![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8226 closed defect (limitation)
Unsupported scale factor (0.000000) detected on Display0
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.6.1-arm64-arm-64bit
ChimeraX Version: 1.6.dev202212061854 (2022-12-06 18:54:31 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001002cc580 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 284 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 1100000,
"procLaunch" : "2022-12-22 09:49:40.3289 +0100",
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,4",
"procStartAbsTime" : 26871231372981,
"coalitionID" : 247878,
"osVersion" : {
"train" : "macOS 12.6.1",
"build" : "21G217",
"releaseType" : "User"
},
"captureTime" : "2022-12-23 15:35:20.3367 +0100",
"incident" : "75277C2A-7508-466A-B610-F8FBAE481D1D",
"bug_type" : "309",
"pid" : 4804,
"procExitAbsTime" : 28030116930814,
"translated" : false,
"cpuType" : "ARM-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D91302BD-DBCE-5C53-8136-7D7F3BF49D6F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F0D674B1-5FA4-E9D0-6B9C-8D1ED9987542",
"wakeTime" : 22773,
"sleepWakeUUID" : "078C4E2B-E764-4E06-892C-46AF3304BEDD",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 68719476712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Fault hit memory shortage\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 68719476712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)",
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===== Log before crash start =====
> graphics silhouettes true
> lighting soft
> windowsize 800 800
UCSF ChimeraX version: 1.6.dev202212061854 (2022-12-06)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/kelvinlau/Downloads/cryosparc_P6_J81_004_volume_map_sharp.mrc
Opened cryosparc_P6_J81_004_volume_map_sharp.mrc as #1, grid size 250,250,250,
pixel 1.66, shown at level 0.0934, step 1, values float32
> volume #1 level 0.1699
> surface dust #1 size 16.6
> open
> /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb
Chain information for SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb #2
---
Chain | Description
A | No description available
> open
> /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb
Chain information for SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb #3
---
Chain | Description
A | No description available
> close #3
> select add #2
9282 atoms, 9503 bonds, 1191 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,238.29,0,1,0,160.08,0,0,1,63.535
> view matrix models #2,1,0,0,268.35,0,1,0,103.19,0,0,1,165.1
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.50961,-0.10696,0.85373,262.71,-0.22592,0.94079,0.25272,100.6,-0.83022,-0.32166,0.45528,155.62
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.50961,-0.10696,0.85373,196.11,-0.22592,0.94079,0.25272,230.53,-0.83022,-0.32166,0.45528,200.66
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.49784,-0.19129,0.84591,196.02,-0.15047,0.94153,0.30147,231.4,-0.85412,-0.27737,0.43994,200.36
> view matrix models
> #2,0.13946,0.46657,0.87342,191.49,-0.35554,0.84682,-0.39559,229.07,-0.9242,-0.25537,0.28399,199.53
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.13946,0.46657,0.87342,199.37,-0.35554,0.84682,-0.39559,235.61,-0.9242,-0.25537,0.28399,205.47
> ui mousemode right select
> fitmap #2 inMap #1
Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#2) to map
cryosparc_P6_J81_004_volume_map_sharp.mrc (#1) using 9282 atoms
average map value = 0.086, steps = 84
shifted from previous position = 8.12
rotated from previous position = 6.55 degrees
atoms outside contour = 7068, contour level = 0.16994
Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#2) relative to
cryosparc_P6_J81_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.20825569 0.51136147 0.83374997 206.39416826
-0.42245097 0.81585364 -0.39486454 231.44674363
-0.88213647 -0.26998570 0.38593131 202.15824498
Axis 0.06379456 0.87656343 -0.47703963
Axis point 276.81499655 0.00000000 24.47113983
Rotation angle (degrees) 78.16931126
Shift along axis 119.60708187
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.20826,0.51136,0.83375,89.2,-0.42245,0.81585,-0.39486,239.57,-0.88214,-0.26999,0.38593,203.41
> select clear
> select add #2
9282 atoms, 9503 bonds, 1191 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.2559,0.43621,0.86269,89.795,-0.31797,0.88073,-0.35101,240.75,-0.91291,-0.18449,0.36408,203.01
> view matrix models
> #2,-0.4747,0.87397,0.10415,81.061,-0.72608,-0.32197,-0.60757,236.66,-0.49747,-0.36403,0.7874,207.94
> view matrix models
> #2,0.62893,0.43037,0.64748,94.135,-0.4547,0.87914,-0.14268,239.16,-0.63063,-0.20467,0.74861,206.3
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.62893,0.43037,0.64748,211.11,-0.4547,0.87914,-0.14268,225.04,-0.63063,-0.20467,0.74861,218.81
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.771,0.063459,0.63366,212.96,-0.25069,0.94493,0.2104,227.37,-0.58541,-0.32107,0.74445,219.4
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.771,0.063459,0.63366,208.02,-0.25069,0.94493,0.2104,227.33,-0.58541,-0.32107,0.74445,214.53
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> view matrix models
> #2,0.771,0.063459,0.63366,204.85,-0.25069,0.94493,0.2104,227.07,-0.58541,-0.32107,0.74445,202.91
> view matrix models
> #2,0.771,0.063459,0.63366,204.6,-0.25069,0.94493,0.2104,226.89,-0.58541,-0.32107,0.74445,202.1
> fitmap #2 inMap #1
Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#2) to map
cryosparc_P6_J81_004_volume_map_sharp.mrc (#1) using 9282 atoms
average map value = 0.09942, steps = 128
shifted from previous position = 13.4
rotated from previous position = 12.4 degrees
atoms outside contour = 6548, contour level = 0.16994
Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#2) relative to
cryosparc_P6_J81_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.78888549 -0.13060681 0.60050108 201.64318990
-0.04479087 0.96233622 0.26814695 215.28574743
-0.61290575 -0.23843420 0.75332308 197.44056504
Axis -0.38444217 0.92084902 0.06512533
Axis point 418.32043794 0.00000000 -274.24590614
Rotation angle (degrees) 41.21239498
Shift along axis 133.58390578
> hide #2 models
> open /Users/kelvinlau/Downloads/cryosparc_P6_J103_003_volume_map_sharp.mrc
Opened cryosparc_P6_J103_003_volume_map_sharp.mrc as #3, grid size
300,300,300, pixel 1.38, shown at level 0.105, step 2, values float32
> surface dust #3 size 13.8
> volume #3 step 1
> surface dust #3 size 13.8
> volume #3 level 0.1602
> volume #3 level 0.2099
> open
> /Users/kelvinlau/Downloads/30BRBD_819d3.result/30BRBD_819d3_unrelaxed_rank_1_model_5.pdb
Chain information for 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb #4
---
Chain | Description
A | No description available
> select add #4
12225 atoms, 12521 bonds, 1568 residues, 2 models selected
> select clear
> select #4/A:264
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
60 atoms, 59 bonds, 9 residues, 1 model selected
> select up
2943 atoms, 3018 bonds, 377 residues, 1 model selected
> select clear
Drag select of 132 residues
> delete atoms sel
> delete bonds sel
Drag select of 17 residues
> delete atoms sel
> delete bonds sel
Drag select of 28 residues, 3 pseudobonds
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
Drag select of 4 residues, 2 pseudobonds
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select clear
Drag select of 3 residues, 1 pseudobonds
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select clear
Drag select of 192 residues, 1 pseudobonds
> select clear
Alignment identifier is 2/A
Alignment identifier is 4/A
> select #4/A:293
7 atoms, 7 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/A:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
84 atoms, 86 bonds, 10 residues, 1 model selected
> select up
1526 atoms, 1573 bonds, 192 residues, 1 model selected
> view matrix models #4,1,0,0,72.441,0,1,0,94.915,0,0,1,-80.71
> view matrix models #4,1,0,0,64.732,0,1,0,82.769,0,0,1,189.15
> view matrix models #4,1,0,0,116,0,1,0,91.709,0,0,1,241.17
> view matrix models #4,1,0,0,189.43,0,1,0,188.52,0,0,1,177.36
> volume #3 level 0.1768
> volume #3 level 0.1381
> volume #3 level 0.08296
> volume #3 level 0.1106
> open /Users/kelvinlau/Downloads/cryosparc_P6_J105_000_volume_map_sharp.mrc
Opened cryosparc_P6_J105_000_volume_map_sharp.mrc as #5, grid size
300,300,300, pixel 1.38, shown at level 0.0411, step 2, values float32
> volume #5 step 1
> volume #5 level 0.07638
> volume #5 level 0.05993
> volume #3 color #ffffb280
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting full
> volume #3 color #9fe3ff80
> color #4 #ee4a4fff
> view matrix models #4,1,0,0,153.28,0,1,0,146.66,0,0,1,197.88
> volume #3 color #9fe3ff
> volume #3 level 0.2128
> view matrix models #4,1,0,0,154.28,0,1,0,146.99,0,0,1,194.61
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.55931,0.59264,-0.57961,172.22,0.3337,0.80101,0.49701,147.24,0.75882,0.084566,-0.64578,164.71
> view matrix models
> #4,-0.80216,-0.17769,-0.57006,176.13,-0.47414,0.76984,0.42723,159.07,0.36294,0.613,-0.70179,170.26
> view matrix models
> #4,-0.56047,-0.65909,-0.50147,173.12,0.39694,-0.74522,0.5358,146.7,-0.72685,0.10125,0.6793,202.42
> view matrix models
> #4,-0.087518,-0.99615,0.0057904,171.32,0.81394,-0.068156,0.57694,140.64,-0.57432,0.055206,0.81677,201.55
> view matrix models
> #4,0.24137,-0.93356,-0.26496,163.22,0.72605,-0.0074357,0.6876,143.22,-0.64389,-0.35834,0.67602,201.1
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.24137,-0.93356,-0.26496,204.57,0.72605,-0.0074357,0.6876,157.76,-0.64389,-0.35834,0.67602,176.12
> view matrix models
> #4,0.24137,-0.93356,-0.26496,209.09,0.72605,-0.0074357,0.6876,182.17,-0.64389,-0.35834,0.67602,193.12
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.23746,-0.97127,0.015804,212.23,0.65669,0.1725,0.73416,183.76,-0.7158,-0.16396,0.67879,194.26
> select clear
> hide #!4 models
> show #!4 models
> select add #4
1526 atoms, 1573 bonds, 192 residues, 1 model selected
> fitmap #4 inMap #3
Fit molecule 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) to map
cryosparc_P6_J103_003_volume_map_sharp.mrc (#3) using 1526 atoms
average map value = 0.08419, steps = 100
shifted from previous position = 2.68
rotated from previous position = 7.78 degrees
atoms outside contour = 1170, contour level = 0.21283
Position of 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) relative to
cryosparc_P6_J103_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.36206110 -0.93104562 0.04545116 211.40525616
0.63727304 0.28281559 0.71686708 181.56403030
-0.68029025 -0.23058489 0.69572680 192.78660277
Axis -0.48074878 0.36825012 0.79578418
Axis point 61.05282466 246.49229503 0.00000000
Rotation angle (degrees) 80.19463617
Shift along axis 118.64468512
> view matrix models
> #4,0.34203,-0.9275,-0.15084,209.56,0.86024,0.24446,0.44747,175.13,-0.37815,-0.28281,0.88149,190.11
> view matrix models
> #4,0.42032,-0.84767,-0.32371,206.44,0.86893,0.27328,0.41264,174.61,-0.26131,-0.45472,0.85144,187.96
> view matrix models
> #4,0.56188,-0.74319,-0.36326,203.8,0.75057,0.27342,0.60158,178.53,-0.34776,-0.61066,0.71144,187.78
> view matrix models
> #4,0.44402,-0.76285,-0.47002,204.47,0.79699,0.096531,0.59623,177.75,-0.40946,-0.63933,0.65084,188.08
> select clear
> volume flip #3
Opened cryosparc_P6_J103_003_volume_map_sharp.mrc z flip as #6, grid size
300,300,300, pixel 1.38, shown at step 1, values float32
> fitmap #4 inMap #6
Fit molecule 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) to map
cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) using 1526 atoms
average map value = 0.06091, steps = 100
shifted from previous position = 6.54
rotated from previous position = 6.37 degrees
atoms outside contour = 1263, contour level = 0.21283
Position of 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) relative to
cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.49114731 -0.70417853 -0.51274449 206.07445746
0.76098264 0.06041915 0.64595274 184.69476976
-0.42388646 -0.70744761 0.56554235 186.38457813
Axis -0.67786324 -0.04450538 0.73383970
Axis point 56.04003946 241.43186192 0.00000000
Rotation angle (degrees) 86.64315955
Shift along axis -11.13380684
> fitmap #4 inMap #6
Fit molecule 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) to map
cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) using 1526 atoms
average map value = 0.0609, steps = 60
shifted from previous position = 0.0193
rotated from previous position = 0.0396 degrees
atoms outside contour = 1267, contour level = 0.21283
Position of 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) relative to
cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.49138650 -0.70443574 -0.51216169 206.06131280
0.76076653 0.06088596 0.64616344 184.70546684
-0.42399716 -0.70715146 0.56582967 186.37997272
Axis -0.67784031 -0.04415932 0.73388178
Axis point 55.95166640 241.48671085 0.00000000
Rotation angle (degrees) 86.61465388
Shift along axis -11.05226510
> fitmap #4 inMap #6
Fit molecule 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) to map
cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) using 1526 atoms
average map value = 0.06087, steps = 44
shifted from previous position = 0.025
rotated from previous position = 0.0733 degrees
atoms outside contour = 1266, contour level = 0.21283
Position of 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) relative to
cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.49101548 -0.70389658 -0.51325764 206.06476567
0.76119997 0.06014995 0.64572176 184.70941009
-0.42364892 -0.70775108 0.56534061 186.38554941
Axis -0.67788758 -0.04488057 0.73379436
Axis point 56.07098321 241.40822333 0.00000000
Rotation angle (degrees) 86.66045746
Shift along axis -11.20994306
> surface dust #6 size 13.8
> hide #!4 models
> show #!4 models
> select add #4
1526 atoms, 1573 bonds, 192 residues, 1 model selected
> view matrix models
> #4,-0.89146,0.45095,0.043991,233.72,-0.01105,0.075423,-0.99709,178.73,-0.45296,-0.88936,-0.062254,179.96
> view matrix models
> #4,-0.91028,0.38768,-0.14523,231.94,0.16457,0.016954,-0.98622,176.11,-0.37988,-0.92164,-0.079232,178.63
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.91028,0.38768,-0.14523,248.08,0.16457,0.016954,-0.98622,102.95,-0.37988,-0.92164,-0.079232,207.95
> view matrix models
> #4,-0.91028,0.38768,-0.14523,262.5,0.16457,0.016954,-0.98622,107.93,-0.37988,-0.92164,-0.079232,219.32
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.14928,0.85422,0.49802,253.03,-0.48951,0.50146,-0.71339,121.12,-0.85913,-0.13729,0.49301,233.06
> view matrix models
> #4,0.52024,0.71757,0.46307,246.86,-0.47325,0.69359,-0.54311,122.73,-0.71091,0.063398,0.70042,233.02
> view matrix models
> #4,0.010456,-0.0014918,0.99994,260.72,0.45443,0.89078,-0.0034227,114.18,-0.89072,0.45444,0.0099916,228.24
> view matrix models
> #4,-0.60486,-0.13448,0.7849,267.96,0.29107,0.8801,0.3751,120.88,-0.74123,0.45534,-0.49319,220.39
> view matrix models
> #4,0.046977,-0.75109,-0.65853,241.96,-0.83002,0.33744,-0.44408,129.38,0.55576,0.56745,-0.60756,198.9
> view matrix models
> #4,0.47398,-0.65094,-0.59298,236.02,-0.78076,0.00068232,-0.62483,126.64,0.40713,0.75913,-0.5079,202.31
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.47398,-0.65094,-0.59298,183.09,-0.78076,0.00068232,-0.62483,173.32,0.40713,0.75913,-0.5079,244.3
> view matrix models
> #4,0.47398,-0.65094,-0.59298,178.72,-0.78076,0.00068232,-0.62483,184.82,0.40713,0.75913,-0.5079,234.87
> view matrix models
> #4,0.47398,-0.65094,-0.59298,197.08,-0.78076,0.00068232,-0.62483,185.77,0.40713,0.75913,-0.5079,233.28
> view matrix models
> #4,0.47398,-0.65094,-0.59298,195.81,-0.78076,0.00068232,-0.62483,181.62,0.40713,0.75913,-0.5079,237.62
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.19048,-0.50759,-0.84028,197.51,-0.75338,0.4732,-0.45662,183.03,0.62939,0.72003,-0.29227,236.52
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.19048,-0.50759,-0.84028,198.54,-0.75338,0.4732,-0.45662,190.6,0.62939,0.72003,-0.29227,241.97
> fitmap #4 inMap #6
Fit molecule 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) to map
cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) using 1526 atoms
average map value = 0.1316, steps = 84
shifted from previous position = 4.3
rotated from previous position = 8.9 degrees
atoms outside contour = 1061, contour level = 0.21283
Position of 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) relative to
cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.24636656 -0.38602508 -0.88898153 195.59638625
-0.72305283 0.53758348 -0.43381862 194.12555926
0.64536667 0.74965901 -0.14667393 241.89623326
Axis 0.60171745 -0.78011113 -0.17135556
Axis point 50.47811682 0.00000000 228.12751276
Rotation angle (degrees) 100.44909898
Shift along axis -75.19601607
> view matrix models
> #4,0.24637,-0.38603,-0.88898,195,-0.72305,0.53758,-0.43382,195,0.64537,0.74966,-0.14667,242.93
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.11804,-0.51068,-0.85163,197.42,-0.64468,0.6129,-0.45688,193.52,0.75528,0.60296,-0.25687,240.01
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.11804,-0.51068,-0.85163,197.16,-0.64468,0.6129,-0.45688,193.66,0.75528,0.60296,-0.25687,235.12
> fitmap #4 inMap #6
Fit molecule 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) to map
cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) using 1526 atoms
average map value = 0.3923, steps = 84
shifted from previous position = 1.86
rotated from previous position = 16.9 degrees
atoms outside contour = 483, contour level = 0.21283
Position of 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) relative to
cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.14031735 -0.38665532 -0.91148709 196.13561642
-0.44327644 0.79864567 -0.40702712 190.95763357
0.88533443 0.46115373 -0.05933135 233.46609381
Axis 0.43487873 -0.90004227 -0.02836198
Axis point 23.47046957 0.00000000 237.51027308
Rotation angle (degrees) 93.45038349
Shift along axis -93.19629312
> select subtract #4
Nothing selected
> color #6 #9fe3ffa1 models
> save /Users/kelvinlau/Desktop/image1.png supersample 3
> save /Users/kelvinlau/Downloads/103_sharp_zflipped.ccp4 models #6
> save /Users/kelvinlau/Downloads/RBD-docked-103.pdb models #4 relModel #6
> open /Users/kelvinlau/Downloads/RBD-docked-103-coot-0.pdb
Chain information for RBD-docked-103-coot-0.pdb #7
---
Chain | Description
A | No description available
> hide #!6 models
> color #7 #2166acff
> close #7
> open /Users/kelvinlau/Downloads/RBD-docked-103-coot-0.pdb
Chain information for RBD-docked-103-coot-0.pdb #7
---
Chain | Description
A | No description available
> color #7 #6bffd5ff
> color #4,7 byhetero
> open 7m0j
Summary of feedback from opening 7m0j fetched from pdb
---
note | Fetching compressed mmCIF 7m0j from
http://files.rcsb.org/download/7m0j.cif
7m0j title:
SARS-CoV-2 u1S2q All Down RBD State Spike Protein Trimer - asymmetric
refinement [more info...]
Chain information for 7m0j #8
---
Chain | Description | UniProt
A B C | Spike glycoprotein | SPIKE_SARS2
> mmaker £7 to £8
> matchmaker £7 to £8
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> mmaker #8 to #7
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 RBD-docked-103-coot-0.pdb, chain A (#7) with 7m0j, chain B (#8),
sequence alignment score = 1146.2
RMSD between 138 pruned atom pairs is 0.941 angstroms; (across all 161 pairs:
1.831)
> mmaker #8 to #7
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 RBD-docked-103-coot-0.pdb, chain A (#7) with 7m0j, chain B (#8),
sequence alignment score = 1146.2
RMSD between 138 pruned atom pairs is 0.941 angstroms; (across all 161 pairs:
1.831)
> close #8
> open 7pki format mmcif fromDatabase pdb
7pki title:
Crystal structure of human ACE2 bound to the spike receptor-binding domain
from a cave bat sarbecovirus closely related to SARS-CoV-2. [more info...]
Chain information for 7pki #8
---
Chain | Description | UniProt
A | Processed angiotensin-converting enzyme 2 | ACE2_HUMAN
E | BANAL 236 coronavirus spike receptor-binding domain |
Non-standard residues in 7pki #8
---
CL — chloride ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
PEG — di(hydroxyethyl)ether
SO4 — sulfate ion
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)
ZN — zinc ion
> mmaker #8 to #7
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 RBD-docked-103-coot-0.pdb, chain A (#7) with 7pki, chain E (#8),
sequence alignment score = 703.4
RMSD between 158 pruned atom pairs is 0.966 angstroms; (across all 190 pairs:
2.336)
> open 6m0j
6m0j title:
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
[more info...]
Chain information for 6m0j #9
---
Chain | Description | UniProt
A | Angiotensin-converting enzyme 2 | ACE2_HUMAN
E | Spike protein S1 | SPIKE_SARS2
Non-standard residues in 6m0j #9
---
CL — chloride ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
ZN — zinc ion
> mmaker #9 to #7
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 RBD-docked-103-coot-0.pdb, chain A (#7) with 6m0j, chain E (#9),
sequence alignment score = 786.1
RMSD between 160 pruned atom pairs is 0.959 angstroms; (across all 189 pairs:
2.241)
> hide #8 models
> hide #!4 models
Drag select of 309 residues, 103 atoms, 98 bonds
> show sel atoms
> select clear
> select #7/A:121
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> view matrix models #7,1,0,0,3.1773,0,1,0,0.72743,0,0,1,0.90934
> select add #7
1554 atoms, 1601 bonds, 194 residues, 1 model selected
> select subtract #7
Nothing selected
> mmaker #7 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 6m0j, chain E (#9) with RBD-docked-103-coot-0.pdb, chain A (#7),
sequence alignment score = 786.1
RMSD between 160 pruned atom pairs is 0.959 angstroms; (across all 189 pairs:
2.241)
> select clear
> hide #!9 models
> show #!9 models
> select add #9/A:35
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
279 atoms, 286 bonds, 33 residues, 1 model selected
> select up
4926 atoms, 5070 bonds, 601 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
Drag select of 1 atoms
> hide sel atoms
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/kelvinlau/Desktop/movie1.mp4
Movie saved to /Users/kelvinlau/Desktop/movie1.mp4
> hide #7#!9 atoms
> select
> ::name="CL"::name="GOL"::name="HOH"::name="NAG"::name="PEG"::name="SO4"::name="TRS"::name="ZN"
372 atoms, 269 bonds, 119 residues, 3 models selected
> show (#7#!9 & sel) target ab
> select
> ::name="CL"::name="GOL"::name="HOH"::name="NAG"::name="PEG"::name="SO4"::name="TRS"::name="ZN"
372 atoms, 269 bonds, 119 residues, 3 models selected
> hide sel & #7#!9 atoms
> select ::name="NAG"
210 atoms, 211 bonds, 15 residues, 3 models selected
> show (#7#!9 & sel) target ab
> select clear
Drag select of 14 atoms, 14 bonds
> hide sel atoms
Drag select of 42 atoms, 42 bonds
> hide sel atoms
> select #7/A:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #9/E:343
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
> select clear
> select add #7/A:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save /Users/kelvinlau/Desktop/image2.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/kelvinlau/Desktop/movie2.mp4
Movie saved to /Users/kelvinlau/Desktop/movie2.mp4
> show #!4 models
> hide #!4 models
> select #9?A
Expected an objects specifier or a keyword
> select #9/B
Nothing selected
> select #9/D
Nothing selected
> select #9/C
Nothing selected
> select #9/F
Nothing selected
> select #9/G
Nothing selected
> select #9/A
4999 atoms, 5070 bonds, 3 pseudobonds, 674 residues, 2 models selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> select clear
> save /Users/kelvinlau/Desktop/image3.png supersample 3
> hide #7 models
> show #7 models
> hide #!9 models
> hide #7 models
> show #!6 models
> color #6 #9fe3ffff models
> color #6 #999999ff models
> color #6 #f4a582ff models
> color #6 #4393c3ff models
> color #6 #d1e5f04c models
> color #6 #666666ff models
> color #6 #a4a4a4ff models
> color #6 #c7c7c7ff models
> lighting soft
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/kelvinlau/Desktop/movie3.mp4
Movie saved to /Users/kelvinlau/Desktop/movie3.mp4
> open /Users/kelvinlau/Downloads/cryosparc_P6_J107_map_locres.mrc
Opened cryosparc_P6_J107_map_locres.mrc as #10, grid size 300,300,300, pixel
1.38, shown at level 6.75, step 2, values float32
> volume flip #10
Opened cryosparc_P6_J107_map_locres.mrc z flip as #11, grid size 300,300,300,
pixel 1.38, shown at step 1, values float32
> hide #!11 models
> show #!11 models
> volume #11 level 5.713
> ui tool show "Surface Color"
> color sample #6.1 map #11 palette #ff0000:#ffffff:#0000ff
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette 0,#ff0000:18.07,#ffffff:36.14,#0000ff
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> key red-white-blue :0.0 :18.1 :36.1 showTool true
> ui mousemode right "color key"
> ui mousemode right "translate selected models"
> color sample #6.1 map #11 palette 0,#0000ff:18.07,#00ffff:36.14,#00ff00
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 1,#0000ff:2,#00ffff:3,#00ff00:4,#ffff00:5,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> key rainbow :1 :2 :3 :4 :5 showTool true
> ui mousemode right "color key"
> ui mousemode right "translate selected models"
> color sample #6.1 map #11 palette
> 1.5,#0000ff:2,#00ffff:2.5,#00ff00:3,#ffff00:4,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 2,#0000ff:2.5,#00ffff:3,#00ff00:3.5,#ffff00:4,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 2,#0000ff:2.5,#00ffff:3,#00ff00:3.5,#ffff00:5,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 2,#0000ff:2.5,#00ffff:3,#00ff00:3.5,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 2,#0000ff:3,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 2.5,#0000ff:3,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 3,#0000ff:3,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 3,#0000ff:3.5,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 2,#0000ff:3.5,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 2,#0000ff:2.5,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 2,#0000ff:2.5,#00ffff:3,#00ff00:5,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 2,#0000ff:2.5,#00ffff:3,#00ff00:4,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 2.5,#0000ff:2.75,#00ffff:3,#00ff00:4,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 2.5,#0000ff:3,#00ffff:3,#00ff00:4,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 2.5,#0000ff:3,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color single #6.1
> color sample #6.1 map #11 palette
> 2.5,#0000ff:3,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 2.5,#0000ff:3,#00ffff:3.5,#00ff00:4,#ffff00:5,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> color sample #6.1 map #11 palette
> 3,#0000ff:3.25,#00ffff:3.5,#00ff00:4,#ffff00:5,#ff0000
Map values for surface "surface": minimum 0, mean 3.554, maximum 36.14
> volume #6 level 0.139
> surface dust #6 size 13.8
> volume #6 level 0.1446
> color sample #6.1 map #11 palette
> 3,#0000ff:3.25,#00ffff:3.5,#00ff00:4,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.239, maximum 49.25
> color sample #6.1 map #11 palette
> 3,#0000ff:3.25,#00ffff:3.5,#00ff00:4,#ffff00:7,#ff0000
Map values for surface "surface": minimum 0, mean 3.239, maximum 49.25
> color sample #6.1 map #11 palette
> 3,#0000ff:3.25,#00ffff:3.5,#00ff00:4,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.239, maximum 49.25
> key rainbow :3.00 :3.25 :3.50 :4.00 :6.00 showTool true
> ui mousemode right "color key"
> key delete
> ui mousemode right "translate selected models"
> key rainbow :3.00 :3.25 :3.50 :4.00 :6.00 showTool true
> ui mousemode right "color key"
> ui mousemode right "translate selected models"
> color sample #6.1 map #11 palette
> 3,#0000ff:3.5,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.239, maximum 49.25
> key rainbow :3.0 :3.5 :4.0 :5.0 :6.0 showTool true
> ui mousemode right "color key"
> ui mousemode right "translate selected models"
> save /Users/kelvinlau/Desktop/image4.png supersample 3
> ui tool show "Side View"
> show #!4 models
> show #!4 surfaces
> hide #!4 surfaces
> show #!4 surfaces
> hide #13 models
> volume #6 color #45c0d1
> hide #!4 surfaces
> volume #6 color #45c0d1e6
> rainbow #!4
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting simple
> lighting full
> volume #6 color #45c0d191
> hide #!4 models
> show #7 models
> open
> /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb
Chain information for SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb #14
---
Chain | Description
A | No description available
> select add #14
9282 atoms, 9503 bonds, 1191 residues, 1 model selected
> view matrix models #14,1,0,0,77.646,0,1,0,100.38,0,0,1,258.11
> view matrix models #14,1,0,0,118.78,0,1,0,136,0,0,1,199.53
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.79311,0.30353,-0.52806,116.21,-0.52524,0.7798,-0.34064,130.01,0.30839,0.54752,0.77789,202.82
> view matrix models
> #14,-0.51061,0.61006,-0.60589,100.88,0.74761,0.66308,0.037593,144.88,0.42468,-0.43377,-0.79466,204.71
> view matrix models
> #14,-0.037789,-0.99929,0.00062917,107.26,-0.51217,0.018828,-0.85868,130.58,0.85805,-0.032771,-0.51252,209.53
> select subtract #14
Nothing selected
> mmaker #14 to #7
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 RBD-docked-103-coot-0.pdb, chain A (#7) with
SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence
alignment score = 1592.9
RMSD between 152 pruned atom pairs is 0.944 angstroms; (across all 192 pairs:
2.028)
> select add #14
9282 atoms, 9503 bonds, 1191 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.064575,-0.9537,-0.29374,128.07,-0.70505,0.25192,-0.66291,235.4,0.70622,0.1643,-0.68867,199.47
> view matrix models
> #14,-0.064575,-0.9537,-0.29374,79.561,-0.70505,0.25192,-0.66291,258.78,0.70622,0.1643,-0.68867,179.1
> select subtract #14
Nothing selected
> select #14:1-283
2264 atoms, 2331 bonds, 283 residues, 1 model selected
> save /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/NTD.pdb relModel
> #14
> open /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/NTD.pdb
Summary of feedback from opening
/Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/NTD.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 286
THR A 294 1 9
Start residue of secondary structure not found: HELIX 2 2 PHE A 329 PHE A 333
1 5
Start residue of secondary structure not found: HELIX 3 3 VAL A 341 ALA A 343
1 3
Start residue of secondary structure not found: HELIX 4 4 TYR A 356 LEU A 359
1 4
Start residue of secondary structure not found: HELIX 5 5 PRO A 376 ASP A 381
1 6
207 messages similar to the above omitted
End residue of secondary structure not found: SHEET 16 16 1 SER A 254 TYR A
260 0
Start residue of secondary structure not found: SHEET 17 17 1 GLN A 262 PHE A
270 0
Start residue of secondary structure not found: SHEET 18 18 1 ILE A 276 ASP A
281 0
Start residue of secondary structure not found: SHEET 19 19 1 GLY A 302 THR A
306 0
Start residue of secondary structure not found: SHEET 20 20 1 THR A 315 ARG A
319 0
Start residue of secondary structure not found: SHEET 21 21 1 GLU A 345 ILE A
349 0
77 messages similar to the above omitted
End residue of secondary structure not found: SHEET 16 16 1 SER A 254 TYR A
260 0
Start residue of secondary structure not found: SHEET 17 17 1 GLN A 262 PHE A
270 0
Start residue of secondary structure not found: SHEET 18 18 1 ILE A 276 ASP A
281 0
Start residue of secondary structure not found: SHEET 19 19 1 GLY A 302 THR A
306 0
Start residue of secondary structure not found: SHEET 20 20 1 THR A 315 ARG A
319 0
Start residue of secondary structure not found: SHEET 21 21 1 GLU A 345 ILE A
349 0
31 messages similar to the above omitted
Chain information for NTD.pdb
---
Chain | Description
15.1/A 15.6/A | No description available
15.2/A 15.3/A | No description available
15.4/A | No description available
15.5/A | No description available
15.4/E | No description available
15.5/E | No description available
> hide #!15 models
> hide #14 models
> show #14 models
> hide #14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> select add #15
37076 atoms, 37963 bonds, 3 pseudobonds, 4752 residues, 9 models selected
> hide #!15 models
> show #!15 models
> select add #14
44094 atoms, 45135 bonds, 3 pseudobonds, 5660 residues, 9 models selected
> select subtract #14
34812 atoms, 35632 bonds, 3 pseudobonds, 4469 residues, 8 models selected
> close #15
> show #14 models
> select #14:1-283
2264 atoms, 2331 bonds, 283 residues, 1 model selected
> save /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/NTD.pdb
> selectedOnly true relModel #14
> open /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/NTD.pdb
Summary of feedback from opening
/Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/NTD.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 286
THR A 294 1 9
Start residue of secondary structure not found: HELIX 2 2 PHE A 329 PHE A 333
1 5
Start residue of secondary structure not found: HELIX 3 3 VAL A 341 ALA A 343
1 3
Start residue of secondary structure not found: HELIX 4 4 TYR A 356 LEU A 359
1 4
Start residue of secondary structure not found: HELIX 5 5 PRO A 376 ASP A 381
1 6
60 messages similar to the above omitted
Chain information for NTD.pdb #12
---
Chain | Description
A | No description available
> hide #14 models
> select add #14
9282 atoms, 9503 bonds, 1191 residues, 1 model selected
> select subtract #14
Nothing selected
> hide #12 models
> show #12 models
> show #14 models
> mmaker #12 to #14
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 SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14) with
NTD.pdb, chain A (#12), sequence alignment score = 1473.7
RMSD between 283 pruned atom pairs is 0.000 angstroms; (across all 283 pairs:
0.000)
> select add #12
2264 atoms, 2331 bonds, 283 residues, 1 model selected
> view matrix models
> #12,-0.064575,-0.9537,-0.29374,79.168,-0.70505,0.25192,-0.66291,259.2,0.70622,0.1643,-0.68867,179.81
> mmaker #14 to #7
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 RBD-docked-103-coot-0.pdb, chain A (#7) with
SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence
alignment score = 1592.9
RMSD between 152 pruned atom pairs is 0.944 angstroms; (across all 192 pairs:
2.028)
> mmaker #12 to #14
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 SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14) with
NTD.pdb, chain A (#12), sequence alignment score = 1473.7
RMSD between 283 pruned atom pairs is 0.000 angstroms; (across all 283 pairs:
0.000)
> select clear
> select add #12
2264 atoms, 2331 bonds, 283 residues, 1 model selected
> fitmap #12 inMap #6
Fit molecule NTD.pdb (#12) to map 103_sharp_zflipped.ccp4 (#6) using 2264
atoms
average map value = 0.09224, steps = 116
shifted from previous position = 2.08
rotated from previous position = 14.4 degrees
atoms outside contour = 1596, contour level = 0.14464
Position of NTD.pdb (#12) relative to 103_sharp_zflipped.ccp4 (#6)
coordinates:
Matrix rotation and translation
0.00130686 -0.97036728 -0.24163119 184.93620442
-0.85371786 0.12474320 -0.50557388 212.99101580
0.52073420 0.20694558 -0.82825686 210.29703969
Axis 0.67859241 -0.72606489 0.11109509
Axis point 150.80219786 0.00000000 158.32988633
Rotation angle (degrees) 148.33188418
Shift along axis -5.78602738
> hide #14 models
> view matrix models
> #12,0.0013069,-0.97037,-0.24163,175.33,-0.85372,0.12474,-0.50557,214.14,0.52073,0.20695,-0.82826,202.9
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.55681,-0.60717,-0.56684,159.86,-0.52018,0.78692,-0.33192,198.21,0.64759,0.11004,-0.754,206.82
> fitmap #12 inMap #6
Fit molecule NTD.pdb (#12) to map 103_sharp_zflipped.ccp4 (#6) using 2264
atoms
average map value = 0.08266, steps = 92
shifted from previous position = 5.15
rotated from previous position = 5.35 degrees
atoms outside contour = 1631, contour level = 0.14464
Position of NTD.pdb (#12) relative to 103_sharp_zflipped.ccp4 (#6)
coordinates:
Matrix rotation and translation
-0.49363864 -0.59548276 -0.63381478 162.45050676
-0.51432470 0.78758617 -0.33937903 197.48970209
0.70127812 0.15845599 -0.69505446 206.26089766
Axis 0.34881942 -0.93546318 0.05686524
Axis point 70.29966497 0.00000000 154.67157935
Rotation angle (degrees) 134.47142525
Shift along axis -116.34937655
> volume #6 level 0.2412
> view matrix models
> #12,-0.034324,-0.92637,-0.37504,175.77,-0.84309,0.22835,-0.48688,211.4,0.53667,0.29948,-0.78886,200.83
> fitmap #12 inMap #6
Fit molecule NTD.pdb (#12) to map 103_sharp_zflipped.ccp4 (#6) using 2264
atoms
average map value = 0.108, steps = 84
shifted from previous position = 3.49
rotated from previous position = 8.83 degrees
atoms outside contour = 1787, contour level = 0.24124
Position of NTD.pdb (#12) relative to 103_sharp_zflipped.ccp4 (#6)
coordinates:
Matrix rotation and translation
-0.17565064 -0.92925889 -0.32499965 180.67796779
-0.81419831 0.32270170 -0.48264347 207.16698866
0.55337868 0.17983753 -0.81328378 201.14249518
Axis 0.59888239 -0.79405342 0.10401468
Axis point 129.54834619 0.00000000 152.49202223
Rotation angle (degrees) 146.42020738
Shift along axis -35.37503108
> ui mousemode right select
> select clear
> select add #12
2264 atoms, 2331 bonds, 283 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.11871,-0.94131,-0.31597,180.73,-0.77934,0.28551,-0.55778,205.25,0.61526,0.18003,-0.7675,202.07
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.11871,-0.94131,-0.31597,185.09,-0.77934,0.28551,-0.55778,205.17,0.61526,0.18003,-0.7675,200
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.071375,-0.95287,-0.29486,185.65,-0.70164,0.25808,-0.66415,201.46,0.70895,0.15948,-0.68699,202.37
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.071375,-0.95287,-0.29486,185.88,-0.70164,0.25808,-0.66415,201.41,0.70895,0.15948,-0.68699,201.43
> fitmap #12 inMap #6
Fit molecule NTD.pdb (#12) to map 103_sharp_zflipped.ccp4 (#6) using 2264
atoms
average map value = 0.1143, steps = 76
shifted from previous position = 4.63
rotated from previous position = 5.18 degrees
atoms outside contour = 1724, contour level = 0.24124
Position of NTD.pdb (#12) relative to 103_sharp_zflipped.ccp4 (#6)
coordinates:
Matrix rotation and translation
0.00304568 -0.93921916 -0.34330466 180.66644685
-0.69529462 0.24475271 -0.67576734 204.60385803
0.71871838 0.24075606 -0.65228859 201.64373900
Axis 0.64368451 -0.74587052 0.17131090
Axis point 122.00043841 0.00000000 175.29096637
Rotation angle (degrees) 134.60740732
Shift along axis -1.77202171
> show #14 models
> mmaker #14 to #12
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 NTD.pdb, chain A (#12) with
SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence
alignment score = 1473.7
RMSD between 283 pruned atom pairs is 0.000 angstroms; (across all 283 pairs:
0.000)
> mmaker #14 to #17
No 'to' model specified
> mmaker #14 to #7
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 RBD-docked-103-coot-0.pdb, chain A (#7) with
SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence
alignment score = 1592.9
RMSD between 152 pruned atom pairs is 0.944 angstroms; (across all 192 pairs:
2.028)
> select subtract #12
Nothing selected
> select add #14
9282 atoms, 9503 bonds, 1191 residues, 1 model selected
> view matrix models
> #14,-0.064575,-0.9537,-0.29374,123.48,-0.70505,0.25192,-0.66291,241.1,0.70622,0.1643,-0.68867,166.98
> select clear
Drag select of 280 residues
> delete sel
Drag select of 8 residues, 1 pseudobonds
> delete sel
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 8/A
Alignment identifier is 8/E
Alignment identifier is 9/A
Alignment identifier is 9/E
Alignment identifier is 12/A
> select add #14/A:940
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #14.1 models
> select add #14
6978 atoms, 7126 bonds, 5 pseudobonds, 903 residues, 2 models selected
> view matrix models
> #14,-0.064575,-0.9537,-0.29374,111.24,-0.70505,0.25192,-0.66291,261.75,0.70622,0.1643,-0.68867,156.73
> select clear
Drag select of 168 residues
> delete sel
Drag select of 6 103_sharp_zflipped.ccp4 , 89 residues
> select clear
Drag select of 94 residues
> delete sel
Drag select of 3 residues
> delete sel
Drag select of 6 residues
> delete sel
Drag select of 125 residues
> delete sel
> select add #14
3902 atoms, 3972 bonds, 3 pseudobonds, 507 residues, 2 models selected
> view matrix models
> #14,-0.064575,-0.9537,-0.29374,193.01,-0.70505,0.25192,-0.66291,213.3,0.70622,0.1643,-0.68867,216.04
> view matrix models
> #14,-0.064575,-0.9537,-0.29374,193.57,-0.70505,0.25192,-0.66291,212.78,0.70622,0.1643,-0.68867,214.23
> view matrix models
> #14,-0.064575,-0.9537,-0.29374,192,-0.70505,0.25192,-0.66291,212.94,0.70622,0.1643,-0.68867,205.49
> select subtract #14
Nothing selected
> select add #14
3902 atoms, 3972 bonds, 3 pseudobonds, 507 residues, 2 models selected
> fitmap #14 inMap #6
Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) to map
103_sharp_zflipped.ccp4 (#6) using 3902 atoms
average map value = 0.08889, steps = 80
shifted from previous position = 3.54
rotated from previous position = 5.3 degrees
atoms outside contour = 3133, contour level = 0.24124
Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) relative to
103_sharp_zflipped.ccp4 (#6) coordinates:
Matrix rotation and translation
-0.08749166 -0.97443388 -0.20693918 186.20184862
-0.71402959 0.20619847 -0.66906197 211.51077507
0.69462720 0.08922336 -0.71381527 207.33430825
Axis 0.62850293 -0.74726108 0.21583545
Axis point 135.67300670 0.00000000 175.49880919
Rotation angle (degrees) 142.89717947
Shift along axis 3.72473183
> open 7m0j
7m0j title:
SARS-CoV-2 u1S2q All Down RBD State Spike Protein Trimer - asymmetric
refinement [more info...]
Chain information for 7m0j #15
---
Chain | Description | UniProt
A B C | Spike glycoprotein | SPIKE_SARS2
> mmaker #15 to #7
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 RBD-docked-103-coot-0.pdb, chain A (#7) with 7m0j, chain B (#15),
sequence alignment score = 1146.2
RMSD between 138 pruned atom pairs is 0.941 angstroms; (across all 161 pairs:
1.831)
> select clear
> mmaker #14 to #15
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 7m0j, chain A (#15) with
SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence
alignment score = 3555.4
RMSD between 144 pruned atom pairs is 1.026 angstroms; (across all 424 pairs:
22.222)
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 4 atomic models, 1 maps.
> select add #14
3902 atoms, 3972 bonds, 3 pseudobonds, 507 residues, 2 models selected
> fitmap #14 inMap #6
Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) to map
103_sharp_zflipped.ccp4 (#6) using 3902 atoms
average map value = 0.07006, steps = 60
shifted from previous position = 1.7
rotated from previous position = 3.57 degrees
atoms outside contour = 3260, contour level = 0.24124
Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) relative to
103_sharp_zflipped.ccp4 (#6) coordinates:
Matrix rotation and translation
0.74110998 -0.00998632 0.67130937 227.62585019
-0.02534229 -0.99959289 0.01310748 185.06534394
0.67090518 -0.02672660 -0.74106134 209.81841633
Axis -0.93302746 0.00946719 -0.35968059
Axis point 0.00000000 94.29909756 59.96036905
Rotation angle (degrees) 178.77683225
Shift along axis -286.09673216
> hide #!14 models
> hide #!15 models
> show #!14 models
> view matrix models
> #14,0.74111,-0.0099863,0.67131,222.62,-0.025342,-0.99959,0.013107,192.08,0.67091,-0.026727,-0.74106,208.83
> view matrix models
> #14,0.74111,-0.0099863,0.67131,221.54,-0.025342,-0.99959,0.013107,188.78,0.67091,-0.026727,-0.74106,208.92
> view matrix models
> #14,0.74111,-0.0099863,0.67131,220.48,-0.025342,-0.99959,0.013107,189.93,0.67091,-0.026727,-0.74106,208.73
> view matrix models
> #14,0.74111,-0.0099863,0.67131,219.14,-0.025342,-0.99959,0.013107,188.6,0.67091,-0.026727,-0.74106,208.5
> fitmap #14 inMap #6
Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) to map
103_sharp_zflipped.ccp4 (#6) using 3902 atoms
average map value = 0.1319, steps = 172
shifted from previous position = 7.13
rotated from previous position = 11.3 degrees
atoms outside contour = 2925, contour level = 0.24124
Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) relative to
103_sharp_zflipped.ccp4 (#6) coordinates:
Matrix rotation and translation
0.70249513 0.15150720 0.69537483 225.20282243
0.01747413 -0.98045480 0.19596694 188.67170643
0.71147399 -0.12551475 -0.69141218 205.56812359
Axis -0.92200855 -0.04617235 -0.38440648
Axis point 0.00000000 93.08070335 47.50006476
Rotation angle (degrees) 169.95988165
Shift along axis -295.37206341
> show #!15 models
> view matrix models
> #14,0.7025,0.15151,0.69537,289.13,0.017474,-0.98045,0.19597,224.01,0.71147,-0.12551,-0.69141,170.98
> select #15/B:340
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
49 atoms, 51 bonds, 6 residues, 1 model selected
> select up
2610 atoms, 2673 bonds, 336 residues, 1 model selected
> select up
2750 atoms, 2815 bonds, 353 residues, 1 model selected
> select up
4361 atoms, 4465 bonds, 556 residues, 1 model selected
> select up
4463 atoms, 4567 bonds, 568 residues, 1 model selected
> select up
7245 atoms, 7410 bonds, 929 residues, 1 model selected
> select up
7268 atoms, 7433 bonds, 932 residues, 1 model selected
> select up
7609 atoms, 7789 bonds, 972 residues, 1 model selected
> select up
22827 atoms, 23367 bonds, 2916 residues, 1 model selected
> select down
7609 atoms, 7789 bonds, 972 residues, 1 model selected
> select up
22827 atoms, 23367 bonds, 2916 residues, 1 model selected
> select down
7609 atoms, 7789 bonds, 972 residues, 1 model selected
> select ~sel
46914 atoms, 48010 bonds, 28 pseudobonds, 6012 residues, 24 models selected
> select ~sel
7609 atoms, 7789 bonds, 11 pseudobonds, 972 residues, 2 models selected
> select #15/A,C
15218 atoms, 15578 bonds, 22 pseudobonds, 1944 residues, 2 models selected
> delete atoms (#!15 & sel)
> delete bonds (#!15 & sel)
Drag select of 6 103_sharp_zflipped.ccp4 , 19 residues
> select clear
> mmaker #14 to #15
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 7m0j, chain B (#15) with
SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence
alignment score = 3587.5
RMSD between 147 pruned atom pairs is 1.000 angstroms; (across all 424 pairs:
22.421)
> hide #!15 models
> select add #14
3902 atoms, 3972 bonds, 3 pseudobonds, 507 residues, 2 models selected
> view matrix models
> #14,-0.272,0.8417,-0.46643,217.94,0.70201,0.50508,0.50207,231.22,0.65818,-0.19088,-0.72826,207.77
> ui tool show "Side View"
> view matrix models
> #14,-0.272,0.8417,-0.46643,215.34,0.70201,0.50508,0.50207,231.83,0.65818,-0.19088,-0.72826,208.77
> view matrix models
> #14,-0.272,0.8417,-0.46643,217.03,0.70201,0.50508,0.50207,230.24,0.65818,-0.19088,-0.72826,208.4
> select subtract #14
Nothing selected
> select add #14
3902 atoms, 3972 bonds, 3 pseudobonds, 507 residues, 2 models selected
> view matrix models
> #14,-0.272,0.8417,-0.46643,148.43,0.70201,0.50508,0.50207,261.82,0.65818,-0.19088,-0.72826,195.75
> select clear
Drag select of 63 residues
> select clear
Drag select of 72 residues
> delete sel
Drag select of 8 residues
> delete sel
Drag select of 9 residues
> delete sel
> hide #!6 models
> hide #7 models
> hide #12 models
Drag select of 24 residues
Drag select of 20 residues
Drag select of 7 residues
> delete sel
Drag select of 30 residues
> delete sel
Drag select of 9 residues
> delete sel
Drag select of 130 residues
> delete sel
> show #12 models
> show #7 models
> show #!6 models
> show #!15 models
> mmaker #14 to #15
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 7m0j, chain B (#15) with
SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence
alignment score = 3403.3
RMSD between 147 pruned atom pairs is 1.000 angstroms; (across all 223 pairs:
5.995)
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 4 atomic models, 1 maps.
> select add #14
1857 atoms, 1874 bonds, 5 pseudobonds, 242 residues, 2 models selected
> fitmap #14 inMap #6
Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) to map
103_sharp_zflipped.ccp4 (#6) using 1857 atoms
average map value = 0.2211, steps = 104
shifted from previous position = 6.64
rotated from previous position = 8.26 degrees
atoms outside contour = 1102, contour level = 0.24124
Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) relative to
103_sharp_zflipped.ccp4 (#6) coordinates:
Matrix rotation and translation
-0.35566557 0.78596340 -0.50573069 215.16698249
0.60314833 0.60637167 0.51819445 231.94554747
0.71394263 -0.12072670 -0.68971804 205.55029546
Axis -0.45999554 -0.87811193 -0.13161892
Axis point 9.54006040 -0.00000000 99.99657948
Rotation angle (degrees) 136.01370802
Shift along axis -329.70431277
> select subtract #14
Nothing selected
> hide #7 models
> hide #!6 models
> delete #14:902-906
> delete #14:902-967
> mmaker #14 to #15
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 7m0j, chain B (#15) with
SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence
alignment score = 3331.9
RMSD between 135 pruned atom pairs is 0.954 angstroms; (across all 157 pairs:
4.833)
> show #!6 models
> select add #14
1358 atoms, 1373 bonds, 5 pseudobonds, 176 residues, 2 models selected
> fitmap #14 inMap #6
Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) to map
103_sharp_zflipped.ccp4 (#6) using 1358 atoms
average map value = 0.1302, steps = 88
shifted from previous position = 5.52
rotated from previous position = 5.53 degrees
atoms outside contour = 971, contour level = 0.24124
Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) relative to
103_sharp_zflipped.ccp4 (#6) coordinates:
Matrix rotation and translation
-0.29473057 0.79460140 -0.53079422 217.14718767
0.64777107 0.57449873 0.50034372 231.94420529
0.70251443 -0.19636655 -0.68404214 210.08107646
Axis -0.48923405 -0.86603659 -0.10310512
Axis point 0.50862202 0.00000000 104.83151306
Rotation angle (degrees) 134.59870751
Shift along axis -328.76840174
> hide #!15 models
> select clear
> select #14
1358 atoms, 1373 bonds, 5 pseudobonds, 176 residues, 2 models selected
> save
> /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/round1-twohelices.pdb
> selectedOnly true relModel #7
> show #2 models
> hide #2 models
> close #4
> close #8
> close #9
> hide #!6 models
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
> graphics silhouettes true
> lighting soft
> windowsize 800 800
UCSF ChimeraX version: 1.6.dev202212061854 (2022-12-06)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.0, Qt 6.4.0
Qt runtime version: 6.4.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,4
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 8419.41.10
OS Loader Version: 7459.141.1
Software:
System Software Overview:
System Version: macOS 12.6.1 (21G217)
Kernel Version: Darwin 21.6.0
Time since boot: 46 days 17:26
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.5.7
ChimeraX-AddH: 2.2.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.8
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.43.4
ChimeraX-AtomicLibrary: 8.0.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.dev202212061854
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.9
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.7
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.3
ChimeraX-PDB: 2.6.9
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.4
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.25.2
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.6
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
contourpy: 1.0.6
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.6.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.8
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.6.0
prompt-toolkit: 3.0.36
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.4.0
PyQt6-Qt6: 6.4.1
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.1
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.3
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (4)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Unsupported scale factor (0.000000) detected on Display0 |
comment:2 by , 3 years ago
| Status: | accepted → feedback |
|---|
follow-up: 3 comment:3 by , 3 years ago
Yes indeed.
Connected to external monitor too.
I thought it had to do something with the resolution
--
Kelvin Lau
Protein production and structure core facility - PTPSP
EPFL SV PTECH PTPSP
AI 2146 (Bâtiment AI)
Station 19
CH-1015 Lausanne
Switzerland
Email: kelvin.lau@epfl.ch<mailto:kelvin.lau@epfl.ch>
Phone: +41 21 69 34494
On 27 Dec 2022, at 18:33, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:
#8226: Unsupported scale factor (0.000000) detected on Display0
-------------------------------------+----------------------
Reporter: kelvin.lau@… | Owner: pett
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Window Toolkit | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------+----------------------
Changes (by pett):
* status: accepted => feedback
Comment:
Hi Kelvin,
Were you connecting or disconnecting a display, or changing screen
resolution when this crash occurred?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8226#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:4 by , 3 years ago
| Resolution: | → limitation |
|---|---|
| Status: | feedback → closed |
Hi Kelvin,
Thanks for that info. This isn't a problem with the ChimeraX code per se, but with the Qt windowing toolkit that ChimeraX uses to render window, buttons, etc. on the various operating systems it supports. We just have to hope that future releases of Qt will have fixes for this issue. In the interim, I guess make sure to save a ChimeraX session before changing screen resolution or connecting/disconnecting monitors.
--Eric
Note:
See TracTickets
for help on using tickets.
Hi Kelvin,
--Eric