![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7758 closed defect (nonchimerax)
Crash during application exit
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 21000,
"procLaunch" : "2022-10-06 14:20:52.2157 +0100",
"procRole" : "Foreground",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"procStartAbsTime" : 472541712785,
"coalitionID" : 3524,
"osVersion" : {
"train" : "macOS 12.6",
"build" : "21G115",
"releaseType" : "User"
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"captureTime" : "2022-10-06 14:53:17.3103 +0100",
"incident" : "65C44702-4080-4DE8-B6D9-97E94769247F",
"bug_type" : "309",
"pid" : 27955,
"procExitAbsTime" : 519223372959,
"translated" : true,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1B3929A5-06BD-2925-9E37-3A27C05B98A2",
"sip" : "enabled",
"vmRegionInfo" : "0x100000030 is not in any region. Bytes before following region: 12095440\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100b89000-100b8a000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000100000030","rawCodes":[1,4294967344],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000100000030"},
"ktriageinfo" : "VM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\n",
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"uuid" : "1f0f0114-cfb6-304b-8183-8ef52c21f8b4",
"path" : "\/usr\/libexec\/rosetta\/runtime",
"name" : "runtime"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5168123904,
"size" : 165068800,
"uuid" : "c9795830-14cd-3b40-983d-a3143cd9cbd9",
"path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703199690752,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5246976,
"uuid" : "bddb824d-15df-3210-88e8-6aac5c154403",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1866"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703243399168,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15269888,
"uuid" : "06015263-62ac-3b08-a298-dc835c18452a",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2113.60.148"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4544606208,
"size" : 63488000,
"uuid" : "10431d8f-5e3b-3bbc-abd5-81f6a73a5269",
"path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
}
],
"sharedCache" : {
"base" : 140703196119040,
"size" : 19331678208,
"uuid" : "3765e290-e8ae-3af7-92bf-da62dfb8ac4f"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=2.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 5056K 4 \nCG image 444K 41 \nColorSync 228K 27 \nCoreAnimation 4020K 68 \nCoreGraphics 12K 2 \nCoreUI image data 5080K 42 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 867.1M 536 \nMALLOC guard page 192K 8 \nMALLOC_MEDIUM (reserved) 776.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1516K 376 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 620K 62 \nRosetta Thread Context 620K 62 \nSTACK GUARD 44K 11 \nStack 105.7M 31 \nStack Guard 56.1M 20 \nVM_ALLOCATE 139.9M 193 \nVM_ALLOCATE (reserved) 128.1M 11 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 44.5M 674 \n__DATA_CONST 31.3M 346 \n__DATA_DIRTY 1665K 219 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 733.8M 146 \n__OBJC_RO 82.8M 1 \n__OBJC_RW 3200K 2 \n__TEXT 797.9M 673 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 5.3G 1153 \nshared memory 812K 16 \nunshared pmap 10.2M 8 \n=========== ======= ======= \nTOTAL 9.5G 4762 \nTOTAL, minus reserved VM space 8.2G 4762 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60f8ddccefea4203d95cbeef",
"factorPackIds" : {
},
"deploymentId" : 240000020
},
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
}
],
"experiments" : [
{
"treatmentId" : "5b729754-3882-4560-826f-9c0bc27d77c6",
"experimentId" : "6192fb082171a2330e561df0",
"deploymentId" : 400000035
}
]
}
}
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/palcon/Desktop/220909.cxs
Log from Fri Sep 9 17:19:50 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/palcon/Desktop/220909.cxs
Log from Fri Sep 9 15:20:29 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/palcon/Desktop/220909.cxs
Log from Fri Sep 9 15:10:40 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/palcon/Desktop/30T_29ds_30T.pdb
Chain information for 30T_29ds_30T.pdb #1
---
Chain | Description
? | No description available
> open /Users/palcon/Desktop/30T_overhang.pdb
Chain information for 30T_overhang.pdb #2
---
Chain | Description
? | No description available
> set bgColor white
> hide #2 models
> show #1 cartoons
> show #1 surfaces
> hide #!1 cartoons
> select #1/?:129@C2'
1 atom, 1 residue, 1 model selected
> select up
32 atoms, 34 bonds, 1 residue, 2 models selected
> select up
4302 atoms, 4667 bonds, 135 residues, 2 models selected
> color (#!1 & sel) orange
> select clear
> show #!1 cartoons
> hide #!1 surfaces
> select #1/?:62
32 atoms, 34 bonds, 1 residue, 1 model selected
> select up
4302 atoms, 4667 bonds, 135 residues, 2 models selected
> select down
32 atoms, 34 bonds, 1 residue, 2 models selected
> select add #1/?:63
64 atoms, 67 bonds, 2 residues, 2 models selected
> select add #1/?:64
94 atoms, 98 bonds, 3 residues, 2 models selected
> select add #1/?:65
126 atoms, 131 bonds, 4 residues, 2 models selected
> select add #1/?:60
224 atoms, 164 bonds, 7 residues, 2 models selected
> select add #1/?:59
256 atoms, 197 bonds, 8 residues, 2 models selected
> select add #1/?:58
288 atoms, 231 bonds, 9 residues, 2 models selected
> select add #1/?:57
321 atoms, 266 bonds, 10 residues, 2 models selected
> select add #1/?:56
354 atoms, 301 bonds, 11 residues, 2 models selected
> select add #1/?:55
386 atoms, 335 bonds, 12 residues, 2 models selected
> select add #1/?:54
416 atoms, 366 bonds, 13 residues, 2 models selected
> select add #1/?:53
448 atoms, 399 bonds, 14 residues, 2 models selected
> select add #1/?:52
478 atoms, 430 bonds, 15 residues, 2 models selected
> select add #1/?:51
511 atoms, 465 bonds, 16 residues, 2 models selected
> select add #1/?:49
573 atoms, 496 bonds, 18 residues, 2 models selected
> select add #1/?:50
605 atoms, 529 bonds, 19 residues, 2 models selected
> select add #1/?:48
638 atoms, 564 bonds, 20 residues, 2 models selected
> select add #1/?:46
668 atoms, 595 bonds, 21 residues, 2 models selected
> select add #1/?:44
733 atoms, 630 bonds, 23 residues, 2 models selected
> select add #1/?:43
765 atoms, 664 bonds, 24 residues, 2 models selected
> select add #1/?:42
797 atoms, 697 bonds, 25 residues, 2 models selected
> select add #1/?:41
827 atoms, 728 bonds, 26 residues, 2 models selected
> select add #1/?:40
859 atoms, 761 bonds, 27 residues, 2 models selected
> select add #1/?:39
889 atoms, 792 bonds, 28 residues, 2 models selected
> select add #1/?:38
921 atoms, 825 bonds, 29 residues, 2 models selected
> select add #1/?:37
954 atoms, 860 bonds, 30 residues, 2 models selected
> select add #1/?:36
986 atoms, 893 bonds, 31 residues, 2 models selected
> select add #1/?:35
1018 atoms, 927 bonds, 32 residues, 2 models selected
> select add #1/?:34
1051 atoms, 962 bonds, 33 residues, 2 models selected
> select add #1/?:33
1081 atoms, 993 bonds, 34 residues, 2 models selected
> select add #1/?:32
1113 atoms, 1026 bonds, 35 residues, 2 models selected
> select add #1/?:31
1145 atoms, 1060 bonds, 36 residues, 2 models selected
> color (#!1 & sel) yellow
> select clear
> show #!1 surfaces
> lighting soft
> lighting flat
> lighting simple
> lighting soft
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> graphics silhouettes false
> lighting soft
> show #2 models
> hide #2 models
> open /Users/palcon/Downloads/91881959ABD.pdb
Chain information for 91881959ABD.pdb #3
---
Chain | Description
? | No description available
> close #3
> open /Users/palcon/Downloads/16058187ABD.pdb
Chain information for 16058187ABD.pdb #3
---
Chain | Description
? | No description available
> hide #!1 models
> select #3/?:466
32 atoms, 34 bonds, 1 residue, 1 model selected
> select add #3/?:467
64 atoms, 67 bonds, 2 residues, 1 model selected
> select add #3/?:468
94 atoms, 98 bonds, 3 residues, 1 model selected
> select add #3/?:469
127 atoms, 133 bonds, 4 residues, 1 model selected
> select add #3/?:470
159 atoms, 167 bonds, 5 residues, 1 model selected
> select add #3/?:471
191 atoms, 200 bonds, 6 residues, 1 model selected
> select add #3/?:473
255 atoms, 233 bonds, 8 residues, 1 model selected
> select add #3/?:474
287 atoms, 267 bonds, 9 residues, 1 model selected
> select add #3/?:475
317 atoms, 298 bonds, 10 residues, 1 model selected
> select add #3/?:477
350 atoms, 333 bonds, 11 residues, 1 model selected
> select add #3/?:476
382 atoms, 367 bonds, 12 residues, 1 model selected
> select add #3/?:478
414 atoms, 401 bonds, 13 residues, 1 model selected
> select add #3/?:479
446 atoms, 434 bonds, 14 residues, 1 model selected
> select add #3/?:480
476 atoms, 465 bonds, 15 residues, 1 model selected
> select add #3/?:481
508 atoms, 499 bonds, 16 residues, 1 model selected
> select add #3/?:482
540 atoms, 533 bonds, 17 residues, 1 model selected
> select add #3/?:483
572 atoms, 566 bonds, 18 residues, 1 model selected
> select add #3/?:484
602 atoms, 597 bonds, 19 residues, 1 model selected
> select add #3/?:485
632 atoms, 628 bonds, 20 residues, 1 model selected
> select add #3/?:487
665 atoms, 663 bonds, 21 residues, 1 model selected
> select add #3/?:486
697 atoms, 696 bonds, 22 residues, 1 model selected
> select add #3/?:488
729 atoms, 730 bonds, 23 residues, 1 model selected
> select add #3/?:489
762 atoms, 765 bonds, 24 residues, 1 model selected
> select add #3/?:490
792 atoms, 796 bonds, 25 residues, 1 model selected
> select add #3/?:491
824 atoms, 830 bonds, 26 residues, 1 model selected
> select add #3/?:492
857 atoms, 865 bonds, 27 residues, 1 model selected
> select add #3/?:493
887 atoms, 896 bonds, 28 residues, 1 model selected
> select add #3/?:494
919 atoms, 929 bonds, 29 residues, 1 model selected
> select add #3/?:495
952 atoms, 964 bonds, 30 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #3/?:165
32 atoms, 33 bonds, 1 residue, 1 model selected
> select up
19121 atoms, 20618 bonds, 600 residues, 1 model selected
> show sel surfaces
> hide sel cartoons
> show sel surfaces
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
16058187ABD.pdb #3/? DT 316 OP1
16058187ABD.pdb #3/? DT 316 OP2
16058187ABD.pdb #3/? DT 316 P
Treating 5' terminal nucleic acids with phosphates as non-standard
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue DT (net charge -2) with am1-bcc method
Running ANTECHAMBER command:
/private/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/AppTranslocation/C5AE9BC0-0479-4C32-8D2C-AA6CD24C9531/d/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/tmp859wzru7/ante.in.mol2 -fi
mol2 -o
/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/tmp859wzru7/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(DT) ``
(DT) `Welcome to antechamber 20.0: molecular input file processor.`
(DT) ``
(DT) `Info: Finished reading file
(/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/tmp859wzru7/ante.in.mol2);
atoms read (39), bonds read (40).`
(DT) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(DT) `Running:
/private/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/AppTranslocation/C5AE9BC0-0479-4C32-8D2C-AA6CD24C9531/d/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(DT) ``
(DT) ``
(DT) `Running:
/private/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/AppTranslocation/C5AE9BC0-0479-4C32-8D2C-AA6CD24C9531/d/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(DT) `Info: Total number of electrons: 200; net charge: -3`
(DT) ``
(DT) `Running:
/private/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/AppTranslocation/C5AE9BC0-0479-4C32-8D2C-AA6CD24C9531/d/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(DT)
`/private/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/AppTranslocation/C5AE9BC0-0479-4C32-8D2C-AA6CD24C9531/d/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(DT) `Cannot properly run
"/private/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/AppTranslocation/C5AE9BC0-0479-4C32-8D2C-AA6CD24C9531/d/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out".`
Failure running ANTECHAMBER for residue DT Check reply log for details
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> show sel atoms
> select clear
> select #3/?:496
32 atoms, 33 bonds, 1 residue, 1 model selected
> select add #3/?:497
62 atoms, 64 bonds, 2 residues, 2 models selected
> select add #3/?:498
94 atoms, 97 bonds, 3 residues, 2 models selected
> select add #3/?:499
126 atoms, 131 bonds, 4 residues, 2 models selected
> select add #3/?:500
159 atoms, 166 bonds, 5 residues, 2 models selected
> select add #3/?:501
191 atoms, 200 bonds, 6 residues, 2 models selected
> select add #3/?:502
224 atoms, 235 bonds, 7 residues, 2 models selected
> select add #3/?:505
288 atoms, 269 bonds, 9 residues, 2 models selected
> select add #3/?:504
318 atoms, 300 bonds, 10 residues, 2 models selected
> select add #3/?:506
350 atoms, 333 bonds, 11 residues, 2 models selected
> select add #3/?:507
380 atoms, 364 bonds, 12 residues, 2 models selected
> select add #3/?:510
477 atoms, 397 bonds, 15 residues, 2 models selected
> select add #3/?:511
509 atoms, 431 bonds, 16 residues, 2 models selected
> select add #3/?:513
541 atoms, 465 bonds, 17 residues, 2 models selected
> select subtract #3/?:513
509 atoms, 431 bonds, 16 residues, 2 models selected
> select add #3/?:512
541 atoms, 465 bonds, 17 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #3/?:465
30 atoms, 31 bonds, 1 residue, 1 model selected
> select add #3/?:464
62 atoms, 65 bonds, 2 residues, 2 models selected
> select add #3/?:463
95 atoms, 100 bonds, 3 residues, 2 models selected
> select add #3/?:461
160 atoms, 135 bonds, 5 residues, 2 models selected
> select add #3/?:460
192 atoms, 169 bonds, 6 residues, 2 models selected
> select add #3/?:459
224 atoms, 202 bonds, 7 residues, 2 models selected
> select add #3/?:458
254 atoms, 233 bonds, 8 residues, 2 models selected
> select add #3/?:457
286 atoms, 266 bonds, 9 residues, 2 models selected
> select add #3/?:456
319 atoms, 301 bonds, 10 residues, 2 models selected
> select add #3/?:455
351 atoms, 334 bonds, 11 residues, 2 models selected
> select add #3/?:454
381 atoms, 365 bonds, 12 residues, 2 models selected
> select add #3/?:453
414 atoms, 400 bonds, 13 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #3/?
Alignment identifier is 3/
> select #3/*:513
32 atoms, 34 bonds, 1 residue, 1 model selected
> select #3/*:513-572
1920 atoms, 2099 bonds, 60 residues, 1 model selected
> select #3/*:1
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #3/*:1-450
14327 atoms, 15389 bonds, 450 residues, 1 model selected
> select #3/*:630
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #3/*:1-630
18104 atoms, 19519 bonds, 1 pseudobond, 568 residues, 2 models selected
> select clear
> select #3/*:1-2
62 atoms, 65 bonds, 2 residues, 1 model selected
> select #3/*:1-450
14327 atoms, 15389 bonds, 450 residues, 1 model selected
> select clear
> select #3/*:1-2
62 atoms, 65 bonds, 2 residues, 1 model selected
> select #3/*:1-315
10044 atoms, 10768 bonds, 315 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold
[Repeated 1 time(s)]
> select clear
> select #3/*:316-317
62 atoms, 65 bonds, 2 residues, 1 model selected
> select #3/*:316-630
8060 atoms, 8751 bonds, 1 pseudobond, 253 residues, 2 models selected
> color sel yellow
> show sel surfaces
Drag select of 16058187ABD.pdb_ SES surface, 56091 of 1862060 triangles, 38
residues, 72 shapes
> select up
18104 atoms, 19519 bonds, 568 residues, 2 models selected
> select up
18104 atoms, 19519 bonds, 1 pseudobond, 568 residues, 3 models selected
> select up
18104 atoms, 19519 bonds, 1 pseudobond, 568 residues, 3 models selected
> show sel surfaces
> hide sel cartoons
> select clear
> lighting soft
> lighting full
> lighting soft
> lighting full
> hide #!3 surfaces
> show #!3 cartoons
> nucleotides #!3 tube/slab shape box
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> select #3/*:316
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #3/*:316-630
8060 atoms, 8751 bonds, 1 pseudobond, 253 residues, 2 models selected
> color sel gold
> select #3/*:315
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #3/*:1-315
10044 atoms, 10768 bonds, 315 residues, 1 model selected
> color sel orange
> select clear
> select #3/*:315
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #3/*:1-315
10044 atoms, 10768 bonds, 315 residues, 1 model selected
> color sel khaki
> select clear
> show #!3 surfaces
> hide #!3 cartoons
> lighting soft
> lighting full
> ~hbonds
> interfaces #!3 & ~solvent
0 buried areas:
> color #!3 bypolymer
> undo
> nucleotides #!3 ladder
> hide #!3 surfaces
> show #!3 cartoons
> nucleotides #!3 fill
> style nucleic & #!3 stick
Changed 18104 atom styles
> hide #!3 atoms
[Repeated 1 time(s)]
> show #!3 atoms
> hide #!3 atoms
> nucleotides #!3 fill
> style nucleic & #!3 stick
Changed 18104 atom styles
> nucleotides #!3 fill
> style nucleic & #!3 stick
Changed 18104 atom styles
> nucleotides #!3 ladder
> cartoon style width 4 thickness 1
> cartoon style width 3 thickness 1.5
> cartoon style width 5 thickness 1.5
> cartoon style width 5 thickness 1
> show #!3 atoms
> cartoon style width 5 thickness 1
> cartoon style width 4 thickness 1
> cartoon style width 4 thickness 0.5
> select #3/*:315
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #3/*:1-315
10044 atoms, 10768 bonds, 315 residues, 1 model selected
> ui tool show "Color Actions"
> color sel wheat
> color sel navajo white
> select clear
> select #3/*:209-315
3406 atoms, 3672 bonds, 107 residues, 1 model selected
> select #3/*:1-315
10044 atoms, 10768 bonds, 315 residues, 1 model selected
> color sel gold
> select clear
> select #3/*:1
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #3/*:1-312
9947 atoms, 10663 bonds, 312 residues, 1 model selected
> select #3/*:315
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #3/*:1-315
10044 atoms, 10768 bonds, 315 residues, 1 model selected
> color sel sandy brown
> color sel light salmon
> select clear
> select #3/*:161-315
4933 atoms, 5317 bonds, 155 residues, 1 model selected
> select #3/*:1-315
10044 atoms, 10768 bonds, 315 residues, 1 model selected
> color sel orange
> select clear
> hide #!3 atoms
> open /Users/palcon/6vad.pdb
6vad.pdb title:
Fanconi anemia id complex [more info...]
Chain information for 6vad.pdb #4
---
Chain | Description | UniProt
A | fanconi anemia, complementation group I | B7ZMF2_HUMAN
B | protein FACD2 | FACD2_HUMAN
> select add #3
18104 atoms, 19519 bonds, 1 pseudobond, 568 residues, 2 models selected
> select subtract #3
1 model selected
> hide #!3 models
> select add #3
18104 atoms, 19519 bonds, 1 pseudobond, 568 residues, 2 models selected
> select subtract #3
1 model selected
> select #4/B:463
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
321 atoms, 326 bonds, 19 residues, 1 model selected
> select up
4015 atoms, 4046 bonds, 251 residues, 1 model selected
> select up
4120 atoms, 4150 bonds, 258 residues, 1 model selected
> select up
8607 atoms, 8677 bonds, 537 residues, 1 model selected
> select up
8643 atoms, 8712 bonds, 539 residues, 1 model selected
> select up
9875 atoms, 9954 bonds, 614 residues, 1 model selected
> select up
18734 atoms, 18908 bonds, 1153 residues, 1 model selected
> select up
37613 atoms, 37931 bonds, 2321 residues, 1 model selected
> select down
18734 atoms, 18908 bonds, 1153 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel light sea green
> color sel dark turquoise
> color sel steel blue
> color sel cornflower blue
> select clear
> select #4/B:963
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
330 atoms, 332 bonds, 20 residues, 1 model selected
> select up
356 atoms, 358 bonds, 22 residues, 1 model selected
> select up
492 atoms, 494 bonds, 30 residues, 1 model selected
> select up
878 atoms, 886 bonds, 53 residues, 1 model selected
> select up
18734 atoms, 18908 bonds, 1153 residues, 1 model selected
> select up
37613 atoms, 37931 bonds, 2321 residues, 1 model selected
> select down
18734 atoms, 18908 bonds, 1153 residues, 1 model selected
> color sel sky blue
> color sel powder blue
> color sel light blue
> color sel pale turquoise
> color sel light steel blue
> select clear
> select #4/A:240
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
394 atoms, 396 bonds, 25 residues, 1 model selected
> select up
1588 atoms, 1600 bonds, 99 residues, 1 model selected
> select up
1689 atoms, 1701 bonds, 105 residues, 1 model selected
> select up
3902 atoms, 3925 bonds, 245 residues, 1 model selected
> select up
18879 atoms, 19023 bonds, 1168 residues, 1 model selected
> select up
37613 atoms, 37931 bonds, 2321 residues, 1 model selected
> select down
18879 atoms, 19023 bonds, 1168 residues, 1 model selected
> color sel misty rose
> color sel pink
> color sel light pink
[Repeated 1 time(s)]
> select clear
> cartoon style width 4 thickness 0.5
> cartoon style width 4 thickness 1
> cartoon style width 3 thickness 1
> lighting soft
> cartoon style width 5 thickness 1
> cartoon style width 4 thickness 1
> show #!3 models
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> ui mousemode right "translate selected models"
Drag select of 306 residues, 3 pseudobonds
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.57621,0.53103,-0.62127,75.31,0.21709,0.6334,0.74275,-85.916,0.78794,-0.56286,0.24969,72.463
Drag select of 611 residues, 3 pseudobonds
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.57621,0.53103,-0.62127,-75.512,0.21709,0.6334,0.74275,-202.15,0.78794,-0.56286,0.24969,135.23
> view matrix models
> #4,0.87798,-0.14383,-0.45657,-48.57,0.05193,0.97678,-0.20785,-90.829,0.47587,0.15878,0.86507,-7.7479
> view matrix models
> #4,0.7877,0.10953,-0.60625,-49.458,0.015793,0.98015,0.19761,-143.86,0.61586,-0.16523,0.77033,30.621
> view matrix models
> #4,0.73508,0.28865,-0.61347,-65.714,-0.016571,0.91222,0.40936,-159.99,0.67778,-0.29074,0.67534,52.687
> view matrix models
> #4,0.18475,0.34588,-0.91991,48.337,-0.43716,0.86725,0.23828,-69.542,0.8802,0.35812,0.31143,-14.09
> view matrix models
> #4,0.42227,-0.45645,-0.78316,106.04,-0.20567,0.79319,-0.5732,23.242,0.88283,0.40312,0.24106,-10.672
> view matrix models
> #4,0.42227,-0.45645,-0.78316,117.07,-0.20567,0.79319,-0.5732,31.329,0.88283,0.40312,0.24106,-12.115
> view matrix models
> #4,0.44251,-0.33887,-0.83028,104.63,-0.3772,0.76964,-0.51515,50.746,0.81358,0.54114,0.21275,-17.316
> view matrix models
> #4,0.44251,-0.33887,-0.83028,114.11,-0.3772,0.76964,-0.51515,41.285,0.81358,0.54114,0.21275,-16.149
> view matrix models
> #4,0.19957,-0.60072,-0.77415,176.93,-0.4871,0.62469,-0.61032,90.527,0.85024,0.49889,-0.16794,38.659
> view matrix models
> #4,0.13962,-0.64055,-0.75511,188.27,-0.40213,0.66019,-0.63438,76.946,0.90487,0.39223,-0.16541,45.274
> view matrix models
> #4,0.13962,-0.64055,-0.75511,198.74,-0.40213,0.66019,-0.63438,69.104,0.90487,0.39223,-0.16541,44.639
> view matrix models
> #4,0.11706,-0.65133,-0.74971,202.68,-0.42301,0.65029,-0.63101,72.965,0.89853,0.391,-0.1994,50.55
> view matrix models
> #4,0.11706,-0.65133,-0.74971,207.21,-0.42301,0.65029,-0.63101,75.564,0.89853,0.391,-0.1994,51.057
> view matrix models
> #4,0.18868,-0.61474,-0.76583,194.24,-0.33916,0.69106,-0.63828,59.021,0.92161,0.38017,-0.078107,32.005
> ui tool show "Side View"
> select clear
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.15719,-0.62854,-0.76173,200.05,-0.33085,0.69323,-0.64029,57.825,0.9305,0.35267,-0.098984,37.515
> view matrix models
> #4,0.15719,-0.62854,-0.76173,201.47,-0.33085,0.69323,-0.64029,53.888,0.9305,0.35267,-0.098984,37.535
> view matrix models
> #4,0.15719,-0.62854,-0.76173,199.54,-0.33085,0.69323,-0.64029,52.688,0.9305,0.35267,-0.098984,39.349
> view matrix models
> #4,0.20568,-0.64645,-0.73471,191.27,-0.30865,0.66959,-0.67556,57.816,0.92867,0.36572,-0.061808,32.513
> view matrix models
> #4,0.22322,-0.59839,-0.76948,187.07,-0.25462,0.7262,-0.6386,37.033,0.94093,0.33847,0.0097396,24.354
> view matrix models
> #4,0.11707,-0.64045,-0.75902,206.52,-0.29338,0.70787,-0.64254,45.648,0.9488,0.29791,-0.10502,45.178
> select clear
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.12564,-0.66907,-0.7325,205.48,-0.28222,0.68374,-0.67294,51.724,0.95109,0.29128,-0.10293,45.471
> view matrix models
> #4,0.095677,-0.56234,-0.82135,207.63,-0.32308,0.76292,-0.55997,30.509,0.94152,0.31893,-0.10869,43.826
> view matrix models
> #4,0.22268,-0.51378,-0.82852,183.85,-0.22128,0.80104,-0.55621,10.209,0.94945,0.30719,0.064684,19.647
> view matrix models
> #4,0.22268,-0.51378,-0.82852,179,-0.22128,0.80104,-0.55621,6.2715,0.94945,0.30719,0.064684,18.487
> view matrix models
> #4,0.22268,-0.51378,-0.82852,179.22,-0.22128,0.80104,-0.55621,9.5465,0.94945,0.30719,0.064684,18.462
> view matrix models
> #4,0.051693,-0.5639,-0.82422,209.88,-0.32784,0.77001,-0.54737,27.751,0.94332,0.29851,-0.14506,50.389
> select clear
> open /Users/palcon/Downloads/Chimera/PDB/6VAE.pdb
6VAE.pdb title:
Mono-ubiquitinated fanconi anemia id complex bound to icl DNA [more info...]
Chain information for 6VAE.pdb #5
---
Chain | Description | UniProt
A | fanconi anemia, complementation group I | B7ZMF2_HUMAN
B | protein FACD2 | FACD2_HUMAN
C D | ubiquitin | UBC_HUMAN
S | DNA (29-mer) |
T | DNA (29-mer) |
> select add #5
42474 atoms, 42951 bonds, 19 pseudobonds, 2563 residues, 2 models selected
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> cartoon style width 4 thickness 1
> select clear
> select #5/S:19
33 atoms, 35 bonds, 1 residue, 1 model selected
> select up
923 atoms, 995 bonds, 29 residues, 1 model selected
> select up
42474 atoms, 42951 bonds, 2563 residues, 1 model selected
> select down
923 atoms, 995 bonds, 29 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5/T:32
32 atoms, 34 bonds, 1 residue, 1 model selected
> select up
917 atoms, 988 bonds, 29 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #5/D:14
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
81 atoms, 80 bonds, 5 residues, 1 model selected
> select up
1231 atoms, 1237 bonds, 76 residues, 1 model selected
> hide sel cartoons
> select clear
> select #5/C:58
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
77 atoms, 77 bonds, 5 residues, 1 model selected
> select up
1231 atoms, 1237 bonds, 76 residues, 1 model selected
> hide sel cartoons
> select clear
> select #5/B:1023
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
483 atoms, 489 bonds, 30 residues, 1 model selected
> select up
609 atoms, 617 bonds, 37 residues, 1 model selected
> select up
18808 atoms, 18983 bonds, 1155 residues, 1 model selected
> select up
40634 atoms, 40968 bonds, 2505 residues, 1 model selected
> select down
18808 atoms, 18983 bonds, 1155 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light blue
> select clear
> select #5/B:810
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
500 atoms, 502 bonds, 29 residues, 1 model selected
> select up
1892 atoms, 1912 bonds, 116 residues, 1 model selected
> select up
1911 atoms, 1930 bonds, 117 residues, 1 model selected
> select up
2414 atoms, 2440 bonds, 147 residues, 1 model selected
> select up
2433 atoms, 2458 bonds, 148 residues, 1 model selected
> select up
2770 atoms, 2798 bonds, 169 residues, 1 model selected
> select up
18808 atoms, 18983 bonds, 1155 residues, 1 model selected
> select up
40634 atoms, 40968 bonds, 2505 residues, 1 model selected
> select down
18808 atoms, 18983 bonds, 1155 residues, 1 model selected
> color sel sky blue
> color sel light steel blue
[Repeated 2 time(s)]
> select clear
> select #5/A:1054
18 atoms, 18 bonds, 1 residue, 1 model selected
> select up
270 atoms, 272 bonds, 17 residues, 1 model selected
> select up
2620 atoms, 2639 bonds, 162 residues, 1 model selected
> select up
2639 atoms, 2657 bonds, 163 residues, 1 model selected
> select up
6455 atoms, 6502 bonds, 401 residues, 1 model selected
> select up
6488 atoms, 6535 bonds, 403 residues, 1 model selected
> select up
8239 atoms, 8303 bonds, 511 residues, 1 model selected
> select up
8296 atoms, 8359 bonds, 514 residues, 1 model selected
> select up
10592 atoms, 10673 bonds, 654 residues, 1 model selected
> select up
10692 atoms, 10773 bonds, 660 residues, 1 model selected
> select up
12876 atoms, 12977 bonds, 794 residues, 1 model selected
> select up
19364 atoms, 19509 bonds, 1198 residues, 1 model selected
> select up
40634 atoms, 40968 bonds, 2505 residues, 1 model selected
> select down
19364 atoms, 19509 bonds, 1198 residues, 1 model selected
> color sel light pink
> select clear
> select add #5
40634 atoms, 40968 bonds, 19 pseudobonds, 2505 residues, 2 models selected
> view matrix models #5,1,0,0,-108.24,0,1,0,-150.04,0,0,1,211
> view matrix models
> #5,0.97897,-0.0043194,-0.20396,-77.928,-0.045164,0.97038,-0.23733,-108.65,0.19894,0.24155,0.94978,158.04
> view matrix models
> #5,0.99573,0.0042728,-0.092249,-96.08,-0.014328,0.99398,-0.10861,-132.97,0.09123,0.10947,0.98979,185.2
> view matrix models
> #5,0.88898,-0.086369,-0.44974,-22.263,-0.17487,0.84362,-0.50767,-38.324,0.42325,0.52995,0.73485,117.02
> view matrix models
> #5,0.84799,-0.12855,-0.51418,-2.5208,-0.22912,0.78589,-0.57435,-14.39,0.47792,0.60485,0.63698,112.39
> view matrix models
> #5,0.92811,-0.04802,-0.3692,-43.359,-0.12114,0.89874,-0.42142,-64.416,0.35205,0.43585,0.82831,127.06
> view matrix models
> #5,0.92811,-0.04802,-0.3692,-55.108,-0.12114,0.89874,-0.42142,-66.012,0.35205,0.43585,0.82831,165.08
> view matrix models
> #5,0.5072,0.62438,-0.59405,-59.222,0.74723,-0.66204,-0.057858,-20.868,-0.42941,-0.41454,-0.80235,600.71
> view matrix models
> #5,0.75885,-0.0079621,-0.65122,-0.41009,0.38911,-0.7963,0.46315,-22.859,-0.52225,-0.60485,-0.60117,612.48
> view matrix models
> #5,0.76688,-0.6085,0.20403,-33.113,-0.63496,-0.67311,0.37914,110.38,-0.093373,-0.4203,-0.90257,569.15
> view matrix models
> #5,0.86185,-0.42224,-0.28093,-7.2276,-0.19533,-0.78756,0.58447,39.187,-0.46804,-0.44885,-0.76123,605.16
> view matrix models
> #5,0.24553,-0.62499,0.74101,-30.986,0.14681,-0.73162,-0.66572,150.01,0.95821,0.27224,-0.08788,225.75
> view matrix models
> #5,0.54076,-0.23901,0.80651,-131.75,0.015185,-0.95585,-0.29345,149.07,0.84104,0.17093,-0.51326,311.37
> view matrix models
> #5,0.25969,-0.17326,0.95002,-121.45,-0.19929,-0.97221,-0.12283,157.87,0.9449,-0.15744,-0.287,311.81
> view matrix models
> #5,0.6109,-0.60386,0.51201,-53.183,-0.78396,-0.55164,0.28477,126.61,0.11048,-0.57536,-0.8104,550.31
> view matrix models
> #5,-0.072647,-0.58951,0.80449,-1.0165,-0.73953,-0.50937,-0.44004,210.39,0.6692,-0.62691,-0.39896,427.33
> view matrix models
> #5,-0.51259,-0.62209,0.59182,91.037,-0.48058,-0.36331,-0.79815,202.76,0.71154,-0.69354,-0.11274,392.87
> view matrix models
> #5,-0.78248,-0.6226,0.0098847,204.37,-0.022222,0.012056,-0.99968,116.51,0.62229,-0.78244,-0.023269,405.18
> view matrix models
> #5,-0.90908,-0.40424,0.10081,180.06,-0.18337,0.17094,-0.96807,112.73,0.3741,-0.89854,-0.22952,481.67
> view matrix models
> #5,-0.90908,-0.40424,0.10081,191.4,-0.18337,0.17094,-0.96807,123.24,0.3741,-0.89854,-0.22952,485.93
> view matrix models
> #5,-0.91729,-0.38322,0.10832,188.69,-0.1595,0.10431,-0.98167,130.79,0.36489,-0.91775,-0.1568,480.19
> view matrix models
> #5,-0.91729,-0.38322,0.10832,184.59,-0.1595,0.10431,-0.98167,141.58,0.36489,-0.91775,-0.1568,481.03
> hide #!4 models
> view matrix models
> #5,-0.91729,-0.38322,0.10832,187.15,-0.1595,0.10431,-0.98167,145.61,0.36489,-0.91775,-0.1568,480.56
> view matrix models
> #5,-0.95979,-0.21713,0.17792,161.31,-0.22729,0.22909,-0.9465,133.32,0.16476,-0.94888,-0.26923,526.71
> show #!4 models
> select clear
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.051693,-0.5639,-0.82422,206.51,-0.32784,0.77001,-0.54737,26.763,0.94332,0.29851,-0.14506,-61.211
> select clear
> select add #5
40634 atoms, 40968 bonds, 19 pseudobonds, 2505 residues, 2 models selected
> view matrix models
> #5,-0.95979,-0.21713,0.17792,157.47,-0.22729,0.22909,-0.9465,137.34,0.16476,-0.94888,-0.26923,524.99
> view matrix models
> #5,-0.96153,-0.21415,0.17207,158.08,-0.22121,0.23217,-0.94719,136.19,0.16289,-0.94881,-0.27061,525.42
> view matrix models
> #5,-0.96333,-0.2172,0.15757,160.64,-0.20731,0.22957,-0.95096,135.15,0.17037,-0.94875,-0.26618,523.81
> view matrix models
> #5,-0.94297,-0.23466,0.23609,149.89,-0.28603,0.20844,-0.93528,146.61,0.17026,-0.94947,-0.26367,523.59
> view matrix models
> #5,-0.93947,-0.25247,0.23165,152.41,-0.29012,0.22641,-0.92982,144.02,0.18231,-0.94074,-0.28595,523.72
> select clear
> scene one
Unknown command: scene one
> scene save one
Unknown command: scene save one
> save scene one
Cannot determine format for 'scene'
> scene one save
Unknown command: scene one save
> savepos one
Unknown command: savepos one
> ~savepos one
Unknown command: ~savepos one
> savepos one
Unknown command: savepos one
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> toolshed show
> save position one
Cannot determine format for 'position'
> save pos one
Cannot determine format for 'pos'
> savepos one
Unknown command: savepos one
> save positions 5 one
Cannot determine format for 'positions'
> save position 5 one
Cannot determine format for 'position'
> savepos #5 one
Unknown command: savepos #5 one
> view name pos1
> select add #3
18104 atoms, 19519 bonds, 1 pseudobond, 568 residues, 2 models selected
> select subtract #3
1 model selected
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.051693,-0.5639,-0.82422,206.8,-0.32784,0.77001,-0.54737,26.154,0.94332,0.29851,-0.14506,69.854
> view matrix models
> #4,0.051693,-0.5639,-0.82422,206.39,-0.32784,0.77001,-0.54737,25.835,0.94332,0.29851,-0.14506,70.894
> view name pos2
> view pos1
> view list
Named views: pos1, pos2
> select clear
> fly pos1 10 pos2 10 pos1
> fly pos1 20 pos2 20 pos1
> wait
wait requires a frame count argument unless motion is in progress
> fly pos1 20 pos2 20 pos1
> wait
[Repeated 1 time(s)]
wait requires a frame count argument unless motion is in progress
> fly pos1 pos2 pos1
> wait
[Repeated 1 time(s)]
wait requires a frame count argument unless motion is in progress
> fly pos1 2 pos2 2 pos1
> wait
[Repeated 1 time(s)]
wait requires a frame count argument unless motion is in progress
> fly pos1 4 pos2 4 pos1
> wait
[Repeated 1 time(s)]
wait requires a frame count argument unless motion is in progress
> fly pos1 1 pos2 1 pos1
> wait
[Repeated 1 time(s)]
wait requires a frame count argument unless motion is in progress
> fly pos1 1 pos2 1 pos1
> wait
[Repeated 1 time(s)]
wait requires a frame count argument unless motion is in progress
> fly pos1 100 pos2 1 pos1
> wait
[Repeated 1 time(s)]
wait requires a frame count argument unless motion is in progress
> fly pos1 0 pos2 1 pos1
> wait
> fly pos1 1 pos2 1 pos1
> wait
> fly pos1 1 pos2 1 pos1
[Repeated 1 time(s)]
> move pos1 1 pos2 1 pos1
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> move pos1 pos2 1 pos1
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> fly pos1 pos2 1 pos1
> fly 2 pos1 pos2 pos1
> fly 5 pos1 pos2 pos1
[Repeated 1 time(s)]
> movie encode 220909_1.mp4 quality medium
No frames have been recorded
> movie record
> fly 5 pos1 pos2 pos1
> movie encode 220909_1.mp4 quality medium
Movie encoding failed because no images were recorded.
> movie record
> fly 5 pos1 pos2 pos1
> movie encode 09052022.mp4 quality medium
Movie encoding failed because no images were recorded.
> movie record
> fly 5 pos1 pos2 pos1
> movie encode 220909_1.mp4 quality medium
Movie encoding failed because no images were recorded.
> fly 5 pos1 pos2 pos1
> movie encode 220909_1.mp4 quality medium
Movie encoding failed because no images were recorded.
> fly 5 pos1 pos2 pos1
> movie encode 220909_1.mp4 quality medium
Movie encoding failed because no images were recorded.
> movie record
> fly 5 pos1 pos2 pos1
> movie encode 220909_1.mp4 quality medium
Movie encoding failed because no images were recorded.
> movie record
> fly 5 pos1 pos2 pos1
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> fly 5 pos1 pos2 pos1
> movie record
> fly 25 pos1 pos2 pos1
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> hide #!5 models
> view matrix models
> #4,0.051693,-0.5639,-0.82422,198.42,-0.32784,0.77001,-0.54737,23.336,0.94332,0.29851,-0.14506,48.901
> view name topbound
> view matrix models
> #4,0.051693,-0.5639,-0.82422,199.63,-0.32784,0.77001,-0.54737,24.712,0.94332,0.29851,-0.14506,22.476
> view name topbound
[Repeated 1 time(s)]
> view matrix models
> #4,0.051693,-0.5639,-0.82422,276.06,-0.32784,0.77001,-0.54737,-33.248,0.94332,0.29851,-0.14506,21.558
> view matrix models
> #4,0.41359,-0.55085,-0.72492,208.6,0.40148,0.82496,-0.39781,-165.97,0.81716,-0.12652,0.56235,-2.3771
> view matrix models
> #4,0.20234,-0.4547,-0.86736,245.65,0.5633,0.77854,-0.27672,-199.82,0.8011,-0.43259,0.41366,63.41
> view matrix models
> #4,0.14822,-0.47073,-0.86974,255.91,0.53306,0.77878,-0.33066,-187.88,0.83299,-0.41462,0.36636,63.115
> view name topunbound
> fly 5 topunbound topbound
> view topunbound
> fly 25 topunbound topbound
> view topbound
> view matrix models
> #4,-0.063015,0.63062,-0.77353,43.522,-0.28977,0.73012,0.61884,-141.18,0.95502,0.26314,0.13672,-14.405
> view sidebound
Expected an objects specifier or a view name or a keyword
> view name sidebound
> view topunbound
> fly 25 topunbound sidebound
> view matrix models
> #4,-0.063015,0.63062,-0.77353,41.255,-0.28977,0.73012,0.61884,-150.38,0.95502,0.26314,0.13672,111.3
> view name sidebound1
> view matrix models
> #4,-0.47145,0.03421,-0.88123,197.23,-0.88161,-0.043372,0.46997,62.065,-0.022142,0.99847,0.050608,160.97
> view sidebound1
> view matrix models
> #4,-0.063015,0.63062,-0.77353,49.82,-0.28977,0.73012,0.61884,-138.76,0.95502,0.26314,0.13672,-97.318
> view sidebound2
Expected an objects specifier or a view name or a keyword
> view name sidebound2
> view matrix models
> #4,-0.063015,0.63062,-0.77353,49.239,-0.28977,0.73012,0.61884,-140.77,0.95502,0.26314,0.13672,-69.066
> view sidebound2
> view matrix models
> #4,-0.063015,0.63062,-0.77353,51.374,-0.28977,0.73012,0.61884,-137.54,0.95502,0.26314,0.13672,-124.94
> view sidebound2
> view matrix models
> #4,-0.063015,0.63062,-0.77353,49.318,-0.28977,0.73012,0.61884,-138.38,0.95502,0.26314,0.13672,-97.315
> view name zoomout1
> view matrix models
> #4,-0.063015,0.63062,-0.77353,42.352,-0.28977,0.73012,0.61884,-144.13,0.95502,0.26314,0.13672,29.852
> view name zoomout2
> view matrix models
> #4,-0.063015,0.63062,-0.77353,46.352,-0.28977,0.73012,0.61884,-142.05,0.95502,0.26314,0.13672,-29.044
> view name zoomout3
> view zoomout1
> view matrix models
> #4,0.36379,-0.50386,-0.78344,146.89,0.11946,0.85936,-0.49722,-55.669,0.92379,0.087291,0.37282,-102.15
> view matrix models
> #4,0.36379,-0.50386,-0.78344,147.65,0.11946,0.85936,-0.49722,-49.095,0.92379,0.087291,0.37282,-101.8
> view matrix models
> #4,0.44154,-0.48644,-0.75394,129.97,-0.15782,0.78508,-0.59896,15.139,0.88325,0.38345,0.26987,-122.34
> view matrix models
> #4,0.44154,-0.48644,-0.75394,133.96,-0.15782,0.78508,-0.59896,22.885,0.88325,0.38345,0.26987,-121.87
> view matrix models
> #4,0.35847,-0.5122,-0.78048,153.13,-0.20533,0.77231,-0.60115,31.729,0.91068,0.37575,0.17168,-110.74
> view matrix models
> #4,0.35847,-0.5122,-0.78048,151.59,-0.20533,0.77231,-0.60115,30.457,0.91068,0.37575,0.17168,-110.73
> view matrix models
> #4,0.32744,-0.52591,-0.78498,158.55,-0.22564,0.76322,-0.60546,35.218,0.91754,0.37537,0.13124,-105.9
> view matrix models
> #4,0.32744,-0.52591,-0.78498,156.26,-0.22564,0.76322,-0.60546,31.044,0.91754,0.37537,0.13124,-105.91
> view name zoomout1
> view matrix models
> #4,0.32744,-0.52591,-0.78498,150.88,-0.22564,0.76322,-0.60546,15.207,0.91754,0.37537,0.13124,119.26
> view matrix models
> #4,0.30555,-0.55367,-0.77465,156.36,-0.24922,0.7387,-0.62627,24.919,0.91898,0.38442,0.08772,123.99
> view name zoomout2
> view matrix models
> #4,0.30555,-0.55367,-0.77465,162.46,-0.24922,0.7387,-0.62627,29.586,0.91898,0.38442,0.08772,16.172
> view matrix models
> #4,0.30688,-0.56977,-0.76236,162.75,-0.24551,0.72651,-0.6418,32.953,0.91954,0.38412,0.083069,16.795
> view matrix models
> #4,0.25299,-0.58584,-0.76993,173.72,-0.20328,0.74586,-0.63432,23.199,0.94587,0.31699,0.069609,24.248
> view name zoomout3
> view name zoomout4
> show #!5 models
> hide #!5 models
> view matrix models
> #4,0.25299,-0.58584,-0.76993,165.47,-0.20328,0.74586,-0.63432,15.301,0.94587,0.31699,0.069609,187.69
> show #!5 models
> hide #!5 models
> view name zoomout5
> view list
Named views: pos1, pos2, sidebound, sidebound1, sidebound2, topbound,
topunbound, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5
> view sidebound
> view sidebound1
> view topunbound
> view topbound
> view topunbound
> movie record
> fly 25 topunbound topbound zoomout1 zoomout2 zoomout3 zoomout4 zoomout 5
fly: Unknown position name "zoomout"
> movie record
Already recording a movie
> movie record
Already recording a movie
> fly 25 topunbound topbound zoomout1 zoomout2 zoomout3 zoomout4 zoomout5
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> view topunbound
> view name topunbound
> view topbound
> view name topbound
> view list
Named views: pos1, pos2, sidebound, sidebound1, sidebound2, topbound,
topunbound, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5
> view zoomout1
> view name zoomout1
> view zoomout2
> select clear
> view name zoomout2
> view zoomout3
> view zoomout2
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.30555,-0.55367,-0.77465,159.89,-0.24922,0.7387,-0.62627,30.879,0.91898,0.38442,0.08772,25.454
Drag select of 73 residues, 1 pseudobonds
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.30555,-0.55367,-0.77465,163.63,-0.24922,0.7387,-0.62627,33.974,0.91898,0.38442,0.08772,-43.204
> view name zoomout3
> view zoomout3
> view zoomout4
> view zoomout3
> view matrix models
> #4,0.30555,-0.55367,-0.77465,165.37,-0.24922,0.7387,-0.62627,35.445,0.91898,0.38442,0.08772,-75.518
> view name zoomout3
> view zoomout2
> view matrix models
> #4,0.30555,-0.55367,-0.77465,164.65,-0.24922,0.7387,-0.62627,33.581,0.91898,0.38442,0.08772,-48.286
> view name zoomout3
> view name zoomout4
> view matrix models
> #4,0.30555,-0.55367,-0.77465,149.16,-0.24922,0.7387,-0.62627,24.043,0.91898,0.38442,0.08772,199.84
> view matrix models
> #4,0.23712,-0.58313,-0.777,163.32,-0.33327,0.70245,-0.62888,41.393,0.91253,0.40807,-0.027775,213.92
> view name junctionopen
> show #!5 models
> matchmaker #4 ¢5
Expected a keyword
> matchmaker #4 #5
Missing required "to" argument
> matchmaker #4 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 6VAE.pdb, chain B (#5) with 6vad.pdb, chain B (#4), sequence
alignment score = 5565.9
RMSD between 635 pruned atom pairs is 1.074 angstroms; (across all 1131 pairs:
12.571)
> morph #4 to #5
Expected a keyword
> morph #4 #5
models have different number of chains, 2 (Morph - 6vad.pdb #/A,Morph -
6vad.pdb #/B) and 4 (6VAE.pdb #5/A,6VAE.pdb #5/B,6VAE.pdb #5/C,6VAE.pdb #5/D)
> hide #!5 models
> show #!5 models
> hide #!4 models
> select #5/B:296
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
220 atoms, 219 bonds, 13 residues, 1 model selected
> select up
2998 atoms, 3018 bonds, 182 residues, 1 model selected
> select up
3069 atoms, 3087 bonds, 186 residues, 1 model selected
> select up
8281 atoms, 8342 bonds, 510 residues, 1 model selected
> select up
8293 atoms, 8353 bonds, 511 residues, 1 model selected
> select up
9875 atoms, 9955 bonds, 614 residues, 1 model selected
> select up
18808 atoms, 18983 bonds, 1155 residues, 1 model selected
> select up
40634 atoms, 40968 bonds, 2505 residues, 1 model selected
> select up
105913 atoms, 108770 bonds, 5694 residues, 5 models selected
> select down
40634 atoms, 40968 bonds, 2505 residues, 3 models selected
> show sel cartoons
> select clear
> select #5/C:2
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
108 atoms, 108 bonds, 6 residues, 1 model selected
> select up
1231 atoms, 1237 bonds, 76 residues, 1 model selected
> select up
40634 atoms, 40968 bonds, 2505 residues, 1 model selected
> select down
1231 atoms, 1237 bonds, 76 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #5/D:24
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
224 atoms, 223 bonds, 14 residues, 1 model selected
> select up
1231 atoms, 1237 bonds, 76 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> view junctionopen
> morph #4 #5
Computed 51 frame morph #6
> coordset #6 1,51
> cartoon style width 4 thickness 1
> view name junctionclosed
> view list
Named views: junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1,
sidebound2, topbound, topunbound, zoomout1, zoomout2, zoomout3, zoomout4,
zoomout5
> view topunbound
[Repeated 1 time(s)]
> view topbound
> view topunbound
> view zoomout1
> view topunbound
> view topbound
> show #!5 models
> hide #!6 models
> view list
Named views: junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1,
sidebound2, topbound, topunbound, zoomout1, zoomout2, zoomout3, zoomout4,
zoomout5
> view topunbound
> show #!4 models
> hide #!5 models
> view topunbound
> view topbound
> view zoomout1
> view zoomout2
> view zoomout3
> view zoomout4
> view zoomout5
> view junctionopen
> movie record
> fly 25 topunbound topbound zoomout1 zoomout2 zoomout3 zoomout4 zoomout5
> junctionopen
> view list
Named views: junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1,
sidebound2, topbound, topunbound, zoomout1, zoomout2, zoomout3, zoomout4,
zoomout5
> view topunbound
> view topbound
> view zoomout1
> view zoomout2
> view zoomout3
> view zoomout4
> view zoomout5
> view topunbound
> view name topunbound
> view topbound
> view name topbound
> view zoomout1
> view name zoomout1
> view zoomout2
> view name zoomout2
> view zoomout3
> view name zoomout3
> view zoomout4
> view name zoomout4
> view zoomout5
> view name zoomout5
> view junctionopen
> view name junctionopen
> view junctionclosed
> view name junctionclosed
> view topunbound
> movie record
Already recording a movie
> movie record
Already recording a movie
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> movie record
> fly 25 topunbound topbound zoomout1 zoomout2 zoomout3 zoomout4 zoomout5
> junctionopen
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> view list
Named views: junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1,
sidebound2, topbound, topunbound, zoomout1, zoomout2, zoomout3, zoomout4,
zoomout5
> view topunbound
> view topbound
> view zoomout1
> view topunbound
> view topbound
> view topunbound
> view topbound
> view zoomout1
> view topbound
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.051693,-0.5639,-0.82422,205.96,-0.32784,0.77001,-0.54737,27.356,0.94332,0.29851,-0.14506,-63.261
> view name topbound1
> view matrix models
> #4,0.051693,-0.5639,-0.82422,198.72,-0.32784,0.77001,-0.54737,15.567,0.94332,0.29851,-0.14506,135.75
> view name topbound2
> view matrix models
> #4,0.051693,-0.5639,-0.82422,202.66,-0.32784,0.77001,-0.54737,25.713,0.94332,0.29851,-0.14506,-15.507
> view name topbound3
> view matrix models
> #4,0.051693,-0.5639,-0.82422,201.55,-0.32784,0.77001,-0.54737,27.267,0.94332,0.29851,-0.14506,-23.706
> undo
> view name zo1
> view matrix models
> #4,0.051693,-0.5639,-0.82422,196.74,-0.32784,0.77001,-0.54737,20.935,0.94332,0.29851,-0.14506,91.214
> view name zo2
> view matrix models
> #4,0.051693,-0.5639,-0.82422,200.32,-0.32784,0.77001,-0.54737,22.219,0.94332,0.29851,-0.14506,45.155
> view name zo3
> view matrix models
> #4,0.051693,-0.5639,-0.82422,194.39,-0.32784,0.77001,-0.54737,10.085,0.94332,0.29851,-0.14506,236.62
> view matrix models
> #4,0.13823,-0.53956,-0.83052,179.6,-0.21401,0.80248,-0.55697,-9.2463,0.967,0.25473,-0.0045496,219.3
> view matrix models
> #4,0.061681,-0.51263,-0.85639,190.46,-0.30616,0.80694,-0.50509,-4.1288,0.94998,0.29334,-0.10717,230.99
> view matrix models
> #4,0.083525,-0.50619,-0.85837,184.42,-0.27489,0.81625,-0.5081,-7.7796,0.95784,0.2784,-0.07097,227.94
> view matrix models
> #4,0.1278,-0.6,-0.78973,181.32,-0.22977,0.75668,-0.61208,8.8344,0.96482,0.25968,-0.041161,225.3
> view matrix models
> #4,0.1611,-0.58561,-0.79442,175.26,-0.18414,0.77297,-0.60714,-0.6177,0.96961,0.2441,0.016693,218.54
> view matrix models
> #4,0.23587,-0.56054,-0.79382,161.06,-0.12396,0.79285,-0.59668,-13.423,0.96384,0.23915,0.11753,205.69
> view matrix models
> #4,0.23587,-0.56054,-0.79382,175.63,-0.12396,0.79285,-0.59668,3.2911,0.96384,0.23915,0.11753,207.14
> view matrix models
> #4,0.34499,-0.52906,-0.77529,153.1,-0.19666,0.76692,-0.61086,19.245,0.91777,0.36321,0.16054,190.42
> view matrix models
> #4,0.34499,-0.52906,-0.77529,162.07,-0.19666,0.76692,-0.61086,26.643,0.91777,0.36321,0.16054,191.33
> view name jo1
> view list
Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound,
sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topunbound,
zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5
> view topbound2
> view topunbound
> movie record
> fly 5 topunbound topbound topbound1
> topbound2
Unknown command: topbound2
> topbound3
Unknown command: topbound3
> zo1
Unknown command: zo1
> zo2
Unknown command: zo2
> zo3
Unknown command: zo3
> jo1
Unknown command: jo1
> view topunbound
> view zo1
> view topunbound
> movie record
Already recording a movie
> view topunbound
> movie record
Already recording a movie
> view topunbound
> view topbound
> view topbound1
> view topbound2
> view topbound3
> view zo1
> view zo2
> view zo3
> view jo1
> view topunbound
> view topbound3
> view topunbound
> view zo3
> view jo1
> view zo3
> view jo1
> view topunbound
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> movie record
> fly 5 topunbound topbound topbound1 topbound2 topbound3 zo1 zo2 zo3 jo1
> view topunbound
> view sidebound
> view topunbound
[Repeated 1 time(s)]
> view sidebound2
> view topunbound
> view sidebound1
> view sidebound2
> view sidebound1
> view topunbound
> view sidebound1
> view topunbound
> view pos2
> view topunbound
> view name topunbound
> view topbound
> view name topbound
> view zoomout1
> view topbound1
> view list
Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound,
sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topunbound,
zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5
> view topbound
> view topunbound
> view topbound
> view topunbound
> view topbound
> view topbound1
> view name topbound1
> view topbound2
> view name topbound2
> view topbound3
> view name topbound3
> view list
Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound,
sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topunbound,
zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5
> view zo1
> view name zo1
> view zo2
> view name zo2
> view zo3
> view name zo3
> view jo1
> view name jo1
> view topunbound
> select clear
> movie record
Already recording a movie
> view list
Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound,
sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topunbound,
zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5
> view topbound3
> view topunbound
[Repeated 1 time(s)]
> view zoomout5
> view topunbound
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> movie record
> fly 5 topunbound topbound topbound1 topbound2 topbound3 zo1 zo2 zo3 jo1
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> save /Users/palcon/Desktop/220909.cxs
> view list
Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound,
sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topunbound,
zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5
> view topunbound
> view name topunbound
[Repeated 2 time(s)]
> view topbound
> view topunbound
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view topunbound
> view matrix models
> #4,0.14822,-0.47073,-0.86974,185.3,0.53306,0.77878,-0.33066,-133.96,0.83299,-0.41462,0.36636,59.764
> view matrix models
> #4,0.14822,-0.47073,-0.86974,183.03,0.53306,0.77878,-0.33066,-132.16,0.83299,-0.41462,0.36636,58.823
> view matrix models
> #4,0.30287,-0.58794,-0.75006,160.19,-0.3314,0.67294,-0.66131,52.62,0.89356,0.44886,0.0089741,-18.371
> view matrix models
> #4,0.30287,-0.58794,-0.75006,162.12,-0.3314,0.67294,-0.66131,58.912,0.89356,0.44886,0.0089741,-16.993
> view matrix models
> #4,0.30287,-0.58794,-0.75006,160.11,-0.3314,0.67294,-0.66131,55.051,0.89356,0.44886,0.0089741,-17.957
> view matrix models
> #4,0.30287,-0.58794,-0.75006,165.41,-0.3314,0.67294,-0.66131,67.334,0.89356,0.44886,0.0089741,-15.048
> view matrix models
> #4,0.38976,-0.54137,-0.74498,145.88,-0.17327,0.7514,-0.63669,30.463,0.90447,0.37724,0.19907,-33.75
> view matrix models
> #4,0.5674,-0.45279,-0.68778,100.19,-0.31303,0.65393,-0.68876,71.256,0.76162,0.6061,0.2293,-49.371
> view matrix models
> #4,0.58607,-0.45581,-0.66989,95.406,-0.28704,0.65635,-0.69772,68.496,0.75771,0.6012,0.25383,-51.629
> view matrix models
> #4,0.58607,-0.45581,-0.66989,95.082,-0.28704,0.65635,-0.69772,68.704,0.75771,0.6012,0.25383,-34.943
> view matrix models
> #4,0.58607,-0.45581,-0.66989,96.115,-0.28704,0.65635,-0.69772,67.769,0.75771,0.6012,0.25383,-36.009
> view matrix models
> #4,0.58607,-0.45581,-0.66989,96.533,-0.28704,0.65635,-0.69772,67.383,0.75771,0.6012,0.25383,-34.977
> view matrix models
> #4,0.4698,-0.52989,-0.70605,128.48,-0.18162,0.72468,-0.66472,38.225,0.86389,0.44052,0.24422,-26.499
> view matrix models
> #4,0.16497,-0.67017,-0.72364,193.79,-0.24192,0.68378,-0.68842,55.84,0.95617,0.28863,-0.049321,23.15
> view matrix models
> #4,0.10326,-0.68492,-0.72127,204.28,-0.18764,0.69871,-0.69036,46.324,0.9768,0.20663,-0.056366,32.56
> view matrix models
> #4,0.10326,-0.68492,-0.72127,210.03,-0.18764,0.69871,-0.69036,42.095,0.9768,0.20663,-0.056366,32.666
> view matrix models
> #4,0.10326,-0.68492,-0.72127,210.47,-0.18764,0.69871,-0.69036,41.415,0.9768,0.20663,-0.056366,16.55
> view name topbound
Drag select of 39 residues
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.10326,-0.68492,-0.72127,259.37,-0.18764,0.69871,-0.69036,-37.784,0.9768,0.20663,-0.056366,5.2566
> view matrix models
> #4,0.11734,-0.39276,-0.91212,244.12,-0.18196,0.89442,-0.40855,-105.77,0.97628,0.21391,0.033484,-8.4656
> view name topunbound
> fly topunbound topbound
> view list
Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound,
sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topunbound,
zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5
> view topunbound
> select clear
> view topbound
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.10326,-0.68492,-0.72127,211.53,-0.18764,0.69871,-0.69036,40.298,0.9768,0.20663,-0.056366,-62.737
> fly topunbound topbound1
> view topunbound
[Repeated 1 time(s)]
> view topbound
> view topunbound
> view topbound
> view matrix models
> #4,0.10326,-0.68492,-0.72127,212.61,-0.18764,0.69871,-0.69036,38.564,0.9768,0.20663,-0.056366,-64.535
> view name topbound1
> view matrix models
> #4,0.10326,-0.68492,-0.72127,210.68,-0.18764,0.69871,-0.69036,40.534,0.9768,0.20663,-0.056366,87.191
> view name topbound2
> view name topbound3
> view matrix models
> #4,0.10326,-0.68492,-0.72127,210.75,-0.18764,0.69871,-0.69036,41.382,0.9768,0.20663,-0.056366,-38.145
> view name topbound4
> view matrix models
> #4,0.10326,-0.68492,-0.72127,209.86,-0.18764,0.69871,-0.69036,40.843,0.9768,0.20663,-0.056366,222.23
> view name topbound5
> view list
Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound,
sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topbound4,
topbound5, topunbound, zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4,
zoomout5
> view topunbound
> fly 25 topunbound topbound topbound1 topbound2 topbound3 topbound4 topbound5
> view topunbound
> movie record
> fly 50 topunbound 5 topbound 5 topbound1 5 topbound2 5 topbound3 5 topbound4
> 5 topbound5
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> view topunbound
> movie record
> fly 50 topunbound 50 topbound 50 topbound1 50 topbound2 50 topbound3 50
> topbound4 50 topbound5
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> select clear
> view topunbound
> movie record
> fly 20 topunbound 20 topbound 20 topbound1 20 topbound2 20 topbound3 20
> topbound4 20 topbound5
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> view list
Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound,
sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topbound4,
topbound5, topunbound, zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4,
zoomout5
> view topunbound
> view topbound
> view topbound1
> view topbound2
> view topbound3
> view topunbound
> movie record
> fly topunbound 20 topbound 20 topbound1 20 topbound2 20 topbound3 20
> topbound4 20 topbound5
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> fly topunbound 20 topbound
> view topunbound
> fly topunbound 20 topbound 20 topbound1
> fly topunbound 20
> wait 10
> fly topbound 20
> wait 10
> fly topbound1
> view topunbound
> fly topunbound 20
> wait 10
> fly topbound 20
> wait 10
> fly topbound1
> fly topunbound 20 wait 10 fly topbound 20 wait 10 fly topbound1
fly: Unknown position name "wait"
> fly topunbound 20 topbound 20 topbound1
> rock #4 y 10
Expected an axis vector or a keyword
> rock y #4 y 10
Expected a number or a keyword
> rock y #4
Expected a number or a keyword
> rock
> stop
> view topunbound
> fly topunbound 20 topbound 20 topbound1
> view topunbound
> fly topunbound 20 topbound 20 topbound1 20 topbound2
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.10326,-0.68492,-0.72127,291.58,-0.18764,0.69871,-0.69036,-91.31,0.9768,0.20663,-0.056366,175.92
> view matrix models
> #4,0.12272,-0.36664,-0.92224,273.39,-0.17817,0.90602,-0.3839,-164.95,0.97632,0.21143,0.045863,160.78
> view matrix models
> #4,-0.34564,-0.23765,-0.90778,320.17,0.58308,0.70357,-0.4062,-242.16,0.73522,-0.66971,-0.10461,338.4
> select clear
> view name one
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,-0.26647,-0.22071,-0.93823,310.89,0.63114,0.69575,-0.34292,-256.93,0.72846,-0.68354,-0.0461,332.95
> view matrix models
> #4,0.0014736,-0.3587,-0.93345,291.15,0.19476,0.91568,-0.35157,-223.99,0.98085,-0.18128,0.071209,210.84
> view matrix models
> #4,0.0014736,-0.3587,-0.93345,214.07,0.19476,0.91568,-0.35157,-98.458,0.98085,-0.18128,0.071209,139.79
> view matrix models
> #4,-0.089649,-0.26302,-0.96062,217.67,0.15891,0.94837,-0.2745,-108.84,0.98321,-0.17726,-0.043223,155.18
> view matrix models
> #4,-0.0156,-0.27174,-0.96224,208.57,0.038721,0.96147,-0.27215,-93.879,0.99913,-0.041505,-0.004477,128.62
> select clear
> view name two
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,-0.0156,-0.27174,-0.96224,207.25,0.038721,0.96147,-0.27215,-90.472,0.99913,-0.041505,-0.004477,-38.073
> view name three
> view matrix models
> #4,-0.0156,-0.27174,-0.96224,205.65,0.038721,0.96147,-0.27215,-89.391,0.99913,-0.041505,-0.004477,159.94
> view matrix models
> #4,-0.0022613,-0.37577,-0.92671,213.09,0.049959,0.92551,-0.37541,-71.321,0.99875,-0.047146,0.01668,157.77
> view matrix models
> #4,-0.0022613,-0.37577,-0.92671,212.53,0.049959,0.92551,-0.37541,-70.15,0.99875,-0.047146,0.01668,122.89
> view name four
> view matrix models
> #4,-0.0022613,-0.37577,-0.92671,213.43,0.049959,0.92551,-0.37541,-70.83,0.99875,-0.047146,0.01668,19.134
> view name five
> view matrix models
> #4,-0.0022613,-0.37577,-0.92671,213.73,0.049959,0.92551,-0.37541,-73.106,0.99875,-0.047146,0.01668,255.18
> view name junction
> view list
Named views: five, four, jo1, junction, junctionclosed, junctionopen, one,
pos1, pos2, sidebound, sidebound1, sidebound2, three, topbound, topbound1,
topbound2, topbound3, topbound4, topbound5, topunbound, two, zo1, zo2, zo3,
zoomout1, zoomout2, zoomout3, zoomout4, zoomout5
> view one
> select clear
> fly 50 one two three four five junction
> view one
> movie record
> fly 50 one
> wait 10
> fly 100 two three four five junction
> view one
> movie record
Already recording a movie
> stop
> save /Users/palcon/Desktop/220909.cxs
——— End of log from Fri Sep 9 15:10:40 2022 ———
opened ChimeraX session
> movie record
> fly 50 one 50 two
> wait 10
> fly two 50 three 50 four 50 five 50 junction
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> ui tool show "Side View"
> view onw
Expected an objects specifier or a view name or a keyword
> view one
> fly 50 one 50 two
> wait 20
> fly two 50 three 50 four 50 five 50 junction
> stop
> veiw onw
Unknown command: veiw onw
> veiw one
Unknown command: veiw one
> view one
> fly 50 one 50 two
> wait 120
> fly two 50 three 50 four 50 five 50 junction
> movei record; fly 50 one 50 two; wait 110; fly two 50 three 40 four 30 five
> 50 junction
Unknown command: movei record; fly 50 one 50 two; wait 110; fly two 50 three
40 four 30 five 50 junction
> movie record
> fly 50 one 50 two
> wait 110
> fly two 50 three 40 four 30 five 50 junction
> movie encode 220909_1.mp4 quality medium
Movie saved to 220909_1.mp4
> view one
> movie record
> fly 50 one 50 two
> wait 50
> fly two 50 three 40 four 30 five 50 junction
> view one
> movie record
Already recording a movie
> view one
> stop
> save /Users/palcon/Desktop/220909.cxs
——— End of log from Fri Sep 9 15:20:29 2022 ———
opened ChimeraX session
> show #!6 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 210
> morph #4,5
Computed 51 frame morph #7
> coordset #7 1,51
> cartoon style width 4 thickness 1
> hide #!7 models
> show #!4 models
> view one
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 160
> hide #4 models
> show #7 models
> coordset #7 1,51
> view one
> hide #!7 models
> show #!4 models
> movie record
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> show #7 models
> coordset #7 1,51
> view one
> hide #!7 models
> show #!4 models
> movie encode 220909_1.mp4 quality high
Movie saved to 220909_1.mp4
> ui tool show "Side View"
> lighting full
> lighting soft
> movie record
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> show #7 models
> coordset #7 1,51
> wait
wait requires a frame count argument unless motion is in progress
> movie encode 220909_1.mp4 quality high
Movie saved to 220909_1.mp4
> view one
> show #!4 models
> hide #!7 models
> 2dlabels text 'wild-type D2-I + DNA (open)’ color black size 26 x 0.05 y 0.1
Invalid "text" argument: incomplete quoted text
> text 'wild-type D2-I + DNA (open)’ color black size 26 x 0.05 y 0.1
Unknown command: text 'wild-type D2-I + DNA (open)’ color black size 26 x 0.05
y 0.1
> text 'wild-type D2-I + DNA (open)’
Unknown command: text 'wild-type D2-I + DNA (open)’
> 2dlabels'wild-type D2-I + DNA (open)’
incomplete quoted text
> 2dlabels text 'wild-type D2-I + DNA (open)’
Invalid "text" argument: incomplete quoted text
> 2dlabels text 'D2-I’
Invalid "text" argument: incomplete quoted text
> 2dlabels text 'D2-I’
Invalid "text" argument: incomplete quoted text
> 2dlabels text 'D2-I’
Invalid "text" argument: incomplete quoted text
> text 'D2-I’
Unknown command: text 'D2-I’
> 2dlabels text 2
> 2dlabels text D2-I
> close #8.1
> view one
> 2dlabels text #8.2 color blue size 26 xpos 0.62 ypos 0.1
> 2dlabels text D2-I color blue size 26 xpos 0.62 ypos 0.1
> close #8.1-3
> 2dlabels text FANCD2 color blue size 26 xpos 0.62 ypos 0.1
> 2dlabels text FANCD2 size 26 xpos 0.62 ypos 0.1
> close #9.1
> 2dlabels text FANCD2 size 26 xpos 0.22 ypos 0.1
> 2dlabels text FANCD2 size 26 xpos 0.25 ypos 0.4
> 2dlabels text FANCD2 size 26 xpos 0.25 ypos 0.7
> 2dlabels text FANCD2 size 26 xpos 0.25 ypos 0.8
> 2dlabels text FANCD2 size 26 xpos 0.3 ypos 0.9
> 2dlabels text FANCD2 size 26 xpos 0.28 ypos 0.9
> 2dlabels text FANCD2 size 26 xpos 0.35 ypos 0.9
> 2dlabels text FANCD2 size 26 xpos 0.35 ypos 0.8
> 2dlabels text FANCD2 size 26 xpos 0.35 ypos 0.85
> close #9.1-9
> 2dlabels text FANCD2 size 20 xpos 0.35 ypos 0.85
> close #9.1
> close #9.10
> 2dlabels text FANCD2 size 20 xpos 0.35 ypos 0.85
> 2dlabels text FANCI size 20 xpos 0.55 ypos 0.65
> close #10.2
> 2dlabels text FANCI size 20 xpos 0.65 ypos 0.65
> 2dlabels text FANCI size 20 xpos 0.6 ypos 0.65
> close #10.2
> wait 40
> 2dlabels change #10.1
> 2dlabels change #10.3 visibility false
> wait 10
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> view one
> show #10.3 models
> movie record
> wait 40
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> show #7 models
> coordset #7 1,51
> wait
wait requires a frame count argument unless motion is in progress
> movie encode 220909_1.mp4 quality high
Movie saved to 220909_1.mp4
> view one
> hide #!7 models
> show #!4 models
> show #10.1 models
> show #10.3 models
> 2dlabels text DNA loading size 20 x 0.5 y 0.6
Expected a keyword
> 2dlabels text DNA loading
Expected a keyword
> 2dlabels text "DNA loading"
> 2dlabels text "DNA loading" size 20 xpos 0.4 ypos 0.4
> 2dlabels text "DNA loading" size 20 xpos 0.4 ypos 0.6
> 2dlabels text "DNA loading" size 20 xpos 0.3 ypos 0.6
> close #10.2,4-5
> hide #10.6 models
> wait 40
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> show #10.6 models
> 2dlabels change #10.6 visibility false
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> show #7 models
> coordset #7 1,51
> wait
wait requires a frame count argument unless motion is in progress
> movie encode 220909_1.mp4 quality high
No frames have been recorded
> view one
> hide #!10 models
> show #!4 models
> hide #!7 models
> show #10.1 models
> show #10.3 models
> movie record
> wait 40
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> show #10.6 models
> 2dlabels change #10.6 visibility false
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> show #7 models
> coordset #7 1,51
> wait
wait requires a frame count argument unless motion is in progress
> movie encode 220909_1.mp4 quality high
Movie saved to 220909_1.mp4
> view one
> show #!4 models
> hide #!7 models
> show #10.1 models
> show #10.3 models
> wait 40
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> show #10.6 models
> 2dlabels change #10.6 visibility false
> show #10.1 models
> show #10.3 models
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> show #10.6 models
> 2dlabels change #10.6 visibility false
> show #10.1 models
> show #10.3 models
> wait 40
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> show #10.6 models
> 2dlabels change #10.6 visibility false
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> view one
> show #10.1 models
> show #10.3 models
> show #!4 models
> show #10.6
> hide #10.6 models
> movie record
> wait 40
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> show #10.6
> 2dlabels change #10.6 visibility false
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> show #7 models
> coordset #7 1,51
> wait
wait requires a frame count argument unless motion is in progress
> view one
> movie encode 220909_1.mp4 quality high
Movie saved to 220909_1.mp4
> close #10.6
> show #10.1 models
> show #10.3 models
> hide #!7 models
> show #!4 models
> wait 40
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> 2dlabels text "DNA loading" size 20 xpos 0.3 ypos 0.6
> wait 60
> 2dlabels change #10.6 visibility false
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> show #7 models
> hide #10.2 models
> show #10.1 models
> show #10.3 models
> hide #!7 models
> show #!4 models
> view onw
Expected an objects specifier or a view name or a keyword
> view one
> wait 40
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> 2dlabels text "DNA loading" size 20 xpos 0.3 ypos 0.6
> wait 60
> 2dlabels change #10.2 visibility false
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> show #7 models
> coordset #7 1,51
> wait
wait requires a frame count argument unless motion is in progress
> close #10.4
> close #10.2
> 2dlabels text "DNA loading" size 20 xpos 0.3 ypos 0.6
> close #10.2
> show #10.1 models
> show #10.3 models
> hide #!7 models
> show #!4 models
> view one
> movie record
> wait 40
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> show #7 models
> coordset #7 1,51
> wait
wait requires a frame count argument unless motion is in progress
> movie encode 220909_1.mp4 quality highest
Movie saved to 220909_1.mp4
> view one
> show #10.1 models
> show #10.3 models
> hide #!7 models
> show #!4 models
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> select clear
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.34564,-0.23765,-0.90778,315.46,0.58308,0.70357,-0.4062,-234.82,0.73522,-0.66971,-0.10461,378.21
> view save one
Expected an objects specifier or a view name or a keyword
> view name one
> view matrix models
> #4,-0.34564,-0.23765,-0.90778,237.07,0.58308,0.70357,-0.4062,-106.56,0.73522,-0.66971,-0.10461,226.51
> view matrix models
> #4,0.06272,-0.37565,-0.92464,200.42,-0.081025,0.92149,-0.37986,-45.9,0.99474,0.098744,0.027359,64.486
> view matrix models
> #4,0.06272,-0.37565,-0.92464,204.01,-0.081025,0.92149,-0.37986,-51.709,0.99474,0.098744,0.027359,61.51
> view name two
> view matrix models
> #4,0.06272,-0.37565,-0.92464,204.09,-0.081025,0.92149,-0.37986,-51.452,0.99474,0.098744,0.027359,11.818
> view name three
> view matrix models
> #4,0.06272,-0.37565,-0.92464,204.69,-0.081025,0.92149,-0.37986,-52.865,0.99474,0.098744,0.027359,70.237
> view name four
> view matrix models
> #4,0.06272,-0.37565,-0.92464,204.86,-0.081025,0.92149,-0.37986,-52.168,0.99474,0.098744,0.027359,-59.245
> view name five
> view matrix models
> #4,0.06272,-0.37565,-0.92464,203.69,-0.081025,0.92149,-0.37986,-52.574,0.99474,0.098744,0.027359,243.84
> view name junction
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> view matrix models
> #4,0.06272,-0.37565,-0.92464,203.93,-0.081025,0.92149,-0.37986,-52.914,0.99474,0.098744,0.027359,237.26
> view name junction
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> view matrix models
> #4,0.06272,-0.37565,-0.92464,203.93,-0.081025,0.92149,-0.37986,-52.832,0.99474,0.098744,0.027359,227.11
> show #!7 models
> hide #!7 models
> view name junction
> view one
> wait 40
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> show #7 models
> coordset #7 1,51
> wait
wait requires a frame count argument unless motion is in progress
> view one
> show #10.1 models
> show #10.3 models
> hide #!7 models
> show #!4 models
> select subtract #4
Nothing selected
> movie record
> wait 40
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> show #7 models
> coordset #7 1,51
> wait
wait requires a frame count argument unless motion is in progress
> movie encode 220909_1.mp4 quality highest
Movie saved to 220909_1.mp4
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.06272,-0.37565,-0.92464,203.75,-0.081025,0.92149,-0.37986,-52.644,0.99474,0.098744,0.027359,240.56
> select up
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> select up
177971 atoms, 181442 bonds, 18 pseudobonds, 10136 residues, 8 models selected
> select up
177971 atoms, 181442 bonds, 18 pseudobonds, 10136 residues, 8 models selected
> select up
177971 atoms, 181442 bonds, 19 pseudobonds, 10136 residues, 11 models selected
> select down
177971 atoms, 181442 bonds, 18 pseudobonds, 10136 residues, 10 models selected
> select down
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 4 models selected
> select clear
> view name junction
> show #10.1 models
> show #10.3 models
> hide #!7 models
> view one
> movie record
> wait 40
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> show #7 models
> coordset #7 1,51
> wait
wait requires a frame count argument unless motion is in progress
> movie encode 220909_1.mp4 quality highest
Movie saved to 220909_1.mp4
> show #!4 models
> hide #!4 models
> show #!4 models
> select add #4
37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected
> view matrix models
> #4,0.0182,-0.37787,-0.92568,210.55,-0.0088749,0.92573,-0.37807,-63.759,0.99979,0.015096,0.013495,253.38
> view matrix models
> #4,0.0182,-0.37787,-0.92568,210.61,-0.0088749,0.92573,-0.37807,-63.837,0.99979,0.015096,0.013495,249.67
> view name junction
> show #10.1 models
> show #10.3 models
> view one
> select subtract #4
Nothing selected
> hide #!7 models
> movie record
> wait 40
> 2dlabels change #10.1 visibility false
> 2dlabels change #10.3 visibility false
> wait 10
> fly one 50 two
> wait 55
> fly two 50 three 50 four 25 five 25 junction
> wait 170
> hide #4 models
> show #7 models
> coordset #7 1,51
> wait
wait requires a frame count argument unless motion is in progress
> movie encode 220909_1.mp4 quality highest
Movie saved to 220909_1.mp4
> save /Users/palcon/Desktop/220909.cxs
——— End of log from Fri Sep 9 17:19:50 2022 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 16 MB
Memory: 32 GB
Software:
System Software Overview:
System Version: macOS 12.6 (21G115)
Kernel Version: Darwin 21.6.0
Time since boot: 1 day 3:58
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
DELL U3223QE:
Resolution: 6720 x 3780
UI Looks like: 3360 x 1890 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash during application exit |
comment:2 by , 3 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
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Qt or PyQt clean-up problem. It is a know problem that PyQt does not clean up Qt objects at exit in a robust way. We even have bug reporter code that looks for this kind of crash and does not ask the user to report it. But this traceback didn't have the usual function call associated with those crashes.