![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Closed 12 months ago
#16237 closed defect (duplicate)
Crash on Mac waking from sleep
| 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-14.7.1-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202404140648 (2024-04-14 06:48:11 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
{"app_name":"ChimeraX","timestamp":"2024-11-03 13:32:52.00 +0000","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.7.1 (23H222)","roots_installed":0,"name":"ChimeraX","incident_id":"8C20CE5E-FABC-4912-A369-A5A10ED877E3"}
{
"uptime" : 43000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 1155,
"osVersion" : {
"train" : "macOS 14.7.1",
"build" : "23H222",
"releaseType" : "User"
},
"captureTime" : "2024-11-03 13:32:28.7943 +0000",
"codeSigningMonitor" : 0,
"incident" : "8C20CE5E-FABC-4912-A369-A5A10ED877E3",
"pid" : 1219,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-11-02 17:41:53.4238 +0000",
"procStartAbsTime" : 1936882213565,
"procExitAbsTime" : 43451533175214,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7FF298D8-9CAA-50B0-B14E-B75862530066","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "29B489BC-839B-868D-A960-82E747B97847",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 2497,
"bridgeVersion" : {"build":"22P1072","train":"9.1"},
"sleepWakeUUID" : "B4E5AE8B-A518-4EC0-9768-1A12D40BB6BB",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000002, 0x0000000000000000","rawCodes":[2,0],"type":"EXC_BREAKPOINT","signal":"SIGTRAP"},
"termination" : {"flags":0,"code":5,"namespace":"SIGNAL","indicator":"Trace\/BPT trap: 5","byProc":"exc handler","byPid":1219},
"os_fault" : {"process":"ChimeraX"},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202404140648 (2024-04-14)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/chitrajoshi/Desktop/Chimera session nov 24.cxs"
Opened cryosparc_P71_J32_class_03_final_volume.mrc as #1, grid size
192,192,192, pixel 1.25, shown at level 0.122, step 1, values float32
Opened cryosparc_P70_J10_class_00_final_volume.mrc as #2, grid size
256,256,256, pixel 0.936, shown at step 1, values float32
Opened cryosparc_P70_J20_class_00_final_volume.mrc as #3, grid size
192,192,192, pixel 1.25, shown at step 1, values float32
Opened cryosparc_P71_J32_class_03_final_volume.mrc z flip as #5, grid size
192,192,192, pixel 1.25, shown at step 1, values float32
Opened cryosparc_P71_J40_class_00_final_volume.mrc as #6, grid size
256,256,256, pixel 0.936, shown at step 1, values float32
Opened cryosparc_P71_J40_class_00_final_volume.mrc z flip as #7, grid size
256,256,256, pixel 0.936, shown at step 1, values float32
Opened cryosparc_P70_J21_class_00_final_volume.mrc as #8, grid size
256,256,256, pixel 0.936, shown at step 1, values float32
Opened cryosparc_P71_J45_002_volume_map.mrc as #10, grid size 288,288,288,
pixel 0.832, shown at step 2, values float32
Opened cryosparc_P71_J44_class_01_final_volume.mrc as #11, grid size
192,192,192, pixel 1.25, shown at step 1, values float32
Opened cryosparc_P71_J44_class_01_final_volume.mrc z flip as #12, grid size
192,192,192, pixel 1.25, shown at step 1, values float32
Opened cryosparc_P71_J51_002_volume_map.mrc as #14, grid size 288,288,288,
pixel 0.832, shown at step 2, values float32
Opened cryosparc_P71_J51_002_volume_map.mrc z flip as #15, grid size
288,288,288, pixel 0.832, shown at step 1, values float32
Opened cryosparc_P71_J53_class_00_final_volume.mrc as #16, grid size
256,256,256, pixel 0.936, shown at step 1, values float32
Opened cryosparc_P71_J54_002_volume_map.mrc as #17, grid size 288,288,288,
pixel 0.832, shown at level 0.341, step 1, values float32
Opened cryosparc_P71_J46_class_00_final_volume.mrc as #18, grid size
256,256,256, pixel 0.936, shown at level 0.295, step 1, values float32
Opened cryosparc_P124_J314_009_volume_map_sharp.mrc as #19, grid size
196,196,196, pixel 1.46, shown at level 2.9, step 1, values float32
Log from Sat Nov 2 16:14:23 2024UCSF ChimeraX version: 1.8.dev202404140648
(2024-04-14)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P71_J32_class_03_final_volume.mrc"
Opened cryosparc_P71_J32_class_03_final_volume.mrc as #1, grid size
192,192,192, pixel 1.25, shown at level 0.307, step 1, values float32
> volume #1 level 0.5272
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P70_J10_class_00_final_volume.mrc"
Opened cryosparc_P70_J10_class_00_final_volume.mrc as #2, grid size
256,256,256, pixel 0.936, shown at level 0.217, step 1, values float32
> volume #2 level 0.4561
> surface dust #1 size 12.5
> surface dust #2 size 9.36
> ui tool show Matchmaker
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit map cryosparc_P71_J32_class_03_final_volume.mrc in map
cryosparc_P70_J10_class_00_final_volume.mrc using 10046 points
correlation = 0.811, correlation about mean = 0.1363, overlap = 2278
steps = 84, shift = 2.47, angle = 7.24 degrees
Position of cryosparc_P71_J32_class_03_final_volume.mrc (#1) relative to
cryosparc_P70_J10_class_00_final_volume.mrc (#2) coordinates:
Matrix rotation and translation
0.99251463 -0.05806448 -0.10743942 21.02444294
0.06136158 0.99773288 0.02763813 -9.83268125
0.10559105 -0.03402390 0.99382740 -5.56019290
Axis -0.24480095 -0.84574019 0.47412659
Axis point 66.29078364 -0.00000000 192.28207205
Rotation angle (degrees) 7.23522848
Shift along axis 0.53285480
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P70_J20_class_00_final_volume.mrc"
Opened cryosparc_P70_J20_class_00_final_volume.mrc as #3, grid size
192,192,192, pixel 1.25, shown at level 0.302, step 1, values float32
> hide #!2 models
> volume #3 level 0.429
> ui tool show "Fit in Map"
> open "/Users/chitrajoshi/Desktop/SLCO2A1/structure/Justin outward
> open_AF_combined_coot3_P2E.pdb"
Justin outward open_AF_combined_coot3_P2E.pdb title:
Alphafold monomer V2.0 prediction for solute carrier organic anion transporter
family member 2A1 (Q00910) [more info...]
Chain information for Justin outward open_AF_combined_coot3_P2E.pdb #4
---
Chain | Description | UniProt
A | solute carrier organic anion transporter family member 2A1 | SO2A1_RAT 1-644
Non-standard residues in Justin outward open_AF_combined_coot3_P2E.pdb #4
---
P2E — (P2E)
> hide #!3 models
> fitmap #4 inMap #1
Fit molecule Justin outward open_AF_combined_coot3_P2E.pdb (#4) to map
cryosparc_P71_J32_class_03_final_volume.mrc (#1) using 4317 atoms
average map value = 0.3009, steps = 384
shifted from previous position = 29.6
rotated from previous position = 63.5 degrees
atoms outside contour = 3730, contour level = 0.52718
Position of Justin outward open_AF_combined_coot3_P2E.pdb (#4) relative to
cryosparc_P71_J32_class_03_final_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.74376239 0.66447785 0.07270967 -86.62507971
-0.31472623 0.44407402 -0.83889550 231.22239098
-0.58971595 0.60105528 0.53941416 39.82642388
Axis 0.77288286 0.35555202 -0.52558049
Axis point -0.00000000 100.64381691 211.33546488
Rotation angle (degrees) 68.67699510
Shift along axis -5.67144272
> rename #4 model
> ui mousemode right rotate
[Repeated 1 time(s)]
> ui mousemode right "rotate selected models"
> select add #4
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> view matrix models
> #4,0.90608,0.13192,-0.40202,38.265,-0.42057,0.17693,-0.88984,293.49,-0.046254,0.97534,0.2158,-39.765
> volume #1 level 0.4043
> view matrix models
> #4,0.91033,-0.058117,-0.40978,66.582,-0.40574,-0.32078,-0.85585,359.07,-0.081709,0.94537,-0.31559,48.442
> volume #1 level 0.5026
> view matrix models
> #4,0.78391,-0.61956,0.04043,99.273,0.014722,0.083648,0.99639,-33.406,-0.6207,-0.78048,0.074693,317.36
> view matrix models
> #4,0.79944,-0.57762,-0.16509,121.51,-0.0082627,-0.28535,0.95839,29.318,-0.6007,-0.7648,-0.23289,357.97
> view matrix models
> #4,0.77465,-0.60436,-0.18619,131.99,0.038937,-0.24827,0.96791,15.938,-0.63119,-0.75704,-0.16879,351.55
> ui mousemode right "move picked models"
> view matrix models
> #4,0.77465,-0.60436,-0.18619,125.77,0.038937,-0.24827,0.96791,12.675,-0.63119,-0.75704,-0.16879,350.93
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.73072,-0.62463,-0.27547,148.08,0.51748,0.24362,0.82028,-103.67,-0.44526,-0.74195,0.50126,223.42
> view matrix models
> #4,0.76916,-0.54199,-0.33858,140.05,0.5629,0.32377,0.76047,-112.8,-0.30254,-0.77551,0.55412,200.66
> fitmap #4 inMap #1
Fit molecule model (#4) to map cryosparc_P71_J32_class_03_final_volume.mrc
(#1) using 4317 atoms
average map value = 0.2833, steps = 108
shifted from previous position = 7.84
rotated from previous position = 15.6 degrees
atoms outside contour = 3615, contour level = 0.5026
Position of model (#4) relative to cryosparc_P71_J32_class_03_final_volume.mrc
(#1) coordinates:
Matrix rotation and translation
0.89374646 -0.37421461 -0.24734731 78.93054950
0.42192267 0.51406960 0.74680232 -117.63574421
-0.15231061 -0.77181337 0.61733751 163.56805580
Axis -0.88431312 -0.05534132 0.46360290
Axis point 0.00000000 95.83884071 218.95043329
Rotation angle (degrees) 59.16437890
Shift along axis 12.54142272
> view matrix models
> #4,0.93704,-0.19663,-0.28862,52.894,0.26955,0.93267,0.23971,-82.237,0.22205,-0.30242,0.92695,-1.7691
> fitmap #4 inMap #1
Fit molecule model (#4) to map cryosparc_P71_J32_class_03_final_volume.mrc
(#1) using 4317 atoms
average map value = 0.3081, steps = 124
shifted from previous position = 8.39
rotated from previous position = 9.47 degrees
atoms outside contour = 3514, contour level = 0.5026
Position of model (#4) relative to cryosparc_P71_J32_class_03_final_volume.mrc
(#1) coordinates:
Matrix rotation and translation
0.94721156 -0.30840708 -0.08760900 39.62490239
0.31999327 0.92634104 0.19873746 -90.56721134
0.01986377 -0.21628071 0.97612913 7.80329782
Axis -0.54556791 -0.14127982 0.82607243
Axis point 300.83240356 72.78625015 0.00000000
Rotation angle (degrees) 22.35562875
Shift along axis -2.37666719
> volume #1 level 0.4535
> volume #1 level 0.4719
> volume flip #1
Opened cryosparc_P71_J32_class_03_final_volume.mrc z flip as #5, grid size
192,192,192, pixel 1.25, shown at step 1, values float32
> select subtract #4
Nothing selected
> select add #5
2 models selected
> select subtract #5
Nothing selected
> select add #4
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> volume #1 level 0.478
> hide #!1 models
> volume #5 level 0.5517
> view matrix models
> #4,0.90242,-0.35174,-0.24882,76.083,0.26056,0.90548,-0.33499,0.24636,0.34313,0.23747,0.90877,-91.761
> view matrix models
> #4,0.99625,-0.055454,0.066371,-27.016,-0.056151,-0.99838,0.0086845,271.23,0.065782,-0.012379,-0.99776,266.34
> ui mousemode right "move picked models"
> view matrix models
> #4,0.99625,-0.055454,0.066371,-20.411,-0.056151,-0.99838,0.0086845,270.86,0.065782,-0.012379,-0.99776,256.85
> ui mousemode right "rotate selected models"
> fitmap #4 inMap #5
Fit molecule model (#4) to map cryosparc_P71_J32_class_03_final_volume.mrc z
flip (#5) using 4317 atoms
average map value = 0.3715, steps = 112
shifted from previous position = 6.94
rotated from previous position = 17.7 degrees
atoms outside contour = 3367, contour level = 0.55175
Position of model (#4) relative to cryosparc_P71_J32_class_03_final_volume.mrc
z flip (#5) coordinates:
Matrix rotation and translation
0.91767601 -0.37436118 -0.13313320 58.30158307
-0.34867923 -0.91941722 0.18191968 276.06459756
-0.19050862 -0.12052255 -0.97425909 303.74251721
Axis -0.97907586 0.18573759 0.08313844
Axis point 0.00000000 155.54970180 143.53663780
Rotation angle (degrees) 171.11493176
Shift along axis 19.44658162
> transparency 30 surfaces
> view matrix models
> #4,0.91443,-0.3538,-0.19657,66.011,-0.14049,-0.73293,0.66564,148,-0.37957,-0.58106,-0.71992,360.86
> undo
> ui mousemode right zoom
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P71_J40_class_00_final_volume.mrc"
Opened cryosparc_P71_J40_class_00_final_volume.mrc as #6, grid size
256,256,256, pixel 0.936, shown at level 0.199, step 1, values float32
> volume flip #6
Opened cryosparc_P71_J40_class_00_final_volume.mrc z flip as #7, grid size
256,256,256, pixel 0.936, shown at step 1, values float32
> hide #!5 models
> fitmap #4 inMap #7
Fit molecule model (#4) to map cryosparc_P71_J40_class_00_final_volume.mrc z
flip (#7) using 4317 atoms
average map value = 0.201, steps = 92
shifted from previous position = 6.72
rotated from previous position = 11.5 degrees
atoms outside contour = 2610, contour level = 0.1994
Position of model (#4) relative to cryosparc_P71_J40_class_00_final_volume.mrc
z flip (#7) coordinates:
Matrix rotation and translation
0.88313868 -0.46866698 -0.02042891 66.78740230
-0.45045608 -0.85937184 0.24201107 271.93534086
-0.13097863 -0.20452701 -0.97005840 305.49237044
Axis -0.96993510 0.24012745 0.03955630
Axis point 0.00000000 162.57689958 137.93623643
Rotation angle (degrees) 166.69176113
Shift along axis 12.60384223
> volume #7 level 0.3156
> fitmap #4 inMap #7
Fit molecule model (#4) to map cryosparc_P71_J40_class_00_final_volume.mrc z
flip (#7) using 4317 atoms
average map value = 0.201, steps = 44
shifted from previous position = 0.00363
rotated from previous position = 0.011 degrees
atoms outside contour = 3432, contour level = 0.31557
Position of model (#4) relative to cryosparc_P71_J40_class_00_final_volume.mrc
z flip (#7) coordinates:
Matrix rotation and translation
0.88315976 -0.46862241 -0.02053979 66.79185172
-0.45040976 -0.85943739 0.24186444 271.95678244
-0.13099576 -0.20435362 -0.97009263 305.47388938
Axis -0.96994122 0.24009741 0.03958870
Axis point 0.00000000 162.57220402 137.93901903
Rotation angle (degrees) 166.70155935
Shift along axis 12.60526278
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> fitmap #4 inMap #6
Fit molecule model (#4) to map cryosparc_P71_J40_class_00_final_volume.mrc
(#6) using 4317 atoms
average map value = 0.2407, steps = 80
shifted from previous position = 7.15
rotated from previous position = 8.87 degrees
atoms outside contour = 2152, contour level = 0.1994
Position of model (#4) relative to cryosparc_P71_J40_class_00_final_volume.mrc
(#6) coordinates:
Matrix rotation and translation
0.91231187 -0.38290467 -0.14515878 61.86983110
-0.34781470 -0.91166657 0.21883556 269.56066549
-0.21612956 -0.14915792 -0.96490410 311.47976365
Axis -0.97763011 0.18854458 0.09322178
Axis point 0.00000000 155.78485592 145.77659964
Rotation angle (degrees) 169.15184037
Shift along axis 19.37508951
> volume #6 level 0.3053
> surface dust #6 size 9.36
> transparency 30 surfaces
> transparency 10 surfaces
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P70_J21_class_00_final_volume.mrc"
Opened cryosparc_P70_J21_class_00_final_volume.mrc as #8, grid size
256,256,256, pixel 0.936, shown at level 0.194, step 1, values float32
> hide #!6 models
> color #8 #fffb00ff models
> color #8 #ffd479ff models
> color #8 #ffd479b1 models
> color #8 #ffd479c9 models
> color #8 #ffd479a1 models
> color #8 #ffd479b0 models
> surface dust #8 size 9.36
> volume #8 level 0.3112
> fitmap #4 inMap #8
Fit molecule model (#4) to map cryosparc_P70_J21_class_00_final_volume.mrc
(#8) using 4317 atoms
average map value = 0.2291, steps = 76
shifted from previous position = 1.87
rotated from previous position = 9.39 degrees
atoms outside contour = 3180, contour level = 0.31124
Position of model (#4) relative to cryosparc_P70_J21_class_00_final_volume.mrc
(#8) coordinates:
Matrix rotation and translation
0.89732899 -0.43406316 -0.07993662 62.98775001
-0.42739517 -0.89976440 0.08807608 297.96743146
-0.11015471 -0.04486869 -0.99290117 284.05066512
Axis -0.97396333 0.22137995 0.04885020
Axis point 0.00000000 161.10830764 138.45071857
Rotation angle (degrees) 176.08655711
Shift along axis 18.49218865
> volume #8 level 0.3743
> volume #8 level 0.2645
> show #!6 models
> hide #!8 models
> fitmap #4 inMap #6
Fit molecule model (#4) to map cryosparc_P71_J40_class_00_final_volume.mrc
(#6) using 4317 atoms
average map value = 0.2407, steps = 76
shifted from previous position = 1.87
rotated from previous position = 9.39 degrees
atoms outside contour = 3056, contour level = 0.30532
Position of model (#4) relative to cryosparc_P71_J40_class_00_final_volume.mrc
(#6) coordinates:
Matrix rotation and translation
0.91232204 -0.38286226 -0.14520666 61.87437914
-0.34774735 -0.91167342 0.21891403 269.53819625
-0.21619497 -0.14922486 -0.96487910 311.49980983
Axis -0.97763258 0.18851713 0.09325144
Axis point 0.00000000 155.78011966 145.78365969
Rotation angle (degrees) 169.14752928
Shift along axis 19.36996451
> open
> /Users/chitrajoshi/Desktop/SLCO2A1/structure/fold_rnslco2a1_cya_mut/fold_rnslco2a1_cya_mut_model_0.cif
Chain information for fold_rnslco2a1_cya_mut_model_0.cif #9
---
Chain | Description
A | .
> hide #!4 models
> hide #9 models
> show #9 models
> select subtract #4
Nothing selected
> fitmap #9 inMap #6
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P71_J40_class_00_final_volume.mrc (#6) using 4940 atoms
average map value = 1.425e-07, steps = 252
shifted from previous position = 2.22
rotated from previous position = 5.99 degrees
atoms outside contour = 4940, contour level = 0.30532
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P71_J40_class_00_final_volume.mrc (#6) coordinates:
Matrix rotation and translation
0.99548491 -0.09207393 -0.02306909 1.51529390
0.09299440 0.99475312 0.04264125 -1.76334272
0.01902190 -0.04459401 0.99882408 -0.29209680
Axis -0.41762822 -0.20150549 0.88599222
Axis point 20.85749642 13.00200465 0.00000000
Rotation angle (degrees) 5.99497777
Shift along axis -0.53630174
> fitmap #9 inMap #6
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P71_J40_class_00_final_volume.mrc (#6) using 4940 atoms
average map value = 1.443e-07, steps = 60
shifted from previous position = 0.0212
rotated from previous position = 0.0703 degrees
atoms outside contour = 4940, contour level = 0.30532
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P71_J40_class_00_final_volume.mrc (#6) coordinates:
Matrix rotation and translation
0.99537264 -0.09322918 -0.02327300 1.53275456
0.09416387 0.99462972 0.04295223 -1.77684487
0.01914362 -0.04494496 0.99880602 -0.29349157
Axis -0.41601297 -0.20075575 0.88692183
Axis point 20.76473712 12.99492905 0.00000000
Rotation angle (degrees) 6.06417741
Shift along axis -0.54123803
> ui mousemode right "rotate selected models"
> select add #9
4940 atoms, 5064 bonds, 644 residues, 1 model selected
> view matrix models
> #9,0.99584,-0.090597,-0.0096523,1.4715,0.0909,0.99514,0.037905,-1.7981,0.0061713,-0.038624,0.99923,-0.48003
> view matrix models
> #9,0.81805,-0.12113,-0.56224,1.7002,0.27663,0.93994,0.19999,0.033653,0.50425,-0.31914,0.80243,7.5815
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.81805,-0.12113,-0.56224,82.205,0.27663,0.93994,0.19999,-6.2536,0.50425,-0.31914,0.80243,131.23
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.44416,-0.43288,0.78443,83.447,0.4576,-0.86233,-0.21677,33.519,0.77028,0.26267,0.5811,119.8
> view matrix models
> #9,-0.36711,-0.33424,0.86805,81.577,0.19774,-0.93992,-0.27828,34.221,0.90892,0.069491,0.41115,124.58
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.36711,-0.33424,0.86805,112.81,0.19774,-0.93992,-0.27828,118.98,0.90892,0.069491,0.41115,103.02
> fitmap #9 inMap #6
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P71_J40_class_00_final_volume.mrc (#6) using 4940 atoms
average map value = 0.1588, steps = 176
shifted from previous position = 8.66
rotated from previous position = 11.2 degrees
atoms outside contour = 4508, contour level = 0.30532
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P71_J40_class_00_final_volume.mrc (#6) coordinates:
Matrix rotation and translation
-0.23813766 -0.42319810 0.87418180 112.14398912
0.33797430 -0.87992950 -0.33391233 111.22404853
0.91052942 0.21593388 0.35257444 99.41683913
Axis 0.58512974 -0.03868004 0.81001669
Axis point 2.18573349 62.47541541 0.00000000
Rotation angle (degrees) 151.97545147
Shift along axis 141.84593171
> fitmap #9 inMap #6
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P71_J40_class_00_final_volume.mrc (#6) using 4940 atoms
average map value = 0.1588, steps = 64
shifted from previous position = 0.0182
rotated from previous position = 0.0083 degrees
atoms outside contour = 4507, contour level = 0.30532
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P71_J40_class_00_final_volume.mrc (#6) coordinates:
Matrix rotation and translation
-0.23802073 -0.42328280 0.87417264 112.13164356
0.33800997 -0.87987809 -0.33401169 111.21289986
0.91054675 0.21597736 0.35250303 99.40972713
Axis 0.58516834 -0.03870074 0.80998782
Axis point 2.17523777 62.47063354 0.00000000
Rotation angle (degrees) 151.96954140
Shift along axis 141.83253495
> view matrix models
> #9,-0.23802,-0.42328,0.87417,111.42,0.33801,-0.87988,-0.33401,132.36,0.91055,0.21598,0.3525,173.73
> view matrix models
> #9,-0.23802,-0.42328,0.87417,117.91,0.33801,-0.87988,-0.33401,114.41,0.91055,0.21598,0.3525,198.52
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.77504,0.27778,0.56759,100.86,-0.13141,-0.94941,0.28522,113.82,0.6181,0.14647,0.77233,198.7
> view matrix models
> #9,-0.60241,0.56932,0.55945,95.24,0.76577,0.21449,0.60629,92.015,0.22518,0.79364,-0.56518,183.84
> view matrix models
> #9,-0.6311,0.20205,0.74892,102.97,0.58216,-0.51469,0.62943,107.03,0.51264,0.83323,0.2072,183.74
> view matrix models
> #9,-0.68867,0.33555,0.64276,99.913,0.61886,-0.18989,0.7622,100.1,0.37781,0.92268,-0.076887,181.42
> view matrix models
> #9,-0.61917,0.31731,0.71829,100.54,0.63358,-0.33853,0.69569,103.4,0.46391,0.88584,0.00857,182.51
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.61917,0.31731,0.71829,113.95,0.63358,-0.33853,0.69569,124.07,0.46391,0.88584,0.00857,124
> fitmap #9 inMap #6
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P71_J40_class_00_final_volume.mrc (#6) using 4940 atoms
average map value = 0.1856, steps = 260
shifted from previous position = 6.04
rotated from previous position = 19.9 degrees
atoms outside contour = 3966, contour level = 0.30532
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P71_J40_class_00_final_volume.mrc (#6) coordinates:
Matrix rotation and translation
-0.75147912 0.12363269 0.64806952 113.77438067
0.49600769 -0.54183665 0.67852002 118.80169371
0.43503507 0.83134109 0.34585617 120.52885338
Axis 0.33556581 0.46778286 0.81766422
Axis point 30.11998362 28.39780177 0.00000000
Rotation angle (degrees) 166.83791579
Shift along axis 192.30431986
> fitmap #9 inMap #6
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P71_J40_class_00_final_volume.mrc (#6) using 4940 atoms
average map value = 0.1856, steps = 40
shifted from previous position = 0.0141
rotated from previous position = 0.0447 degrees
atoms outside contour = 3966, contour level = 0.30532
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P71_J40_class_00_final_volume.mrc (#6) coordinates:
Matrix rotation and translation
-0.75142238 0.12317508 0.64822243 113.77230667
0.49655844 -0.54137596 0.67848493 118.81382679
0.43450447 0.83170907 0.34563838 120.52290473
Axis 0.33550827 0.46796895 0.81758135
Axis point 30.11768498 28.39923927 0.00000000
Rotation angle (degrees) 166.80026870
Shift along axis 192.31001012
> fitmap #9 inMap #6
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P71_J40_class_00_final_volume.mrc (#6) using 4940 atoms
average map value = 0.1856, steps = 44
shifted from previous position = 0.00488
rotated from previous position = 0.0181 degrees
atoms outside contour = 3968, contour level = 0.30532
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P71_J40_class_00_final_volume.mrc (#6) coordinates:
Matrix rotation and translation
-0.75148330 0.12294975 0.64819459 113.77231582
0.49670429 -0.54121042 0.67851023 118.81157996
0.43423233 0.83185013 0.34564092 120.51870756
Axis 0.33542635 0.46803591 0.81757663
Axis point 30.12319826 28.39905067 0.00000000
Rotation angle (degrees) 166.78683196
Shift along axis 192.30359752
> volume #6 level 0.3053
> surface dust #6 size 9.36
> transparency 30 surfaces
> fitmap #9 inMap #6
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P71_J40_class_00_final_volume.mrc (#6) using 4940 atoms
average map value = 0.1856, steps = 28
shifted from previous position = 0.0187
rotated from previous position = 0.0142 degrees
atoms outside contour = 3967, contour level = 0.30532
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P71_J40_class_00_final_volume.mrc (#6) coordinates:
Matrix rotation and translation
-0.75134218 0.12296754 0.64835478 113.76899449
0.49688534 -0.54112789 0.67844349 118.82030463
0.43426938 0.83190120 0.34547144 120.53533053
Axis 0.33551477 0.46806914 0.81752133
Axis point 30.10936833 28.39390729 0.00000000
Rotation angle (degrees) 166.78004496
Shift along axis 192.32749894
> fitmap #9 inMap #6
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P71_J40_class_00_final_volume.mrc (#6) using 4940 atoms
average map value = 0.1856, steps = 28
shifted from previous position = 0.0213
rotated from previous position = 0.0179 degrees
atoms outside contour = 3968, contour level = 0.30532
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P71_J40_class_00_final_volume.mrc (#6) coordinates:
Matrix rotation and translation
-0.75144754 0.12306695 0.64821379 113.77189129
0.49663017 -0.54130136 0.67849194 118.80223287
0.43437895 0.83177363 0.34564082 120.52405305
Axis 0.33547188 0.46799837 0.81757944
Axis point 30.11988595 28.39320190 0.00000000
Rotation angle (degrees) 166.79376398
Shift along axis 192.30450964
> fitmap #9 inMap #6
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P71_J40_class_00_final_volume.mrc (#6) using 4940 atoms
average map value = 0.1856, steps = 40
shifted from previous position = 0.00911
rotated from previous position = 0.00673 degrees
atoms outside contour = 3967, contour level = 0.30532
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P71_J40_class_00_final_volume.mrc (#6) coordinates:
Matrix rotation and translation
-0.75150041 0.12298709 0.64816766 113.77263815
0.49664105 -0.54125815 0.67851845 118.80993808
0.43427504 0.83181356 0.34567528 120.51930585
Axis 0.33542364 0.46801651 0.81758885
Axis point 30.12424018 28.39902400 0.00000000
Rotation angle (degrees) 166.79065256
Shift along axis 192.30228579
> show #!8 models
> hide #!6 models
> fitmap #9 inMap #8
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P70_J21_class_00_final_volume.mrc (#8) using 4940 atoms
average map value = 0.1852, steps = 120
shifted from previous position = 2.63
rotated from previous position = 12.5 degrees
atoms outside contour = 3678, contour level = 0.26449
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P70_J21_class_00_final_volume.mrc (#8) coordinates:
Matrix rotation and translation
-0.70508512 0.09501383 0.70272851 116.02410289
0.63032927 -0.37002179 0.68247263 119.85426768
0.32486920 0.92415164 0.20100686 121.04655377
Axis 0.34605149 0.54104318 0.76649895
Axis point 29.17680577 22.80142120 0.00000000
Rotation angle (degrees) 159.56190503
Shift along axis 197.77870451
> surface dust #8 size 9.36
> volume #8 level 0.2898
> volume #8 level 0.3441
> fitmap #9 inMap #8
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P70_J21_class_00_final_volume.mrc (#8) using 4940 atoms
average map value = 0.1852, steps = 28
shifted from previous position = 0.00185
rotated from previous position = 0.00451 degrees
atoms outside contour = 4181, contour level = 0.34411
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P70_J21_class_00_final_volume.mrc (#8) coordinates:
Matrix rotation and translation
-0.70503231 0.09500394 0.70278282 116.02328242
0.63037539 -0.37004607 0.68241687 119.85605439
0.32489430 0.92414294 0.20100629 121.04658234
Axis 0.34608170 0.54102688 0.76649682
Axis point 29.17328843 22.80324920 0.00000000
Rotation angle (degrees) 159.55961130
Shift along axis 197.78070204
> fitmap #9 inMap #8
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P70_J21_class_00_final_volume.mrc (#8) using 4940 atoms
average map value = 0.1852, steps = 28
shifted from previous position = 0.00107
rotated from previous position = 0.00347 degrees
atoms outside contour = 4181, contour level = 0.34411
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P70_J21_class_00_final_volume.mrc (#8) coordinates:
Matrix rotation and translation
-0.70499536 0.09501038 0.70281902 116.02416662
0.63041755 -0.37002196 0.68239099 119.85611755
0.32489270 0.92415192 0.20096756 121.04709758
Axis 0.34610193 0.54103461 0.76648223
Axis point 29.17164416 22.80183548 0.00000000
Rotation angle (degrees) 159.55778017
Shift along axis 197.78294503
> select subtract #9
Nothing selected
> hide #9 models
> show #!4 models
> fitmap #4 inMap #8
Fit molecule model (#4) to map cryosparc_P70_J21_class_00_final_volume.mrc
(#8) using 4317 atoms
average map value = 0.2291, steps = 92
shifted from previous position = 1.87
rotated from previous position = 9.39 degrees
atoms outside contour = 3385, contour level = 0.34411
Position of model (#4) relative to cryosparc_P70_J21_class_00_final_volume.mrc
(#8) coordinates:
Matrix rotation and translation
0.89735065 -0.43402749 -0.07988703 62.97246560
-0.42736206 -0.89978049 0.08807236 297.96589603
-0.11010662 -0.04489110 -0.99290549 284.04726905
Axis -0.97396889 0.22136109 0.04882484
Axis point 0.00000000 161.10574307 138.44716599
Rotation angle (degrees) 176.08602818
Shift along axis 18.49339271
> volume #8 level 0.3242
> volume #8 level 0.2989
> show #9 models
> hide #!4 models
> fitmap #9 inMap #8
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P70_J21_class_00_final_volume.mrc (#8) using 4940 atoms
average map value = 0.1852, steps = 28
shifted from previous position = 0.0006
rotated from previous position = 0.00199 degrees
atoms outside contour = 3928, contour level = 0.29887
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P70_J21_class_00_final_volume.mrc (#8) coordinates:
Matrix rotation and translation
-0.70501139 0.09501578 0.70280221 116.02406357
0.63039275 -0.37004299 0.68240250 119.85554144
0.32490604 0.92414295 0.20098727 121.04690434
Axis 0.34609567 0.54102750 0.76649007
Axis point 29.17236418 22.80233805 0.00000000
Rotation angle (degrees) 159.55920330
Shift along axis 197.78182075
> fitmap #9 inMap #8
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P70_J21_class_00_final_volume.mrc (#8) using 4940 atoms
average map value = 0.1852, steps = 28
shifted from previous position = 0.000145
rotated from previous position = 0.000765 degrees
atoms outside contour = 3928, contour level = 0.29887
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P70_J21_class_00_final_volume.mrc (#8) coordinates:
Matrix rotation and translation
-0.70501721 0.09501915 0.70279592 116.02402970
0.63038311 -0.37005105 0.68240703 119.85540348
0.32491210 0.92413938 0.20099389 121.04685974
Axis 0.34609371 0.54102489 0.76649280
Axis point 29.17259413 22.80251268 0.00000000
Rotation angle (degrees) 159.55979817
Shift along axis 197.78148981
> fitmap #9 inMap #8
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P70_J21_class_00_final_volume.mrc (#8) using 4940 atoms
average map value = 0.1852, steps = 28
shifted from previous position = 5.75e-05
rotated from previous position = 0.000288 degrees
atoms outside contour = 3928, contour level = 0.29887
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P70_J21_class_00_final_volume.mrc (#8) coordinates:
Matrix rotation and translation
-0.70501914 0.09502075 0.70279376 116.02402063
0.63037957 -0.37005423 0.68240858 119.85534647
0.32491478 0.92413794 0.20099617 121.04684816
Axis 0.34609320 0.54102385 0.76649377
Axis point 29.17266191 22.80256748 0.00000000
Rotation angle (degrees) 159.56003028
Shift along axis 197.78137979
> fitmap #9 inMap #8
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P70_J21_class_00_final_volume.mrc (#8) using 4940 atoms
average map value = 0.1852, steps = 28
shifted from previous position = 2.83e-05
rotated from previous position = 0.000138 degrees
atoms outside contour = 3928, contour level = 0.29887
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P70_J21_class_00_final_volume.mrc (#8) coordinates:
Matrix rotation and translation
-0.70502004 0.09502156 0.70279276 116.02402258
0.63037789 -0.37005577 0.68240930 119.85531744
0.32491611 0.92413724 0.20099725 121.04684414
Axis 0.34609298 0.54102334 0.76649422
Axis point 29.17269527 22.80259256 0.00000000
Rotation angle (degrees) 159.56014234
Shift along axis 197.78133077
> fitmap #9 inMap #8
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P70_J21_class_00_final_volume.mrc (#8) using 4940 atoms
average map value = 0.1852, steps = 28
shifted from previous position = 2.98e-05
rotated from previous position = 0.000103 degrees
atoms outside contour = 3928, contour level = 0.29887
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P70_J21_class_00_final_volume.mrc (#8) coordinates:
Matrix rotation and translation
-0.70502079 0.09502183 0.70279197 116.02400826
0.63037664 -0.37005697 0.68240980 119.85529403
0.32491689 0.92413673 0.20099831 121.04683173
Axis 0.34609271 0.54102292 0.76649464
Axis point 29.17272284 22.80262578 0.00000000
Rotation angle (degrees) 159.56021462
Shift along axis 197.78127245
> fitmap #9 inMap #8
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P70_J21_class_00_final_volume.mrc (#8) using 4940 atoms
average map value = 0.1852, steps = 28
shifted from previous position = 1.3e-05
rotated from previous position = 1.03e-05 degrees
atoms outside contour = 3928, contour level = 0.29887
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P70_J21_class_00_final_volume.mrc (#8) coordinates:
Matrix rotation and translation
-0.70502069 0.09502196 0.70279205 116.02401598
0.63037668 -0.37005700 0.68240974 119.85530081
0.32491703 0.92413670 0.20099822 121.04683966
Axis 0.34609279 0.54102290 0.76649461
Axis point 29.17271747 22.80262336 0.00000000
Rotation angle (degrees) 159.56021714
Shift along axis 197.78128957
> fitmap #9 inMap #8
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P70_J21_class_00_final_volume.mrc (#8) using 4940 atoms
average map value = 0.1852, steps = 28
shifted from previous position = 1.46e-05
rotated from previous position = 5.34e-05 degrees
atoms outside contour = 3928, contour level = 0.29887
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P70_J21_class_00_final_volume.mrc (#8) coordinates:
Matrix rotation and translation
-0.70502116 0.09502191 0.70279159 116.02400794
0.63037605 -0.37005756 0.68241003 119.85529088
0.32491724 0.92413649 0.20099887 121.04683213
Axis 0.34609257 0.54102270 0.76649486
Axis point 29.17273891 22.80264617 0.00000000
Rotation angle (degrees) 159.56024729
Shift along axis 197.78125474
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P71_J45_002_volume_map.mrc"
Failed opening file /Users/chitrajoshi/Desktop/SLCO2A1/Grid screening
/Cryosparc volumes/cryosparc_P71_J45_002_volume_map.mrc:
File size 19398656 too small for grid size (288,288,288)
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P71_J45_002_volume_map.mrc"
Failed opening file /Users/chitrajoshi/Desktop/SLCO2A1/Grid screening
/Cryosparc volumes/cryosparc_P71_J45_002_volume_map.mrc:
File size 49020928 too small for grid size (288,288,288)
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P71_J45_002_volume_map.mrc"
Opened cryosparc_P71_J45_002_volume_map.mrc as #10, grid size 288,288,288,
pixel 0.832, shown at level 0.176, step 2, values float32
> hide #!8 models
> volume #10 level 0.2805
> hide #9 models
> show #!4 models
> fitmap #4 inMap #10
Fit molecule model (#4) to map cryosparc_P71_J45_002_volume_map.mrc (#10)
using 4317 atoms
average map value = 0.2173, steps = 80
shifted from previous position = 1.98
rotated from previous position = 9.75 degrees
atoms outside contour = 2928, contour level = 0.28052
Position of model (#4) relative to cryosparc_P71_J45_002_volume_map.mrc (#10)
coordinates:
Matrix rotation and translation
0.91261466 -0.37918450 -0.15281883 62.48229894
-0.34258744 -0.91330184 0.22025802 268.70413102
-0.22308815 -0.14865689 -0.96339649 312.33257754
Axis -0.97770724 0.18622944 0.09699040
Axis point 0.00000000 155.41571512 146.35985734
Rotation angle (degrees) 169.12521515
Shift along axis 19.24448606
> volume #10 level 0.3558
> surface dust #10 size 8.32
> transparency 30 surfaces
[Repeated 1 time(s)]
> transparency 20 surfaces
> volume #10 level 0.3444
> select ::name="P2E"
56 atoms, 56 bonds, 1 residue, 1 model selected
> hide sel target a
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P71_J44_class_01_final_volume.mrc"
Opened cryosparc_P71_J44_class_01_final_volume.mrc as #11, grid size
192,192,192, pixel 1.25, shown at level 0.297, step 1, values float32
> hide #!10 models
> volume #11 level 0.1581
> view matrix models
> #4,0.91261,-0.37918,-0.15282,30.428,-0.34259,-0.9133,0.22026,260.56,-0.22309,-0.14866,-0.9634,380.36
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.94701,0.32027,0.024597,160.07,0.28571,0.87484,-0.39118,2.9905,-0.1468,-0.36342,-0.91998,394.69
> volume #11 level 0.4763
> surface dust #11 size 12.5
> volume #11 level 0.4962
> view matrix models
> #4,-0.81948,0.57309,0.0030771,108.64,0.32124,0.46379,-0.82566,122.61,-0.4746,-0.67562,-0.56417,432.95
> ui mousemode right "move picked models"
> view matrix models
> #4,-0.81948,0.57309,0.0030771,142.12,0.32124,0.46379,-0.82566,84.013,-0.4746,-0.67562,-0.56417,391.41
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.81948,0.57309,0.0030771,138.89,0.32124,0.46379,-0.82566,88.675,-0.4746,-0.67562,-0.56417,396.58
> fitmap #4 inMap #11
Fit molecule model (#4) to map cryosparc_P71_J44_class_01_final_volume.mrc
(#11) using 4317 atoms
average map value = 0.2429, steps = 284
shifted from previous position = 31.4
rotated from previous position = 15 degrees
atoms outside contour = 3858, contour level = 0.49622
Position of model (#4) relative to cryosparc_P71_J44_class_01_final_volume.mrc
(#11) coordinates:
Matrix rotation and translation
-0.65392916 0.75157502 -0.08666974 118.69668018
0.45861540 0.30268399 -0.83549645 110.98467985
-0.60170472 -0.58610357 -0.54261776 377.09220066
Axis 0.38793609 0.80114820 -0.45570511
Axis point 69.60088814 0.00000000 206.40640379
Rotation angle (degrees) 161.25023876
Shift along axis -36.88093965
> fitmap #4 inMap #11
Fit molecule model (#4) to map cryosparc_P71_J44_class_01_final_volume.mrc
(#11) using 4317 atoms
average map value = 0.2429, steps = 40
shifted from previous position = 0.0494
rotated from previous position = 0.214 degrees
atoms outside contour = 3856, contour level = 0.49622
Position of model (#4) relative to cryosparc_P71_J44_class_01_final_volume.mrc
(#11) coordinates:
Matrix rotation and translation
-0.65206344 0.75318674 -0.08673527 118.17834547
0.46121363 0.30326615 -0.83385348 110.26849068
-0.60174352 -0.58372885 -0.54512876 377.09645888
Axis 0.38918692 0.80133841 -0.45430198
Axis point 69.41732464 0.00000000 206.15376544
Rotation angle (degrees) 161.25586434
Shift along axis -36.95982533
> ui mousemode right "move picked models"
> view matrix models
> #4,-0.65206,0.75319,-0.086735,110.24,0.46121,0.30327,-0.83385,139.08,-0.60174,-0.58373,-0.54513,360.14
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.958,0.064873,0.27934,198.87,-0.25144,0.27841,-0.92697,255.47,-0.13791,-0.95827,-0.2504,306.69
> ui mousemode right "move picked models"
> view matrix models
> #4,-0.958,0.064873,0.27934,200.95,-0.25144,0.27841,-0.92697,248.41,-0.13791,-0.95827,-0.2504,310.84
> fitmap #4 inMap #11
Fit molecule model (#4) to map cryosparc_P71_J44_class_01_final_volume.mrc
(#11) using 4317 atoms
average map value = 0.2659, steps = 92
shifted from previous position = 7.36
rotated from previous position = 8.57 degrees
atoms outside contour = 3710, contour level = 0.49622
Position of model (#4) relative to cryosparc_P71_J44_class_01_final_volume.mrc
(#11) coordinates:
Matrix rotation and translation
-0.94717747 0.02120883 0.32000785 207.00580445
-0.28387595 0.40884603 -0.86732887 227.18847740
-0.14922897 -0.91235690 -0.38122907 325.11011339
Axis -0.08019173 0.83567758 -0.54333440
Axis point 142.11186535 -0.00000000 218.69105607
Rotation angle (degrees) 163.69488980
Shift along axis -3.38734728
> volume #11 level 0.4714
> view matrix models
> #4,-0.94718,0.021209,0.32001,205.21,-0.28388,0.40885,-0.86733,229.82,-0.14923,-0.91236,-0.38123,324.67
> fitmap #4 inMap #11
Fit molecule model (#4) to map cryosparc_P71_J44_class_01_final_volume.mrc
(#11) using 4317 atoms
average map value = 0.2659, steps = 72
shifted from previous position = 3.21
rotated from previous position = 0.0138 degrees
atoms outside contour = 3622, contour level = 0.47136
Position of model (#4) relative to cryosparc_P71_J44_class_01_final_volume.mrc
(#11) coordinates:
Matrix rotation and translation
-0.94711825 0.02137114 0.32017228 206.95165185
-0.28396828 0.40882246 -0.86730975 227.21217004
-0.14942902 -0.91236367 -0.38113449 325.14595337
Axis -0.08017430 0.83566439 -0.54335726
Axis point 142.11001457 0.00000000 218.71069413
Rotation angle (degrees) 163.68160627
Shift along axis -3.38950005
> view matrix models
> #4,-0.94712,0.021371,0.32017,200.76,-0.28397,0.40882,-0.86731,236.76,-0.14943,-0.91236,-0.38113,329.07
> fitmap #4 inMap #11
Fit molecule model (#4) to map cryosparc_P71_J44_class_01_final_volume.mrc
(#11) using 4317 atoms
average map value = 0.2992, steps = 200
shifted from previous position = 7.13
rotated from previous position = 43.5 degrees
atoms outside contour = 3645, contour level = 0.47136
Position of model (#4) relative to cryosparc_P71_J44_class_01_final_volume.mrc
(#11) coordinates:
Matrix rotation and translation
-0.59908962 -0.59150657 0.53964025 202.26075173
-0.74649032 0.16888887 -0.64360605 301.60377970
0.28955798 -0.78841393 -0.54273350 274.50702402
Axis -0.44159740 0.76263586 -0.47262912
Axis point 203.58564119 0.00000000 219.50324193
Rotation angle (degrees) 170.56322460
Shift along axis 10.95602060
> view matrix models
> #4,-0.59909,-0.59151,0.53964,202.58,-0.74649,0.16889,-0.64361,300.88,0.28956,-0.78841,-0.54273,274.48
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.78085,-0.18252,0.59747,159.49,-0.62323,0.29375,-0.72478,277.59,-0.043221,-0.9383,-0.34312,312.92
> fitmap #4 inMap #11
Fit molecule model (#4) to map cryosparc_P71_J44_class_01_final_volume.mrc
(#11) using 4317 atoms
average map value = 0.2977, steps = 136
shifted from previous position = 2.92
rotated from previous position = 23.8 degrees
atoms outside contour = 3635, contour level = 0.47136
Position of model (#4) relative to cryosparc_P71_J44_class_01_final_volume.mrc
(#11) coordinates:
Matrix rotation and translation
-0.64877657 -0.56182481 0.51326586 209.51165280
-0.73195384 0.27621392 -0.62285588 280.61419706
0.20816471 -0.77978122 -0.59043095 293.09487097
Axis -0.40977260 0.79669794 -0.44425084
Axis point 194.89847007 0.00000000 211.89222094
Rotation angle (degrees) 168.96091572
Shift along axis 7.50497491
> hide #!4 models
> select add #4
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> volume flip #11
Opened cryosparc_P71_J44_class_01_final_volume.mrc z flip as #12, grid size
192,192,192, pixel 1.25, shown at step 1, values float32
> volume #12 level 0.5211
> surface dust #12 size 12.5
> show #!4 models
> view matrix models
> #4,-0.96288,0.24993,0.10193,195.64,-0.21076,-0.9321,0.29456,248.5,0.16863,0.26215,0.95018,-82.357
> fitmap #4 inMap #12
Fit molecule model (#4) to map cryosparc_P71_J44_class_01_final_volume.mrc z
flip (#12) using 4317 atoms
average map value = 0.3523, steps = 108
shifted from previous position = 16.5
rotated from previous position = 12.4 degrees
atoms outside contour = 3353, contour level = 0.52108
Position of model (#4) relative to cryosparc_P71_J44_class_01_final_volume.mrc
z flip (#12) coordinates:
Matrix rotation and translation
-0.91716669 0.38396409 0.10666231 183.75720012
-0.36694012 -0.91810813 0.14977449 282.71513932
0.15543556 0.09822949 0.98295002 -57.84539854
Axis -0.06833942 -0.06466458 -0.99556427
Axis point 121.83388251 124.98728665 0.00000000
Rotation angle (degrees) 157.84429247
Shift along axis 26.74929577
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.91717,0.38396,0.10666,182.22,-0.36694,-0.91811,0.14977,283.24,0.15544,0.098229,0.98295,-57.132
> fitmap #4 inMap #12
Fit molecule model (#4) to map cryosparc_P71_J44_class_01_final_volume.mrc z
flip (#12) using 4317 atoms
average map value = 0.3524, steps = 56
shifted from previous position = 1.78
rotated from previous position = 0.014 degrees
atoms outside contour = 3354, contour level = 0.52108
Position of model (#4) relative to cryosparc_P71_J44_class_01_final_volume.mrc
z flip (#12) coordinates:
Matrix rotation and translation
-0.91707403 0.38417042 0.10671604 183.70251168
-0.36712591 -0.91801799 0.14987170 282.73492485
0.15554352 0.09826522 0.98292938 -57.88118745
Axis -0.06838484 -0.06470233 -0.99555870
Axis point 121.82736031 124.99408218 0.00000000
Rotation angle (degrees) 157.83197840
Shift along axis 26.76804526
> transparency 20 surfaces
> hide #!12 models
> show (#!4 & sel) target ab
> hide (#!4 & sel) target a
> ui tool show H-Bonds
> hbonds select true reveal true
1235 hydrogen bonds found
> hbonds select true reveal true
1235 hydrogen bonds found
> ui tool show Clashes
> show #9 models
> hide #!4 models
> show #!4 models
> hide #13 models
> hide #9 models
> show #9 models
> hide #!4 models
> show #13 models
> show #!12 models
> hide #13 models
> hide #9 models
> show #!4 models
> fitmap #4 inMap #12
Fit molecule model (#4) to map cryosparc_P71_J44_class_01_final_volume.mrc z
flip (#12) using 4317 atoms
average map value = 0.3523, steps = 28
shifted from previous position = 0.0269
rotated from previous position = 0.018 degrees
atoms outside contour = 3353, contour level = 0.52108
Position of model (#4) relative to cryosparc_P71_J44_class_01_final_volume.mrc
z flip (#12) coordinates:
Matrix rotation and translation
-0.91719417 0.38391136 0.10661578 183.77436619
-0.36689440 -0.91812888 0.14975933 282.71490785
0.15538133 0.09824165 0.98295738 -57.84122997
Axis -0.06831229 -0.06466298 -0.99556624
Axis point 121.83743065 124.98802577 0.00000000
Rotation angle (degrees) 157.84739738
Shift along axis 26.74953843
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P71_J51_002_volume_map.mrc"
Opened cryosparc_P71_J51_002_volume_map.mrc as #14, grid size 288,288,288,
pixel 0.832, shown at level 0.175, step 2, values float32
> hide #!12 models
> volume #14 level 0.06821
> volume #14 level 0.3398
> fitmap #4 inMap #14
Fit molecule model (#4) to map cryosparc_P71_J51_002_volume_map.mrc (#14)
using 4317 atoms
average map value = 0.1548, steps = 96
shifted from previous position = 2.21
rotated from previous position = 12.9 degrees
atoms outside contour = 3641, contour level = 0.33978
Position of model (#4) relative to cryosparc_P71_J51_002_volume_map.mrc (#14)
coordinates:
Matrix rotation and translation
-0.86201001 0.45773300 0.21775960 149.10620185
-0.37829284 -0.86687388 0.32469092 253.15245304
0.33739186 0.19750992 0.92041108 -87.12694876
Axis -0.14891264 -0.14007404 -0.97887910
Axis point 110.62108629 115.25927680 0.00000000
Rotation angle (degrees) 154.72063526
Shift along axis 27.62286362
> surface dust #14 size 8.32
> view matrix models
> #4,-0.86201,0.45773,0.21776,105.2,-0.37829,-0.86687,0.32469,269.79,0.33739,0.19751,0.92041,-16.92,#9,-0.70502,0.095022,0.70279,72.117,0.63038,-0.37006,0.68241,136.49,0.32492,0.92414,0.201,191.25
> view matrix models
> #4,-0.86201,0.45773,0.21776,69.302,-0.37829,-0.86687,0.32469,241.96,0.33739,0.19751,0.92041,-40.009,#9,-0.70502,0.095022,0.70279,36.22,0.63038,-0.37006,0.68241,108.66,0.32492,0.92414,0.201,168.17
> view matrix models
> #4,-0.86201,0.45773,0.21776,84.72,-0.37829,-0.86687,0.32469,245.83,0.33739,0.19751,0.92041,-41.249,#9,-0.70502,0.095022,0.70279,51.638,0.63038,-0.37006,0.68241,112.54,0.32492,0.92414,0.201,166.93
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.89312,-0.41537,0.17264,-24.699,0.43916,0.88825,-0.13474,-55.791,-0.097382,0.19616,0.97572,11.095,#9,0.82254,0.23289,-0.51883,74.113,-0.55191,0.54693,-0.62949,116.42,0.13717,0.80413,0.57841,162.02
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.89312,-0.41537,0.17264,22.509,0.43916,0.88825,-0.13474,-47.955,-0.097382,0.19616,0.97572,-32.002,#9,0.82254,0.23289,-0.51883,121.32,-0.55191,0.54693,-0.62949,124.25,0.13717,0.80413,0.57841,118.93
> fitmap #4 inMap #14
Fit molecule model (#4) to map cryosparc_P71_J51_002_volume_map.mrc (#14)
using 4317 atoms
average map value = 0.2097, steps = 124
shifted from previous position = 5.45
rotated from previous position = 17.6 degrees
atoms outside contour = 3299, contour level = 0.33978
Position of model (#4) relative to cryosparc_P71_J51_002_volume_map.mrc (#14)
coordinates:
Matrix rotation and translation
0.91175378 -0.39153560 -0.12411653 60.53472492
0.38618065 0.92008601 -0.06562192 -59.58094427
0.13989120 0.01189963 0.99009537 -43.66460597
Axis 0.09397055 -0.32002647 0.94273676
Axis point 191.74575644 115.32994854 0.00000000
Rotation angle (degrees) 24.36059116
Shift along axis -16.40826862
> volume flip #14
Opened cryosparc_P71_J51_002_volume_map.mrc z flip as #15, grid size
288,288,288, pixel 0.832, shown at step 1, values float32
> fitmap #4 inMap #15
Fit molecule model (#4) to map cryosparc_P71_J51_002_volume_map.mrc z flip
(#15) using 4317 atoms
average map value = 0.1705, steps = 124
shifted from previous position = 2.94
rotated from previous position = 14.7 degrees
atoms outside contour = 3585, contour level = 0.33978
Position of model (#4) relative to cryosparc_P71_J51_002_volume_map.mrc z flip
(#15) coordinates:
Matrix rotation and translation
0.84809331 -0.48615624 -0.21068899 95.44617061
0.42178601 0.86011998 -0.28686265 -26.73310659
0.32067788 0.15442062 0.93451590 -82.14994219
Axis 0.38681673 -0.46578153 0.79587711
Axis point 136.27282014 166.48573928 0.00000000
Rotation angle (degrees) 34.77837074
Shift along axis -16.00929601
> surface dust #15 size 8.32
> view matrix models
> #4,0.84809,-0.48616,-0.21069,109.45,0.42179,0.86012,-0.28686,-9.2405,0.32068,0.15442,0.93452,-149.05,#9,0.82254,0.23289,-0.51883,135.32,-0.55191,0.54693,-0.62949,141.75,0.13717,0.80413,0.57841,52.023
> view matrix models
> #4,0.84809,-0.48616,-0.21069,85.673,0.42179,0.86012,-0.28686,-11.739,0.32068,0.15442,0.93452,-146.74,#9,0.82254,0.23289,-0.51883,111.55,-0.55191,0.54693,-0.62949,139.25,0.13717,0.80413,0.57841,54.335
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.76502,-0.61066,-0.20453,114.47,0.63948,0.7579,0.12904,-88.789,0.076215,-0.22951,0.97032,-62.052,#9,0.88723,0.11932,-0.44563,110.27,-0.30684,0.87396,-0.37689,137.58,0.34449,0.47113,0.81201,50.359
> view matrix models
> #4,0.7888,-0.53559,-0.30155,114.62,0.47473,0.84251,-0.25459,-21.309,0.39042,0.057664,0.91883,-139.96,#9,0.82428,0.11885,-0.55357,111.61,-0.50629,0.59238,-0.6267,139.5,0.25345,0.79684,0.54846,55.047
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.7888,-0.53559,-0.30155,122.89,0.47473,0.84251,-0.25459,-23.532,0.39042,0.057664,0.91883,-75.996,#9,0.82428,0.11885,-0.55357,119.89,-0.50629,0.59238,-0.6267,137.28,0.25345,0.79684,0.54846,119.01
> fitmap #4 inMap #15
Fit molecule model (#4) to map cryosparc_P71_J51_002_volume_map.mrc z flip
(#15) using 4317 atoms
average map value = 0.1644, steps = 156
shifted from previous position = 6.64
rotated from previous position = 17.8 degrees
atoms outside contour = 3597, contour level = 0.33978
Position of model (#4) relative to cryosparc_P71_J51_002_volume_map.mrc z flip
(#15) coordinates:
Matrix rotation and translation
0.89239127 -0.29039225 -0.34541302 81.33191299
0.30142427 0.95322132 -0.02263870 -55.12462247
0.33582916 -0.08391329 0.93817766 -51.19349344
Axis -0.06774531 -0.75318278 0.65431359
Axis point 189.88124525 0.00000000 176.80063332
Rotation angle (degrees) 26.88763711
Shift along axis 2.51246295
> hide #!15 models
> select add #15
1911 atoms, 1017 residues, 4 models selected
> show #!15 models
> select subtract #15
1911 atoms, 1017 residues, 2 models selected
> hide #!15 models
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P71_J53_class_00_final_volume.mrc"
Opened cryosparc_P71_J53_class_00_final_volume.mrc as #16, grid size
256,256,256, pixel 0.936, shown at level 0.219, step 1, values float32
> hide #!4 models
> select add #4
5343 atoms, 4429 bonds, 483 pseudobonds, 1087 residues, 4 models selected
> select subtract #4
1026 atoms, 533 residues, 1 model selected
> volume #16 level 0.5228
> surface dust #16 size 9.36
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P71_J53_class_01_final_volume.mrc"
Opened cryosparc_P71_J53_class_01_final_volume.mrc as #17, grid size
256,256,256, pixel 0.936, shown at level 0.221, step 1, values float32
> hide #!16 models
> volume #17 level 0.4652
> surface dust #17 size 9.36
> hide #!17 models
> show #!4 models
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P70_J44_001_volume_map.mrc"
Failed opening file /Users/chitrajoshi/Desktop/SLCO2A1/Grid screening
/Cryosparc volumes/cryosparc_P70_J44_001_volume_map.mrc:
File size 53739520 too small for grid size (288,288,288)
> hide #!4 models
> select add #9
4940 atoms, 5064 bonds, 569 pseudobonds, 644 residues, 2 models selected
> select subtract #9
Nothing selected
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P70_J44_001_volume_map.mrc"
Opened cryosparc_P70_J44_001_volume_map.mrc as #18, grid size 288,288,288,
pixel 0.832, shown at level 0.201, step 2, values float32
> surface dust #18 size 8.32
> volume #18 level 0.3265
> volume #18 level 0.2011
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P70_J41_class_00_00142_volume.mrc"
Opened cryosparc_P70_J41_class_00_00142_volume.mrc as #19, grid size
128,128,128, pixel 1.87, shown at level 0.667, step 1, values float32
> hide #!18 models
> volume #19 level 1.078
> surface dust #19 size 18.7
> volume #19 level 0.8153
> hide #!19 models
> select add #19
2 models selected
> hide target m
> select subtract #19
Nothing selected
> select add #19
2 models selected
> show #!19 models
> hide #!19 target m
> show #!19 target m
> select subtract #19
Nothing selected
> hide #!19 models
> select add #19
2 models selected
> show #!19 target m
> select subtract #19
Nothing selected
> hide #!19 models
> show #!18 models
> volume #18 level 0.1183
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.1215
> show #!19 models
> show #!17 models
> close #19
> close #18
> close #17
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P71_J54_002_volume_map.mrc"
Failed opening file /Users/chitrajoshi/Desktop/SLCO2A1/Grid screening
/Cryosparc volumes/cryosparc_P71_J54_002_volume_map.mrc:
File size 27000832 too small for grid size (288,288,288)
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P71_J54_002_volume_map.mrc"
Opened cryosparc_P71_J54_002_volume_map.mrc as #17, grid size 288,288,288,
pixel 0.832, shown at level 0.173, step 2, values float32
> hide #!1 models
> volume #17 level 0.283
> show #!4 models
> fitmap #4 inMap #17
Fit molecule model (#4) to map cryosparc_P71_J54_002_volume_map.mrc (#17)
using 4317 atoms
average map value = 0.218, steps = 124
shifted from previous position = 4.07
rotated from previous position = 14.6 degrees
atoms outside contour = 2874, contour level = 0.28303
Position of model (#4) relative to cryosparc_P71_J54_002_volume_map.mrc (#17)
coordinates:
Matrix rotation and translation
0.90743528 -0.40269833 -0.11998022 62.32954785
0.39649906 0.91514658 -0.07276829 -59.46478200
0.13910316 0.01846047 0.99010581 -44.50156107
Axis 0.10795257 -0.30657786 0.94570411
Axis point 188.07150611 116.14045770 0.00000000
Rotation angle (degrees) 24.99511152
Shift along axis -17.12608909
> surface dust #17 size 8.32
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P71_J46_class_00_final_volume.mrc"
Failed opening file /Users/chitrajoshi/Desktop/SLCO2A1/Grid screening
/Cryosparc volumes/cryosparc_P71_J46_class_00_final_volume.mrc:
File size 43253760 too small for grid size (256,256,256)
> hide #!17 models
> hide #!4 models
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/cryosparc_P71_J46_class_00_final_volume.mrc"
Opened cryosparc_P71_J46_class_00_final_volume.mrc as #18, grid size
256,256,256, pixel 0.936, shown at level 0.192, step 1, values float32
> volume #18 level 0.2954
> surface dust #18 size 9.36
> show #!17 models
> volume #17 level 0.3412
> volume #17 step 1
> hide #!18 models
> hide #!17 models
> show #!18 models
> open
> /Users/chitrajoshi/Downloads/cryosparc_P124_J314_009_volume_map_sharp.mrc
Opened cryosparc_P124_J314_009_volume_map_sharp.mrc as #19, grid size
196,196,196, pixel 1.46, shown at level 0.402, step 1, values float32
> hide #!18 models
> volume #19 level 3.73
> volume #19 level 2.898
> save "/Users/chitrajoshi/Desktop/Chimera session nov 24.cxs"
——— End of log from Sat Nov 2 16:14:23 2024 ———
opened ChimeraX session
> hide #!19 models
> show #!18 models
> show #!19 models
> hide #!18 models
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/PGE2
> bound/PGE2-bound-selected/cryosparc_P124_J82_009_volume_map_sharp (1).mrc"
Opened cryosparc_P124_J82_009_volume_map_sharp (1).mrc as #20, grid size
392,392,392, pixel 0.732, shown at level 0.0315, step 2, values float32
> hide #!19 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #20 step 1
> volume #20 level 0.1373
> volume #20 level 0.2114
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/PGE2
> bound/PGE2-bound-selected/cryosparc_P124_J89_map_sharp_deepEMhanced.mrc"
Opened cryosparc_P124_J89_map_sharp_deepEMhanced.mrc as #21, grid size
392,392,392, pixel 0.732, shown at level 0.000869, step 2, values float32
> hide #!20 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #21 step 1
> volume #21 step 2
> volume #21 level 0.1951
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by
> Justin/Dinoprost/dinoprost-
> selected/cryosparc_P124_J500_map_deepEMhanced.mrc"
Opened cryosparc_P124_J500_map_deepEMhanced.mrc as #22, grid size 392,392,392,
pixel 0.732, shown at level 0.000931, step 2, values float32
> hide #!21 models
> volume #22 level 0.1019
> volume #22 level 0.0498
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/Tolcapone/cryosparc_P73_J12_class_00_final_volume.mrc"
Opened cryosparc_P73_J12_class_00_final_volume.mrc as #23, grid size
192,192,192, pixel 1.3, shown at level 0.3, step 1, values float32
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/Tolcapone/cryosparc_P73_J12_class_01_final_volume.mrc"
Opened cryosparc_P73_J12_class_01_final_volume.mrc as #24, grid size
192,192,192, pixel 1.3, shown at level 0.296, step 1, values float32
> hide #!22 models
> hide #!24 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #24 step 2
> volume #24 step 1
> volume #24 level 0.3202
> hide #!24 models
> volume #23 level 0.0892
> volume #23 level 0.4439
> hide #!23 models
> show #!24 models
> volume #24 level 0.1516
> volume #24 level 0.3262
> surface dust #24 size 13
> volume #24 level 0.3864
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/PGE2
> bound/PGE2-bound-selected/AF_combined_coot3_P2E.pdb"
AF_combined_coot3_P2E.pdb title:
Alphafold monomer V2.0 prediction for solute carrier organic anion transporter
family member 2A1 (Q00910) [more info...]
Chain information for AF_combined_coot3_P2E.pdb #25
---
Chain | Description | UniProt
A | solute carrier organic anion transporter family member 2A1 | SO2A1_RAT 1-644
Non-standard residues in AF_combined_coot3_P2E.pdb #25
---
P2E — (P2E)
> hide #!24 models
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/PGE2
> bound/PGE2-bound-selected/cryosparc_P124_J82_009_volume_map (6).mrc"
Opened cryosparc_P124_J82_009_volume_map (6).mrc as #26, grid size
392,392,392, pixel 0.732, shown at level 0.0253, step 2, values float32
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/PGE2
> bound/PGE2-bound-selected/cryosparc_P124_J82_009_volume_map_sharp (1).mrc"
Opened cryosparc_P124_J82_009_volume_map_sharp (1).mrc as #27, grid size
392,392,392, pixel 0.732, shown at level 0.0315, step 2, values float32
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/PGE2
> bound/PGE2-bound-selected/cryosparc_P124_J89_map_sharp_deepEMhanced.mrc"
Opened cryosparc_P124_J89_map_sharp_deepEMhanced.mrc as #28, grid size
392,392,392, pixel 0.732, shown at level 0.000869, step 2, values float32
> hide #!25 models
> hide #!26 models
> hide #!27 models
> hide #!28 models
> show #!25 models
> show #!26 models
> hide #!25 models
> volume #28 level 0.05198
> hide #!28 models
> volume #28 level 0.1644
> hide #!28 models
> volume #26 level 0.05897
> show #!27 models
> hide #!26 models
> volume #27 level 0.2079
> hide #!27 models
> show #!28 models
> volume #28 level 0.09627
> show #!25 models
> hide #!28 models
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> rainbow #!25
> show #!25 cartoons
> cartoon style #25 xsection oval modeHelix default
> select add #25
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> hide (#!25 & sel) target a
> select ::name="P2E"
112 atoms, 112 bonds, 2 residues, 2 models selected
> show (#!25 & sel) target ab
> surface (#!25 & sel)
> surface style #25 mesh
> transparency (#!25 & sel) 20
> transparency (#!25 & sel) 40
> transparency (#!25 & sel) 70
> color (#!25 & sel) magenta
> transparency (#!25 & sel) 70
> set bgColor white
> set bgColor #ffffff00
> transparency (#!25 & sel) 80
> color (#!25 & sel) byhetero
> color (#!25 & sel) byelement
> transparency (#!25 & sel) 80
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting soft
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/PGE2
> bound/Images/PGE2 bound structure overview.png" width 866 height 663
> supersample 3 transparentBackground true
> save "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/PGE2
> bound/Images/PGE2 bound structure overview second.png" width 866 height 663
> supersample 4
> show #9 models
> select add #4
4373 atoms, 4485 bonds, 483 pseudobonds, 555 residues, 5 models selected
> select subtract #4
56 atoms, 56 bonds, 1 residue, 2 models selected
> hide #!25 models
> select add #25
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 3 models selected
> select subtract #25
1 model selected
> select add #9
4940 atoms, 5064 bonds, 569 pseudobonds, 644 residues, 2 models selected
> hide (#9 & sel) target a
> rainbow sel
> lighting soft
> select subtract #9
Nothing selected
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> lighting full
> lighting soft
> save "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/PGE2
> bound/Images/Alphafold model.png" width 866 height 663 supersample 4
> show #!25 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!25 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 fold_rnslco2a1_cya_mut_model_0.cif, chain A (#9) with
AF_combined_coot3_P2E.pdb, chain A (#25), sequence alignment score = 3079.6
RMSD between 318 pruned atom pairs is 0.651 angstroms; (across all 553 pairs:
6.740)
> toolshed show
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> morph #25,9,25,9 frames 50
Computed 51 frame morph #29
> coordset #29 1,51
> morph #25,9,25,9,25 frames 50
Computed 51 frame morph #30
> coordset #30 1,51
> hide #!29 models
> hide #!30 models
> show #!25 models
> hide #!25 models
> show #9 models
> matchmaker #!25 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 fold_rnslco2a1_cya_mut_model_0.cif, chain A (#9) with
AF_combined_coot3_P2E.pdb, chain A (#25), sequence alignment score = 3079.6
RMSD between 318 pruned atom pairs is 0.651 angstroms; (across all 553 pairs:
6.740)
> show #!26 models
> hide #9 models
> show #!27 models
> show #!28 models
> hide #!27 models
> hide #!26 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #28 step 1
> surface dust #28 size 7.32
> volume #28 level 0.0315
> volume #28 level 0.02468
> volume #28 level 0.01105
> surface dust #28 size 7.32
> show #!26 models
> hide #!28 models
> volume #26 level 0.03315
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> surface dust #26 size 7.32
> volume zone #26 nearAtoms sel newMap
Missing "newMap" keyword's argument
> volume zone #26 nearAtoms sel newMap map truei must true true
Invalid "newMap" argument: Expected true or false (or 1 or 0)
> volume zone #26 nearAtoms sel newMap map true i must true true
Invalid "newMap" argument: Expected true or false (or 1 or 0)
> volume zone #26 nearAtoms Atoms CA invert true
Invalid "nearAtoms" argument: invalid atoms specifier
> volume zone #26 nearAtoms Atoms CA invert true
Invalid "nearAtoms" argument: invalid atoms specifier
> volume zone #26 nearAtoms Atoms CA invert true
Invalid "nearAtoms" argument: invalid atoms specifier
> volume zone #26 nearAtoms Atoms CA invert true
Invalid "nearAtoms" argument: invalid atoms specifier
> volume #26 level 0.03988
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #26 style mesh
> volume #26 style surface
> save "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/PGE2
> bound/Images/detergent micelle surface.png" width 866 height 663 supersample
> 4
> surface dust #26 size 7.32
> ui tool show "Side View"
> save "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/PGE2
> bound/Images/detergent micelle surface sliced.png" width 866 height 663
> supersample 4
> open "/Users/chitrajoshi/Desktop/SLCO2A1/structure/PDB
> release/P2E/8kgw-2.pdb"
8kgw-2.pdb title:
Molecular mechanism of prostaglandin transporter SLCO2A1 [more info...]
Chain information for 8kgw-2.pdb #31
---
Chain | Description | UniProt
A | solute carrier organic anion transporter family member 2A1 | SO2A1_HUMAN 1-643
Non-standard residues in 8kgw-2.pdb #31
---
P2E — (Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-
cyclopentyl]hept-5-enoic acid (prostaglandin E2)
> hide #!26 models
> view
> show #31 target ab
> hide #31 target a
> select ::name="P2E"
137 atoms, 137 bonds, 3 residues, 3 models selected
> show (#!31 & sel) target ab
> color (#!31 & sel) byelement
No visible Surface models selected
> surface (#!31 & sel)
> surface style #31 mesh
> transparency (#!31 & sel) 70
> transparency (#!31 & sel) 80
> select clear
> rainbow #!31
> lighting soft
> save "/Users/chitrajoshi/Desktop/SLCO2A1/structure/PDB release/PDB release
> 8KGW.png" width 866 height 663 supersample 4
> show #!25 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!31 to #25
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 AF_combined_coot3_P2E.pdb, chain A (#25) with 8kgw-2.pdb, chain A
(#31), sequence alignment score = 2463.3
RMSD between 414 pruned atom pairs is 1.192 angstroms; (across all 526 pairs:
1.849)
> matchmaker #!31 to #25
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 AF_combined_coot3_P2E.pdb, chain A (#25) with 8kgw-2.pdb, chain A
(#31), sequence alignment score = 2463.3
RMSD between 414 pruned atom pairs is 1.192 angstroms; (across all 526 pairs:
1.849)
> select #25/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> color (#!25 & sel) cornflower blue
> undo
> select clear
> select #31/A
4036 atoms, 4144 bonds, 3 pseudobonds, 533 residues, 2 models selected
> color (#!31 & sel) purple
> select #25/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> color (#!25 & sel) hot pink
> select clear
> select ::name="P2E"
137 atoms, 137 bonds, 3 residues, 3 models selected
> surface style #25,31 mesh
> color (#!25,31 & sel) byelement
> transparency (#!25,31 & sel) 80
> select clear
> select #25/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> color (#!25 & sel) #ff8ad8ff
> color (#!25 & sel) #ff8ad8fe
> color (#!25 & sel) #ff8ad8ed
> color (#!25 & sel) #ff8ad8e8
> color (#!25 & sel) #ff8ad8e1
> color (#!25 & sel) #ff8ad8dc
> color (#!25 & sel) #ff8ad8da
> color (#!25 & sel) #ff8ad8d3
> color (#!25 & sel) #ff8ad8c4
> color (#!25 & sel) #ff8ad8c0
> select clear
> undo
> color (#!25 & sel) hot pink
> select clear
> select #25/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> color (#!25 & sel) hot pink
> select ::name="P2E"
137 atoms, 137 bonds, 3 residues, 3 models selected
> surface style #25,31 mesh
> transparency (#!25,31 & sel) 80
> color (#!25,31 & sel) byelement
> transparency (#!25,31 & sel) 80
> select clear
> select ::name="P2E"
137 atoms, 137 bonds, 3 residues, 3 models selected
> show (#!25,31 & sel) target ab
> select #25/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> show (#!25 & sel) target ab
> hide #* target a
> show (#!25 & sel) target ab
> hide (#!25 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!25 & sel-residues)
> show (#!25 & sel-residues & backbone) target ab
> show (#!25 & sel) target ab
> hide (#!25 & sel) target a
> show (#!25 & sel) target ab
> hide (#!25 & sel) target a
> cartoon (#!25 & sel)
> select ::name="P2E"
137 atoms, 137 bonds, 3 residues, 3 models selected
> show (#!25,31 & sel) target ab
> select ligand
137 atoms, 137 bonds, 3 residues, 3 models selected
> show (#!25,31 & sel) target ab
> style sel & #!25,31 stick
Changed 81 atom styles
> style sel & #!25,31 stick
Changed 81 atom styles
> hide #!25 models
> hide #!31 models
> show #!31 models
> select add #25
4398 atoms, 4510 bonds, 1 pseudobond, 556 residues, 6 models selected
> select ::name="P2E"
137 atoms, 137 bonds, 3 residues, 3 models selected
> select clear
> show #!25 models
> select ligand
137 atoms, 137 bonds, 3 residues, 3 models selected
> show (#!25,31 & sel) target ab
> hide #!31 models
> color (#!25 & sel) hot pink
> show (#!25 & sel) target ab
> hide #* target a
> show (#!25 & sel) target ab
> surface style #25 mesh
> transparency (#!25 & sel) 80
> style (#!25 & sel) stick
Changed 56 atom styles
> show (#!25 & sel) target ab
> surface hidePatches (#!25 & sel)
> color (#!25 & sel) byelement
> show #!31 models
> select ::name="P2E"
137 atoms, 137 bonds, 3 residues, 3 models selected
> show (#!25,31 & sel) target ab
> surface hidePatches (#!25,31 & sel)
> select clear
> save "/Users/chitrajoshi/Desktop/SLCO2A1/structure/PDB release/Overlay of
> 8KGW and our structure.png" width 866 height 663 supersample 4
> select #25/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> hide #* target a
> show (#!25 & sel) target ab
> undo
> cartoon hide (#!25 & sel)
> select ligand
137 atoms, 137 bonds, 3 residues, 3 models selected
> show (#!25,31 & sel) target ab
> select #31/A
4036 atoms, 4144 bonds, 3 pseudobonds, 533 residues, 2 models selected
> cartoon hide (#!31 & sel)
> select ::name="P2E"
137 atoms, 137 bonds, 3 residues, 3 models selected
> show (#!25,31 & sel) target ab
> select clear
> select ligand
137 atoms, 137 bonds, 3 residues, 3 models selected
> select #31/A
4036 atoms, 4144 bonds, 3 pseudobonds, 533 residues, 2 models selected
> color (#!31 & sel) purple
> select #25/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> color (#!25 & sel) hot pink
> select clear
> save "/Users/chitrajoshi/Desktop/SLCO2A1/structure/PDB release/overlay of
> ligand.png" width 866 height 663 supersample 4
> surface #25,31
> surface style #25,31 mesh
> transparency #25,31 80
> undo
> redo
> surface hidePatches #25,31
> select ::name="P2E"
137 atoms, 137 bonds, 3 residues, 3 models selected
> surface (#!25,31 & sel)
> transparency (#!25,31 & sel) 80
> select clear
> transparency #25,31 90
> save "/Users/chitrajoshi/Desktop/SLCO2A1/structure/PDB release/overlay of
> ligand surface.png" width 866 height 663 supersample 4
> select #25/A
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> cartoon (#!25 & sel)
> ui tool show "Side View"
> view
> select ligand
137 atoms, 137 bonds, 3 residues, 3 models selected
> show (#!25,31 & sel) target ab
> surface hidePatches (#!25,31 & sel)
> select clear
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Grid screening /Cryosparc
> volumes/Tolcapone/cryosparc_P73_J20_class_00_final_volume.mrc"
Opened cryosparc_P73_J20_class_00_final_volume.mrc as #32, grid size
256,256,256, pixel 0.975, shown at level 0.191, step 1, values float32
> hide #!25 models
> hide #!31 models
> view
> volume #32 level 0.3059
> volume #32 level 0.2183
> volume #32 level 0.3197
> show #!25 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #25 inMap #32
Fit molecule AF_combined_coot3_P2E.pdb (#25) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4317 atoms
average map value = 0.2321, steps = 196
shifted from previous position = 3.11
rotated from previous position = 23 degrees
atoms outside contour = 3353, contour level = 0.31972
Position of AF_combined_coot3_P2E.pdb (#25) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
-0.85079680 0.51206939 0.11802433 149.19728367
0.38484189 0.76009191 -0.52360005 49.29647444
-0.35782890 -0.40005654 -0.84374952 347.87195911
Axis 0.24327974 0.93704194 -0.25053418
Axis point 92.07737044 0.00000000 170.17249458
Rotation angle (degrees) 165.29084768
Shift along axis -4.66427613
> select add #25
4317 atoms, 4429 bonds, 1 pseudobond, 554 residues, 2 models selected
> ui mousemode right "move picked models"
> view matrix models
> #25,-0.8508,0.51207,0.11802,149.35,0.38484,0.76009,-0.5236,42.304,-0.35783,-0.40006,-0.84375,368.81
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.87502,-0.47824,-0.075038,326.01,0.41981,-0.82684,0.3743,135.88,-0.24105,0.29602,0.92427,-11.598
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.87502,-0.47824,-0.075038,335.82,0.41981,-0.82684,0.3743,128.13,-0.24105,0.29602,0.92427,-14.49
> fitmap #25 inMap #32
Fit molecule AF_combined_coot3_P2E.pdb (#25) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4317 atoms
average map value = 0.2597, steps = 220
shifted from previous position = 14.9
rotated from previous position = 32.1 degrees
atoms outside contour = 2979, contour level = 0.31972
Position of AF_combined_coot3_P2E.pdb (#25) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
-0.50416102 -0.85579395 -0.11592403 333.71098303
0.67752211 -0.47518377 0.56139485 22.59309066
-0.53552353 0.20449231 0.81938845 49.33489444
Axis -0.21905752 0.25753929 0.94110962
Axis point 164.93709318 94.70838809 0.00000000
Rotation angle (degrees) 125.44900733
Shift along axis -20.85374845
> fitmap #25 inMap #32
Fit molecule AF_combined_coot3_P2E.pdb (#25) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4317 atoms
average map value = 0.2597, steps = 44
shifted from previous position = 0.00317
rotated from previous position = 0.0134 degrees
atoms outside contour = 2980, contour level = 0.31972
Position of AF_combined_coot3_P2E.pdb (#25) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
-0.50405940 -0.85585510 -0.11591444 333.70178266
0.67768198 -0.47513651 0.56124187 22.58394883
-0.53541690 0.20434611 0.81949461 49.32594201
Axis -0.21902895 0.25745104 0.94114041
Axis point 164.93232305 94.71960982 0.00000000
Rotation angle (degrees) 125.44003908
Shift along axis -20.85345232
> fitmap #25 inMap #32
Fit molecule AF_combined_coot3_P2E.pdb (#25) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4317 atoms
average map value = 0.2597, steps = 44
shifted from previous position = 0.00702
rotated from previous position = 0.0117 degrees
atoms outside contour = 2981, contour level = 0.31972
Position of AF_combined_coot3_P2E.pdb (#25) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
-0.50400793 -0.85589635 -0.11583362 333.68513720
0.67763860 -0.47501530 0.56139682 22.54595658
-0.53552023 0.20445512 0.81939989 49.33403894
Axis -0.21904969 0.25755529 0.94110707
Axis point 164.93444876 94.70006311 0.00000000
Rotation angle (degrees) 125.43729759
Shift along axis -20.85818236
> view matrix models
> #25,-0.50401,-0.8559,-0.11583,335.67,0.67764,-0.47502,0.5614,-6.3036,-0.53552,0.20446,0.8194,30.712
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.48551,-0.87373,-0.029544,322.89,0.8657,-0.47579,-0.15551,74.16,0.12181,-0.10108,0.98739,-40.86
> view matrix models
> #25,0.11771,0.93232,-0.34195,21.784,0.6564,-0.33144,-0.67771,159.68,-0.74518,-0.14468,-0.65098,329.15
> view matrix models
> #25,0.15787,0.95524,-0.2502,-0.76177,0.67167,-0.28961,-0.6819,152.07,-0.72384,-0.060399,-0.68732,319.27
> ui mousemode right "move picked models"
> view matrix models
> #25,0.15787,0.95524,-0.2502,-2.6805,0.67167,-0.28961,-0.6819,177.38,-0.72384,-0.060399,-0.68732,332.58
> fitmap #25 inMap #32
Fit molecule AF_combined_coot3_P2E.pdb (#25) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4317 atoms
average map value = 0.2583, steps = 104
shifted from previous position = 4.06
rotated from previous position = 11.7 degrees
atoms outside contour = 3025, contour level = 0.31972
Position of AF_combined_coot3_P2E.pdb (#25) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
0.18945876 0.97973108 -0.06505678 -35.05522050
0.74224340 -0.18627851 -0.64371970 143.93771262
-0.64279087 0.07367038 -0.76249103 311.60527081
Axis 0.75417637 0.60735912 -0.24966557
Axis point 0.00000000 34.51565506 175.85928663
Rotation angle (degrees) 151.60082076
Shift along axis -16.81304194
> fitmap #25 inMap #32
Fit molecule AF_combined_coot3_P2E.pdb (#25) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4317 atoms
average map value = 0.2583, steps = 44
shifted from previous position = 0.00425
rotated from previous position = 0.00691 degrees
atoms outside contour = 3024, contour level = 0.31972
Position of AF_combined_coot3_P2E.pdb (#25) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
0.18952282 0.97971238 -0.06515173 -35.04715852
0.74224339 -0.18639082 -0.64368719 143.94642806
-0.64277200 0.07363496 -0.76251036 311.60742093
Axis 0.75420410 0.60731928 -0.24967873
Axis point 0.00000000 34.52459794 175.85813593
Rotation angle (degrees) 151.60489235
Shift along axis -16.81301512
> select subtract #25
2 models selected
> hide #!25 models
> show #9 models
> select add #9
4940 atoms, 5064 bonds, 569 pseudobonds, 644 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.73451,0.60997,-0.29739,108.83,-0.65848,0.53471,-0.52962,137.89,-0.16403,0.58483,0.7944,121.87,#13,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #9,0.18161,-0.84347,0.50555,137.69,-0.95327,-0.024779,0.30111,148.44,-0.24145,-0.53661,-0.80855,146.5,#13,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "move picked models"
> view matrix models
> #9,0.18161,-0.84347,0.50555,126.64,-0.95327,-0.024779,0.30111,125.43,-0.24145,-0.53661,-0.80855,122.02
> fitmap #9 inMap #32
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4940 atoms
average map value = 0.2265, steps = 184
shifted from previous position = 4
rotated from previous position = 20.7 degrees
atoms outside contour = 3728, contour level = 0.31972
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
0.44398842 -0.63622740 0.63094292 122.30857404
-0.88775648 -0.21685910 0.40603023 125.18578312
-0.12150185 -0.74039639 -0.66109793 121.32144042
Axis -0.82229537 0.53970471 -0.18041382
Axis point -0.00000000 130.23610582 9.02454481
Rotation angle (degrees) 135.80605728
Shift along axis -54.89848126
> fitmap #9 inMap #32
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4940 atoms
average map value = 0.2265, steps = 28
shifted from previous position = 0.0243
rotated from previous position = 0.0154 degrees
atoms outside contour = 3726, contour level = 0.31972
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
0.44406706 -0.63603497 0.63108157 122.32566745
-0.88771988 -0.21682066 0.40613077 125.19939283
-0.12148185 -0.74057296 -0.66090380 121.33101384
Axis -0.82230538 0.53966594 -0.18048416
Axis point 0.00000000 130.25400343 9.00470792
Rotation angle (degrees) 135.79326895
Shift along axis -54.92153212
> view matrix models
> #9,0.44407,-0.63603,0.63108,122.21,-0.88772,-0.21682,0.40613,127.38,-0.12148,-0.74057,-0.6609,133.79
> view matrix models
> #9,0.44407,-0.63603,0.63108,122.63,-0.88772,-0.21682,0.40613,122.73,-0.12148,-0.74057,-0.6609,126.25
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.56903,-0.21338,-0.79415,110.26,-0.73837,0.55768,0.37922,106.61,0.36197,0.80216,-0.47488,94.744,#13,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.56903,-0.21338,-0.79415,115.99,-0.73837,0.55768,0.37922,114.93,0.36197,0.80216,-0.47488,128,#13,1,0,0,0,0,1,0,0,0,0,1,0
> fitmap #9 inMap #32
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4940 atoms
average map value = 0.2123, steps = 208
shifted from previous position = 16.1
rotated from previous position = 11.4 degrees
atoms outside contour = 3787, contour level = 0.31972
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
-0.57467564 -0.09361019 -0.81300986 122.73235623
-0.62698091 0.68883576 0.36386842 128.63930884
0.52596848 0.71884798 -0.45454894 122.81332709
Axis 0.23914474 -0.90205089 -0.35932436
Axis point 59.74594273 0.00000000 73.72157289
Rotation angle (degrees) 132.08207108
Shift along axis -130.81822444
> fitmap #9 inMap #32
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4940 atoms
average map value = 0.2122, steps = 44
shifted from previous position = 0.0219
rotated from previous position = 0.017 degrees
atoms outside contour = 3786, contour level = 0.31972
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
-0.57465146 -0.09390582 -0.81299286 122.71154272
-0.62710692 0.68881059 0.36369888 128.64000921
0.52584465 0.71883354 -0.45471500 122.80641837
Axis 0.23927355 -0.90204770 -0.35924660
Axis point 59.74483302 0.00000000 73.71550394
Rotation angle (degrees) 132.08851972
Shift along axis -130.79558567
> view matrix models
> #9,-0.57465,-0.093906,-0.81299,117.77,-0.62711,0.68881,0.3637,126.31,0.52584,0.71883,-0.45471,120.99,#13,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.16776,0.64145,-0.7486,103.45,-0.41538,0.64267,0.64377,127.99,0.89405,0.41895,0.15862,128.6,#13,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.16776,0.64145,-0.7486,122.11,-0.41538,0.64267,0.64377,129.27,0.89405,0.41895,0.15862,138.16,#13,1,0,0,0,0,1,0,0,0,0,1,0
> fitmap #9 inMap #32
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4940 atoms
average map value = 0.2238, steps = 204
shifted from previous position = 15.8
rotated from previous position = 20.9 degrees
atoms outside contour = 3737, contour level = 0.31972
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
-0.37360141 0.38597220 -0.84347343 125.75546552
-0.35136092 0.78267279 0.51377893 128.63385130
0.85846810 0.48831214 -0.15679211 123.42727809
Axis -0.01372895 -0.91750354 -0.39749059
Axis point 41.19277957 -0.00000000 79.26204009
Rotation angle (degrees) 111.95389394
Shift along axis -168.80968641
> volume #32 level 0.4276
> fitmap #9 inMap #32
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4940 atoms
average map value = 0.2238, steps = 28
shifted from previous position = 0.0243
rotated from previous position = 0.00515 degrees
atoms outside contour = 4189, contour level = 0.42759
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
-0.37359925 0.38603931 -0.84344368 125.77835343
-0.35129130 0.78267226 0.51382735 128.64108640
0.85849753 0.48825994 -0.15679352 123.43051897
Axis -0.01378319 -0.91750332 -0.39748922
Axis point 41.20125533 0.00000000 79.26717618
Rotation angle (degrees) 111.95388711
Shift along axis -168.82455152
> fitmap #9 inMap #32
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4940 atoms
average map value = 0.2238, steps = 44
shifted from previous position = 0.0243
rotated from previous position = 0.00824 degrees
atoms outside contour = 4188, contour level = 0.42759
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
-0.37360564 0.38591668 -0.84349697 125.75525969
-0.35138180 0.78269327 0.51373346 128.63429500
0.85845772 0.48832320 -0.15681452 123.42862718
Axis -0.01369849 -0.91751185 -0.39747245
Axis point 41.19286241 0.00000000 79.26540536
Rotation angle (degrees) 111.95408407
Shift along axis -168.80562652
> fitmap #9 inMap #32
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4940 atoms
average map value = 0.2238, steps = 44
shifted from previous position = 0.0165
rotated from previous position = 0.00904 degrees
atoms outside contour = 4190, contour level = 0.42759
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
-0.37365429 0.38582277 -0.84351838 125.77092194
-0.35130825 0.78277544 0.51365855 128.63962808
0.85846664 0.48826569 -0.15694468 123.43003056
Axis -0.01368940 -0.91754748 -0.39739052
Axis point 41.19754574 -0.00000000 79.27379374
Rotation angle (degrees) 111.95706921
Shift along axis -168.80461906
> fitmap #9 inMap #32
Fit molecule fold_rnslco2a1_cya_mut_model_0.cif (#9) to map
cryosparc_P73_J20_class_00_final_volume.mrc (#32) using 4940 atoms
average map value = 0.2238, steps = 28
shifted from previous position = 0.0222
rotated from previous position = 0.00513 degrees
atoms outside contour = 4188, contour level = 0.42759
Position of fold_rnslco2a1_cya_mut_model_0.cif (#9) relative to
cryosparc_P73_J20_class_00_final_volume.mrc (#32) coordinates:
Matrix rotation and translation
-0.37361920 0.38586530 -0.84351446 125.74999340
-0.35136019 0.78273216 0.51368899 128.63248813
0.85846066 0.48830148 -0.15686606 123.42773043
Axis -0.01368631 -0.91752810 -0.39743536
Axis point 41.18893076 0.00000000 79.26579470
Rotation angle (degrees) 111.95489413
Shift along axis -168.79952083
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by
> Justin/nab_B9/nab_B9-selected/cryosparc_P124_J314_009_volume_map (1).mrc"
Opened cryosparc_P124_J314_009_volume_map (1).mrc as #33, grid size
196,196,196, pixel 1.46, shown at level 0.304, step 1, values float32
> hide #9 models
> select subtract #9
Nothing selected
> hide #!32 models
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by
> Justin/nab_B9/nab_B9-selected/cryosparc_P124_J314_009_volume_map_sharp.mrc"
Opened cryosparc_P124_J314_009_volume_map_sharp.mrc as #34, grid size
196,196,196, pixel 1.46, shown at level 0.402, step 1, values float32
> hide #!33 models
> volume #34 level 1.552
> show #!33 models
> hide #!34 models
> volume #33 level 0.3814
> ui tool show "Side View"
> volume #33 level 0.5213
> save "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/nab_B9/Image of
> B9 bound.png" width 866 height 682 supersample 4
> volume #33 level 0.529
> save "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by Justin/nab_B9/60 degree
> rotated view.png" width 866 height 682 supersample 4
> volume #33 level 1.236
> open "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by
> Justin/Dinoprost/dinoprost-
> selected/cryosparc_P124_J500_map_deepEMhanced.mrc"
Opened cryosparc_P124_J500_map_deepEMhanced.mrc as #35, grid size 392,392,392,
pixel 0.732, shown at level 0.000931, step 2, values float32
> hide #!33 models
> volume #35 color #531b93
> volume #35 color #76d6ff
> volume #35 color #7a81ff
> volume #35 color #9437ff
> volume #35 color #ffd479
> volume #35 color #ff9300
> volume #35 color #009051
> volume #35 color #7a81ff
> volume #35 color #73fcd6
> volume #35 color #00fdff
> view
> surface dust #35 size 7.32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #35 step 1
> volume #35 step 2
> volume #35 level 0.04943
> surface dust #35 size 7.32
> volume #35 level 0.007079
> ui tool show "Side View"
> volume #35 level 0.01685
> volume #35 level 0.01359
> surface dust #35 size 7.32
> volume #35 level 0.02011
> save "/Users/chitrajoshi/Desktop/SLCO2A1/Volumes by
> Justin/Dinoprost/dinoprost-selected/Image.png" width 866 height 682
> supersample 4
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202404140648 (2024-04-14)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-22.5.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0)
OS Loader Version: 580.140.1~51
Software:
System Software Overview:
System Version: macOS 14.7.1 (23H222)
Kernel Version: Darwin 23.6.0
Time since boot: 20 hours, 24 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56.1
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
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: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202404140648
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.3
fonttools: 4.51.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.6
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 12 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 12 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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