![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16858 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-14.0-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 0x00000001e4ec5300 (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, chimerax.surface._surface, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 61)
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
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"modelCode" : "MacBookPro17,1",
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"releaseType" : "User"
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"codeSigningMonitor" : 1,
"incident" : "07B0C8DF-EE93-4696-AA53-F1E6703D7C3A",
"pid" : 99790,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-14 08:53:21.8597 +0100",
"procStartAbsTime" : 5399221935799,
"procExitAbsTime" : 5472250691208,
"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":"AEB5C07D-D805-55B7-BE78-CBE4CE346859","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "64F1A385-9340-A007-6408-CDF73347C0DD",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 3541,
"sleepWakeUUID" : "8C891D3F-4C30-45E4-8B59-B4C31DDC1FEF",
"sip" : "enabled",
"vmRegionInfo" : "0x134e95d023c8 is not in any region. Bytes after previous region: 20747205485513 Bytes before following region: 84324874443832\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":99790},
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"faultingThread" : 0,
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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/amaliebenfeldt/Desktop/Updated models/Drs2p_PS_BeFx-
> coot-11.pdb"
Chain information for Drs2p_PS_BeFx-coot-11.pdb #1
---
Chain | Description
A | No description available
C | No description available
> open 8oxa
Summary of feedback from opening 8oxa fetched from pdb
---
notes | Fetching compressed mmCIF 8oxa from http://files.rcsb.org/download/8oxa.cif
Fetching CCD D39 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/D39/D39.cif
Fetching CCD VN4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/VN4/VN4.cif
8oxa title:
Cryo-EM structure of ATP8B1-CDC50A in E2-Pi conformation with occluded PS
[more info...]
Chain information for 8oxa #2
---
Chain | Description | UniProt
A | Phospholipid-transporting ATPase IC | AT8B1_HUMAN 1-1185
B | Cell cycle control protein 50A | CC50A_HUMAN 1-361
Non-standard residues in 8oxa #2
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
D39 —
(2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-
propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid
MG — magnesium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
VN4 — oxido(dioxo)vanadium
> open 7bsv
Summary of feedback from opening 7bsv fetched from pdb
---
notes | Fetching compressed mmCIF 7bsv from http://files.rcsb.org/download/7bsv.cif
Fetching CCD P5S from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/P5S/P5S.cif
7bsv title:
Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdSer-occluded E2-AlF
state [more info...]
Chain information for 7bsv #3
---
Chain | Description
A | ATP11C
C | CDC50A
Non-standard residues in 7bsv #3
---
ALF — tetrafluoroaluminate ion
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
MG — magnesium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
P5S —
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
(phosphatidyl serine)
> open 6k7m
Summary of feedback from opening 6k7m fetched from pdb
---
note | Fetching compressed mmCIF 6k7m from http://files.rcsb.org/download/6k7m.cif
6k7m title:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2Pi-PL state)
[more info...]
Chain information for 6k7m #4
---
Chain | Description | UniProt
A | Phospholipid-transporting ATPase | Q59EX4_HUMAN 1-1149
C | Cell cycle control protein 50A | CC50A_HUMAN 1-361
Non-standard residues in 6k7m #4
---
ALF — tetrafluoroaluminate ion
D39 —
(2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-
propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
MG — magnesium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Y01 — cholesterol hemisuccinate
> ui tool show Matchmaker
> matchmaker #!2-4 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 Drs2p_PS_BeFx-coot-11.pdb, chain A (#1) with 8oxa, chain A (#2),
sequence alignment score = 2515.2
RMSD between 446 pruned atom pairs is 0.912 angstroms; (across all 998 pairs:
6.683)
Matchmaker Drs2p_PS_BeFx-coot-11.pdb, chain A (#1) with 7bsv, chain A (#3),
sequence alignment score = 1924.9
RMSD between 425 pruned atom pairs is 1.095 angstroms; (across all 772 pairs:
6.022)
Matchmaker Drs2p_PS_BeFx-coot-11.pdb, chain A (#1) with 6k7m, chain A (#4),
sequence alignment score = 2910.7
RMSD between 508 pruned atom pairs is 0.988 angstroms; (across all 978 pairs:
5.954)
> hide #1 models
> close #1
> open "/Users/amaliebenfeldt/Desktop/Updated models/Drs2p_PS_AlFx-
> coot-10.pdb"
Chain information for Drs2p_PS_AlFx-coot-10.pdb #1
---
Chain | Description
A | No description available
C | No description available
> ui tool show Matchmaker
> matchmaker #!2-4 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 Drs2p_PS_AlFx-coot-10.pdb, chain A (#1) with 8oxa, chain A (#2),
sequence alignment score = 2542.6
RMSD between 759 pruned atom pairs is 1.069 angstroms; (across all 1010 pairs:
4.071)
Matchmaker Drs2p_PS_AlFx-coot-10.pdb, chain A (#1) with 7bsv, chain A (#3),
sequence alignment score = 1947.7
RMSD between 570 pruned atom pairs is 1.162 angstroms; (across all 785 pairs:
2.461)
Matchmaker Drs2p_PS_AlFx-coot-10.pdb, chain A (#1) with 6k7m, chain A (#4),
sequence alignment score = 2905.8
RMSD between 802 pruned atom pairs is 1.053 angstroms; (across all 971 pairs:
2.322)
> set bgColor white
> hide atoms
> select ::name="D39"
156 atoms, 153 bonds, 3 residues, 3 models selected
> show sel atoms
> select ::name="P5S"
136 atoms, 135 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #3
9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected
> select subtract #3
Nothing selected
> ui mousemode right zoom
> select add #2
11138 atoms, 11391 bonds, 11 pseudobonds, 1382 residues, 4 models selected
> select add #3
20559 atoms, 21044 bonds, 17 pseudobonds, 2533 residues, 8 models selected
> select add #4
31150 atoms, 31888 bonds, 23 pseudobonds, 3849 residues, 12 models selected
> hide sel cartoons
> color #1 silver
> color #3 #4f8f00ff
> color #3 #008f00ff
> color #3 #945200ff
> color #3 #941100ff
> color #3 #009193ff
> color #4 #00fa92ff
> color #4 #8efa00ff
> color #4 #fffb00ff
> color #4 #ff9300ff
> color #4 #0433ffff
> color #4 #005493ff
> color #4 #011993ff
> color #4 #0433ffff
> color #4 #0096ffff
> color #4 #0433ffff
> color #4 #929000ff
> ui tool show "Side View"
> select subtract #2
20012 atoms, 20497 bonds, 12 pseudobonds, 2467 residues, 8 models selected
> select subtract #3
10591 atoms, 10844 bonds, 6 pseudobonds, 1316 residues, 4 models selected
> select subtract #4
Nothing selected
> color :D39 byhetero
> color :P5S byhetero
> select h
Expected an objects specifier or a keyword
> select H
11513 atoms, 1421 residues, 2 models selected
> hide sel
> select add #3
20852 atoms, 9653 bonds, 6 pseudobonds, 2571 residues, 5 models selected
> select subtract #3
11431 atoms, 1420 residues, 1 model selected
> select add #1
22985 atoms, 23251 bonds, 3 pseudobonds, 1427 residues, 2 models selected
> select subtract #1
Nothing selected
> lighting shadows false
> lighting soft
> graphics silhouettes true
> cartoon style width 1.2 thickness 0.25 xsection oval sides 20
> save AlFx_PS_comparison.png format png width 3600 height 3600 supersample 2
> transparentBackground true
> select add #1
22985 atoms, 23251 bonds, 3 pseudobonds, 1427 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #2
11138 atoms, 11391 bonds, 11 pseudobonds, 1382 residues, 4 models selected
> select add #3
20559 atoms, 21044 bonds, 17 pseudobonds, 2533 residues, 8 models selected
> select add #4
31150 atoms, 31888 bonds, 23 pseudobonds, 3849 residues, 12 models selected
> select add #1
54135 atoms, 55139 bonds, 26 pseudobonds, 5276 residues, 14 models selected
> show sel cartoons
> select /A:507-510,1047,237,245
247 atoms, 239 bonds, 23 residues, 4 models selected
> show sel atoms
> hide sel atoms
> select #1/A:507-510,1047,237,245
105 atoms, 102 bonds, 7 residues, 1 model selected
> show sel atoms
> select #4/A:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/A:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/A:96
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color #4/A:96 by het
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #4/A:96 byhetero
> color #3/A:86 byhetero
> select #3/A:86
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color #2/A:139 byhetero
> color #3/A:79
> select #3/A:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color #3/A:79 byhetero
> select #4/A:88
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color #4/A:88 byhetero
> select #2/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/A:879
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> color #4/A:879 byhetero
> select #3/A:909
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color #3/A:909 byhetero
> hide #!3 models
> select #2/A:986 byhet
Expected a keyword
> select #2/A:986
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!3 models
> color #1/A:507-510,1047,237,245 byhetero
> select H
11513 atoms, 1421 residues, 2 models selected
> hide sel
> select add #3
20852 atoms, 9653 bonds, 6 pseudobonds, 2571 residues, 5 models selected
> select add #1
32406 atoms, 32904 bonds, 9 pseudobonds, 2578 residues, 6 models selected
> select subtract #1
9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected
> select subtract #3
Nothing selected
> select add #3
9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected
> select subtract #3
Nothing selected
> ~label #1-4 residues
> ui mousemode right select
No visible residues selected
> ui mousemode right translate
> ui mousemode right zoom
> select #4/A:356-359
29 atoms, 29 bonds, 4 residues, 1 model selected
> show sel atoms
> color #4/A:356-359 byhetero
> select #3/A:356-359
28 atoms, 28 bonds, 4 residues, 1 model selected
> color #3/A:356-359 byhetero
> select #2/A:401-404 byhet
Expected a keyword
> select #2/A:401-404
29 atoms, 29 bonds, 4 residues, 1 model selected
> color #2/A:401-404 byhetero
> select add #2
11138 atoms, 11391 bonds, 11 pseudobonds, 1382 residues, 4 models selected
> select subtract #2
Nothing selected
> select #2/A:401-404
29 atoms, 29 bonds, 4 residues, 1 model selected
> show sel atoms
> select #3/A:356-359
28 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> select add #3
9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected
> select subtract #3
Nothing selected
> open /Users/amaliebenfeldt/Downloads/emd_9941.map
Opened emd_9941.map as #5, grid size 260,260,260, pixel 0.83, shown at level
0.0122, step 2, values float32
> volume #5 step 1
> hide #!5 models
> save AlFx_PS_comparison_residue.png format png width 3600 height 3600
> supersample 2 transparentBackground true
> show #!5 models
> volume #5 level 0.02482
> select add #5
4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.99088,0.049565,-0.12526,224.15,-0.09401,-0.92042,0.37946,184.94,-0.096486,0.38778,0.91669,-24.083
> view matrix models
> #5,-0.98157,0.19111,0.0022948,192.51,-0.18143,-0.93552,0.30313,204.83,0.060077,0.29712,0.95295,-34.872
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.98157,0.19111,0.0022948,208.55,-0.18143,-0.93552,0.30313,266.6,0.060077,0.29712,0.95295,20.617
> view matrix models
> #5,-0.98157,0.19111,0.0022948,251.75,-0.18143,-0.93552,0.30313,257.1,0.060077,0.29712,0.95295,22.924
> select subtract #5
Nothing selected
> ui tool show "Fit in Map"
> fitmap #4 inMap #5
Fit molecule 6k7m (#4) to map emd_9941.map (#5) using 10591 atoms
average map value = 0.03523, steps = 128
shifted from previous position = 3.16
rotated from previous position = 16 degrees
atoms outside contour = 4387, contour level = 0.024815
Position of 6k7m (#4) relative to emd_9941.map (#5) coordinates:
Matrix rotation and translation
0.99999999 -0.00007255 -0.00002499 0.01510218
0.00007255 0.99999999 0.00001998 -0.01007013
0.00002498 -0.00001999 0.99999999 0.00530739
Axis -0.25202896 -0.31509735 0.91498364
Axis point 120.46426379 222.81896502 0.00000000
Rotation angle (degrees) 0.00454324
Shift along axis 0.00422307
> ui tool show Matchmaker
> matchmaker #!1-3 to #4
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 6k7m, chain A (#4) with Drs2p_PS_AlFx-coot-10.pdb, chain A (#1),
sequence alignment score = 2905.8
RMSD between 802 pruned atom pairs is 1.053 angstroms; (across all 971 pairs:
2.322)
Matchmaker 6k7m, chain A (#4) with 8oxa, chain A (#2), sequence alignment
score = 2604.3
RMSD between 777 pruned atom pairs is 0.959 angstroms; (across all 948 pairs:
2.203)
Matchmaker 6k7m, chain A (#4) with 7bsv, chain A (#3), sequence alignment
score = 1989
RMSD between 629 pruned atom pairs is 1.058 angstroms; (across all 755 pairs:
2.162)
> volume #5 style mesh
> volume #5 color #005493
> ui mousemode right zoom
> hide #!3 models
> hide #!2 models
> hide #!1 models
> volume #5 level 0.02001
> volume #5 level 0.02145
> show #!1 models
> hide #!1 models
> open /Users/amaliebenfeldt/Downloads/emd_17262.map
Opened emd_17262.map as #6, grid size 256,256,256, pixel 1.05, shown at level
2.47, step 1, values float32
> show #!1 models
> show #!2 models
> show #!3 models
> save "/Users/amaliebenfeldt/Desktop/Updated models/AlFx_PS_comparison.cxs"
> volume #6 level 0.79
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/amaliebenfeldt/Desktop/Updated models/AlFx_PS_comparison.cxs"
Opened emd_9941.map as #5, grid size 260,260,260, pixel 0.83, shown at level
0.0215, step 1, values float32
Opened emd_17262.map as #6, grid size 256,256,256, pixel 1.05, shown at level
2.47, step 1, values float32
Log from Fri Feb 14 09:43:52 2025 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/amaliebenfeldt/Desktop/Updated models/Drs2p_PS_BeFx-
> coot-11.pdb"
Chain information for Drs2p_PS_BeFx-coot-11.pdb #1
---
Chain | Description
A | No description available
C | No description available
> open 8oxa
Summary of feedback from opening 8oxa fetched from pdb
---
notes | Fetching compressed mmCIF 8oxa from http://files.rcsb.org/download/8oxa.cif
Fetching CCD D39 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/D39/D39.cif
Fetching CCD VN4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/VN4/VN4.cif
8oxa title:
Cryo-EM structure of ATP8B1-CDC50A in E2-Pi conformation with occluded PS
[more info...]
Chain information for 8oxa #2
---
Chain | Description | UniProt
A | Phospholipid-transporting ATPase IC | AT8B1_HUMAN 1-1185
B | Cell cycle control protein 50A | CC50A_HUMAN 1-361
Non-standard residues in 8oxa #2
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
D39 —
(2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-
propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid
MG — magnesium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
VN4 — oxido(dioxo)vanadium
> open 7bsv
Summary of feedback from opening 7bsv fetched from pdb
---
notes | Fetching compressed mmCIF 7bsv from http://files.rcsb.org/download/7bsv.cif
Fetching CCD P5S from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/P5S/P5S.cif
7bsv title:
Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdSer-occluded E2-AlF
state [more info...]
Chain information for 7bsv #3
---
Chain | Description
A | ATP11C
C | CDC50A
Non-standard residues in 7bsv #3
---
ALF — tetrafluoroaluminate ion
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
MG — magnesium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
P5S —
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
(phosphatidyl serine)
> open 6k7m
Summary of feedback from opening 6k7m fetched from pdb
---
note | Fetching compressed mmCIF 6k7m from http://files.rcsb.org/download/6k7m.cif
6k7m title:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2Pi-PL state)
[more info...]
Chain information for 6k7m #4
---
Chain | Description | UniProt
A | Phospholipid-transporting ATPase | Q59EX4_HUMAN 1-1149
C | Cell cycle control protein 50A | CC50A_HUMAN 1-361
Non-standard residues in 6k7m #4
---
ALF — tetrafluoroaluminate ion
D39 —
(2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-
propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
MG — magnesium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Y01 — cholesterol hemisuccinate
> ui tool show Matchmaker
> matchmaker #!2-4 to #1
Computing secondary structure
[Repeated 3 time(s)] 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 Drs2p_PS_BeFx-coot-11.pdb, chain A (#1) with 8oxa, chain A (#2),
sequence alignment score = 2515.2
RMSD between 446 pruned atom pairs is 0.912 angstroms; (across all 998 pairs:
6.683)
Matchmaker Drs2p_PS_BeFx-coot-11.pdb, chain A (#1) with 7bsv, chain A (#3),
sequence alignment score = 1924.9
RMSD between 425 pruned atom pairs is 1.095 angstroms; (across all 772 pairs:
6.022)
Matchmaker Drs2p_PS_BeFx-coot-11.pdb, chain A (#1) with 6k7m, chain A (#4),
sequence alignment score = 2910.7
RMSD between 508 pruned atom pairs is 0.988 angstroms; (across all 978 pairs:
5.954)
> hide #1 models
> close #1
> open "/Users/amaliebenfeldt/Desktop/Updated models/Drs2p_PS_AlFx-
> coot-10.pdb"
Chain information for Drs2p_PS_AlFx-coot-10.pdb #1
---
Chain | Description
A | No description available
C | No description available
> ui tool show Matchmaker
> matchmaker #!2-4 to #1
Computing secondary structure
[Repeated 3 time(s)] 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 Drs2p_PS_AlFx-coot-10.pdb, chain A (#1) with 8oxa, chain A (#2),
sequence alignment score = 2542.6
RMSD between 759 pruned atom pairs is 1.069 angstroms; (across all 1010 pairs:
4.071)
Matchmaker Drs2p_PS_AlFx-coot-10.pdb, chain A (#1) with 7bsv, chain A (#3),
sequence alignment score = 1947.7
RMSD between 570 pruned atom pairs is 1.162 angstroms; (across all 785 pairs:
2.461)
Matchmaker Drs2p_PS_AlFx-coot-10.pdb, chain A (#1) with 6k7m, chain A (#4),
sequence alignment score = 2905.8
RMSD between 802 pruned atom pairs is 1.053 angstroms; (across all 971 pairs:
2.322)
> set bgColor white
> hide atoms
> select ::name="D39"
156 atoms, 153 bonds, 3 residues, 3 models selected
> show sel atoms
> select ::name="P5S"
136 atoms, 135 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #3
9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected
> select subtract #3
Nothing selected
> ui mousemode right zoom
> select add #2
11138 atoms, 11391 bonds, 11 pseudobonds, 1382 residues, 4 models selected
> select add #3
20559 atoms, 21044 bonds, 17 pseudobonds, 2533 residues, 8 models selected
> select add #4
31150 atoms, 31888 bonds, 23 pseudobonds, 3849 residues, 12 models selected
> hide sel cartoons
> color #1 silver
> color #3 #4f8f00ff
> color #3 #008f00ff
> color #3 #945200ff
> color #3 #941100ff
> color #3 #009193ff
> color #4 #00fa92ff
> color #4 #8efa00ff
> color #4 #fffb00ff
> color #4 #ff9300ff
> color #4 #0433ffff
> color #4 #005493ff
> color #4 #011993ff
> color #4 #0433ffff
> color #4 #0096ffff
> color #4 #0433ffff
> color #4 #929000ff
> ui tool show "Side View"
> select subtract #2
20012 atoms, 20497 bonds, 12 pseudobonds, 2467 residues, 8 models selected
> select subtract #3
10591 atoms, 10844 bonds, 6 pseudobonds, 1316 residues, 4 models selected
> select subtract #4
Nothing selected
> color :D39 byhetero
> color :P5S byhetero
> select h
Expected an objects specifier or a keyword
> select H
11513 atoms, 1421 residues, 2 models selected
> hide sel
> select add #3
20852 atoms, 9653 bonds, 6 pseudobonds, 2571 residues, 5 models selected
> select subtract #3
11431 atoms, 1420 residues, 1 model selected
> select add #1
22985 atoms, 23251 bonds, 3 pseudobonds, 1427 residues, 2 models selected
> select subtract #1
Nothing selected
> lighting shadows false
> lighting soft
> graphics silhouettes true
> cartoon style width 1.2 thickness 0.25 xsection oval sides 20
> save AlFx_PS_comparison.png format png width 3600 height 3600 supersample 2
> transparentBackground true
> select add #1
22985 atoms, 23251 bonds, 3 pseudobonds, 1427 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #2
11138 atoms, 11391 bonds, 11 pseudobonds, 1382 residues, 4 models selected
> select add #3
20559 atoms, 21044 bonds, 17 pseudobonds, 2533 residues, 8 models selected
> select add #4
31150 atoms, 31888 bonds, 23 pseudobonds, 3849 residues, 12 models selected
> select add #1
54135 atoms, 55139 bonds, 26 pseudobonds, 5276 residues, 14 models selected
> show sel cartoons
> select /A:507-510,1047,237,245
247 atoms, 239 bonds, 23 residues, 4 models selected
> show sel atoms
> hide sel atoms
> select #1/A:507-510,1047,237,245
105 atoms, 102 bonds, 7 residues, 1 model selected
> show sel atoms
> select #4/A:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/A:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/A:96
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color #4/A:96 by het
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #4/A:96 byhetero
> color #3/A:86 byhetero
> select #3/A:86
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color #2/A:139 byhetero
> color #3/A:79
> select #3/A:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color #3/A:79 byhetero
> select #4/A:88
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color #4/A:88 byhetero
> select #2/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/A:879
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> color #4/A:879 byhetero
> select #3/A:909
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color #3/A:909 byhetero
> hide #!3 models
> select #2/A:986 byhet
Expected a keyword
> select #2/A:986
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!3 models
> color #1/A:507-510,1047,237,245 byhetero
> select H
11513 atoms, 1421 residues, 2 models selected
> hide sel
> select add #3
20852 atoms, 9653 bonds, 6 pseudobonds, 2571 residues, 5 models selected
> select add #1
32406 atoms, 32904 bonds, 9 pseudobonds, 2578 residues, 6 models selected
> select subtract #1
9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected
> select subtract #3
Nothing selected
> select add #3
9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected
> select subtract #3
Nothing selected
> ~label #1-4 residues
[Repeated 1 time(s)]
> ui mousemode right select
No visible residues selected
> ui mousemode right translate
> ui mousemode right zoom
> select #4/A:356-359
29 atoms, 29 bonds, 4 residues, 1 model selected
> show sel atoms
> color #4/A:356-359 byhetero
> select #3/A:356-359
28 atoms, 28 bonds, 4 residues, 1 model selected
> color #3/A:356-359 byhetero
> select #2/A:401-404 byhet
Expected a keyword
> select #2/A:401-404
29 atoms, 29 bonds, 4 residues, 1 model selected
> color #2/A:401-404 byhetero
> select add #2
11138 atoms, 11391 bonds, 11 pseudobonds, 1382 residues, 4 models selected
> select subtract #2
Nothing selected
> select #2/A:401-404
29 atoms, 29 bonds, 4 residues, 1 model selected
> show sel atoms
> select #3/A:356-359
28 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> select add #3
9421 atoms, 9653 bonds, 6 pseudobonds, 1151 residues, 4 models selected
> select subtract #3
Nothing selected
> open /Users/amaliebenfeldt/Downloads/emd_9941.map
Opened emd_9941.map as #5, grid size 260,260,260, pixel 0.83, shown at level
0.0122, step 2, values float32
> volume #5 step 1
> hide #!5 models
> save AlFx_PS_comparison_residue.png format png width 3600 height 3600
> supersample 2 transparentBackground true
> show #!5 models
> volume #5 level 0.02482
> select add #5
4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.99088,0.049565,-0.12526,224.15,-0.09401,-0.92042,0.37946,184.94,-0.096486,0.38778,0.91669,-24.083
> view matrix models
> #5,-0.98157,0.19111,0.0022948,192.51,-0.18143,-0.93552,0.30313,204.83,0.060077,0.29712,0.95295,-34.872
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.98157,0.19111,0.0022948,208.55,-0.18143,-0.93552,0.30313,266.6,0.060077,0.29712,0.95295,20.617
> view matrix models
> #5,-0.98157,0.19111,0.0022948,251.75,-0.18143,-0.93552,0.30313,257.1,0.060077,0.29712,0.95295,22.924
> select subtract #5
Nothing selected
> ui tool show "Fit in Map"
> fitmap #4 inMap #5
Fit molecule 6k7m (#4) to map emd_9941.map (#5) using 10591 atoms
average map value = 0.03523, steps = 128
shifted from previous position = 3.16
rotated from previous position = 16 degrees
atoms outside contour = 4387, contour level = 0.024815
Position of 6k7m (#4) relative to emd_9941.map (#5) coordinates:
Matrix rotation and translation
0.99999999 -0.00007255 -0.00002499 0.01510218
0.00007255 0.99999999 0.00001998 -0.01007013
0.00002498 -0.00001999 0.99999999 0.00530739
Axis -0.25202896 -0.31509735 0.91498364
Axis point 120.46426379 222.81896502 0.00000000
Rotation angle (degrees) 0.00454324
Shift along axis 0.00422307
> ui tool show Matchmaker
> matchmaker #!1-3 to #4
Computing secondary structure
[Repeated 3 time(s)] 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 6k7m, chain A (#4) with Drs2p_PS_AlFx-coot-10.pdb, chain A (#1),
sequence alignment score = 2905.8
RMSD between 802 pruned atom pairs is 1.053 angstroms; (across all 971 pairs:
2.322)
Matchmaker 6k7m, chain A (#4) with 8oxa, chain A (#2), sequence alignment
score = 2604.3
RMSD between 777 pruned atom pairs is 0.959 angstroms; (across all 948 pairs:
2.203)
Matchmaker 6k7m, chain A (#4) with 7bsv, chain A (#3), sequence alignment
score = 1989
RMSD between 629 pruned atom pairs is 1.058 angstroms; (across all 755 pairs:
2.162)
> volume #5 style mesh
> volume #5 color #005493
> ui mousemode right zoom
> hide #!3 models
> hide #!2 models
> hide #!1 models
> volume #5 level 0.02001
> volume #5 level 0.02145
> show #!1 models
> hide #!1 models
> open /Users/amaliebenfeldt/Downloads/emd_17262.map
Opened emd_17262.map as #6, grid size 256,256,256, pixel 1.05, shown at level
2.47, step 1, values float32
> show #!1 models
> show #!2 models
> show #!3 models
> save "/Users/amaliebenfeldt/Desktop/Updated models/AlFx_PS_comparison.cxs"
——— End of log from Fri Feb 14 09:43:52 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1
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: MacBookPro17,1
Model Number: MYDC2DK/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 10 dage og 12 minutter
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
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
HP E24m G4:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
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 (3)
comment:1 by , 9 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 , 9 months ago
comment:3 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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I hope most of our Mac users are simply ignoring the wall of red text that says this is a known crash that we can't fix and pressing the "Report" button. Because if most actually read a bit of the text and decide not to report, then there must be a ton of crashes happening.