![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 hours ago
#19516 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.0.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202510240114 (2025-10-24 01:14:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 290000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 51292,
"osVersion" : {
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"build" : "25A362",
"releaseType" : "User"
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"captureTime" : "2025-12-14 15:51:18.7135 -0600",
"codeSigningMonitor" : 1,
"incident" : "24C1EB09-D93E-4078-9E63-1936AF65994C",
"pid" : 92226,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-12-14 14:42:01.5300 -0600",
"procStartAbsTime" : 7050471516635,
"procExitAbsTime" : 7143029215358,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "6FF9CF12-F27B-F6D1-E7B7-B87E880328F6",
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"sleepWakeUUID" : "429F2E6B-0403-4391-B87F-621D875F6BBF",
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"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4333535224
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 1024c8000-1024cc000 [ 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: 4333535224
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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Log:
UCSF ChimeraX version: 1.11.dev202510240114 (2025-10-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/jason/Desktop/Postdoc Work/VDAC2-BAK/VDAC2-BAK1 Structures/BAK1
> structure/AF3-VDAC2-BAK1 8UKY-monomer and 7LK4.cxs"
Updated animation length to 0:05.00
[Repeated 1 time(s)]Log from Sun Dec 14 15:41:23 2025UCSF ChimeraX version:
1.11.dev202510240114 (2025-10-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/jason/Desktop/Postdoc Work/VDAC2-BAK/VDAC2-BAK1 Structures/BAK1
> structure/AF3-VDAC2-BAK1 complex with 8UKY-monomer.cxs"
Updated animation length to 0:05.00
[Repeated 1 time(s)]Log from Tue Dec 9 17:05:55 2025UCSF ChimeraX version:
1.11.dev202510240114 (2025-10-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/jason/Desktop/ Papers to MBP/VDAC2/VDAC2-BAK1 Structures/AF of
> VDAC-BAK/Sessions for check/Monomer of VDAC2-BAK1.cxs"
Updated animation length to 0:05.00
Log from Sat Jul 12 21:05:13 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10.dev202501140846 (2025-01-14)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/haofeng/Desktop/Immunity
> Paper/dimer_of_bak1_and_vdac2/fold_dimer_of_bak1_and_vdac2_model_0.cif"
Chain information for fold_dimer_of_bak1_and_vdac2_model_0.cif #1
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> lighting soft
> set bgColor white
> select /A:1-211
1653 atoms, 1694 bonds, 211 residues, 1 model selected
Drag select of 35 residues
> select up
2100 atoms, 2154 bonds, 267 residues, 1 model selected
> select up
3306 atoms, 3388 bonds, 422 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> select clear
Drag select of 49 residues
Drag select of 29 residues
> select up
1670 atoms, 1698 bonds, 214 residues, 1 model selected
> select up
4436 atoms, 4522 bonds, 588 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
> color sel dark salmon
> color sel violet
> color sel misty rose
> color sel pink
> color sel plum
> color sel light pink
> color sel hot pink
> color sel light salmon
> color sel dark salmon
> color sel gold
> color sel orange
> color sel olive drab
> color sel old lace
> color sel light salmon
> select clear
> save "/Users/haofeng/Desktop/Immunity Paper/VDAC2-BAK1 Projects/Dimer of
> VDAC2-BAK1.cxs" includeMaps true
> save "/Users/haofeng/Desktop/Immunity Paper/VDAC2-BAK1 Projects/Dimer of
> VDAC2-BAK1.cxs"
Drag select of 321 residues
> select up
2790 atoms, 2847 bonds, 363 residues, 1 model selected
> select up
3871 atoms, 3955 bonds, 505 residues, 1 model selected
> hide sel cartoons
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> save "/Users/haofeng/Desktop/Immunity Paper/VDAC2-BAK1 Projects/Monomer of
> VDAC2-BAK1.cxs"
——— End of log from Sat Jul 12 21:05:13 2025 ———
> view name session-start
opened ChimeraX session
> open "/Users/jason/Desktop/ Papers to MBP/VDAC2/VDAC2-BAK1 AF3 files/BAK
> structure/8UKY-monomer.pdb" format pdb
No such file/path: /Users/jason/Desktop/ Papers to MBP/VDAC2/VDAC2-BAK1 AF3
files/BAK structure/8UKY-monomer.pdb
> open "/Users/jason/Desktop/ Papers to MBP/VDAC2/VDAC2-BAK1 Structures/BAK
> structure/8UKY-monomer.pdb"
8UKY-monomer.pdb title:
Crystal structure of bak In complex with inhibiting antibody 14G6 [more
info...]
Chain information for 8UKY-monomer.pdb #2
---
Chain | Description | UniProt
A | 14G6 fab light chain |
B | 14G6 fab heavy chain |
D | BCL-2 homologous antagonist/killer | BAK_HUMAN 23-186
Non-standard residues in 8UKY-monomer.pdb #2
---
144 — tris-hydroxymethyl-methyl-ammonium
1PE — pentaethylene glycol (PEG400)
EDO — 1,2-ethanediol (ethylene glycol)
PEG — di(hydroxyethyl)ether
PGE — triethylene glycol
SO4 — sulfate ion
4486 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> lighting soft
> graphics silhouettes true
> ui tool show Matchmaker
> matchmaker #1 to #2
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 8UKY-monomer.pdb, chain D (#2) with
fold_dimer_of_bak1_and_vdac2_model_0.cif, chain A (#1), sequence alignment
score = 795.2
RMSD between 134 pruned atom pairs is 0.770 angstroms; (across all 153 pairs:
3.312)
Drag select of 359 residues, 297 atoms, 256 bonds
> select clear
Drag select of 79 atoms, 140 residues, 1 pseudobonds, 61 bonds
> select up
1077 atoms, 1066 bonds, 1 pseudobond, 149 residues, 2 models selected
> select up
1101 atoms, 1093 bonds, 1 pseudobond, 149 residues, 2 models selected
> select up
1866 atoms, 1886 bonds, 1 pseudobond, 250 residues, 2 models selected
> select up
4213 atoms, 4306 bonds, 1 pseudobond, 553 residues, 2 models selected
> select up
4254 atoms, 4347 bonds, 1 pseudobond, 560 residues, 2 models selected
> select up
4512 atoms, 4610 bonds, 1 pseudobond, 590 residues, 2 models selected
> select up
4711 atoms, 4666 bonds, 1 pseudobond, 733 residues, 2 models selected
> hide sel atoms
> select clear
Drag select of 27 residues
> select up
574 atoms, 588 bonds, 69 residues, 1 model selected
> select up
1653 atoms, 1694 bonds, 211 residues, 1 model selected
> select down
574 atoms, 588 bonds, 69 residues, 1 model selected
> select up
1653 atoms, 1694 bonds, 211 residues, 1 model selected
Drag select of 35 residues
> select up
2585 atoms, 2647 bonds, 320 residues, 2 models selected
> select up
2880 atoms, 2949 bonds, 364 residues, 2 models selected
> select up
2906 atoms, 2955 bonds, 384 residues, 2 models selected
> select up
12453 atoms, 12576 bonds, 1743 residues, 2 models selected
> select down
2906 atoms, 2955 bonds, 384 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #1 to #2 & sel
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 8UKY-monomer.pdb, chain D (#2) with
fold_dimer_of_bak1_and_vdac2_model_0.cif, chain A (#1), sequence alignment
score = 795.2
RMSD between 134 pruned atom pairs is 0.770 angstroms; (across all 153 pairs:
3.312)
> matchmaker #1 to #2 & sel
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 8UKY-monomer.pdb, chain D (#2) with
fold_dimer_of_bak1_and_vdac2_model_0.cif, chain A (#1), sequence alignment
score = 795.2
RMSD between 134 pruned atom pairs is 0.770 angstroms; (across all 153 pairs:
3.312)
No reference and/or match structure/chain chosen
> ui tool show Matchmaker
> matchmaker #2/D to #1/B & sel pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_dimer_of_bak1_and_vdac2_model_0.cif, chain B (#1) with 8UKY-
monomer.pdb, chain D (#2), sequence alignment score = 795.2
RMSD between 134 pruned atom pairs is 0.778 angstroms; (across all 153 pairs:
3.308)
> select clear
> save "/Users/jason/Desktop/ Papers to MBP/VDAC2/VDAC2-BAK1 Structures/BAK
> structure/AF3-VDAC2-BAK1 complex with 8UKY-monomer.cxs" includeMaps true
Drag select of 134 residues
> select up
1212 atoms, 1234 bonds, 164 residues, 1 model selected
> select up
3259 atoms, 3336 bonds, 430 residues, 1 model selected
> select up
3458 atoms, 3405 bonds, 560 residues, 1 model selected
> select up
4711 atoms, 4666 bonds, 733 residues, 1 model selected
> color sel orange
> color sel magenta
> select clear
> lighting soft
> save "/Users/jason/Desktop/ Papers to MBP/VDAC2/VDAC2-BAK1 Structures/BAK
> structure/AF3-VDAC2-BAK1 complex with 8UKY-monomer.cxs" includeMaps true
——— End of log from Tue Dec 9 17:05:55 2025 ———
> view name session-start
opened ChimeraX session
> open "/Users/jason/Desktop/Postdoc Work/VDAC2-BAK/VDAC2-BAK1 Structures/BAK1
> structure/9CPH-Structural basis of BAK sequestration by MCL-1 and
> consequences for apoptosis initiation.cif" "/Users/jason/Desktop/Postdoc
> Work/VDAC2-BAK/VDAC2-BAK1 Structures/BAK1 structure/5W5Z-Crystal structure
> of BAXP168G in complex with an activating antibody at high resolution
> 3C10.pdb" "/Users/jason/Desktop/Postdoc Work/VDAC2-BAK/VDAC2-BAK1
> Structures/BAK1 structure/7LK4-dimer.pdb"
9CPH-Structural basis of BAK sequestration by MCL-1 and consequences for
apoptosis initiation.cif title:
Structural basis of BAK sequestration by MCL-1 and consequences for apoptosis
initiation [more info...]
Chain information for 9CPH-Structural basis of BAK sequestration by MCL-1 and
consequences for apoptosis initiation.cif #3
---
Chain | Description | UniProt
A | Induced myeloid leukemia cell differentiation protein Mcl-1 |
B | Bcl-2 homologous antagonist/killer | BAK_HUMAN 69-89
H | Synthetic antibody, Fab fragment, Heavy Chain |
L | Synthetic antibody, Fab fragment, Light Chain |
Non-standard residues in 9CPH-Structural basis of BAK sequestration by MCL-1
and consequences for apoptosis initiation.cif #3
---
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)
36 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5W5Z-Crystal structure of BAXP168G in complex with an activating antibody at
high resolution 3C10.pdb title:
Crystal structure of BAXP168G In complex with an activating antibody At high
resolution [more info...]
Chain information for 5W5Z-Crystal structure of BAXP168G in complex with an
activating antibody at high resolution 3C10.pdb #4
---
Chain | Description | UniProt
A | apoptosis regulator bax | BAX_HUMAN 32-192
H | 3C10 fab heavy chain |
L | 3C10 fab light chain |
Non-standard residues in 5W5Z-Crystal structure of BAXP168G in complex with an
activating antibody at high resolution 3C10.pdb #4
---
EDO — 1,2-ethanediol (ethylene glycol)
MES — 2-(N-morpholino)-ethanesulfonic acid
PCA — pyroglutamic acid
PG4 — tetraethylene glycol
PGE — triethylene glycol
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
4022 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
7LK4-dimer.pdb title:
Crystal structure of bak L100A In complex with activating antibody fragments
[more info...]
Chain information for 7LK4-dimer.pdb #5
---
Chain | Description | UniProt
C G | 7D10 antibody VL fragment |
D H | 7D10 antibody VH fragment |
Q S | BCL-2 homologous antagonist/killer | BAK_HUMAN 23-186
Non-standard residues in 7LK4-dimer.pdb #5
---
MPD — (4S)-2-methyl-2,4-pentanediol
17 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5807 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> hide #1 models
> hide #!2 models
> close #3
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> close #5
> open "/Users/jason/Desktop/Postdoc Work/VDAC2-BAK/VDAC2-BAK1 Structures/BAK1
> structure/7LK4-monomerpdb.pdb"
7LK4-monomerpdb.pdb title:
Crystal structure of bak L100A In complex with activating antibody fragments
[more info...]
Chain information for 7LK4-monomerpdb.pdb #3
---
Chain | Description | UniProt
G | 7D10 antibody VL fragment |
H | 7D10 antibody VH fragment |
Q | BCL-2 homologous antagonist/killer | BAK_HUMAN 23-186
Non-standard residues in 7LK4-monomerpdb.pdb #3
---
MPD — (4S)-2-methyl-2,4-pentanediol
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2820 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Drag select of 33 atoms, 28 bonds
> select up
40 atoms, 28 bonds, 12 residues, 1 model selected
> select up
2866 atoms, 2914 bonds, 385 residues, 1 model selected
> select down
40 atoms, 28 bonds, 12 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #1 models
Drag select of 19 residues
> select up
533 atoms, 543 bonds, 64 residues, 1 model selected
> select up
1653 atoms, 1694 bonds, 211 residues, 1 model selected
Drag select of 38 residues
> select up
2194 atoms, 2247 bonds, 281 residues, 2 models selected
> select up
2368 atoms, 2425 bonds, 303 residues, 2 models selected
> select up
2476 atoms, 2533 bonds, 320 residues, 2 models selected
> select down
2368 atoms, 2425 bonds, 303 residues, 2 models selected
Drag select of 63 residues
> select up
3274 atoms, 3348 bonds, 418 residues, 3 models selected
> select up
3545 atoms, 3627 bonds, 457 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #!4 to #1 & sel
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 fold_dimer_of_bak1_and_vdac2_model_0.cif, chain B (#1) with
5W5Z-Crystal structure of BAXP168G in complex with an activating antibody at
high resolution 3C10.pdb, chain A (#4), sequence alignment score = 166.7
RMSD between 38 pruned atom pairs is 1.041 angstroms; (across all 107 pairs:
11.507)
> matchmaker #!3 to #1 & sel
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 fold_dimer_of_bak1_and_vdac2_model_0.cif, chain B (#1) with
7LK4-monomerpdb.pdb, chain Q (#3), sequence alignment score = 751.3
RMSD between 97 pruned atom pairs is 0.673 angstroms; (across all 137 pairs:
16.033)
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> show #!4 models
> hide #!2 models
> hide #!3 models
> select clear
> hide #!4 models
> show #!4 models
> select add #4
4198 atoms, 4181 bonds, 4 pseudobonds, 645 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.068996,0.17991,-0.98126,-45.986,-0.81343,0.5593,0.15974,38.114,0.57756,0.80921,0.10775,61.696
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.46832,-0.81861,0.33251,-57.887,0.76528,-0.5639,-0.31043,61.236,0.44163,0.10908,0.89054,55.945
> undo
> ui mousemode right zoom
> ui mousemode right translate
> select clear
> select add #1/B:29
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #4/A:162
17 atoms, 15 bonds, 2 residues, 2 models selected
> select up
330 atoms, 337 bonds, 39 residues, 2 models selected
> select up
1983 atoms, 2033 bonds, 253 residues, 2 models selected
> select up
2014 atoms, 2064 bonds, 257 residues, 2 models selected
> select up
2231 atoms, 2289 bonds, 283 residues, 2 models selected
> select up
2264 atoms, 2321 bonds, 287 residues, 2 models selected
> select up
2368 atoms, 2425 bonds, 303 residues, 2 models selected
> select up
2476 atoms, 2533 bonds, 320 residues, 2 models selected
> select up
2481 atoms, 2533 bonds, 325 residues, 2 models selected
> select up
11940 atoms, 12091 bonds, 1655 residues, 2 models selected
> select down
2481 atoms, 2533 bonds, 325 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!3 to #1/B & sel pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_dimer_of_bak1_and_vdac2_model_0.cif, chain B (#1) with
7LK4-monomerpdb.pdb, chain Q (#3), sequence alignment score = 751.3
RMSD between 97 pruned atom pairs is 0.673 angstroms; (across all 137 pairs:
16.033)
> matchmaker #!3 to #1 & sel
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 fold_dimer_of_bak1_and_vdac2_model_0.cif, chain B (#1) with
7LK4-monomerpdb.pdb, chain Q (#3), sequence alignment score = 751.3
RMSD between 97 pruned atom pairs is 0.673 angstroms; (across all 137 pairs:
16.033)
> ui tool show Matchmaker
> matchmaker #!4 to #2 & sel
No 'to' model specified
> hide #!4 models
> show #!3 models
> select clear
> hide #1 models
> show #!4 models
Drag select of 150 residues, 2 pseudobonds
> select up
1609 atoms, 1642 bonds, 2 pseudobonds, 205 residues, 4 models selected
> select up
1892 atoms, 1933 bonds, 2 pseudobonds, 246 residues, 4 models selected
> select up
1897 atoms, 1933 bonds, 2 pseudobonds, 251 residues, 4 models selected
> select down
1892 atoms, 1933 bonds, 2 pseudobonds, 246 residues, 4 models selected
> select up
1897 atoms, 1933 bonds, 2 pseudobonds, 251 residues, 4 models selected
> select up
7024 atoms, 7067 bonds, 6 pseudobonds, 1018 residues, 4 models selected
> select down
1897 atoms, 1933 bonds, 2 pseudobonds, 251 residues, 4 models selected
> select clear
Drag select of 82 residues
> select up
1222 atoms, 1251 bonds, 148 residues, 2 models selected
> select up
1784 atoms, 1825 bonds, 229 residues, 2 models selected
> select down
1222 atoms, 1251 bonds, 148 residues, 2 models selected
> select up
1784 atoms, 1825 bonds, 229 residues, 2 models selected
> select up
1892 atoms, 1933 bonds, 246 residues, 2 models selected
> select clear
> hide #!3 models
> show #!2 models
Drag select of 131 residues, 2 pseudobonds
> select up
1809 atoms, 1844 bonds, 2 pseudobonds, 227 residues, 3 models selected
> select up
2050 atoms, 2094 bonds, 2 pseudobonds, 262 residues, 3 models selected
> select up
2081 atoms, 2100 bonds, 2 pseudobonds, 287 residues, 3 models selected
> select up
8909 atoms, 8847 bonds, 4 pseudobonds, 1378 residues, 3 models selected
> select down
2081 atoms, 2100 bonds, 2 pseudobonds, 287 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #!4 to #2 & sel
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 8UKY-monomer.pdb, chain D (#2) with 5W5Z-Crystal structure of
BAXP168G in complex with an activating antibody at high resolution 3C10.pdb,
chain A (#4), sequence alignment score = 151.8
RMSD between 39 pruned atom pairs is 1.104 angstroms; (across all 81 pairs:
5.244)
> show #1 models
> show #!3 models
> close #4
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #1 models
> show #!3 models
> hide #!3 models
> show #1 models
> select clear
> show #!3 models
> save "/Users/jason/Desktop/Postdoc Work/VDAC2-BAK/VDAC2-BAK1 Structures/BAK1
> structure/AF3-VDAC2-BAK1 8UKY-monomer and 7LK4.cxs" includeMaps true
——— End of log from Sun Dec 14 15:41:23 2025 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGP3KH/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 13822.1.2
OS Loader Version: 13822.1.2
Software:
System Software Overview:
System Version: macOS 26.0.1 (25A362)
Kernel Version: Darwin 25.0.0
Time since boot: 10 days, 19 hours, 18 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.11.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.10.2
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: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.19
ChimeraX-AtomicLibrary: 14.2.1
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
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202510240114
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: 1.1.4
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: 1.7.2
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.1
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: 0.1.0
ChimeraX-MDcrds: 2.17.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.15.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
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: 1.4
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.2.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.2
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-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
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: 1.48.4
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.1
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: 8.3.0
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.11.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.17
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.60.1
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: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.7
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.15
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: 3.10.5
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.0
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: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
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: 4.5.0
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: 2.12.3
pydantic-settings: 2.11.0
pydantic_core: 2.41.4
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 8.4.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.1.1
python-multipart: 0.0.20
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals-py: 3.1.0
rpds-py: 0.28.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
sniffio: 1.3.1
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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: 3.0.2
stack-data: 0.6.3
starlette: 0.48.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
yarl: 1.22.0
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