![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 hours ago
Last modified 40 minutes ago
#20051 assigned defect
Crash in QWindowContainer::parentWasChanged
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202602270247 (2026-02-27 02:47:46 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,12",
"coalitionID" : 17924,
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"build" : "25D771280a",
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"codeSigningMonitor" : 2,
"incident" : "15E06847-EF0C-43B8-BD8D-30AB8C7920F1",
"pid" : 37129,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-03-23 16:29:05.7881 +0100",
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"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "2A13C616-385F-83D8-2186-2B719B7CA831",
"appleIntelligenceStatus" : {"state":"available"},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
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"sleepWakeUUID" : "5AC39FF0-53E2-4703-9E9E-ADEBAAD30A67",
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"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4329783288
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 102134000-102138000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
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"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4329783288
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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{"imageOffset":3124,"symbol": "mach_msg2_trap" ,"symbolLocation":8,"imageIndex":141},
{"imageOffset":77864,"symbol": "mach_msg2_internal" ,"symbolLocation":76,"imageIndex":141},
{"imageOffset":39308,"symbol": "mach_msg_overwrite" ,"symbolLocation":484,"imageIndex":141},
{"imageOffset":4020,"symbol": "mach_msg" ,"symbolLocation":24,"imageIndex":141},
{"imageOffset":84303928,"imageIndex":57},
{"imageOffset":83753404,"imageIndex":57},
{"imageOffset":84018040,"imageIndex":57},
{"imageOffset":84020700,"imageIndex":57},
{"imageOffset":84019912,"imageIndex":57},
{"imageOffset":84019668,"imageIndex":57},
{"imageOffset":84187692,"imageIndex":57},
{"imageOffset":27656,"symbol": "_pthread_start" ,"symbolLocation":136,"imageIndex":142},
{"imageOffset":7080,"symbol": "thread_start" ,"symbolLocation":8,"imageIndex":142}]},{"id":1981609,"frames":[
],
"threadState":{"x":[{"value":6315831296},{"value":0},{"value":6315294720},{"value":0},{"value":278532},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":0},"fp":{"value":0},"sp":{"value":6315831296},"esr":{"value":0},"pc":{"value":6466513812},"far":{"value":0}}},{"id":1982033,"name":"ThreadPoolForegroundWorker",
"threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":717031905165312},{"value":0},{"value":717031905165312},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":166947},{"value":0},{"value":18446744073709551569},{"value":52805210112},{"value":0},{"value":0},{"value":32},{"value":717031905165312},{"value":0},{"value":717031905165312},{"value":6333803744},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6466334760},"cpsr":{"value":0},"fp":{"value":6333803088},"sp":{"value":6333803008},"esr":{"value":1442840704,"description":"(Syscall)"},"pc":{"value":6466260020},"far":{"value":0}},"frames":[
{"imageOffset":3124,"symbol": "mach_msg2_trap" ,"symbolLocation":8,"imageIndex":141},
{"imageOffset":77864,"symbol": "mach_msg2_internal" ,"symbolLocation":76,"imageIndex":141},
{"imageOffset":39308,"symbol": "mach_msg_overwrite" ,"symbolLocation":484,"imageIndex":141},
{"imageOffset":4020,"symbol": "mach_msg" ,"symbolLocation":24,"imageIndex":141},
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{"imageOffset":84187692,"imageIndex":57},
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REGION TYPE SIZE COUNT (non-coalesced)
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Accelerate framework 256K 2
Activity Tracing 256K 1
AttributeGraph Data 1024K 1
CG image 5104K 5
CG raster data 3296K 7
ColorSync 96K 6
CoreAnimation 1456K 90
CoreGraphics 64K 4
CoreServices 240K 1
CoreUI image data 1408K 16
Foundation 48K 2
Kernel Alloc Once 112K 3
MALLOC 436.5M 121
MALLOC guard page 3504K 4
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 704K 44
Stack 203.5M 45
Stack Guard 56.0M 1
VM_ALLOCATE 250.8M 211
VM_ALLOCATE (reserved) 192.0M 1 reserved VM address space (unallocated)
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TOTAL, minus reserved VM space 4.0G 6886
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Log:
UCSF ChimeraX version: 1.12.dev202602270247 (2026-02-27)
© 2016-2026 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs 260223 GLS.cxs"
Log from Tue Feb 24 10:12:16 2026UCSF ChimeraX version: 1.11.dev202511180234
(2025-11-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs 260222.cxs" format session
Log from Sat Feb 21 18:41:51 2026UCSF ChimeraX version: 1.11.dev202511180234
(2025-11-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025 experiments/XX25-36
> GST pull-down DMC1 mutants negatively charged/260127 54B positive and DMC1
> negative residues tested in XX25-36.cxs"
Log from Wed Jan 28 15:35:48 2026UCSF ChimeraX version: 1.11.dev202511180234
(2025-11-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025
> experiments/251020_lysines.cxs"
Log from Tue Oct 21 09:05:15 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025
> experiments/251009_lysines.cxs"
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
pixel 0.73, shown at level 0.0225, step 2, values float32
Log from Mon Oct 13 17:24:42 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/anz/Desktop/251009_lysines.cxs
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
pixel 0.73, shown at level 0.0225, step 2, values float32
Log from Thu Oct 9 18:29:50 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/anz/Desktop/251009_lysines.cxs
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
pixel 0.73, shown at level 0.0225, step 2, values float32
Log from Thu Oct 9 14:13:54 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/250904 TMM
> RAD54B/preparation/ForAlexRAD54B movies TMM peptide 2.cxs"
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
pixel 0.73, shown at level 0.0225, step 2, values float32
Log from Thu Sep 4 04:53:36 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
> structures RAD54B PhePP from Sophie/ForAlexRAD54B movies TMM.cxs"
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
pixel 0.73, shown at level 0.0225, step 2, values float32
Log from Wed Sep 3 19:35:27 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
> structures RAD54B PhePP from Sophie/ForAlexRAD54B.cxs"
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
pixel 0.73, shown at level 0.0225, step 2, values float32
Log from Fri Jul 11 19:20:58 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/RAD54B.cxs" format session
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened cryosparc_P26_J362_012_volume_map_sharp.mrc as #6, grid size
336,336,336, pixel 0.73, shown at level 0.05, step 2, values float32
Opened cryosparc_P26_J362_012_volume_map.mrc as #8, grid size 336,336,336,
pixel 0.73, shown at level 0.0236, step 2, values float32
Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #9, grid size
336,336,336, pixel 0.73, shown at level 0.0229, step 2, values float32
restore_snapshot for "Redust" returned None
Log from Thu Jul 10 10:47:21 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
> RAD54/BRCA2-07072025.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened cryosparc_P26_J362_012_volume_map_sharp.mrc as #6, grid size
336,336,336, pixel 0.73, shown at level 0.035, step 2, values float32
Opened cryosparc_P26_J402_011_volume_map.mrc as #1, grid size 336,336,336,
pixel 0.745, shown at level 0.0227, step 2, values float32
Opened cryosparc_P26_J402_011_volume_map_sharp.mrc as #2, grid size
336,336,336, pixel 0.745, shown at level 0.0194, step 2, values float32
Log from Mon Jul 7 15:58:39 2025 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
> open /Users/sz140275local/Downloads/J216_011_volume_map_ABCEF.pdb
Chain information for J216_011_volume_map_ABCEF.pdb #1
---
Chain | Description
A B C D E F | No description available
M N O P Q R | No description available
X | No description available
> open
> /Users/sz140275local/Downloads/cryosparc_P26_J216_011_volume_map_sharp.mrc
Opened cryosparc_P26_J216_011_volume_map_sharp.mrc as #2, grid size
336,336,336, pixel 0.745, shown at level 0.0337, step 2, values float32
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> volume #2 level 0.1509
> hide #!2 models
> hide atoms
> show cartoons
Computing secondary structure
> select #1/B
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> color sel light green
> select #1/C
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> color sel light blue
> select #1/D
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> color sel light green
> select #1/F
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> color sel light green
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!2 models
> volume #2 level 0.08302
> transparency 50
> volume #2 level 0.03522
> surface dust #2 size 7.45
> color zone #2 near #1 distance 4.47
> transparency 0
> transparency 50
> ui mousemode right zoom
> select #1/O
55 atoms, 58 bonds, 7 residues, 1 model selected
> show sel atoms
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #1
Nothing selected
> ui mousemode right translate
> select #1/P
55 atoms, 58 bonds, 7 residues, 1 model selected
> show sel atoms
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #1
Nothing selected
> volume #2 level 0.02134
> surface dust #2 size 7.45
> color zone #2 near #1 distance 4.47
> transparency 0
> transparency 50
> volume #2 level 0.02443
> color zone #2 near #1 distance 4.47
> transparency 0
> transparency 50
> open /Users/sz140275local/Downloads/cryosparc_P26_J216_011_volume_map.mrc
Opened cryosparc_P26_J216_011_volume_map.mrc as #3, grid size 336,336,336,
pixel 0.745, shown at level 0.0204, step 2, values float32
> hide #!2 models
> ui tool show "Fit in Map"
> fitmap #1 inMap #3
Fit molecule J216_011_volume_map_ABCEF.pdb (#1) to map
cryosparc_P26_J216_011_volume_map.mrc (#3) using 15318 atoms
average map value = 0.04976, steps = 44
shifted from previous position = 0.00864
rotated from previous position = 0.0468 degrees
atoms outside contour = 2325, contour level = 0.020397
Position of J216_011_volume_map_ABCEF.pdb (#1) relative to
cryosparc_P26_J216_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999981 0.00023261 0.00057087 -0.10686852
-0.00023292 0.99999983 0.00053698 -0.03534062
-0.00057074 -0.00053712 0.99999969 0.14093574
Axis -0.65688580 0.69817168 -0.28470573
Axis point 249.53117123 0.00000000 181.07164593
Rotation angle (degrees) 0.04684334
Shift along axis 0.00540138
> fitmap #1 inMap #3
Fit molecule J216_011_volume_map_ABCEF.pdb (#1) to map
cryosparc_P26_J216_011_volume_map.mrc (#3) using 15318 atoms
average map value = 0.04976, steps = 40
shifted from previous position = 0.0138
rotated from previous position = 0.00839 degrees
atoms outside contour = 2325, contour level = 0.020397
Position of J216_011_volume_map_ABCEF.pdb (#1) relative to
cryosparc_P26_J216_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999978 0.00031309 0.00057735 -0.11718292
-0.00031333 0.99999986 0.00041488 -0.02267100
-0.00057722 -0.00041506 0.99999975 0.12663259
Axis -0.53414014 0.74307156 -0.40316122
Axis point 215.58542420 0.00000000 207.95751060
Rotation angle (degrees) 0.04451256
Shift along axis -0.00530742
> transparency #3.1 50
> volume #3 level 0.01092
> surface dust #3 size 7.45
> color zone #3 near #1 distance 4.47
> transparency #3.1 0
> transparency #3.1 50
> hide #!3 models
> select #1/P
55 atoms, 58 bonds, 7 residues, 1 model selected
> color sel red
> hide #!1 models
> show #!1 models
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!3 models
> color zone #3 near #1 distance 4.47
> transparency #3.1 0
> transparency #3.1 50
> label sel
> label #1/P
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #1/D
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 2438 atom styles
> show #!3 models
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #1
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> volume #3 level 0.01255
> color zone #3 near #1 distance 4.47
> transparency #3.1 0
> transparency #3.1 50
> volume #3 level 0.01549
> color zone #3 near #1 distance 4.47
> select #1/O
55 atoms, 58 bonds, 7 residues, 1 model selected
> color sel red
> color zone #3 near sel & #1 distance 4.47
[Repeated 2 time(s)]
> select #1/P
55 atoms, 58 bonds, 7 residues, 1 model selected
> select #1/P
55 atoms, 58 bonds, 7 residues, 1 model selected
> color sel red
> color zone #3 near sel & #1 distance 4.47
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> color zone #3 near sel & #1 distance 4.47
> select #1/Q
55 atoms, 58 bonds, 7 residues, 1 model selected
> select #1/Q,N
110 atoms, 116 bonds, 14 residues, 1 model selected
> color sel red
> color zone #3 near sel & #1 distance 4.47
[Repeated 1 time(s)]
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> color zone #3 near sel & #1 distance 4.47
> select subtract #1
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> transparency #3.1 0
> transparency #3.1 50
> label #1/O
> label #1/D
> hide atoms
> unlabel #1/D
Unknown command: unlabel #1/D
> unlabel
Unknown command: unlabel
> ~label #1,3 residues
> hide #!3 models
> show #!3 models
> select #1/O
55 atoms, 58 bonds, 7 residues, 1 model selected
> show sel atoms
> label #1/O
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> select #1/C:20
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #1/C
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for J216_011_volume_map_ABCEF.pdb_C SES surface #1.3:
minimum, -26.80, mean -0.75, maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for J216_011_volume_map_ABCEF.pdb_C SES surface #1.3:
minimum, -26.80, mean -0.75, maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!3 models
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 4 models selected
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> select subtract #1
1 model selected
> select #1/D:89
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> transparency #1.3 50
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #1
1 model selected
> show #!3 models
> hide #!3 models
> hide surfaces
> show #!3 models
> hide #!3 models
> select #1/M
55 atoms, 58 bonds, 7 residues, 1 model selected
> color sel red
> show #!3 models
> color zone #3 near sel & #1 distance 4.47
[Repeated 1 time(s)]
> select add #1
15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected
> select subtract #1
1 model selected
> color zone #3 near #1 distance 4.47
> hide #!1 models
> open emdb:16432
Summary of feedback from opening 16432 fetched from emdb
---
notes | Fetching compressed map 16432 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16432/map/emd_16432.map.gz
Fetching map header 16432 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16432/header/emd-16432.xml
Opened emdb 16432 as #4, grid size 600,600,600, pixel 0.73, shown at level
0.0272, step 4, values float32
> hide #!3 models
> open 7bdx
Summary of feedback from opening 7bdx fetched from pdb
---
note | Fetching compressed mmCIF 7bdx from http://files.rcsb.org/download/7bdx.cif
7bdx title:
Armadillo domain of HSF2BP in complex with BRCA2 peptide [more info...]
Chain information for 7bdx #5
---
Chain | Description | UniProt
A B C D | Heat shock factor 2-binding protein | HSF2B_HUMAN 122-334
E F | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 2291-2343
Non-standard residues in 7bdx #5
---
MG — magnesium ion
> hide #!4 models
> view #5 clip false
> hide #!5 atoms
> show #!5 cartoons
> select #5/E,F
871 atoms, 854 bonds, 135 residues, 1 model selected
> color sel red
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 2 models selected
> select subtract #5
Nothing selected
> color #5/A
> color #5/A light blue
> color #5/B lime
> color #5/B pale green
> color #5/C pale green
> color #5/C green
> color #5/D cyan
> show #!4 models
> color #4 #fef6d9ff models
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,105.96,0,1,0,63.522,0,0,1,-12.452
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.13885,0.16272,0.97685,70.836,-0.45432,0.88695,-0.083165,90.344,-0.87995,-0.43226,0.19708,88.131
> view matrix models
> #5,-0.6185,0.067994,0.78284,113.07,-0.18461,0.95579,-0.22887,85.24,-0.76379,-0.28608,-0.5786,118.91
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.6185,0.067994,0.78284,191.52,-0.18461,0.95579,-0.22887,93.923,-0.76379,-0.28608,-0.5786,219.64
> view matrix models
> #5,-0.6185,0.067994,0.78284,99.843,-0.18461,0.95579,-0.22887,143.12,-0.76379,-0.28608,-0.5786,226.59
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.84821,-0.4082,-0.3375,198.72,-0.52089,0.75833,0.39192,131.54,0.095959,0.50824,-0.85585,165.61
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.84821,-0.4082,-0.3375,196.64,-0.52089,0.75833,0.39192,111.25,0.095959,0.50824,-0.85585,238.08
> view matrix models
> #5,-0.84821,-0.4082,-0.3375,207.57,-0.52089,0.75833,0.39192,117.01,0.095959,0.50824,-0.85585,237.86
> ui tool show "Fit in Map"
> fitmap #5 inMap #4
Fit molecule 7bdx (#5) to map emdb 16432 (#4) using 7434 atoms
average map value = 0.03421, steps = 112
shifted from previous position = 7.2
rotated from previous position = 12.8 degrees
atoms outside contour = 2925, contour level = 0.0272
Position of 7bdx (#5) relative to emdb 16432 (#4) coordinates:
Matrix rotation and translation
-0.86382345 -0.47543336 -0.16664985 204.71782263
-0.50378895 0.81675834 0.28125168 124.65891763
0.00239623 0.32690815 -0.94505308 252.37451155
Axis 0.25738757 -0.95299437 -0.15985418
Axis point 113.70622837 0.00000000 121.14343579
Rotation angle (degrees) 174.91163309
Shift along axis -106.45054436
> view matrix models
> #5,-0.86382,-0.47543,-0.16665,208.23,-0.50379,0.81676,0.28125,121.73,0.0023962,0.32691,-0.94505,248.04
> transparency #4.1 50
> view matrix models
> #5,-0.86382,-0.47543,-0.16665,205.91,-0.50379,0.81676,0.28125,124.41,0.0023962,0.32691,-0.94505,248.61
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.41993,0.90484,0.070133,95.392,0.15485,-0.0047059,0.98793,111.38,0.89425,0.42572,-0.13814,167.25
> view matrix models
> #5,0.98295,0.008792,-0.18369,115.29,-0.1418,-0.59977,-0.78751,256.29,-0.11709,0.80013,-0.58829,204.52
> view matrix models
> #5,0.44654,0.73647,-0.50815,108.35,-0.66072,-0.11156,-0.7423,242.32,-0.60337,0.66721,0.43678,171.56
> view matrix models
> #5,0.89516,-0.19084,-0.40283,142.43,0.34388,0.87068,0.35167,88.464,0.28362,-0.45333,0.84502,185.29
> view matrix models
> #5,0.65334,-0.40245,-0.64124,176.59,0.62631,0.76315,0.15916,96.048,0.42531,-0.5056,0.75065,188.87
> view matrix models
> #5,0.414,-0.69992,0.58199,133.95,0.24703,0.70175,0.66822,84.089,-0.87611,-0.13288,0.46343,226.97
> view matrix models
> #5,-0.54647,0.35217,0.75984,93.982,0.65193,0.7484,0.12199,98.137,-0.5257,0.56202,-0.63857,235.39
> view matrix models
> #5,-0.2605,0.068669,0.96303,89.77,-0.38401,0.90781,-0.1686,140.11,-0.88582,-0.41373,-0.21011,281.73
> view matrix models
> #5,-0.2192,-0.95749,-0.1875,213.88,-0.32214,-0.11037,0.94024,136.55,-0.92097,0.2665,-0.28425,246.58
> view matrix models
> #5,0.82463,0.2605,-0.50212,123.51,-0.067718,-0.83581,-0.54483,254.24,-0.5616,0.48329,-0.67159,243.15
> view matrix models
> #5,-0.97664,-0.20844,-0.052222,187.44,-0.045686,-0.036052,0.99831,119.48,-0.20997,0.97737,0.025687,162.75
> view matrix models
> #5,-0.73345,-0.15296,-0.66231,210.03,-0.66497,-0.040621,0.74577,154.93,-0.14098,0.9874,-0.071922,165.27
> view matrix models
> #5,-0.74012,0.53192,-0.41145,155.43,-0.3207,-0.81697,-0.47929,258.04,-0.59108,-0.22278,0.77524,205.19
> fitmap #5 inMap #4
Fit molecule 7bdx (#5) to map emdb 16432 (#4) using 7434 atoms
average map value = 0.03392, steps = 280
shifted from previous position = 3.51
rotated from previous position = 37.7 degrees
atoms outside contour = 2888, contour level = 0.0272
Position of 7bdx (#5) relative to emdb 16432 (#4) coordinates:
Matrix rotation and translation
-0.82631357 0.55436000 0.09945286 126.03120258
-0.56321014 -0.81347234 -0.14511058 249.18468833
0.00045865 -0.17591970 0.98440441 173.51218129
Axis -0.02745009 0.08820113 -0.99572439
Axis point 101.14138831 113.49827864 0.00000000
Rotation angle (degrees) 145.86224811
Shift along axis -154.25150712
> view matrix models
> #5,-0.97364,0.19603,0.11663,151.41,-0.22375,-0.7214,-0.65538,260.74,-0.044342,-0.6642,0.74624,217.44
> view matrix models
> #5,-0.58332,-0.28277,0.76143,130.56,-0.44822,-0.66973,-0.59209,261.74,0.67737,-0.68666,0.26392,221.26
> view matrix models
> #5,0.94524,0.30301,0.12123,79.591,0.32533,-0.90438,-0.27615,231.75,0.025962,0.30047,-0.95344,252.77
> fitmap #5 inMap #4
Fit molecule 7bdx (#5) to map emdb 16432 (#4) using 7434 atoms
average map value = 0.02864, steps = 252
shifted from previous position = 21.4
rotated from previous position = 12.1 degrees
atoms outside contour = 3611, contour level = 0.0272
Position of 7bdx (#5) relative to emdb 16432 (#4) coordinates:
Matrix rotation and translation
0.87261982 0.43976226 0.21247070 88.01929926
0.48814924 -0.79925673 -0.35056954 233.42789236
0.01565138 0.40963134 -0.91211688 245.34569372
Axis 0.96624770 0.25016573 0.06150191
Axis point 0.00000000 80.33356484 140.42171784
Rotation angle (degrees) 156.83515700
Shift along axis 158.53333505
> view matrix models
> #5,-0.57905,-0.80598,0.12284,216.52,-0.72635,0.57842,0.37127,152.25,-0.37029,0.12576,-0.92036,275.82
> view matrix models
> #5,-0.74829,-0.61836,0.24019,204.53,-0.049114,0.41273,0.90953,108.97,-0.66155,0.6688,-0.33921,220.85
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.74829,-0.61836,0.24019,197.97,-0.049114,0.41273,0.90953,100.11,-0.66155,0.6688,-0.33921,228.27
> view matrix models
> #5,-0.74829,-0.61836,0.24019,199.07,-0.049114,0.41273,0.90953,97.48,-0.66155,0.6688,-0.33921,224.41
> vop flip #4
Opened emdb 16432 z flip as #6, grid size 600,600,600, pixel 0.73, shown at
step 1, values float32
> view matrix models
> #5,-0.74829,-0.61836,0.24019,182.9,-0.049114,0.41273,0.90953,88.945,-0.66155,0.6688,-0.33921,216
> view matrix models
> #5,-0.74829,-0.61836,0.24019,175.75,-0.049114,0.41273,0.90953,96.632,-0.66155,0.6688,-0.33921,222.71
> volume #6 level 0.06538
> view matrix models
> #5,-0.74829,-0.61836,0.24019,180.22,-0.049114,0.41273,0.90953,87.231,-0.66155,0.6688,-0.33921,240.87
> view matrix models
> #5,-0.74829,-0.61836,0.24019,208.61,-0.049114,0.41273,0.90953,90.379,-0.66155,0.6688,-0.33921,243.87
> volume #6 level 0.03871
> view matrix models
> #5,-0.74829,-0.61836,0.24019,202.27,-0.049114,0.41273,0.90953,112.3,-0.66155,0.6688,-0.33921,212.48
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.88601,-0.4493,0.11449,203.92,0.07525,0.10432,0.99169,121.84,-0.45751,0.88727,-0.058616,176.83
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.88601,-0.4493,0.11449,199.26,0.07525,0.10432,0.99169,116.35,-0.45751,0.88727,-0.058616,182.47
> fitmap #5 inMap #6
Fit molecule 7bdx (#5) to map emdb 16432 z flip (#6) using 7434 atoms
average map value = 0.05131, steps = 436
shifted from previous position = 12.5
rotated from previous position = 67.8 degrees
atoms outside contour = 2238, contour level = 0.038713
Position of 7bdx (#5) relative to emdb 16432 z flip (#6) coordinates:
Matrix rotation and translation
-0.86719186 -0.45679819 -0.19827678 205.88171390
-0.49796702 0.79334082 0.35019880 121.99409785
-0.00266912 0.40242484 -0.91544913 245.49065594
Axis 0.25278458 -0.94678047 -0.19926540
Axis point 113.12491740 0.00000000 116.31534353
Rotation angle (degrees) 174.07068315
Shift along axis -112.37570003
> color zone #6 near sel & #5 distance 4.38
> hide #!5 models
> select subtract #5
Nothing selected
> volume #6 level 0.05326
> color #6 #b1ada080 models
> show #!5 models
> color zone #6 near #5 distance 4.38
> volume #6 level 0.03629
> volume #6 level 0.04114
> hide #!5 models
> transparency #6.1 0
> show #!5 models
> transparency #6.1 50
> hide #!6 models
> open
> /Users/sz140275local/Downloads/ZCWPW1idr_ARMdimer_c8acb/predictions/ZCWPW1idr_ARMdimer/models/ZCWPW1idr_ARMdimer_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_38557.pdb
Chain information for
ZCWPW1idr_ARMdimer_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_38557.pdb
#7
---
Chain | Description
A | No description available
B C | No description available
Computing secondary structure
> hide #!5 models
> view #7 clip false
> color bfactor alphafold palette
> color byattribute bfactor alphafold palette
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor #1 alphafold palette
> color byattribute bfactor #1 alphafold palette
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor #1 palette alphafold
15318 atoms, 1944 residues, 1 surfaces, atom bfactor range 20 to 100
> color bfactor #1
15318 atoms, 1944 residues, 1 surfaces, atom bfactor range 20 to 100
> color bfactor #7 palette alphafold
4539 atoms, 584 residues, atom bfactor range 16.5 to 98.8
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:33-135
819 atoms, 830 bonds, 103 residues, 1 model selected
> select #7/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:33-106
594 atoms, 599 bonds, 74 residues, 1 model selected
> select #7/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:33-112
634 atoms, 641 bonds, 80 residues, 1 model selected
> select #7/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:33-115
649 atoms, 656 bonds, 83 residues, 1 model selected
> select #7/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:33-62
254 atoms, 256 bonds, 30 residues, 1 model selected
> select #7/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:33-57
210 atoms, 212 bonds, 25 residues, 1 model selected
> mmaker #7 to #5
Computing secondary structure
[Repeated 1 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 7bdx, chain C (#5) with
ZCWPW1idr_ARMdimer_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_38557.pdb,
chain C (#7), sequence alignment score = 1049.6
RMSD between 210 pruned atom pairs is 0.672 angstroms; (across all 213 pairs:
0.782)
> view #5 clip false
No displayed objects specified.
> show #!5 target m
> view #5 clip false
> view matrix models
> #7,0.38841,0.91274,0.12662,136.83,0.17641,0.06122,-0.98241,181.76,-0.90444,0.40392,-0.13724,230.2
> select add #7
4539 atoms, 4604 bonds, 584 residues, 1 model selected
> select subtract #7
Nothing selected
> select #7/A:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:36-52
144 atoms, 145 bonds, 17 residues, 1 model selected
> label sel
> view matrix models
> #7,0.38841,0.91274,0.12662,138.59,0.17641,0.06122,-0.98241,183.35,-0.90444,0.40392,-0.13724,226.78
> view matrix models
> #7,0.38841,0.91274,0.12662,138.52,0.17641,0.06122,-0.98241,184.68,-0.90444,0.40392,-0.13724,230.11
> view matrix models
> #7,0.38841,0.91274,0.12662,138.35,0.17641,0.06122,-0.98241,183.75,-0.90444,0.40392,-0.13724,231.43
> select add #7
4539 atoms, 4604 bonds, 584 residues, 2 models selected
> select subtract #7
Nothing selected
> select #5/E
448 atoms, 442 bonds, 66 residues, 1 model selected
> label sel
> view matrix models
> #5,-0.86719,-0.4568,-0.19828,205.03,-0.49797,0.79334,0.3502,122.26,-0.0026691,0.40242,-0.91545,245.62
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected
> select subtract #5
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/E
Alignment identifier is 5/E
> select #5/E:2312
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/E:2296-2312
131 atoms, 131 bonds, 17 residues, 1 model selected
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected
> select subtract #5
Nothing selected
> select #5/E:2306
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/E:2302-2306
37 atoms, 36 bonds, 5 residues, 1 model selected
> select #7/A:41
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #7/A:38-41
34 atoms, 33 bonds, 4 residues, 1 model selected
> open
> /Users/sz140275local/Downloads/fold_zcwpw2_hsf2bp/fold_zcwpw2_hsf2bp_model_0.cif
Chain information for fold_zcwpw2_hsf2bp_model_0.cif #8
---
Chain | Description
A | .
B C | .
Computing secondary structure
> select add #7
4539 atoms, 4604 bonds, 584 residues, 2 models selected
> select subtract #7
Nothing selected
> hide #!7 models
> hide #!5 models
> view #8 clip false
> color #8 bychain
> mmaker #8 to #5
Computing secondary structure
[Repeated 1 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 7bdx, chain C (#5) with fold_zcwpw2_hsf2bp_model_0.cif, chain B
(#8), sequence alignment score = 1052
RMSD between 208 pruned atom pairs is 0.657 angstroms; (across all 213 pairs:
0.799)
> view #5 clip false
No displayed objects specified.
> show #!5 target m
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected
> show #!5 target m
> view #5 clip false
> select subtract #5
Nothing selected
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected
> view matrix models
> #5,-0.86719,-0.4568,-0.19828,205.93,-0.49797,0.79334,0.3502,120.58,-0.0026691,0.40242,-0.91545,245.72
> select subtract #5
Nothing selected
> select add #5
7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected
> view matrix models
> #5,-0.86719,-0.4568,-0.19828,213.03,-0.49797,0.79334,0.3502,112.79,-0.0026691,0.40242,-0.91545,246.87
> view matrix models
> #5,-0.86719,-0.4568,-0.19828,205.33,-0.49797,0.79334,0.3502,120.04,-0.0026691,0.40242,-0.91545,246.3
> view matrix models
> #5,-0.86719,-0.4568,-0.19828,205.33,-0.49797,0.79334,0.3502,120.92,-0.0026691,0.40242,-0.91545,245.8
> select subtract #5
Nothing selected
> close #8#1-7
> open
> /Users/sz140275local/Downloads/fold_zcwpw2_hsf2bp/fold_zcwpw2_hsf2bp_model_0.cif
Chain information for fold_zcwpw2_hsf2bp_model_0.cif #1
---
Chain | Description
A | .
B C | .
Computing secondary structure
> close
> open
> /Users/sz140275local/Downloads/fold_brh2_myst/fold_brh2_myst_model_0.cif
Chain information for fold_brh2_myst_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> open
> /Users/sz140275local/Downloads/Myst_BRC2_9deb6/predictions/Myst_BRC2/models/Myst_BRC2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_97616.pdb
Chain information for
Myst_BRC2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_97616.pdb #2
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> mmaker #1 to #2
Computing secondary structure
[Repeated 1 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
Myst_BRC2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_97616.pdb,
chain B (#2) with fold_brh2_myst_model_0.cif, chain B (#1), sequence alignment
score = 1958.5
RMSD between 160 pruned atom pairs is 0.648 angstroms; (across all 394 pairs:
56.902)
> hide #2 models
> select #1
5188 atoms, 5286 bonds, 653 residues, 1 model selected
> color bfactor #1 palette alphafold
5188 atoms, 653 residues, atom bfactor range 14.1 to 98.7
> color bfactor #2 palette alphafold
5186 atoms, 653 residues, atom bfactor range 12.5 to 97.9
> select subtract #1
Nothing selected
> hide #1 models
> show #2 models
> color #2 bychain
> hide #2 models
> show #1 models
> color #1 bychain
> color bfactor #1 palette alphafold
5188 atoms, 653 residues, atom bfactor range 14.1 to 98.7
> color #1 bychain
[deleted to fit within ticket limits]
> movie encode /Users/anz/Desktop/FPP.mp4
No frames have been recorded
> select up
283 atoms, 279 bonds, 45 residues, 4 models selected
> select up
355 atoms, 368 bonds, 45 residues, 4 models selected
> select up
4630 atoms, 4711 bonds, 596 residues, 7 models selected
> select up
20410 atoms, 20483 bonds, 2840 residues, 20 models selected
> select up
35858 atoms, 36207 bonds, 4794 residues, 32 models selected
> select down
20410 atoms, 20483 bonds, 2840 residues, 21 models selected
> select down
4630 atoms, 4711 bonds, 596 residues, 7 models selected
> select down
355 atoms, 368 bonds, 45 residues, 4 models selected
> select down
283 atoms, 279 bonds, 45 residues, 4 models selected
> select down
269 atoms, 279 bonds, 35 residues, 4 models selected
> movie record
> fly core1 core2 core3 core1
> save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
> structures RAD54B PhePP from Sophie/ForAlexRAD54B movies TMM peptide 2.cxs"
> ~cartoon #3.1,4,5,6
> ~cartoon #3.7,9-12
> select ~sel & ##selected
86 atoms, 89 bonds, 10 residues, 4 models selected
> ~cartoon #3.7,9-13
> hide FPP
> show #3.8 | #1.11
> color #3.8 coral
> hide #3.8
> hide #1.11
> crossfade
> show #3.8
> movie stop
> movie reset
> ~select
Nothing selected
> color #3.8 byhetero
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting full
> color #1.11 byhetero
> view name cryo1
> select ~sel & ##selected
Nothing selected
> view name cryo2
> select ~sel & ##selected
Nothing selected
> view name cryo3
> view name cryo4
> view cryo1
> movie record
> fly cryo1 cryo2 cryo3 cryo4 cryo1
> crossfade
> show #1.11
> wait 20
> fly cryo1 30 cryo2
> fly cryo2 30 cryo3 30 cryo4 30 cryo1
> movie encode cryo.mp4
Movie saved to cryo.mp4
> movie record
> crossfade
> hide peptides & ~FPP
> crossfade
> show FPP
> fly cryo1 20 cryo2 40 cryo3 30 cryo4 10 cryo1
> movie encode FPP2.mp4
Movie saved to FPP2.mp4
> view core1
> view name core2
> select ~sel & ##selected
Nothing selected
> view name core3
> hide FPP
> show #3.8
> view core1
> movie record
> fly core1 core2 core3 core1
> crossfade
> show #1.11
> fly core1 core2 core1
> movie stop
> movie reset
> view core1
> hide #1.11
> movie record
> fly core1 core2 core3 core1
> crossfade
> show #1.11
> fly core1 30 core2
> fly core2 20 core3 20 core1
> movie encode cryo.mp4
Movie saved to cryo.mp4
> view core1
> hide peptides
> movie record
> crossfade 10
> show #3.8
> wait 10
> crossfade 20
> show #1.1
> hide #1.1
> resest
Unknown command: movie resest
> movie stop
> movie reset
> hide peptides
> movie record
> crossfade 10
> show #3.8
> wait 10
> crossfade 20
> show #1.11
> fly core1 core2 core3 core1
> movie encode cryo.mp4
Movie saved to cryo.mp4
> view core1
> movie record
> crossfade 10
> show #4.3
> crossfade 10
> show #6.12
> show #6.12 models
> crossfade 10
> show #6.12
> crossfade 10
> hide peptids & ~FPP
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> crossfade 10
> hide peptides & ~FPP
> fly core1 core2 core3 core1
> movie encode FPP.mp4
Movie saved to FPP.mp4
> hide peptides
> show #3.8 | #1.11
> movie record
> crossfade 20
> show #4.3
> wait 10
> crossfade 20
> show #6.12
> wait 15
> crossfade 20
> hide peptides & ~FPP
> fly core1 core2
> fly core2 core3 core1
> movie encode FPP.mp4
Movie saved to FPP.mp4
> hide FPP
> show #3.8 | #1.11
> movie record
> crossfade 40
> show #6.2
> movie stop
> movie reset
> hide #6.2
> movie record
> crossfade 40
> show #6.12
> movie stop
> movie reset
> movie record
> movie stop
> hide #6.12
> movie record
> crossfade 40
> show #4.3
> crossfade 40
> show #6.12
> wait 20
> crossfade 30
> hide peptides & ~FPP
> fly core1 core2 core3 core1
> movie encode FPP2.mp4
Movie saved to FPP2.mp4
> hide FPP
> show #1.11
> hide #1.11
> show #3.8
> view name r54b1
> select ~sel & ##selected
Nothing selected
> view name r54b2
> view name r54b3
> view r54b1
> movie record
> fly r54b1 r54b2 r54b3 r54b4
fly: Unknown position name "r54b4"
> fly r54b1 r54b2 r54b3 r54b1
> movie encode r54b.mp4
Movie saved to r54b.mp4
> movie record
> crossfade 30
> coulombic #3.2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for RAD54-J402_m4_real_space_refined_000.pdb B_B SES surface
#3.2.2: minimum, -19.17, mean -0.61, maximum 13.24
> movie encode r54b-es.mp4
Movie saved to r54b-es.mp4
> view r54b1
> ~surface #3.2
> surface #3.2
> hide #3.8
> show #1.11
> movie record
> fly r54b1 r54b3
> crossfade 40
> show #4.3
> movie stop
> view name phepp1
> view r54b3
> movie record
> fly r54b3 phepp1
> wait 30
> fly phepp1 r54b1
> movie encode phepp.mp4
Movie saved to phepp.mp4
> save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
> structures RAD54B PhePP from Sophie/ForAlexRAD54B movies TMM peptide 2.cxs"
——— End of log from Thu Sep 4 04:53:36 2025 ———
> view name session-start
opened ChimeraX session
> label listfonts
221 fonts available:
.Apple Symbols Fallback
.AppleSystemUIFont
.Times Fallback
Academy Engraved LET
Al Bayan
Al Nile
Al Tarikh
Aller
Aller Display
American Typewriter
Andale Mono
Apple Braille
Apple Chancery
Apple Color Emoji
Apple SD Gothic Neo
Apple Symbols
AppleGothic
AppleMyungjo
Aptos
Aptos Mono
Aptos Narrow
Aptos Serif
Arial
Arial Black
Arial Hebrew
Arial Hebrew Scholar
Arial Narrow
Arial Rounded MT Bold
Arial Unicode MS
Avenir
Avenir Next
Avenir Next Condensed
Ayuthaya
Baghdad
Bahnschrift
Bangla MN
Bangla Sangam MN
Baskerville
Beirut
Big Caslon
Bodoni 72
Bodoni 72 Oldstyle
Bodoni 72 Smallcaps
Bodoni Ornaments
Bradley Hand
Braggadocio
Brush Script MT
Canela Text
Chalkboard
Chalkboard SE
Chalkduster
Charter
Cochin
Comic Sans MS
Consolas
Copperplate
Corsiva Hebrew
Courier New
DIN Alternate
DIN Condensed
Damascus
Darkwoman
DecoType Naskh
Devanagari MT
Devanagari Sangam MN
Didot
Diwan Kufi
Diwan Thuluth
Euphemia UCAS
Farah
Farisi
Futura
GB18030 Bitmap
Galvji
Geeza Pro
Geneva
Georgia
Gill Sans
Gloucester MT Extra Condensed
Grantha Sangam MN
Gujarati MT
Gujarati Sangam MN
Gurmukhi MN
Gurmukhi MT
Gurmukhi Sangam MN
Heiti SC
Heiti TC
Helvetica
Helvetica Neue
Herculanum
Hiragino Maru Gothic ProN
Hiragino Mincho ProN
Hiragino Sans
Hiragino Sans GB
Hobo Std
Hoefler Text
ITF Devanagari
ITF Devanagari Marathi
Impact
InaiMathi
Kailasa
Kannada MN
Kannada Sangam MN
Kefa III
Khmer MN
Khmer Sangam MN
Kohinoor Bangla
Kohinoor Devanagari
Kohinoor Gujarati
Kohinoor Telugu
Kokonor
Kotyhoroshko
Koziyar
Krungthep
KufiStandardGK
KurkaLapoyu
Lao MN
Lao Sangam MN
LevType Hryvnia
Lucida Blackletter
Lucida Grande
Lugatype
Luminari
Malayalam MN
Malayalam Sangam MN
Marker Felt
Matura MT Script Capitals
Menlo
Microsoft Sans Serif
Mishafi
Mishafi Gold
Monaco
Montserrat
Mshtakan
Mukta Mahee
Muna
Myanmar MN
Myanmar Sangam MN
Nadeem
New Peninim MT
Noteworthy
Noto Emoji
Noto Nastaliq Urdu
Noto Sans
Noto Sans Armenian
Noto Sans Batak
Noto Sans Condensed
Noto Sans ExtraCondensed
Noto Sans Kannada
Noto Sans Myanmar
Noto Sans NKo
Noto Sans Oriya
Noto Sans SemiCondensed
Noto Sans Syriac
Noto Sans Tagalog
Noto Sans Zawgyi
Noto Serif Myanmar
Open Sans
Open Sans Condensed
Open Sans SemiCondensed
Optima
Oriya MN
Oriya Sangam MN
PT Mono
PT Sans
PT Sans Caption
PT Sans Narrow
PT Serif
PT Serif Caption
Palatino
Papyrus
Party LET
Phosphate
PingFang HK
PingFang MO
PingFang SC
PingFang TC
Plantagenet Cherokee
Proxima Nova
Publico Text
Raanana
Roboto
Roboto Condensed
Roboto SemiCondensed
Rockwell
STIX Two Math
STIX Two Text
STSong
Sana
Sathu
Savoye LET
Segoe UI
Shree Devanagari 714
SignPainter
Silom
Sinhala MN
Sinhala Sangam MN
Skia
Snell Roundhand
Songti SC
Songti TC
Sukhumvit Set
Symbol
Tahoma
Tamil MN
Tamil Sangam MN
Telugu MN
Telugu Sangam MN
Thonburi
Times New Roman
Trattatello
Trebuchet MS
Veles
Verdana
Waseem
Webdings
Wingdings
Wingdings 2
Wingdings 3
Zapf Dingbats
Zapfino
> label #3.2/B:182
> label #3.2/B:182,180
> label #3.2/B:182 hight 5
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label #3.2/B:182 residues hight 5
Expected a keyword
> label #3.2/B:182 residues height 5
> label #3.2/B:182 residues height 2
> label #3.2/B:182 residues height 1
> label #3.2/B:172,175,180,182,186 residues height 1
> label #3.2/B:172,175,180,182,186 residues height 1 font "Aller Display"
> label #3.2/B:172,175,180,182,186 residues height 1.5 font "Aller Display"
> label #3.2/B:168,172,175,180,182,186 residues height 1.5 font "Aller
> Display"
> log metadata #3.10
The model has no metadata
> log chains #3.10
Chain information for RAD54-J402_m4_real_space_refined_000.pdb P #3.10
---
Chain | Description
P | No description available
> ui tool show "Renumber Residues"
> show #3.10 target m
> ui tool show "Show Sequence Viewer"
> sequence chain #6.12/L #6.13/M #6.14/N #6.15/O #6.16/P #6.17/Q #6.18/R
> #6.19/S #6.20/T #6.21/U
Alignment identifier is 1
> pwd
Current working directory is: /Users/anz/Desktop
> save 251009_lysines
Cannot determine format for '251009_lysines'
> save 251009_lysines.csx
No known data format for file suffix '.csx'
> save 251009_lysines.cxs
> cartoon #3.2
> select ~sel & ##selected
Nothing selected
> cartoon #3.1
> select add #3.1
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for RAD54-J402_m4_real_space_refined_000.pdb A_A SES surface
#3.1.2: minimum, -27.47, mean -0.69, maximum 13.40
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show "Show Sequence Viewer"
> sequence chain #3.8/N #3.9/O #3.10/P #3.11/Q
Alignment identifier is 1
> ui tool show "Renumber Residues"
> hide #1
> select ~sel & ##selected
Nothing selected
> hide #4
> show #3.4
> hide #3.4
> show #3.10
> select ~sel & ##selected
Nothing selected
> hide #3.10
> show #!4.2 models
> hide #!4.2 models
> show #4
> select ~sel & ##selected
Nothing selected
> hide #4
Cell requested for row 12 is out of bounds for table with 26 rows! Resizing
table model.
> show #3.2
> hide #3.2
> show #3.8,9,10,11
> save 251009_lysines.cxs
——— End of log from Thu Oct 9 14:13:54 2025 ———
> view name session-start
opened ChimeraX session
> surface #3.2 transparency 80
> surface #3.2 transparency 60
> select #3.3:57,57,255
20 atoms, 18 bonds, 2 residues, 1 model selected
> style sel ball
Changed 20 atom styles
> show sel atoms
> select #3.3:56,57,255
31 atoms, 29 bonds, 3 residues, 1 model selected
> show sel atoms
> select #3.3:56,57,255,252
42 atoms, 39 bonds, 4 residues, 1 model selected
> show sel atoms
> select ~sel & ##selected
2429 atoms, 2470 bonds, 1 pseudobond, 313 residues, 2 models selected
> select ~sel & ##selected
42 atoms, 39 bonds, 4 residues, 1 model selected
> label #3.2:197,201,204,238
> select ~sel & ##selected
2429 atoms, 2470 bonds, 1 pseudobond, 313 residues, 2 models selected
> label #3.2:197,201,204,238 residues height 1.5 font "Aller Display"
> label #3.2:197,201,204,238,232,238,241 residues height 1.5 font "Aller
> Display"
> ~label #3.2:197,201,204,238,232,238,241 residues height 1.5 font "Aller
> Display"
> label delete #3.2:197,201,204,238,232,238,241 residues height 1.5 font
> "Aller Display"
Expected a keyword
> ~label #3.2:197,201,204,238,232,238,241
> label #3.2:197,201,204,238 residues height 1.5 font "Aller Display"
> label #3.1:232,238,241 residues height 1.5 font "Aller Display"
> save 251009_lysines.cxs
> select up
2435 atoms, 2470 bonds, 1 pseudobond, 317 residues, 2 models selected
> select add #3
15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 22 models selected
> select subtract #3
2 models selected
> ui tool show "Renumber Residues"
> renumber #3.8/N #3.9/O #3.10/P #3.11/Q seqStart 18
32 residues renumbered
> hide #3.10,11
> hide #3.9-11
> save 251009_lysines.cxs
> lighting shadows false
> lighting shadows true
> lighting shadows false
> select #3.1
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 3 models selected
> mlp sel
Map values for surface "RAD54-J402_m4_real_space_refined_000.pdb A_A SES
surface": minimum -28.84, mean -5.01, maximum 21.74
To also show corresponding color key, enter the above mlp command and add key
true
> save 251009_lysines.cxs
——— End of log from Thu Oct 9 18:29:50 2025 ———
> view name session-start
opened ChimeraX session
> surface #3.2 transparency 10
> label #3.2:23,212
> label #3.2:23,212 residues height 1.5 font "Aller Display"
> label #3.2:23,212,213 residues height 1.5 font "Aller Display"
> save /Users/anz/Desktop/251009_lysines.cxs
> select #3.2:212,213,23
26 atoms, 24 bonds, 3 residues, 1 model selected
> show sel atoms
> surface #3.2 transparency 90
Alignment identifier is 3.2/B
> select
> #3.2/B:24-30,34-43,48-53,56-61,67-80,88-97,106-112,132-144,167-176,181-187,196-212,227-232,236-260,290-296
1179 atoms, 1180 bonds, 145 residues, 1 model selected
> select
> #3.2/B:121-126,155-160,188-192,217-223,263-268,270-272,285-287,299-305,310-317,325-331,334-337
494 atoms, 491 bonds, 62 residues, 1 model selected
> select #3.2/B:23
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.2/B:23-25
24 atoms, 23 bonds, 3 residues, 1 model selected
> select
> #3.2/B:24-30,34-43,48-53,56-61,67-80,88-97,106-112,132-144,167-176,181-187,196-212,227-232,236-260,290-296
1179 atoms, 1180 bonds, 145 residues, 1 model selected
> select #3.2/B:23-25
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #3.2:25
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> label #3.2:23,25,212,213 residues height 1.5 font "Aller Display"
> select up
60 atoms, 60 bonds, 7 residues, 2 models selected
> select up
2013 atoms, 2044 bonds, 257 residues, 2 models selected
> select down
60 atoms, 60 bonds, 7 residues, 2 models selected
> select down
8 atoms, 7 bonds, 1 residue, 2 models selected
> select down
8 atoms, 7 bonds, 1 residue, 2 models selected
> surface #3.2 transparency 30
> save /Users/anz/Desktop/251009_lysines.cxs
——— End of log from Mon Oct 13 17:24:42 2025 ———
> view name session-start
opened ChimeraX session
> pwd
Current working directory is: /Users/anz/Desktop/P-motifs/2025 RAD54B
paper/2025 experiments/250915 AF Models DMC1 RAD54B
> open "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025 experiments/250915
> AF Models DMC1 RAD54B/all_AF_models.cif"
Summary of feedback from opening /Users/anz/Desktop/P-motifs/2025 RAD54B
paper/2025 experiments/250915 AF Models DMC1 RAD54B/all_AF_models.cif
---
warnings | Unknown polymer entity '1' on line 116
Unknown polymer entity '2' on line 1396
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for all_AF_models.cif #7
---
Chain | Description
A B C D E | No description available
F G | No description available
> split #7
Split all_AF_models.cif (#7) into 7 models
Chain information for all_AF_models.cif A #7.1
---
Chain | Description
A | No description available
Chain information for all_AF_models.cif B #7.2
---
Chain | Description
B | No description available
Chain information for all_AF_models.cif C #7.3
---
Chain | Description
C | No description available
Chain information for all_AF_models.cif D #7.4
---
Chain | Description
D | No description available
Chain information for all_AF_models.cif E #7.5
---
Chain | Description
E | No description available
Chain information for all_AF_models.cif F #7.6
---
Chain | Description
F | No description available
Chain information for all_AF_models.cif G #7.7
---
Chain | Description
G | No description available
> view #7
> cartoon #7
> hide #7
> delete #2
[Repeated 1 time(s)]
Cell requested for row 1 is out of bounds for table with 33 rows! Resizing
table model.
> close #2
> hide #7.1 models
> show #7.1 models
> select add #7
6582 atoms, 6695 bonds, 846 residues, 9 models selected
> color sel bychain
> select subtract #7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #7.1
264 atoms, 269 bonds, 34 residues, 2 models selected
> select subtract #7.1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3.2
2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 5 models selected
> view #3
> mmaker #7.7 to #3.2 bring #7.1-6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RAD54-J402_m4_real_space_refined_000.pdb B, chain B (#3.2) with
all_AF_models.cif G, chain G (#7.7), sequence alignment score = 1569
RMSD between 312 pruned atom pairs is 0.526 angstroms; (across all 314 pairs:
0.761)
> select
74534 atoms, 75562 bonds, 93 pseudobonds, 9756 residues, 111 models selected
> ~select
Nothing selected
> ~cartoon #7.4
Unsupported scale factor (0.000000) detected on Display1
[Repeated 2 time(s)]
> save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025
> experiments/251020_lysines.cxs"
> select #7.6:1-20
160 atoms, 161 bonds, 20 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for all_AF_models.cif F_F SES surface #7.6.1: minimum,
-19.36, mean -2.31, maximum 14.11
To also show corresponding color key, enter the above coulombic command and
add key true
> select #7.:1-20
Expected an objects specifier or a keyword
> select #7.7:1-20
160 atoms, 161 bonds, 20 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for all_AF_models.cif G_G SES surface #7.7.1: minimum,
-22.31, mean -2.76, maximum 12.63
To also show corresponding color key, enter the above coulombic command and
add key true
> ~select
Nothing selected
> rename #7.6 "DMC1 in model 1"
> rename #7.7 "DMC1 in model 4"
> rename #7.6 "DMC1 in model 0"
> rename #7.1 "54B model 0"
> rename #7.2 "54B model 1"
> rename #7.3 "54B model 2"
> rename #7.4 "54B model 3"
> rename #7.5 "54B model 4"
Alignment identifier is 4.1/A
Alignment identifier is 4.2/B
Alignment identifier is 4.3/C
Alignment identifier is 4.4/D
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 3.7/M
Alignment identifier is 4
Alignment identifier is 3.12/R
Alignment identifier is 5.1/A
Alignment identifier is 5.2/B
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 6.22/V
Alignment identifier is 7
Alignment identifier is 8
>
Unknown command: sequence #7.7
>
Incomplete command: sequence
> select #7.7
2647 atoms, 2689 bonds, 340 residues, 1 model selected
Alignment identifier is 7.7/G
> ~select #7.7
1 model selected
> select #7.7/G:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7.7/G:3-4
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #7.7/G:9
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7.7/G:9-10
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #7.7/G:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7.7/G:15-18
35 atoms, 34 bonds, 4 residues, 1 model selected
> label #7.6-7:3,4,9,10,15-18 residues height 1.5 font "Aller Display"
> save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025
> experiments/251020_lysines.cxs"
——— End of log from Tue Oct 21 09:05:15 2025 ———
> view name session-start
opened ChimeraX session
> ~label #3.2
> surface #7.7/1-18 transparency 90
No atoms specified by #7.7/1-18
> surface #7.7:1-18 transparency 90
> surface #7.6:1-18 transparency 90
> transparency #7.6:1-18 90 cartoons
> transparency #7.6:1-18 70 cartoons
> transparency #7.6:1-18 50 cartoons
> transparency #7.6:1-18 10 cartoons
> transparency #7.6:1-18 0.2 cartoons
> transparency #7.6:1-18 1 cartoons
> transparency #7.6:1-18 15 cartoons
> transparency #7.6:1-18 10 cartoons
> transparency #7.6:1-18 1 cartoons
> transparency #7.6:1-18 2 cartoons
> transparency #7.6:1-18 0.2 cartoons
> transparency #7.6:1-18 0.3 cartoons
> transparency #7.6:1-18 50 cartoons
> select up
80 atoms, 81 bonds, 10 residues, 1 model selected
> select up
2647 atoms, 2689 bonds, 340 residues, 2 models selected
> select up
2647 atoms, 2689 bonds, 340 residues, 3 models selected
> surface #7.7:1-18 transparency 80
> surface #7.6,7:1-18 transparency 80
> surface #7.6,7:1-18 transparency 86
> ~select
Nothing selected
> hide #!7.7 models
> show #!7.7 models
> hide #!7.7 models
> show #!7.7 models
> transparency #7.6:1-18 50 cartoons
> hide #!7.7 models
> show #!7.7 models
> transparency #7.6:1-18 50 ccartoons
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #7.6:1-18 50 cartoons
> transparency #7.7:1-18 50 cartoons
> coulombic #3.1
Coulombic values for RAD54-J402_m4_real_space_refined_000.pdb A_A SES surface
#3.1.2: minimum, -27.47, mean -0.69, maximum 13.40
> transparency #3.1 80 surfaces
> transparency #3.1 80 cartoons
> transparency #3.1 79 cartoons
> transparency #3.1 81 cartoons
> lighting soft
> lighting simple
> lighting soft
> lighting full
> ~cartoon #7
> cartoon #7.1-5
> lighting soft
> transparency #3.3 90 cartoons
> select ~sel & ##selected
Nothing selected
> pwd
Current working directory is: /Users/anz/Desktop
> save 260127_lysines.cxs
> select #7.1-5:LYS,ARG
300 atoms, 280 bonds, 30 residues, 5 models selected
> style sel ball
Changed 300 atom styles
> style sel ball
Changed 300 atom styles
> show sel atoms
> color sel byhetero
> transparency #7.1-5 60 cartoons
> ~select
Nothing selected
> hide #7.1-5 atoms
> hide #7.7 atoms
> hide #3.8 atoms
> show #7.1-5:LYS,ARG atoms
> select ~sel & ##selected
Nothing selected
> color #7.1-5:LYS,ARG blue
> hide #3 atoms
> hide #3.2 cartoons
[Repeated 1 time(s)]
> hide #3.2 cartoonsd
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #3.2 cartoons
> hide #7.6-7 cartoons
> hide #3.2 cartoons
> hide #3.2
> hide #!3.2 models
> show #!3.2 models
> hide #4.3 models
> show #4.3 models
> hide #3.2.2 models
> show #3.2.2 models
> select ~sel & ##selected
Nothing selected
> hide #1.4
> hide #1.4 cartoons
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> graphics silhouettes false
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> save 260127_lysines.cxs
> hide #!7 models
> ~label #3.1
> ~surface #3.1,2
> cartoon 3.2
Expected an atoms specifier or a keyword
> show #3.2 cartoons
> show #3.8 cartoons
> color #3.8 red
> save view1.png
[Repeated 1 time(s)]
> show #7.6,7:1-19 cartoons
> show #7.6:1-19 cartoons
> hide #!7.6 models
> show #!7.6 models
> hide #!7.7 models
> show #!7.7 models
> hide #!7.7 models
> hide #!7.6 models
> hide #!7 models
> show #7.6:1-19 cartoons transparency 0
Expected ',' or a keyword
> transparency #7.6,7:1-19 0 cartoons
> show #7.6:1-19 cartoons
> show #7.6 cartoons
> show #!7 models
> show #!7.7 models
> show #!7.6 models
> hide #7.6,7 cartoons
> hide #7.6,7 surfaces
> hide #7.1-5 surfaces
> hide #7.1-5
> hide #7.1-5 cartoons
> show #7.1-5 cartoons
> select ~sel & ##selected
Nothing selected
> show #3.2 surfaces
> label #3.2/B:213 residues height 1.5 font "Aller Display"
> hide #7.4
> hide #7.4 cartoons
> select zone #7.5:2 5 #3.1
Nothing selected
> select zone #7.5:2 8 #3.1
Nothing selected
> select zone #7.5:2 8 #3.1
Nothing selected
> distance #7.5:2 #3.1:234
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 17 atoms and 0
measurable objects
> save 260127_lysines.cxs
> label #3.2/B:201,204,212,213 residues height 1.5 font "Aller Display"
> show #3.2/B:201,204,212,213 atoms
> ~surface #3.2
> surface #7.6:1-18
> select ~sel & ##selected
Nothing selected
> ~surface #7.6:1-18
> surface #7.7:1-18
> surface #7.7:1-18 transparency 50
> save 260127_lysines.cxs
> ~label
> label
> show #3.2/B:201,204,212,213,238 atoms
> label #3.2/B:201,204,212,213,238 residues height 1.5 font "Aller Display"
> label #3.2/B:201,204,212,213 OR #3.1:238 residues height 1.5 font "Aller
> Display"
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label #3.2/B:201,204,212,213 | #3.1:238 residues height 1.5 font "Aller Display"
> cd "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/2025 experiments/XX25-36
> GST pull-down DMC1 mutants negatively charged"
Current working directory is: /Users/anz/Desktop/P-motifs/2025 RAD54B
paper/2025 experiments/XX25-36 GST pull-down DMC1 mutants negatively charged
> save 260127_lysines_XX25-36.cxs
> save "260127 54B positive and DMC1 negative residues tested in XX25-36.cxs"
——— End of log from Wed Jan 28 15:35:48 2026 ———
> view name session-start
opened ChimeraX session
> rename #4 "8qqe our DMC1 Xray"
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> show #5.1 models
> rename #5 "RAD54 on RAD51 2025.cif"
> rename #5.1 RAD51
> rename #5.2 "RAD54 1-118"
> rename #5.2 "RAD54 1-150"
> rename #1 "DMC1-PhePP Cryo.pdb"
> rename #3 "DMC1-RAD54 Cryo"
> rename #1 "DMC1-PhePP Cryo"
> rename #5 "RAD54 on RAD51 2025 AF_0"
> rename #7 "54B on DMC1 AF models"
> rename #6 "8pbc TR2 RAD51 Cryo"
> hide #!1 models
> rename #1 "PhePP DMC1 Cryo"
> rename #3 "RAD54B DMC1 Cryo"
> rename #4 "PhePP DMC1 Xray 8qqe"
> rename #6 "TR2 RAD51 Cryo 8pbc "
> rename #7 "RAD54B on DMC1 AF models"
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7.7 models
> hide #!7.6 models
> show #!7.6 models
> hide #!7.6 models
> hide #7.5 models
> show #7.5 models
> hide #5.2 models
> show #5.2 models
> hide #5.2 models
> show #5.2 models
> hide #5.2 models
> show #5.2 models
> hide #5.1 models
> show #5.1 models
> rename #5.1 "RAD54 1-150"
> rename #5.2 RAD51
> hide #5.2 models
> select add #5.1
1187 atoms, 1216 bonds, 150 residues, 1 model selected
> color bfactor sel
1187 atoms, 150 residues, atom bfactor range 21.3 to 96.6
> save "/Users/anz/Desktop/P-motifs 260222.cxs"
——— End of log from Sat Feb 21 18:41:51 2026 ———
> view name session-start
opened ChimeraX session
> rename #3.13 DNA
> rename #3.7 "54B peptide 1"
> rename #3.8 "54B peptide 2"
> rename #3.9 "54B peptide 3"
> rename #3.10 "54B peptide 4"
> rename #3.11 "54B peptide 5"
> rename #3.12 "54B peptide 6"
> rename #3.1 DMC1
> rename #3.2 DMC1
> rename #3.3 DMC1
> rename #3.5-6 DMC1
> rename #3.4-6 DMC1
> save "/Users/anz/Desktop/P-motifs 260222.cxs"
[Repeated 1 time(s)]
> open 9QNC
Summary of feedback from opening 9QNC fetched from pdb
---
notes | Fetching compressed mmCIF 9qnc from http://files.rcsb.org/download/9qnc.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
9qnc title:
RAD51 filament in complex with magnesium and ATP bound by the RAD51AP1
C-terminus [more info...]
Chain information for 9qnc #2
---
Chain | Description | UniProt
A C E G I K | DNA repair protein RAD51 homolog 1 | RAD51_HUMAN 1-339
B D F H J L | RAD51-associated protein 1 | R51A1_HUMAN 328-352
Z | DNA |
Non-standard residues in 9qnc #2
---
ATP — adenosine-5'-triphosphate
K — potassium ion
MG — magnesium ion
> split #8
> rename #2 "AP1 RAD51 XZ 9qnc"
> hide
> split #2
Split AP1 RAD51 XZ 9qnc (#2) into 13 models
Chain information for AP1 RAD51 XZ 9qnc A #2.1
---
Chain | Description
A | No description available
Chain information for AP1 RAD51 XZ 9qnc B #2.2
---
Chain | Description
B | No description available
Chain information for AP1 RAD51 XZ 9qnc C #2.3
---
Chain | Description
C | No description available
Chain information for AP1 RAD51 XZ 9qnc D #2.4
---
Chain | Description
D | No description available
Chain information for AP1 RAD51 XZ 9qnc E #2.5
---
Chain | Description
E | No description available
Chain information for AP1 RAD51 XZ 9qnc F #2.6
---
Chain | Description
F | No description available
Chain information for AP1 RAD51 XZ 9qnc G #2.7
---
Chain | Description
G | No description available
Chain information for AP1 RAD51 XZ 9qnc H #2.8
---
Chain | Description
H | No description available
Chain information for AP1 RAD51 XZ 9qnc I #2.9
---
Chain | Description
I | No description available
Chain information for AP1 RAD51 XZ 9qnc J #2.10
---
Chain | Description
J | No description available
Chain information for AP1 RAD51 XZ 9qnc K #2.11
---
Chain | Description
K | No description available
Chain information for AP1 RAD51 XZ 9qnc L #2.12
---
Chain | Description
L | No description available
Chain information for AP1 RAD51 XZ 9qnc Z #2.13
---
Chain | Description
Z | No description available
> save "/Users/anz/Desktop/P-motifs 260221.cxs"
> hide #!3 models
> cartoon #2
> rename #2.13 DNA
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #2.2 models
> show #2.2 models
> rename #2.1,3,5,7,9,11 RAD51
> rename #2.1 RAD51 1
Expected a keyword
> rename #2.1 "RAD51 1"
> rename #2.3 "RAD51 2"
> rename #2.5 "RAD51 3"
> rename #2.7 "RAD51 4"
> hide #!2.7 models
> show #!2.7 models
> hide #!2.7 models
> show #!2.7 models
> rename #2.9 "RAD51 5"
> rename #2.11 "RAD51 6"
> rename #2.2 "AP1 pep 1"
> rename #2.4 "AP1 pep 2"
> select down
1187 atoms, 1216 bonds, 150 residues, 1 model selected
> select down
1187 atoms, 1216 bonds, 150 residues, 1 model selected
> rename #2.6 "AP1 pep 3"
> rename #2.8 "AP1 pep 4"
> rename #2.10 "AP1 pep 5"
> rename #2.12 "AP1 pep 6"
> help mmaker
> mmaker #2.3 to #3.2 bring #2.1,2,4-13
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 DMC1, chain B (#3.2) with RAD51 2, chain C (#2.3), sequence
alignment score = 1035.4
RMSD between 283 pruned atom pairs is 0.842 angstroms; (across all 312 pairs:
1.769)
> ~cartoon #2.1,2,5-13
> cartoon #2.1,2,5-13
> show #!3 models
> ~cartoon #2.1,2,5-13
> color #2.4 red
> save "/Users/anz/Desktop/P-motifs 260221.cxs"
> hide #7
> ~cartoon #7
> ~select
Nothing selected
> ~cartoon @2.3
> cartoon hide @2.3
Expected an atoms specifier or a keyword
> ~cartoon #2.3
> select ~sel & ##selected
Nothing selected
> color #2.4 magenta
Cell requested for row 2 is out of bounds for table with 46 rows! Resizing
table model.
> rename #2 "AP1 RAD51 Cryo 9qnc"
> cartoon #3.8
> select clear
> show #2.4:335-338
> show #2.4:335-338 stick
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #2.4:335-338 atoms
> help show
> style ball
Changed 90630 atom styles
> show #2.4:335-338 atoms
> show #2.4:334-338 atoms
> label #2.4:335-338
> help label
> label #5.1:95-104
> select ~sel & ##selected
Nothing selected
> label #5.1:95-104 color red
> save "/Users/anz/Desktop/P-motifs 260221.cxs"
> open /Users/anz/Downloads/fold_mnd1_rad51/fold_mnd1_rad51_model_0.cif
Chain information for fold_mnd1_rad51_model_0.cif #8
---
Chain | Description
A | .
B | .
Computing secondary structure
> close #8
> help label
> label listfonts
336 fonts available:
.Apple Color Emoji UI
.Apple Symbols Fallback
.AppleHongKongChineseFont
.AppleIndicFont
.AppleJapaneseFont
.AppleKoreanFont
.AppleMacaoChineseFont
.AppleSimplifiedChineseFont
.AppleSystemFallback
.AppleSystemUIFont
.AppleTraditionalChineseFont
.AppleUrduFont
.Lucida Grande UI
.SF Arabic
.SF Armenian
.SF Georgian
.SF Hebrew
.ThonburiUI
.Times Fallback
Academy Engraved LET
Adelle Sans Devanagari
AkayaKanadaka
AkayaTelivigala
Al Bayan
Al Nile
Al Tarikh
Aller
Aller Display
American Typewriter
Andale Mono
Annai MN
Apple Braille
Apple Chancery
Apple Color Emoji
Apple LiGothic
Apple LiSung
Apple SD Gothic Neo
Apple Symbols
AppleGothic
AppleMyungjo
Arial
Arial Black
Arial Hebrew
Arial Hebrew Scholar
Arial Narrow
Arial Rounded MT Bold
Arial Unicode MS
Arima Koshi
Arima Madurai
Avenir
Avenir Next
Avenir Next Condensed
Ayuthaya
BM Dohyeon
BM Hanna 11yrs Old
BM Hanna Air
BM Hanna Pro
BM Jua
BM Kirang Haerang
BM Yeonsung
Baghdad
Bai Jamjuree
Baloo 2
Baloo Bhai 2
Baloo Bhaijaan
Baloo Bhaina 2
Baloo Chettan 2
Baloo Da 2
Baloo Paaji 2
Baloo Tamma 2
Baloo Tammudu 2
Baloo Thambi 2
Bangla MN
Bangla Sangam MN
Baoli SC
Baoli TC
Baskerville
Beirut
BiauKaiHK
BiauKaiTC
Big Caslon
Bodoni 72
Bodoni 72 Oldstyle
Bodoni 72 Smallcaps
Bodoni Ornaments
Bradley Hand
Brush Script MT
Cambay Devanagari
Chakra Petch
Chalkboard
Chalkboard SE
Chalkduster
Charm
Charmonman
Charter
Cochin
Comic Sans MS
Copperplate
Corsiva Hebrew
Courier New
DIN Alternate
DIN Condensed
Damascus
DecoType Naskh
Devanagari MT
Devanagari Sangam MN
Didot
Diwan Kufi
Diwan Thuluth
Euphemia UCAS
Fahkwang
Farah
Farisi
Futura
GB18030 Bitmap
Galvji
Geeza Pro
Geneva
Georgia
Gill Sans
Gotu
Grantha Sangam MN
Gujarati MT
Gujarati Sangam MN
GungSeo
Gurmukhi MN
Gurmukhi MT
Gurmukhi Sangam MN
Hannotate SC
Hannotate TC
HanziPen SC
HanziPen TC
HeadLineA
Hei
Heiti SC
Heiti TC
Helvetica
Helvetica Neue
Herculanum
Hiragino Maru Gothic ProN
Hiragino Mincho ProN
Hiragino Sans
Hiragino Sans GB
Hiragino Sans TC
Hoefler Text
Hubballi
ITF Devanagari
ITF Devanagari Marathi
Impact
InaiMathi
Jaini
Jaini Purva
K2D
Kai
Kailasa
Kaiti SC
Kaiti TC
Kannada MN
Kannada Sangam MN
Katari
Kavivanar
Kefa III
Khmer MN
Khmer Sangam MN
Klee
KoHo
Kodchasan
Kohinoor Bangla
Kohinoor Devanagari
Kohinoor Gujarati
Kohinoor Telugu
Kokonor
Krub
Krungthep
KufiStandardGK
Lahore Gurmukhi
Lantinghei SC
Lantinghei TC
Lao MN
Lao Sangam MN
Lava Devanagari
Lava Kannada
Lava Telugu
LiHei Pro
LiSong Pro
Libian SC
Libian TC
LingWai SC
LingWai TC
Lucida Grande
Luminari
Maku
Malayalam MN
Malayalam Sangam MN
Mali
Marker Felt
Menlo
Microsoft Sans Serif
Mishafi
Mishafi Gold
Modak
Monaco
Montserrat
Mshtakan
Mukta
Mukta Mahee
Mukta Malar
Mukta Vaani
Muna
Myanmar MN
Myanmar Sangam MN
Nadeem
Nanum Brush Script
Nanum Gothic
Nanum Myeongjo
Nanum Pen Script
New Peninim MT
Niramit
Noteworthy
Noto Nastaliq Urdu
Noto Sans Armenian
Noto Sans Batak
Noto Sans Kannada
Noto Sans Myanmar
Noto Sans NKo
Noto Sans Oriya
Noto Sans Syriac
Noto Sans Tagalog
Noto Sans Zawgyi
Noto Serif Kannada
Noto Serif Myanmar
October Compressed Devanagari
October Compressed Tamil
October Condensed Devanagari
October Condensed Tamil
October Devanagari
October Tamil
Optima
Oriya MN
Oriya Sangam MN
Osaka
PCMyungjo
PSL Ornanong Pro
PT Mono
PT Sans
PT Sans Caption
PT Sans Narrow
PT Serif
PT Serif Caption
Padyakke Expanded One
Palatino
Papyrus
Party LET
Phosphate
PilGi
PingFang HK
PingFang MO
PingFang SC
PingFang TC
Plantagenet Cherokee
Raanana
Rockwell
STFangsong
STHeiti
STIX Two Math
STIX Two Text
STKaiti
STSong
Sama Devanagari
Sama Gujarati
Sama Gurmukhi
Sama Kannada
Sama Malayalam
Sama Tamil
Sana
Sarabun
Sathu
Savoye LET
Shobhika
Shree Devanagari 714
SignPainter
Silom
SimSong
Sinhala MN
Sinhala Sangam MN
Skia
Snell Roundhand
Songti SC
Songti TC
Srisakdi
Sukhumvit Set
Symbol
Tahoma
Tamil MN
Tamil Sangam MN
Telugu MN
Telugu Sangam MN
Thonburi
Times New Roman
Tiro Bangla
Tiro Devanagari Hindi
Tiro Devanagari Marathi
Tiro Devanagari Sanskrit
Tiro Gurmukhi
Tiro Kannada
Tiro Tamil
Tiro Telugu
Toppan Bunkyu Gothic
Toppan Bunkyu Midashi Gothic
Toppan Bunkyu Midashi Mincho
Toppan Bunkyu Mincho
Trattatello
Trebuchet MS
Tsukushi A Round Gothic
Tsukushi B Round Gothic
Verdana
Waseem
Wawati SC
Wawati TC
Webdings
Wingdings
Wingdings 2
Wingdings 3
Xingkai SC
Xingkai TC
YuGothic
YuKyokasho
YuKyokasho Yoko
YuMincho
YuMincho +36p Kana
Yuanti SC
Yuanti TC
Yuppy SC
Yuppy TC
Zapf Dingbats
Zapfino
> label #5.1:95-104 color red height 1.5 font "Arial Black"
> label #5.1:95-104 color red height 1 font "Arial Black"
> label #2.4:333-340 hight 1 font 'Arial Black'
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label #2.4:335-338
> label #2.4:335-338 font "Arial Black"
> label #2.4:331-340 font "Arial Black"
> label #2.4:331-340 font "Arial Black" color magenta
> show #2.4:333
> show #5.1:102
> show #3.2:102
> ~show #3.2:102
> ~show #3.2:117-119
> show #3.2:117-119
Unsupported scale factor (0.000000) detected on Display1
[Repeated 2 time(s)]
> save "/Users/anz/Desktop/P-motifs 260223 GLS.cxs"
——— End of log from Tue Feb 24 10:12:16 2026 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PySide6 6.10.1, Qt 6.10.1
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac16,12
Model Number: Z1GS000EYN/A
Chip: Apple M4
Total Number of Cores: 10 (4 Performance and 6 Efficiency)
Memory: 24 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (a) (25D771280a)
Kernel Version: Darwin 25.3.0
Time since boot: 3 days, 15 hours, 25 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
HP Z23n:
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:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.0.0
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.64.1
ChimeraX-AtomicLibrary: 14.2.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12.dev202602270247
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.3
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.18
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.5
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.5.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.5
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.2
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: 1.50.3
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.1
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.4
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.6
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.9.2
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.13.1
pydantic_core: 2.41.5
pydata-sphinx-theme: 0.16.1
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.0
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PySide6: 6.10.1
PySide6_Addons: 6.10.1
PySide6_Essentials: 6.10.1
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.22
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.1
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
shiboken6: 6.10.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.41.0
wcwidth: 0.6.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 40 minutes ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in QWindowContainer::parentWasChanged |
comment:2 by , 40 minutes ago
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Seemingly the same as #19970