![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 17 months ago
Closed 17 months ago
#15244 closed defect (can't reproduce)
Crash giving widget focus
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| 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: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 14000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,1",
"coalitionID" : 1444,
"osVersion" : {
"train" : "macOS 13.6.6",
"build" : "22G630",
"releaseType" : "User"
},
"captureTime" : "2024-05-17 21:42:19.7346 -0700",
"incident" : "EF96BC6C-99FA-49FF-BA2B-936F7D97B11E",
"pid" : 7187,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-05-17 21:39:18.4071 -0700",
"procStartAbsTime" : 14691723790889,
"procExitAbsTime" : 14872980099145,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"840A055B-A76B-563D-B314-53AF546F5152","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7696617D-CAD3-F661-560A-9FD813E482F7",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 594,
"sleepWakeUUID" : "8AF9EA36-24F5-4DB2-AE9E-8BD4619791EC",
"sip" : "enabled",
"vmRegionInfo" : "0x40 is not in any region. Bytes before following region: 140737486299072\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe0a000-7fffffe0b000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000040","rawCodes":[1,64],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000040"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":7187},
"vmregioninfo" : "0x40 is not in any region. Bytes before following region: 140737486299072\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe0a000-7fffffe0b000 [ 4K] r-x\/r-x SM=SHM ",
"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: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/biq2001/Documents/Work/Cys-story-figures-scrach/figure-2/all-
> ligand-color-map.cxs
Opened cryosparc_P61_J150_008_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.825, shown at level 0.62, step 1, values float32
Opened cryosparc_P59_J39_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.08, shown at level 0.614, step 1, values float32
Opened cryosparc_P100_J155_008_volume_map_sharp.mrc as #5, grid size
240,240,240, pixel 1.16, shown at level 0.614, step 1, values float32
Opened cryosparc_P113_J33_009_volume_map_sharp.mrc as #7, grid size
320,320,320, pixel 0.844, shown at level 0.34, step 1, values float32
Log from Fri May 17 17:01:07 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/biq2001/Documents/Work/Cys-story-figures-scrach/figure-2/all-
> ligand-color-map.cxs
Opened cryosparc_P61_J150_008_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.825, shown at level 0.62, step 1, values float32
Opened cryosparc_P59_J39_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.08, shown at level 0.614, step 1, values float32
Opened cryosparc_P100_J155_008_volume_map_sharp.mrc as #5, grid size
240,240,240, pixel 1.16, shown at level 0.614, step 1, values float32
Opened cryosparc_P113_J33_009_volume_map_sharp.mrc as #7, grid size
320,320,320, pixel 0.844, shown at level 0.34, step 1, values float32
Log from Fri May 17 16:45:44 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/biq2001/Documents/Work/Cys-story-figures-scrach/figure-2/all-
> ligand-color-map.cxs
Opened cryosparc_P61_J150_008_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.825, shown at level 0.62, step 1, values float32
Opened cryosparc_P59_J39_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.08, shown at level 0.614, step 1, values float32
Log from Thu May 16 16:26:30 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/biq2001/Documents/Work/Cys-story-figures-scrach/figure-2/Cys-
> timer-color-map.cxs
Opened cryosparc_P61_J150_008_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.825, shown at level 0.62, step 1, values float32
Log from Wed May 15 11:30:14 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/biq2001/Dropbox/Biao's_folder/Cys-and-D-Asp/Cys-
> Trimer/cryosparc_P61_J150_008_volume_map_sharp.mrc
Opened cryosparc_P61_J150_008_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.825, shown at level 0.285, step 2, values float32
> hide #!1 models
> show #!1 models
> volume #1 step 1
> volume #1 level 0.6637
> set bgColor white
> open /Users/biq2001/Dropbox/Biao's_folder/Cys-and-D-Asp/Cys-
> Trimer/iOFS*-GlufitJ150.pdb
Chain information for iOFS*-GlufitJ150.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.7497
> view orient
> turn x 90
> view orient
> turn x 90
> hide atoms
> view name Cys-trimer-side
> color #2:13-83, 125-275 wheat
> hide #!1 models
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near #2 distance 4.95
> hide #!2 models
> show #!2 models
> color single #1
> color zone #1 near #2 distance 4.95
[Repeated 1 time(s)]
> color single #1
> color #2: 84-124, 276-500 skyblue
> color zone #1 near #2 distance 4.95
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide cartoons
[Repeated 1 time(s)]
> select #2:13-500
9255 atoms, 9393 bonds, 6 pseudobonds, 1218 residues, 2 models selected
> color zone #1 near sel distance 4.95
> hide #!1 models
> show #!1 models
> color zone #1 near sel distance 1
> color zone #1 near sel distance 1.5
[Repeated 3 time(s)]
> color zone #1 near sel distance 1
[Repeated 1 time(s)]
> color zone #1 near sel distance 1.5
[Repeated 1 time(s)]
> color zone #1 near sel distance 2
[Repeated 1 time(s)]
> volume #1 level 0.6
> surface dust #1 size 8.25
> color zone #1 near sel distance 2.5
[Repeated 1 time(s)]
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show sel atoms
> style sel sphere
Changed 9255 atom styles
> show #!1 models
> color zone #1 near sel distance 2
> color zone #1 near sel distance 3
[Repeated 1 time(s)]
> color zone #1 near sel distance 5
[Repeated 1 time(s)]
> hide #!2 models
> show #!2 models
> hide #!1 models
> style sel stick
Changed 9255 atom styles
> style sel ball
Changed 9255 atom styles
> show #!1 models
> style sel sphere
Changed 9255 atom styles
> style sel stick
Changed 9255 atom styles
> volume #1 color #b2b2b282
> ui windowfill toggle
[Repeated 1 time(s)]
> select clear
> volume #1 color #b2b2b2
No atoms selected for color zoning
> select #2:13-500
9255 atoms, 9393 bonds, 6 pseudobonds, 1218 residues, 2 models selected
> color zone #1 near sel distance 5
> color zone #1 near sel distance 2
[Repeated 1 time(s)]
> color zone #1 near sel distance 2.5
[Repeated 2 time(s)]
> view list
Named views: Cys-trimer-side
> view list
Named views: Cys-trimer-side
> ui windowfill toggle
[Repeated 1 time(s)]
> ui tool show Log
> view Cys-trimer-side
> hide #!2 models
> view Cys-trimer-side
> turn y 45
> turn y -45
> turn y 5
[Repeated 9 time(s)]
> volume #1 level 0.62
> view name cys-trimer-side-view2
> color #2: 84-124, 276-500 #1F78B4
> color zone #1 near sel distance 2.5
> color zone #1 near sel distance 2
> color zone #1 near sel distance 3
[Repeated 1 time(s)]
> color zone #1 near sel distance 3.5
[Repeated 1 time(s)]
> color zone #1 near sel distance 3
[Repeated 2 time(s)]
> color zone #1 near sel distance 5
[Repeated 1 time(s)]
> color zone #1 near sel distance 6
> hide #!1 models
> show #!2 models
> style sel sphere
Changed 9255 atom styles
> show #!1 models
> hide #!1 models
> hide sel cartoons
> hide sel atoms
> show sel atoms
> style sel stick
Changed 9255 atom styles
> style sel ball
Changed 9255 atom styles
> show #!1 models
> hide #!2 models
> color zone #1 near sel distance 3
> color zone #1 near sel distance 5
[Repeated 1 time(s)]
> color zone #1 near sel distance 300
> color zone #1 near sel distance 3
[Repeated 1 time(s)]
> show #!2 models
> hide #!1 models
> style sel stick
Changed 9255 atom styles
> show #!1 models
> hide #!2 models
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view cys-trimer-side-view2
> view Cys-trimer-side
> view cys-trimer-side-view2
> save /Users/biq2001/Documents/Work/Cys-story-figures-scrach/figure-2/Cys-
> timer-color-map.cxs
——— End of log from Wed May 15 11:30:14 2024 ———
opened ChimeraX session
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view cys-trimer-side-view2
> open /Users/biq2001/Dropbox/Biao's_folder/Cys-and-D-
> Asp/D-Asp/cryosparc_P59_J39_008_volume_map_sharp.mrc
Opened cryosparc_P59_J39_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.08, shown at level 0.278, step 1, values float32
> volume #3 level 0.5221
> hide #!1 models
> view orient
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view cys-trimer-side-view2
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> volume #3 level 0.5832
> show #!1 models
> select #3
2 models selected
> ui mousemode right translate
> undo
> select #3
2 models selected
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view cys-trimer-side-view2
> select #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-10.058,0,1,0,-11.987,0,0,1,-21.186
> select clear
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit map cryosparc_P59_J39_008_volume_map_sharp.mrc in map
cryosparc_P61_J150_008_volume_map_sharp.mrc using 44135 points
correlation = 0.2536, correlation about mean = 0.0612, overlap = 1.221e+04
steps = 84, shift = 0.984, angle = 3.62 degrees
Position of cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) relative to
cryosparc_P61_J150_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99991380 0.01102271 -0.00713362 -10.30561405
-0.01144282 0.99802235 -0.06180974 -1.91480729
0.00643820 0.06188604 0.99806246 -29.57859378
Axis 0.97822081 -0.10732969 -0.17766368
Axis point 0.00000000 489.50611572 -54.66462081
Rotation angle (degrees) 3.62493611
Shift along axis -4.62060860
> select #3
2 models selected
> view matrix models
> #3,0.99991,0.011023,-0.0071336,-10.855,-0.011443,0.99802,-0.06181,-3.2356,0.0064382,0.061886,0.99806,-31
> fitmap #3 inMap #1
Fit map cryosparc_P59_J39_008_volume_map_sharp.mrc in map
cryosparc_P61_J150_008_volume_map_sharp.mrc using 44135 points
correlation = 0.2536, correlation about mean = 0.06103, overlap = 1.221e+04
steps = 68, shift = 2.02, angle = 0.00625 degrees
Position of cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) relative to
cryosparc_P61_J150_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99991308 0.01111236 -0.00709520 -10.31114501
-0.01152961 0.99802441 -0.06176037 -1.91436172
0.00639488 0.06183681 0.99806579 -29.56350258
Axis 0.97801118 -0.10674552 -0.17916341
Axis point 0.00000000 489.66143107 -54.58168901
Rotation angle (degrees) 3.62282061
Shift along axis -4.58336752
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.94589,0.32339,0.02668,-50.56,-0.31394,0.93284,-0.17675,66.272,-0.082047,0.15881,0.98389,-28.404
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.94589,0.32339,0.02668,-52.716,-0.31394,0.93284,-0.17675,66.3,-0.082047,0.15881,0.98389,-27.57
> fitmap #3 inMap #1
Fit map cryosparc_P59_J39_008_volume_map_sharp.mrc in map
cryosparc_P61_J150_008_volume_map_sharp.mrc using 44135 points
correlation = 0.9155, correlation about mean = 0.8071, overlap = 6.729e+04
steps = 132, shift = 5.38, angle = 14.2 degrees
Position of cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) relative to
cryosparc_P61_J150_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.98798460 0.15455222 -0.00019946 -33.56844060
-0.15455221 0.98798462 0.00007039 8.95092523
0.00020795 -0.00003872 0.99999998 -23.54676633
Axis -0.00035297 -0.00131803 -0.99999907
Axis point 40.98681707 220.33071720 0.00000000
Rotation angle (degrees) 8.89083564
Shift along axis 23.54679548
> select clear
> hide #!1 models
> volume #3 level 0.614
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> open /Users/biq2001/Dropbox/Biao's_folder/Cys-and-D-Asp/D-Asp/iOFS*-DAS-
> fitJ39-RSR-45-coot-14.pdb
Summary of feedback from opening /Users/biq2001/Dropbox/Biao's_folder/Cys-and-
D-Asp/D-Asp/iOFS*-DAS-fitJ39-RSR-45-coot-14.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
6193 messages similar to the above omitted
Chain information for iOFS*-DAS-fitJ39-RSR-45-coot-14.pdb #4
---
Chain | Description
A B C | No description available
> ui tool show Matchmaker
> matchmaker #!4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker iOFS*-GlufitJ150.pdb, chain A (#2) with iOFS*-DAS-
fitJ39-RSR-45-coot-14.pdb, chain A (#4), sequence alignment score = 1972.4
RMSD between 401 pruned atom pairs is 0.505 angstroms; (across all 406 pairs:
0.601)
> color #4:13-83, 125-275 wheat
> hide #!3 models
> hide #!4 cartoons
> hide #!4 atoms
> show #!4 cartoons
> color #4: 84-124, 276-500 plum
> show #!2 models
> hide #!4 models
> show #!2 cartoons
> hide #!2 cartoons
> hide #!2 atoms
> show #!2 cartoons
> hide #!2 models
> show #!4 models
> show #!3 models
> ui tool show "Color Zone"
> color zone #3 near #4 distance 6.46
> color zone #3 near #4 distance 5
[Repeated 1 time(s)]
> color zone #3 near #4 distance 3
[Repeated 1 time(s)]
> surface dust #3 size 10.8
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view cys-trimer-side-view2
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 cartoons
[Repeated 1 time(s)]
> show #!4 atoms
> hide #!4 cartoons
[Repeated 2 time(s)]
> hide #!4 atoms
> show #!4 cartoons
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> select $3:10-500
Expected an objects specifier or a keyword
> select #3:10-500
Nothing selected
> select #4:10-500
9255 atoms, 9393 bonds, 6 pseudobonds, 1218 residues, 2 models selected
> color zone #3 near sel distance 3
> show #!3 models
> show #!2 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> show #!3 models
> hide #!1 models
> view name
Missing or invalid "name" argument: Expected a text string
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> log
> color zone #3 near sel distance 2
[Repeated 1 time(s)]
> select #4:10-500
9255 atoms, 9393 bonds, 6 pseudobonds, 1218 residues, 2 models selected
> color zone #3 near sel distance 2
> select #4:10-500
9255 atoms, 9393 bonds, 6 pseudobonds, 1218 residues, 2 models selected
> show #!4 models
> color zone #3 near sel distance 2
[Repeated 1 time(s)]
> color zone #3 near sel distance 3
[Repeated 7 time(s)]
> color zone #3 near sel distance 5
[Repeated 1 time(s)]
> color zone #3 near sel distance 3
[Repeated 2 time(s)]
> color zone #3 near sel distance 2
[Repeated 5 time(s)]
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> color zone #3 near sel distance 3
[Repeated 2 time(s)]
> color zone #3 near sel distance 3.5
[Repeated 1 time(s)]
> color zone #3 near sel distance 2.05
[Repeated 1 time(s)]
> color zone #3 near sel distance 2.12
> color zone #3 near sel distance 5.58
> color zone #3 near sel distance 5.27
> color zone #3 near sel distance 3
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view cys-trimer-side-view2
> hide #!4 models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 9255 atom styles
> style sel ball
Changed 9255 atom styles
> show #!3 models
> hide #!3 models
> style sel stick
Changed 9255 atom styles
> show #!3 models
> volume #3 level 0.1657
> volume #3 level 0.614
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view cys-trimer-side-view2
> save /Users/biq2001/Documents/Work/Cys-story-figures-scrach/figure-2/all-
> ligand-color-map.cxs
——— End of log from Thu May 16 16:26:30 2024 ———
opened ChimeraX session
> hide #!3 models
> show #!1 models
> hide #!4 models
> select add #4
9297 atoms, 9417 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> open /Users/biq2001/Dropbox/Biao's_folder/Cys-and-D-Asp/iOFS-L-Asp-
> Trimer/cryosparc_P100_J155_008_volume_map_sharp.mrc
Opened cryosparc_P100_J155_008_volume_map_sharp.mrc as #5, grid size
240,240,240, pixel 1.16, shown at level 0.238, step 1, values float32
> hide #!1 models
> volume #5 level 0.5038
> show #!3 models
> hide #!3 models
> select #5
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.33855,-0.72667,-0.59778,282.92,-0.71099,0.21858,-0.66837,308.02,0.61635,0.65129,-0.44265,39.142
> view matrix models
> #5,0.12434,-0.98778,0.094018,245.6,-0.92369,-0.080622,0.37456,223.18,-0.36241,-0.13342,-0.92242,357.28
> show #!1 models
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.12434,-0.98778,0.094018,245.72,-0.92369,-0.080622,0.37456,234.64,-0.36241,-0.13342,-0.92242,343.26
> view matrix models
> #5,0.12434,-0.98778,0.094018,236.1,-0.92369,-0.080622,0.37456,210.44,-0.36241,-0.13342,-0.92242,332.37
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.22084,-0.97531,0.0018087,234.53,-0.90313,-0.20379,0.37792,223.95,-0.36822,-0.085091,-0.92584,327.06
> view matrix models
> #5,0.70144,-0.71272,0.0011371,130.53,-0.70313,-0.69173,0.16467,294.62,-0.11658,-0.1163,-0.98635,304.79
> view matrix models
> #5,0.64103,-0.73393,-0.22458,175.77,-0.75726,-0.65245,-0.029259,325.9,-0.12505,0.18882,-0.97402,262.21
> view matrix models
> #5,0.66075,-0.70287,0.2634,95.695,-0.68643,-0.7078,-0.16683,344.07,0.3037,-0.070573,-0.95015,233.62
> view matrix models
> #5,0.70933,-0.69412,0.12263,108.68,-0.68313,-0.71985,-0.1231,338.72,0.17372,0.0035526,-0.98479,247.01
> view matrix models
> #5,0.90043,-0.42625,0.086751,50.192,-0.40415,-0.89354,-0.19557,333.95,0.16088,0.14104,-0.97685,228.74
> view matrix models
> #5,0.75412,-0.6558,-0.03509,120.68,-0.64504,-0.72959,-0.2272,350.24,0.1234,0.19397,-0.97322,226.23
> ui tool show "Fit in Map"
> fitmap #5 inMap #1
Fit map cryosparc_P100_J155_008_volume_map_sharp.mrc in map
cryosparc_P61_J150_008_volume_map_sharp.mrc using 42254 points
correlation = 0.2219, correlation about mean = 0.03239, overlap = 9620
steps = 92, shift = 2.03, angle = 4.76 degrees
Position of cryosparc_P100_J155_008_volume_map_sharp.mrc (#5) relative to
cryosparc_P61_J150_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.77036592 -0.63611202 0.04356409 105.61079017
-0.61105813 -0.75607860 -0.23442080 350.59906350
0.18205577 0.15396961 -0.97115861 222.18562015
Axis 0.94017631 -0.33524668 0.06064795
Axis point 0.00000000 181.77647009 127.06380850
Rotation angle (degrees) 168.07963887
Shift along axis -4.76930740
> fitmap #5 inMap #3
Fit map cryosparc_P100_J155_008_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 42254 points
correlation = 0.2794, correlation about mean = 0.03792, overlap = 1.236e+04
steps = 112, shift = 1.63, angle = 7.1 degrees
Position of cryosparc_P100_J155_008_volume_map_sharp.mrc (#5) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.90048967 -0.43153651 0.05380142 71.23710333
-0.42093825 -0.89600200 -0.14139098 346.30685931
0.10922155 0.10467404 -0.98849077 264.69452092
Axis 0.97470255 -0.21952792 0.04198141
Axis point 0.00000000 172.57779889 142.10226702
Rotation angle (degrees) 172.74845604
Shift along axis 4.52320995
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> view matrix models
> #5,0.91591,-0.39926,0.041284,53.138,-0.38143,-0.89777,-0.22026,337.23,0.12501,0.18599,-0.97457,225.68
> fitmap #5 inMap #3
Fit map cryosparc_P100_J155_008_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 42254 points
correlation = 0.2844, correlation about mean = 0.06045, overlap = 1.293e+04
steps = 168, shift = 3.7, angle = 5.39 degrees
Position of cryosparc_P100_J155_008_volume_map_sharp.mrc (#5) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.93692161 -0.32707435 0.12328933 38.29272450
-0.30067741 -0.93401597 -0.19289182 340.98515961
0.17824417 0.14365420 -0.97344362 245.86383568
Axis 0.98398515 -0.16067564 0.07717873
Axis point 0.00000000 162.86356567 136.36862016
Rotation angle (degrees) 170.15335131
Shift along axis 1.86692228
> fitmap #5 inMap #3
Fit map cryosparc_P100_J155_008_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 42254 points
correlation = 0.2845, correlation about mean = 0.06058, overlap = 1.294e+04
steps = 40, shift = 0.014, angle = 0.0582 degrees
Position of cryosparc_P100_J155_008_volume_map_sharp.mrc (#5) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.93661885 -0.32796262 0.12323008 38.45880372
-0.30161880 -0.93376555 -0.19263435 341.03277028
0.17824487 0.14325645 -0.97350211 245.93206335
Axis 0.98390811 -0.16115207 0.07716764
Axis point 0.00000000 162.92703997 136.37122359
Rotation angle (degrees) 170.17193494
Shift along axis 1.85978909
> view matrix models
> #5,0.79963,-0.59231,0.098792,84.321,-0.57293,-0.8018,-0.1699,342.84,0.17985,0.07926,-0.9805,232.02
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.79963,-0.59231,0.098792,82.009,-0.57293,-0.8018,-0.1699,340.99,0.17985,0.07926,-0.9805,232.95
> fitmap #5 inMap #3
Fit map cryosparc_P100_J155_008_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 42254 points
correlation = 0.3878, correlation about mean = 0.1191, overlap = 1.897e+04
steps = 132, shift = 2.58, angle = 13.5 degrees
Position of cryosparc_P100_J155_008_volume_map_sharp.mrc (#5) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.94080033 -0.33896115 0.00026654 53.87686734
-0.33896101 -0.94080030 -0.00046289 315.99131341
0.00040766 0.00034514 -0.99999985 297.08399870
Axis 0.98508882 -0.17204647 0.00017083
Axis point 0.00000000 162.66955152 148.57019566
Rotation angle (degrees) 179.97650110
Shift along axis -1.24094134
> fitmap #5 inMap #3
Fit map cryosparc_P100_J155_008_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 42254 points
correlation = 0.3877, correlation about mean = 0.1188, overlap = 1.896e+04
steps = 28, shift = 0.0264, angle = 0.0178 degrees
Position of cryosparc_P100_J155_008_volume_map_sharp.mrc (#5) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.94069777 -0.33924570 0.00025699 53.93193243
-0.33924553 -0.94069771 -0.00053006 316.02750096
0.00042158 0.00041144 -0.99999982 297.09922376
Axis 0.98506280 -0.17219537 0.00017198
Axis point 0.00000000 162.69154302 148.58320706
Rotation angle (degrees) 179.97261895
Shift along axis -1.24103709
> view matrix models
> #5,0.87696,-0.48056,0.00037145,67.57,-0.48056,-0.87696,-0.0006338,310.66,0.00063032,0.00037732,-1,272.8
> fitmap #5 inMap #3
Fit map cryosparc_P100_J155_008_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 42254 points
correlation = 0.3877, correlation about mean = 0.1188, overlap = 1.896e+04
steps = 60, shift = 2.51, angle = 0.00722 degrees
Position of cryosparc_P100_J155_008_volume_map_sharp.mrc (#5) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.94065549 -0.33936292 0.00023881 53.95719752
-0.33936276 -0.94065543 -0.00052778 316.03757417
0.00040375 0.00041541 -0.99999983 297.10014316
Axis 0.98505207 -0.17225675 0.00016285
Axis point 0.00000000 162.70045468 148.58398552
Rotation angle (degrees) 179.97256951
Shift along axis -1.24057449
> fitmap #5 inMap #3
Fit map cryosparc_P100_J155_008_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 42254 points
correlation = 0.3879, correlation about mean = 0.119, overlap = 1.897e+04
steps = 28, shift = 0.0251, angle = 0.0123 degrees
Position of cryosparc_P100_J155_008_volume_map_sharp.mrc (#5) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.94072624 -0.33916672 0.00026887 53.91680347
-0.33916657 -0.94072621 -0.00048715 316.01382397
0.00041816 0.00036708 -0.99999984 297.07982204
Axis 0.98507002 -0.17215407 0.00017410
Axis point 0.00000000 162.68556005 148.56989705
Rotation angle (degrees) 179.97515719
Shift along axis -1.23951695
> view matrix models
> #5,0.877,-0.48048,0.00038981,65.724,-0.48048,-0.877,-0.00059324,307.79,0.00062691,0.00033298,-1,274.79
> view matrix models
> #5,0.877,-0.48048,0.00038981,65.744,-0.48048,-0.877,-0.00059324,307.83,0.00062691,0.00033298,-1,274.8
> view matrix models
> #5,0.877,-0.48048,0.00038981,66.394,-0.48048,-0.877,-0.00059324,309.16,0.00062691,0.00033298,-1,273.65
> view matrix models
> #5,0.877,-0.48048,0.00038981,68.158,-0.48048,-0.877,-0.00059324,308.97,0.00062691,0.00033298,-1,273.01
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.82496,-0.56462,0.025344,83.352,-0.56401,-0.81954,0.10118,297.66,-0.036357,-0.097763,-0.99455,290.91
> fitmap #5 inMap #3
Fit map cryosparc_P100_J155_008_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 42254 points
correlation = 0.9602, correlation about mean = 0.8774, overlap = 6.895e+04
steps = 100, shift = 5.97, angle = 7.35 degrees
Position of cryosparc_P100_J155_008_volume_map_sharp.mrc (#5) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.93167673 -0.36328839 -0.00006493 58.61574286
-0.36328839 -0.93167674 0.00004534 317.97969905
-0.00007697 -0.00001866 -0.99999999 291.84096413
Axis -0.98277202 0.18482195 0.00003266
Axis point 0.00000000 164.50396003 145.91882412
Rotation angle (degrees) 179.99813436
Shift along axis 1.17324751
> hide #!2 models
> show #!1 models
> select clear
> fitmap #5 inMap #1
Fit map cryosparc_P100_J155_008_volume_map_sharp.mrc in map
cryosparc_P61_J150_008_volume_map_sharp.mrc using 42254 points
correlation = 0.8958, correlation about mean = 0.7764, overlap = 6.158e+04
steps = 40, shift = 0.0035, angle = 0.00485 degrees
Position of cryosparc_P100_J155_008_volume_map_sharp.mrc (#5) relative to
cryosparc_P61_J150_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.86429891 -0.50297849 0.00016509 73.43999913
-0.50297850 -0.86429892 0.00002232 314.06928799
0.00013147 -0.00010233 -0.99999998 268.30361728
Axis -0.96547979 0.26047798 -0.00007880
Axis point 0.00000000 166.94586249 134.14360939
Rotation angle (degrees) 179.99630154
Shift along axis 10.88215617
> fitmap #5 inMap #1
Fit map cryosparc_P100_J155_008_volume_map_sharp.mrc in map
cryosparc_P61_J150_008_volume_map_sharp.mrc using 42254 points
correlation = 0.8958, correlation about mean = 0.7764, overlap = 6.158e+04
steps = 28, shift = 0.00213, angle = 0.00901 degrees
Position of cryosparc_P100_J155_008_volume_map_sharp.mrc (#5) relative to
cryosparc_P61_J150_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.86422684 -0.50310234 0.00010050 73.47888859
-0.50310234 -0.86422684 0.00002764 314.07494354
0.00007295 -0.00007445 -0.99999999 268.30782702
Axis -0.96546132 0.26054641 -0.00004737
Axis point 0.00000000 166.95591868 134.14784966
Rotation angle (degrees) 179.99697055
Shift along axis 10.87736417
> open /Users/biq2001/Dropbox/Biao's_folder/Cys-and-D-Asp/iOFS-L-Asp-
> Trimer/iOFS_-LAsp-fit-J155-RSR18-coot-13.pdb
Summary of feedback from opening /Users/biq2001/Dropbox/Biao's_folder/Cys-and-
D-Asp/iOFS-L-Asp-Trimer/iOFS_-LAsp-fit-J155-RSR18-coot-13.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
6199 messages similar to the above omitted
Chain information for iOFS_-LAsp-fit-J155-RSR18-coot-13.pdb #6
---
Chain | Description
A B C | No description available
> ui tool show Matchmaker
> matchmaker #!6 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker iOFS*-GlufitJ150.pdb, chain A (#2) with iOFS_-LAsp-
fit-J155-RSR18-coot-13.pdb, chain A (#6), sequence alignment score = 2003
RMSD between 401 pruned atom pairs is 0.499 angstroms; (across all 406 pairs:
0.606)
> hide #!1 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> hide #!6 atoms
> color #6: 84-124, 276-500 skyblue
> color #4:13-83, 125-275 wheat
> color #6:13-83, 125-275 wheat
> select #5:1-500
Nothing selected
> select #6:1-500
9255 atoms, 9393 bonds, 6 pseudobonds, 1218 residues, 2 models selected
> ui tool show "Color Zone"
> color zone #5 near sel distance 3
> show #!5 models
> view matrix models
> #6,-0.67762,-0.72448,0.12632,300.46,-0.7324,0.68034,-0.026877,135.28,-0.066467,-0.11073,-0.99163,291.79
> view matrix models
> #6,-0.83986,-0.53079,0.11357,297.93,-0.53464,0.84507,-0.0041147,81.061,-0.093794,-0.064177,-0.99352,289.37
> undo
[Repeated 1 time(s)]
> select clear
> ui mousemode right "translate selected models"
> surface dust #5 size 11.6
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view cys-trimer-side-view2
> volume #5 level 0.614
> hide #!6 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!5 models
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view cys-trimer-side-view2
> lighting simple
> lighting soft
> show #!1 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> show #!3 models
> show #!5 models
> hide #!3 models
> hide #!5 models
> open
> /Users/biq2001/Dropbox/Biao's_folder/R-2HG-300Kv/cryosparc_P113_J33_009_volume_map_sharp.mrc
Opened cryosparc_P113_J33_009_volume_map_sharp.mrc as #7, grid size
320,320,320, pixel 0.844, shown at level 0.13, step 2, values float32
> volume #7 step 1
> volume #7 level 0.2588
> hide #!1 models
> show #!3 models
> select #7
2 models selected
> view matrix models #7,1,0,0,-13.679,0,1,0,-7.8079,0,0,1,-16.462
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.92031,-0.39099,0.012182,49.073,0.39022,0.91979,0.041453,-55.017,-0.027413,-0.033396,0.99907,-8.0573
> view matrix models
> #7,0.8899,-0.45597,0.012985,61.982,0.45536,0.88966,0.033848,-58.609,-0.026987,-0.024209,0.99934,-9.4142
> ui tool show "Fit in Map"
[Repeated 1 time(s)]
> fitmap #7 inMap #3
Fit map cryosparc_P113_J33_009_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 111734 points
correlation = 0.7367, correlation about mean = 0.557, overlap = 5.634e+04
steps = 120, shift = 4.27, angle = 6.98 degrees
Position of cryosparc_P113_J33_009_volume_map_sharp.mrc (#7) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.73524340 -0.67780312 0.00026368 129.93217046
0.67780317 0.73524337 -0.00020318 -53.12548622
-0.00005615 0.00032811 0.99999994 6.20312125
Axis 0.00039192 0.00023593 0.99999990
Axis point 132.97001462 139.75302306 0.00000000
Rotation angle (degrees) 42.67221631
Shift along axis 6.24150962
> fitmap #7 inMap #3
Fit map cryosparc_P113_J33_009_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 111734 points
correlation = 0.7365, correlation about mean = 0.5563, overlap = 5.634e+04
steps = 36, shift = 0.013, angle = 0.0162 degrees
Position of cryosparc_P113_J33_009_volume_map_sharp.mrc (#7) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.73543410 -0.67759620 0.00028675 129.88092975
0.67759625 0.73543408 -0.00018346 -53.12569439
-0.00008658 0.00032922 0.99999994 6.21884555
Axis 0.00037831 0.00027548 0.99999989
Axis point 132.97326341 139.75635184 0.00000000
Rotation angle (degrees) 42.65609372
Shift along axis 6.25334495
> volume #7 level 0.3741
> view matrix models
> #7,0.84088,-0.54106,0.013416,81.41,0.54097,0.84098,0.010147,-64.368,-0.016773,-0.0012749,0.99986,-14.837
> fitmap #7 inMap #3
Fit map cryosparc_P113_J33_009_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 76350 points
correlation = 0.7588, correlation about mean = 0.5537, overlap = 5.336e+04
steps = 44, shift = 0.0501, angle = 1.39 degrees
Position of cryosparc_P113_J33_009_volume_map_sharp.mrc (#7) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.73546285 -0.67756498 0.00028914 129.86850420
0.67756502 0.73546287 -0.00006145 -53.14460946
-0.00017102 0.00024111 0.99999996 6.22633133
Axis 0.00022327 0.00033957 0.99999992
Axis point 132.99652522 139.74244929 0.00000000
Rotation angle (degrees) 42.65365998
Shift along axis 6.23728048
> select clear
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view cys-trimer-side-view2
> select #7
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.83135,-0.55576,7.6709e-05,86.597,0.55576,0.83135,-3.5013e-05,-63.821,-4.4313e-05,7.1739e-05,1,-16.124
> ui tool show "Fit in Map"
> select clear
> open /Users/biq2001/Dropbox/Biao's_folder/R-2HG-300Kv/8cv3-iofs-Na-
> fit-J33.pdb
Chain information for 8cv3-iofs-Na-fit-J33.pdb #8
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!8 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker iOFS*-GlufitJ150.pdb, chain A (#2) with 8cv3-iofs-Na-fit-J33.pdb,
chain A (#8), sequence alignment score = 1933.4
RMSD between 272 pruned atom pairs is 1.066 angstroms; (across all 406 pairs:
2.311)
> hide #!3 models
> volume #7 level 0.238
> surface dust #7 size 8.44
> volume #7 level 0.34
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view cys-trimer-side-view2
> color #8:13-83, 125-275 wheat
> hide #!8 atoms
> color #8: 84-124, 276-500 lightblue greenwheat
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #8: 84-124, 276-500 light green
> open /Users/biq2001/Dropbox/Biao's_folder/R-2HG-300Kv/OFS-Na-fit-J33.pdb
Chain information for OFS-Na-fit-J33.pdb #9
---
Chain | Description
A B C | No description available
> ui tool show Matchmaker
> matchmaker #!2 to #9
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 OFS-Na-fit-J33.pdb, chain A (#9) with iOFS*-GlufitJ150.pdb, chain A
(#2), sequence alignment score = 1934.6
RMSD between 170 pruned atom pairs is 0.633 angstroms; (across all 406 pairs:
4.309)
> ui tool show Matchmaker
> matchmaker #!9 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker iOFS*-GlufitJ150.pdb, chain A (#2) with OFS-Na-fit-J33.pdb, chain A
(#9), sequence alignment score = 1934.6
RMSD between 170 pruned atom pairs is 0.633 angstroms; (across all 406 pairs:
4.309)
> hide #!8 models
> show #!8 models
> show #!2 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!7 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> close #8
> close #9
> show #!4 models
> ui tool show Matchmaker
> matchmaker #!2 to #4
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 iOFS*-DAS-fitJ39-RSR-45-coot-14.pdb, chain A (#4) with
iOFS*-GlufitJ150.pdb, chain A (#2), sequence alignment score = 1972.4
RMSD between 401 pruned atom pairs is 0.505 angstroms; (across all 406 pairs:
0.601)
> open /Users/biq2001/Dropbox/Biao's_folder/R-2HG-300Kv/OFS-Na-fit-J33.pdb
Chain information for OFS-Na-fit-J33.pdb #8
---
Chain | Description
A B C | No description available
> ui tool show Matchmaker
> matchmaker #!8 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker iOFS*-GlufitJ150.pdb, chain A (#2) with OFS-Na-fit-J33.pdb, chain A
(#8), sequence alignment score = 1934.6
RMSD between 170 pruned atom pairs is 0.633 angstroms; (across all 406 pairs:
4.309)
> hide #!2 models
> hide #!7 models
> hide #!4,8 cartoons
> show #!4,8 cartoons
> hide #!4,8 atoms
> ui tool show "Fit in Map"
> fitmap #8 inMap #7
Fit molecule OFS-Na-fit-J33.pdb (#8) to map
cryosparc_P113_J33_009_volume_map_sharp.mrc (#7) using 9882 atoms
average map value = 0.6546, steps = 68
shifted from previous position = 1.44
rotated from previous position = 1.58 degrees
atoms outside contour = 3067, contour level = 0.34
Position of OFS-Na-fit-J33.pdb (#8) relative to
cryosparc_P113_J33_009_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.50001312 -0.86601783 -0.00002826 319.62473921
0.86601783 -0.50001312 0.00006628 85.63380241
-0.00007153 0.00000867 1.00000000 0.00932509
Axis -0.00003326 0.00002498 1.00000000
Axis point 135.09245274 135.08300175 0.00000000
Rotation angle (degrees) 120.00086800
Shift along axis 0.00083368
> show #!7 models
> hide #!7 models
> hide #!8 models
> hide #!4 models
> show #!3 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select #7
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.83135,-0.55576,7.6709e-05,86.268,0.55576,0.83135,-3.5013e-05,-63.572,-4.4313e-05,7.1739e-05,1,-16.469
> view matrix models
> #7,0.83135,-0.55576,7.6709e-05,86.055,0.55576,0.83135,-3.5013e-05,-63.157,-4.4313e-05,7.1739e-05,1,-17.146
> view matrix models
> #7,0.83135,-0.55576,7.6709e-05,86.264,0.55576,0.83135,-3.5013e-05,-63.27,-4.4313e-05,7.1739e-05,1,-17.499
> fitmap #7 inMap #3
Fit map cryosparc_P113_J33_009_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 84675 points
correlation = 0.7523, correlation about mean = 0.5538, overlap = 5.425e+04
steps = 40, shift = 0.494, angle = 0.00559 degrees
Position of cryosparc_P113_J33_009_volume_map_sharp.mrc (#7) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.73545234 -0.67757640 0.00026944 129.87532572
0.67757645 0.73545233 -0.00015573 -53.13708384
-0.00009264 0.00029710 0.99999995 6.21315379
Axis 0.00033416 0.00026719 0.99999991
Axis point 132.98781870 139.75047451 0.00000000
Rotation angle (degrees) 42.65455030
Shift along axis 6.24235451
> fitmap #7 inMap #3
Fit map cryosparc_P113_J33_009_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 84675 points
correlation = 0.7523, correlation about mean = 0.5537, overlap = 5.425e+04
steps = 28, shift = 0.0234, angle = 0.00342 degrees
Position of cryosparc_P113_J33_009_volume_map_sharp.mrc (#7) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.73545746 -0.67757083 0.00032865 129.85427072
0.67757089 0.73545745 -0.00015470 -53.11693771
-0.00013689 0.00033646 0.99999993 6.21612344
Axis 0.00036244 0.00034354 0.99999988
Axis point 132.95277375 139.73497491 0.00000000
Rotation angle (degrees) 42.65411830
Shift along axis 6.24493931
> fitmap #7 inMap #3
Fit map cryosparc_P113_J33_009_volume_map_sharp.mrc in map
cryosparc_P59_J39_008_volume_map_sharp.mrc using 84675 points
correlation = 0.7524, correlation about mean = 0.5538, overlap = 5.425e+04
steps = 28, shift = 0.021, angle = 0.00405 degrees
Position of cryosparc_P113_J33_009_volume_map_sharp.mrc (#7) relative to
cryosparc_P59_J39_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.73544331 -0.67758620 0.00027881 129.87321998
0.67758625 0.73544329 -0.00020035 -53.13004019
-0.00006930 0.00033626 0.99999994 6.20473431
Axis 0.00039597 0.00025687 0.99999989
Axis point 132.97613447 139.74756737 0.00000000
Rotation angle (degrees) 42.65531465
Shift along axis 6.24251236
> fitmap #8 inMap #7
Fit molecule OFS-Na-fit-J33.pdb (#8) to map
cryosparc_P113_J33_009_volume_map_sharp.mrc (#7) using 9882 atoms
average map value = 0.6545, steps = 52
shifted from previous position = 1.2
rotated from previous position = 0.00869 degrees
atoms outside contour = 3071, contour level = 0.34
Position of OFS-Na-fit-J33.pdb (#8) relative to
cryosparc_P113_J33_009_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.49993042 -0.86606557 -0.00002676 319.61976063
0.86606557 -0.49993042 0.00006905 85.61572117
-0.00007318 0.00001134 1.00000000 -0.00564482
Axis -0.00003332 0.00002680 1.00000000
Axis point 135.09245735 135.08269789 0.00000000
Rotation angle (degrees) 119.99539673
Shift along axis -0.01399909
> fitmap #8 inMap #7
Fit molecule OFS-Na-fit-J33.pdb (#8) to map
cryosparc_P113_J33_009_volume_map_sharp.mrc (#7) using 9882 atoms
average map value = 0.6545, steps = 40
shifted from previous position = 0.00401
rotated from previous position = 0.00962 degrees
atoms outside contour = 3070, contour level = 0.34
Position of OFS-Na-fit-J33.pdb (#8) relative to
cryosparc_P113_J33_009_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.50007001 -0.86598498 -0.00002809 319.62829963
0.86598498 -0.50007001 0.00002190 85.65576180
-0.00003301 -0.00001337 1.00000000 -0.00717938
Axis -0.00002036 0.00000284 1.00000000
Axis point 135.08976932 135.08801026 0.00000000
Rotation angle (degrees) 120.00463194
Shift along axis -0.01344468
> show #!8 models
> select clear
> view list
Named views: Cys-trimer-side, cys-trimer-side-view2
> view cys-trimer-side-view2
> hide #!3 models
> color #8: 84-124, 276-500 light green
> color #8:13-83, 125-275 wheat
> hide #!7 models
> lighting simple
> lighting soft
> ui tool show "Color Zone"
> color zone #7 near #8 distance 5.07
> show #!7 models
> color zone #7 near #8 distance 3
[Repeated 2 time(s)]
> show target m
> hide target m
> show #!7 models
> show #!8 models
> show target m
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> select add #7.1
1 model selected
> view #7.1 clip false
> show #7.1 target m
> ui tool show "Model Panel"
[Repeated 1 time(s)]
> save /Users/biq2001/Documents/Work/Cys-story-figures-scrach/figure-2/all-
> ligand-color-map.cxs
——— End of log from Fri May 17 16:45:44 2024 ———
opened ChimeraX session
> volume #7 level 0.204
> select #8:1-500
9876 atoms, 10023 bonds, 3 pseudobonds, 1299 residues, 2 models selected
> ui tool show "Color Zone"
> color zone #5 near #8 distance 1.16
> color zone #7 near sel distance 3
[Repeated 1 time(s)]
> hide #!8 models
> show #!8 models
> hide #!7 models
> hide #!8 models
> show #!8 models
> show #!7 models
> hide #!8 models
> volume #7 level 0.34
> hide #!5 models
> show #!7 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!7 models
> hide #!7 models
> show #!7 models
> color #7 gray
> hide #!7 models
> show #!1 models
> show #!7 models
> color #7 dark gray
> color #7 darkgray
> color #7 silver
> hide #!7 models
> show #!7 models
> hide #!7 models
> color #7 light gray
> color #5 #bfbfbfff models
> show #!7 models
> hide #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!7 models
> color #7 dark gray
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> color #7 light gray
> color #7 silver
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> initial color
Unknown command: initial color
> initial colors
Unknown command: initial colors
> initialColors
Unknown command: initialColors
> save /Users/biq2001/Documents/Work/Cys-story-figures-scrach/figure-2/all-
> ligand-color-map.cxs
——— End of log from Fri May 17 17:01:07 2024 ———
opened ChimeraX session
OpenGL version: 4.1 INTEL-20.7.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 526.0.0.0.0
OS Loader Version: 577.140.2~22
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.6.6 (22G630)
Kernel Version: Darwin 22.6.0
Time since boot: 13 hours, 11 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL U2917W:
Resolution: 2560 x 1080 (UW-UXGA - Ultra Wide - Ultra Extended Graphics Array)
UI Looks like: 2560 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 0PRH47BPALTL
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 17 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash giving widget focus |
comment:2 by , 17 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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