![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 months ago
Closed 2 months ago
#18703 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 380000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 6974,
"osVersion" : {
"train" : "macOS 15.6",
"build" : "24G84",
"releaseType" : "User"
},
"captureTime" : "2025-09-04 16:44:13.2700 +0800",
"codeSigningMonitor" : 0,
"incident" : "15D1DE78-B928-4B14-9BF2-4DCE5311F2EA",
"pid" : 42604,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-04 15:39:47.9188 +0800",
"procStartAbsTime" : 377217083004435,
"procExitAbsTime" : 381082509252630,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"9AF340B5-A10A-5B99-A5D6-B07C114305A4","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4BECD708-46BC-5D82-C5A2-600CD697911F",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["deviceNotCapable"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570490881,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"bootSessionUUID" : "34587B2B-51D2-4F88-92D9-A4ED6DA438FD",
"wakeTime" : 24856,
"bridgeVersion" : {"build":"22P6083","train":"9.6"},
"sleepWakeUUID" : "1C106410-823E-4CF1-A4CE-86DB54EE5E0B",
"sip" : "disabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4378197847\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104f60000-104f64000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":42604},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 4378197847\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104f60000-104f64000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
"threads" : 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Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs"
Log from Thu Sep 4 14:59:35 2025UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs"
Log from Thu Sep 4 14:44:21 2025UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs"
Log from Thu Sep 4 13:33:38 2025UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs"
Log from Thu Sep 4 12:58:57 2025UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd.cxs"
> format session
Log from Wed Sep 3 18:54:37 2025 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo107-coot-0.pdb"
Summary of feedback from opening /Users/julia/Desktop/cryo-EM data
processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo107-coot-0.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
714 messages similar to the above omitted
Chain information for Fit_6596_redo107-coot-0.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo104-coot-0.pdb"
Summary of feedback from opening /Users/julia/Desktop/cryo-EM data
processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo104-coot-0.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
714 messages similar to the above omitted
Chain information for Fit_6596_redo104-coot-0.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo106-coot-0.pdb"
Summary of feedback from opening /Users/julia/Desktop/cryo-EM data
processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo106-coot-0.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
655 messages similar to the above omitted
Chain information for Fit_6596_redo106-coot-0.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo108-coot-0.pdb"
Summary of feedback from opening /Users/julia/Desktop/cryo-EM data
processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo108-coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 12 12 GLN C
33 SER C 41 1 9
Start residue of secondary structure not found: HELIX 13 13 ALA C 71 LEU C 81
1 11
Start residue of secondary structure not found: SHEET 15 1515 ASN C 21 ASN C
25 0
Start residue of secondary structure not found: SHEET 16 1616 VAL C 46 LEU C
51 0
Start residue of secondary structure not found: SHEET 17 1717 TYR C 63 TYR C
68 0
1 messages similar to the above omitted
Chain information for Fit_6596_redo108-coot-0.pdb #4
---
Chain | Description
A | No description available
B | No description available
> set bgColor white
> matchmaker #2-4 to #1 showAlignment true
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 Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo104-coot-0.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo106-coot-0.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo108-coot-0.pdb #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
> matchmaker #2-4 to #1
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 Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
> ui tool show Matchmaker
> matchmaker #!2-4 to #1
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 Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
> ui tool show "Render by Attribute"
> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 5,#fffb00:5,blue:5,red noValueColor grey
46518 atoms, 6313 residues, atom seq_rmsd range 0 to 0.000844
> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 1.66667,#0433ff:3,#fffb00:5,#fffb00:5,blue:5,red:5,#ff2600:5,yellow
> noValueColor grey
46518 atoms, 6313 residues, atom seq_rmsd range 0 to 0.000844
> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 1.66667,#0433ff:3,#fffb00:5,#fffb00:5,blue:5,red:5,#ff2600:5,yellow
46518 atoms, 6313 residues, atom seq_rmsd range 0 to 0.000844
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!4 models
> hide #!1 models
> show #!1 models
> matchmaker #2-4 to #1
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 Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
> show #!2 models
> show #!3 models
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> sequence header 3 rmsd show
Chains used in RMSD evaluation for alignment 3: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo104-coot-0.pdb #2/A, Fit_6596_redo106-coot-0.pdb #3/A,
Fit_6596_redo108-coot-0.pdb #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
> sequence header 2 rmsd show
Chains used in RMSD evaluation for alignment 2: Fit_6596_redo107-coot-0.pdb
#1/C, Fit_6596_redo104-coot-0.pdb #2/C, Fit_6596_redo106-coot-0.pdb #3/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
> sequence header 1 rmsd show
Chains used in RMSD evaluation for alignment 1: Fit_6596_redo107-coot-0.pdb
#1/B, Fit_6596_redo104-coot-0.pdb #2/B, Fit_6596_redo106-coot-0.pdb #3/B,
Fit_6596_redo108-coot-0.pdb #4/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
> ui tool show "Render by Attribute"
> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 1.66667,#0433ff:3,#fffb00:5,#fffb00:5,blue:5,red:5,#ff2600:5,yellow
> noValueColor grey
46518 atoms, 6313 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute seq_rmsd #1 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute seq_rmsd #2 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute seq_rmsd #3 palette blue:yellow:red
11765 atoms, 1599 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute seq_rmsd #4 palette blue:yellow:red
11105 atoms, 1514 residues, atom seq_rmsd range 0.000165 to 3.4
> hide #!2 models
> hide #!3 models
> hide #!4 models
> ui tool show "Render by Attribute"
[Repeated 1 time(s)]
> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 0.000165002,blue:0.760137,white:1.69034,red
46518 atoms, 6313 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 0.000165002,blue:0.760137,#fffb00:1.69034,red
46518 atoms, 6313 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute seq_rmsd #4 palette blue:yellow:red
11105 atoms, 1514 residues, atom seq_rmsd range 0.000165 to 3.4
> color byattribute seq_rmsd #1 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5
> show #!2 models
> show #!3 models
> show #!4 models
> color byattribute seq_rmsd #2 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute seq_rmsd #3 palette blue:yellow:red
11765 atoms, 1599 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute seq_rmsd #4 palette blue:yellow:red
11105 atoms, 1514 residues, atom seq_rmsd range 0.000165 to 3.4
> hide #!4 models
> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 0.000165002,blue:1,#fffb00:3,red noValueColor grey
46518 atoms, 6313 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute seq_rmsd #4 palette blue:yellow:red
11105 atoms, 1514 residues, atom seq_rmsd range 0.000165 to 3.4
> show #!4 models
> color byattribute seq_rmsd #3 palette blue:yellow:red
11765 atoms, 1599 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute seq_rmsd #2 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute seq_rmsd #1 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #1/A#2/A#3/A#4/A
32112 atoms, 32688 bonds, 4 pseudobonds, 4528 residues, 8 models selected
> show #!1 models
> show #!2 models
> show #!3 models
> cartoon hide (#!1-4 & sel)
> select add #1
35908 atoms, 36569 bonds, 8 pseudobonds, 4996 residues, 9 models selected
> select add #2
39704 atoms, 40450 bonds, 12 pseudobonds, 5464 residues, 10 models selected
> select add #3
43441 atoms, 44267 bonds, 16 pseudobonds, 5931 residues, 11 models selected
> select add #4
46518 atoms, 47416 bonds, 20 pseudobonds, 6313 residues, 12 models selected
> select subtract #3
34753 atoms, 35427 bonds, 15 pseudobonds, 4714 residues, 9 models selected
> select subtract #2
22929 atoms, 23374 bonds, 10 pseudobonds, 3114 residues, 6 models selected
> select subtract #1
11105 atoms, 11321 bonds, 5 pseudobonds, 1514 residues, 3 models selected
> select subtract #4
Nothing selected
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> show #!2 models
> show #!3 models
> ui tool show "Render by Attribute"
> key blue:0 #fffb00:1 red:3 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> ui tool show "Render by Attribute"
> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 0.000165002,blue:1.5,#fffb00:3,red noValueColor grey
46518 atoms, 6313 residues, atom seq_rmsd range 0.000165 to 12.5
> close #5
> key blue:0.0 #fffb00:1.5 red:3.0 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> color byattribute seq_rmsd #1 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute seq_rmsd #2 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute seq_rmsd #3 palette blue:yellow:red
11765 atoms, 1599 residues, atom seq_rmsd range 0.000165 to 12.5
> color byattribute seq_rmsd #4 palette blue:yellow:red
11105 atoms, 1514 residues, atom seq_rmsd range 0.000165 to 3.4
> hide #6 models
> show #6 models
> ui tool show "Render by Attribute"
> hide #6 models
> save "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd.cxs"
> includeMaps true
——— End of log from Wed Sep 3 18:54:37 2025 ———
opened ChimeraX session
> show #!4 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/B
Alignment identifier is 4/B
> select #4/B:338
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/B:338-339
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #4/B:341
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/B:341-361
157 atoms, 162 bonds, 21 residues, 1 model selected
> select clear
> show #!1 models
> hide #!4 models
> hide #!1 models
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class1-model-
> coot-11.pdb"
Chain information for Fit_class1-model-coot-11.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class2-model-
> coot-10.pdb"
Chain information for Fit_class2-model-coot-10.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class4-model-
> coot-3.pdb"
Chain information for Fit_class4-model-coot-3.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class3-model-
> coot-2.pdb"
Chain information for Fit_class3-model-coot-2.pdb #9
---
Chain | Description
A | No description available
B | No description available
> hide #!5 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> show #!5 models
> hide #!5 models
> show #!7 models
> show #!5 models
> hide #!5 models
> hide #!7 models
> show #!1 models
> show #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!7 models
> hide #!7 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!5 models
> show #!7 models
> show #!8 models
> hide #!5 models
> hide #!7 models
> hide #!1 models
> hide #!8 models
> show #!8 models
> show #!7 models
> hide #!8 models
> show #!5 models
> show #!9 models
> hide #!5 models
> hide #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #6 models
> hide #6 models
> show #!7 models
> show #!8 models
> show #!9 models
> close #6
> close #5
> close #7
> close #8
> close #9
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class1-model-
> coot-11.pdb"
Chain information for Fit_class1-model-coot-11.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class2-model-
> coot-10.pdb"
Chain information for Fit_class2-model-coot-10.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class4-model-
> coot-3.pdb"
Chain information for Fit_class4-model-coot-3.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class3-model-
> coot-2.pdb"
Chain information for Fit_class3-model-coot-2.pdb #8
---
Chain | Description
A | No description available
B | No description available
> ui tool show "Show Sequence Viewer"
[Repeated 2 time(s)]
> sequence chain #5/A
Alignment identifier is 5/A
> sequence chain #5/B
Alignment identifier is 5/B
> sequence chain #5/C
Alignment identifier is 5/C
> sequence chain #6/A
Alignment identifier is 6/A
> sequence chain #6/B
Alignment identifier is 6/B
> sequence chain #6/C
Alignment identifier is 6/C
> sequence chain #7/A
Alignment identifier is 7/A
> sequence chain #7/B
Alignment identifier is 7/B
> sequence chain #7/C
Alignment identifier is 7/C
> sequence chain #8/A
Alignment identifier is 8/A
> sequence chain #8/B
Alignment identifier is 8/B
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A
Alignment identifier is 1
> sequence header rmsd show
Chains used in RMSD evaluation for alignment 1: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo104-coot-0.pdb #2/A, Fit_6596_redo106-coot-0.pdb #3/A,
Fit_6596_redo108-coot-0.pdb #4/A, Fit_class1-model-coot-11.pdb #5/A,
Fit_class2-model-coot-10.pdb #6/A, Fit_class4-model-coot-3.pdb #7/A,
Fit_class3-model-coot-2.pdb #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B #2/B #3/B #4/B #5/B #6/B #7/B #8/B
Alignment identifier is 2
> sequence header 2 rmsd show
Chains used in RMSD evaluation for alignment 2: Fit_6596_redo107-coot-0.pdb
#1/B, Fit_6596_redo104-coot-0.pdb #2/B, Fit_6596_redo106-coot-0.pdb #3/B,
Fit_6596_redo108-coot-0.pdb #4/B, Fit_class1-model-coot-11.pdb #5/B,
Fit_class2-model-coot-10.pdb #6/B, Fit_class4-model-coot-3.pdb #7/B,
Fit_class3-model-coot-2.pdb #8/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C #2/C #3/C #5/C #6/C #7/C
Alignment identifier is 3
> sequence header 3 rmsd show
Chains used in RMSD evaluation for alignment 3: Fit_6596_redo107-coot-0.pdb
#1/C, Fit_6596_redo104-coot-0.pdb #2/C, Fit_6596_redo106-coot-0.pdb #3/C,
Fit_class1-model-coot-11.pdb #5/C, Fit_class2-model-coot-10.pdb #6/C,
Fit_class4-model-coot-3.pdb #7/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
> ui tool show "Render by Attribute"
> key blue:0.18 #fffb00:1.00 red:3.00 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> color byattribute r:seq_rmsd #!5-8 target csab palette
> 0.180098,blue:1,#fffb00:3,red noValueColor grey
45869 atoms, 6220 residues, atom seq_rmsd range 0.18 to 10.2
> color byattribute r:seq_rmsd #!5-8 target csab palette
> 0.180098,blue:1,#fffb00:3,red noValueColor grey
45869 atoms, 6220 residues, atom seq_rmsd range 0.18 to 10.2
> ui tool show "Render by Attribute"
> key blue:0.18 #fffb00:1.50 red:3.00 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> color byattribute r:seq_rmsd #!5-8 target csab palette
> 0.180098,blue:1.5,#fffb00:3,red noValueColor grey
45869 atoms, 6220 residues, atom seq_rmsd range 0.18 to 10.2
> color byattribute seq_rmsd #5 palette blue:yellow:red
11817 atoms, 1600 residues, atom seq_rmsd range 0.18 to 10.2
> color byattribute seq_rmsd #6 palette blue:yellow:red
11817 atoms, 1600 residues, atom seq_rmsd range 0.18 to 10.2
> color byattribute seq_rmsd #7 palette blue:yellow:red
11078 atoms, 1505 residues, atom seq_rmsd range 0.18 to 4.34
> color byattribute seq_rmsd #8 palette blue:yellow:red
11157 atoms, 1515 residues, atom seq_rmsd range 0.18 to 4.43
> hide #9 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> show #!5 models
> show #!8 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!5 models
> hide #!8 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!8 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!8 models
> show #!1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> show #!5 models
> show #!1 models
> hide #!1 models
> hide #!5 models
> show #!8 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!5 models
> hide #!8 models
> show #!1 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!1 models
> show #!8 models
> ui tool show "Render by Attribute"
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B #2/B #3/B #4/B #5/B #6/B #7/B #8/B
Alignment identifier is 1
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B #2/B #3/B #4/B #5/B #6/B #7/B #8/B
Alignment identifier is 1
> sequence header rmsd show
Chains used in RMSD evaluation for alignment 1: Fit_6596_redo107-coot-0.pdb
#1/B, Fit_6596_redo104-coot-0.pdb #2/B, Fit_6596_redo106-coot-0.pdb #3/B,
Fit_6596_redo108-coot-0.pdb #4/B, Fit_class1-model-coot-11.pdb #5/B,
Fit_class2-model-coot-10.pdb #6/B, Fit_class4-model-coot-3.pdb #7/B,
Fit_class3-model-coot-2.pdb #8/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> hide #!8 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> matchmaker #2-8 to #1
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 Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with Fit_class1-model-
coot-11.pdb, chain A (#5), sequence alignment score = 5752
RMSD between 1128 pruned atom pairs is 0.191 angstroms; (across all 1132
pairs: 0.280)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with Fit_class2-model-
coot-10.pdb, chain A (#6), sequence alignment score = 5741.2
RMSD between 1128 pruned atom pairs is 0.185 angstroms; (across all 1132
pairs: 0.277)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with Fit_class4-model-
coot-3.pdb, chain A (#7), sequence alignment score = 5741.2
RMSD between 1128 pruned atom pairs is 0.185 angstroms; (across all 1132
pairs: 0.277)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with Fit_class3-model-
coot-2.pdb, chain A (#8), sequence alignment score = 5741.2
RMSD between 1128 pruned atom pairs is 0.185 angstroms; (across all 1132
pairs: 0.277)
> show #9 models
> hide #9 models
> color byattribute seq_rmsd #1 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #2 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #3 palette blue:yellow:red
11765 atoms, 1599 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #4 palette blue:yellow:red
11105 atoms, 1514 residues, atom seq_rmsd range 0.00785 to 5.08
> color byattribute seq_rmsd #5 palette blue:yellow:red
11817 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #6 palette blue:yellow:red
11817 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #7 palette blue:yellow:red
11078 atoms, 1505 residues, atom seq_rmsd range 0.00785 to 4.34
> color byattribute seq_rmsd #8 palette blue:yellow:red
11157 atoms, 1515 residues, atom seq_rmsd range 0.00785 to 5.08
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!3 models
> hide #!1 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!7 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!8 models
> show #!4 models
> hide #!8 models
> hide #!4 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #9 models
> show #!6 models
> show #!7 models
> show #!8 models
> ui tool show "Render by Attribute"
> color byattribute r:seq_rmsd #!1-8 target csab palette
> 0.00785371,blue:1.96353,#fffb00:5,red noValueColor grey
92387 atoms, 12533 residues, atom seq_rmsd range 0.00785 to 10.2
> key blue:0.01 #fffb00:1.96 red:5.00 showTool true
> ui mousemode right "color key"
> key blue:0.01 #fffb00:2 red:5.00
> ui mousemode right translate
> key blue:0.01 #fffb00:1.96 red:4.00 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> key blue:0.01 #fffb00:1.96 red:4.00 showTool true
> ui mousemode right "color key"
> key blue:0.01 #fffb00:2 red:4.00
> ui mousemode right translate
> hide #9 models
> color byattribute seq_rmsd #1 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #2 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #3 palette blue:yellow:red
11765 atoms, 1599 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #4 palette blue:yellow:red
11105 atoms, 1514 residues, atom seq_rmsd range 0.00785 to 5.08
> color byattribute seq_rmsd #5 palette blue:yellow:red
11817 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #6 palette blue:yellow:red
11817 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #7 palette blue:yellow:red
11078 atoms, 1505 residues, atom seq_rmsd range 0.00785 to 4.34
> color byattribute seq_rmsd #8 palette blue:yellow:red
11157 atoms, 1515 residues, atom seq_rmsd range 0.00785 to 5.08
> show #9 models
> hide #9 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!8 models
> hide #!4 models
> show #9 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> ui tool show "Render by Attribute"
> color byattribute r:seq_rmsd #!1-8 target csab palette
> 1,blue:2,#fffb00:4,red noValueColor grey
92387 atoms, 12533 residues, atom seq_rmsd range 0.00785 to 10.2
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> color byattribute r:seq_rmsd #!1-8 target csab palette
> 0,blue:1.99367,#fffb00:3.99521,red noValueColor grey
92387 atoms, 12533 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute r:seq_rmsd #!1-8 target csab palette
> 1.2,blue:1.99367,#fffb00:3.99521,red noValueColor grey
92387 atoms, 12533 residues, atom seq_rmsd range 0.00785 to 10.2
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> color byattribute r:seq_rmsd #!1-8 target csab palette
> 1.2,blue:1.99367,#fffb00:3.99521,red noValueColor grey
92387 atoms, 12533 residues, atom seq_rmsd range 0.00785 to 10.2
> ui tool show "Render by Attribute"
> key blue:1 #fffb00:2 red:3 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> color byattribute r:seq_rmsd #!1-8 target csab palette
> 1,blue:2,#fffb00:3,red noValueColor grey
92387 atoms, 12533 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #1 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #2 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #3 palette blue:yellow:red
11765 atoms, 1599 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #4 palette blue:yellow:red
11105 atoms, 1514 residues, atom seq_rmsd range 0.00785 to 5.08
> color byattribute seq_rmsd #5 palette blue:yellow:red
11817 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #6 palette blue:yellow:red
11817 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2
> color byattribute seq_rmsd #7 palette blue:yellow:red
11078 atoms, 1505 residues, atom seq_rmsd range 0.00785 to 4.34
> color byattribute seq_rmsd #8 palette blue:yellow:red
11157 atoms, 1515 residues, atom seq_rmsd range 0.00785 to 5.08
> hide #9 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> show #!1 models
> show #!4 models
> hide #!1 models
> show #!8 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> hide #!8 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> matchmaker #2-4 to #1
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 Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> matchmaker #6-8 to #5
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 Fit_class1-model-coot-11.pdb, chain A (#5) with Fit_class2-model-
coot-10.pdb, chain A (#6), sequence alignment score = 5767.6
RMSD between 1132 pruned atom pairs is 0.041 angstroms; (across all 1132
pairs: 0.041)
Matchmaker Fit_class1-model-coot-11.pdb, chain A (#5) with Fit_class4-model-
coot-3.pdb, chain A (#7), sequence alignment score = 5767.6
RMSD between 1132 pruned atom pairs is 0.041 angstroms; (across all 1132
pairs: 0.041)
Matchmaker Fit_class1-model-coot-11.pdb, chain A (#5) with Fit_class3-model-
coot-2.pdb, chain A (#8), sequence alignment score = 5767.6
RMSD between 1132 pruned atom pairs is 0.041 angstroms; (across all 1132
pairs: 0.041)
> hide #!6 models
> hide #!7 models
> hide #!8 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A
Alignment identifier is 2
> sequence header 2 rmsd show
Chains used in RMSD evaluation for alignment 2: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo104-coot-0.pdb #2/A, Fit_6596_redo106-coot-0.pdb #3/A,
Fit_6596_redo108-coot-0.pdb #4/A, Fit_class1-model-coot-11.pdb #5/A,
Fit_class2-model-coot-10.pdb #6/A, Fit_class4-model-coot-3.pdb #7/A,
Fit_class3-model-coot-2.pdb #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B #2/B #3/B #4/B #5/B #6/B #7/B #8/B
Alignment identifier is 3
> sequence header 3 rmsd show
Chains used in RMSD evaluation for alignment 3: Fit_6596_redo107-coot-0.pdb
#1/B, Fit_6596_redo104-coot-0.pdb #2/B, Fit_6596_redo106-coot-0.pdb #3/B,
Fit_6596_redo108-coot-0.pdb #4/B, Fit_class1-model-coot-11.pdb #5/B,
Fit_class2-model-coot-10.pdb #6/B, Fit_class4-model-coot-3.pdb #7/B,
Fit_class3-model-coot-2.pdb #8/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
> save "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd.cxs"
> includeMaps true
——— End of log from Thu Sep 4 12:58:57 2025 ———
opened ChimeraX session
> close #5
> close #6
> close #7
> close #8
> close #9
> matchmaker #2-4 to #1
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 Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A #3/A #4/A
Alignment identifier is 1
> sequence header rmsd show
Chains used in RMSD evaluation for alignment 1: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo104-coot-0.pdb #2/A, Fit_6596_redo106-coot-0.pdb #3/A,
Fit_6596_redo108-coot-0.pdb #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B #2/B #3/B #4/B
Alignment identifier is 2
> sequence header 2 rmsd show
Chains used in RMSD evaluation for alignment 2: Fit_6596_redo107-coot-0.pdb
#1/B, Fit_6596_redo104-coot-0.pdb #2/B, Fit_6596_redo106-coot-0.pdb #3/B,
Fit_6596_redo108-coot-0.pdb #4/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C #2/C #3/C
Alignment identifier is 3
> sequence header 3 rmsd show
Chains used in RMSD evaluation for alignment 3: Fit_6596_redo107-coot-0.pdb
#1/C, Fit_6596_redo104-coot-0.pdb #2/C, Fit_6596_redo106-coot-0.pdb #3/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
> ui tool show "Render by Attribute"
> key blue:0 #fffb00:2 red:4 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> color byattribute r:seq_rmsd #!1-4 target cabs palette
> 0,blue:1.99986,#fffb00:3.99989,red noValueColor grey
46518 atoms, 6313 residues, atom seq_rmsd range 0.000164 to 12.5
> color byattribute seq_rmsd #1 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.000164 to 12.5
> color byattribute seq_rmsd #2 palette blue:yellow:red
11824 atoms, 1600 residues, atom seq_rmsd range 0.000164 to 12.5
> color byattribute seq_rmsd #3 palette blue:yellow:red
11765 atoms, 1599 residues, atom seq_rmsd range 0.000164 to 12.5
> color byattribute seq_rmsd #4 palette blue:yellow:red
11105 atoms, 1514 residues, atom seq_rmsd range 0.000164 to 3.4
> hide #5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> save "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs" includeMaps true
> show #!4 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> hide #!4 models
> show #5 models
> save "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs" includeMaps true
——— End of log from Thu Sep 4 13:33:38 2025 ———
opened ChimeraX session
> hide #5 models
> show #!4 models
> matchmaker #4 to #1
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 Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)
> rmsd #4/B #1/B
Missing required "to" argument
> rmsd #4/B to #1/B
RMSD between 3077 atom pairs is 1.011
> ui tool show Log
> save "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs" includeMaps true
——— End of log from Thu Sep 4 14:44:21 2025 ———
opened ChimeraX session
> rmsd #8/B:145-155 to #5/B:145-155
Given atom specs don't contain any atoms
> rmsd #4/B:145-155 to #1/B:145-155
RMSD between 93 atom pairs is 2.964
> rmsd #4/B:42-74 to #1/B:42-74
RMSD between 241 atom pairs is 1.463
> rmsd #4/B:125-130 to #1/B:125-130
RMSD between 51 atom pairs is 2.027
> rmsd #4/B:173-177 to #1/B:173-177
RMSD between 35 atom pairs is 0.290
> rmsd #4/B:375-383 to #1/B:375-383
RMSD between 74 atom pairs is 3.151
> rmsd #4/B:368-375 to #1/B:368-375
RMSD between 60 atom pairs is 0.985
> save "/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs" includeMaps true
——— End of log from Thu Sep 4 14:59:35 2025 ———
opened ChimeraX session
OpenGL version: 4.1 INTEL-23.7.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2075.140.4.0.0 (iBridge: 22.16.16083.0.0,0)
OS Loader Version: 583~2210
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 13 days, 20 hours, 44 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL SE2723DS:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: 1JF2WP3
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Adapter Firmware Version: 15.75
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 2 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 2 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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