![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 17 months ago
Closed 17 months ago
#15398 closed defect (can't reproduce)
Crash destroying main window
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
{"app_name":"ChimeraX","timestamp":"2024-06-08 15:16:01.00 -0700","app_version":"1.2.5","slice_uuid":"74b1c996-e1f3-331c-8c86-116411356099","build_version":"1.2.5.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.6.6 (22G630)","roots_installed":0,"name":"ChimeraX","incident_id":"FF9C7960-B5AA-449E-AB16-EC26B957223F"}
{
"uptime" : 1400000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 210403,
"osVersion" : {
"train" : "macOS 13.6.6",
"build" : "22G630",
"releaseType" : "User"
},
"captureTime" : "2024-06-08 15:14:24.7294 -0700",
"incident" : "FF9C7960-B5AA-449E-AB16-EC26B957223F",
"pid" : 47173,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-06-07 14:08:50.3049 -0700",
"procStartAbsTime" : 34987624666579,
"procExitAbsTime" : 35626066192080,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.2.5.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.2.5","CFBundleVersion":"1.2.5.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"C6124183-FF04-5BE0-B07C-B4ED688FD23C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "0F2DDC60-B324-657A-0510-56E25E58E004",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 33,
"sleepWakeUUID" : "4CFE80FA-083B-42DA-B380-F29768C18EC7",
"sip" : "enabled",
"vmRegionInfo" : "0x6f185c1c39c8 is not in any region. Bytes after previous region: 16596762114505 Bytes before following region: 18324114359864\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)\n---> GAP OF 0x1fc2a6700000 BYTES\n MALLOC_TINY 7fc2c6700000-7fc2c6800000 [ 1024K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00006f185c1c39c8","rawCodes":[1,122150415251912],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00006f185c1c39c8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":47173},
"ktriageinfo" : "VM - (arg = 0x0) pmap_enter retried due to resource shortage\n",
"vmregioninfo" : "0x6f185c1c39c8 is not in any region. Bytes after previous region: 16596762114505 Bytes before following region: 18324114359864\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)\n---> GAP OF 0x1fc2a6700000 BYTES\n MALLOC_TINY 7fc2c6700000-7fc2c6800000 [ 1024K] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh 7.1-AvrPikC.cxs"
Log from Sat Jun 8 15:14:22 2024UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh-AvrPikC_7a8x.pdb"
Pikh-AvrPikC_7a8x.pdb title:
Complex of rice blast (magnaporthe oryzae) effector protein avr-pikc with the
hma domain of pikh-1 from rice (oryza sativa) [more info...]
Chain information for Pikh-AvrPikC_7a8x.pdb #1
---
Chain | Description
A B D E | NBS-LRR class disease resistance protein PIKH-1
C F | avr-pik protein
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> sequence chain /B
Alignment identifier is 1/B
> sequence chain /C
Alignment identifier is 1/C
> sequence chain /D
Alignment identifier is 1/D
> sequence chain /E
Alignment identifier is 1/E
> sequence chain /F
Alignment identifier is 1/F
> select /E:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /E:186-262
544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected
> hide sel atoms
> select /B:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:186-262
544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected
> select /B:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:186-262
544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected
> hide sel atoms
> select /A:188-259
530 atoms, 531 bonds, 72 residues, 1 model selected
> select /A:188-259
530 atoms, 531 bonds, 72 residues, 1 model selected
> select /D:187-259
522 atoms, 522 bonds, 1 pseudobond, 71 residues, 2 models selected
> select /A:188-259
530 atoms, 531 bonds, 72 residues, 1 model selected
> select /F:32-113
668 atoms, 693 bonds, 82 residues, 1 model selected
> select /C:33-112
651 atoms, 675 bonds, 80 residues, 1 model selected
> select /F:32-113
668 atoms, 693 bonds, 82 residues, 1 model selected
> select /A:188-259
530 atoms, 531 bonds, 72 residues, 1 model selected
> select /C:33-112
651 atoms, 675 bonds, 80 residues, 1 model selected
> select /F:32-113
668 atoms, 693 bonds, 82 residues, 1 model selected
> select /A:188-259
530 atoms, 531 bonds, 72 residues, 1 model selected
> select /D:187-259
522 atoms, 522 bonds, 1 pseudobond, 71 residues, 2 models selected
> hide sel atoms
> select /A:188-259
530 atoms, 531 bonds, 72 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select /C:109-112
31 atoms, 31 bonds, 4 residues, 1 model selected
> select /C:33-112
651 atoms, 675 bonds, 80 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel atoms
> select /F:60-113
431 atoms, 444 bonds, 54 residues, 1 model selected
> select /F:32-113
668 atoms, 693 bonds, 82 residues, 1 model selected
> show sel cartoons
> show sel cartoons
> hide sel atoms
> select /A:188-259
530 atoms, 531 bonds, 72 residues, 1 model selected
> select /A:188-191
35 atoms, 34 bonds, 4 residues, 1 model selected
> select /A:188-199
92 atoms, 91 bonds, 12 residues, 1 model selected
> select /A:251-259
69 atoms, 68 bonds, 9 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /F
Alignment identifier is 1/F
> sequence chain /A
Alignment identifier is 1/A
> sequence chain /B
Alignment identifier is 1/B
> sequence chain /C
Alignment identifier is 1/C
> sequence chain /D
Alignment identifier is 1/D
> sequence chain /E
Alignment identifier is 1/E
> select /F:95
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /F:32-95
528 atoms, 546 bonds, 64 residues, 1 model selected
> select /B:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:186-262
544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected
> show sel atoms
> show sel cartoons
> hide sel atoms
> select /C:33-112
651 atoms, 675 bonds, 80 residues, 1 model selected
> select /B:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:202-212,237-249
179 atoms, 178 bonds, 24 residues, 1 model selected
> select /B:197
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:186-197
91 atoms, 90 bonds, 12 residues, 1 model selected
> select /B:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:186-262
544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected
> select /E:261
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /E:261-262
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /E:186-262
544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected
> select /E:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /E:186-262
544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected
> show sel cartoons
> select /D:187
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:187-259
522 atoms, 522 bonds, 1 pseudobond, 71 residues, 2 models selected
> show sel cartoons
> select /F:32-46
127 atoms, 129 bonds, 15 residues, 1 model selected
> select /F:32-113
668 atoms, 693 bonds, 82 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> select /D:199
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /D:197-199
21 atoms, 20 bonds, 3 residues, 1 model selected
> select /D:197
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:197-198
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /D:198-199
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /D:198-199
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /D:187-259
522 atoms, 522 bonds, 1 pseudobond, 71 residues, 2 models selected
> hide sel cartoons
> select /A:188-259
530 atoms, 531 bonds, 72 residues, 1 model selected
> select /F:35
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /F:35-41
60 atoms, 60 bonds, 7 residues, 1 model selected
> select /A:188-259
530 atoms, 531 bonds, 72 residues, 1 model selected
> select /A:188-259
530 atoms, 531 bonds, 72 residues, 1 model selected
> select /A:198
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:198-199
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:188-259
530 atoms, 531 bonds, 72 residues, 1 model selected
> hide sel cartoons
> select /B:196-197
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /B:195
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:195-207
73 atoms, 71 bonds, 1 pseudobond, 10 residues, 2 models selected
> select /E:195-196
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /E:195-204
51 atoms, 49 bonds, 1 pseudobond, 7 residues, 2 models selected
> select /E:202-212,237-249
179 atoms, 178 bonds, 24 residues, 1 model selected
> select /E:189-195,216-222,228-233,252-259
210 atoms, 206 bonds, 28 residues, 1 model selected
> select /E:195-204
51 atoms, 49 bonds, 1 pseudobond, 7 residues, 2 models selected
> select /F:32-109
634 atoms, 657 bonds, 78 residues, 1 model selected
> select /D:187-259
522 atoms, 522 bonds, 1 pseudobond, 71 residues, 2 models selected
> select /E:224
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /E:224-225
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /C:33-112
651 atoms, 675 bonds, 80 residues, 1 model selected
> select /B:215
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:213-215
15 atoms, 14 bonds, 3 residues, 1 model selected
> select /A:213-259
346 atoms, 347 bonds, 47 residues, 1 model selected
> select /A:213-259
346 atoms, 347 bonds, 47 residues, 1 model selected
> select /A:198
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:193-198
46 atoms, 45 bonds, 6 residues, 1 model selected
> select /A:189-195,216-222,228-233,252-258
201 atoms, 197 bonds, 27 residues, 1 model selected
> select /A:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:188-189
18 atoms, 17 bonds, 2 residues, 1 model selected
> select solvent
116 atoms, 116 residues, 1 model selected
> hide sel atoms
> select /E:197
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /E:197
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /F:32-113
668 atoms, 693 bonds, 82 residues, 1 model selected
> hide sel cartoons
> select /E:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /E:186-262
544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select /B:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:186-262
544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected
> style sel sphere
Changed 544 atom styles
> show sel atoms
> hide sel atoms
> style sel ball
Changed 544 atom styles
> show sel atoms
> show sel atoms
> hide sel atoms
> select /B:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:189-190
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /B:197
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:197
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:262
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:262
9 atoms, 8 bonds, 1 residue, 1 model selected
> save "/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh 7.1-AvrPikC.cxs"
> select /B:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> swapaa /B:189 arg
Using Dunbrack library
/B GLN 189: phi -103.3, psi 148.2 trans
Applying ARG rotamer (chi angles: -64.9 -179.8 -178.2 -87.3) to /B ARG 189
> show sel atoms
> select /B:189
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:189
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select /B:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> swapaa /B:190 ile
Using Dunbrack library
/B LYS 190: phi -119.0, psi 123.4 trans
Applying ILE rotamer (chi angles: -59.9 171.3) to /B ILE 190
> select /B:190
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:190
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select /B:197
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:197
8 atoms, 7 bonds, 1 residue, 1 model selected
> swapaa /B:197 arg
Using Dunbrack library
/B MET 197: phi -152.9, psi none trans
Applying ARG rotamer (chi angles: 64.1 -175.8 68.0 -172.6) to /B ARG 197
> show sel atoms
> style sel stick
Changed 4 atom styles
> show sel atoms
> select /B:197
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:197
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:197
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> style sel stick
Changed 11 atom styles
> swapaa /B:198 gly
No amino acid residues specified for swapping
> save "/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh 7.1-AvrPikC.cxs"
> select /B:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:186-262
548 atoms, 548 bonds, 1 pseudobond, 74 residues, 2 models selected
> color (#!1 & sel) white
> select /C:33-112
651 atoms, 675 bonds, 80 residues, 1 model selected
> color sel gray
> color sel byhetero
> undo
> color sel bychain
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for Pikh-AvrPikC_7a8x.pdb_C SES surface #1.2: minimum,
-14.58, mean -1.64, maximum 7.77
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "Pikh-AvrPikC_7a8x.pdb_C SES surface": minimum -26.66,
mean -5.066, maximum 23.1
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Coulombic values for Pikh-AvrPikC_7a8x.pdb_C SES surface #1.2: minimum,
-14.58, mean -1.64, maximum 7.77
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for Pikh-AvrPikC_7a8x.pdb_C SES surface #1.2: minimum,
-14.58, mean -1.64, maximum 7.77
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel bychain
> rainbow sel
> style sel stick
Changed 651 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 651 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> hide sel atoms
> show sel cartoons
> hide sel atoms
> hide sel surfaces
> coulombic sel
Coulombic values for Pikh-AvrPikC_7a8x.pdb_C SES surface #1.2: minimum,
-14.58, mean -1.64, maximum 7.77
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel byhetero
> color sel bychain
> hide sel surfaces
> show sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> coulombic sel
Coulombic values for Pikh-AvrPikC_7a8x.pdb_C SES surface #1.2: minimum,
-14.58, mean -1.64, maximum 7.77
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> show sel surfaces
> color sel bychain
> select /B:186-262
548 atoms, 548 bonds, 1 pseudobond, 74 residues, 2 models selected
> select /C:33-112
651 atoms, 675 bonds, 80 residues, 1 model selected
> select /B:189
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:189-190
19 atoms, 18 bonds, 2 residues, 1 model selected
> select /B:191
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:190-191
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /B:191
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:190-191
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /B:189
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:188-189
20 atoms, 19 bonds, 2 residues, 1 model selected
> select /B:190
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:189-190
19 atoms, 18 bonds, 2 residues, 1 model selected
> color sel yellow
> select /B:197
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:197
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel yellow
> lighting soft
> lighting full
> lighting simple
> select /B:189-195,216-222,228-233,252-259
211 atoms, 207 bonds, 28 residues, 1 model selected
> select /B:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> save "/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh 7.1-AvrPikC.cxs"
> select /B:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:186-262
548 atoms, 548 bonds, 1 pseudobond, 74 residues, 2 models selected
> hide sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> select /B:186-262
548 atoms, 548 bonds, 1 pseudobond, 74 residues, 2 models selected
> ui mousemode right select
> ui mousemode right select
Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000026141b0>
contents scale of 2 - updating layer to match.
> undo
> view sel
> ui tool show "Command Line Interface"
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 705 of 86524 triangles
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 154 of 86524 triangles, 1
residues
Drag select of 2 residues
> select clear
> select clear
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 44 of 86524 triangles
> select clear
Drag select of 2 residues
> select clear
> select clear
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 722 of 86524 triangles
> save "/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh 7.1-AvrPikC.cxs"
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 597 of 86524 triangles, 1
residues
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 3328 of 86524 triangles, 6
residues
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 81 of 86524 triangles
> select clear
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 346 of 86524 triangles
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 465 of 86524 triangles
> select clear
> select clear
Drag select of 3 residues
> select clear
> select clear
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 85 of 86524 triangles
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 2742 of 86524 triangles, 5
atoms, 8 residues, 5 bonds
> select clear
> select clear
> select clear
> set bgColor white
> set bgColor black
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting simple
Permission denied reading directory "/Users/yrim/Desktop" while trying to
determine next unused file name image#.png.
Permission denied reading directory "/Users/yrim/Desktop" while trying to
determine next unused file name image#.png.
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 335 of 86524 triangles, 9
residues, 2 bonds
> select clear
> select /C:33-112
651 atoms, 675 bonds, 80 residues, 1 model selected
> ui tool show "Color Actions"
> ui tool show "Side View"
> transparency (#!1 & sel) 70
> cartoon hide (#!1 & sel)
> transparency (#!1 & sel) 20
> transparency (#!1 & sel) 40
> select clear
> select /C:60-112
419 atoms, 431 bonds, 53 residues, 1 model selected
> select /C:33-112
651 atoms, 675 bonds, 80 residues, 1 model selected
> select /C:33-36
30 atoms, 29 bonds, 4 residues, 1 model selected
> select /C:33-112
651 atoms, 675 bonds, 80 residues, 1 model selected
> transparency (#!1 & sel) 60
> select clear
Drag select of 8 residues
> select clear
> select clear
> save "/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh 7.1-AvrPikC.cxs"
——— End of log from Sat Jun 8 15:14:22 2024 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MJ123LL/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.101.3
OS Loader Version: 8422.141.2.700.1
Software:
System Software Overview:
System Version: macOS 13.6.6 (22G630)
Kernel Version: Darwin 22.6.0
Time since boot: 58 days, 17 hours, 23 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U2720Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
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: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 17 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash destroying main window |
comment:2 by , 17 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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