![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17940 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x000000020520c240 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, tables._comp_lzo, tables._comp_bzip2, tables.utilsextension, numexpr.interpreter, tables.hdf5extension, tables.linkextension, tables.lrucacheextension, tables.tableextension, tables.indexesextension, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, psutil._psutil_osx, psutil._psutil_posix (total: 72)
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{
"uptime" : 830000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 936,
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"build" : "24C101",
"releaseType" : "User"
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"captureTime" : "2025-06-08 22:54:12.4238 +0200",
"codeSigningMonitor" : 1,
"incident" : "91D578B5-B57F-4BFE-A1F7-29343111B73B",
"pid" : 907,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-28 11:17:00.9767 +0200",
"procStartAbsTime" : 4384240681,
"procExitAbsTime" : 19965440510483,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"9287E029-B919-5F84-921E-C986DAEAFE45","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "749779CA-88A6-02AD-11B4-F559E016BA64",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "DCCD0C54-6325-46FD-AD91-1FA2CF5F0E52",
"wakeTime" : 34691,
"sleepWakeUUID" : "C6037DA5-F6A9-4011-9023-B2A525A18357",
"sip" : "enabled",
"vmRegionInfo" : "0x168 is not in any region. Bytes before following region: 4331585176\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1022ec000-1022f0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000168","rawCodes":[1,360],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000168"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":907},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/Prediction_Fernando/CyaB_2_PilG2_model_0.cif
CyaB_2_PilG2_model_0.cif title:
. [more info...]
Chain information for CyaB_2_PilG2_model_0.cif #1
---
Chain | Description
A B | .
C D | .
Color CyaB_2_PilG2_model_0.cif by residue attribute pLDDT_score
Computing secondary structure
> set bgColor white
> set bgColor #ffffff00
> select /C:1-135
1029 atoms, 1044 bonds, 135 residues, 1 model selected
> select /D:1-135
1029 atoms, 1044 bonds, 135 residues, 1 model selected
> select /C:1-135
1029 atoms, 1044 bonds, 135 residues, 1 model selected
> select /A:1-463
3610 atoms, 3677 bonds, 463 residues, 1 model selected
> select /B:1-463
3610 atoms, 3677 bonds, 463 residues, 1 model selected
> open /Users/ctsai/Documents/AlphaFold_CyaB/H0N27-0934_PAO-CyaB-
> copy-2/pred.model_idx_0.rank_1.cif
pred.model_idx_0.rank_1.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.model_idx_0.rank_1.cif #2
---
Chain | Description
A B | protein-0-1
Color pred.model_idx_0.rank_1.cif by residue attribute pLDDT_score
Computing secondary structure
> close #1
> select #2/A:1-489
4021 atoms, 4120 bonds, 489 residues, 1 model selected
> select #2/B:1-489
4021 atoms, 4120 bonds, 489 residues, 1 model selected
> close session
> open /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2/pred.rank_0.cif
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #1
---
Chain | Description
A B | Entity A
Color pred.rank_0.cif by residue attribute pLDDT_score
Computing secondary structure
> color #1 #2ea9dfff
> color #1 #7ab8bfff
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-ATP-2-Mg2-4/pred.rank_0.cif
Summary of feedback from opening
/Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-ATP-2-Mg2-4/pred.rank_0.cif
---
warnings | Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Unable to fetch template for 'LIG6': will connect using distance criteria
Unable to fetch template for 'LIG7': will connect using distance criteria
1 messages similar to the above omitted
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #2
---
Chain | Description
A B | Entity A
Non-standard residues in pred.rank_0.cif #2
---
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
LIG6 — (LIG6)
LIG7 — (LIG7)
LIG8 — (LIG8)
Color pred.rank_0.cif by residue attribute pLDDT_score
Computing secondary structure
> color #2 #f28f6bff
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
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 pred.rank_0.cif, chain A (#1) with pred.rank_0.cif, chain A (#2),
sequence alignment score = 2362.3
RMSD between 426 pruned atom pairs is 1.015 angstroms; (across all 463 pairs:
1.421)
> close #1
> close
> open "/Volumes/Gani_sv_WS/Optical_tweezer/20241104_wt/20241104-141211 Marker
> 2.h5"
Summary of feedback from opening
/Volumes/Gani_sv_WS/Optical_tweezer/20241104_wt/20241104-141211 Marker 2.h5
---
notes | /Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tables/group.py:1192: UserWarning: problems loading leaf ``/Calibration/17/JSON``::
variable length strings are not supported yet
The leaf will become an ``UnImplemented`` node.
warnings.warn(
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/group.py:1192: UserWarning: problems loading leaf
``/Marker/2``::
variable length strings are not supported yet
The leaf will become an ``UnImplemented`` node.
warnings.warn(
Failed opening file
/Volumes/Gani_sv_WS/Optical_tweezer/20241104_wt/20241104-141211 Marker 2.h5:
HDF5 file /Volumes/Gani_sv_WS/Optical_tweezer/20241104_wt/20241104-141211
Marker 2.h5 contains no 3d arrays
> open /Users/ctsai/Documents/Model_building/Phenix/Final_models/SS-
> bond/final_SS_resampled_WT_solid_woG1_Q23.pdb
Chain information for final_SS_resampled_WT_solid_woG1_Q23.pdb #1
---
Chain | Description
A B C D E F G H I J K L M N O P Q R S T U V | No description available
> show cartoons
> hide surfaces
> hide cartoons
> show cartoons
> hide cartoons
> hide atoms
> show cartoons
> dssp
Computing secondary structure
> select /C
1042 atoms, 1057 bonds, 143 residues, 1 model selected
> select ~sel
21882 atoms, 22197 bonds, 3003 residues, 1 model selected
> surface hidePatches sel
> hide sel target a
> cartoon hide sel
> select /C:E48
Nothing selected
Alignment identifier is 1
> select /N,A-M,O-V:48
198 atoms, 176 bonds, 22 residues, 1 model selected
> select /N,A-M,O-V:48
198 atoms, 176 bonds, 22 residues, 1 model selected
> select /C:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> color #1 #d92b04ff
> select /C:23
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C:75
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /C:30
11 atoms, 10 bonds, 1 residue, 1 model selected
> close
> open "/Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-173350
> Marker 10.h5"
Failed opening file
/Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-173350 Marker
10.h5:
HDF5 error back trace
File "H5F.c", line 836, in H5Fopen
unable to synchronously open file
File "H5F.c", line 796, in H5F__open_api_common
unable to open file
File "H5VLcallback.c", line 3863, in H5VL_file_open
open failed
File "H5VLcallback.c", line 3675, in H5VL__file_open
open failed
File "H5VLnative_file.c", line 128, in H5VL__native_file_open
unable to open file
File "H5Fint.c", line 1910, in H5F_open
unable to lock the file
File "H5FD.c", line 2412, in H5FD_lock
driver lock request failed
File "H5FDsec2.c", line 941, in H5FD__sec2_lock
unable to lock file, errno = 35, error message = 'Resource temporarily
unavailable'
End of HDF5 error back trace
Unable to open/create file
'/Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-173350 Marker
10.h5'
> open "/Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-181112
> Marker 14.h5"
Summary of feedback from opening
/Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-181112 Marker 14.h5
---
notes | /Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tables/group.py:1192: UserWarning: problems loading leaf ``/Calibration/123/JSON``::
variable length strings are not supported yet
The leaf will become an ``UnImplemented`` node.
warnings.warn(
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/group.py:1192: UserWarning: problems loading leaf
``/Marker/14``::
variable length strings are not supported yet
The leaf will become an ``UnImplemented`` node.
warnings.warn(
Failed opening file
/Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-181112 Marker
14.h5:
HDF5 file /Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-181112
Marker 14.h5 contains no 3d arrays
> open "/Volumes/Gani_sv_WS/Optical_tweezer/20250303_wt/20250303-153026 Marker
> 1.h5"
Summary of feedback from opening
/Volumes/Gani_sv_WS/Optical_tweezer/20250303_wt/20250303-153026 Marker 1.h5
---
notes | /Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tables/group.py:1192: UserWarning: problems loading leaf ``/Calibration/52/JSON``::
variable length strings are not supported yet
The leaf will become an ``UnImplemented`` node.
warnings.warn(
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/group.py:1192: UserWarning: problems loading leaf
``/Calibration/53/JSON``::
variable length strings are not supported yet
The leaf will become an ``UnImplemented`` node.
warnings.warn(
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/group.py:1192: UserWarning: problems loading leaf
``/Marker/1``::
variable length strings are not supported yet
The leaf will become an ``UnImplemented`` node.
warnings.warn(
Failed opening file
/Volumes/Gani_sv_WS/Optical_tweezer/20250303_wt/20250303-153026 Marker 1.h5:
HDF5 file /Volumes/Gani_sv_WS/Optical_tweezer/20250303_wt/20250303-153026
Marker 1.h5 contains no 3d arrays
> open "/Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-183158
> Marker 16.h5"
Summary of feedback from opening
/Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-183158 Marker 16.h5
---
notes | /Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tables/group.py:1192: UserWarning: problems loading leaf ``/Calibration/141/JSON``::
variable length strings are not supported yet
The leaf will become an ``UnImplemented`` node.
warnings.warn(
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/group.py:1192: UserWarning: problems loading leaf
``/Marker/16``::
variable length strings are not supported yet
The leaf will become an ``UnImplemented`` node.
warnings.warn(
Failed opening file
/Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-183158 Marker
16.h5:
HDF5 file /Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-183158
Marker 16.h5 contains no 3d arrays
> open
> /Users/ctsai/Documents/Fernando_binders/all_binders/1846_binder_AF_16_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
> format pdb
Chain information for
1846_binder_AF_16_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> close session
> open /Users/ctsai/Documents/Model_building/mm_PilTs_I_9ewx_N.cxs format
> session
> set bgColor transparent
opened ChimeraX session
> set bgColor white
> set bgColor #ffffff00
> hide #2 models
> select #1:30
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1:75
4 atoms, 3 bonds, 1 residue, 1 model selected
> color #1 #d92b04ff
> select #1:23
9 atoms, 8 bonds, 1 residue, 1 model selected
> close session
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-ATP-2-Mg2-4/pred.rank_0.cif
Summary of feedback from opening
/Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-ATP-2-Mg2-4/pred.rank_0.cif
---
warnings | Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Unable to fetch template for 'LIG6': will connect using distance criteria
Unable to fetch template for 'LIG7': will connect using distance criteria
1 messages similar to the above omitted
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #1
---
Chain | Description
A B | Entity A
Non-standard residues in pred.rank_0.cif #1
---
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
LIG6 — (LIG6)
LIG7 — (LIG7)
LIG8 — (LIG8)
Color pred.rank_0.cif by residue attribute pLDDT_score
Computing secondary structure
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/pred.rank_0.cif
Summary of feedback from opening
/Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/pred.rank_0.cif
---
warnings | Unable to fetch template for 'LIG10': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Unable to fetch template for 'LIG6': will connect using distance criteria
Unable to fetch template for 'LIG7': will connect using distance criteria
Unable to fetch template for 'LIG8': will connect using distance criteria
1 messages similar to the above omitted
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #2
---
Chain | Description
A B | Entity A
C D | Entity C
Non-standard residues in pred.rank_0.cif #2
---
LIG10 — (LIG10)
LIG5 — (LIG5)
LIG6 — (LIG6)
LIG7 — (LIG7)
LIG8 — (LIG8)
LIG9 — (LIG9)
Color pred.rank_0.cif by residue attribute pLDDT_score
Computing secondary structure
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> close #1
> show #2 models
> select ::name="LIG10"
1 atom, 1 residue, 1 model selected
> select :LIG10
1 atom, 1 residue, 1 model selected
> hide sel target a
> select :LIG5
31 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel target a
> select :LIG6
31 atoms, 33 bonds, 1 residue, 1 model selected
> hide sel target a
> select :LIG7
1 atom, 1 residue, 1 model selected
> hide sel target a
> select :LIG8
1 atom, 1 residue, 1 model selected
> hide sel target a
> select :LIG9
1 atom, 1 residue, 1 model selected
> hide sel target a
> show sel surfaces
> hide sel cartoons
> hide sel atoms
> show sel surfaces
> select :LIG9
1 atom, 1 residue, 1 model selected
> select :LIG9
1 atom, 1 residue, 1 model selected
> hide (#!2 & sel) target a
> hide sel atoms
> hide sel cartoons
> show sel surfaces
> select clear
> show surfaces
> hide cartoons
> color #2 #986db2ff
> select #2/C:1-135
1029 atoms, 1044 bonds, 135 residues, 1 model selected
> select #2/D:1-135
1029 atoms, 1044 bonds, 135 residues, 1 model selected
> select /C
1029 atoms, 1044 bonds, 135 residues, 1 model selected
> color (#!2 & sel) #f28f6bff
> select /D
1029 atoms, 1044 bonds, 135 residues, 1 model selected
> color (#!2 & sel) #ebaaa9ff
> color (#!2 & sel) #f28f6bff
> graphics silhouettes true
> lighting full
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> select clear
> save
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/colored.cxs
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif
Summary of feedback from opening
/Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif
---
warnings | Atom C_1 is not in the residue template for LIG /C:1
Atom C_1 is not in the residue template for LIG /D:1
pred.model_idx_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.model_idx_0.cif #1
---
Chain | Description
A B | protein-0-1
E F | protein-2-1
Non-standard residues in pred.model_idx_0.cif #1
---
LIG — (LIG)
Color pred.model_idx_0.cif by residue attribute pLDDT_score
Computing secondary structure
> hide #1 models
> show #1 models
> close #1
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-fimL-2-ATP-2-Mg-4/pred.rank_0.cif
Summary of feedback from opening
/Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-fimL-2-ATP-2-Mg-4/pred.rank_0.cif
---
warnings | Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Unable to fetch template for 'LIG6': will connect using distance criteria
Unable to fetch template for 'LIG7': will connect using distance criteria
Unable to fetch template for 'LIG8': will connect using distance criteria
1 messages similar to the above omitted
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #1
---
Chain | Description
A B | Entity A
C | Entity C
Non-standard residues in pred.rank_0.cif #1
---
LIG4 — (LIG4)
LIG5 — (LIG5)
LIG6 — (LIG6)
LIG7 — (LIG7)
LIG8 — (LIG8)
LIG9 — (LIG9)
Color pred.rank_0.cif by residue attribute pLDDT_score
Computing secondary structure
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-fimL-2-ATP-2-Mg-4/pred.rank_0.cif
Summary of feedback from opening
/Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-fimL-2-ATP-2-Mg-4/pred.rank_0.cif
---
warnings | Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Unable to fetch template for 'LIG6': will connect using distance criteria
Unable to fetch template for 'LIG7': will connect using distance criteria
Unable to fetch template for 'LIG8': will connect using distance criteria
1 messages similar to the above omitted
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #3
---
Chain | Description
A B | Entity A
C | Entity C
Non-standard residues in pred.rank_0.cif #3
---
LIG4 — (LIG4)
LIG5 — (LIG5)
LIG6 — (LIG6)
LIG7 — (LIG7)
LIG8 — (LIG8)
LIG9 — (LIG9)
Color pred.rank_0.cif by residue attribute pLDDT_score
Computing secondary structure
> close #3
> select #1/A,B #2/A,B
14440 atoms, 14708 bonds, 1852 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!2 & sel to #1 & sel
Computing secondary structure
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 pred.rank_0.cif, chain A (#1) with pred.rank_0.cif, chain A (#2),
sequence alignment score = 2392.3
RMSD between 272 pruned atom pairs is 0.683 angstroms; (across all 463 pairs:
4.626)
> select #1/A,B
7220 atoms, 7354 bonds, 926 residues, 1 model selected
> select #1
11561 atoms, 11758 bonds, 1494 residues, 1 model selected
> show sel surfaces
> hide sel cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select #1/C,D
4306 atoms, 4371 bonds, 563 residues, 1 model selected
> select #1/C
4275 atoms, 4338 bonds, 562 residues, 1 model selected
> color (#!1 & sel) #bdc0baff
> color (#!1 & sel) #2ea9dfff
> select #1/a,B
7220 atoms, 7354 bonds, 926 residues, 1 model selected
> color (#!1 & sel) #986db2ff
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> select clear
> show #!1 cartoons
> hide #!1 surfaces
> show #!1 surfaces
> hide #!1 surfaces
> show #!1 surfaces
> hide #!1 surfaces
> show #!1 surfaces
> hide #!1 surfaces
> show #!2 models
> hide #!2 models
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-fimL-1-ATP-2-Mg-4/pred.rank_0.cif
Summary of feedback from opening
/Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-fimL-1-ATP-2-Mg-4/pred.rank_0.cif
---
warnings | Unable to fetch template for 'LIG10': will connect using distance criteria
Unable to fetch template for 'LIG11': will connect using distance criteria
Unable to fetch template for 'LIG6': will connect using distance criteria
Unable to fetch template for 'LIG7': will connect using distance criteria
Unable to fetch template for 'LIG8': will connect using distance criteria
1 messages similar to the above omitted
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #3
---
Chain | Description
A B | Entity A
C D | Entity C
E | Entity E
Non-standard residues in pred.rank_0.cif #3
---
LIG10 — (LIG10)
LIG11 — (LIG11)
LIG6 — (LIG6)
LIG7 — (LIG7)
LIG8 — (LIG8)
LIG9 — (LIG9)
Color pred.rank_0.cif by residue attribute pLDDT_score
> show #3#!1 surfaces
> hide #!1,3 surfaces
> hide #!1,3 cartoons
> hide #!1,3 atoms
> show #!1,3 surfaces
> select #2/A,B #3/A,B
14440 atoms, 14708 bonds, 1852 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!3 & sel to #2 & sel
Computing secondary structure
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 pred.rank_0.cif, chain A (#2) with pred.rank_0.cif, chain B (#3),
sequence alignment score = 2381.5
RMSD between 397 pruned atom pairs is 0.718 angstroms; (across all 463 pairs:
3.708)
> color #1 #bdc0baff
> color #2 #986db2ff
> color #2 #448f91ff
> color #3 #448f91ff
> color #1 #bdc0baff
> color #2 #986db2ff
> color #3 #7ba23fff
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> select #2/C,D
2058 atoms, 2088 bonds, 270 residues, 1 model selected
> select #3/C,D
2058 atoms, 2088 bonds, 270 residues, 1 model selected
> color (#!3 & sel) #eb7a77ff
> select clear
> show #!3 cartoons
> hide #!3 surfaces
> show #!2 models
> hide #!3 models
> hide #!2 cartoons
> show #!2 cartoons
> hide #!2 surfaces
> show #!2 surfaces
> show #!1 models
> hide #!2 models
> color #1 #986db2ff
> select #2/C
1029 atoms, 1044 bonds, 135 residues, 1 model selected
> select #1/C
4275 atoms, 4338 bonds, 562 residues, 1 model selected
> color (#!1 & sel) #2ea9dfff
> select clear
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif
Summary of feedback from opening
/Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif
---
warnings | Atom C_1 is not in the residue template for LIG /C:1
Atom C_1 is not in the residue template for LIG /D:1
pred.model_idx_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.model_idx_0.cif #4
---
Chain | Description
A B | protein-0-1
E F | protein-2-1
Non-standard residues in pred.model_idx_0.cif #4
---
LIG — (LIG)
Color pred.model_idx_0.cif by residue attribute pLDDT_score
Computing secondary structure
> hide #!1 models
> close #4
> hide #2.1 models
> show #2.1 models
> select add #2.1
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> hide #!2 models
> show #!2 models
> select subtract #2.1
1 model selected
> show #!2 cartoons
> hide #!2 surfaces
> select add #2.1
1 atom, 1 residue, 1 model selected
> select subtract #2.1
1 model selected
> select add #2.2
3610 atoms, 463 residues, 1 model selected
> select subtract #2.2
1 model selected
> select add #2.1
1 atom, 1 residue, 1 model selected
> select subtract #2.1
1 model selected
> select add #2.4
1029 atoms, 135 residues, 1 model selected
> select subtract #2.4
1 model selected
> select add #2.5
1029 atoms, 135 residues, 1 model selected
> select subtract #2.5
1 model selected
> close #3
> show #!1 models
> hide #!2 models
> select add #1.3
4275 atoms, 562 residues, 1 model selected
> select subtract #1.3
1 model selected
> select add #1.2
3610 atoms, 463 residues, 1 model selected
> select subtract #1.2
1 model selected
> select add #1.1
3610 atoms, 463 residues, 1 model selected
> select subtract #1.1
1 model selected
> select add #1.3
4275 atoms, 562 residues, 1 model selected
> select subtract #1.3
1 model selected
> hide #!1 cartoons
> show #!1 cartoons
> hide #!1 surfaces
> close #1
> show #!2 models
> hide #!2 models
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-fimL-2-ATP-2-Mg-4/pred.rank_1.cif
Summary of feedback from opening
/Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-fimL-2-ATP-2-Mg-4/pred.rank_1.cif
---
warnings | Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Unable to fetch template for 'LIG6': will connect using distance criteria
Unable to fetch template for 'LIG7': will connect using distance criteria
Unable to fetch template for 'LIG8': will connect using distance criteria
1 messages similar to the above omitted
pred.rank_1.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_1.cif #1
---
Chain | Description
A B | Entity A
C | Entity C
Non-standard residues in pred.rank_1.cif #1
---
LIG4 — (LIG4)
LIG5 — (LIG5)
LIG6 — (LIG6)
LIG7 — (LIG7)
LIG8 — (LIG8)
LIG9 — (LIG9)
Color pred.rank_1.cif by residue attribute pLDDT_score
Computing secondary structure
> color #1 #2ea9dfff
> color #1 #bdc0baff
> color #1 #986db2ff
> color #1 #bdc0baff
> ui tool show Matchmaker
> matchmaker #1 to #2
Computing secondary structure
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 pred.rank_0.cif, chain A (#2) with pred.rank_1.cif, chain B (#1),
sequence alignment score = 2377.9
RMSD between 335 pruned atom pairs is 0.991 angstroms; (across all 463 pairs:
3.127)
> show #!2 models
> select #1/A,B #2/A,B
14440 atoms, 14708 bonds, 1852 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #1 & sel to #2 & sel
Computing secondary structure
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 pred.rank_0.cif, chain A (#2) with pred.rank_1.cif, chain B (#1),
sequence alignment score = 2377.9
RMSD between 335 pruned atom pairs is 0.991 angstroms; (across all 463 pairs:
3.127)
> select clear
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> hide #1 models
> show #!2 models
> show #1 models
> hide #!2 models
> hide #1 models
> show #!2 models
> show #!2 surfaces
> select #12/C,D
Nothing selected
> select #2/C,D
2058 atoms, 2088 bonds, 270 residues, 1 model selected
> color (#!2 & sel) #f28f6bff
> select clear
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/pred.rank_0.cif
Summary of feedback from opening
/Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/pred.rank_0.cif
---
warnings | Unable to fetch template for 'LIG10': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Unable to fetch template for 'LIG6': will connect using distance criteria
Unable to fetch template for 'LIG7': will connect using distance criteria
Unable to fetch template for 'LIG8': will connect using distance criteria
1 messages similar to the above omitted
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #3
---
Chain | Description
A B | Entity A
C D | Entity C
Non-standard residues in pred.rank_0.cif #3
---
LIG10 — (LIG10)
LIG5 — (LIG5)
LIG6 — (LIG6)
LIG7 — (LIG7)
LIG8 — (LIG8)
LIG9 — (LIG9)
Color pred.rank_0.cif by residue attribute pLDDT_score
Computing secondary structure
> hide #!2 models
> close #3
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif
Summary of feedback from opening
/Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif
---
warnings | Atom C_1 is not in the residue template for LIG /C:1
Atom C_1 is not in the residue template for LIG /D:1
pred.model_idx_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.model_idx_0.cif #3
---
Chain | Description
A B | protein-0-1
E F | protein-2-1
Non-standard residues in pred.model_idx_0.cif #3
---
LIG — (LIG)
Color pred.model_idx_0.cif by residue attribute pLDDT_score
Computing secondary structure
> select :LIG
66 atoms, 66 bonds, 6 residues, 1 model selected
> select #3/E:1-135
1029 atoms, 1044 bonds, 135 residues, 1 model selected
> select #3/F:1-135
1029 atoms, 1044 bonds, 135 residues, 1 model selected
> select #3/B:1-463
3610 atoms, 3677 bonds, 463 residues, 1 model selected
> select #3/A:1-463
3610 atoms, 3677 bonds, 463 residues, 1 model selected
> select #3/E:1-135
1029 atoms, 1044 bonds, 135 residues, 1 model selected
> select #3/F:1-135
1029 atoms, 1044 bonds, 135 residues, 1 model selected
> select :LIG
66 atoms, 66 bonds, 6 residues, 1 model selected
> close #3
> show #1 models
> show #!2 models
> hide #1 models
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/Prediction_Fernando/CyaB_2_PilG2_model_0.cif
CyaB_2_PilG2_model_0.cif title:
. [more info...]
Chain information for CyaB_2_PilG2_model_0.cif #3
---
Chain | Description
A B | .
C D | .
Color CyaB_2_PilG2_model_0.cif by residue attribute pLDDT_score
Computing secondary structure
> color #3 #7ab8bfff
> select #3/A,B
7220 atoms, 7354 bonds, 926 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #3 & sel to #2 & sel
No 'to' model specified
> matchmaker #3 & sel to #2
Computing secondary structure
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 pred.rank_0.cif, chain A (#2) with CyaB_2_PilG2_model_0.cif, chain
A (#3), sequence alignment score = 2361.7
RMSD between 281 pruned atom pairs is 1.236 angstroms; (across all 463 pairs:
4.894)
> show sel surfaces
> select clear
> close #1
> select #3/A,B #2/A,B
14440 atoms, 14708 bonds, 1852 residues, 2 models selected
> show sel surfaces
> color (#!2-3 & sel) #ffffffff
> color (#!2-3 & sel) #ebebebff
> color (#!2-3 & sel) #d6d6d6ff
> select #3/C,D
2058 atoms, 2088 bonds, 270 residues, 1 model selected
> color sel #7ba23fff
> color sel #bec23fff
> color sel #ddd23bff
> surface hidePatches sel
> select #2/C,D
2058 atoms, 2088 bonds, 270 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> select #3/C,D
2058 atoms, 2088 bonds, 270 residues, 1 model selected
> color sel #2ea9dfff
> select clear
> select #3/A,B #2/A,B
14440 atoms, 14708 bonds, 1852 residues, 2 models selected
> color (#!2-3 & sel) #ffffffff
> color (#!2-3 & sel) #ebebebff
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting full
> lighting soft
> lighting simple
> lighting soft
> color (#!2-3 & sel) #ebebebff
> color (#!2-3 & sel) #ebebebf9
> color (#!2-3 & sel) #ebebebf2
> color (#!2-3 & sel) #ebebebeb
> color (#!2-3 & sel) #ebebebd7
> color (#!2-3 & sel) #ebebebca
> color (#!2-3 & sel) #ebebebc7
> color (#!2-3 & sel) #ebebebbe
> color (#!2-3 & sel) #ebebebbc
> color (#!2-3 & sel) #ebebebbe
> color (#!2-3 & sel) #ebebebc3
> color (#!2-3 & sel) #ebebebc9
> color (#!2-3 & sel) #ebebebcb
> color (#!2-3 & sel) #ebebebd2
> color (#!2-3 & sel) #ebebebd8
> color (#!2-3 & sel) #ebebebde
> color (#!2-3 & sel) #ebebebdf
> color (#!2-3 & sel) #ebebebcc
> color (#!2-3 & sel) #ebebebc9
> color (#!2-3 & sel) #ebebebbe
> color (#!2-3 & sel) #c0c0c0ff
> color (#!2-3 & sel) #c0c0c0f0
> select clear
> select #3/A,B #2/A,B
14440 atoms, 14708 bonds, 1852 residues, 2 models selected
> color (#!2-3 & sel) #c0c0c0ef
> color (#!2-3 & sel) #c0c0c0ea
> color (#!2-3 & sel) #c0c0c0e6
> color (#!2-3 & sel) #c0c0c0e2
> color (#!2-3 & sel) #c0c0c0e0
> color (#!2-3 & sel) #c0c0c0dc
> color (#!2-3 & sel) #c0c0c0d9
> color (#!2-3 & sel) #c0c0c0d4
> color (#!2-3 & sel) #c0c0c0ce
> color (#!2-3 & sel) #c0c0c0c4
> color (#!2-3 & sel) #c0c0c0b9
> color (#!2-3 & sel) #c0c0c0ae
> color (#!2-3 & sel) #c0c0c0ab
> color (#!2-3 & sel) #c0c0c0aa
> color (#!2-3 & sel) #c0c0c0a6
> color (#!2-3 & sel) #c0c0c0a0
> color (#!2-3 & sel) #c0c0c09d
> color (#!2-3 & sel) #c0c0c09a
> color (#!2-3 & sel) #c0c0c097
> color (#!2-3 & sel) #c0c0c090
> color (#!2-3 & sel) #c0c0c08a
> color (#!2-3 & sel) #c0c0c082
> color (#!2-3 & sel) #c0c0c07d
> color (#!2-3 & sel) #c0c0c078
> color (#!2-3 & sel) #c0c0c06d
> color (#!2-3 & sel) #c0c0c066
> color (#!2-3 & sel) #c0c0c060
> color (#!2-3 & sel) #c0c0c05d
> color (#!2-3 & sel) #c0c0c055
> color (#!2-3 & sel) #c0c0c051
> color (#!2-3 & sel) #c0c0c04e
> color (#!2-3 & sel) #c0c0c04b
> color (#!2-3 & sel) #c0c0c049
> color (#!2-3 & sel) #c0c0c046
> color (#!2-3 & sel) #c0c0c042
> color (#!2-3 & sel) #c0c0c03f
> color (#!2-3 & sel) #c0c0c03c
> color (#!2-3 & sel) #c0c0c03a
> color (#!2-3 & sel) #c0c0c032
> color (#!2-3 & sel) #c0c0c031
> color (#!2-3 & sel) #c0c0c027
> color (#!2-3 & sel) #c0c0c018
> color (#!2-3 & sel) #c0c0c014
> color (#!2-3 & sel) #c0c0c00e
> color (#!2-3 & sel) #c0c0c00d
> color (#!2-3 & sel) #c0c0c00b
> color (#!2-3 & sel) #c0c0c009
> color (#!2-3 & sel) #c0c0c018
> color (#!2-3 & sel) #c0c0c03b
> color (#!2-3 & sel) #c0c0c057
> color (#!2-3 & sel) #c0c0c061
> color (#!2-3 & sel) #c0c0c064
> color (#!2-3 & sel) #c0c0c067
> color (#!2-3 & sel) #c0c0c068
> color (#!2-3 & sel) #c0c0c060
> color (#!2-3 & sel) #c0c0c05a
> color (#!2-3 & sel) #c0c0c056
> color (#!2-3 & sel) #c0c0c053
> color (#!2-3 & sel) #c0c0c052
> color (#!2-3 & sel) #c0c0c051
> color (#!2-3 & sel) #c0c0c04d
> color (#!2-3 & sel) #c0c0c043
> select clear
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/ACIAD1397-copy-2/pred.model_idx_0.rank_3.cif
pred.model_idx_0.rank_3.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.model_idx_0.rank_3.cif #1
---
Chain | Description
A B | protein-0-1
Color pred.model_idx_0.rank_3.cif by residue attribute pLDDT_score
Computing secondary structure
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #1 models
> show #1 models
> close #1
> save
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/chai1_alphafold3.cxs
> close session
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/colored.cxs
opened ChimeraX session
> lighting soft
> save /Users/ctsai/Desktop/image16.png supersample 3
> hide surfaces
> show cartoons
> hide atoms
> save /Users/ctsai/Desktop/image17.png supersample 3
> open /Users/ctsai/Desktop/image17.png
Opened multi-channel map image17.png as #1, 3 channels, grid size 1344,850,1,
pixel 1, shown at step 1, values uint8
> open /Users/ctsai/Desktop/image16.png
Opened multi-channel map image16.png as #3, 3 channels, grid size 1344,850,1,
pixel 1, shown at step 1, values uint8
> undo
> close session
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/chai1_alphafold3.cxs
opened ChimeraX session
> close session
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/colored.cxs
> format session
opened ChimeraX session
> hide surfaces
> show cartoons
> hide atoms
> lighting flat
> lighting soft
> lighting simple
> lighting flat
> save /Users/ctsai/Desktop/image18.png supersample 3
> open /Volumes/Gani_sv_WS/colloborative_projects/Fernando/CyaB-PilG-
> MD/Chai1_CyaB2_PIlG2_ATP2_Mg4_POPE.cif
Summary of feedback from opening
/Volumes/Gani_sv_WS/colloborative_projects/Fernando/CyaB-PilG-
MD/Chai1_CyaB2_PIlG2_ATP2_Mg4_POPE.cif
---
warnings | Atom C_1 is not in the residue template for LIG /I:1
Atom C_1 is not in the residue template for LIG /J:1
Atom C_1 is not in the residue template for LIG /K:1
Atom C_1 is not in the residue template for LIG /L:1
Atom C_1 is not in the residue template for LIG /M:1
9 messages similar to the above omitted
Chai1_CyaB2_PIlG2_ATP2_Mg4_POPE.cif title:
Chai-1 predicted structure [more info...]
Chain information for Chai1_CyaB2_PIlG2_ATP2_Mg4_POPE.cif #1
---
Chain | Description
A B | CyaB_PilG_membrane_protein_2
C D | CyaB_PilG_membrane_protein_4
Non-standard residues in Chai1_CyaB2_PIlG2_ATP2_Mg4_POPE.cif #1
---
LIG — (LIG)
Color Chai1_CyaB2_PIlG2_ATP2_Mg4_POPE.cif by residue attribute pLDDT_score
Computing secondary structure
> close #1
> close session
No visible models!
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/chai1_alphafold3.cxs
> format session
opened ChimeraX session
> hide #!3 models
> color #2 #986db2ff
> select #1/C,D
Nothing selected
> select #2/C,D
2058 atoms, 2088 bonds, 270 residues, 1 model selected
> color (#!2 & sel) #f28f6bff
> select clear
> select #2/C,D@58
Nothing selected
> select #2/C,D
2058 atoms, 2088 bonds, 270 residues, 1 model selected
Alignment identifier is 1
> select #2/C-D:58
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/C-D:58
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select clear
> color #2 white
> color #2 #ebebebff
> close session
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-ATP-2-Mg2-4/pred.rank_0.cif
Summary of feedback from opening
/Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-ATP-2-Mg2-4/pred.rank_0.cif
---
warnings | Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Unable to fetch template for 'LIG6': will connect using distance criteria
Unable to fetch template for 'LIG7': will connect using distance criteria
1 messages similar to the above omitted
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #1
---
Chain | Description
A B | Entity A
Non-standard residues in pred.rank_0.cif #1
---
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
LIG6 — (LIG6)
LIG7 — (LIG7)
LIG8 — (LIG8)
Color pred.rank_0.cif by residue attribute pLDDT_score
Computing secondary structure
> hide atoms
> show surfaces
> color #1 #ebebebff
> select #1/A,B:1-17
252 atoms, 256 bonds, 34 residues, 1 model selected
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif
Summary of feedback from opening
/Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif
---
warnings | Atom C_1 is not in the residue template for LIG /C:1
Atom C_1 is not in the residue template for LIG /D:1
pred.model_idx_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.model_idx_0.cif #2
---
Chain | Description
A B | protein-0-1
E F | protein-2-1
Non-standard residues in pred.model_idx_0.cif #2
---
LIG — (LIG)
Color pred.model_idx_0.cif by residue attribute pLDDT_score
Computing secondary structure
> color #2 #bdc0baff
> color #2 #787d7bff
> select #1/A,B #2/A,B
14440 atoms, 14708 bonds, 1852 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #2 & sel to #1 & sel
Computing secondary structure
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 pred.rank_0.cif, chain A (#1) with pred.model_idx_0.cif, chain A
(#2), sequence alignment score = 2360.5
RMSD between 383 pruned atom pairs is 0.857 angstroms; (across all 463 pairs:
4.441)
> select #1/A,B
7220 atoms, 7354 bonds, 926 residues, 1 model selected
> select #1/A,B
7220 atoms, 7354 bonds, 926 residues, 1 model selected
> color #2 #4f4f48ff
> color #2 #d6d6d6ff
> color #2 silver
> color #2 #919191ff
> color #2 #797979ff
> color #2 #ebebebff
> color #2 #ebebeb53
> color #2 #ebebebff
> select #1/A,B
7220 atoms, 7354 bonds, 926 residues, 1 model selected
> color (#!1 & sel) #ebebebff
> color (#!1 & sel) #ebebebfe
> color (#!1 & sel) #ebebebaf
> color (#!1 & sel) #ebebebae
> color (#!1 & sel) #ebebebad
> color (#!1 & sel) #ebebeba5
> color (#!1 & sel) #ebebeba1
> color (#!1 & sel) #ebebeba0
> color (#!1 & sel) #ebebeb9f
> color (#!1 & sel) #ebebeb99
> color (#!1 & sel) #ebebeb95
> color (#!1 & sel) #ebebeb90
> color (#!1 & sel) #ebebeb8a
> color (#!1 & sel) #ebebeb87
> color (#!1 & sel) #ebebeb86
> color (#!1 & sel) #ebebeb84
> color (#!1 & sel) #ebebeb82
> color (#!1 & sel) #ebebeb7d
> color (#!1 & sel) #ebebeb7a
> color (#!1 & sel) #ebebeb78
> color (#!1 & sel) #ebebeb74
> hide #2 models
> show #2 models
> hide #2 models
> color (#!1 & sel) #ebebeb74
> color (#!1 & sel) #ebebeb6f
> color (#!1 & sel) #ebebeb69
> color (#!1 & sel) #ebebeb67
> color (#!1 & sel) #ebebeb65
> color (#!1 & sel) #ebebeb64
> color (#!1 & sel) #ebebeb62
> color (#!1 & sel) #ebebeb60
> color (#!1 & sel) #ebebeb5f
> color (#!1 & sel) #ebebeb5d
> color (#!1 & sel) #ebebeb5c
> color (#!1 & sel) #ebebeb5a
> color (#!1 & sel) #ebebeb58
> color (#!1 & sel) #ebebeb51
> color (#!1 & sel) #ebebeb4a
> color (#!1 & sel) #ebebeb47
> color (#!1 & sel) #ebebeb45
> color (#!1 & sel) #ebebeb43
> color (#!1 & sel) #ebebeb42
> color (#!1 & sel) #ebebeb41
> color (#!1 & sel) #ebebeb3e
> color (#!1 & sel) #ebebeb3b
> color (#!1 & sel) #ebebeb39
> color (#!1 & sel) #ebebeb3b
> color (#!1 & sel) #ebebeb3d
> color (#!1 & sel) #ebebeb3e
> color (#!1 & sel) #ebebeb40
> color (#!1 & sel) #ebebeb45
> color (#!1 & sel) #ebebeb4b
> color (#!1 & sel) #ebebeb4e
> color (#!1 & sel) #ebebeb50
> color (#!1 & sel) #ebebeb51
> select #1/A,B:1-17
252 atoms, 256 bonds, 34 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> color (#!1 & sel) #986db2ff
> select #2/A,B
7220 atoms, 7354 bonds, 926 residues, 1 model selected
> show #2 models
> hide #!1 models
> show sel surfaces
> select #2/
Expected an objects specifier or a keyword
> select #2
9344 atoms, 9508 bonds, 1202 residues, 1 model selected
> show sel surfaces
> select #2/A,B
7220 atoms, 7354 bonds, 926 residues, 1 model selected
> color (#!2 & sel) #4f4f48ff
> color (#!2 & sel) #787d7bff
> color (#!2 & sel) #787d7bfe
> color (#!2 & sel) #787d7bf9
> color (#!2 & sel) #787d7bf6
> color (#!2 & sel) #787d7bf4
> color (#!2 & sel) #787d7be8
> color (#!2 & sel) #787d7bdc
> color (#!2 & sel) #787d7bd9
> color (#!2 & sel) #787d7bd3
> color (#!2 & sel) #787d7bcd
> color (#!2 & sel) #787d7bc9
> color (#!2 & sel) #787d7bc2
> color (#!2 & sel) #787d7bb9
> color (#!2 & sel) #787d7bb5
> color (#!2 & sel) #787d7bb2
> color (#!2 & sel) #787d7bb0
> color (#!2 & sel) #787d7bad
> color (#!2 & sel) #787d7ba5
> color (#!2 & sel) #787d7ba2
> color (#!2 & sel) #787d7b9f
> color (#!2 & sel) #787d7b9c
> color (#!2 & sel) #787d7b98
> color (#!2 & sel) #787d7b94
> color (#!2 & sel) #787d7b90
> color (#!2 & sel) #787d7b8c
> color (#!2 & sel) #787d7b88
> color (#!2 & sel) #787d7b87
> color (#!2 & sel) #787d7b84
> color (#!2 & sel) #787d7b82
> color (#!2 & sel) #787d7b79
> color (#!2 & sel) #787d7b75
> color (#!2 & sel) #787d7b73
> color (#!2 & sel) #787d7b72
> color (#!2 & sel) #787d7b71
> color (#!2 & sel) #787d7b70
> color (#!2 & sel) #787d7b6c
> color (#!2 & sel) #787d7b69
> color (#!2 & sel) #787d7b68
> color (#!2 & sel) #787d7b66
> color (#!2 & sel) #787d7b65
> color (#!2 & sel) #787d7b64
> color (#!2 & sel) #787d7b61
> color (#!2 & sel) #787d7b5d
> color (#!2 & sel) #787d7b5c
> color (#!2 & sel) #787d7b5b
> color (#!2 & sel) #787d7b5a
> color (#!2 & sel) #787d7b59
> show #!1 models
> hide #!1 models
> color (#!2 & sel) #4f4f48ff
> color (#!2 & sel) #4f4f48f2
> color (#!2 & sel) #4f4f48e9
> color (#!2 & sel) #4f4f48e4
> color (#!2 & sel) #4f4f48e1
> color (#!2 & sel) #4f4f48de
> color (#!2 & sel) #4f4f48db
> color (#!2 & sel) #4f4f48d9
> color (#!2 & sel) #4f4f48d7
> color (#!2 & sel) #4f4f48d6
> color (#!2 & sel) #4f4f48d5
> color (#!2 & sel) #4f4f48d1
> color (#!2 & sel) #4f4f48d0
> color (#!2 & sel) #4f4f48ce
> color (#!2 & sel) #4f4f48cc
> color (#!2 & sel) #4f4f48cb
> color (#!2 & sel) #4f4f48c9
> color (#!2 & sel) #4f4f48c8
> color (#!2 & sel) #4f4f48c7
> color (#!2 & sel) #4f4f48c5
> color (#!2 & sel) #4f4f48c4
> color (#!2 & sel) #4f4f48bf
> color (#!2 & sel) #4f4f48ba
> color (#!2 & sel) #4f4f48ad
> color (#!2 & sel) #4f4f48aa
> color (#!2 & sel) #4f4f48a9
> color (#!2 & sel) #4f4f48a5
> color (#!2 & sel) #4f4f48a3
> color (#!2 & sel) #4f4f4899
> color (#!2 & sel) #4f4f4893
> color (#!2 & sel) #4f4f4891
> color (#!2 & sel) #4f4f4890
> color (#!2 & sel) #4f4f488f
> show #!1 models
> hide #!1 models
> color (#!2 & sel) #4f4f488e
> color (#!2 & sel) #4f4f488a
> color (#!2 & sel) #4f4f4888
> color (#!2 & sel) #4f4f487d
> color (#!2 & sel) #4f4f4877
> color (#!2 & sel) #4f4f4875
> color (#!2 & sel) #4f4f4873
> color (#!2 & sel) #4f4f4871
> color (#!2 & sel) #4f4f486f
> color (#!2 & sel) #4f4f486d
> color (#!2 & sel) #4f4f486c
> color (#!2 & sel) #4f4f486a
> color (#!2 & sel) #4f4f4868
> color (#!2 & sel) #4f4f4866
> color (#!2 & sel) #4f4f4865
> color (#!2 & sel) #4f4f4862
> color (#!2 & sel) #4f4f485f
> color (#!2 & sel) #4f4f485d
> color (#!2 & sel) #4f4f485b
> color (#!2 & sel) #4f4f4859
> color (#!2 & sel) #4f4f4858
> color (#!2 & sel) #4f4f4857
> color (#!2 & sel) #4f4f4855
> color (#!2 & sel) #4f4f4853
> color (#!2 & sel) #4f4f4851
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2/C,D
62 atoms, 66 bonds, 2 residues, 1 model selected
> select #2/C,D
62 atoms, 66 bonds, 2 residues, 1 model selected
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> select #2/C
31 atoms, 33 bonds, 1 residue, 1 model selected
> select #2/C,D
62 atoms, 66 bonds, 2 residues, 1 model selected
> select #2/E,F
2058 atoms, 2088 bonds, 270 residues, 1 model selected
> color (#!2 & sel) #f28f6bff
> color (#!2 & sel) #f28f6bf6
> color (#!2 & sel) #f28f6beb
> color (#!2 & sel) #f28f6bdc
> color (#!2 & sel) #f28f6bcd
> color (#!2 & sel) #f28f6bbe
> color (#!2 & sel) #f28f6bb0
> color (#!2 & sel) #f28f6ba5
> color (#!2 & sel) #f28f6b9f
> color (#!2 & sel) #f28f6b98
> color (#!2 & sel) #f28f6b8f
> color (#!2 & sel) #f28f6b85
> color (#!2 & sel) #f28f6b76
> color (#!2 & sel) #f28f6b6b
> color (#!2 & sel) #f28f6b69
> color (#!2 & sel) #f28f6b67
> color (#!2 & sel) #f28f6b66
> color (#!2 & sel) #f28f6b64
> color (#!2 & sel) #f28f6b63
> color (#!2 & sel) #f28f6b61
> color (#!2 & sel) #f28f6b60
> color (#!2 & sel) #f28f6b5f
> color (#!2 & sel) #f28f6b5e
> color (#!2 & sel) #f28f6b5d
> color (#!2 & sel) #f28f6b5b
> color (#!2 & sel) #f28f6b5a
> color (#!2 & sel) #f28f6b59
> color (#!2 & sel) #f28f6b57
> color (#!2 & sel) #f28f6b55
> color (#!2 & sel) #f28f6b52
> color (#!2 & sel) #f28f6b51
> select #2/A,B:1-17
252 atoms, 256 bonds, 34 residues, 1 model selected
> color (#!2 & sel) #2ea9dfff
> hide sel surfaces
> show #!1 models
> select clear
> view
> ui tool show "Side View"
> save
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/cyaB-w-
> wo-pilG-1-17.cxs
> select #2/C,D
62 atoms, 66 bonds, 2 residues, 1 model selected
> select #2/E,F
2058 atoms, 2088 bonds, 270 residues, 1 model selected
Alignment identifier is 1
> select #2/E-F:91
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/E-F:91-108
278 atoms, 280 bonds, 36 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> cartoon hide (#!2 & sel)
> undo
> show surfaces
> hide surfaces
> undo
> close session
> open
> /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/cyaB-w-
> wo-pilG-1-17.cxs format session
opened ChimeraX session
> select #2/E,F
2058 atoms, 2088 bonds, 270 residues, 1 model selected
Alignment identifier is 1
> select #2/E-F:61
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/E-F:61-76
252 atoms, 254 bonds, 32 residues, 1 model selected
> select #2/E-F:78
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #2/E-F:78-84
104 atoms, 106 bonds, 14 residues, 1 model selected
> select #2/E-F:93
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/E-F:93-112
322 atoms, 328 bonds, 40 residues, 1 model selected
> select #2/E-F:74-75
34 atoms, 32 bonds, 4 residues, 1 model selected
> select #2/E-F:74-111
580 atoms, 588 bonds, 76 residues, 1 model selected
> hide (#!2 & sel) target a
> surface hidePatches (#!2 & sel)
> cartoon hide (#!2 & sel)
> surface (#!2 & sel)
> select #2/E,F
2058 atoms, 2088 bonds, 270 residues, 1 model selected
> surface (#!2 & sel)
> cartoon (#!2 & sel)
> select clear
> select #2/A,B
7220 atoms, 7354 bonds, 926 residues, 1 model selected
> color (#!2 & sel) #ebebebff
> color (#!2 & sel) #ebebebfd
> color (#!2 & sel) #ebebebfb
> color (#!2 & sel) #ebebebf7
> color (#!2 & sel) #ebebebe6
> color (#!2 & sel) #ebebebd2
> color (#!2 & sel) #ebebebc8
> color (#!2 & sel) #ebebebc6
> color (#!2 & sel) #ebebebc4
> color (#!2 & sel) #ebebebb2
> color (#!2 & sel) #ebebeb9f
> color (#!2 & sel) #ebebeb7c
> color (#!2 & sel) #ebebeb65
> color (#!2 & sel) #ebebeb5b
> color (#!2 & sel) #ebebeb59
> color (#!2 & sel) #ebebeb58
> color (#!2 & sel) #ebebeb50
> color (#!2 & sel) #ebebeb4c
> color (#!2 & sel) #ebebeb49
> color (#!2 & sel) #ebebeb46
> color (#!2 & sel) #ebebeb44
> color (#!2 & sel) #ebebeb41
> color (#!2 & sel) #ebebeb3a
> color (#!2 & sel) #ebebeb37
> color (#!2 & sel) #ebebeb36
> color (#!2 & sel) #ebebeb33
> color (#!2 & sel) #ebebeb32
> color (#!2 & sel) #ebebeb30
> color (#!2 & sel) #ebebeb2e
> color (#!2 & sel) #ebebeb30
> color (#!2 & sel) #ebebeb33
> color (#!2 & sel) #ebebeb35
> color (#!2 & sel) #ebebeb36
> color (#!2 & sel) #ebebeb37
> color (#!2 & sel) #ebebeb38
> color (#!2 & sel) #ebebeb39
> color (#!2 & sel) #ebebeb3b
> color (#!2 & sel) #ebebeb3d
> color (#!2 & sel) #ebebeb3f
> color (#!2 & sel) #ebebeb40
> color (#!2 & sel) #ebebeb41
> color (#!2 & sel) #ebebeb43
> color (#!2 & sel) #ebebeb44
> color (#!2 & sel) #ebebeb45
> color (#!2 & sel) #ebebeb46
> color (#!2 & sel) #ebebeb47
> color (#!2 & sel) #ebebeb48
> color (#!2 & sel) #ebebeb49
> color (#!2 & sel) #ebebeb4a
> color (#!2 & sel) #ebebeb4b
> color (#!2 & sel) #ebebeb4d
> color (#!2 & sel) #ebebeb4e
> color (#!2 & sel) #ebebeb4f
> color (#!2 & sel) #ebebeb51
> color (#!2 & sel) #ebebeb50
> select clear
> select #2/A,B:1-17
252 atoms, 256 bonds, 34 residues, 1 model selected
> color (#!2 & sel) #2ea9dfff
> color (#!2 & sel) #006284ff
> color (#!2 & sel) #2ea9dfff
> select clear
> ui tool show "Side View"
> hide #!2 models
> save /Users/ctsai/Desktop/image19.png supersample 3
> hide #!1 models
> show #!2 models
> save /Users/ctsai/Desktop/image20.png supersample 3
> show #!1 models
> save /Users/ctsai/Desktop/image21.png supersample 3
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16S00188SM/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.61.3
OS Loader Version: 11881.61.3
Software:
System Software Overview:
System Version: macOS 15.2 (24C101)
Kernel Version: Darwin 24.2.0
Time since boot: 41 days, 23 hours, 2 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
BenQ GC2870:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
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: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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