![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#10030 closed defect (nonchimerax)
Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 655
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5rc202211182308 (2022-11-18 23:08:37 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff856c4e4c0 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 235 in swap_buffers
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 497 in swap_buffers
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 191 in draw
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX.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" : 33000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 1294,
"osVersion" : {
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"build" : "22A400",
"releaseType" : "User"
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"captureTime" : "2023-10-20 10:27:51.9425 +0200",
"incident" : "3F5FDB72-2CBE-4F9E-A987-A1D7398F42C5",
"pid" : 7834,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-10-20 10:07:53.0692 +0200",
"procStartAbsTime" : 32300862440466,
"procExitAbsTime" : 33499754145774,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"4118825E-EA91-5E09-A29F-34B7D8399597","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "DAE5A66E-5B02-652B-9AB4-D1348B2E5EC8",
"wakeTime" : 1361,
"bridgeVersion" : {"build":"20P420","train":"7.0"},
"sleepWakeUUID" : "808FE6FC-54FC-4FF5-8966-3B38C6ED5D2E",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
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"faultingThread" : 0,
"threads" : 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"arch" : "x86_64",
"base" : 4497993728,
"size" : 2801664,
"uuid" : "babd94e3-ec19-3110-ab5b-11c39432d8c5",
"path" : "\/Applications\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703451049984,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4820992,
"uuid" : "dbc459f3-81bb-398a-8f74-3f7392392bb7",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1953.1"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703611674624,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3112947,
"uuid" : "ff73b93b-3c5b-3f73-948f-0a35a80f7fad",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4400611328,
"CFBundleShortVersionString" : "1.5.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 4096,
"uuid" : "5df621ee-554e-36a8-b448-93b2334e5480",
"path" : "\/Applications\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.5.0.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703447302144,
"size" : 607568,
"uuid" : "28fd2071-57f3-3873-87bf-e4f674a82de6",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4517572608,
"size" : 64028672,
"uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
"path" : "\/Applications\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5030002688,
"size" : 165052416,
"uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
"path" : "\/Applications\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
}
],
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "62b4513af75dc926494899c6",
"factorPackIds" : {
"COREOS_ICD" : "62fbe3cfa9a700130f60b3ea"
},
"deploymentId" : 240000019
},
{
"rolloutId" : "61675b89201f677a9a4cbd65",
"factorPackIds" : {
"HEALTH_FEATURE_AVAILABILITY" : "64d14f3e1008ca2fac17a163"
},
"deploymentId" : 240000064
}
],
"experiments" : [
{
"treatmentId" : "6dd670af-0633-45e4-ae5f-122ae4df02be",
"experimentId" : "64406ba83deb637ac8a04419",
"deploymentId" : 900000017
}
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5rc202211182308 (2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v2/ChimeraX/ModelBuilding_20SCP-OG_PI31_v2.cxs
Opened cryosparc_P175_J266_map_sharp.mrc as #3, grid size 384,384,384, pixel
0.851, shown at level 0.483, step 1, values float32
Opened cryosparc_P175_J267_map_sharp.mrc as #4, grid size 384,384,384, pixel
0.851, shown at level 0.05, step 1, values float32
Opened cryosparc_P175_J268_map_sharp.mrc as #5, grid size 384,384,384, pixel
0.851, shown at level 0.385, step 1, values float32
Opened cryosparc_P175_J269_map_sharp.mrc as #6, grid size 384,384,384, pixel
0.851, shown at level 0.04, step 1, values float32
Opened cryosparc_P175_J270_map_sharp.mrc as #7, grid size 384,384,384, pixel
0.851, shown at level 0.391, step 1, values float32
Opened cryosparc_P175_J271_map_sharp.mrc as #8, grid size 384,384,384, pixel
0.851, shown at level 0.02, step 1, values float32
Opened cryosparc_P175_J169_008_volume_map_sharp.mrc as #9, grid size
384,384,384, pixel 0.851, shown at level 0.6, step 1, values float32
Opened cryosparc_P175_J206_009_volume_map_sharp.mrc as #10, grid size
384,384,384, pixel 0.851, shown at level 0.8, step 1, values float32
Log from Fri Oct 20 00:11:03 2023UCSF ChimeraX version: 1.5rc202211182308
(2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v2/ChimeraX/ModelBuilding_20SCP-OG_PI31_v2.cxs
Opened cryosparc_P175_J266_map_sharp.mrc as #3, grid size 384,384,384, pixel
0.851, shown at level 0.483, step 1, values float32
Opened cryosparc_P175_J267_map_sharp.mrc as #4, grid size 384,384,384, pixel
0.851, shown at level 0.05, step 1, values float32
Opened cryosparc_P175_J268_map_sharp.mrc as #5, grid size 384,384,384, pixel
0.851, shown at level 0.385, step 1, values float32
Opened cryosparc_P175_J269_map_sharp.mrc as #6, grid size 384,384,384, pixel
0.851, shown at level 0.04, step 1, values float32
Opened cryosparc_P175_J270_map_sharp.mrc as #7, grid size 384,384,384, pixel
0.851, shown at level 0.391, step 1, values float32
Opened cryosparc_P175_J271_map_sharp.mrc as #8, grid size 384,384,384, pixel
0.851, shown at level 0.02, step 1, values float32
Opened cryosparc_P175_J272_map_sharp.mrc as #9, grid size 384,384,384, pixel
0.851, shown at level 0.329, step 1, values float32
Opened cryosparc_P175_J273_map_sharp.mrc as #10, grid size 384,384,384, pixel
0.851, shown at level 0.01, step 1, values float32
Log from Wed Oct 11 16:38:26 2023UCSF ChimeraX version: 1.5rc202211182308
(2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v2/ChimeraX/ModelBuilding_20SCP-OG_PI31_new2.cxs
Opened cryosparc_P175_J253_map_sharp.mrc as #1, grid size 384,384,384, pixel
0.851, shown at level 0.35, step 1, values float32
Opened cryosparc_P175_J256_map_sharp.mrc as #2, grid size 384,384,384, pixel
0.851, shown at level 0.118, step 1, values float32
Log from Tue Oct 10 14:37:41 2023UCSF ChimeraX version: 1.5rc202211182308
(2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs
Opened cryosparc_P175_J228_009_volume_map.mrc as #6.2, grid size 384,384,384,
pixel 0.851, shown at level 0.396, step 1, values float32
Opened cryosparc_P175_J177_map_sharp.mrc as #7, grid size 384,384,384, pixel
0.851, shown at level 0.08, step 1, values float32
Opened cryosparc_P175_J214_009_volume_map.mrc as #8, grid size 384,384,384,
pixel 0.851, shown at level 0.392, step 1, values float32
Opened cryosparc_P175_J222_009_volume_map.mrc as #9, grid size 384,384,384,
pixel 0.851, shown at level 0.25, step 1, values float32
Opened cryosparc_P175_J227_008_volume_map.mrc as #10, grid size 384,384,384,
pixel 0.851, shown at level 0.398, step 1, values float32
Opened cryosparc_P175_J228_009_volume_map.mrc as #11, grid size 384,384,384,
pixel 0.851, shown at level 0.396, step 1, values float32
Opened cryosparc_P175_J236_008_volume_map.mrc as #12, grid size 384,384,384,
pixel 0.851, shown at level 0.395, step 1, values float32
Opened cryosparc_P175_J206_009_volume_map.mrc as #13, grid size 384,384,384,
pixel 0.851, shown at level 0.395, step 1, values float32
Opened cryosparc_P175_J189_009_volume_map.mrc as #14, grid size 400,400,400,
pixel 0.851, shown at level 0.297, step 1, values float32
Opened cryosparc_P175_J169_008_volume_map.mrc as #15, grid size 384,384,384,
pixel 0.851, shown at level 0.395, step 1, values float32
Opened cryosparc_P175_J161_009_volume_map.mrc as #16, grid size 384,384,384,
pixel 0.851, shown at level 0.394, step 1, values float32
Opened cryosparc_P175_J160_008_volume_map.mrc as #17, grid size 384,384,384,
pixel 0.851, shown at level 0.394, step 1, values float32
Opened cryosparc_P175_J158_009_volume_map.mrc as #18, grid size 384,384,384,
pixel 0.851, shown at level 0.395, step 1, values float32
Log from Tue Oct 10 10:03:50 2023UCSF ChimeraX version: 1.5rc202211182308
(2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs
Opened cryosparc_P175_J177_map_sharp.mrc as #8, grid size 384,384,384, pixel
0.851, shown at level 0.08, step 1, values float32
Log from Tue Oct 10 00:42:27 2023UCSF ChimeraX version: 1.5rc202211182308
(2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs
Opened cryosparc_P175_J149_map_sharp.mrc as #3, grid size 384,384,384, pixel
0.851, shown at level 0.12, step 1, values float32
Log from Mon Oct 9 16:59:21 2023UCSF ChimeraX version: 1.5rc202211182308
(2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v1/ChimeraX/EMD_29604_PDB_8fz6.cxs
Opened emd_29604.map as #1, grid size 352,352,352, pixel 0.828, shown at level
0.671, step 1, values float32
Log from Thu Jul 13 14:39:19 2023UCSF ChimeraX version: 1.5rc202211182308
(2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/fadlof/Downloads/EMDB/emd_29604.map
Opened emd_29604.map as #1, grid size 352,352,352, pixel 0.828, shown at level
0.439, step 2, values float32
> volume #1 level 0.6294
> volume #1 step 1
> open 8fz6
Summary of feedback from opening 8fz6 fetched from pdb
---
note | Fetching compressed mmCIF 8fz6 from
http://files.rcsb.org/download/8fz6.cif
8fz6 title:
The human PI31 complexed with bovine 20S proteasome [more info...]
Chain information for 8fz6 #2
---
Chain | Description | UniProt
A O | Proteasome subunit alpha type-6 | PSA6_BOVIN
B P | Proteasome subunit alpha type-2 | PSA2_BOVIN
C Q | Proteasome subunit alpha type-4 | PSA4_BOVIN
D R | Proteasome subunit alpha type-7 | PSA7_BOVIN
E S | Proteasome subunit alpha type-5 | PSA5_BOVIN
F T | Proteasome subunit alpha type-1 | PSA1_BOVIN
G U | Proteasome subunit alpha type-3 | PSA3_BOVIN
H V | Proteasome subunit beta type-6 | PSB6_BOVIN
I W | Proteasome subunit beta type-7 | PSB7_BOVIN
J X | Proteasome subunit beta type-3 | PSB3_BOVIN
K Y | Proteasome subunit beta type-2 | PSB2_BOVIN
L Z | Proteasome subunit beta type-5 | PSB5_BOVIN
M a | Proteasome subunit beta type-1 | PSB1_BOVIN
N b | Proteasome subunit beta type-4 | PSB4_BOVIN
c d | Proteasome inhibitor PI31 subunit | PSMF1_BOVIN
> show atoms
> hide atoms
> hide cartoons
> show cartoons
[Repeated 1 time(s)]
> set bgColor white
> select add #2
49780 atoms, 50698 bonds, 6404 residues, 1 model selected
> split sel
Split 8fz6 (#2) into 30 models
Chain information for 8fz6 A #2.1
---
Chain | Description
A | No description available
Chain information for 8fz6 B #2.2
---
Chain | Description
B | No description available
Chain information for 8fz6 C #2.3
---
Chain | Description
C | No description available
Chain information for 8fz6 D #2.4
---
Chain | Description
D | No description available
Chain information for 8fz6 E #2.5
---
Chain | Description
E | No description available
Chain information for 8fz6 F #2.6
---
Chain | Description
F | No description available
Chain information for 8fz6 G #2.7
---
Chain | Description
G | No description available
Chain information for 8fz6 H #2.8
---
Chain | Description
H | No description available
Chain information for 8fz6 I #2.9
---
Chain | Description
I | No description available
Chain information for 8fz6 J #2.10
---
Chain | Description
J | No description available
Chain information for 8fz6 K #2.11
---
Chain | Description
K | No description available
Chain information for 8fz6 L #2.12
---
Chain | Description
L | No description available
Chain information for 8fz6 M #2.13
---
Chain | Description
M | No description available
Chain information for 8fz6 N #2.14
---
Chain | Description
N | No description available
Chain information for 8fz6 O #2.15
---
Chain | Description
O | No description available
Chain information for 8fz6 P #2.16
---
Chain | Description
P | No description available
Chain information for 8fz6 Q #2.17
---
Chain | Description
Q | No description available
Chain information for 8fz6 R #2.18
---
Chain | Description
R | No description available
Chain information for 8fz6 S #2.19
---
Chain | Description
S | No description available
Chain information for 8fz6 T #2.20
---
Chain | Description
T | No description available
Chain information for 8fz6 U #2.21
---
Chain | Description
U | No description available
Chain information for 8fz6 V #2.22
---
Chain | Description
V | No description available
Chain information for 8fz6 W #2.23
---
Chain | Description
W | No description available
Chain information for 8fz6 X #2.24
---
Chain | Description
X | No description available
Chain information for 8fz6 Y #2.25
---
Chain | Description
Y | No description available
Chain information for 8fz6 Z #2.26
---
Chain | Description
Z | No description available
Chain information for 8fz6 a #2.27
---
Chain | Description
a | No description available
Chain information for 8fz6 b #2.28
---
Chain | Description
b | No description available
Chain information for 8fz6 c #2.29
---
Chain | Description
c | No description available
Chain information for 8fz6 d #2.30
---
Chain | Description
d | No description available
> volume #1 level 0.6294
> volume #1 level 0.6543
> volume #1 level 0.6377
> volume #1 level 0.6045
> volume #1 level 0.563
> volume #1 level 0.5381
> ui tool show "Side View"
> transparency 50
> volume #1 level 0.4385
> select add #2.29
470 atoms, 488 bonds, 65 residues, 1 model selected
> select add #2
49780 atoms, 50698 bonds, 6404 residues, 31 models selected
> combine sel
> select add #3
99560 atoms, 101396 bonds, 12808 residues, 32 models selected
> select subtract #2
49780 atoms, 50698 bonds, 6404 residues, 1 model selected
> color zone #1 near sel & #3 distance 4.97
> select subtract #3
Nothing selected
> view
> volume #1 level 0.5132
> volume #1 level 0.5381
> color #2.30 #ff40ffff
> color #2.29 #0433ffff
Color zone shortcut requires 1 displayed atomic model and 1 map, got 31 atomic
models, 1 maps.
> close #3
> select add #2
49780 atoms, 50698 bonds, 6404 residues, 31 models selected
> combine sel
> select add #3
99560 atoms, 101396 bonds, 12808 residues, 32 models selected
> select subtract #2
49780 atoms, 50698 bonds, 6404 residues, 1 model selected
> color zone #1 near sel & #3 distance 4.97
> select subtract #3
Nothing selected
> volume #1 level 0.3555
> volume #1 level 0.2974
> volume #1 level 0.397
> surface dust #1 size 8.28
> view
> color #2.1 #c7e4faff
> color #2.2 #a3d1f6ff
> color #2.3 #90c8f5ff
> color #2.4 #59acefff
> color #2.5 #2590eaff
> color #2.6 #176fbbff
> color #2.7 #326cb1ff
> color #2.8 #f4d5ffff
> color #2.9 #efc1ffff
> color #2.10 #e497ffff
> color #2.10 #d356ffff
> color #2.10 #e497ffff
> color #2.11 #d356ffff
> color #2.12 #c300ffff
> color #2.13 #a500e0ff
> color #2.14 #9600ccff
> select add #2.14
1671 atoms, 1704 bonds, 214 residues, 1 model selected
> select add #2.13
3316 atoms, 3380 bonds, 427 residues, 2 models selected
> select add #2.12
4873 atoms, 4968 bonds, 628 residues, 3 models selected
> select add #2.11
6457 atoms, 6586 bonds, 825 residues, 4 models selected
> select add #2.10
8051 atoms, 8209 bonds, 1029 residues, 5 models selected
> select subtract #2.10
6457 atoms, 6586 bonds, 825 residues, 4 models selected
> select add #2.9
8117 atoms, 8273 bonds, 1045 residues, 5 models selected
> select add #2.10
9711 atoms, 9896 bonds, 1249 residues, 6 models selected
> select add #2.8
11230 atoms, 11443 bonds, 1451 residues, 7 models selected
> select add #2.7
13118 atoms, 13366 bonds, 1692 residues, 8 models selected
> select add #2.6
14991 atoms, 15274 bonds, 1930 residues, 9 models selected
> select add #2
49780 atoms, 50698 bonds, 6404 residues, 31 models selected
> select subtract #2
Nothing selected
> color #2.15 #c7e4faff
> color #2.16 #a3d1f6ff
> color #2.17 #90c8f5ff
> color #2.18 #59acefff
> color #2.19 #2590eaff
> color #2.20 #176fbbff
> color #2.21 #326cb1ff
> color #2.22 #f4d5ffff
> color #2.23 #efc1ffff
> color #2.24 #e497ffff
> color #2.25 #d356ffff
> color #2.26 #c300ffff
> color #2.27 #a500e0ff
> color #2.28 #9600ccff
> color #2.30 #fe9000ff
> color #2.29 #fe9000ff
> color #2.30 #dfb503ff
> close #3
> select add #2
49780 atoms, 50698 bonds, 6404 residues, 31 models selected
> combine sel
Color zone shortcut requires 1 displayed atomic model and 1 map, got 31 atomic
models, 1 maps.
> select add #3
99560 atoms, 101396 bonds, 12808 residues, 32 models selected
> select subtract #2
49780 atoms, 50698 bonds, 6404 residues, 1 model selected
> color zone #1 near sel & #3 distance 4.97
> select subtract #3
Nothing selected
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
> volume #1 level 0.4717
> volume #1 level 0.6045
> select add #2.29
470 atoms, 488 bonds, 65 residues, 1 model selected
> select add #2.30
940 atoms, 976 bonds, 130 residues, 2 models selected
> combine sel
> select add #3
50720 atoms, 51674 bonds, 6534 residues, 3 models selected
> select add #4
51660 atoms, 52650 bonds, 6664 residues, 4 models selected
> select subtract #3
1880 atoms, 1952 bonds, 260 residues, 3 models selected
> select add #2
50720 atoms, 51674 bonds, 6534 residues, 32 models selected
> select subtract #2
940 atoms, 976 bonds, 130 residues, 1 model selected
> hide #!2 models
> hide #3 models
> show sel atoms
> style sel stick
Changed 940 atom styles
> show sel cartoons
> select subtract #4
Nothing selected
> volume #1 level 0.4634
> lighting simple
> volume #1 level 0.4053
> view
> volume #1 level 0.48
> volume #1 level 0.4883
> volume #1 level 0.5381
> volume #1 level 0.6709
> save /Users/fadlof/Desktop/EMD_29604_PDB_8fz6.cxs includeMaps true
——— End of log from Thu Jul 13 14:39:19 2023 ———
opened ChimeraX session
> volume #1 level 0.4551
> color #2.1 #a3d1f6ff
> color #2.2 #90c8f5ff
> color #2.3 #59acefff
> color #2.4 #2590eaff
> color #2.5 #176fbbff
> color #2.6 #326cb1ff
> color #2.7 #c7e4faff
> color #2.21 #c7e4faff
> color #2.15 #a3d1f6ff
> color #2.16 #90c8f5ff
> color #2.17 #59acefff
> color #2.18 #2590eaff
> color #2.19 #176fbbff
> color #2.20 #326cb1ff
> hide #4 models
> hide #!1 models
> show #4 models
> show #3 models
> hide #4 models
> close #3
> rename #4 PI31
> rename #4 8fz6_PI31
> show #!2 models
> combine #2
> rename #3 8fz6
> hide #!2 models
> show #!1 models
> color zone #1 near #3 distance 4.97
[Repeated 1 time(s)]
> hide #!1 models
> select add #2.8
1519 atoms, 1547 bonds, 202 residues, 1 model selected
> select subtract #2.8
Nothing selected
> select add #2.8
1519 atoms, 1547 bonds, 202 residues, 1 model selected
> select subtract #2.8
Nothing selected
> select add #2.8
1519 atoms, 1547 bonds, 202 residues, 1 model selected
> select subtract #2.8
Nothing selected
> select add #2.8
1519 atoms, 1547 bonds, 202 residues, 1 model selected
> select subtract #2.8
Nothing selected
> select add #2.8
1519 atoms, 1547 bonds, 202 residues, 1 model selected
> select subtract #2.8
Nothing selected
> select add #2.8
1519 atoms, 1547 bonds, 202 residues, 1 model selected
> select subtract #2.8
Nothing selected
> show #!2 models
> hide #3 models
> select add #2.8
1519 atoms, 1547 bonds, 202 residues, 1 model selected
> select subtract #2.8
Nothing selected
> select add #2.8
1519 atoms, 1547 bonds, 202 residues, 1 model selected
> select subtract #2.8
Nothing selected
> color #2.8 #9600ccff
> color #2.8 #f4d5ffff
> show #!1 models
> color #2.8 #efc1ffff
> color #2.9 #e497ffff
> color #2.10 #d356ffff
> color #2.11 #c300ffff
> color #2.12 #a500e0ff
> color #2.13 #9600ccff
> color #2.14 #f4d5ffff
> color #2.22 #efc1ffff
> color #2.22 #9600ccff
> color #2.23 #f4d5ffff
> color #2.24 #efc1ffff
> color #2.25 #e497ffff
> color #2.26 #d356ffff
> color #2.27 #c300ffff
> color #2.28 #a500e0ff
> color #2.8 #f4d5ffff
> color #2.9 #efc1ffff
> color #2.10 #e497ffff
> color #2.8 #efc1ffff
> color #2.9 #e497ffff
> color #2.10 #d356ffff
> close #3
> combine #2
> hide #!2 models
> color zone #1 near #3 distance 4.97
> color #2.1 #c7e4faff
> color #2.2 #a3d1f6ff
> color #2.3 #90c8f5ff
> color #2.4 #59acefff
> color #2.5 #2590eaff
> color #2.5 #176fbbff
> color #2.7 #326cb1ff
> color #2.6 #176fbbff
> color #2.5 #2590eaff
> color #2.15 #c7e4faff
> color #2.16 #a3d1f6ff
> color #2.17 #90c8f5ff
> color #2.18 #59acefff
> color #2.19 #2590eaff
> color #2.20 #176fbbff
> color #2.21 #326cb1ff
> color #2.29 #bed5acff
> color #2.30 #f4ffcdff
> close #4
> close #3
> combine #2
> color zone #1 near #3 distance 4.97
> close #3
> color #2.8 #9600ccff
> color #2.9 #f4d5ffff
> color #2.10 #efc1ffff
> color #2.11 #e497ffff
> color #2.11 #d356ffff
> color #2.11 #e497ffff
> color #2.12 #d356ffff
> color #2.13 #c300ffff
> color #2.14 #a500e0ff
> rename #2 8FZ6
> combine #2
> color zone #1 near #3 distance 4.97
> ui tool show "Side View"
> color zone #1 near #3 distance 4.97
> volume #1 level 0.4
> volume #1 level 0.3
> color #2.29 #b1ea98ff
> color #2.29 #dcffb7ff
> color #2.30 #fffc79ff
> close #3
> combine #2
> color zone #1 near #3 distance 4.97
> volume #1 level 0.5
> color zone #1 near #3 distance 4.97
> hide #!1 models
> rename #3 8FZ6
> select #3/c,d
940 atoms, 976 bonds, 130 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 940 atom styles
> transparency 0
> select add #3
49780 atoms, 50698 bonds, 6404 residues, 1 model selected
> select subtract #3
Nothing selected
> transparency 50
> volume #1 level 0.4
> color zone #1 near #3 distance 4.97
> transparency 0
> transparency 50
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/c
Alignment identifier is 3/c
> select #3/c:194-199,211-215
81 atoms, 80 bonds, 11 residues, 1 model selected
> select #3/c:189
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/c
470 atoms, 488 bonds, 65 residues, 1 model selected
> select add #3
49780 atoms, 50698 bonds, 6404 residues, 1 model selected
> select subtract #3
Nothing selected
> show #!1 models
> save /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v2/PDBs/8FZ6.pdb models #3
> save /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v1/ChimeraX/20SCP-OG_PI31_v2.pdb
> color zone #1 near #3 distance 4.97
> save /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v1/ChimeraX/EMD_29604_PDB_8fz6.cxs includeMaps true
> open /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v1/ChimeraX/20SCP-OG_PI31_v2.pdb
Summary of feedback from opening
/Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
OG_PI31_v1/ChimeraX/20SCP-OG_PI31_v2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 22
GLN A 34 1 13
Start residue of secondary structure not found: HELIX 2 2 ASP A 62 VAL A 66 1
5
Start residue of secondary structure not found: HELIX 3 3 MET A 83 GLY A 106 1
24
Start residue of secondary structure not found: HELIX 4 4 PRO A 110 ASN A 128
1 19
Start residue of secondary structure not found: HELIX 5 5 LYS A 171 LYS A 185
1 15
488 messages similar to the above omitted
Chain information for 20SCP-OG_PI31_v2.pdb
---
Chain | Description
4.1/A 4.31/A 4.15/O 4.31/O | No description available
4.2/B 4.31/B 4.16/P 4.31/P | No description available
4.3/C 4.31/C 4.17/Q 4.31/Q | No description available
4.4/D 4.31/D 4.18/R 4.31/R | No description available
4.5/E 4.31/E 4.19/S 4.31/S | No description available
4.6/F 4.31/F 4.20/T 4.31/T | No description available
4.7/G 4.31/G 4.21/U 4.31/U | No description available
4.8/H 4.31/H 4.22/V 4.31/V | No description available
4.9/I 4.31/I 4.23/W 4.31/W | No description available
4.10/J 4.31/J 4.24/X 4.31/X | No description available
4.11/K 4.31/K 4.25/Y 4.31/Y | No description available
4.12/L 4.31/L 4.26/Z 4.31/Z | No description available
4.13/M 4.31/M 4.27/a 4.31/a | No description available
4.14/N 4.31/N 4.28/b 4.31/b | No description available
4.29/c 4.31/c 4.30/d 4.31/d | No description available
> hide #3 models
> hide #!1 models
> style #4.1-31 stick
Changed 99560 atom styles
> show #4.1-31 cartoons
> hide #4.1-31 cartoons
> show #4.1-31 cartoons
> hide #4.1-31 atoms
> close #4
> open /Users/fadlof/Downloads/20SCP-OG+PI31_v2.pdb
Chain information for 20SCP-OG+PI31_v2.pdb #4
---
Chain | Description
A O | No description available
B P | No description available
C Q | No description available
D R | No description available
E S | No description available
F T | No description available
G U | No description available
H V | No description available
I W | No description available
J X | No description available
K Y | No description available
L Z | No description available
M a | No description available
N b | No description available
c d | No description available
> hide #!4 cartoons
> show #!4 cartoons
> style #!4 stick
Changed 47322 atom styles
> hide #!4 atoms
> close #4
> show #3 models
> close #2
> close #1
> open /Users/fadlof/Downloads/20SCP-OG+PI31_v2.pdb
Chain information for 20SCP-OG+PI31_v2.pdb #1
---
Chain | Description
A O | No description available
B P | No description available
C Q | No description available
D R | No description available
E S | No description available
F T | No description available
G U | No description available
H V | No description available
I W | No description available
J X | No description available
K Y | No description available
L Z | No description available
M a | No description available
N b | No description available
c d | No description available
> open /Users/fadlof/Downloads/cryosparc_P175_J149_map_sharp.mrc
Opened cryosparc_P175_J149_map_sharp.mrc as #2, grid size 384,384,384, pixel
0.851, shown at level 0.0228, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J177_map_sharp.mrc
Opened cryosparc_P175_J177_map_sharp.mrc as #4, grid size 384,384,384, pixel
0.851, shown at level 0.0281, step 2, values float32
> rename #2 id #5
> rename #4 id #6
> color #6 darkgrey models
> hide #!6 models
> hide #!5 models
> hide #3 models
> show #!6 models
> hide #!6 models
> show #!5 models
> style #!1 stick
Changed 47322 atom styles
> hide #!1 cartoons
[Repeated 1 time(s)]
> show #!1 cartoons
> hide #!1 atoms
> hide #!5 models
> show #3 models
> hide #3 models
> split #1
Split 20SCP-OG+PI31_v2.pdb (#1) into 30 models
Chain information for 20SCP-OG+PI31_v2.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for 20SCP-OG+PI31_v2.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for 20SCP-OG+PI31_v2.pdb C #1.3
---
Chain | Description
C | No description available
Chain information for 20SCP-OG+PI31_v2.pdb D #1.4
---
Chain | Description
D | No description available
Chain information for 20SCP-OG+PI31_v2.pdb E #1.5
---
Chain | Description
E | No description available
Chain information for 20SCP-OG+PI31_v2.pdb F #1.6
---
Chain | Description
F | No description available
Chain information for 20SCP-OG+PI31_v2.pdb G #1.7
---
Chain | Description
G | No description available
Chain information for 20SCP-OG+PI31_v2.pdb H #1.8
---
Chain | Description
H | No description available
Chain information for 20SCP-OG+PI31_v2.pdb I #1.9
---
Chain | Description
I | No description available
Chain information for 20SCP-OG+PI31_v2.pdb J #1.10
---
Chain | Description
J | No description available
Chain information for 20SCP-OG+PI31_v2.pdb K #1.11
---
Chain | Description
K | No description available
Chain information for 20SCP-OG+PI31_v2.pdb L #1.12
---
Chain | Description
L | No description available
Chain information for 20SCP-OG+PI31_v2.pdb M #1.13
---
Chain | Description
M | No description available
Chain information for 20SCP-OG+PI31_v2.pdb N #1.14
---
Chain | Description
N | No description available
Chain information for 20SCP-OG+PI31_v2.pdb O #1.15
---
Chain | Description
O | No description available
Chain information for 20SCP-OG+PI31_v2.pdb P #1.16
---
Chain | Description
P | No description available
Chain information for 20SCP-OG+PI31_v2.pdb Q #1.17
---
Chain | Description
Q | No description available
Chain information for 20SCP-OG+PI31_v2.pdb R #1.18
---
Chain | Description
R | No description available
Chain information for 20SCP-OG+PI31_v2.pdb S #1.19
---
Chain | Description
S | No description available
Chain information for 20SCP-OG+PI31_v2.pdb T #1.20
---
Chain | Description
T | No description available
Chain information for 20SCP-OG+PI31_v2.pdb U #1.21
---
Chain | Description
U | No description available
Chain information for 20SCP-OG+PI31_v2.pdb V #1.22
---
Chain | Description
V | No description available
Chain information for 20SCP-OG+PI31_v2.pdb W #1.23
---
Chain | Description
W | No description available
Chain information for 20SCP-OG+PI31_v2.pdb X #1.24
---
Chain | Description
X | No description available
Chain information for 20SCP-OG+PI31_v2.pdb Y #1.25
---
Chain | Description
Y | No description available
Chain information for 20SCP-OG+PI31_v2.pdb Z #1.26
---
Chain | Description
Z | No description available
Chain information for 20SCP-OG+PI31_v2.pdb a #1.27
---
Chain | Description
a | No description available
Chain information for 20SCP-OG+PI31_v2.pdb b #1.28
---
Chain | Description
b | No description available
Chain information for 20SCP-OG+PI31_v2.pdb c #1.29
---
Chain | Description
c | No description available
Chain information for 20SCP-OG+PI31_v2.pdb d #1.30
---
Chain | Description
d | No description available
> color #1.1 #c7e4faff
> color #1.2 #a3d1f6ff
> color #1.1 #a3d1f6ff
> color #1.2 #90c8f5ff
> color #1.3 #59acefff
> color #1.4 #2590eaff
> color #1.5 #176fbbff
> color #1.6 #326cb1ff
> color #1.7 #c7e4faff
> color #1.8 #f4d5ffff
> color #1.9 #efc1ffff
> color #1.10 #e497ffff
> color #1.11 #d356ffff
> color #1.12 #c300ffff
> color #1.13 #a500e0ff
> color #1.14 #9600ccff
> color #1.15 #a3d1f6ff
> color #1.16 #90c8f5ff
> color #1.17 #59acefff
> color #1.18 #2590eaff
> color #1.19 #176fbbff
> color #1.20 #326cb1ff
> color #1.21 #c7e4faff
> color #1.22 #f4d5ffff
> color #1.23 #efc1ffff
> color #1.24 #e497ffff
> color #1.25 #d356ffff
> color #1.26 #c300ffff
> color #1.27 #a500e0ff
> color #1.28 #9600ccff
> color #1.29 #dcffb7ff
> color #1.30 #fffc79ff
> combine #1
> rename #1 20SCP-OG_PI31_v2.pdb
> rename #2 20SCP-OG_PI31_v2.pdb
> hide #!1 models
> rename #3 id #4
> rename #4 id #10
> rename #5 id #3
> rename #6 id #4
> show #!3 models
> color zone #3 near #2 distance 5.11
> volume #3 level 0.06
> volume #3 step 1
Error processing trigger "graphics update":
You deleted or moved a volume file that is still open in ChimeraX.
/Users/fadlof/Downloads/cryosparc_P175_J149_map_sharp.mrc
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.
> volume #4 step 1
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
You deleted or moved a volume file that is still open in ChimeraX.
/Users/fadlof/Downloads/cryosparc_P175_J149_map_sharp.mrc
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.
[Repeated 1 time(s)]
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
> volume #4 level 0.1171
> volume #3 level 0.1158
> volume #3 level 0.1
> volume #4 level 0.1
> color zone #3 near #2 distance 5.11
> close #3
> close #4
> open /Users/fadlof/Downloads/cryosparc_P175_J149_map_sharp.mrc
Opened cryosparc_P175_J149_map_sharp.mrc as #3, grid size 384,384,384, pixel
0.851, shown at level 0.0228, step 2, values float32
> volume #3 step 1
> color zone #3 near #2 distance 5.11
> volume #3 level 0.1542
> volume #3 level 0.12
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
——— End of log from Mon Oct 9 16:59:21 2023 ———
opened ChimeraX session
> rename #3 id #5
> rename #2 id #4
> rename #1 id #3
> rename #10 id #1
> show #1 models
> hide #!4 models
> ui tool show "Side View"
> select add #1
49780 atoms, 50698 bonds, 6404 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.84259,-0.48557,-0.23292,126.2,0.49544,0.86845,-0.018206,-50.748,0.21112,-0.10006,0.97233,-12.441
> view matrix models
> #1,0.27663,-0.76558,-0.58082,299.52,-0.22817,-0.63945,0.73419,158.7,-0.9335,-0.070572,-0.35158,344.38
> view matrix models
> #1,-0.60335,0.38602,-0.69783,280.98,-0.76303,-0.025015,0.64588,162.12,0.23187,0.92215,0.30964,-63.614
> view matrix models
> #1,-0.26343,0.27021,-0.92606,281.47,-0.93367,0.17001,0.3152,207.76,0.24261,0.94767,0.20751,-53.815
> view matrix models
> #1,-0.40422,0.060573,-0.91266,329.83,-0.85598,0.32659,0.40079,161.61,0.32234,0.94322,-0.080164,-22.56
> view matrix models
> #1,-0.22424,0.17269,-0.95911,294.49,-0.7051,0.65062,0.282,110.97,0.67272,0.73951,-0.02413,-52.817
> view matrix models
> #1,-0.15319,0.18265,-0.97117,284.5,-0.72921,0.64236,0.23584,122.44,0.66692,0.74432,0.034788,-61.307
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.15319,0.18265,-0.97117,301.11,-0.72921,0.64236,0.23584,137.86,0.66692,0.74432,0.034788,-46.264
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.14116,0.20776,-0.96794,295.31,-0.98156,0.097948,0.16417,262.58,0.12891,0.97326,0.1901,-23.303
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.14116,0.20776,-0.96794,295.8,-0.98156,0.097948,0.16417,263.55,0.12891,0.97326,0.1901,-22.961
> ui tool show "Fit in Map"
> fitmap #1 inMap #5
Fit molecule 8FZ6 (#1) to map cryosparc_P175_J149_map_sharp.mrc (#5) using
49780 atoms
average map value = 0.1364, steps = 216
shifted from previous position = 5.16
rotated from previous position = 16.1 degrees
atoms outside contour = 32439, contour level = 0.12
Position of 8FZ6 (#1) relative to cryosparc_P175_J149_map_sharp.mrc (#5)
coordinates:
Matrix rotation and translation
-0.33364190 0.01187962 -0.94262504 349.17566374
-0.94230615 0.02469453 0.33384024 247.83638201
0.02724357 0.99962446 0.00295511 12.82892312
Axis 0.43954204 -0.64029459 -0.62994098
Axis point 258.05964941 0.00000000 11.52002166
Rotation angle (degrees) 130.76788007
Shift along axis -13.29237400
> fitmap #1 inMap #5
Fit molecule 8FZ6 (#1) to map cryosparc_P175_J149_map_sharp.mrc (#5) using
49780 atoms
average map value = 0.1364, steps = 44
shifted from previous position = 0.0027
rotated from previous position = 0.0066 degrees
atoms outside contour = 32438, contour level = 0.12
Position of 8FZ6 (#1) relative to cryosparc_P175_J149_map_sharp.mrc (#5)
coordinates:
Matrix rotation and translation
-0.33356871 0.01179781 -0.94265197 349.18180636
-0.94233221 0.02471810 0.33376492 247.85036480
0.02723826 0.99962485 0.00287228 12.84159457
Axis 0.43958854 -0.64030378 -0.62989919
Axis point 258.07051015 0.00000000 11.53141529
Rotation angle (degrees) 130.76735311
Shift along axis -13.29211688
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
> split #1
Split 8FZ6 (#1) into 30 models
Chain information for 8FZ6 A #1.1
---
Chain | Description
A | No description available
Chain information for 8FZ6 B #1.2
---
Chain | Description
B | No description available
Chain information for 8FZ6 C #1.3
---
Chain | Description
C | No description available
Chain information for 8FZ6 D #1.4
---
Chain | Description
D | No description available
Chain information for 8FZ6 E #1.5
---
Chain | Description
E | No description available
Chain information for 8FZ6 F #1.6
---
Chain | Description
F | No description available
Chain information for 8FZ6 G #1.7
---
Chain | Description
G | No description available
Chain information for 8FZ6 H #1.8
---
Chain | Description
H | No description available
Chain information for 8FZ6 I #1.9
---
Chain | Description
I | No description available
Chain information for 8FZ6 J #1.10
---
Chain | Description
J | No description available
Chain information for 8FZ6 K #1.11
---
Chain | Description
K | No description available
Chain information for 8FZ6 L #1.12
---
Chain | Description
L | No description available
Chain information for 8FZ6 M #1.13
---
Chain | Description
M | No description available
Chain information for 8FZ6 N #1.14
---
Chain | Description
N | No description available
Chain information for 8FZ6 O #1.15
---
Chain | Description
O | No description available
Chain information for 8FZ6 P #1.16
---
Chain | Description
P | No description available
Chain information for 8FZ6 Q #1.17
---
Chain | Description
Q | No description available
Chain information for 8FZ6 R #1.18
---
Chain | Description
R | No description available
Chain information for 8FZ6 S #1.19
---
Chain | Description
S | No description available
Chain information for 8FZ6 T #1.20
---
Chain | Description
T | No description available
Chain information for 8FZ6 U #1.21
---
Chain | Description
U | No description available
Chain information for 8FZ6 V #1.22
---
Chain | Description
V | No description available
Chain information for 8FZ6 W #1.23
---
Chain | Description
W | No description available
Chain information for 8FZ6 X #1.24
---
Chain | Description
X | No description available
Chain information for 8FZ6 Y #1.25
---
Chain | Description
Y | No description available
Chain information for 8FZ6 Z #1.26
---
Chain | Description
Z | No description available
Chain information for 8FZ6 a #1.27
---
Chain | Description
a | No description available
Chain information for 8FZ6 b #1.28
---
Chain | Description
b | No description available
Chain information for 8FZ6 c #1.29
---
Chain | Description
c | No description available
Chain information for 8FZ6 d #1.30
---
Chain | Description
d | No description available
> combine #1
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
> open /Users/fadlof/Downloads/cryosparc_P175_J177_map_sharp.mrc
Opened cryosparc_P175_J177_map_sharp.mrc as #6, grid size 384,384,384, pixel
0.851, shown at level 0.0281, step 2, values float32
> volume #6 step 1
> hide #2 models
> hide #!1 models
> volume #6 level 0.12
> volume #6 level 0.1
> volume #5 level 0.1
> select add #6
2 models selected
> view matrix models #6,1,0,0,4.472,0,1,0,2.1786,0,0,1,-0.60727
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.010143,-0.91039,0.41362,251.95,0.59789,0.32603,0.73228,-101.99,-0.80151,0.25473,0.54101,161.67
> fitmap #6 inMap #5
Fit map cryosparc_P175_J177_map_sharp.mrc in map
cryosparc_P175_J149_map_sharp.mrc using 375975 points
correlation = 0.5934, correlation about mean = 0.218, overlap = 2.368e+04
steps = 220, shift = 7.41, angle = 15.7 degrees
Position of cryosparc_P175_J177_map_sharp.mrc (#6) relative to
cryosparc_P175_J149_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.18341600 -0.95636838 0.22741615 252.91895108
0.59760805 0.29216167 0.74666337 -103.07254211
-0.78052751 -0.00104428 0.62512056 189.84607603
Axis -0.37432859 0.50461184 0.77797493
Axis point 242.14440944 58.10043896 0.00000000
Rotation angle (degrees) 87.11398809
Shift along axis 1.00906749
> view matrix models
> #6,0.28363,-0.95815,-0.038646,278.82,0.95651,0.28555,-0.059585,-33.433,0.068127,-0.020065,0.99747,-4.6663
> fitmap #6 inMap #5
Fit map cryosparc_P175_J177_map_sharp.mrc in map
cryosparc_P175_J149_map_sharp.mrc using 375975 points
correlation = 0.9681, correlation about mean = 0.8911, overlap = 5.31e+04
steps = 76, shift = 3.97, angle = 4.1 degrees
Position of cryosparc_P175_J177_map_sharp.mrc (#6) relative to
cryosparc_P175_J149_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.29252014 -0.95625936 0.00004114 271.96708864
0.95625936 0.29252014 -0.00001060 -40.66748702
-0.00000189 0.00004244 1.00000000 1.25575098
Axis 0.00002774 0.00002250 1.00000000
Axis point 163.46748408 163.46726330 0.00000000
Rotation angle (degrees) 72.99110653
Shift along axis 1.26237912
> select subtract #6
Nothing selected
> hide #!5 models
> show #!4 models
> color zone #6 near #4 distance 5.11
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
> ui tool show "Side View"
> hide #!4 models
> hide #!6 models
> rename #2 8FZ6
> show #!1 models
> hide #1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #1.4 models
> hide #1.5 models
> hide #1.6 models
> hide #1.7 models
> hide #1.9 models
> hide #1.8 models
> hide #1.10 models
> hide #1.11 models
> hide #1.12 models
> hide #1.13 models
> hide #1.14 models
> hide #1.15 models
> hide #1.16 models
> hide #1.17 models
> hide #1.18 models
> hide #1.19 models
> hide #1.21 models
> hide #1.20 models
> hide #1.23 models
> hide #1.22 models
> hide #1.24 models
> hide #1.25 models
> hide #1.26 models
> hide #1.27 models
> hide #1.28 models
> select add #1.29
470 atoms, 488 bonds, 65 residues, 1 model selected
> select add #1.30
940 atoms, 976 bonds, 130 residues, 2 models selected
> hide #!3.29 models
> hide #!3.30 models
> show #!3 models
> select add #3
48262 atoms, 49132 bonds, 24 pseudobonds, 6264 residues, 45 models selected
> select subtract #3.29
47912 atoms, 48772 bonds, 22 pseudobonds, 6215 residues, 43 models selected
> select subtract #3.30
47562 atoms, 48412 bonds, 20 pseudobonds, 6166 residues, 41 models selected
> combine sel
> rename #7 id #9
> rename #6 id #8
> rename #5 id #7
> rename #9 id #5
> rename #5 20SCP-OG_PI31-8FZ6.pdb
> hide #!3 models
> hide #!1 models
> select add #3
48262 atoms, 49132 bonds, 24 pseudobonds, 6264 residues, 45 models selected
> select add #1
97102 atoms, 98854 bonds, 24 pseudobonds, 12538 residues, 74 models selected
> select subtract #3
49780 atoms, 50698 bonds, 6404 residues, 31 models selected
> select subtract #1
Nothing selected
> show #!7 models
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
> split 5
Expected a structures specifier or a keyword
> split #5
Split 20SCP-OG_PI31-8FZ6.pdb (#5) into 30 models
Chain information for 20SCP-OG_PI31-8FZ6.pdb A #5.1
---
Chain | Description
A | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb B #5.2
---
Chain | Description
B | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb C #5.3
---
Chain | Description
C | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb D #5.4
---
Chain | Description
D | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb E #5.5
---
Chain | Description
E | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb F #5.6
---
Chain | Description
F | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb G #5.7
---
Chain | Description
G | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb H #5.8
---
Chain | Description
H | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb I #5.9
---
Chain | Description
I | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb J #5.10
---
Chain | Description
J | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb K #5.11
---
Chain | Description
K | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb L #5.12
---
Chain | Description
L | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb M #5.13
---
Chain | Description
M | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb N #5.14
---
Chain | Description
N | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb O #5.15
---
Chain | Description
O | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb P #5.16
---
Chain | Description
P | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb Q #5.17
---
Chain | Description
Q | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb R #5.18
---
Chain | Description
R | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb S #5.19
---
Chain | Description
S | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb T #5.20
---
Chain | Description
T | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb U #5.21
---
Chain | Description
U | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb V #5.22
---
Chain | Description
V | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb W #5.23
---
Chain | Description
W | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb X #5.24
---
Chain | Description
X | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb Y #5.25
---
Chain | Description
Y | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb Z #5.26
---
Chain | Description
Z | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb a #5.27
---
Chain | Description
a | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb b #5.28
---
Chain | Description
b | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb c #5.29
---
Chain | Description
c | No description available
Chain information for 20SCP-OG_PI31-8FZ6.pdb d #5.30
---
Chain | Description
d | No description available
> combine #5
> rename #6 20SCP-OG_PI31-8FZ6.pdb
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
> hide #!5 models
> close #6
> select add #5.29
470 atoms, 488 bonds, 65 residues, 1 model selected
> transparency #7.1 50
> show #!5 models
> fitmap #5.29 inMap #7
Fit molecule 20SCP-OG_PI31-8FZ6.pdb c (#5.29) to map
cryosparc_P175_J149_map_sharp.mrc (#7) using 470 atoms
average map value = 0.1675, steps = 52
shifted from previous position = 0.677
rotated from previous position = 0.317 degrees
atoms outside contour = 222, contour level = 0.1
Position of 20SCP-OG_PI31-8FZ6.pdb c (#5.29) relative to
cryosparc_P175_J149_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.33432157 0.01726460 -0.94230092 348.59245183
-0.94200477 0.02491929 0.33467306 248.28823756
0.02925947 0.99954038 0.00793228 11.96951455
Axis 0.43781312 -0.63976958 -0.63167598
Axis point 258.08017383 0.00000000 10.89657296
Rotation angle (degrees) 130.59704045
Shift along axis -13.78976815
> fitmap #5.29 inMap #7
Fit molecule 20SCP-OG_PI31-8FZ6.pdb c (#5.29) to map
cryosparc_P175_J149_map_sharp.mrc (#7) using 470 atoms
average map value = 0.1674, steps = 60
shifted from previous position = 0.0192
rotated from previous position = 0.0192 degrees
atoms outside contour = 219, contour level = 0.1
Position of 20SCP-OG_PI31-8FZ6.pdb c (#5.29) relative to
cryosparc_P175_J149_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.33450905 0.01722255 -0.94223516 348.59779176
-0.94194647 0.02464908 0.33485710 248.28248493
0.02899232 0.99954780 0.00797738 11.98899085
Axis 0.43779879 -0.63969935 -0.63175705
Axis point 258.07993632 0.00000000 10.84936867
Rotation angle (degrees) 130.61260892
Shift along axis -13.78458354
> select add #5.30
940 atoms, 976 bonds, 130 residues, 2 models selected
> select subtract #5.29
470 atoms, 488 bonds, 65 residues, 1 model selected
> fitmap #5.30 inMap #7
Fit molecule 20SCP-OG_PI31-8FZ6.pdb d (#5.30) to map
cryosparc_P175_J149_map_sharp.mrc (#7) using 470 atoms
average map value = 0.1853, steps = 64
shifted from previous position = 0.629
rotated from previous position = 0.385 degrees
atoms outside contour = 198, contour level = 0.1
Position of 20SCP-OG_PI31-8FZ6.pdb d (#5.30) relative to
cryosparc_P175_J149_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.33548382 0.00548132 -0.94203003 350.21204800
-0.94173938 0.02355921 0.33551739 247.05534929
0.02403256 0.99970742 -0.00274176 14.28010304
Axis 0.44067805 -0.64096502 -0.62846377
Axis point 257.86630768 0.00000000 12.27511391
Rotation angle (degrees) 131.09680165
Shift along axis -12.99760269
> fitmap #5.30 inMap #7
Fit molecule 20SCP-OG_PI31-8FZ6.pdb d (#5.30) to map
cryosparc_P175_J149_map_sharp.mrc (#7) using 470 atoms
average map value = 0.1853, steps = 48
shifted from previous position = 0.00837
rotated from previous position = 0.0321 degrees
atoms outside contour = 200, contour level = 0.1
Position of 20SCP-OG_PI31-8FZ6.pdb d (#5.30) relative to
cryosparc_P175_J149_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.33562339 0.00505369 -0.94198270 350.29535184
-0.94170114 0.02322916 0.33564770 247.08075903
0.02357773 0.99971740 -0.00303718 14.39061847
Axis 0.44079347 -0.64091576 -0.62843306
Axis point 257.90655266 0.00000000 12.26860729
Rotation angle (degrees) 131.12589134
Shift along axis -12.99358795
> fitmap #5.30 inMap #7
Fit molecule 20SCP-OG_PI31-8FZ6.pdb d (#5.30) to map
cryosparc_P175_J149_map_sharp.mrc (#7) using 470 atoms
average map value = 0.1853, steps = 40
shifted from previous position = 0.0135
rotated from previous position = 0.0417 degrees
atoms outside contour = 199, contour level = 0.1
Position of 20SCP-OG_PI31-8FZ6.pdb d (#5.30) relative to
cryosparc_P175_J149_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.33514375 0.00553037 -0.94215078 350.16349988
-0.94186286 0.02344026 0.33517892 247.13994214
0.02393792 0.99970995 -0.00264701 14.28474438
Axis 0.44082372 -0.64086522 -0.62846338
Axis point 257.91047915 0.00000000 12.25583505
Rotation angle (degrees) 131.08479533
Shift along axis -13.00045375
> select subtract #5.30
Nothing selected
> hide #!7 models
> combine #5
> rename #6 20SCP-OG_PI31-8FZ6.pdb
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> select #4/c,d
700 atoms, 720 bonds, 4 pseudobonds, 98 residues, 2 models selected
> show sel atoms
> select add #4
47322 atoms, 48156 bonds, 24 pseudobonds, 6134 residues, 2 models selected
> select subtract #4
Nothing selected
> show #!7 models
> hide #!4 models
> color zone #7 near #6 distance 5.11
> volume #7 level 0.06963
> color zone #8 near #6 distance 5.11
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!8 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!8 models
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
> view
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
> open /Users/fadlof/Downloads/cryosparc_P175_J149_map_sharp.mrc
Opened cryosparc_P175_J149_map_sharp.mrc as #9, grid size 384,384,384, pixel
0.851, shown at level 0.0228, step 2, values float32
> close #9
> open /Users/fadlof/Downloads/cryosparc_P175_J160_008_volume_map.mrc
Opened cryosparc_P175_J160_008_volume_map.mrc as #9, grid size 384,384,384,
pixel 0.851, shown at level 0.394, step 2, values float32
> volume #9 step 1
> fitmap #9 inMap #7
Fit map cryosparc_P175_J160_008_volume_map.mrc in map
cryosparc_P175_J149_map_sharp.mrc using 564819 points
correlation = 0.89, correlation about mean = 0.805, overlap = 1.018e+05
steps = 116, shift = 1.32, angle = 8.91 degrees
Position of cryosparc_P175_J160_008_volume_map.mrc (#9) relative to
cryosparc_P175_J149_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.98793120 0.15489336 0.00001707 -23.30423642
-0.15489336 0.98793120 0.00001783 27.31964984
-0.00001410 -0.00002026 1.00000000 1.31972340
Axis -0.00012295 0.00010061 -0.99999999
Axis point 163.66147367 163.20645801 0.00000000
Rotation angle (degrees) 8.91061153
Shift along axis -1.31410957
> color #9 darkgrey models
> hide #!8 models
> color zone #9 near #6 distance 5.11
> volume #9 level 0.394
> volume #9 level 0.3432
> volume #9 level 0.3082
> volume #9 level 0.3051
> volume #9 level 0.2701
> color zone #9 near #6 distance 5.11
> transparency #9.1 50
> color zone #9 near #6 distance 5.11
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!7 models
> transparency #9.1 50
> transparency #9.1 0
> hide #!9 models
> show #!9 models
> volume #9 level 0.3
> color zone #9 near #6 distance 5.11
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> transparency #8.1 50
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> transparency #7.1 50
> transparency #7.1 0
> hide #!7 models
> show #!9 models
> hide #!9 models
> show #!9 models
> transparency #9.1 50
> hide #!6 models
> show #!6 models
> hide #!9 models
> show #!9 models
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
> open /Users/fadlof/Downloads/cryosparc_P175_J48_007_volume_map.mrc
Opened cryosparc_P175_J48_007_volume_map.mrc as #10, grid size 384,384,384,
pixel 0.851, shown at level 0.345, step 2, values float32
> hide #!9 models
> volume #10 step 1
> volume #10 level 0.2018
> color zone #10 near #6 distance 5.11
> transparency #10.1 50
> volume #10 color darkgrey
> color #10 darkgrey models
> color zone #10 near #6 distance 5.11
> volume #10 level 0.25
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!8 models
> hide #!8 models
> hide #!9 models
> show #!9 models
> show #!8 models
> hide #!9 models
> hide #!10 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.2
> volume #8 level 0.05
> color zone #8 near #6 distance 5.11
> transparency #8.1 50
> show #!6 atoms
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> transparency #7.1 50
> show #!8 models
> hide #!7 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> close #9
> close #10
> hide #!6 models
> transparency #8.1 0
> volume #8 level 0.08
> show #!6 models
> color zone #8 near #6 distance 5.11
> close #7
> open /Users/fadlof/Downloads/cryosparc_P175_J176_map_sharp.mrc
Opened cryosparc_P175_J176_map_sharp.mrc as #7, grid size 384,384,384, pixel
0.851, shown at level 0.484, step 2, values float32
> volume #7 step 1
> volume #7 color darkgrey
> color #7 darkgrey models
> select add #7
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.25907,0.96426,0.055597,39.096,-0.96419,-0.26158,0.043787,356.6,0.056765,-0.042262,0.99749,-1.9604
> volume #7 level 0.6824
> volume #7 level 0.7532
> ui tool show "Fit in Map"
> fitmap #7 inMap #8
Fit map cryosparc_P175_J176_map_sharp.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 371778 points
correlation = 0.9511, correlation about mean = 0.8492, overlap = 2.493e+05
steps = 84, shift = 1.34, angle = 4.48 degrees
Position of cryosparc_P175_J176_map_sharp.mrc (#7) relative to
cryosparc_P175_J177_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
-1.00000000 -0.00002778 -0.00000972 326.92680859
0.00002778 -0.99999999 0.00011076 326.90105660
-0.00000972 0.00011076 0.99999999 0.05607983
Axis -0.00003467 0.00002006 1.00000000
Axis point 163.46113464 163.45279855 0.00000000
Rotation angle (degrees) 179.99840811
Shift along axis 0.05130517
> select subtract #7
Nothing selected
> hide #!8 models
> color zone #7 near #6 distance 5.11
> hide #!7 models
> show #!7 models
> volume #7 level 0.7274
> volume #7 level 0.5855
> undo
> close #7
> view
> hide #!6 atoms
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
——— End of log from Tue Oct 10 00:42:27 2023 ———
opened ChimeraX session
> open /Users/fadlof/Downloads/cryosparc_P175_J214_009_volume_map.mrc
Opened cryosparc_P175_J214_009_volume_map.mrc as #7, grid size 384,384,384,
pixel 0.851, shown at level 0.392, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J222_009_volume_map.mrc
Opened cryosparc_P175_J222_009_volume_map.mrc as #9, grid size 384,384,384,
pixel 0.851, shown at level 0.394, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J227_008_volume_map.mrc
Opened cryosparc_P175_J227_008_volume_map.mrc as #10, grid size 384,384,384,
pixel 0.851, shown at level 0.398, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J228_009_volume_map.mrc
Opened cryosparc_P175_J228_009_volume_map.mrc as #11, grid size 384,384,384,
pixel 0.851, shown at level 0.396, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J236_008_volume_map.mrc
Opened cryosparc_P175_J236_008_volume_map.mrc as #12, grid size 384,384,384,
pixel 0.851, shown at level 0.395, step 2, values float32
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> hide #!9 models
> show #!9 models
> hide #!6 models
> select add #9
2 models selected
> view matrix models
> #9,0.20701,-0.97688,-0.053339,298.18,-0.077592,-0.070741,0.99447,21.158,-0.97526,-0.20173,-0.090442,374.94
> view matrix models
> #9,0.1785,-0.90069,-0.39609,347.78,-0.4242,0.29278,-0.85693,328.39,0.8878,0.32099,-0.32981,25.111
> view matrix models
> #9,-0.083826,-0.99559,-0.042034,346.88,-0.99277,0.087076,-0.082609,325.28,0.085905,0.034805,-0.9957,314.43
> ui tool show "Fit in Map"
> fitmap #9 inMap #8
Fit map cryosparc_P175_J222_009_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 70753 points
correlation = 0.8702, correlation about mean = 0.7874, overlap = 1.436e+04
steps = 124, shift = 7.59, angle = 6.9 degrees
Position of cryosparc_P175_J222_009_volume_map.mrc (#9) relative to
cryosparc_P175_J177_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
-0.99099679 -0.13388565 -0.00000046 347.32099452
-0.13388565 0.99099679 -0.00007026 23.41274127
0.00000986 -0.00006956 -1.00000000 326.02732231
Axis 0.06725725 -0.99773566 -0.00013714
Axis point 174.44919969 0.00000000 163.01250247
Rotation angle (degrees) 179.99970352
Shift along axis -0.04458194
> fitmap #9 inMap #8
Fit map cryosparc_P175_J222_009_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 70753 points
correlation = 0.8705, correlation about mean = 0.7876, overlap = 1.436e+04
steps = 28, shift = 0.0156, angle = 0.00726 degrees
Position of cryosparc_P175_J222_009_volume_map.mrc (#9) relative to
cryosparc_P175_J177_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
-0.99101372 -0.13376032 0.00000350 347.28773871
-0.13376033 0.99101371 -0.00006235 23.38435061
0.00000488 -0.00006226 -1.00000000 326.02962634
Axis 0.06825286 -0.99766726 -0.00125733
Axis point 174.44370328 0.00000000 163.00013805
Rotation angle (degrees) 179.99996040
Shift along axis -0.03634420
> color #9 darkgrey models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 2 maps.
[Repeated 1 time(s)]
> hide #!8 models
> select subtract #9
Nothing selected
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> rename #10 id #15
> rename #11 id #6
> close #12,15
> show #!6 models
> hide #!6 models
> hide #!9 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!7 models
> rename #7 id #10
> rename #9 id #11
> rename #10 id #9
> rename #11 id #10
> show #!8 models
> select add #8
2 models selected
> hide #!9 models
> hide #!8 models
> show #!8 models
> select subtract #8
Nothing selected
> show #!9 models
> select add #9
2 models selected
> select subtract #9
Nothing selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #9
2 models selected
> select subtract #9
Nothing selected
> select add #9
2 models selected
> select add #8
4 models selected
> select add #6
47562 atoms, 48412 bonds, 20 pseudobonds, 6166 residues, 8 models selected
> select add #10
47562 atoms, 48412 bonds, 20 pseudobonds, 6166 residues, 10 models selected
> show #!10 models
> select subtract #8
47562 atoms, 48412 bonds, 20 pseudobonds, 6166 residues, 8 models selected
> select subtract #6
4 models selected
> select subtract #9
2 models selected
> hide #!8 models
> hide #!6 models
> hide #!9 models
> hide #!10 models
> show #!10 models
> show #!8 models
> fitmap #3.11 inMap #8
Fit molecule 20SCP-OG+PI31_v2.pdb K (#3.11) to map
cryosparc_P175_J177_map_sharp.mrc (#8) using 1543 atoms
average map value = 0.01871, steps = 2000
shifted from previous position = 6.49
rotated from previous position = 8.17 degrees
atoms outside contour = 1465, contour level = 0.08
Position of 20SCP-OG+PI31_v2.pdb K (#3.11) relative to
cryosparc_P175_J177_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.17307855 0.98373647 0.04802475 -30.23001218
-0.98277402 0.17570621 -0.05729349 296.54976117
-0.06479994 -0.03728120 0.99720162 14.96993924
Axis 0.01015931 0.05727589 -0.99830670
Axis point 161.78930392 166.74655672 0.00000000
Rotation angle (degrees) 80.03810464
Shift along axis 1.73344500
> fitmap #3.11 inMap #8
Fit molecule 20SCP-OG+PI31_v2.pdb K (#3.11) to map
cryosparc_P175_J177_map_sharp.mrc (#8) using 1543 atoms
average map value = 0.03173, steps = 280
shifted from previous position = 5.8
rotated from previous position = 15.5 degrees
atoms outside contour = 1409, contour level = 0.08
Position of 20SCP-OG+PI31_v2.pdb K (#3.11) relative to
cryosparc_P175_J177_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.15086099 0.96165119 0.22905881 -46.93236512
-0.94610981 0.20762210 -0.24853429 312.38617278
-0.28656097 -0.17922066 0.94114970 70.94810037
Axis 0.03505242 0.26075279 -0.96476904
Axis point 164.31366246 194.30721868 0.00000000
Rotation angle (degrees) 81.38371342
Shift along axis 11.36194302
> hide #!8 models
> show #!6 models
> color zone #10 near #6 distance 5.11
> lighting soft
> hide #!10 models
> select subtract #10
Nothing selected
> show #!10 models
> hide #!6 models
> show #!6 models
> volume #10 level 0.3572
> volume #10 level 0.3112
> volume #10 level 0.25
> open /Users/fadlof/Downloads/cryosparc_P175_J227_008_volume_map.mrc
Opened cryosparc_P175_J227_008_volume_map.mrc as #7, grid size 384,384,384,
pixel 0.851, shown at level 0.398, step 2, values float32
> view
> volume #7 step 1
> rename #7 id #11
> color #11 darkgrey models
> hide #!10 models
> show #!8 models
> hide #!6 models
> fitmap #11 inMap #8
Fit map cryosparc_P175_J227_008_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 566699 points
correlation = 0.8988, correlation about mean = 0.8165, overlap = 1.157e+05
steps = 200, shift = 0.142, angle = 18.7 degrees
Position of cryosparc_P175_J227_008_volume_map.mrc (#11) relative to
cryosparc_P175_J177_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.58431564 0.81152648 0.00000906 -64.64905295
-0.81152648 0.58431564 0.00006633 200.59955637
0.00004853 -0.00004612 1.00000000 -1.13391101
Axis -0.00006928 -0.00002432 -1.00000000
Axis point 163.48739670 163.40579262 0.00000000
Rotation angle (degrees) 54.24534219
Shift along axis 1.13351205
> open /Users/fadlof/Downloads/cryosparc_P175_J228_009_volume_map.mrc
Opened cryosparc_P175_J228_009_volume_map.mrc as #7, grid size 384,384,384,
pixel 0.851, shown at level 0.396, step 2, values float32
> rename #7 id #12
> color #12 #dcffb7ff models
> color #12 darkgrey models
> hide #!11 models
> select add #12
2 models selected
> view matrix models
> #12,0.096559,-0.66356,0.74186,139.53,-0.010667,0.74461,0.66741,-61.385,-0.99527,-0.072358,0.064821,321.42
> view matrix models
> #12,0.017526,-0.99753,-0.067995,334.28,0.99007,0.026801,-0.138,18.926,0.13948,-0.064901,0.9881,-10.318
> fitmap #12 inMap #8
Fit map cryosparc_P175_J228_009_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 70770 points
correlation = 0.8991, correlation about mean = 0.8152, overlap = 1.405e+04
steps = 148, shift = 2.58, angle = 11.9 degrees
Position of cryosparc_P175_J228_009_volume_map.mrc (#12) relative to
cryosparc_P175_J177_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99067767 -0.13622688 -0.00001497 23.82937651
0.13622688 0.99067766 0.00010623 -20.71203060
0.00000036 -0.00010728 0.99999999 1.22846119
Axis -0.00078365 -0.00005629 0.99999969
Axis point 163.24668535 163.75978867 0.00000000
Rotation angle (degrees) 7.82957291
Shift along axis 1.21095272
> hide #!12 models
> select subtract #12
Nothing selected
> hide #!8 models
> view
[Repeated 1 time(s)]
> volume #12 color #dcffb7
> volume #12 color darkgrey
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting simple
> color #12 darkgrey models
> show #!8 models
> fitmap #12 inMap #8
Fit map cryosparc_P175_J228_009_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 70770 points
correlation = 0.8991, correlation about mean = 0.8151, overlap = 1.405e+04
steps = 28, shift = 0.0142, angle = 0.0105 degrees
Position of cryosparc_P175_J228_009_volume_map.mrc (#12) relative to
cryosparc_P175_J177_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99069551 -0.13609703 0.00003887 23.80752011
0.13609703 0.99069551 -0.00000980 -20.68413968
-0.00003717 0.00001500 1.00000000 1.21567940
Axis 0.00009114 0.00027937 0.99999996
Axis point 163.17996496 163.77362851 0.00000000
Rotation angle (degrees) 7.82206068
Shift along axis 1.21207063
> open /Users/fadlof/Downloads/cryosparc_P175_J236_008_volume_map.mrc
Opened cryosparc_P175_J236_008_volume_map.mrc as #7, grid size 384,384,384,
pixel 0.851, shown at level 0.395, step 2, values float32
> fitmap #12 inMap #8
Fit map cryosparc_P175_J228_009_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 70770 points
correlation = 0.8992, correlation about mean = 0.8152, overlap = 1.405e+04
steps = 28, shift = 0.0171, angle = 0.00384 degrees
Position of cryosparc_P175_J228_009_volume_map.mrc (#12) relative to
cryosparc_P175_J177_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99069434 -0.13610560 0.00000678 23.79890898
0.13610560 0.99069433 0.00004836 -20.68706112
-0.00001330 -0.00004699 1.00000000 1.22227631
Axis -0.00035028 0.00007378 0.99999994
Axis point 163.18585259 163.70216169 0.00000000
Rotation angle (degrees) 7.82255668
Shift along axis 1.21241364
> rename #7 id #13
> rename #8 id #7
> rename #9 id #8
> rename #10 id #9
> rename #11 id #10
> rename #12 id #11
> rename #13 id #12
> fitmap #12 inMap #7
Fit map cryosparc_P175_J236_008_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 70767 points
correlation = 0.3636, correlation about mean = 0.07341, overlap = 2782
steps = 84, shift = 0.597, angle = 0.827 degrees
Position of cryosparc_P175_J236_008_volume_map.mrc (#12) relative to
cryosparc_P175_J177_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.30602724 0.95202159 0.00148758 -42.46585817
-0.95201895 0.30603006 -0.00234786 269.40552285
-0.00269046 -0.00069769 0.99999614 -0.11475579
Axis 0.00086666 0.00219429 -0.99999722
Axis point 163.55767190 163.83137574 0.00000000
Rotation angle (degrees) 72.18005581
Shift along axis 0.66910700
> hide #!11 models
> select add #12
2 models selected
> view matrix models
> #12,0.86798,-0.46047,-0.18596,127.92,-0.36994,-0.34973,-0.86072,424.66,0.3313,0.81588,-0.4739,59.127
> view matrix models
> #12,0.9967,0.053242,-0.061325,2.1212,0.048608,-0.99602,-0.074726,330.69,-0.06506,0.071498,-0.99532,332.59
> fitmap #12 inMap #7
Fit map cryosparc_P175_J236_008_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 70767 points
correlation = 0.9012, correlation about mean = 0.8154, overlap = 1.424e+04
steps = 120, shift = 7.55, angle = 7.77 degrees
Position of cryosparc_P175_J236_008_volume_map.mrc (#12) relative to
cryosparc_P175_J177_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.25023666 -0.96818470 -0.00000540 280.81910251
-0.96818470 -0.25023666 -0.00007254 362.61752833
0.00006888 0.00002339 -1.00000000 325.58465279
Axis 0.79065033 -0.61226796 0.00001001
Axis point 0.00000000 290.03360656 162.79750471
Rotation angle (degrees) 179.99652422
Shift along axis 0.01387835
> color #12 darkgrey models
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
> open /Users/fadlof/Downloads/cryosparc_P175_J206_009_volume_map.mrc
Opened cryosparc_P175_J206_009_volume_map.mrc as #13, grid size 384,384,384,
pixel 0.851, shown at level 0.395, step 2, values float32
> select subtract #12
Nothing selected
> hide #!12 models
> select add #13
2 models selected
> view matrix models
> #13,-0.054898,-0.93858,0.34068,271.46,0.37955,0.29596,0.87655,-86.776,-0.92354,0.17743,0.33999,227.21
> view matrix models
> #13,0.24791,-0.96476,0.088169,266.52,0.96639,0.25267,0.047453,-43.369,-0.068059,0.073441,0.99497,-0.078089
> fitmap #13 inMap #7
Fit map cryosparc_P175_J206_009_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 70741 points
correlation = 0.8788, correlation about mean = 0.7989, overlap = 1.456e+04
steps = 88, shift = 0.457, angle = 5.75 degrees
Position of cryosparc_P175_J206_009_volume_map.mrc (#13) relative to
cryosparc_P175_J177_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.99895375 -0.04573185 0.00001289 7.69132885
0.04573185 0.99895375 0.00009828 -7.27036256
-0.00001737 -0.00009758 0.99999999 -0.88569101
Axis -0.00214136 0.00033090 0.99999765
Axis point 162.73312062 164.41786401 0.00000000
Rotation angle (degrees) 2.62116212
Shift along axis -0.90456461
> open /Users/fadlof/Downloads/cryosparc_P175_J189_009_volume_map.mrc
Opened cryosparc_P175_J189_009_volume_map.mrc as #14, grid size 400,400,400,
pixel 0.851, shown at level 0.297, step 2, values float32
> hide #!13 models
> select subtract #13
Nothing selected
> color #13 darkgrey models
> color #14 darkgrey models
> select add #14
2 models selected
> view matrix models
> #14,0.55127,0.24068,0.79886,-106.37,0.57319,0.5865,-0.57225,75.619,-0.60626,0.77336,0.18537,110.93
> view matrix models
> #14,0.099176,-0.17729,0.97915,9.9089,-0.088012,-0.98171,-0.16884,386.33,0.99117,-0.069433,-0.11297,40.986
> fitmap #13 inMap #7
Fit map cryosparc_P175_J206_009_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 70741 points
correlation = 0.8786, correlation about mean = 0.7988, overlap = 1.457e+04
steps = 40, shift = 0.00849, angle = 0.00429 degrees
Position of cryosparc_P175_J206_009_volume_map.mrc (#13) relative to
cryosparc_P175_J177_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.99895524 -0.04569936 0.00003682 7.67652579
0.04569936 0.99895524 0.00003525 -7.26140603
-0.00003839 -0.00003353 1.00000000 -0.89102143
Axis -0.00075244 0.00082294 0.99999938
Axis point 162.63381519 164.24590903 0.00000000
Rotation angle (degrees) 2.61929426
Shift along axis -0.90277271
> fitmap #14 inMap #7
Fit map cryosparc_P175_J189_009_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 79999 points
correlation = 0.8566, correlation about mean = 0.7438, overlap = 1.212e+04
steps = 176, shift = 19.7, angle = 6.66 degrees
Position of cryosparc_P175_J189_009_volume_map.mrc (#14) relative to
cryosparc_P175_J177_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.16531393 -0.98050340 0.10622800 340.81006736
-0.08785599 -0.09264099 -0.99181599 369.91811032
0.98232002 -0.17329376 -0.07082825 35.71245169
Axis 0.54759101 -0.58610517 0.59718072
Axis point 16.90585116 332.44237860 0.00000000
Rotation angle (degrees) 131.63566643
Shift along axis -8.85960299
> select subtract #14
Nothing selected
> hide #!14 models
> open /Users/fadlof/Downloads/cryosparc_P175_J169_008_volume_map.mrc
Opened cryosparc_P175_J169_008_volume_map.mrc as #15, grid size 384,384,384,
pixel 0.851, shown at level 0.395, step 2, values float32
> select add #15
2 models selected
> view matrix models
> #15,0.56367,-0.69598,0.44484,110.67,-0.27926,0.34626,0.89561,2.7282,-0.77736,-0.62906,0.00081275,396.92
> view matrix models
> #15,0.184,-0.98042,-0.07015,305.32,-0.97739,-0.19007,0.092662,338.73,-0.10418,0.051513,-0.99322,341.89
> fitmap #15 inMap #7
Fit map cryosparc_P175_J169_008_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 70741 points
correlation = 0.8941, correlation about mean = 0.8103, overlap = 1.405e+04
steps = 124, shift = 7.41, angle = 8.26 degrees
Position of cryosparc_P175_J169_008_volume_map.mrc (#15) relative to
cryosparc_P175_J177_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.92082904 -0.38996649 -0.00003527 377.70891251
-0.38996649 0.92082904 -0.00004752 76.72516086
0.00005101 -0.00003000 -1.00000000 325.73091118
Axis 0.19898513 -0.98000251 0.00000456
Axis point 196.64014901 0.00000000 162.86987569
Rotation angle (degrees) 179.99747776
Shift along axis -0.03090704
> open /Users/fadlof/Downloads/cryosparc_P175_J161_009_volume_map.mrc
Opened cryosparc_P175_J161_009_volume_map.mrc as #16, grid size 384,384,384,
pixel 0.851, shown at level 0.394, step 2, values float32
> select subtract #15
Nothing selected
> hide #!15 models
> select add #16
2 models selected
> view matrix models
> #16,0.20294,-0.56641,0.79875,96.329,-0.71777,0.4688,0.51481,122.59,-0.66604,-0.6778,-0.31141,427.32
> view matrix models
> #16,-0.20345,-0.97772,-0.051765,364.67,-0.92757,0.2094,-0.30945,329.81,0.31339,-0.014941,-0.94951,259.98
> view matrix models
> #16,0.062182,-0.98212,-0.17768,341.92,0.15222,0.18528,-0.97083,262.03,0.98639,0.033322,0.16102,-33.777
> view matrix models
> #16,0.3097,-0.9483,0.069427,256.8,0.95083,0.30854,-0.027051,-38.105,0.0042313,0.074391,0.99722,-12.409
> fitmap #16 inMap #7
Fit map cryosparc_P175_J161_009_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 70755 points
correlation = 0.8897, correlation about mean = 0.8079, overlap = 1.423e+04
steps = 92, shift = 1.45, angle = 5.02 degrees
Position of cryosparc_P175_J161_009_volume_map.mrc (#16) relative to
cryosparc_P175_J177_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.99796191 0.06381242 0.00002377 -10.06134572
-0.06381242 0.99796191 0.00001486 10.80356362
-0.00002277 -0.00001635 1.00000000 0.16506253
Axis -0.00024449 0.00036470 -0.99999990
Axis point 164.09957962 162.91239386 0.00000000
Rotation angle (degrees) 3.65866864
Shift along axis -0.15866254
> open /Users/fadlof/Downloads/cryosparc_P175_J160_008_volume_map.mrc
Opened cryosparc_P175_J160_008_volume_map.mrc as #17, grid size 384,384,384,
pixel 0.851, shown at level 0.394, step 2, values float32
> hide #!16 models
> color #16 darkgrey models
> select subtract #16
Nothing selected
> select add #17
2 models selected
> color #17 darkgrey models
> view matrix models
> #17,0.99611,0.088157,0.00042867,-13.839,-0.087994,0.99454,-0.056058,24.145,-0.0053682,0.055802,0.99843,-7.9935
> fitmap #17 inMap #7
Fit map cryosparc_P175_J160_008_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 70763 points
correlation = 0.8773, correlation about mean = 0.7957, overlap = 1.443e+04
steps = 104, shift = 1.34, angle = 5.01 degrees
Position of cryosparc_P175_J160_008_volume_map.mrc (#17) relative to
cryosparc_P175_J177_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.14094994 0.99001672 0.00003766 -21.37017827
-0.99001672 0.14094994 -0.00000004 302.23694392
-0.00000535 -0.00003728 1.00000000 0.05593822
Axis -0.00001880 0.00002172 -1.00000000
Axis point 163.47218332 163.43255988 0.00000000
Rotation angle (degrees) 81.89718087
Shift along axis -0.04897110
> open /Users/fadlof/Downloads/cryosparc_P175_J158_009_volume_map.mrc
Opened cryosparc_P175_J158_009_volume_map.mrc as #18, grid size 384,384,384,
pixel 0.851, shown at level 0.395, step 2, values float32
> hide #!17 models
> select subtract #17
Nothing selected
> select add #18
2 models selected
> view matrix models
> #18,0.42551,0.88462,-0.19073,-20.441,0.33683,-0.35044,-0.87392,304.23,-0.83993,0.30762,-0.44708,316.46
> view matrix models
> #18,-0.3461,0.92156,0.17591,41.488,-0.9231,-0.36799,0.11165,356.73,0.16762,-0.12374,0.97805,-3.6915
> fitmap #18 inMap #7
Fit map cryosparc_P175_J158_009_volume_map.mrc in map
cryosparc_P175_J177_map_sharp.mrc using 70765 points
correlation = 0.854, correlation about mean = 0.7808, overlap = 1.51e+04
steps = 148, shift = 1.52, angle = 12.7 degrees
Position of cryosparc_P175_J158_009_volume_map.mrc (#18) relative to
cryosparc_P175_J177_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.99999999 -0.00006218 -0.00001101 326.92760056
0.00006217 -0.99999998 0.00013904 326.88678008
-0.00001102 0.00013904 0.99999999 0.04801276
Axis -0.00002642 0.00006709 1.00000000
Axis point 163.45871988 163.44847010 0.00000000
Rotation angle (degrees) 179.99643764
Shift along axis 0.06130438
> color #18 darkgrey models
> volume all step 1
> select subtract #18
Nothing selected
> hide #!18 models
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
> show #!6 models
> hide #!7 models
> view
[Repeated 1 time(s)]
> view orient
> select #6/b:35
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> view matrix models
> #6,-0.30847,0.016593,-0.95109,346.08,-0.95015,-0.053063,0.30724,264.01,-0.04537,0.99845,0.032134,19.288
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new.cxs includeMaps
> true
——— End of log from Tue Oct 10 10:03:50 2023 ———
opened ChimeraX session
> close #2#1,3-18
> open /Users/fadlof/Downloads/20SCP-OG_PI31-8FZ6-coot-0.pdb
Summary of feedback from opening /Users/fadlof/Downloads/20SCP-
OG_PI31-8FZ6-coot-0.pdb
---
warning | PDB SEQRES record for chain c is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb #1
---
Chain | Description
A O | No description available
B P | No description available
C Q | No description available
D R | No description available
E S | No description available
F T | No description available
G U | No description available
H V | No description available
I W | No description available
J X | No description available
K Y | No description available
L Z | No description available
M a | No description available
N b | No description available
c | No description available
d | No description available
> style stick
Changed 47639 atom styles
> show cartoons
> hide atoms
> open /Users/fadlof/Downloads/cryosparc_P175_J253_map_sharp.mrc
Opened cryosparc_P175_J253_map_sharp.mrc as #2, grid size 384,384,384, pixel
0.851, shown at level 0.415, step 2, values float32
> volume #2 step 1
> color zone #2 near #1 distance 5.11
> view
> ui tool show "Side View"
> split #1
Split 20SCP-OG_PI31-8FZ6-coot-0.pdb (#1) into 30 models
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb C #1.3
---
Chain | Description
C | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb D #1.4
---
Chain | Description
D | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb E #1.5
---
Chain | Description
E | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb F #1.6
---
Chain | Description
F | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb G #1.7
---
Chain | Description
G | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb H #1.8
---
Chain | Description
H | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb I #1.9
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I | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb J #1.10
---
Chain | Description
J | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb K #1.11
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Chain | Description
K | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb L #1.12
---
Chain | Description
L | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb M #1.13
---
Chain | Description
M | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb N #1.14
---
Chain | Description
N | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb O #1.15
---
Chain | Description
O | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb P #1.16
---
Chain | Description
P | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb Q #1.17
---
Chain | Description
Q | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb R #1.18
---
Chain | Description
R | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb S #1.19
---
Chain | Description
S | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb T #1.20
---
Chain | Description
T | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb U #1.21
---
Chain | Description
U | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb V #1.22
---
Chain | Description
V | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb W #1.23
---
Chain | Description
W | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb X #1.24
---
Chain | Description
X | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb Y #1.25
---
Chain | Description
Y | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb Z #1.26
---
Chain | Description
Z | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb a #1.27
---
Chain | Description
a | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb b #1.28
---
Chain | Description
b | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb c #1.29
---
Chain | Description
c | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb d #1.30
---
Chain | Description
d | No description available
> color #1.29 #dcffb7ff
> color #1 darkgrey models
> color #1.29 #dcffb7ff
> color #1.30 #fffc79ff
> combine #1
> rename #2 id #4
> rename #4 id #2
> rename #2 id #4
> rename #3 id #2
> rename #4 id #3
> hide #!1 models
> rename #2 20SCP-OG_PI31-8FZ6-coot-0.pdb
> color zone #3 near #2 distance 5.11
> volume #3 level 0.7449
> volume #3 level 0.8983
> volume #3 level 0.7449
> volume #3 level 0.7755
> volume #3 level 0.7832
> close #2
> close #1
> rename #3 id #2
> rename #2 id #3
> rename #3 id #1
> open /Users/fadlof/Downloads/cryosparc_P175_J256_map_sharp.mrc
Opened cryosparc_P175_J256_map_sharp.mrc as #2, grid size 384,384,384, pixel
0.851, shown at level 0.0383, step 2, values float32
> volume #2 level 0.03833
> volume #2 level 0.02668
> volume #2 level 0.02086
> volume #2 level 0.04707
> volume #2 level 0.06164
> volume #2 step 1
> volume #2 level 0.1177
> volume #2 color darkgrey
> open /Users/fadlof/Downloads/20SCP-OG_PI31-8FZ6-coot-0.pdb
Summary of feedback from opening /Users/fadlof/Downloads/20SCP-
OG_PI31-8FZ6-coot-0.pdb
---
warning | PDB SEQRES record for chain c is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb #3
---
Chain | Description
A O | No description available
B P | No description available
C Q | No description available
D R | No description available
E S | No description available
F T | No description available
G U | No description available
H V | No description available
I W | No description available
J X | No description available
K Y | No description available
L Z | No description available
M a | No description available
N b | No description available
c | No description available
d | No description available
> color #3 darkgrey
> split #3
Split 20SCP-OG_PI31-8FZ6-coot-0.pdb (#3) into 30 models
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb A #3.1
---
Chain | Description
A | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb B #3.2
---
Chain | Description
B | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb C #3.3
---
Chain | Description
C | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb D #3.4
---
Chain | Description
D | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb E #3.5
---
Chain | Description
E | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb F #3.6
---
Chain | Description
F | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb G #3.7
---
Chain | Description
G | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb H #3.8
---
Chain | Description
H | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb I #3.9
---
Chain | Description
I | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb J #3.10
---
Chain | Description
J | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb K #3.11
---
Chain | Description
K | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb L #3.12
---
Chain | Description
L | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb M #3.13
---
Chain | Description
M | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb N #3.14
---
Chain | Description
N | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb O #3.15
---
Chain | Description
O | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb P #3.16
---
Chain | Description
P | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb Q #3.17
---
Chain | Description
Q | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb R #3.18
---
Chain | Description
R | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb S #3.19
---
Chain | Description
S | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb T #3.20
---
Chain | Description
T | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb U #3.21
---
Chain | Description
U | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb V #3.22
---
Chain | Description
V | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb W #3.23
---
Chain | Description
W | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb X #3.24
---
Chain | Description
X | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb Y #3.25
---
Chain | Description
Y | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb Z #3.26
---
Chain | Description
Z | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb a #3.27
---
Chain | Description
a | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb b #3.28
---
Chain | Description
b | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb c #3.29
---
Chain | Description
c | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb d #3.30
---
Chain | Description
d | No description available
> style stick
Changed 47639 atom styles
> hide cartoons
> show cartoons
> hide atoms
> hide #!2 models
> color #3.1 #a3d1f6ff
> color #3.2 #90c8f5ff
> color #3.3 #59acefff
> color #3.4 #2590eaff
> color #3.5 #176fbbff
> color #3.6 #326cb1ff
> color #3.7 #c7e4faff
> color #3.8 #f4d5ffff
> color #3.9 #efc1ffff
> color #3.10 #e497ffff
> color #3.11 #d356ffff
> color #3.12 #c300ffff
> color #3.13 #a500e0ff
> color #3.14 #9600ccff
> color #3.15 #a3d1f6ff
> color #3.16 #90c8f5ff
> color #3.17 #59acefff
> color #3.18 #2590eaff
> color #3.19 #176fbbff
> color #3.20 #326cb1ff
> color #3.21 #c7e4faff
> color #3.22 #f4d5ffff
> color #3.23 #efc1ffff
> color #3.24 #e497ffff
> color #3.25 #d356ffff
> color #3.26 #c300ffff
> color #3.27 #a500e0ff
> color #3.28 #9600ccff
> color #3.29 #dcffb7ff
> color #3.30 #fffc79ff
> select add #3.29
547 atoms, 570 bonds, 74 residues, 1 model selected
> select add #3.30
1017 atoms, 1058 bonds, 139 residues, 2 models selected
> show sel atoms
> select subtract #3.29
470 atoms, 488 bonds, 65 residues, 1 model selected
> select add #3
47639 atoms, 48494 bonds, 20 pseudobonds, 6175 residues, 41 models selected
> select subtract #3
Nothing selected
> combine #3
> rename #4 20SCP-OG_PI31-8FZ6-coot-0.pdb
> save /Users/fadlof/Downloads/ModelBuilding_20SCP-OG_PI31_new2.cxs
> includeMaps true
——— End of log from Tue Oct 10 14:37:41 2023 ———
opened ChimeraX session
> show #!2 models
> close #2
> close #1
> save /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v2/ChimeraX/ModelBuilding_20SCP-OG_PI31_v2.cxs includeMaps true
> open /Users/fadlof/Downloads/cryosparc_P175_J245_009_volume_map_sharp.mrc
Opened cryosparc_P175_J245_009_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.851, shown at level 0.577, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J245_009_volume_map.mrc
Opened cryosparc_P175_J245_009_volume_map.mrc as #2, grid size 400,400,400,
pixel 0.851, shown at level 0.359, step 2, values float32
> close #3
> volume #2 step 1
> volume #1 step 1
> volume #1 level 0.6
> volume #1 level 1.2
> hide #!4 models
> hide #!2 models
> show #!2 models
> volume #2 color darkgrey
> volume #2 level 0.4307
> volume #2 level 0.518
> ui tool show "Fit in Map"
> fitmap #4 inMap #1
Fit molecule 20SCP-OG_PI31-8FZ6-coot-0.pdb (#4) to map
cryosparc_P175_J245_009_volume_map_sharp.mrc (#1) using 47639 atoms
average map value = 0.2585, steps = 136
shifted from previous position = 0.807
rotated from previous position = 2.62 degrees
atoms outside contour = 43172, contour level = 1.2
Position of 20SCP-OG_PI31-8FZ6-coot-0.pdb (#4) relative to
cryosparc_P175_J245_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99898984 -0.03757422 -0.02464696 10.76049040
0.03777412 0.99925667 0.00769567 -7.40733690
0.02433948 -0.00861891 0.99966660 -1.89250370
Axis -0.17861141 -0.53630193 0.82491103
Axis point 194.72439690 283.47133689 0.00000000
Rotation angle (degrees) 2.61764233
Shift along axis 0.48947554
> show #!1 models
> show #!4 models
> fitmap #4 inMap #1
Fit molecule 20SCP-OG_PI31-8FZ6-coot-0.pdb (#4) to map
cryosparc_P175_J245_009_volume_map_sharp.mrc (#1) using 47639 atoms
average map value = 0.2585, steps = 80
shifted from previous position = 0.0141
rotated from previous position = 0.00761 degrees
atoms outside contour = 43182, contour level = 1.2
Position of 20SCP-OG_PI31-8FZ6-coot-0.pdb (#4) relative to
cryosparc_P175_J245_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99899299 -0.03745622 -0.02469876 10.74132668
0.03765583 0.99926136 0.00766689 -7.37739702
0.02439334 -0.00858922 0.99966554 -1.91564710
Axis -0.17826101 -0.53833342 0.82366264
Axis point 194.63737648 283.81653009 0.00000000
Rotation angle (degrees) 2.61338556
Shift along axis 0.47889271
> select add #4
47639 atoms, 48494 bonds, 20 pseudobonds, 6175 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99899,0.010422,-0.043803,5.9253,-0.016657,0.98937,-0.14448,27.069,0.041831,0.14506,0.98854,-28.125
> view matrix models
> #4,0.63311,0.02252,0.77374,-64.948,0.37857,0.86287,-0.33487,13.114,-0.67518,0.50492,0.53776,101.22
> view matrix models
> #4,0.36165,0.47721,0.80092,-99.167,0.03294,0.85199,-0.52252,100.93,-0.93173,0.21535,0.29241,229.11
> view matrix models
> #4,-0.26224,0.96005,-0.097673,65.362,-0.38339,-0.19654,-0.90243,400.14,-0.88557,-0.19921,0.41962,269.29
> view matrix models
> #4,-0.19303,0.10976,0.97503,24.141,-0.31437,0.93442,-0.16743,88.323,-0.92947,-0.33884,-0.14587,388.3
> view matrix models
> #4,-0.18121,0.12621,0.97531,19.476,-0.31533,0.93191,-0.17918,90.741,-0.93152,-0.34002,-0.12907,386.19
> view matrix models
> #4,0.96424,-0.26083,0.046924,41.652,0.25787,0.96425,0.061017,-46.049,-0.061162,-0.046735,0.99703,18.717
> view matrix models
> #4,0.94,-0.33817,-0.045139,72.747,0.3391,0.94063,0.014647,-48.168,0.037506,-0.029075,0.99887,-0.58632
> view matrix models
> #4,0.94368,-0.32397,-0.067171,73.292,0.32587,0.94522,0.019357,-47.495,0.05722,-0.040156,0.99755,-1.79
> view matrix models
> #4,0.93896,-0.31789,-0.13155,83.207,0.32233,0.94653,0.013396,-46.193,0.12026,-0.054982,0.99122,-8.6738
> fitmap #4 inMap #1
Fit molecule 20SCP-OG_PI31-8FZ6-coot-0.pdb (#4) to map
cryosparc_P175_J245_009_volume_map_sharp.mrc (#1) using 47639 atoms
average map value = 2.077, steps = 188
shifted from previous position = 11.6
rotated from previous position = 11.2 degrees
atoms outside contour = 11574, contour level = 1.2
Position of 20SCP-OG_PI31-8FZ6-coot-0.pdb (#4) relative to
cryosparc_P175_J245_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.98320200 -0.18252069 -0.00003236 39.38742002
0.18252069 0.98320200 0.00006704 -20.27548604
0.00001958 -0.00007181 0.99999998 7.04058525
Axis -0.00038037 -0.00014226 0.99999992
Axis point 129.84256575 203.86181776 0.00000000
Rotation angle (degrees) 10.51661834
Shift along axis 7.02848741
> select subtract #4
Nothing selected
> view
> ui tool show "Side View"
> hide #!1 models
> color zone #2 near #4 distance 5.11
> open /Users/fadlof/Downloads/cryosparc_P175_J250_006_volume_map_sharp.mrc
Opened cryosparc_P175_J250_006_volume_map_sharp.mrc as #3, grid size
384,384,384, pixel 0.851, shown at level 0.618, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J250_006_volume_map.mrc
Opened cryosparc_P175_J250_006_volume_map.mrc as #5, grid size 384,384,384,
pixel 0.851, shown at level 0.389, step 2, values float32
> view
> show #!1 models
> close #1
> close #2
> rename #5 id #1
> rename #3 id #2
> volume #2 step 1
> volume #1 step 1
> volume #2 level 1
> volume #1 level 0.4
> select add #4
47639 atoms, 48494 bonds, 20 pseudobonds, 6175 residues, 2 models selected
> view matrix models
> #4,-0.012842,0.14937,0.9887,-7.6962,-0.97194,-0.23414,0.022749,363.8,0.23489,-0.96066,0.14819,259.73
> view matrix models
> #4,0.73281,-0.46011,-0.50129,204.59,0.41225,-0.28589,0.86505,13.412,-0.54133,-0.84058,-0.019828,393.43
> view matrix models
> #4,-0.056551,0.17806,-0.98239,305.06,0.9766,-0.19462,-0.091494,56.834,-0.20749,-0.96458,-0.16289,381.65
> view matrix models
> #4,0.27531,-0.091683,-0.95697,290.89,0.89013,-0.35172,0.28978,36.62,-0.36315,-0.93161,-0.015223,378.46
> view matrix models
> #4,0.39003,-0.21471,-0.89542,282.56,0.80941,-0.38369,0.44457,30.672,-0.43902,-0.89815,0.02414,379.2
> view matrix models
> #4,0.085156,0.12448,-0.98856,291.62,0.99319,-0.089727,0.074257,10.885,-0.079457,-0.98816,-0.13127,359.6
> view matrix models
> #4,0.27421,0.1483,-0.95017,250.78,0.9596,0.022512,0.28045,-34.427,0.06298,-0.98869,-0.13614,337.17
> view
> view matrix models
> #4,0.051538,0.14563,-0.988,293.57,0.99435,-0.099405,0.037217,18.108,-0.092791,-0.98433,-0.14993,364.09
> fitmap #4 inMap #2
Fit molecule 20SCP-OG_PI31-8FZ6-coot-0.pdb (#4) to map
cryosparc_P175_J250_006_volume_map_sharp.mrc (#2) using 47639 atoms
average map value = 0.2664, steps = 96
shifted from previous position = 3.71
rotated from previous position = 4.1 degrees
atoms outside contour = 42019, contour level = 1
Position of 20SCP-OG_PI31-8FZ6-coot-0.pdb (#4) relative to
cryosparc_P175_J250_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.12027467 0.14407441 -0.98223041 282.30542171
0.98649903 -0.12812001 0.10200461 11.72926292
-0.11114711 -0.98123793 -0.15753885 370.89055750
Axis -0.66645247 -0.53592395 0.51829203
Axis point -0.00000000 35.67838298 291.15356940
Rotation angle (degrees) 125.64011367
Shift along axis -2.19952008
> fitmap #4 inMap #2
Fit molecule 20SCP-OG_PI31-8FZ6-coot-0.pdb (#4) to map
cryosparc_P175_J250_006_volume_map_sharp.mrc (#2) using 47639 atoms
average map value = 0.2665, steps = 48
shifted from previous position = 0.0171
rotated from previous position = 0.00871 degrees
atoms outside contour = 42023, contour level = 1
Position of 20SCP-OG_PI31-8FZ6-coot-0.pdb (#4) relative to
cryosparc_P175_J250_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.12031322 0.14410532 -0.98222116 282.27603498
0.98647886 -0.12826589 0.10201639 11.75026731
-0.11128436 -0.98121433 -0.15758893 370.91838521
Axis -0.66649148 -0.53587102 0.51829659
Axis point 0.00000000 35.70100214 291.14028432
Rotation angle (degrees) 125.64566239
Shift along axis -2.18546720
> fitmap #4 inMap #1
Fit molecule 20SCP-OG_PI31-8FZ6-coot-0.pdb (#4) to map
cryosparc_P175_J250_006_volume_map.mrc (#1) using 47639 atoms
average map value = 0.7083, steps = 116
shifted from previous position = 8.39
rotated from previous position = 8.36 degrees
atoms outside contour = 7331, contour level = 0.4
Position of 20SCP-OG_PI31-8FZ6-coot-0.pdb (#4) relative to
cryosparc_P175_J250_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.18364689 0.05576524 -0.98140923 281.01445601
0.98259028 -0.03896441 0.18165388 -20.88747923
-0.02811006 -0.99768335 -0.06195007 347.56604650
Axis -0.66357390 -0.53638979 0.52149368
Axis point 0.00000000 34.09470360 292.32069931
Rotation angle (degrees) 117.29898368
Shift along axis 5.98346876
> volume #2 level 0.9232
> volume #2 level 0.8
> color zone #2 near sel & #4 distance 5.11
> select subtract #4
Nothing selected
> select add #4
47639 atoms, 48494 bonds, 20 pseudobonds, 6175 residues, 2 models selected
> select subtract #4
Nothing selected
> show #!1 models
> hide #!2 models
> color zone #1 near #4 distance 5.11
> hide #!1 models
> show #!2 models
> volume #2 level 0.8
> volume #2 level 0.6925
> volume #1 level 0.3962
> volume #1 level 0.3466
> volume #1 level 0.3
> volume #1 level 0.25
> split #4
Split 20SCP-OG_PI31-8FZ6-coot-0.pdb (#4) into 30 models
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb A #4.1
---
Chain | Description
A | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb B #4.2
---
Chain | Description
B | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb C #4.3
---
Chain | Description
C | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb D #4.4
---
Chain | Description
D | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb E #4.5
---
Chain | Description
E | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb F #4.6
---
Chain | Description
F | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb G #4.7
---
Chain | Description
G | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb H #4.8
---
Chain | Description
H | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb I #4.9
---
Chain | Description
I | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb J #4.10
---
Chain | Description
J | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb K #4.11
---
Chain | Description
K | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb L #4.12
---
Chain | Description
L | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb M #4.13
---
Chain | Description
M | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb N #4.14
---
Chain | Description
N | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb O #4.15
---
Chain | Description
O | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb P #4.16
---
Chain | Description
P | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb Q #4.17
---
Chain | Description
Q | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb R #4.18
---
Chain | Description
R | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb S #4.19
---
Chain | Description
S | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb T #4.20
---
Chain | Description
T | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb U #4.21
---
Chain | Description
U | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb V #4.22
---
Chain | Description
V | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb W #4.23
---
Chain | Description
W | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb X #4.24
---
Chain | Description
X | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb Y #4.25
---
Chain | Description
Y | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb Z #4.26
---
Chain | Description
Z | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb a #4.27
---
Chain | Description
a | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb b #4.28
---
Chain | Description
b | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb c #4.29
---
Chain | Description
c | No description available
Chain information for 20SCP-OG_PI31-8FZ6-coot-0.pdb d #4.30
---
Chain | Description
d | No description available
> view
[Repeated 1 time(s)]
> volume #1 level 0.3
> transparency #1.1 50
> hide #!1 models
> select add #4.14
1479 atoms, 1505 bonds, 197 residues, 1 model selected
> select add #4.28
2958 atoms, 3010 bonds, 394 residues, 2 models selected
> select add #4.29
3505 atoms, 3580 bonds, 468 residues, 3 models selected
> select add #4.30
3975 atoms, 4068 bonds, 533 residues, 4 models selected
> select add #4.22
5620 atoms, 5740 bonds, 753 residues, 5 models selected
> select subtract #4.22
3975 atoms, 4068 bonds, 533 residues, 4 models selected
> select add #4.23
5562 atoms, 5684 bonds, 737 residues, 5 models selected
> select add #4.9
7149 atoms, 7300 bonds, 941 residues, 6 models selected
> rename #4 id #3
> combine sel
> show #!1 models
> hide #!3 models
> select add #3
47639 atoms, 48494 bonds, 20 pseudobonds, 6175 residues, 41 models selected
> select subtract #3
Nothing selected
> volume zone #1 nearAtoms #4 range 5.11
> volume #1 level 0.3322
> color zone #1 near #4 distance 5.11
> select add #3.30
470 atoms, 488 bonds, 65 residues, 1 model selected
> volume #!1 region all imageMode "full region"
> volume unzone #!1
> mousemode rightMode "crop volume"
> select add #3
47639 atoms, 48494 bonds, 20 pseudobonds, 6175 residues, 41 models selected
> select subtract #3
Nothing selected
> show #!3 models
> hide #!1 models
> select add #3.14
1479 atoms, 1505 bonds, 197 residues, 1 model selected
> select add #3.8
3124 atoms, 3177 bonds, 417 residues, 2 models selected
> select add #3.29
3671 atoms, 3747 bonds, 491 residues, 3 models selected
> combine sel
> hide #4 models
> hide #!3 models
> close #5
> close #4
> show #!3 models
> select add #3.30
4141 atoms, 4235 bonds, 556 residues, 4 models selected
> select subtract #3.29
3594 atoms, 3665 bonds, 482 residues, 3 models selected
> combine sel
> hide #!3 models
> select add #3
47639 atoms, 48494 bonds, 20 pseudobonds, 6175 residues, 41 models selected
> select subtract #3
Nothing selected
> hide #4 models
> close #4
> show #!3 models
> select add #3.29
547 atoms, 570 bonds, 74 residues, 1 model selected
> select add #3.30
1017 atoms, 1058 bonds, 139 residues, 2 models selected
> select add #3.8
2662 atoms, 2730 bonds, 359 residues, 3 models selected
> select add #3.14
4141 atoms, 4235 bonds, 556 residues, 4 models selected
> combine sel
> hide #!3 models
> show #!1 models
> volume zone #1 nearAtoms #4 range 5.11
> hide #4 models
> close #4
> select add #3.13
5775 atoms, 5901 bonds, 766 residues, 5 models selected
> select add #3.28
7254 atoms, 7406 bonds, 963 residues, 6 models selected
> select add #3.27
8888 atoms, 9072 bonds, 1173 residues, 7 models selected
> select add #3.22
10533 atoms, 10744 bonds, 1393 residues, 8 models selected
> combine sel
> volume zone #1 nearAtoms #4 range 5.11
> color zone #1 near #4 distance 5.11
> close #4
> select add #3.9
12120 atoms, 12360 bonds, 1597 residues, 9 models selected
> select add #3.10
13700 atoms, 13973 bonds, 1793 residues, 10 models selected
> select add #3.11
15243 atoms, 15547 bonds, 1992 residues, 11 models selected
> select add #3.12
16884 atoms, 17218 bonds, 2205 residues, 12 models selected
> select add #3.23
18471 atoms, 18834 bonds, 2409 residues, 13 models selected
> select add #3.24
20051 atoms, 20447 bonds, 2605 residues, 14 models selected
> select add #3.25
21594 atoms, 22021 bonds, 2804 residues, 15 models selected
> select add #3.26
23235 atoms, 23692 bonds, 3017 residues, 16 models selected
> combine sel
> volume zone #1 nearAtoms #4 range 5.11
> color zone #1 near #4 distance 5.11
> transparency #1.1 50
> volume #1 level 0.323
> volume #1 level 0.2125
> volume #1 level 0.2171
> volume #1 level 0.2862
> volume zone #1 nearAtoms #4 range 5.11
[Repeated 2 time(s)]
> volume #!1 region all imageMode "full region"
> volume unzone #!1
> mousemode rightMode "crop volume"
> volume zone #1 nearAtoms #4 range 5.11
> hide #!1 models
> show #!1 models
> select add #3
47639 atoms, 48494 bonds, 20 pseudobonds, 6175 residues, 41 models selected
> hide #4 models
> show #!2 models
> hide #!1 models
> volume #2 level 1.017
> select subtract #3
Nothing selected
> show #4 models
> hide #!2 models
> show #!1 models
> close #1-2
> rename #3 id #1
> rename #4 id #2
> show #!1 models
> hide #2 models
> open /Users/fadlof/Downloads/cryosparc_P175_J266_map_sharp.mrc
Opened cryosparc_P175_J266_map_sharp.mrc as #3, grid size 384,384,384, pixel
0.851, shown at level 0.461, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J268_map_sharp.mrc
Opened cryosparc_P175_J268_map_sharp.mrc as #4, grid size 384,384,384, pixel
0.851, shown at level 0.431, step 2, values float32
> show #2 models
> select add #2
23235 atoms, 23692 bonds, 3017 residues, 1 model selected
> select add #1
70874 atoms, 72186 bonds, 20 pseudobonds, 9192 residues, 42 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.74374,-0.39799,-0.53708,441.91,0.48824,0.22536,-0.84311,189.07,0.45658,-0.88928,0.026708,234.47,#2,-0.51255,0.50987,0.69089,54.552,0.3348,0.8596,-0.386,28.529,-0.7907,0.033466,-0.61129,390.63
> view matrix models
> #1,-0.8625,0.49237,0.11693,205.63,-0.054765,0.1389,-0.98879,316.58,-0.50309,-0.85923,-0.092833,405.99,#2,0.32211,-0.18394,0.92866,-6.3889,0.15422,0.97803,0.14023,-45.379,-0.93406,0.098042,0.34341,250.29
> view matrix models
> #1,0.086459,0.99442,0.060399,-20.522,0.079589,0.053538,-0.99539,309.69,-0.99307,0.090867,-0.074517,327.27,#2,0.99129,-0.094185,0.092048,3.9958,0.095203,0.99544,-0.0067198,-15.024,-0.090995,0.015424,0.99573,20.41
> view matrix models
> #1,0.051995,0.99526,0.082165,-18.675,0.073536,0.078238,-0.99422,306.48,-0.99594,0.057737,-0.069119,332.21,#2,0.98517,-0.11786,0.12467,3.7062,0.11833,0.99297,0.0036353,-20.045,-0.12423,0.011171,0.99219,27.107
> hide #2 models
> select subtract #2
47639 atoms, 48494 bonds, 20 pseudobonds, 6175 residues, 41 models selected
> combine#1
Unknown command: combine#1
> combine #1
> rename #5 20SCP-OG_PI31-8FZ6-coot-0.pdb
> close #1
> rename #5 id #1
> color #2 darkgrey
> hide #!3 models
> hide #!4 models
> show #2 models
> hide #!1 models
> undo
[Repeated 4 time(s)]
> fitmap #1 inMap #3
Fit molecule 20SCP-OG_PI31-8FZ6-coot-0.pdb (#1) to map
cryosparc_P175_J266_map_sharp.mrc (#3) using 47639 atoms
average map value = 1.64, steps = 104
shifted from previous position = 6.69
rotated from previous position = 7.24 degrees
atoms outside contour = 4817, contour level = 0.46066
Position of 20SCP-OG_PI31-8FZ6-coot-0.pdb (#1) relative to
cryosparc_P175_J266_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99067482 -0.13624758 -0.00003809 23.79610858
0.13624758 0.99067483 0.00009384 -20.74574944
0.00002496 -0.00009816 1.00000000 1.14830088
Axis -0.00070460 -0.00023138 0.99999972
Axis point 163.45167546 163.47221180 0.00000000
Rotation angle (degrees) 7.83076965
Shift along axis 1.13633393
> show #2 models
> hide #!1 models
> fitmap #2 inMap #3
Fit molecule combination (#2) to map cryosparc_P175_J266_map_sharp.mrc (#3)
using 23235 atoms
average map value = 2.07, steps = 88
shifted from previous position = 6.66
rotated from previous position = 7.25 degrees
atoms outside contour = 1366, contour level = 0.46066
Position of combination (#2) relative to cryosparc_P175_J266_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
0.99064509 -0.13646350 -0.00015449 23.86187034
0.13646352 0.99064511 0.00013186 -20.79348775
0.00013505 -0.00015171 0.99999998 1.14458627
Axis -0.00103901 -0.00106087 0.99999890
Axis point 163.58394655 163.65359967 0.00000000
Rotation angle (degrees) 7.84326489
Shift along axis 1.14185155
> show #!1 models
> hide #!3 models
> hide #!4 models
> volume #3 step 1
> volume #4 step 1
> hide #!1 models
> volume zone #4 nearAtoms #2 range 5.11
> color zone #4 near #2 distance 5.11
> volume #4 level 0.5
> volume #4 level 0.6
> 6
Unknown command: 6
> volume #3 level 0.6
> lighting simple
> volume #!4 region all imageMode "full region"
> volume unzone #!4
> mousemode rightMode "crop volume"
> volume zone #4 nearAtoms #2 range 5.11
> volume #!4 region all imageMode "full region"
> volume unzone #!4
> mousemode rightMode "crop volume"
> transparency #4.1 50
> volume #4 region 0,0,0,383,383,383
[Repeated 1 time(s)]
> volume #4 level 0.5502
> volume #3 level 0.5485
> transparency #3.1 50
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #2/b
1479 atoms, 1505 bonds, 197 residues, 1 model selected
> show sel atoms
> show #!3 models
> hide sel atoms
> select add #2
23235 atoms, 23692 bonds, 3017 residues, 1 model selected
> select subtract #2
Nothing selected
> view orient
> color zone #3 near #2 distance 5.11
> open /Users/fadlof/Downloads/cryosparc_P175_J270_map_sharp.mrc
Opened cryosparc_P175_J270_map_sharp.mrc as #5, grid size 384,384,384, pixel
0.851, shown at level 0.415, step 2, values float32
> volume #5 step 1
> volume #!3,5 region all imageMode "full region"
> volume unzone #!3,5
> mousemode rightMode "crop volume"
> hide #!3 models
> volume zone #5 nearAtoms #2 range 5.11
> color zone #5 near #2 distance 5.11
> transparency #5.1 50
> volume #5 region 0,0,0,383,383,383
[Repeated 2 time(s)]
> hide #!5 models
> show #!5 models
> volume #5 region 0,0,0,383,381,383
> transparency #5.1 50
> color zone #5 near #2 distance 5.11
> volume #!5 region all imageMode "full region"
> volume unzone #!5
> mousemode rightMode "crop volume"
> volume #5 level 0.6015
> volume #5 level 0.6502
> volume #5 level 0.4553
> hide #!5 models
> show #!5 models
> volume #5 level 0.3903
> transparency #5.1 0
> transparency #5.1 50
> volume #5 level 0.3822
> open /Users/fadlof/Downloads/cryosparc_P175_J267_map_sharp.mrc
Opened cryosparc_P175_J267_map_sharp.mrc as #6, grid size 384,384,384, pixel
0.851, shown at level 0.0309, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J269_map_sharp.mrc
Opened cryosparc_P175_J269_map_sharp.mrc as #7, grid size 384,384,384, pixel
0.851, shown at level 0.0349, step 2, values float32
> rename #7 id #10
> rename #6 id #11
> rename #5 id #9
> rename #4 id #8
> close #3,8-11
> open /Users/fadlof/Downloads/cryosparc_P175_J266_map_sharp.mrc
Opened cryosparc_P175_J266_map_sharp.mrc as #3, grid size 384,384,384, pixel
0.851, shown at level 0.461, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J267_map_sharp.mrc
Opened cryosparc_P175_J267_map_sharp.mrc as #4, grid size 384,384,384, pixel
0.851, shown at level 0.0309, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J268_map_sharp.mrc
Opened cryosparc_P175_J268_map_sharp.mrc as #5, grid size 384,384,384, pixel
0.851, shown at level 0.431, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J269_map_sharp.mrc
Opened cryosparc_P175_J269_map_sharp.mrc as #6, grid size 384,384,384, pixel
0.851, shown at level 0.0349, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J270_map_sharp.mrc
Opened cryosparc_P175_J270_map_sharp.mrc as #7, grid size 384,384,384, pixel
0.851, shown at level 0.415, step 2, values float32
> volume #3 step 1
> volume all setp 1
Expected a keyword
> volume all setp 1
Expected a keyword
> volume all level 1
> show #!1 models
> hide #2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!7 models
> show #!3 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> volume #4 step 1
> volume #5 step 1
> volume #4 level 0.1707
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> volume #4 level 0.8
> volume #4 level 0.1
> volume #4 level 0.05
> hide #!3 models
> color zone #4 near #1 distance 5.11
> hide #!4 models
> show #!5 models
> volume #5 level 0.385
> color zone #5 near #1 distance 5.11
> volume #5 region 0,0,0,383,383,383
[Repeated 2 time(s)]
> show #!6 models
> hide #!5 models
> show #!5 models
> volume #6 level 0.04
> hide #!5 models
> volume #6 step 1
> volume #7 step 1
> color zone #6 near #1 distance 5.11
> show #!7 models
> hide #!6 models
> color zone #7 near #1 distance 5.11
> transparency #7.1 50
> volume #7 level 0.472
> volume #7 level 0.4152
> open /Users/fadlof/Downloads/cryosparc_P175_J271_map_sharp.mrc
Opened cryosparc_P175_J271_map_sharp.mrc as #8, grid size 384,384,384, pixel
0.851, shown at level 0.0381, step 2, values float32
> hide #!7 models
> volume #8 step 1
> volume #8 level 0.03
> volume #8 level 0.02
> show #!7 models
> hide #!8 models
> color zone #7 near #1 distance 5.11
> transparency #7.1 50
> open /Users/fadlof/Downloads/cryosparc_P175_J272_map_sharp.mrc
Opened cryosparc_P175_J272_map_sharp.mrc as #9, grid size 384,384,384, pixel
0.851, shown at level 0.41, step 2, values float32
> hide #!7 models
> volume #9 step 1
> volume #9 region 0,0,5,383,383,383
> volume #9 region 0,0,8,383,383,383
> volume #9 region 0,0,6,383,383,383
> volume #9 region 0,0,3,383,383,383
> volume #9 region 0,0,1,383,383,383
> volume #9 region 0,0,3,383,383,383
> volume #9 region 0,0,4,383,383,383
[Repeated 1 time(s)]
> volume #9 level 0.4536
> color zone #9 near #1 distance 5.11
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!4 models
> volume #3 level 0.7747
> volume #3 level 0.6023
> volume #!3 region all imageMode "full region"
> volume unzone #!3
> mousemode rightMode "crop volume"
> color zone #3 near #1 distance 5.11
> volume #3 level 0.5228
> volume #3 level 0.483
> volume #3 region 0,0,0,383,381,383
> show #!5 models
> hide #!4 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> transparency #6.1 50
> show #!7 models
> volume #7 level 0.3989
> hide #!8 models
> hide #!6 models
> volume #9 level 0.3
[Repeated 1 time(s)]
> volume #9 level 0.3146
> volume #9 level 0.3876
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> split #2
Split combination (#2) into 16 models
Chain information for combination H #2.1
---
Chain | Description
H | No description available
Chain information for combination I #2.2
---
Chain | Description
I | No description available
Chain information for combination J #2.3
---
Chain | Description
J | No description available
Chain information for combination K #2.4
---
Chain | Description
K | No description available
Chain information for combination L #2.5
---
Chain | Description
L | No description available
Chain information for combination M #2.6
---
Chain | Description
M | No description available
Chain information for combination N #2.7
---
Chain | Description
N | No description available
Chain information for combination V #2.8
---
Chain | Description
V | No description available
Chain information for combination W #2.9
---
Chain | Description
W | No description available
Chain information for combination X #2.10
---
Chain | Description
X | No description available
Chain information for combination Y #2.11
---
Chain | Description
Y | No description available
Chain information for combination Z #2.12
---
Chain | Description
Z | No description available
Chain information for combination a #2.13
---
Chain | Description
a | No description available
Chain information for combination b #2.14
---
Chain | Description
b | No description available
Chain information for combination c #2.15
---
Chain | Description
c | No description available
Chain information for combination d #2.16
---
Chain | Description
d | No description available
> transparency #9.1 50
> transparency #9.1 0
> transparency #9.1 50
> open /Users/fadlof/.Trash/cryosparc_P175_J272_map_sharp(1).mrc
Opened cryosparc_P175_J272_map_sharp(1).mrc as #10, grid size 384,384,384,
pixel 0.851, shown at level 0.41, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J273_map_sharp.mrc
Opened cryosparc_P175_J273_map_sharp.mrc as #11, grid size 384,384,384, pixel
0.851, shown at level 0.0393, step 2, values float32
> hide #!9 models
> hide #!10 models
> volume #11 step 1
> volume #11 level 0.03
> close #10
> color zone #11 near #1 distance 5.11
> volume #11 level 0.02
> show #!9 models
> hide #!11 models
> volume #9 region 0,0,2,383,383,383
> volume #9 region 0,0,0,383,383,383
> transparency #9.1 50
> show #!11 models
> hide #!9 models
> transparency #11.1 50
> show #2.15 models
> select add #2.15
547 atoms, 570 bonds, 74 residues, 1 model selected
> combine sel
> rename #10 id #12
> rename #11 id #10
> rename #12 id #11
> hide #!10 models
> hide #!2 models
> select add #2
23235 atoms, 23692 bonds, 3017 residues, 17 models selected
> hide #11 models
> show #11 models
> select subtract #2
Nothing selected
> hide #!1 models
> show #!10 models
> volume zone #10 nearAtoms #11 range 5.11
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!10 models
> volume zone #9 nearAtoms #11 range 5.11
> volume #9 level 0.3365
> show #!10 models
> hide #11 models
> hide #!9 models
> show #11 models
> volume #10 level 0.01
> hide #!10 models
> hide #11 models
> show #11 models
> show #!9 models
> hide #!10 models
> volume #9 level 0.227
> volume #9 level 0.3292
> hide #!9 models
> show #!10 models
> hide #11 models
> hide #!10 models
> show #!10 models
> show #11 models
> hide #!10 models
> setattr #11/c res ss_type 0
Assigning ss_type attribute to 74 items
> hide #11 models
> show #!1 models
> setattr #1/c,d res ss_type 0
Assigning ss_type attribute to 139 items
> setattr #2/c,d res ss_type 0
Assigning ss_type attribute to 139 items
> hide #!1 models
> show #11 models
> close #11
> save /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v2/ChimeraX/ModelBuilding_20SCP-OG_PI31_v2.cxs includeMaps true
——— End of log from Wed Oct 11 16:38:26 2023 ———
opened ChimeraX session
> close #9
> close #10
> save /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v2/ChimeraX/ModelBuilding_20SCP-OG_PI31_v2.cxs includeMaps true
> open /Users/fadlof/Downloads/cryosparc_P175_J169_008_volume_map_sharp.mrc
Opened cryosparc_P175_J169_008_volume_map_sharp.mrc as #9, grid size
384,384,384, pixel 0.851, shown at level 0.6, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J206_009_volume_map_sharp.mrc
Opened cryosparc_P175_J206_009_volume_map_sharp.mrc as #10, grid size
384,384,384, pixel 0.851, shown at level 0.614, step 2, values float32
> view
> show #!3 models
> hide #!10 models
> hide #!3 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!3 models
> select add #9
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.41711,-0.011602,0.90878,-50.725,-0.68617,0.65167,0.32325,116.47,-0.59598,-0.75841,0.26386,341.14
> view matrix models
> #9,-0.83607,-0.42532,0.34652,313.19,-0.54508,0.57244,-0.61253,258.63,0.06216,-0.70101,-0.71044,382.74
> view matrix models
> #9,-0.92812,-0.36972,0.043539,368.45,-0.36897,0.92912,0.024369,67.919,-0.049463,0.0065524,-0.99875,332.26
> ui tool show "Fit in Map"
> fitmap #9 inMap #3
Fit map cryosparc_P175_J169_008_volume_map_sharp.mrc in map
cryosparc_P175_J266_map_sharp.mrc using 70704 points
correlation = 0.9739, correlation about mean = 0.9125, overlap = 1.276e+05
steps = 84, shift = 0.231, angle = 3.12 degrees
Position of cryosparc_P175_J169_008_volume_map_sharp.mrc (#9) relative to
cryosparc_P175_J266_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.92087024 -0.38986921 0.00001971 377.64213663
-0.38986921 0.92087024 -0.00005043 76.66589122
0.00000151 -0.00005413 -1.00000000 325.69051039
Axis -0.19889689 0.98002042 0.00002697
Axis point 196.60157960 0.00000000 162.84330546
Rotation angle (degrees) 179.99946789
Shift along axis 0.03107650
> select subtract #9
Nothing selected
> hide #!9 models
> show #!10 models
> fitmap #10 inMap #3
Fit map cryosparc_P175_J206_009_volume_map_sharp.mrc in map
cryosparc_P175_J266_map_sharp.mrc using 70657 points
correlation = 0.9762, correlation about mean = 0.9211, overlap = 1.357e+05
steps = 80, shift = 0.967, angle = 2.63 degrees
Position of cryosparc_P175_J206_009_volume_map_sharp.mrc (#10) relative to
cryosparc_P175_J266_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99894321 -0.04596149 0.00000003 7.68415482
0.04596149 0.99894321 0.00000030 -7.33878996
-0.00000004 -0.00000030 1.00000000 -0.96690830
Axis -0.00000647 0.00000073 1.00000000
Axis point 163.43026724 163.42892943 0.00000000
Rotation angle (degrees) 2.63432756
Shift along axis -0.96696334
> hide #!10 models
> show #!9 models
> hide #!3 models
> show #!1 models
> color zone #9 near #1 distance 5.11
> color zone #10 near #1 distance 5.11
[Repeated 1 time(s)]
> ui tool show "Side View"
> volume #10 step 1
> volume #9 step 1
> color zone #10 near #1 distance 5.11
> volume #10 level 0.7254
> volume #10 level 0.8
> save /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v2/ChimeraX/ModelBuilding_20SCP-OG_PI31_v2.cxs includeMaps true
——— End of log from Fri Oct 20 00:11:03 2023 ———
opened ChimeraX session
> view
> show #!9 models
> hide #!10 models
> show #!10 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> hide #!9 models
> volume #3 level 0.6
> volume #4 level 0.08
> close #9
> close #10
> open /Users/fadlof/Downloads/cryosparc_P175_J290_006_volume_map_sharp.mrc
Opened cryosparc_P175_J290_006_volume_map_sharp.mrc as #9, grid size
420,420,420, pixel 0.851, shown at level 0.537, step 2, values float32
> volume #9 step 1
> volume #9 level 0.6
> volume #9 level 0.65
> volume #9 level 0.8
> select add #9
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.89575,0.44278,0.039677,-67.523,-0.44304,0.8965,-0.0024463,98.127,-0.036653,-0.015387,0.99921,9.442
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.89575,0.44278,0.039677,-71.415,-0.44304,0.8965,-0.0024463,83.584,-0.036653,-0.015387,0.99921,-7.043
> view matrix models
> #9,0.89575,0.44278,0.039677,-80.499,-0.44304,0.8965,-0.0024463,85.582,-0.036653,-0.015387,0.99921,-7.3475
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.94807,0.30298,0.096789,-74.951,-0.31597,0.93202,0.17747,24.731,-0.036439,-0.19884,0.97935,28.914
> ui tool show "Fit in Map"
> fitmap #1 inMap #9
Fit molecule 20SCP-OG_PI31-8FZ6-coot-0.pdb (#1) to map
cryosparc_P175_J290_006_volume_map_sharp.mrc (#9) using 47639 atoms
average map value = 1.893, steps = 164
shifted from previous position = 6.39
rotated from previous position = 11.7 degrees
atoms outside contour = 6150, contour level = 0.8
Position of 20SCP-OG_PI31-8FZ6-coot-0.pdb (#1) relative to
cryosparc_P175_J290_006_volume_map_sharp.mrc (#9) coordinates:
Matrix rotation and translation
0.88993863 -0.45608029 -0.00005356 107.85185898
0.45608028 0.88993865 0.00002382 -41.22936491
0.00003681 -0.00004562 1.00000000 12.11406587
Axis -0.00007613 -0.00009907 0.99999999
Axis point 139.34852491 202.85001579 0.00000000
Rotation angle (degrees) 27.13446323
Shift along axis 12.10993961
> fitmap #1 inMap #9
Fit molecule 20SCP-OG_PI31-8FZ6-coot-0.pdb (#1) to map
cryosparc_P175_J290_006_volume_map_sharp.mrc (#9) using 47639 atoms
average map value = 1.893, steps = 28
shifted from previous position = 0.0058
rotated from previous position = 0.000475 degrees
atoms outside contour = 6147, contour level = 0.8
Position of 20SCP-OG_PI31-8FZ6-coot-0.pdb (#1) relative to
cryosparc_P175_J290_006_volume_map_sharp.mrc (#9) coordinates:
Matrix rotation and translation
0.88994170 -0.45607430 -0.00005508 107.85503793
0.45607430 0.88994172 0.00002844 -41.22587644
0.00003605 -0.00005042 1.00000000 12.11492988
Axis -0.00008646 -0.00009990 0.99999999
Axis point 139.34418785 202.86190572 0.00000000
Rotation angle (degrees) 27.13407796
Shift along axis 12.10972327
> hide #!4 models
> color zone #9 near #1 distance 5.11
> select subtract #9
Nothing selected
> save /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v2/ChimeraX/ModelBuilding_20SCP-OG_PI31_v2.cxs includeMaps true
> view
> ui tool show "Side View"
> color zone #9 near #1 distance 5.11
> volume #9 level 0.9
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> transparency #9.1 50
> volume #9 level 0.8485
> volume #9 level 0.5652
> volume #9 level 0.7455
> volume #9 level 0.8871
> volume #9 level 0.8614
> color zone #9 near #1 distance 5.11
> close #8
> close #1
> close #2
> close #3-7
> close
> open /Users/fadlof/Downloads/cryosparc_P175_J290_006_volume_map_sharp.mrc
Opened cryosparc_P175_J290_006_volume_map_sharp.mrc as #1, grid size
420,420,420, pixel 0.851, shown at level 0.537, step 2, values float32
> open /Users/fadlof/Downloads/cryosparc_P175_J290_006_volume_map.mrc
Opened cryosparc_P175_J290_006_volume_map.mrc as #2, grid size 420,420,420,
pixel 0.851, shown at level 0.318, step 2, values float32
> volume #1 step 1
> volume #2 step 1
> volume #1 level 0.7024
> volume #2 level 0.3576
> volume #1 level 0.7464
> volume #1 level 0.85
> volume #2 level 0.3895
> open /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP-
> OG_PI31_v2/PDBs/20SCP-OG_PI31-8FZ6-coot-0-2.pdb
20SCP-OG_PI31-8FZ6-coot-0-2.pdb title:
Alphafold monomer V2.0 prediction for proteasome inhibitor Π31 subunit
(Q92530) [more info...]
Chain information for 20SCP-OG_PI31-8FZ6-coot-0-2.pdb #3
---
Chain | Description | UniProt
A | proteasome inhibitor Π31 subunit |
B | No description available |
C | No description available |
D | No description available |
E | No description available |
F | No description available |
G | No description available |
H | No description available |
I | No description available |
J | No description available |
K | No description available |
L | No description available |
M | No description available |
N | No description available |
c | No description available |
d | No description available |
e | No description available | PSMF1_HUMAN
Non-standard residues in 20SCP-OG_PI31-8FZ6-coot-0-2.pdb #3
---
6V1 — (6V1)
> select add #3
24373 atoms, 24824 bonds, 10 pseudobonds, 3163 residues, 2 models selected
> view matrix models
> #3,0.58887,-0.55473,0.5878,83.553,0.80702,0.36378,-0.46518,30.034,0.044218,0.74829,0.66189,-86.445
> view matrix models
> #3,-0.84408,-0.50266,0.18672,374.62,-0.18092,-0.060843,-0.98161,339.58,0.50478,-0.86234,-0.039582,196.81
> view matrix models
> #3,-0.89703,0.061682,0.43765,256.09,-0.37907,0.4018,-0.83358,276.71,-0.22727,-0.91365,-0.33704,370.92
> hide sel atoms
> show sel cartoons
> style sel stick
Changed 24373 atom styles
> view matrix models
> #3,-0.56958,0.80478,-0.16708,157.44,0.0096741,-0.1967,-0.98042,329.15,-0.82188,-0.56004,0.10425,355.04
> view matrix models
> #3,-0.48382,-0.86133,0.155,376.62,-0.14184,-0.097594,-0.98507,339.37,0.8636,-0.49858,-0.074957,78.7
> view matrix models
> #3,0.90025,0.18226,0.39539,-67.783,0.40081,0.0076964,-0.91613,219.12,-0.17002,0.98322,-0.066123,8.8619
> view matrix models
> #3,-0.84761,0.49883,0.1809,209.39,0.059354,0.42791,-0.90187,206.06,-0.52729,-0.7537,-0.39231,403.4
> view matrix models
> #3,-0.22366,0.8523,0.47282,3.8045,0.025555,0.49007,-0.87131,197.42,-0.97433,-0.18279,-0.13139,350.23
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.22366,0.8523,0.47282,14.276,0.025555,0.49007,-0.87131,245,-0.97433,-0.18279,-0.13139,385.18
> view matrix models
> #3,-0.22366,0.8523,0.47282,17.682,0.025555,0.49007,-0.87131,247.08,-0.97433,-0.18279,-0.13139,390.06
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.35441,0.81588,0.45687,-73.652,0.23321,0.39602,-0.88813,229.23,-0.90554,0.42131,-0.04992,266.7
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.35441,0.81588,0.45687,-85.772,0.23321,0.39602,-0.88813,228.03,-0.90554,0.42131,-0.04992,252.32
> view matrix models
> #3,0.35441,0.81588,0.45687,-84.707,0.23321,0.39602,-0.88813,224.18,-0.90554,0.42131,-0.04992,251.66
> fitmap #3 inMap #2
Fit molecule 20SCP-OG_PI31-8FZ6-coot-0-2.pdb (#3) to map
cryosparc_P175_J290_006_volume_map.mrc (#2) using 24373 atoms
average map value = 0.7672, steps = 136
shifted from previous position = 9.12
rotated from previous position = 14.5 degrees
atoms outside contour = 2419, contour level = 0.38948
Position of 20SCP-OG_PI31-8FZ6-coot-0-2.pdb (#3) relative to
cryosparc_P175_J290_006_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.13592894 0.89185442 0.43141512 -61.59789813
0.13735763 0.41428607 -0.89972214 242.02089701
-0.98115045 0.18155644 -0.06618955 313.71377313
Axis 0.55958208 0.73102936 -0.39046634
Axis point 45.45720711 0.00000000 259.71682945
Rotation angle (degrees) 104.95066750
Shift along axis 19.96063354
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5rc202211182308 (2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.2.44
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2,7 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1916.40.8.0.0 (iBridge: 20.16.420.0.0,0)
OS Loader Version: 564.40.4~27
Software:
System Software Overview:
System Version: macOS 13.0.1 (22A400)
Kernel Version: Darwin 22.1.0
Time since boot: 1 Tag und 6 Minuten
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2718Q:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 30.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: FN84K91L0H2L
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 7,55
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
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: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
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: 2.7.1
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: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5rc202211182308
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
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: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 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: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
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: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
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: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
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
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.3
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: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.0.0
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: 5.0.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
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: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.32
psutil: 5.9.1
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: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
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: 1.9.0
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: 0.6.1
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.12
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.10.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 2 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 655 |
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Apple Intel graphics driver crash.