #8
23202 atoms, 23097 bonds, 3502 residues, 2 models selected
> select subtract #8
8802 atoms, 8397 bonds, 1620 residues, 6 models selected
> select subtract #7
Nothing selected
> select add #6.1
7881 atoms, 8049 bonds, 1020 residues, 1 model selected
> view matrix models
> #6.1,0.37848,-0.91798,-0.1186,51.317,0.022432,-0.119,0.99264,-119.61,-0.92534,-0.37835,-0.024447,125.58
> view matrix models
> #6.1,0.73765,0.26873,0.6194,37.672,-0.44186,-0.50152,0.7438,-111.06,0.51052,-0.82235,-0.2512,111.95
> view matrix models
> #6.1,0.6456,-0.76202,0.050278,45.98,-0.73454,-0.60161,0.31388,-101.68,-0.20893,-0.23957,-0.94813,130.55
> view matrix models
> #6.1,0.69744,-0.69165,0.18761,43.495,-0.60893,-0.70998,-0.35372,-93.754,0.37786,0.13246,-0.91634,123.65
> view matrix models
> #6.1,0.68424,-0.64673,0.33697,41.566,-0.5713,-0.76257,-0.30349,-94.939,0.45324,0.015145,-0.89126,122.34
> view matrix models
> #6.1,0.74644,-0.56817,0.34643,40.78,-0.50471,-0.82265,-0.26174,-96.342,0.4337,0.020525,-0.90082,122.7
> view matrix models
> #6.1,0.74232,-0.61109,0.27482,41.808,-0.53861,-0.78819,-0.29775,-95.415,0.39857,0.073007,-0.91423,123.34
> view matrix models
> #6.1,0.74051,-0.60311,0.29649,41.528,-0.48733,-0.78568,-0.38107,-94.822,0.46277,0.1377,-0.87572,122.1
> view matrix models
> #6.1,0.70678,-0.49079,0.5095,38.986,-0.40148,-0.87127,-0.28233,-97.274,0.58247,-0.0050023,-0.81284,119.73
> view matrix models
> #6.1,0.72045,-0.51024,0.46969,39.377,-0.43786,-0.85987,-0.26249,-97.128,0.53781,-0.016546,-0.8429,120.66
> ui mousemode right "move picked models"
> view matrix models
> #6.1,0.72045,-0.51024,0.46969,76.971,-0.43786,-0.85987,-0.26249,-100.12,0.53781,-0.016546,-0.8429,127.07
> select subtract #6.1
Nothing selected
> ui mousemode right select
Drag select of 49 residues
Drag select of 2058 residues
> coulombic sel
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8rc202405250712 (2024-05-25)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Max
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: Mac15,11
Model Number: MRW33B/A
Chip: Apple M3 Max
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 36 GB
System Firmware Version: 11881.41.5
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.1 (23H222)
Kernel Version: Darwin 23.6.0
Time since boot: 80 days, 17 hours, 24 minutes
Graphics/Displays:
Apple M3 Max:
Chipset Model: Apple M3 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
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: 1.6.3
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
ChimeraX-AtomicLibrary: 14.0.5
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: 1.8rc202405250712
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: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
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: 1.13.4
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: 3.0.12
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: 1.4.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
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: 4.52.4
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: 8.1.2
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
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: 3.0.44
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
traitlets: 5.14.2
typing-extensions: 4.12.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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