![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#17099 closed defect (duplicate)
Crash moving window between screens
| 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-12.7.6-x86_64-i386-64bit
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 0x0000000110d73600 (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.surface._surface, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 56)
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"version" : 2,
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"deployVersion" : 210,
"modelCode" : "MacBookPro15,1",
"procStartAbsTime" : 653117923653566,
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"captureTime" : "2025-03-14 14:26:29.9553 -0400",
"incident" : "BC3406E0-44E4-4C27-A90C-13B4228F2763",
"bug_type" : "309",
"pid" : 94491,
"procExitAbsTime" : 1053102473890440,
"cpuType" : "X86-64",
"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":"6D374710-34C2-5DCC-97F1-7AD66A8EBA1D","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "EE1E0E94-F120-C3A3-E922-1FF53A6A9CB7",
"wakeTime" : 4211,
"bridgeVersion" : {"build":"21P6074","train":"8.6"},
"sleepWakeUUID" : "71CE57A2-13FA-4A5F-9F97-53A1B953C439",
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"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4460359680\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 109dbb000-109dbf000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"isCorpse" : 1,
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"vmregioninfo" : "0 is not in any region. Bytes before following region: 4460359680\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 109dbb000-109dbf000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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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 22758 fromDatabase emdb format ccp4
Summary of feedback from opening 22758 fetched from emdb
---
notes | Fetching compressed map 22758 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22758/map/emd_22758.map.gz
Fetching map header 22758 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22758/header/emd-22758.xml
Opened emdb 22758 as #1, grid size 300,300,300, pixel 0.91, shown at level
0.0201, step 2, values float32, fit PDB 7ka4
> volume #1 step 1
> ui tool show AlphaFold
> alphafold match P00883
1 AlphaFold model found using UniProt identifier: P00883 (UniProt P00883)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P00883 | P00883 | 100.0 | 100.0
Opened 1 AlphaFold model
> ui tool show "Local EM Fitting"> marker #3 position 146.641,136.5,122.638
> radius 38.4176 color 100,65,0,50> ui mousemode right "move markers"> marker
> change #3:1 position 131.1,134.6,134.1> phenix emplaceLocal #2 mapData #1
> resolution 2.8 center 131.061,134.633,134.131 showSharpenedMap false
> applySymmetry true4 fitting solutions
map LLG values: 3062.6, 3062.01, 3061.2, 3061.07
map CC values: 0.601782, 0.601879, 0.602018, 0.601824
Opened sharpened local map as #3, grid size 113,113,113, pixel 0.91, shown at
level 0.00238, step 1, values float32
> measure symmetry #1Symmetry emdb 22758: D2, center 150 150 150
> sym #2 symmetry #1 copies trueMade 4 copies for AlphaFold P00883 symmetry #1
> combine #2,4 close true modelId 2 name "AlphaFold P00883"Remapping chain ID
> 'A' in AlphaFold P00883 #4.1 to 'B'
Remapping chain ID 'A' in AlphaFold P00883 #4.2 to 'C'
Remapping chain ID 'A' in AlphaFold P00883 #4.3 to 'D'
Remapping chain ID 'A' in AlphaFold P00883 #4.4 to 'E'
> transparency #1-2 30> hide #2 models> show #2 models> hide #!1 models> hide #2 models> show #2 models> hide #2 models> open 44511 fromDatabase emdb format ccp4 | Summary of feedback from opening 44511 fetched from emdb
---
notes | Fetching compressed map 44511 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-44511/map/emd_44511.map.gz
Fetching map header 44511 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-44511/header/emd-44511.xml
Opened emdb 44511 as #4, grid size 320,320,320, pixel 0.828, shown at level
0.007, step 2, values float32, fit PDB 9bgf
> volume #4 step 1
> volume #4 level 0.01052
Fetching compressed Q3T906 UniProt info from
https://www.uniprot.org/uniprot/Q3T906.xml
> alphafold match Q3T906
Fetching compressed AlphaFold Q3T906 from
https://alphafold.ebi.ac.uk/files/AF-Q3T906-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: Q3T906 (UniProt Q3T906)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
Q3T906 | Q3T906 | 100.0 | 100.0
Opened 1 AlphaFold model
> ui tool show "Local EM Fitting"Must specify a structure to fit
> ui tool show "Local EM Fitting"> marker #6 position 132.511,147.613,148.125
> radius 98.9356 color 100,65,0,50> phenix emplaceLocal #5 mapData #4
> resolution 2.9 center 132.511,147.613,148.125 showSharpenedMap false
> applySymmetry true2 fitting solutions
map LLG values: 5071.56, 4690.03
map CC values: 0.304397, 0.298342
Opened sharpened local map as #6, grid size 291,283,284, pixel 0.828, shown at
level 0.000204, step 2, values float32
> measure symmetry #4No symmetry found for emdb 44511
Could not determine symmetry for emdb 44511 #4
If you know the symmetry of the map, you can create symmetry copies of the
structure with the sym command and then combine the symmetry copies with the
original structure with the combine command
> delete #5 :1-900> ui tool show "Local EM Fitting"> marker #7 position
> 132.511,146.735,137.049 radius 85.3002 color 100,65,0,50> phenix
> emplaceLocal #5 mapData #4 resolution 2.9 center 132.511,146.735,137.049
> showSharpenedMap false applySymmetry true2 fitting solutions
map LLG values: 5421.2, 4906.56
map CC values: 0.40956, 0.403341
Opened sharpened local map as #7, grid size 263,263,263, pixel 0.828, shown at
level 0.000285, step 2, values float32
> measure symmetry #4No symmetry found for emdb 44511
Could not determine symmetry for emdb 44511 #4
If you know the symmetry of the map, you can create symmetry copies of the
structure with the sym command and then combine the symmetry copies with the
original structure with the combine command
> transparency #4-5 30> volume #4 level 0.01537> combine #5 close false>
> select add #82968 atoms, 3039 bonds, 356 residues, 1 model selected
> ui mousemode right "translate selected models"> view matrix models
> #8,-0.92187,0.38744,0.0065662,121.17,-0.37607,-0.89864,0.22588,175,0.093418,0.20577,0.97413,120.73>
> view #4> ui tool show "Local EM Fitting"> marker #9 position
> 129.541,132.447,132.944 radius 85.3002 color 100,65,0,50> phenix
> emplaceLocal #8 mapData #4 resolution 2.9 center 129.541,132.447,132.944
> showSharpenedMap false applySymmetry false2 fitting solutions
map LLG values: 5421.18, 4906.53
map CC values: 0.409615, 0.4033
Opened sharpened local map as #9, grid size 263,263,263, pixel 0.828, shown at
level 0.000285, step 2, values float32
> ui tool show "Local EM Fitting"> marker #10 position 129.541,132.447,132.944
> radius 85.3002 color 100,65,0,50> ui mousemode right "move markers"> marker
> change #10:1 position 126.6,127.6,205.3> marker change #10:1 position
> 122.9,128,218> phenix emplaceLocal #8 mapData #4 resolution 2.9 center
> 122.893,127.987,217.974 showSharpenedMap false applySymmetry false1 fitting
> solution
map LLG value: 4906.59
map CC value: 0.403454
Opened sharpened local map as #10, grid size 263,263,263, pixel 0.828, shown
at level 0.000285, step 2, values float32
> select subtract #8Nothing selected
> hide #8 models> hide #5 models> hide #!4 models> show #!1 models> show #2
> models> show #!4 models> hide #2 models> hide #!1 models> show #5 models>
> show #8 models> hide #!4 models> hide #5 models> hide #8 models> show #!4
> models> volume #4 level 0.01309> hide #!4 models> open 46853 fromDatabase
> emdb format ccp4Opened emdb 46853 as #11, grid size 288,288,288, pixel 0.73,
> shown at level 0.00814, step 2, values float32, fit PDB 9dgz
> open 52724 fromDatabase emdb format ccp4Opened emdb 52724 as #12, grid size
> 256,256,256, pixel 0.67, shown at level 0.169, step 1, values float32, fit
> PDB 9i8i
> open 39117 fromDatabase emdb format ccp4 | Summary of feedback from opening 39117 fetched from emdb
---
notes | Fetching compressed map 39117 from https://files.wwpdb.org/pub/emdb/structures/EMD-39117/map/emd_39117.map.gz
Fetching map header 39117 from
https://files.wwpdb.org/pub/emdb/structures/EMD-39117/header/emd-39117.xml
Opened emdb 39117 as #13, grid size 300,300,300, pixel 0.705, shown at level
0.165, step 2, values float32, fit PDB 8ybe
> hide #!13 models
> hide #!12 models
> show #!13 models
> show #!12 models
> hide #!3 models
> hide #!13 models
> hide #!12 models
> volume #11 step 1
> volume #11 level 0.01041
> alphafold match o60701
1 AlphaFold model found using UniProt identifier: o60701 (UniProt o60701)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
o60701 | o60701 | 100.0 | 100.0
Opened 1 AlphaFold model
> ui tool show "Local EM Fitting"> marker #15 position 97.952,95.1239,104.39
> radius 53.0401 color 100,65,0,50> marker change #15:1 position
> 109.7,105.6,103.5> marker change #15:1 position 109.5,105.7,99.4> marker
> change #15:1 position 110,105.5,99.69> phenix emplaceLocal #14 mapData #11
> resolution 2.1 center 110.037,105.538,99.6901 showSharpenedMap false
> applySymmetry true5 fitting solutions
map LLG values: 1428.23, 1421.54, 1421.06, 1406.35, 1406.28
map CC values: 0.39165, 0.392323, 0.392366, 0.392139, 0.392041
Opened sharpened local map as #15, grid size 181,181,181, pixel 0.73, shown at
level 0.00253, step 1, values float32
> measure symmetry #11Symmetry emdb 46853: D3, center 144 144 143
> sym #14 symmetry #11 copies trueMade 6 copies for AlphaFold o60701 symmetry
> #11
> combine #14,16 close true modelId 14 name "AlphaFold o60701"Remapping chain
> ID 'A' in AlphaFold o60701 #16.1 to 'B'
Remapping chain ID 'A' in AlphaFold o60701 #16.2 to 'C'
Remapping chain ID 'A' in AlphaFold o60701 #16.3 to 'D'
Remapping chain ID 'A' in AlphaFold o60701 #16.4 to 'E'
Remapping chain ID 'A' in AlphaFold o60701 #16.5 to 'F'
Remapping chain ID 'A' in AlphaFold o60701 #16.6 to 'G'
> transparency #11,14 30> hide #!11 models> show #!12 models> hide #14 models>
> open 9I8I fromDatabase pdb format mmcif9i8i title:
cryoEM structure of HIV-1 KAKA/G225R mature CA hexamer [more info...]
| Chain information for 9i8i #16
---
Chain | Description
A B C D E F | HIV-1 KAKA/G225R CA hexamer
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> surface hidePatches #12,16
> cartoon #12,16
> surface hidePatches #12,16
> hide #12,16 target a
> close #12
> close #16
> show #!13 models
> volume #13 step 1
> volume #13 level 0.2562
> volume #13 level 0.235
> ui mousemode right "translate selected models"
Fetching compressed P0AEX9 UniProt info from
https://www.uniprot.org/uniprot/P0AEX9.xml
> alphafold match P0AEX9
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold P0AEX9 from
https://alphafold.ebi.ac.uk/files/AF-P0AEX9-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: P0AEX9 (UniProt P0AEX9)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P0AEX9 | P0AEX9 | 100.0 | 100.0
Opened 1 AlphaFold model
> ui tool show "Local EM Fitting"> marker #16 position 100.947,100.891,97.3471
> radius 66.4349 color 100,65,0,50> phenix emplaceLocal #12 mapData #13
> resolution 2.1 center 100.947,100.891,97.3471 showSharpenedMap false
> applySymmetry false1 fitting solution
map LLG value: 65281.8
map CC value: 0.57801
Opened sharpened local map as #16, grid size 287,287,287, pixel 0.705, shown
at level 0.000223, step 2, values float32
> ui tool show "Water Placement"> transparency #12-13 30> delete /A:1-31> save
> /Users/Jen/Desktop/Cash_Lab/Conferences/CSHL_CryoEM_2025/Modules/Model_building/MBP.mrc
> models #13> save
> /Users/Jen/Desktop/Cash_Lab/Conferences/CSHL_CryoEM_2025/Modules/Model_building/MBP.pdb
> models #12 relModel #13> hide #12 models> alphafold match P0AEX9Fetching
> AlphaFold database settings from
> https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
1 AlphaFold model found using UniProt identifier: P0AEX9 (UniProt P0AEX9)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P0AEX9 | P0AEX9 | 100.0 | 100.0
Opened 1 AlphaFold model
> ui tool show "Local EM Fitting"> marker #18 position 106.458,100.879,103.888
> radius 66.4349 color 100,65,0,50> phenix emplaceLocal #17 mapData #13
> resolution 2.1 center 106.458,100.879,103.888 showSharpenedMap false
> applySymmetry false1 fitting solution
map LLG value: 65281.5
map CC value: 0.578006
Opened sharpened local map as #18, grid size 287,287,287, pixel 0.705, shown
at level 0.000223, step 2, values float32
> save
> /Users/Jen/Desktop/Cash_Lab/Conferences/CSHL_CryoEM_2025/Modules/Model_building/Build_Me.pdb
> models #17 relModel #13> select add #132 models selected
> select subtract #13Nothing selected
> hide #!13 models> hide #17 models> show #!1 models> show #2 models> close
> session> open 46853 fromDatabase emdb format ccp4Opened emdb 46853 as #1,
> grid size 288,288,288, pixel 0.73, shown at level 0.00814, step 2, values
> float32, fit PDB 9dgz
> volume #1 step 1> volume #1 level 0.01427> volume #1 level 0.01291> ui tool
> show AlphaFold> alphafold match O60701Fetching AlphaFold database settings
> from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
1 AlphaFold model found using UniProt identifier: O60701 (UniProt O60701)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
O60701 | O60701 | 100.0 | 100.0
Opened 1 AlphaFold model
> volume #1 level 0.01563> vop zflip #1> volume zflip #1Expected a density
> maps specifier or a keyword
> vop flip #1Opened emdb 46853 z flip as #3, grid size 288,288,288, pixel
> 0.73, shown at step 1, values float32
> ui tool show "Local EM Fitting"> marker #4 position 106.132,106.795,98.8524
> radius 53.0401 color 100,65,0,50> marker #5 position 113.408,105.686,104.39
> radius 53.0401 color 100,65,0,50> phenix emplaceLocal #2 mapData #1
> resolution 2.1 center 113.408,105.686,104.39 showSharpenedMap false
> applySymmetry true5 fitting solutions
map LLG values: 1433.53, 1421.5, 1421.06, 1406.36, 1406.28
map CC values: 0.391615, 0.39216, 0.392254, 0.392119, 0.392057
Opened sharpened local map as #5, grid size 181,181,181, pixel 0.73, shown at
level 0.00253, step 1, values float32
> measure symmetry #1Symmetry emdb 46853: D3, center 144 144 143
> sym #2 symmetry #1 copies trueMade 6 copies for AlphaFold O60701 symmetry #1
> combine #2,6 close true modelId 2 name "AlphaFold O60701"Remapping chain ID
> 'A' in AlphaFold O60701 #6.1 to 'B'
Remapping chain ID 'A' in AlphaFold O60701 #6.2 to 'C'
Remapping chain ID 'A' in AlphaFold O60701 #6.3 to 'D'
Remapping chain ID 'A' in AlphaFold O60701 #6.4 to 'E'
Remapping chain ID 'A' in AlphaFold O60701 #6.5 to 'F'
Remapping chain ID 'A' in AlphaFold O60701 #6.6 to 'G'
> close #3> close #5> hide #!1 models> hide #2 models> open 44511 fromDatabase
> emdb format ccp4Opened emdb 44511 as #3, grid size 320,320,320, pixel 0.828,
> shown at level 0.007, step 2, values float32, fit PDB 9bgf
> volume #3 step 1> surface dust #3 size 8.28> alphafold match Q3T9061
> AlphaFold model found using UniProt identifier: Q3T906 (UniProt Q3T906)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
Q3T906 | Q3T906 | 100.0 | 100.0
Opened 1 AlphaFold model
> ui tool show "Local EM Fitting"> marker #5 position 131.555,133.933,128.04
> radius 98.9356 color 100,65,0,50> phenix emplaceLocal #4 mapData #3
> resolution 2.9 center 131.555,133.933,128.04 showSharpenedMap false
> applySymmetry true2 fitting solutions
map LLG values: 5071.5, 4689.95
map CC values: 0.304569, 0.298304
Opened sharpened local map as #5, grid size 291,283,284, pixel 0.828, shown at
level 0.000204, step 2, values float32
> measure symmetry #3No symmetry found for emdb 44511
Could not determine symmetry for emdb 44511 #3
If you know the symmetry of the map, you can create symmetry copies of the
structure with the sym command and then combine the symmetry copies with the
original structure with the combine command
> select add #410113 atoms, 10347 bonds, 1256 residues, 1 model selected
> view matrix models
> #4,-0.92503,0.37989,-0.000664,94.816,-0.37026,-0.90121,0.22522,195.98,0.08496,0.20858,0.97431,74.378>
> select subtract #4Nothing selected
> delete #4/A:406-899> ui tool show "Local EM Fitting"> marker #6 position
> 138.638,140.834,135.031 radius 96.6119 color 100,65,0,50> phenix
> emplaceLocal #4 mapData #3 resolution 2.9 center 138.638,140.834,135.031
> showSharpenedMap false applySymmetry true2 fitting solutions
map LLG values: 8764.44, 7867.58
map CC values: 0.375179, 0.365848
Opened sharpened local map as #6, grid size 271,271,267, pixel 0.828, shown at
level 0.000257, step 2, values float32
> measure symmetry #3No symmetry found for emdb 44511
Could not determine symmetry for emdb 44511 #3
If you know the symmetry of the map, you can create symmetry copies of the
structure with the sym command and then combine the symmetry copies with the
original structure with the combine command
> transparency #3-4 30> volume #3 level 0.01214> delete #4/A:77-285> ui tool
> show "Local EM Fitting"> marker #7 position 131.935,132.48,123.502 radius
> 89.2811 color 100,65,0,50> phenix emplaceLocal #4 mapData #3 resolution 2.9
> center 131.935,132.48,123.502 showSharpenedMap false applySymmetry true2
> fitting solutions
map LLG values: 9478.79, 8583.22
map CC values: 0.427983, 0.416669
Opened sharpened local map as #7, grid size 255,255,255, pixel 0.828, shown at
level 0.000332, step 1, values float32
> measure symmetry #3No symmetry found for emdb 44511
Could not determine symmetry for emdb 44511 #3
If you know the symmetry of the map, you can create symmetry copies of the
structure with the sym command and then combine the symmetry copies with the
original structure with the combine command
> close #3> close #4> close #5> close #6> close #7> show #!1 models> show #2
> models> hide #2 models> hide #!1 models> open 22758 fromDatabase emdb format
> ccp4Opened emdb 22758 as #3, grid size 300,300,300, pixel 0.91, shown at
> level 0.0201, step 2, values float32, fit PDB 7ka4
> volume #3 step 1> alphafold match P008831 AlphaFold model found using
> UniProt identifier: P00883 (UniProt P00883)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P00883 | P00883 | 100.0 | 100.0
Opened 1 AlphaFold model
> ui tool show "Local EM Fitting"> marker #5 position 134.084,136.5,132.442
> radius 38.4176 color 100,65,0,50> ui mousemode right "move markers"> marker
> change #5:1 position 133.8,136.8,134.8> alphafold match P008831 AlphaFold
> model found using UniProt identifier: P00883 (UniProt P00883)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P00883 | P00883 | 100.0 | 100.0
Opened 1 AlphaFold model
> close #6> phenix emplaceLocal #4 mapData #3 resolution 2.8 center
> 133.754,136.823,134.758 showSharpenedMap false applySymmetry true4 fitting
> solutions
map LLG values: 3062.01, 3061.2, 3061.08, 3060.16
map CC values: 0.601868, 0.602061, 0.601843, 0.601767
Opened sharpened local map as #5, grid size 113,113,113, pixel 0.91, shown at
level 0.00238, step 1, values float32
> measure symmetry #3Symmetry emdb 22758: D2, center 150 150 150
> sym #4 symmetry #3 copies trueMade 4 copies for AlphaFold P00883 symmetry #3
> combine #4,6 close true modelId 4 name "AlphaFold P00883"Remapping chain ID
> 'A' in AlphaFold P00883 #6.1 to 'B'
Remapping chain ID 'A' in AlphaFold P00883 #6.2 to 'C'
Remapping chain ID 'A' in AlphaFold P00883 #6.3 to 'D'
Remapping chain ID 'A' in AlphaFold P00883 #6.4 to 'E'
> close session> open 22758 fromDatabase emdb format ccp4Opened emdb 22758 as
> #1, grid size 300,300,300, pixel 0.91, shown at level 0.0201, step 2, values
> float32, fit PDB 7ka4
> volume #1 step 1> vop flip #1Opened emdb 22758 z flip as #2, grid size
> 300,300,300, pixel 0.91, shown at step 1, values float32
> show #!1 models> select add #22 models selected
> ui mousemode right "translate selected models"> view matrix models
> #2,1,0,0,0.0014216,0,1,0,-26.149,0,0,1,-0.97763> view matrix models
> #2,1,0,0,-0.55421,0,1,0,-69.693,0,0,1,2.0247> select subtract #2Nothing
> selected
> view #1> select ~sel & ##selectedNothing selected
> view #2> ui tool show AlphaFold> alphafold match P008831 AlphaFold model
> found using UniProt identifier: P00883 (UniProt P00883)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P00883 | P00883 | 100.0 | 100.0
Opened 1 AlphaFold model
> hide #!2 models> view #1> select add #32766 atoms, 2820 bonds, 364 residues,
> 1 model selected
> view matrix models #3,1,0,0,124.08,0,1,0,152.61,0,0,1,88.097> view matrix
> models #3,1,0,0,126.01,0,1,0,117.73,0,0,1,118.23> view matrix models
> #3,1,0,0,132.38,0,1,0,108.5,0,0,1,76.183> view matrix models
> #3,1,0,0,130.43,0,1,0,110.62,0,0,1,73.298> ui mousemode right "rotate
> selected models"> view matrix models
> #3,0.20254,-0.95443,0.21917,136.33,0.92754,0.25876,0.26965,112.39,-0.31408,0.14868,0.93768,73.178>
> view matrix models
> #3,-0.87354,-0.48407,-0.050902,135.71,0.38146,-0.61588,-0.68934,110.58,0.30234,-0.62158,0.72265,72.868>
> view matrix models
> #3,-0.79847,0.39471,-0.45458,130.54,0.36146,-0.28951,-0.8863,108.49,-0.48144,-0.872,0.088497,71.622>
> view matrix models
> #3,0.5584,0.72011,-0.41186,126.82,0.73717,-0.65844,-0.15179,113.08,-0.3805,-0.21885,-0.89851,63.648>
> view matrix models
> #3,0.5265,-0.84815,0.058593,134.36,-0.83403,-0.52864,-0.1579,116.12,0.1649,0.034266,-0.98572,61.176>
> view matrix models
> #3,-0.03351,-0.61388,-0.78868,129.92,-0.85858,0.42162,-0.29169,112.54,0.51159,0.66737,-0.54119,61.123>
> view matrix models
> #3,0.41783,-0.58187,-0.69774,129.36,-0.72124,0.25457,-0.6442,110.67,0.55247,0.77241,-0.3133,62.056>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.41783,-0.58187,-0.69774,127.58,-0.72124,0.25457,-0.6442,128.7,0.55247,0.77241,-0.3133,102.42>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.23818,-0.73876,-0.63047,128.85,-0.62004,0.38399,-0.68418,127.86,0.74754,0.55388,-0.3666,102.33>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.23818,-0.73876,-0.63047,123.13,-0.62004,0.38399,-0.68418,130.92,0.74754,0.55388,-0.3666,110>
> transparency sel 30> select add #12766 atoms, 2820 bonds, 364 residues, 5
> models selected
> transparency (#3 & sel) 30> select subtract #34 models selected
> select subtract #1Nothing selected
> transparency #1,3 30> ui tool show "Fit in Map"> fitmap #3 inMap #1Fit
> molecule AlphaFold P00883 (#3) to map emdb 22758 (#1) using 2766 atoms
average map value = 0.007438, steps = 68
shifted from previous position = 2.17
rotated from previous position = 8 degrees
atoms outside contour = 2230, contour level = 0.0201
Position of AlphaFold P00883 (#3) relative to emdb 22758 (#1) coordinates:
Matrix rotation and translation
0.30076611 -0.65085799 -0.69708222 123.99334994
-0.58822436 0.44873520 -0.67277695 129.69476908
0.75068758 0.61238925 -0.24788619 111.30904940
Axis 0.66351433 -0.74746442 0.03233692
Axis point 61.65075560 0.00000000 126.57205845
Rotation angle (degrees) 104.42972993
Shift along axis -11.07146961
> select add #32766 atoms, 2820 bonds, 364 residues, 1 model selected
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.33674,-0.63651,-0.69388,123.89,-0.5914,0.43046,-0.68188,129.7,0.7327,0.63997,-0.23148,111.36>
> view matrix models
> #3,0.33982,-0.71597,-0.60984,124.61,-0.62105,0.31611,-0.71719,129.9,0.70627,0.62246,-0.33723,110.85>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.33982,-0.71597,-0.60984,122.17,-0.62105,0.31611,-0.71719,130.89,0.70627,0.62246,-0.33723,113.9>
> view matrix models
> #3,0.33982,-0.71597,-0.60984,116.7,-0.62105,0.31611,-0.71719,125.09,0.70627,0.62246,-0.33723,112.46>
> view matrix models
> #3,0.33982,-0.71597,-0.60984,117.41,-0.62105,0.31611,-0.71719,126.4,0.70627,0.62246,-0.33723,116.04>
> ui mousemode right "rotate selected models"> view matrix models
> #3,-0.062976,-0.81005,-0.58297,118.74,-0.60574,0.49525,-0.62274,126.39,0.79317,0.31391,-0.52187,115.68>
> view matrix models
> #3,0.062132,-0.83146,-0.55209,118.71,-0.59124,0.415,-0.69153,126.19,0.8041,0.36938,-0.46581,115.82>
> view matrix models
> #3,0.016564,-0.85632,-0.51617,119.1,-0.70962,0.35362,-0.60942,127.12,0.70439,0.37638,-0.60181,115.22>
> fitmap #3 inMap #1Fit molecule AlphaFold P00883 (#3) to map emdb 22758 (#1)
> using 2766 atoms
average map value = 0.02708, steps = 96
shifted from previous position = 1.09
rotated from previous position = 13.3 degrees
atoms outside contour = 1014, contour level = 0.0201
Position of AlphaFold P00883 (#3) relative to emdb 22758 (#1) coordinates:
Matrix rotation and translation
0.24036807 -0.84542120 -0.47695511 119.24692782
-0.71531986 0.17787207 -0.67578030 128.25324663
0.65615599 0.50361147 -0.56199181 115.71230050
Axis 0.71884311 -0.69063488 0.07929719
Axis point 0.00000000 79.58824754 99.41969532
Rotation angle (degrees) 124.88113761
Shift along axis 6.31932585
> select subtract #3Nothing selected
> ui tool show "Local EM Fitting"> marker #4 position 116.597,136.5,110.571
> radius 38.4176 color 100,65,0,50> ui mousemode right "move markers"> marker
> change #4:1 position 119.6,135.5,114.7> marker change #4:1 position
> 139.5,129.9,133.9> marker change #4:1 position 138.9,130.1,132.3> phenix
> emplaceLocal #3 mapData #1 resolution 2.8 center 138.922,130.085,132.335
> showSharpenedMap false applySymmetry true4 fitting solutions
map LLG values: 3062.02, 3061.09, 3060.18, 3038.85
map CC values: 0.601862, 0.601845, 0.6018, 0.601547
Opened sharpened local map as #4, grid size 113,113,113, pixel 0.91, shown at
level 0.00238, step 1, values float32
> measure symmetry #1Symmetry emdb 22758: D2, center 150 150 150
> sym #3 symmetry #1 copies trueMade 4 copies for AlphaFold P00883 symmetry #1
> combine #3,5 close true modelId 3 name "AlphaFold P00883"Remapping chain ID
> 'A' in AlphaFold P00883 #5.1 to 'B'
Remapping chain ID 'A' in AlphaFold P00883 #5.2 to 'C'
Remapping chain ID 'A' in AlphaFold P00883 #5.3 to 'D'
Remapping chain ID 'A' in AlphaFold P00883 #5.4 to 'E'
> delete #3:346-364> close #4> hide #3 models> hide #!1 models> open
> /Users/Jen/Downloads/cryosparc_P20_J1031_class_03_final_volume.mrcOpened
> cryosparc_P20_J1031_class_03_final_volume.mrc as #4, grid size 128,128,128,
> pixel 2.55, shown at level 0.072, step 1, values float32
> open
> /Users/Jen/Downloads/cryosparc_P20_J1032_class_01_final_volume.mrcOpened
> cryosparc_P20_J1032_class_01_final_volume.mrc as #5, grid size 128,128,128,
> pixel 2.55, shown at level 0.078, step 1, values float32
> view #4> volume #5 level 0.09299> hide #!4 models> show #!4 models> hide #!5
> models> volume #4 level 0.08633> show #!5 models> select add #52 models
> selected
> ui mousemode right "translate selected models"> view matrix models
> #5,1,0,0,11.36,0,1,0,-94.43,0,0,1,15.34> select subtract #5Nothing selected
> hide #!5 models> hide #!4 models> open 39117 fromDatabase emdbOpened emdb
> 39117 as #6, grid size 300,300,300, pixel 0.705, shown at level 0.165, step
> 2, values float32, fit PDB 8ybe
> view #6> volume #6 step 1> surface dust #6 size 7.05> volume #6 level
> 0.1994> hide #!6 models> show #!5 models> show #!4 models> hide #!5 models>
> view #4> show #!5 models> volume #5 level 0.164> volume #6 level 0.164>
> volume #6 level 0.199> volume #4 level 0.164> hide #!5 models> hide #!4
> models> show #!6 models> select ~sel & ##selectedNothing selected
> view #6> show #!5 models> hide #!6 models> view #4No displayed objects
> specified.
> show #!4 models> view #4> volume #4 level 0.08> hide #!5 models> hide #!4
> models> show #!6 models> view #6> ui tool show "Fit in Map"> alphafold match
> P0AEX91 AlphaFold model found using UniProt identifier: P0AEX9 (UniProt
> P0AEX9)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P0AEX9 | P0AEX9 | 100.0 | 100.0
Opened 1 AlphaFold model
> ui tool show "Local EM Fitting"> marker #8 position 104.022,105.79,104.689
> radius 66.4349 color 100,65,0,50> ui tool show "Side View"> phenix
> emplaceLocal #7 mapData #6 resolution 2.3 center 104.022,105.79,104.689
> showSharpenedMap false applySymmetry false1 fitting solution
map LLG value: 61548.2
map CC value: 0.596113
Opened sharpened local map as #8, grid size 289,289,289, pixel 0.705, shown at
level 0.000155, step 2, values float32
> view #6> transparency #6-7 30> volume #6 level 0.1426> view #6:1-24No
> objects specified.
> delete #6:1-24> delete #7:1-24> view #7> save
> /Users/Jen/Desktop/Cash_Lab/Conferences/CSHL_CryoEM_2025/Modules/Model_building/Test_run_from_chimera.pdb
> models #7 relModel #6> open
> /Users/Jen/Desktop/Cash_Lab/Conferences/CSHL_CryoEM_2025/Modules/Model_building/Build_Me.mrcOpened
> Build_Me.mrc as #9, grid size 300,300,300, pixel 0.705, shown at level
> 0.0314, step 2, values float32
> volume #9 step 1> volume #9 level 0.1129> volume #9 level 0.1285> surface
> dust #6 size 7.05> surface dust #9 size 7.05> close session> open 22758
> fromDatabase emdbOpened emdb 22758 as #1, grid size 300,300,300, pixel 0.91,
> shown at level 0.0201, step 2, values float32, fit PDB 7ka4
> volume #1 step 1> ui tool show AlphaFold> alphafold match P00883Fetching
> AlphaFold database settings from
> https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
1 AlphaFold model found using UniProt identifier: P00883 (UniProt P00883)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P00883 | P00883 | 100.0 | 100.0
Opened 1 AlphaFold model
> select add #22766 atoms, 2820 bonds, 364 residues, 1 model selected
> view matrix models #2,1,0,0,-13.666,0,1,0,124.38,0,0,1,106.2> view matrix
> models #2,1,0,0,113.31,0,1,0,100.75,0,0,1,108.42> view matrix models
> #2,1,0,0,109.5,0,1,0,123.97,0,0,1,111.87> transparency sel 30> view matrix
> models #2,1,0,0,117.01,0,1,0,124.01,0,0,1,114.55> ui mousemode right "rotate
> selected models"> view matrix models
> #2,0.98672,0.16096,0.02195,116.68,-0.16123,0.98685,0.011306,124.47,-0.019842,-0.014695,0.9997,114.63>
> view matrix models
> #2,0.78483,0.45132,-0.42468,113.64,-0.44588,0.88717,0.11882,126.03,0.43039,0.096104,0.89751,112.71>
> view matrix models
> #2,0.81047,0.43748,-0.38954,113.83,-0.42873,0.89616,0.11444,125.94,0.39916,0.074256,0.91387,112.94>
> ui mousemode right "translate selected models"> view matrix models
> #2,0.81047,0.43748,-0.38954,109.62,-0.42873,0.89616,0.11444,127.26,0.39916,0.074256,0.91387,108.98>
> view matrix models
> #2,0.81047,0.43748,-0.38954,101.44,-0.42873,0.89616,0.11444,128.15,0.39916,0.074256,0.91387,107.1>
> ui mousemode right "rotate selected models"> view matrix models
> #2,-0.43657,0.89926,0.027145,105.24,-0.44709,-0.24304,0.86084,135.99,0.78071,0.36368,0.50815,103.01>
> ui mousemode right "translate selected models"> view matrix models
> #2,-0.43657,0.89926,0.027145,106.85,-0.44709,-0.24304,0.86084,138.65,0.78071,0.36368,0.50815,106.05>
> view matrix models
> #2,-0.43657,0.89926,0.027145,104.21,-0.44709,-0.24304,0.86084,131.25,0.78071,0.36368,0.50815,112.98>
> ui tool show "Fit in Map"> fitmap #2 inMap #1Fit molecule AlphaFold P00883
> (#2) to map emdb 22758 (#1) using 2766 atoms
average map value = 0.00668, steps = 192
shifted from previous position = 10.3
rotated from previous position = 12.3 degrees
atoms outside contour = 2305, contour level = 0.0201
Position of AlphaFold P00883 (#2) relative to emdb 22758 (#1) coordinates:
Matrix rotation and translation
-0.24093604 0.96740001 0.07801951 113.88288738
-0.48659853 -0.18996089 0.85272312 128.91136545
0.83974501 0.16748755 0.51650385 114.18147420
Axis -0.38523837 -0.42824089 -0.81743571
Axis point 47.39973065 19.70445501 0.00000000
Rotation angle (degrees) 117.20635295
Shift along axis -192.41318977
> view matrix models
> #2,-0.24094,0.9674,0.07802,113.34,-0.4866,-0.18996,0.85272,136.39,0.83975,0.16749,0.5165,110.18>
> ui mousemode right "rotate selected models"> view matrix models
> #2,-0.24951,0.68614,0.68334,117.76,-0.15496,-0.72485,0.67125,136.2,0.95589,0.061595,0.28718,108.9>
> view matrix models
> #2,-0.52009,0.39509,0.75724,119.66,-0.0016739,-0.88705,0.46167,135.12,0.85411,0.23884,0.46201,109.62>
> view matrix models
> #2,-0.68471,-0.18107,0.70597,121.45,0.32424,-0.94319,0.072559,132.28,0.65272,0.27858,0.70452,111.37>
> view matrix models
> #2,-0.6478,-0.11427,0.75319,121.44,0.25624,-0.96376,0.074173,132.5,0.71742,0.24105,0.65361,111.04>
> view matrix models
> #2,-0.65384,0.58468,0.48025,117.76,-0.13937,-0.71693,0.68307,136.21,0.74369,0.37968,0.55024,109.96>
> ui tool show "Local EM Fitting"> marker #3 position 112.523,136.5,115.426
> radius 38.4176 color 100,65,0,50> ui mousemode right "move markers"> marker
> change #3:1 position 111.5,135.9,113.9> phenix emplaceLocal #2 mapData #1
> resolution 2.8 center 111.46,135.861,113.879 showSharpenedMap false
> applySymmetry true1 fitting solution
map LLG value: 3062.1
map CC value: 0.601875
Opened sharpened local map as #3, grid size 113,113,113, pixel 0.91, shown at
level 0.00238, step 1, values float32
> measure symmetry #1Symmetry emdb 22758: D2, center 150 150 150
> sym #2 symmetry #1 copies trueMade 4 copies for AlphaFold P00883 symmetry #1
> combine #2,4 close true modelId 2 name "AlphaFold P00883"Remapping chain ID
> 'A' in AlphaFold P00883 #4.1 to 'B'
Remapping chain ID 'A' in AlphaFold P00883 #4.2 to 'C'
Remapping chain ID 'A' in AlphaFold P00883 #4.3 to 'D'
Remapping chain ID 'A' in AlphaFold P00883 #4.4 to 'E'
> hide #2 models> show #2 models> hide #2 models> show #2 models> delete
> #3:346-364> hide #2 models> show #2 models> hide #2 models> show #2 models>
> delete #2:346-364> hide #!1 models> hide #2 models> open 39117 fromDatabase
> emdbOpened emdb 39117 as #4, grid size 300,300,300, pixel 0.705, shown at
> level 0.165, step 2, values float32, fit PDB 8ybe
> surface dust #4 size 7.05> ui tool show "Local EM Fitting"> ui tool show
> AlphaFold> alphafold match #2/A1 AlphaFold model found using sequence
> similarity searches: P00883 (chain A)
| AlphaFold prediction matching AlphaFold P00883
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | P00883 | ALDOA_RABIT | 0.00 | 364 | 345 | 100
Opened 1 AlphaFold model
> hide #!4 models
> show #!4 models
> hide #!5 models
> hide #5.1 models
> alphafold match p0aex9
1 AlphaFold model found using UniProt identifier: p0aex9 (UniProt p0aex9)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
p0aex9 | p0aex9 | 100.0 | 100.0
Opened 1 AlphaFold model
> ui tool show "Local EM Fitting"Must specify exactly one full map for fitting
> marker #7 position 102.222,105.878,120.496 radius 66.4349 color 100,65,0,50>
> phenix emplaceLocal #6 mapData #4 resolution 2.3 center
> 102.222,105.878,120.496 showSharpenedMap false applySymmetry false1 fitting
> solution
map LLG value: 61548.1
map CC value: 0.596113
Opened sharpened local map as #7, grid size 289,289,289, pixel 0.705, shown at
level 0.000155, step 2, values float32
> close session
===== 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 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
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: MacBookPro15,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
OS Loader Version: 540.120.3~37
Software:
System Software Overview:
System Version: macOS 12.7.6 (21H1320)
Kernel Version: Darwin 21.6.0
Time since boot: 42 days 23:58
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Radeon Pro 560X:
Chipset Model: Radeon Pro 560X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c2
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501U-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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-PhenixUI: 1.3.7
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 , 8 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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