![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#16090 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8rc202405202242 (2024-05-20 22:42:21 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 450000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 32210,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-10-08 16:02:10.2102 +0900",
"codeSigningMonitor" : 1,
"incident" : "C30B377B-1E78-457D-BBA4-6CF1EAE80BDD",
"pid" : 97091,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-07 13:44:28.7040 +0900",
"procStartAbsTime" : 9889321190010,
"procExitAbsTime" : 11039797958629,
"procName" : "ChimeraX",
"procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.8-rc2024.05.20.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"B8EB5343-7017-597D-884C-4F59714DA940","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FCE20E77-29CC-CC3D-AA3B-D6B973E28639",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"IAAg1AAAINQAAEDUIAAg1AAAINQAAEDUIAAg1AAAINQAAEDUIAAg1A==","atPC":"AAAg1AAAQNQgACDUAAAg1AAAQNQgACDUAAAg1AAAQNQgACDUAAAg1A=="},
"wakeTime" : 1357,
"sleepWakeUUID" : "ECF0F10D-64A6-49FD-8690-5CC16B66D311",
"sip" : "enabled",
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"termination" : {"flags":0,"code":5,"namespace":"SIGNAL","indicator":"Trace\/BPT trap: 5","byProc":"exc handler","byPid":97091},
"os_fault" : {"process":"ChimeraX"},
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{
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{
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"path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.8-rc2024.05.20.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bisect.cpython-311-darwin.so",
"name" : "_bisect.cpython-311-darwin.so"
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{
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"path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.8-rc2024.05.20.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_lzma.cpython-311-darwin.so",
"name" : "_lzma.cpython-311-darwin.so"
},
{
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"path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.8-rc2024.05.20.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bz2.cpython-311-darwin.so",
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},
{
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"path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.8-rc2024.05.20.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
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},
{
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"path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.8-rc2024.05.20.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_typing.cpython-311-darwin.so",
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},
{
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{
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=3.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 1952K 52 \nColorSync 656K 31 \nCoreAnimation 3888K 149 \nCoreGraphics 48K 3 \nCoreUI image data 5360K 38 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.5G 99 \nMALLOC guard page 192K 12 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 39 \nStack 155.4M 39 \nVM_ALLOCATE 260.2M 325 \nVM_ALLOCATE (reserved) 160.0M 1 reserved VM address space (unallocated)\n__AUTH 2199K 405 \n__AUTH_CONST 31.8M 624 \n__CTF 824 1 \n__DATA 21.9M 771 \n__DATA_CONST 42.4M 781 \n__DATA_DIRTY 2024K 232 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 554.4M 152 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2200K 1 \n__TEXT 937.3M 798 \ndyld private memory 592K 6 \nmapped file 595.8M 117 \nshared memory 3184K 25 \n=========== ======= ======= \nTOTAL 5.3G 4718 \nTOTAL, minus reserved VM space 5.2G 4718 \n",
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}
===== Log before crash start =====
Startup Messages
---
notes | available bundle cache has not been initialized yet
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'
UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/rnom/Desktop/hAC9-Gs_TM_trimmed_real_space_refined_026.pdb
> format pdb
No such file/path:
/Users/rnom/Desktop/hAC9-Gs_TM_trimmed_real_space_refined_026.pdb
> open /Users/rnom/Desktop/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb
> format pdb
No such file/path:
/Users/rnom/Desktop/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb
> open /Users/rnom/Desktop/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb
> format pdb
No such file/path:
/Users/rnom/Desktop/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb
> open "/Users/rnom/Desktop/論文化/for
> figure/hAC9-Gs_TM_trimmed_real_space_refined_026.pdb"
Chain information for hAC9-Gs_TM_trimmed_real_space_refined_026.pdb #1
---
Chain | Description
A | No description available
> set bgColor white
> set bgColor #ffffff00
> open "/Users/rnom/Desktop/論文化/for
> figure/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb"
Chain information for hAC9-Gs_SD_trimmed_real_space_refined_025.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide #!1 models
> color #2 #43ecb5ff
> color #2 #ec73c5ff
> color #2 #ec5987ff
> undo
> hide #!2 models
> show #!2 models
> close #2
> close #
Expected a models specifier or a keyword
> open "/Users/rnom/Desktop/論文化/for
> figure/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb"
Chain information for hAC9-Gs_SD_trimmed_real_space_refined_025.pdb #2
---
Chain | Description
A | No description available
B | No description available
> open "/Users/rnom/Desktop/hAC/AC9 Hiroaki/pdb6r3q.ent"
pdb6r3q.ent title:
The structure of A membrane adenylyl cyclase bound to an activated stimulatory
G protein [more info...]
Chain information for pdb6r3q.ent #3
---
Chain | Description | UniProt
A | adenylyl cyclase family member (ACY-1)-LIKE | E1BM79_BOVIN 1-1354
B | adenylate cyclase-stimulating G α protein | GNAS2_BOVIN 1-394
Non-standard residues in pdb6r3q.ent #3
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
MG — magnesium ion
> matchmaker #2 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pdb6r3q.ent, chain A (#3) with
hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence
alignment score = 1735.5
RMSD between 434 pruned atom pairs is 0.796 angstroms; (across all 443 pairs:
1.867)
> show #!2-3 atoms
> hide #!2-3 atoms
> undo
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> color #1 #4ad7aeff
> color #1 #1acdd7ff
> color #1 #00d7ccff
> color #1 #00d2d7ff
> matchmaker #1 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pdb6r3q.ent, chain A (#3) with
hAC9-Gs_TM_trimmed_real_space_refined_026.pdb, chain A (#1), sequence
alignment score = 1704.3
RMSD between 368 pruned atom pairs is 0.756 angstroms; (across all 418 pairs:
1.411)
> color #!1,3 bychain
> undo
> graphics silhouettes true
> show #!2 models
> hide #!1 models
> ui tool show "Side View"
> view orient
> view
> close session
> set bgColor white
> open "/Users/rnom/Desktop/論文化/for figure/SD_apo-coot-1.pdb"
> "/Users/rnom/Desktop/論文化/for
> figure/AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb"
Chain information for SD_apo-coot-1.pdb #1
---
Chain | Description
A | No description available
Chain information for
AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb #2
---
Chain | Description
A | No description available
> close session
> open "/Users/rnom/Desktop/論文化/for
> figure/AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb"
Chain information for
AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb #1
---
Chain | Description
A | No description available
> open "/Users/rnom/Desktop/論文化/for figure/pdb6r3q.ent"
pdb6r3q.ent title:
The structure of A membrane adenylyl cyclase bound to an activated stimulatory
G protein [more info...]
Chain information for pdb6r3q.ent #2
---
Chain | Description | UniProt
A | adenylyl cyclase family member (ACY-1)-LIKE | E1BM79_BOVIN 1-1354
B | adenylate cyclase-stimulating G α protein | GNAS2_BOVIN 1-394
Non-standard residues in pdb6r3q.ent #2
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
MG — magnesium ion
> open "/Users/rnom/Desktop/論文化/for figure/SD_apo-coot-1.pdb"
Chain information for SD_apo-coot-1.pdb #3
---
Chain | Description
A | No description available
> hide #!2 models
> hide #!3 models
> dssp #1
> close #2-3
> open "/Users/rnom/Desktop/論文化/for figure/SD_apo-coot-1.pdb"
Chain information for SD_apo-coot-1.pdb #2
---
Chain | Description
A | No description available
> open "/Users/rnom/Desktop/論文化/for figure/pdb6r3q.ent"
pdb6r3q.ent title:
The structure of A membrane adenylyl cyclase bound to an activated stimulatory
G protein [more info...]
Chain information for pdb6r3q.ent #3
---
Chain | Description | UniProt
A | adenylyl cyclase family member (ACY-1)-LIKE | E1BM79_BOVIN 1-1354
B | adenylate cyclase-stimulating G α protein | GNAS2_BOVIN 1-394
Non-standard residues in pdb6r3q.ent #3
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
MG — magnesium ion
> hide #!2 models
> color #1 #20d7d1ff
> matchmaker #1 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pdb6r3q.ent, chain A (#3) with
AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb, chain A
(#1), sequence alignment score = 1600.8
RMSD between 360 pruned atom pairs is 0.770 angstroms; (across all 405 pairs:
1.583)
> close #3
> open "/Users/rnom/Desktop/論文化/for
> figure/hAC9-Gs_TM_trimmed_real_space_refined_026.pdb"
Chain information for hAC9-Gs_TM_trimmed_real_space_refined_026.pdb #3
---
Chain | Description
A | No description available
> close session
> open "/Users/rnom/Desktop/論文化/for
> figure/hAC9-Gs_TM_trimmed_real_space_refined_026.pdb"
Chain information for hAC9-Gs_TM_trimmed_real_space_refined_026.pdb #1
---
Chain | Description
A | No description available
> open "/Users/rnom/Desktop/論文化/for
> figure/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb"
Chain information for hAC9-Gs_SD_trimmed_real_space_refined_025.pdb #2
---
Chain | Description
A | No description available
B | No description available
> color #1 #32d7b9ff
> color #1 #3dd0d7ff
> color #1 #15d7d2ff
> open "/Users/rnom/Desktop/論文化/for figure/pdb6r3q.ent"
pdb6r3q.ent title:
The structure of A membrane adenylyl cyclase bound to an activated stimulatory
G protein [more info...]
Chain information for pdb6r3q.ent #3
---
Chain | Description | UniProt
A | adenylyl cyclase family member (ACY-1)-LIKE | E1BM79_BOVIN 1-1354
B | adenylate cyclase-stimulating G α protein | GNAS2_BOVIN 1-394
Non-standard residues in pdb6r3q.ent #3
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
MG — magnesium ion
> matchmaker #1 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pdb6r3q.ent, chain A (#3) with
hAC9-Gs_TM_trimmed_real_space_refined_026.pdb, chain A (#1), sequence
alignment score = 1704.3
RMSD between 368 pruned atom pairs is 0.756 angstroms; (across all 418 pairs:
1.411)
> matchmaker #2 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pdb6r3q.ent, chain A (#3) with
hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence
alignment score = 1735.5
RMSD between 434 pruned atom pairs is 0.796 angstroms; (across all 443 pairs:
1.867)
> save "/Users/rnom/Desktop/論文化/for figure/chimera hAC9Gs bAC9.pdb"
> open "/Users/rnom/Desktop/論文化/for
> figure/AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb"
Chain information for
AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb #4
---
Chain | Description
A | No description available
> open "/Users/rnom/Desktop/論文化/for figure/SD_apo-coot-1.pdb"
Chain information for SD_apo-coot-1.pdb #5
---
Chain | Description
A | No description available
> dssp #4
> color #5 #23ef16ff
> color #5 #a0efa3ff
> color #4 #18ec0dff
> hide #!2 models
> hide #!1 models
> matchmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pdb6r3q.ent, chain A (#3) with
AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb, chain A
(#4), sequence alignment score = 1600.8
RMSD between 360 pruned atom pairs is 0.770 angstroms; (across all 405 pairs:
1.583)
> matchmaker #5 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pdb6r3q.ent, chain A (#3) with SD_apo-coot-1.pdb, chain A (#5),
sequence alignment score = 1551
RMSD between 351 pruned atom pairs is 1.053 angstroms; (across all 421 pairs:
2.696)
> hide #!3 models
> show #!2 models
> show #!1 models
> save "/Users/rnom/Desktop/論文化/for figure/hAC9Gs to hAC9 apo.pdb"
> matchmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with
SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> hide #!1 models
> hide #!2 models
> show #!2 models
> select #5/A:328
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:331
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
131 atoms, 131 bonds, 16 residues, 1 model selected
> matchmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with
SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> matchmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with
SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> hide #!4 models
> matchmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with
SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> matchmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with
SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.034141,0.43193,0.90126,-38.552,-0.97755,0.17318,-0.12003,241.88,-0.20792,-0.88512,0.41632,198.43
> matchmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with
SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> view matrix models
> #5,-0.037769,0.44792,0.89328,-39.356,-0.9722,0.19027,-0.13651,240.45,-0.23111,-0.8736,0.42828,199.11
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> view matrix models
> #5,-0.01856,0.43326,0.90108,-40.644,-0.97179,0.20413,-0.11817,237.43,-0.23514,-0.87785,0.41725,200.92
> view matrix models
> #5,0.018383,0.51801,0.85518,-51.68,-0.69803,0.61902,-0.35996,173.04,-0.71583,-0.59032,0.37296,231.14
> matchmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with
SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> view matrix models
> #5,0.0005245,0.38052,0.92477,-38.686,-0.97777,0.19412,-0.07932,236.46,-0.2097,-0.90417,0.37216,204.12
> view matrix models
> #5,-0.030638,0.43233,0.90119,-39.032,-0.97431,0.18832,-0.12347,239.97,-0.2231,-0.88183,0.41546,200.01
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right rotate
> select #2/B:129
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
80 atoms, 81 bonds, 9 residues, 1 model selected
> select up
2518 atoms, 2574 bonds, 305 residues, 1 model selected
> hide sel cartoons
> select #2/B:199@CG
1 atom, 1 residue, 1 model selected
> select #2/B:199@CG
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 1 atoms
Drag select of 147 atoms, 32 residues, 137 bonds
> select #2/B:296@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
76 atoms, 75 bonds, 10 residues, 1 model selected
> select up
2518 atoms, 2574 bonds, 305 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 5 atoms, 1 residues, 8 bonds
> select clear
Drag select of 39 atoms, 14 residues, 35 bonds
Drag select of 4 atoms, 5 bonds
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> view sel
No displayed objects specified.
> view sel
No displayed objects specified.
> select #2/A:1228
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
64 atoms, 64 bonds, 8 residues, 1 model selected
> select up
1858 atoms, 1897 bonds, 231 residues, 1 model selected
> select #5/A:1227
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:1228
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #5/A:1227
4 atoms, 3 bonds, 1 residue, 1 model selected
Drag select of 6 residues
> select up
85 atoms, 85 bonds, 12 residues, 1 model selected
> select up
227 atoms, 229 bonds, 29 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 1 atoms
> hide sel cartoons
> hide sel atoms
Drag select of 6 residues
> select up
69 atoms, 55 bonds, 9 residues, 2 models selected
> select up
2668 atoms, 2706 bonds, 344 residues, 2 models selected
> hide sel cartoons
Drag select of 24 residues
> select up
249 atoms, 249 bonds, 31 residues, 2 models selected
> select up
342 atoms, 342 bonds, 42 residues, 2 models selected
> select down
249 atoms, 249 bonds, 31 residues, 2 models selected
> hide sel cartoons
> open "/Users/rnom/Desktop/240617
> 解析関連/cryosparc_P78_J52_007_volume_map_sharp.mrc"
Opened cryosparc_P78_J52_007_volume_map_sharp.mrc as #6, grid size
320,320,320, pixel 0.79, shown at level 0.0733, step 2, values float32
> hide #!2 models
> hide #!6 models
> show #!6 models
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = -0.001662, steps = 96
shifted from previous position = 2.58
rotated from previous position = 5.11 degrees
atoms outside contour = 3488, contour level = 0.073323
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.03600526 0.45927056 0.88756643 -47.55149952
-0.96150180 0.25803345 -0.09451466 229.92837055
-0.27242963 -0.84999370 0.45088004 199.48128659
Axis -0.38084979 0.58477367 -0.71623543
Axis point 60.90157452 223.33171648 0.00000000
Rotation angle (degrees) 97.32749762
Shift along axis 9.69047128
Drag select of 6 cryosparc_P78_J52_007_volume_map_sharp.mrc
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.93048,0.25148,-0.2664,6.1275,-0.27723,0.95872,-0.063269,47.421,0.23949,0.13272,0.96178,-43.103
> view matrix models
> #6,0.45018,0.85133,0.26939,-73.984,-0.48171,0.48556,-0.72951,211.62,-0.75186,0.19865,0.62868,110.61
> view matrix models
> #6,0.41223,0.54124,0.73289,-81.503,-0.2083,0.8391,-0.50252,104.83,-0.88695,0.054493,0.45864,165.98
> color #6 #b2b2b2af models
> color #6 #b2b2b22d models
> color #6 #acacac2d models
> color #6 #acacac2e models
> view matrix models
> #6,0.2871,0.63523,0.71698,-76.369,-0.5901,0.70689,-0.38999,157.19,-0.75455,-0.31112,0.5778,183.86
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.07513, steps = 240
shifted from previous position = 9.46
rotated from previous position = 34.2 degrees
atoms outside contour = 2065, contour level = 0.073323
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.98878045 0.14669790 -0.02815925 -14.93133511
-0.14492117 0.98778755 0.05721541 12.59098993
0.03620874 -0.05249260 0.99796465 -2.48024412
Axis -0.34482880 -0.20231829 -0.91660264
Axis point 85.52431162 96.86518788 0.00000000
Rotation angle (degrees) 9.15327141
Shift along axis 4.87476506
> view matrix models
> #6,0.078253,0.58406,0.80793,-53.878,-0.64902,0.64501,-0.40341,174.25,-0.75674,-0.49279,0.42954,225.02
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.0777, steps = 96
shifted from previous position = 6.95
rotated from previous position = 6.42 degrees
atoms outside contour = 2034, contour level = 0.073323
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.99772083 0.01841915 -0.06491441 4.18488356
-0.02420010 0.99569947 -0.08942545 11.91254364
0.06298810 0.09079257 0.99387585 -22.80120914
Axis 0.80073976 -0.56829293 -0.18936467
Axis point 0.00000000 257.79482173 126.52714719
Rotation angle (degrees) 6.46130668
Shift along axis 0.89893181
> view matrix models
> #6,0.046323,0.60142,0.79759,-50.977,-0.65046,0.62414,-0.43285,180.55,-0.75813,-0.49875,0.42011,227.06
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.0777, steps = 68
shifted from previous position = 1.89
rotated from previous position = 2.18 degrees
atoms outside contour = 2034, contour level = 0.073323
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.99772940 0.01835985 -0.06479944 4.18259708
-0.02415752 0.99566196 -0.08985357 11.94320014
0.06286864 0.09121494 0.99384474 -22.83666976
Axis 0.80262984 -0.56591956 -0.18846853
Axis point 0.00000000 257.01253906 126.19234231
Rotation angle (degrees) 6.47657686
Shift along axis 0.90218026
> view matrix models
> #6,-0.10361,0.63925,0.76198,-33.088,-0.57517,0.58651,-0.57025,191.8,-0.81145,-0.49735,0.30691,246.52
> view matrix models
> #6,0.00059231,0.62064,0.78409,-46.23,-0.78696,0.48408,-0.38258,210.33,-0.61701,-0.61682,0.48871,217.05
> view matrix models
> #6,-0.38948,0.43995,0.80917,23.562,-0.92101,-0.19261,-0.33859,311.15,0.00689,-0.87713,0.48021,174.1
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.1415, steps = 256
shifted from previous position = 10.7
rotated from previous position = 53.6 degrees
atoms outside contour = 1033, contour level = 0.073323
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.99999125 0.00227039 0.00351385 -0.40477670
-0.00227859 0.99999469 0.00232871 0.11727871
-0.00350854 -0.00233670 0.99999111 0.74862997
Axis -0.48700357 0.73303847 -0.47484958
Axis point 203.25802129 0.00000000 125.73379773
Rotation angle (degrees) 0.27444303
Shift along axis -0.07238913
> show #!2 models
> matchmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with
SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> undo
> view matrix models
> #6,0.28316,0.63549,0.71831,-76.062,-0.58937,0.70616,-0.39241,157.47,-0.75661,-0.31224,0.5745,184.64
> view matrix models
> #6,0.082155,0.30908,0.94748,-34.162,-0.48044,0.84521,-0.23406,107.39,-0.87317,-0.43598,0.21794,256.37
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.05886, steps = 132
shifted from previous position = 4.85
rotated from previous position = 6.48 degrees
atoms outside contour = 2338, contour level = 0.073323
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.62396070 0.75885718 -0.18657124 -22.89073700
-0.74126437 0.65033448 0.16610897 125.99194015
0.24738669 0.03465314 0.96829695 -41.79708916
Axis -0.08388200 -0.27690868 -0.95722797
Axis point 128.66236222 93.14297026 0.00000000
Rotation angle (degrees) 51.58915812
Shift along axis 7.04120229
> view matrix models
> #6,0.016458,0.4504,0.89267,-38.25,-0.040171,0.89237,-0.44951,70.679,-0.99906,-0.028461,0.03278,239.72
> view matrix models
> #6,0.10908,0.50046,0.85886,-52.572,-0.063432,0.86576,-0.49642,82.468,-0.99201,-0.00032921,0.12618,224.44
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.10908,0.50046,0.85886,-61.111,-0.063432,0.86576,-0.49642,83.85,-0.99201,-0.00032921,0.12618,225.11
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.05192, steps = 64
shifted from previous position = 3.11
rotated from previous position = 3.75 degrees
atoms outside contour = 2448, contour level = 0.073323
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.28788878 0.93592299 -0.20289948 -0.89561999
-0.79229189 0.35178264 0.49852033 132.41035783
0.53795316 0.01723720 0.84279848 -55.58520203
Axis -0.24796477 -0.38169914 -0.89040398
Axis point 102.16520782 78.90961022 0.00000000
Rotation angle (degrees) 76.04056030
Shift along axis -0.82555257
> view matrix models
> #6,0.10908,0.50046,0.85886,-67.052,-0.063432,0.86576,-0.49642,86.515,-0.99201,-0.00032921,0.12618,222.62
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.05319, steps = 100
shifted from previous position = 3.72
rotated from previous position = 8.8 degrees
atoms outside contour = 2399, contour level = 0.073323
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.42604160 0.88779422 -0.17409761 -18.66873133
-0.76978287 0.45683169 0.44580168 120.71375853
0.47531346 -0.05591270 0.87803808 -37.53274104
Axis -0.27125586 -0.35110925 -0.89618221
Axis point 95.80100050 84.08897101 0.00000000
Rotation angle (degrees) 67.63808831
Shift along axis -3.68354021
> view matrix models
> #6,0.10908,0.50046,0.85886,-65.246,-0.063432,0.86576,-0.49642,83.733,-0.99201,-0.00032921,0.12618,226.79
> view matrix models
> #6,0.10908,0.50046,0.85886,-65.453,-0.063432,0.86576,-0.49642,84.767,-0.99201,-0.00032921,0.12618,225.08
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.1415, steps = 296
shifted from previous position = 8.21
rotated from previous position = 67.6 degrees
atoms outside contour = 1032, contour level = 0.073323
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.99999107 0.00228442 0.00355335 -0.40872594
-0.00229289 0.99999454 0.00237990 0.11395914
-0.00354789 -0.00238802 0.99999085 0.76072823
Axis -0.49147968 0.73199928 -0.47183131
Axis point 204.16680335 0.00000000 125.86171639
Rotation angle (degrees) 0.27791855
Shift along axis -0.07463689
> view matrix models
> #6,0.10908,0.50046,0.85886,-60.387,-0.063432,0.86576,-0.49642,82.945,-0.99201,-0.00032921,0.12618,226.42
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.07771, steps = 168
shifted from previous position = 3.38
rotated from previous position = 6.67 degrees
atoms outside contour = 2031, contour level = 0.073323
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.99772712 0.01834223 -0.06483939 4.18748969
-0.02413117 0.99568029 -0.08965731 11.92606966
0.06291478 0.09101818 0.99385986 -22.83065082
Axis 0.80186453 -0.56699190 -0.18850322
Axis point 0.00000000 257.49363072 126.30050427
Rotation angle (degrees) 6.46865321
Shift along axis 0.89946561
> undo
> show #!2 models
> matchmaker #2 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SD_apo-coot-1.pdb, chain A (#5) with
hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence
alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> hide #!2 models
> view matrix models
> #6,0.10908,0.50046,0.85886,-65.456,-0.063432,0.86576,-0.49642,84.744,-0.99201,-0.00032921,0.12618,225.05
> show #!2 models
> view matrix models
> #6,0.10908,0.50046,0.85886,-76.713,-0.063432,0.86576,-0.49642,73.417,-0.99201,-0.00032921,0.12618,212.87
> undo
> hide #!2 models
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.1415, steps = 72
shifted from previous position = 3.4
rotated from previous position = 6.67 degrees
atoms outside contour = 1032, contour level = 0.073323
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.99999093 0.00230189 0.00358227 -0.41272768
-0.00231046 0.99999447 0.00239007 0.11282165
-0.00357675 -0.00239832 0.99999072 0.76598986
Axis -0.49010819 0.73275135 -0.47209047
Axis point 203.71185785 0.00000000 126.21838261
Rotation angle (degrees) 0.27989268
Shift along axis -0.07666508
> show #!2 models
> matchmaker #2 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SD_apo-coot-1.pdb, chain A (#5) with
hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence
alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> matchmaker #2 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SD_apo-coot-1.pdb, chain A (#5) with
hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence
alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> open /Users/rnom/Desktop/pdb6r3q.ent
pdb6r3q.ent title:
The structure of A membrane adenylyl cyclase bound to an activated stimulatory
G protein [more info...]
Chain information for pdb6r3q.ent #7
---
Chain | Description | UniProt
A | adenylyl cyclase family member (ACY-1)-LIKE | E1BM79_BOVIN 1-1354
B | adenylate cyclase-stimulating G α protein | GNAS2_BOVIN 1-394
Non-standard residues in pdb6r3q.ent #7
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
MG — magnesium ion
> open /Users/rnom/Desktop/pdb6r3q.ent
pdb6r3q.ent title:
The structure of A membrane adenylyl cyclase bound to an activated stimulatory
G protein [more info...]
Chain information for pdb6r3q.ent #8
---
Chain | Description | UniProt
A | adenylyl cyclase family member (ACY-1)-LIKE | E1BM79_BOVIN 1-1354
B | adenylate cyclase-stimulating G α protein | GNAS2_BOVIN 1-394
Non-standard residues in pdb6r3q.ent #8
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
MG — magnesium ion
> open /Users/rnom/Downloads/pdb7pdd.ent
pdb7pdd.ent title:
Focus refinement of soluble domain of adenylyl cyclase 9 In complex with
darpin C4 and mant-GTP [more info...]
Chain information for pdb7pdd.ent #9
---
Chain | Description | UniProt
A | adenylate cyclase 9 | E1BM79_BOVIN 1-1354
B | darpin C4 |
> hide #!7 models
> show #!7 models
> hide #!7 models
> close #7-9
> open "/Users/rnom/Desktop/bAC9 model,map/7pd4.pdb"
7pd4.pdb title:
Structure of adenylyl cyclase 9 In complex with mant-GTP [more info...]
Chain information for 7pd4.pdb #7
---
Chain | Description | UniProt
A | adenylate cyclase 9 | E1BM79_BOVIN 1-1354
> close #7
> close #6
> open "/Users/rnom/Desktop/論文化/for figure/hAC9 model,
> map/AC9_SD/cryosparc_P78_J60_005_volume_map_sharp.mrc"
Opened cryosparc_P78_J60_005_volume_map_sharp.mrc as #6, grid size
320,320,320, pixel 0.79, shown at level 0.0635, step 2, values float32
Drag select of 6 cryosparc_P78_J60_005_volume_map_sharp.mrc
> view matrix models #6,1,0,0,-74.685,0,1,0,-17.294,0,0,1,38.859
> view matrix models #6,1,0,0,-39.269,0,1,0,-8.0412,0,0,1,50.854
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.35591,-0.12873,0.92561,-43.424,-0.19238,0.95916,0.20736,-1.3276,-0.91451,-0.25187,0.31661,274.91
> view matrix models
> #6,0.48889,-0.012202,0.87226,-69.56,-0.66365,0.64376,0.38097,80.254,-0.56617,-0.76513,0.30663,299.11
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.48889,-0.012202,0.87226,-43.821,-0.66365,0.64376,0.38097,87.914,-0.56617,-0.76513,0.30663,246.02
> hide #!2 models
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.0576, steps = 428
shifted from previous position = 28.2
rotated from previous position = 39.2 degrees
atoms outside contour = 2267, contour level = 0.063498
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.06418813 -0.63318352 0.77133554 125.15384509
0.98007258 0.18559561 0.07079547 -29.17775390
-0.18798302 0.75142059 0.63247884 -40.82598727
Axis 0.34090378 0.48049258 0.80802939
Axis point 86.99326752 71.42481315 0.00000000
Rotation angle (degrees) 93.37487970
Shift along axis -4.34287326
> color #6 #b2b2b242 models
> color #6 #b2b2b256 models
> color #6 #b2b2b257 models
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.0576, steps = 40
shifted from previous position = 0.00397
rotated from previous position = 0.00954 degrees
atoms outside contour = 2268, contour level = 0.063498
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.06409108 -0.63308705 0.77142279 125.14551701
0.98007015 0.18557860 0.07087379 -29.18300725
-0.18802884 0.75150607 0.63236365 -40.82295833
Axis 0.34090967 0.48056249 0.80798533
Axis point 86.99033611 71.41488258 0.00000000
Rotation angle (degrees) 93.38145894
Shift along axis -4.34529269
> view matrix models
> #6,0.48889,-0.012202,0.87226,-51.712,-0.66365,0.64376,0.38097,85.631,-0.56617,-0.76513,0.30663,234.53
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.35647,-0.18819,0.91516,-16.718,-0.70197,0.59246,0.39526,95.599,-0.61657,-0.78331,0.079095,268.44
> view matrix models
> #6,0.66049,-0.18784,0.72696,-34.362,-0.7226,0.10399,0.6834,130.2,-0.20397,-0.97668,-0.067049,257.75
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.66049,-0.18784,0.72696,-40.357,-0.7226,0.10399,0.6834,129.13,-0.20397,-0.97668,-0.067049,251.05
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.05396, steps = 184
shifted from previous position = 9.99
rotated from previous position = 20.5 degrees
atoms outside contour = 2262, contour level = 0.063498
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.56092550 -0.53166240 0.63458465 201.89721759
0.77848791 -0.59951514 0.18584449 70.92659522
0.28163658 0.59826139 0.75017608 -86.01878073
Axis 0.29081299 0.24887895 0.92384364
Axis point 98.35061172 92.69261318 0.00000000
Rotation angle (degrees) 134.84023198
Shift along axis -3.10143294
> view matrix models
> #6,0.66049,-0.18784,0.72696,-40.006,-0.7226,0.10399,0.6834,128.66,-0.20397,-0.97668,-0.067049,259.81
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.07375, steps = 232
shifted from previous position = 6.85
rotated from previous position = 17.9 degrees
atoms outside contour = 1943, contour level = 0.063498
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.74629259 -0.54301442 0.38494508 251.38648943
0.65642579 -0.69620280 0.29052858 97.88167330
0.11023863 0.46950720 0.87601966 -57.75740346
Axis 0.14393778 0.22092380 0.96461111
Axis point 112.39700349 100.93081789 0.00000000
Rotation angle (degrees) 141.55799490
Shift along axis 2.09497277
> view matrix models
> #6,0.66049,-0.18784,0.72696,-38.776,-0.7226,0.10399,0.6834,129.55,-0.20397,-0.97668,-0.067049,250.64
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.07513, steps = 88
shifted from previous position = 2.87
rotated from previous position = 9.69 degrees
atoms outside contour = 1985, contour level = 0.063498
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.76523589 -0.60093746 0.23084237 269.35421235
0.64371868 -0.71784510 0.26518800 97.23918505
0.00634766 0.35152892 0.93615551 -35.85225341
Axis 0.06810921 0.17709050 0.98183506
Axis point 118.23408164 100.87294714 0.00000000
Rotation angle (degrees) 140.66586681
Shift along axis 0.36463841
> view matrix models
> #6,0.66049,-0.18784,0.72696,-40.452,-0.7226,0.10399,0.6834,127.55,-0.20397,-0.97668,-0.067049,252.82
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.07115, steps = 124
shifted from previous position = 1.89
rotated from previous position = 5.79 degrees
atoms outside contour = 2038, contour level = 0.063498
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.70690984 -0.64672681 0.28639645 264.38204486
0.70462141 -0.67914550 0.20559683 92.23937195
0.06153988 0.34713949 0.93579219 -37.95810671
Axis 0.10277413 0.16326837 0.98121400
Axis point 115.58274225 102.94958249 0.00000000
Rotation angle (degrees) 136.47979439
Shift along axis 4.98638149
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.65374,-0.23032,0.72082,-33.367,-0.66445,0.28113,0.69244,96.043,-0.36212,-0.93162,0.030747,256.1
> view matrix models
> #6,-0.091081,-0.58969,0.80248,98.695,0.19546,0.77957,0.59504,-67.002,-0.97647,0.21105,0.044259,182.84
> view matrix models
> #6,-0.089335,-0.62056,0.77906,105.1,0.37864,0.7023,0.60283,-80.908,-0.92122,0.34884,0.17223,143.7
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.04426, steps = 196
shifted from previous position = 13
rotated from previous position = 6.14 degrees
atoms outside contour = 2570, contour level = 0.063498
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.75444757 -0.45385825 0.47415352 36.22522290
0.63281065 0.69473638 -0.34189478 -8.73132935
-0.17423994 0.55799108 0.81134851 -20.04509765
Axis 0.57954025 0.41757530 0.69983138
Axis point 41.59126644 53.07478525 0.00000000
Rotation angle (degrees) 50.93023294
Shift along axis 3.31979897
> view matrix models
> #6,-0.13448,-0.56943,0.81097,100.59,0.3635,0.733,0.57496,-79.925,-0.92184,0.37211,0.10841,147.79
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.05375, steps = 124
shifted from previous position = 4.4
rotated from previous position = 9.21 degrees
atoms outside contour = 2359, contour level = 0.063498
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.68545093 -0.56994047 0.45312789 64.51164247
0.72041859 0.62113553 -0.30852507 -16.92140215
-0.10561291 0.53792055 0.83635363 -30.44505651
Axis 0.51573359 0.34043699 0.78620704
Axis point 64.33106263 74.45184289 0.00000000
Rotation angle (degrees) 55.14719991
Shift along axis 3.57403211
> view matrix models
> #6,-0.72884,-0.4357,0.52816,189.48,0.26423,0.53266,0.80403,-66.523,-0.63165,0.72556,-0.2731,107.11
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.05499, steps = 76
shifted from previous position = 1.92
rotated from previous position = 6.74 degrees
atoms outside contour = 2435, contour level = 0.063498
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.90184778 -0.37893425 -0.20755581 76.64071143
0.27337981 0.87247868 -0.40502399 20.03740715
0.33456548 0.30852842 0.89043594 -63.34038632
Axis 0.64376387 -0.48909947 0.58851490
Axis point 0.00000000 205.20654040 -12.40597061
Rotation angle (degrees) 33.65587279
Shift along axis 2.26147457
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.05498, steps = 48
shifted from previous position = 0.0248
rotated from previous position = 0.144 degrees
atoms outside contour = 2437, contour level = 0.063498
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.90282527 -0.37671180 -0.20735180 76.24688757
0.27166607 0.87346854 -0.40404239 20.04831489
0.33332281 0.30844923 0.89092928 -63.22447310
Axis 0.64496256 -0.48943014 0.58692541
Axis point 0.00000000 205.07134507 -11.86871488
Rotation angle (degrees) 33.52846202
Shift along axis 2.25608804
> view matrix models
> #6,0.78289,0.60399,0.14926,-95.549,-0.0941,-0.1222,0.98804,44.015,0.61501,-0.78757,-0.038829,121.5
> view matrix models
> #6,0.79504,0.48543,0.3637,-105.3,-0.18787,-0.37305,0.90859,97.445,0.57673,-0.79069,-0.2054,145.16
> view matrix models
> #6,0.75975,0.17454,0.62635,-89.244,-0.35135,-0.70035,0.62134,192.66,0.54711,-0.69213,-0.47077,165.37
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.75975,0.17454,0.62635,-77.794,-0.35135,-0.70035,0.62134,175.36,0.54711,-0.69213,-0.47077,152.26
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.1606, steps = 148
shifted from previous position = 12.6
rotated from previous position = 18.4 degrees
atoms outside contour = 901, contour level = 0.063498
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.99401473 0.00323811 0.10919811 241.20741140
0.01958709 -0.97808088 0.20730208 212.87036962
0.10747585 0.20820019 0.97216337 -35.66515130
Axis 0.05455038 0.10460789 0.99301634
Axis point 121.14214835 108.81363402 0.00000000
Rotation angle (degrees) 179.52833707
Shift along axis 0.00979704
> show #!2 models
> matchmaker #2 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SD_apo-coot-1.pdb, chain A (#5) with
hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence
alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> hide #!2 models
> select add #5
3488 atoms, 3546 bonds, 4 pseudobonds, 438 residues, 4 models selected
> select subtract #5
2 models selected
> view matrix models
> #6,0.75975,0.17454,0.62635,-76.501,-0.35135,-0.70035,0.62134,176.77,0.54711,-0.69213,-0.47077,151.6
> fitmap #5 inMap #6
Fit molecule SD_apo-coot-1.pdb (#5) to map
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms
average map value = 0.1606, steps = 64
shifted from previous position = 2.01
rotated from previous position = 0.00868 degrees
atoms outside contour = 900, contour level = 0.063498
Position of SD_apo-coot-1.pdb (#5) relative to
cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.99400449 0.00322052 0.10929184 241.20055875
0.01961108 -0.97810542 0.20718397 212.88014700
0.10756618 0.20808512 0.97217802 -35.66997391
Axis 0.05459652 0.10454880 0.99302002
Axis point 121.13853906 108.81896286 0.00000000
Rotation angle (degrees) 179.52713907
Shift along axis 0.00407661
> ui mousemode right "rotate selected models"
> show #!2 models
> matchmaker #2 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SD_apo-coot-1.pdb, chain A (#5) with
hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence
alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> hide #!6 models
> select add #5
3488 atoms, 3546 bonds, 4 pseudobonds, 438 residues, 4 models selected
> select subtract #5
2 models selected
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!6 models
> show #!2 models
> hide #!2 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!2 models
> show #!6 models
> hide #!6 models
> open "/Users/rnom/Desktop/論文化/for figure/hAC9+Gs
> model,map/AC9-Gs_SD/J242_004_volume_map_sharp_trimmed.mrc"
Opened J242_004_volume_map_sharp_trimmed.mrc as #7, grid size 292,292,292,
pixel 0.79, shown at level 0.139, step 2, values float32
> surface dust #7 size 7.9
> color #7 #ffffb249 models
> color #7 #ffffb255 models
> color #7 #ffffb254 models
> color #7 #3fffd854 models
> color #7 #b9ffe654 models
> color #7 #b5fffe54 models
Drag select of 7 J242_004_volume_map_sharp_trimmed.mrc
> view matrix models
> #7,-0.8589,0.26683,-0.43714,248.52,0.18053,-0.64104,-0.74598,270.23,-0.47927,-0.71964,0.50242,207.77
> view matrix models
> #7,-0.82962,0.29912,-0.47144,246.23,0.21869,-0.60282,-0.76732,264.41,-0.51371,-0.73969,0.4347,223.58
> view matrix models
> #7,-0.80378,0.35561,-0.47694,237.55,0.19334,-0.60203,-0.77471,268.32,-0.56263,-0.71491,0.41515,229.23
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.80378,0.35561,-0.47694,248.83,0.19334,-0.60203,-0.77471,252.08,-0.56263,-0.71491,0.41515,183.45
> hide #!5 models
> view matrix models
> #7,-0.80378,0.35561,-0.47694,232.19,0.19334,-0.60203,-0.77471,243.96,-0.56263,-0.71491,0.41515,190.06
> fitmap #2 inMap #7
Fit molecule hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) to map
J242_004_volume_map_sharp_trimmed.mrc (#7) using 6416 atoms
average map value = 0.06654, steps = 140
shifted from previous position = 4.85
rotated from previous position = 8.55 degrees
atoms outside contour = 5130, contour level = 0.13875
Position of hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) relative to
J242_004_volume_map_sharp_trimmed.mrc (#7) coordinates:
Matrix rotation and translation
0.96348241 -0.19216888 -0.18647455 65.93026295
0.17408753 0.97867059 -0.10907527 -5.75243065
0.20345803 0.07262921 0.97638610 -28.99043090
Axis 0.32160957 -0.69016487 0.64825900
Axis point 198.07460760 -0.00000000 303.76792232
Rotation angle (degrees) 16.40901215
Shift along axis 6.38062155
> view matrix models
> #7,-0.80378,0.35561,-0.47694,224.8,0.19334,-0.60203,-0.77471,241.87,-0.56263,-0.71491,0.41515,176.06
> fitmap #2 inMap #7
Fit molecule hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) to map
J242_004_volume_map_sharp_trimmed.mrc (#7) using 6416 atoms
average map value = 0.0704, steps = 192
shifted from previous position = 5.17
rotated from previous position = 10.5 degrees
atoms outside contour = 5081, contour level = 0.13875
Position of hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) relative to
J242_004_volume_map_sharp_trimmed.mrc (#7) coordinates:
Matrix rotation and translation
0.97942469 -0.13254196 -0.15218381 38.51969094
0.14397435 0.98733166 0.06669018 -36.35623404
0.14141664 -0.08722857 0.98609964 -4.17941113
Axis -0.35655192 -0.68012380 0.64054848
Axis point 92.77975956 0.00000000 260.05114793
Rotation angle (degrees) 12.46501192
Shift along axis 8.31535466
> view matrix models
> #7,-0.80378,0.35561,-0.47694,216.63,0.19334,-0.60203,-0.77471,247.94,-0.56263,-0.71491,0.41515,179.48
> view matrix models
> #7,-0.80378,0.35561,-0.47694,220.74,0.19334,-0.60203,-0.77471,246.96,-0.56263,-0.71491,0.41515,176.92
> view matrix models
> #7,-0.80378,0.35561,-0.47694,218.99,0.19334,-0.60203,-0.77471,246.07,-0.56263,-0.71491,0.41515,185.98
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.82508,0.32047,-0.46534,223.85,0.16231,-0.65444,-0.73849,250.58,-0.5412,-0.68484,0.48795,169.84
> fitmap #2 inMap #7
Fit molecule hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) to map
J242_004_volume_map_sharp_trimmed.mrc (#7) using 6416 atoms
average map value = 0.5312, steps = 116
shifted from previous position = 5.95
rotated from previous position = 13.2 degrees
atoms outside contour = 831, contour level = 0.13875
Position of hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) relative to
J242_004_volume_map_sharp_trimmed.mrc (#7) coordinates:
Matrix rotation and translation
0.99999999 0.00007070 0.00007818 -0.02645356
-0.00007069 0.99999999 -0.00007378 0.01482179
-0.00007818 0.00007378 0.99999999 0.00013710
Axis 0.57344071 0.60765315 -0.54947558
Axis point -42.11207468 0.00000000 292.61736079
Rotation angle (degrees) 0.00737159
Shift along axis -0.00623838
> view matrix models
> #7,-0.67891,-0.043491,-0.73294,285.69,0.54975,-0.6918,-0.46817,171.57,-0.48669,-0.72077,0.49358,166.76
> view matrix models
> #7,-0.80853,0.23973,-0.5374,241.21,0.25647,-0.67838,-0.68849,235.27,-0.52962,-0.6945,0.48701,169.71
> fitmap #2 inMap #7
Fit molecule hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) to map
J242_004_volume_map_sharp_trimmed.mrc (#7) using 6416 atoms
average map value = 0.5312, steps = 80
shifted from previous position = 2.32
rotated from previous position = 6.3 degrees
atoms outside contour = 829, contour level = 0.13875
Position of hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) relative to
J242_004_volume_map_sharp_trimmed.mrc (#7) coordinates:
Matrix rotation and translation
0.99999999 -0.00000079 0.00013980 -0.02856000
0.00000083 0.99999996 -0.00026357 0.04123823
-0.00013980 0.00026357 0.99999995 -0.01486838
Axis 0.88342705 0.46856092 0.00270438
Axis point 0.00000000 56.37836338 167.02643506
Rotation angle (degrees) 0.01709426
Shift along axis -0.00594827
> show #!5 models
> hide #!5 models
> hide #!7 models
> show #!5 models
> view matrix models
> #7,-0.80853,0.23973,-0.5374,241.21,0.25647,-0.67838,-0.68849,235.27,-0.52962,-0.6945,0.48701,169.71
> matchmaker #2 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SD_apo-coot-1.pdb, chain A (#5) with
hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence
alignment score = 2132.5
RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs:
1.891)
> show #!2,5 atoms
> hide #!2,5 atoms
> select #2/A:326
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/A:1028
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide #!5 models
> select #2/A:1028
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/A:1025
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/A:326
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
===== Log before crash end =====
Log:
Startup Messages
---
notes | available bundle cache has not been initialized yet
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'
UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/rnom/Desktop/240617 解析関連/240617 hAC9 phenix/240617 hAC9 whole
> P78J52.pdb" format pdb
Chain information for 240617 hAC9 whole P78J52.pdb #1
---
Chain | Description
A | No description available
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MYDC2J/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 13日 20時間 52分
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LCD-MF235XD:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.4
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.4
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202405202242
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.3
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.4
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.51.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 13 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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