![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#10217 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff8592aa700 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-11-23 10:30:13.00 +0100","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.6.1 (22G313)","roots_installed":0,"name":"ChimeraX","incident_id":"9B2C6BFD-0565-4C40-93CC-A513BCAC507E"}
{
"uptime" : 330000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Macmini8,1",
"coalitionID" : 3797,
"osVersion" : {
"train" : "macOS 13.6.1",
"build" : "22G313",
"releaseType" : "User"
},
"captureTime" : "2023-11-23 10:29:53.9247 +0100",
"incident" : "9B2C6BFD-0565-4C40-93CC-A513BCAC507E",
"pid" : 39678,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-11-21 17:13:24.4665 +0100",
"procStartAbsTime" : 250394839595302,
"procExitAbsTime" : 338236134803316,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"793F310D-059A-5737-977A-EA9554F1DECF","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7AB8BCDC-6EA7-29DA-5ACB-ECDCDF5A342B",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 54885,
"bridgeVersion" : {"build":"21P1069","train":"8.1"},
"sleepWakeUUID" : "B30CC306-E34D-4DC0-9A19-DA6CE277B273",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737486790632\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe82000-7fffffe83000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":39678},
"ktriageinfo" : "VM - (arg = 0x0) Waiting on busy page was interrupted\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737486790632\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe82000-7fffffe83000 [ 4K] r-x\/r-x SM=SHM ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Could not find tool "Structural Screening"
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1989.t1.pdb
> format pdb
Chain information for g1989.t1.pdb #1
---
Chain | Description
A | No description available
> set bgColor white
> open 2aai
Summary of feedback from opening 2aai fetched from pdb
---
note | Fetching compressed mmCIF 2aai from
http://files.rcsb.org/download/2aai.cif
2aai title:
Crystallographic refinement of ricin to 2.5 Angstroms [more info...]
Chain information for 2aai #2
---
Chain | Description | UniProt
A | RICIN (A CHAIN) | RICI_RICCO 1-267
B | RICIN (B CHAIN) | RICI_RICCO 1-262
Non-standard residues in 2aai #2
---
BGC — beta-D-glucopyranose
BMA — beta-D-mannopyranose
GAL — beta-D-galactopyranose
MAN — alpha-D-mannopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> mmaker #1 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 2aai, chain B (#2) with g1989.t1.pdb, chain A (#1), sequence
alignment score = 45.4
RMSD between 5 pruned atom pairs is 1.250 angstroms; (across all 89 pairs:
20.196)
> view clip false
> mmaker #1 to #2/B
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 2aai, chain B (#2) with g1989.t1.pdb, chain A (#1), sequence
alignment score = 45.4
RMSD between 5 pruned atom pairs is 1.250 angstroms; (across all 89 pairs:
20.196)
> close
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0B2UDY9.pdb
Chain information for A0A0B2UDY9.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0B2UJ21.pdb
Chain information for A0A0B2UJ21.pdb #2
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0B2UJ51.pdb
Chain information for A0A0B2UJ51.pdb #3
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0B2UKB5.pdb
Chain information for A0A0B2UKB5.pdb #4
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WA85.pdb
Chain information for A0A0F9WA85.pdb #5
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WE74.pdb
Chain information for A0A0F9WE74.pdb #6
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WET1.pdb
Chain information for A0A0F9WET1.pdb #7
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WET7.pdb
Chain information for A0A0F9WET7.pdb #8
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WGX6.pdb
Chain information for A0A0F9WGX6.pdb #9
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WN65.pdb
Chain information for A0A0F9WN65.pdb #10
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WPM0.pdb
Chain information for A0A0F9WPM0.pdb #11
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WSN9.pdb
Chain information for A0A0F9WSN9.pdb #12
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WSP8.pdb
Chain information for A0A0F9WSP8.pdb #13
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9YP43.pdb
Chain information for A0A0F9YP43.pdb #14
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9YP48.pdb
Chain information for A0A0F9YP48.pdb #15
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9YTP2.pdb
Chain information for A0A0F9YTP2.pdb #16
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9YTP9.pdb
Chain information for A0A0F9YTP9.pdb #17
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9Z9D8.pdb
Chain information for A0A0F9Z9D8.pdb #18
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9ZEM9.pdb
Chain information for A0A0F9ZEM9.pdb #19
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g264.t1.pdb
Chain information for g264.t1.pdb #20
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g375.t1.pdb
Chain information for g375.t1.pdb #21
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g724.t1.pdb
Chain information for g724.t1.pdb #22
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g732.t1.pdb
Chain information for g732.t1.pdb #23
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g883.t1.pdb
Chain information for g883.t1.pdb #24
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g884.t1.pdb
Chain information for g884.t1.pdb #25
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g886.t1.pdb
Chain information for g886.t1.pdb #26
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g888.t1.pdb
Chain information for g888.t1.pdb #27
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g957.t1.pdb
Chain information for g957.t1.pdb #28
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g958.t1.pdb
Chain information for g958.t1.pdb #29
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g972.t1.pdb
Chain information for g972.t1.pdb #30
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g973.t1.pdb
Chain information for g973.t1.pdb #31
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g977.t1.pdb
Chain information for g977.t1.pdb #32
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g978.t1.pdb
Chain information for g978.t1.pdb #33
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1726.t1.pdb
Chain information for g1726.t1.pdb #34
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1727.t1.pdb
Chain information for g1727.t1.pdb #35
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1987.t1.pdb
Chain information for g1987.t1.pdb #36
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1988.t1.pdb
Chain information for g1988.t1.pdb #37
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1989.t1.pdb
Chain information for g1989.t1.pdb #38
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1991.t1.pdb
Chain information for g1991.t1.pdb #39
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1992.t1.pdb
Chain information for g1992.t1.pdb #40
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g3022.t1.pdb
Chain information for g3022.t1.pdb #41
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6TKU6.pdb
Chain information for I6TKU6.pdb #42
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6TV97.pdb
Chain information for I6TV97.pdb #43
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6TWE0.pdb
Chain information for I6TWE0.pdb #44
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UDH1.pdb
Chain information for I6UDH1.pdb #45
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UDI1.pdb
Chain information for I6UDI1.pdb #46
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UMG3.pdb
Chain information for I6UMG3.pdb #47
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UMG6.pdb
Chain information for I6UMG6.pdb #48
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UN97.pdb
Chain information for I6UN97.pdb #49
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UQG3.pdb
Chain information for I6UQG3.pdb #50
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UQK2.pdb
Chain information for I6UQK2.pdb #51
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6ZK24.pdb
Chain information for I6ZK24.pdb #52
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6ZUI2.pdb
Chain information for I6ZUI2.pdb #53
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6ZUJ1.pdb
Chain information for I6ZUJ1.pdb #54
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6ZV11.pdb
Chain information for I6ZV11.pdb #55
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I7AF84.pdb
Chain information for I7AF84.pdb #56
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I7AF87.pdb
Chain information for I7AF87.pdb #57
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I7ANB6.pdb
Chain information for I7ANB6.pdb #58
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I7AP33.pdb
Chain information for I7AP33.pdb #59
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I7AT09.pdb
Chain information for I7AT09.pdb #60
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUI3.pdb
Chain information for Q8SUI3.pdb #61
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUI4.pdb
Chain information for Q8SUI4.pdb #62
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUK1.pdb
Chain information for Q8SUK1.pdb #63
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUK2.pdb
Chain information for Q8SUK2.pdb #64
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUK3.pdb
Chain information for Q8SUK3.pdb #65
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUK4.pdb
Chain information for Q8SUK4.pdb #66
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUL9.pdb
Chain information for Q8SUL9.pdb #67
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUY7.pdb
Chain information for Q8SUY7.pdb #68
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUY8.pdb
Chain information for Q8SUY8.pdb #69
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUZ1.pdb
Chain information for Q8SUZ1.pdb #70
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUZ3.pdb
Chain information for Q8SUZ3.pdb #71
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SV68.pdb
Chain information for Q8SV68.pdb #72
---
Chain | Description
A | No description available
> mmaker #2-72 to #1
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 A0A0B2UDY9.pdb, chain A (#1) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 90.8
RMSD between 67 pruned atom pairs is 1.016 angstroms; (across all 207 pairs:
31.340)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0B2UJ51.pdb, chain A (#3),
sequence alignment score = 126.7
RMSD between 48 pruned atom pairs is 1.178 angstroms; (across all 203 pairs:
19.794)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0B2UKB5.pdb, chain A (#4),
sequence alignment score = 48.9
RMSD between 8 pruned atom pairs is 1.368 angstroms; (across all 201 pairs:
50.983)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 94.1
RMSD between 71 pruned atom pairs is 0.906 angstroms; (across all 210 pairs:
42.489)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WE74.pdb, chain A (#6),
sequence alignment score = 149.7
RMSD between 77 pruned atom pairs is 1.121 angstroms; (across all 220 pairs:
12.557)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WET1.pdb, chain A (#7),
sequence alignment score = 48.7
RMSD between 46 pruned atom pairs is 0.810 angstroms; (across all 126 pairs:
9.350)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WET7.pdb, chain A (#8),
sequence alignment score = 58.6
RMSD between 47 pruned atom pairs is 0.913 angstroms; (across all 140 pairs:
16.056)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WGX6.pdb, chain A (#9),
sequence alignment score = 103.7
RMSD between 65 pruned atom pairs is 1.078 angstroms; (across all 198 pairs:
32.837)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WN65.pdb, chain A (#10),
sequence alignment score = 137.6
RMSD between 74 pruned atom pairs is 1.023 angstroms; (across all 191 pairs:
22.979)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WPM0.pdb, chain A (#11),
sequence alignment score = 83.3
RMSD between 53 pruned atom pairs is 0.882 angstroms; (across all 114 pairs:
12.979)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WSN9.pdb, chain A (#12),
sequence alignment score = 68.4
RMSD between 35 pruned atom pairs is 0.802 angstroms; (across all 127 pairs:
13.986)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WSP8.pdb, chain A (#13),
sequence alignment score = 56.4
RMSD between 7 pruned atom pairs is 1.020 angstroms; (across all 159 pairs:
18.708)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9YP43.pdb, chain A (#14),
sequence alignment score = 103
RMSD between 51 pruned atom pairs is 1.097 angstroms; (across all 173 pairs:
12.062)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9YP48.pdb, chain A (#15),
sequence alignment score = 91.6
RMSD between 54 pruned atom pairs is 1.089 angstroms; (across all 211 pairs:
19.286)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9YTP2.pdb, chain A (#16),
sequence alignment score = 100.2
RMSD between 57 pruned atom pairs is 0.810 angstroms; (across all 189 pairs:
28.912)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9YTP9.pdb, chain A (#17),
sequence alignment score = 70.1
RMSD between 53 pruned atom pairs is 0.906 angstroms; (across all 130 pairs:
11.673)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9Z9D8.pdb, chain A (#18),
sequence alignment score = 101.8
RMSD between 51 pruned atom pairs is 0.916 angstroms; (across all 193 pairs:
21.080)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9ZEM9.pdb, chain A (#19),
sequence alignment score = 58.3
RMSD between 42 pruned atom pairs is 0.873 angstroms; (across all 160 pairs:
17.834)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g264.t1.pdb, chain A (#20),
sequence alignment score = 100.5
RMSD between 38 pruned atom pairs is 0.861 angstroms; (across all 156 pairs:
16.781)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g375.t1.pdb, chain A (#21),
sequence alignment score = 112.4
RMSD between 56 pruned atom pairs is 0.962 angstroms; (across all 153 pairs:
11.797)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g724.t1.pdb, chain A (#22),
sequence alignment score = 88.8
RMSD between 47 pruned atom pairs is 0.876 angstroms; (across all 205 pairs:
27.354)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g732.t1.pdb, chain A (#23),
sequence alignment score = 67.1
RMSD between 56 pruned atom pairs is 1.042 angstroms; (across all 154 pairs:
17.782)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g883.t1.pdb, chain A (#24),
sequence alignment score = 130.9
RMSD between 77 pruned atom pairs is 1.133 angstroms; (across all 183 pairs:
23.062)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g884.t1.pdb, chain A (#25),
sequence alignment score = 77
RMSD between 75 pruned atom pairs is 1.058 angstroms; (across all 222 pairs:
21.871)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g886.t1.pdb, chain A (#26),
sequence alignment score = 146
RMSD between 44 pruned atom pairs is 1.045 angstroms; (across all 177 pairs:
21.492)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g888.t1.pdb, chain A (#27),
sequence alignment score = 102.3
RMSD between 72 pruned atom pairs is 1.072 angstroms; (across all 181 pairs:
12.238)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g957.t1.pdb, chain A (#28),
sequence alignment score = 86
RMSD between 57 pruned atom pairs is 1.053 angstroms; (across all 136 pairs:
6.143)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g958.t1.pdb, chain A (#29),
sequence alignment score = 94.5
RMSD between 20 pruned atom pairs is 0.884 angstroms; (across all 199 pairs:
24.531)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g972.t1.pdb, chain A (#30),
sequence alignment score = 108.2
RMSD between 59 pruned atom pairs is 1.020 angstroms; (across all 133 pairs:
8.026)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g973.t1.pdb, chain A (#31),
sequence alignment score = 59.3
RMSD between 35 pruned atom pairs is 0.965 angstroms; (across all 206 pairs:
22.940)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g977.t1.pdb, chain A (#32),
sequence alignment score = 76.6
RMSD between 38 pruned atom pairs is 0.790 angstroms; (across all 101 pairs:
11.360)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g978.t1.pdb, chain A (#33),
sequence alignment score = 74.3
RMSD between 46 pruned atom pairs is 0.937 angstroms; (across all 148 pairs:
11.865)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1726.t1.pdb, chain A (#34),
sequence alignment score = 185.5
RMSD between 84 pruned atom pairs is 0.981 angstroms; (across all 215 pairs:
13.460)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1727.t1.pdb, chain A (#35),
sequence alignment score = 133.9
RMSD between 47 pruned atom pairs is 0.917 angstroms; (across all 153 pairs:
14.894)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1987.t1.pdb, chain A (#36),
sequence alignment score = 101.7
RMSD between 48 pruned atom pairs is 0.862 angstroms; (across all 155 pairs:
21.929)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1988.t1.pdb, chain A (#37),
sequence alignment score = 83.6
RMSD between 46 pruned atom pairs is 1.014 angstroms; (across all 184 pairs:
17.148)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1989.t1.pdb, chain A (#38),
sequence alignment score = 87.9
RMSD between 49 pruned atom pairs is 0.880 angstroms; (across all 147 pairs:
15.561)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1991.t1.pdb, chain A (#39),
sequence alignment score = 131.8
RMSD between 72 pruned atom pairs is 0.912 angstroms; (across all 168 pairs:
24.547)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1992.t1.pdb, chain A (#40),
sequence alignment score = 112.5
RMSD between 45 pruned atom pairs is 0.929 angstroms; (across all 194 pairs:
26.572)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g3022.t1.pdb, chain A (#41),
sequence alignment score = 75.8
RMSD between 56 pruned atom pairs is 1.098 angstroms; (across all 142 pairs:
13.511)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6TKU6.pdb, chain A (#42),
sequence alignment score = 100
RMSD between 55 pruned atom pairs is 0.902 angstroms; (across all 208 pairs:
24.414)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6TV97.pdb, chain A (#43),
sequence alignment score = 43.8
RMSD between 29 pruned atom pairs is 0.853 angstroms; (across all 182 pairs:
48.501)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6TWE0.pdb, chain A (#44),
sequence alignment score = 427.6
RMSD between 100 pruned atom pairs is 0.825 angstroms; (across all 254 pairs:
11.405)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UDH1.pdb, chain A (#45),
sequence alignment score = 65.5
RMSD between 47 pruned atom pairs is 1.141 angstroms; (across all 166 pairs:
15.530)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UDI1.pdb, chain A (#46),
sequence alignment score = 140.6
RMSD between 72 pruned atom pairs is 1.031 angstroms; (across all 181 pairs:
25.019)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UMG3.pdb, chain A (#47),
sequence alignment score = 74.4
RMSD between 43 pruned atom pairs is 1.009 angstroms; (across all 193 pairs:
26.517)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UMG6.pdb, chain A (#48),
sequence alignment score = 89.3
RMSD between 76 pruned atom pairs is 1.022 angstroms; (across all 207 pairs:
28.399)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UN97.pdb, chain A (#49),
sequence alignment score = 68
RMSD between 55 pruned atom pairs is 0.898 angstroms; (across all 187 pairs:
27.666)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UQG3.pdb, chain A (#50),
sequence alignment score = 113.6
RMSD between 65 pruned atom pairs is 0.807 angstroms; (across all 206 pairs:
35.493)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UQK2.pdb, chain A (#51),
sequence alignment score = 178.8
RMSD between 100 pruned atom pairs is 0.880 angstroms; (across all 146 pairs:
3.407)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6ZK24.pdb, chain A (#52),
sequence alignment score = 443.9
RMSD between 106 pruned atom pairs is 0.880 angstroms; (across all 257 pairs:
11.250)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6ZUI2.pdb, chain A (#53),
sequence alignment score = 76.5
RMSD between 47 pruned atom pairs is 1.075 angstroms; (across all 172 pairs:
14.626)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6ZUJ1.pdb, chain A (#54),
sequence alignment score = 158.5
RMSD between 61 pruned atom pairs is 0.950 angstroms; (across all 208 pairs:
32.357)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6ZV11.pdb, chain A (#55),
sequence alignment score = 108.2
RMSD between 49 pruned atom pairs is 0.920 angstroms; (across all 210 pairs:
28.657)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I7AF84.pdb, chain A (#56),
sequence alignment score = 82.1
RMSD between 35 pruned atom pairs is 1.013 angstroms; (across all 209 pairs:
30.878)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I7AF87.pdb, chain A (#57),
sequence alignment score = 118.9
RMSD between 73 pruned atom pairs is 1.079 angstroms; (across all 218 pairs:
31.578)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I7ANB6.pdb, chain A (#58),
sequence alignment score = 37.2
RMSD between 5 pruned atom pairs is 1.196 angstroms; (across all 171 pairs:
35.417)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I7AP33.pdb, chain A (#59),
sequence alignment score = 89.5
RMSD between 60 pruned atom pairs is 0.905 angstroms; (across all 199 pairs:
43.691)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I7AT09.pdb, chain A (#60),
sequence alignment score = 73.6
RMSD between 51 pruned atom pairs is 0.864 angstroms; (across all 182 pairs:
31.243)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUI3.pdb, chain A (#61),
sequence alignment score = 131.3
RMSD between 108 pruned atom pairs is 0.872 angstroms; (across all 144 pairs:
3.728)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUI4.pdb, chain A (#62),
sequence alignment score = 450.6
RMSD between 121 pruned atom pairs is 0.841 angstroms; (across all 259 pairs:
15.316)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUK1.pdb, chain A (#63),
sequence alignment score = 98.6
RMSD between 51 pruned atom pairs is 0.862 angstroms; (across all 193 pairs:
22.742)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUK2.pdb, chain A (#64),
sequence alignment score = 85.1
RMSD between 47 pruned atom pairs is 0.899 angstroms; (across all 196 pairs:
29.044)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUK3.pdb, chain A (#65),
sequence alignment score = 97.7
RMSD between 46 pruned atom pairs is 0.844 angstroms; (across all 214 pairs:
32.127)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUK4.pdb, chain A (#66),
sequence alignment score = 98.9
RMSD between 47 pruned atom pairs is 0.865 angstroms; (across all 212 pairs:
31.768)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUL9.pdb, chain A (#67),
sequence alignment score = 116.9
RMSD between 4 pruned atom pairs is 0.926 angstroms; (across all 230 pairs:
30.068)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUY7.pdb, chain A (#68),
sequence alignment score = 148.1
RMSD between 63 pruned atom pairs is 0.960 angstroms; (across all 233 pairs:
40.480)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUY8.pdb, chain A (#69),
sequence alignment score = 97.7
RMSD between 70 pruned atom pairs is 1.023 angstroms; (across all 215 pairs:
33.292)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUZ1.pdb, chain A (#70),
sequence alignment score = 33.7
RMSD between 11 pruned atom pairs is 1.434 angstroms; (across all 206 pairs:
24.633)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUZ3.pdb, chain A (#71),
sequence alignment score = 72.8
RMSD between 50 pruned atom pairs is 1.107 angstroms; (across all 164 pairs:
12.803)
Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SV68.pdb, chain A (#72),
sequence alignment score = 34
RMSD between 9 pruned atom pairs is 1.166 angstroms; (across all 177 pairs:
43.917)
> color lightgrey
> color &helix orchid
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1-72 &helix orchid
> color #1-72 &strand gold
> tile columns 7 spacingFactor 1
72 models tiled
> color #1-72:cys orange
> color #1-72:glu green
> color #1-72:trp blue
> color #1-72:phe darkblue
> hide #72 models
> hide #71 models
> hide #70 models
> hide #69 models
> hide #67 models
> hide #68 models
> hide #66 models
> hide #65 models
> hide #63 models
> hide #64 models
> hide #62 models
> hide #61 models
> hide #60 models
> hide #59 models
> hide #58 models
> hide #57 models
> hide #56 models
> hide #55 models
> hide #54 models
> hide #53 models
> hide #52 models
> hide #51 models
> hide #50 models
> hide #48 models
> hide #49 models
> hide #47 models
> hide #46 models
> hide #45 models
> hide #44 models
> hide #43 models
> hide #42 models
> hide #41 models
> hide #40 models
> hide #39 models
> hide #38 models
> hide #37 models
> hide #36 models
> hide #35 models
> hide #34 models
> hide #33 models
> hide #32 models
> hide #31 models
> hide #30 models
> hide #29 models
> hide #28 models
> hide #27 models
> hide #26 models
> hide #25 models
> hide #24 models
> hide #23 models
> hide #22 models
> hide #21 models
> hide #20 models
> hide #19 models
> hide #18 models
> hide #17 models
> hide #16 models
> hide #15 models
> hide #14 models
> hide #13 models
> hide #12 models
> hide #11 models
> hide #10 models
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> show #2 models
> show #22 models
> show #67 models
> show #59 models
> show #50 models
> show #5 models
> view #50 clip false
> tile #2,5,22,50,59 columns 5 spacingFactor 1
5 models tiled
> tile #2,5,22,50,59,67 columns 5 spacingFactor 1
6 models tiled
> tile #2,5,22,50,59,67 columns 3 spacingFactor 1
6 models tiled
> hide atoms
> show cartoons
> set bgColor white
> graphics silhouettes true
> set silhouetteWidth 2
> cartoon style width 2 thickness 1
> cartoon style modeHelix wrap
> color #2 #db7a57ff
> color #5 #dadb24ff
> color #22 #7cdb50ff
> color #50 #3ec7dbff
> color #59 #db3ecfff
> color #59 #db52c6ff
> color #67 #c8db9eff
> color #67 #d1dbceff
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> hide #59 models
> hide #67 models
> hide #50 models
> hide #22 models
> hide #5 models
> hide #2:159-404 cartoons
> hide #2 models
> show #2 models
> show #5 models
> hide #5:143-483 cartoons
> show #22 models
> hide #22:143-474 cartoons
> show #50 models
> hide #50:143-368 cartoons
> show #59 models
> hide #59:147-379 cartoons
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
> mmaker #2,5,22,50,59 to #67
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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2),
sequence alignment score = 542.7
RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs:
44.250)
Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5),
sequence alignment score = 505.1
RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs:
41.997)
Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence
alignment score = 467.9
RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs:
40.245)
Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence
alignment score = 1024.4
RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs:
32.941)
Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence
alignment score = 1087.1
RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs:
37.256)
Drag select of 730 residues
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.33671,0.6339,-0.69627,458.61,0.59846,-0.71495,-0.36151,-161.78,-0.72696,-0.29497,-0.62009,-3.8328,#5,0.3239,0.23139,-0.91736,458.3,0.93637,0.060267,0.34581,-161.63,0.1353,-0.97099,-0.19715,-4.6652,#22,-0.55891,0.19842,0.80514,457.1,0.82359,0.019728,0.56685,-162.48,0.096591,0.97992,-0.17444,-2.4225,#50,0.61026,-0.63985,-0.46709,458.33,-0.2272,0.42348,-0.87695,-160.57,0.75892,0.64129,0.11306,-3.2024,#59,0.83419,-0.54951,-0.04659,457.38,-0.25198,-0.30464,-0.91853,-161.5,0.49055,0.77797,-0.39259,-3.8979
> view matrix models
> #2,0.36052,0.060407,-0.93079,462.36,0.81886,-0.49835,0.28482,-163.69,-0.44666,-0.86487,-0.22913,-0.36275,#5,0.77852,-0.071062,-0.62359,461.94,0.53428,0.59638,0.59906,-162.99,0.32932,-0.79955,0.50226,-0.73435,#22,-0.003503,0.46163,0.88707,461.2,0.68518,-0.64501,0.33837,-164.73,0.72836,0.60899,-0.31404,1.167,#50,0.6029,-0.11063,-0.79011,462.94,-0.78869,0.066679,-0.61116,-163.12,0.1203,0.99162,-0.047054,0.76895,#59,0.69139,-0.36768,-0.62193,461.49,-0.69281,-0.58155,-0.42639,-163.14,-0.20491,0.72568,-0.65681,0.37945
> view matrix models
> #2,0.40313,0.91365,-0.052317,455.61,0.76734,-0.30632,0.56335,-165.3,0.49868,-0.26725,-0.82456,-4.3451,#5,-0.19641,0.66491,-0.72064,455.76,0.2276,0.7458,0.62609,-164.45,0.95374,-0.041044,-0.29781,-4.5957,#22,-0.79483,-0.37815,0.4746,454,0.4953,-0.85613,0.14736,-166.29,0.3506,0.3522,0.86778,-5.4443,#50,0.14548,-0.98714,-0.066192,454.59,-0.92791,-0.11293,-0.35529,-165.15,0.34325,0.11311,-0.93241,-3.4044,#59,0.46574,-0.70554,0.53414,454.6,-0.79392,-0.59975,-0.099954,-164.71,0.39087,-0.37751,-0.83947,-4.8438
> view matrix models
> #2,0.089554,0.96993,-0.22633,455.37,-0.60291,0.23367,0.76282,-171.24,0.79277,0.06814,0.6057,-5.7962,#5,-0.29111,0.35682,-0.88766,455.22,-0.95634,-0.083386,0.28011,-171.09,0.025933,0.93044,0.36552,-4.9226,#22,-0.92853,-0.058384,0.36665,454.25,-0.34435,-0.2337,-0.90929,-169.93,0.13877,-0.97055,0.1969,-7.1433,#50,0.45654,-0.88507,0.090657,454.34,-0.2537,-0.031841,0.96676,-172.11,-0.85276,-0.46437,-0.23908,-6.1269,#59,0.70668,-0.43506,0.55797,454.24,-0.3372,0.4862,0.80617,-170.73,-0.62202,-0.75785,0.19689,-5.5363
> view matrix models
> #2,-0.16239,-0.39,0.90638,467.64,-0.89996,0.43519,0.026014,-174.4,-0.40459,-0.81149,-0.42166,-3.1384,#5,-0.48342,0.09472,0.87025,468.18,-0.75016,-0.55721,-0.35606,-174.93,0.45118,-0.82495,0.34042,-3.6185,#22,0.36943,-0.51035,-0.77657,468.69,-0.63303,0.47358,-0.61237,-173.01,0.68029,0.71782,-0.14812,-1.821,#50,-0.78584,0.32419,0.52664,467.51,0.55442,-0.0079688,0.8322,-175.11,0.27398,0.94596,-0.17347,-1.9425,#59,-0.90287,0.30125,0.30673,468.77,0.42877,0.68317,0.59113,-174.62,-0.031466,0.66523,-0.74598,-2.6098
> view matrix models
> #2,-0.29885,-0.76485,0.5707,470.27,-0.87257,0.46115,0.16111,-174.41,-0.3864,-0.44983,-0.8052,-7.7682,#5,-0.15491,-0.30407,0.93997,470.53,-0.83513,-0.46799,-0.28902,-174.84,0.52778,-0.82977,-0.18144,-8.5171,#22,0.69105,-0.10464,-0.71519,471.77,-0.64758,0.3499,-0.67691,-173.04,0.32108,0.93093,0.17403,-6.9688,#50,-0.56899,0.75438,0.32735,470.8,0.43978,-0.057221,0.89628,-175.23,0.69487,0.65394,-0.29921,-6.77,#59,-0.81696,0.56003,-0.13764,471.53,0.32996,0.64966,0.68488,-174.55,0.47298,0.5141,-0.71554,-7.899
> view matrix models
> #2,-0.32498,-0.93153,-0.16321,471.18,-0.55181,0.046618,0.83267,-169.51,-0.76804,0.36067,-0.52918,-15.238,#5,0.3897,-0.69816,0.60058,470.92,-0.87813,-0.085166,0.47079,-169.27,-0.27754,-0.71086,-0.64626,-16.068,#22,0.82374,0.49407,-0.27812,472.55,-0.14843,-0.2855,-0.94682,-168.11,-0.5472,0.82121,-0.16184,-14.28,#50,-0.013679,0.99242,-0.12217,472.37,-0.39602,0.10681,0.91201,-170.19,0.91814,0.060856,0.39155,-15.479,#59,-0.32242,0.63685,-0.70034,472.01,-0.50976,0.50659,0.69535,-168.78,0.79761,0.5812,0.16131,-15.856
> view matrix models
> #2,0.30013,0.93022,0.21123,457.83,0.1036,-0.25192,0.96219,-167.05,0.94826,-0.2669,-0.17198,-10.966,#5,-0.43434,0.6974,-0.57006,458.1,-0.43728,0.39004,0.81034,-166.32,0.78748,0.60125,0.13555,-10.509,#22,-0.82678,-0.51424,0.22803,456.52,0.29939,-0.74543,-0.59556,-166.62,0.47624,-0.42413,0.77026,-12.661,#50,-0.01382,-0.98565,0.16824,456.6,-0.91456,0.080481,0.39637,-167.33,-0.40422,-0.14839,-0.90254,-10.362,#59,0.28918,-0.6127,0.73551,457.04,-0.92951,0.0039759,0.36877,-166.06,-0.22887,-0.79031,-0.56836,-11.033
> view matrix models
> #2,-0.010133,0.95541,0.29512,457.02,-0.88037,-0.14848,0.45045,-167.63,0.47418,-0.25525,0.84262,-11.255,#5,-0.67858,0.48802,-0.54897,457.16,-0.71977,-0.59086,0.36444,-167.83,-0.1465,0.64244,0.7522,-10.391,#22,-0.92136,-0.38524,-0.05188,456.33,-0.047966,0.24512,-0.96831,-165.58,0.38575,-0.88967,-0.24432,-11.594,#50,0.075755,-0.88423,0.46086,455.65,0.0098158,0.46283,0.88639,-167.88,-0.99708,-0.062625,0.043741,-11.395,#59,0.30708,-0.33146,0.8921,456.33,-0.24196,0.87939,0.41003,-166.95,-0.92041,-0.34177,0.18985,-10.43
> view matrix models
> #2,-0.25218,-0.038667,0.96691,465.34,-0.9406,0.24453,-0.23554,-171.96,-0.22733,-0.96887,-0.098035,-5.6535,#5,-0.751,0.1835,0.63429,465.85,-0.5078,-0.77453,-0.37716,-172.69,0.42206,-0.60534,0.67485,-5.8015,#22,0.0089213,-0.56134,-0.82754,466.29,-0.46556,0.73007,-0.50024,-170.44,0.88497,0.38973,-0.25482,-4.4049,#50,-0.67744,0.040928,0.73443,464.73,0.72471,0.20808,0.65688,-172.28,-0.12593,0.97726,-0.17062,-4.439,#59,-0.73234,0.25915,0.6297,466.2,0.53805,0.78701,0.30185,-172.2,-0.41736,0.55986,-0.7158,-4.7498
> view matrix models
> #2,0.51673,0.8313,0.20478,455.88,-0.52399,0.49623,-0.69224,-173.65,-0.67707,0.2504,0.69201,-14.101,#5,-0.25661,0.8337,-0.48897,456.28,-0.10085,-0.52625,-0.84433,-174.45,-0.96124,-0.16735,0.21911,-14.044,#22,-0.68008,-0.62911,0.37644,454.23,-0.62683,0.76526,0.14648,-173.35,-0.38023,-0.13635,-0.91479,-12.695,#50,-0.14521,-0.98893,-0.030422,454.81,0.9772,-0.14817,0.15207,-173.91,-0.15489,-0.0076464,0.9879,-14.968,#59,0.18942,-0.77921,0.59745,455.13,0.94828,0.30303,0.094567,-174.57,-0.25473,0.54863,0.79631,-13.656
> view matrix models
> #2,-0.43048,-0.10712,-0.89622,462.48,0.65711,0.64352,-0.39254,-172.99,0.61878,-0.7579,-0.20663,-7.482,#5,0.38884,-0.77041,-0.50524,461.63,0.30523,0.62516,-0.71834,-172.91,0.86927,0.12511,0.47824,-7.2167,#22,-0.025112,0.96661,0.25503,463.03,-0.48355,-0.23503,0.84318,-175.01,0.87496,-0.10215,0.4733,-8.1194,#50,0.90168,0.37479,-0.21562,463.11,0.21184,-0.81764,-0.53534,-173.42,-0.37694,0.43703,-0.81665,-6.31,#59,0.7486,0.43091,-0.5039,461.96,0.5259,-0.84874,0.055491,-174.06,-0.40377,-0.30654,-0.86198,-7.0371
> view matrix models
> #2,-0.0076623,-0.94501,0.32694,466.61,-0.62505,0.25973,0.73611,-172.8,-0.78055,-0.19871,-0.59267,-14.116,#5,0.26013,-0.23779,0.93584,466.88,-0.96481,-0.10257,0.24212,-172.68,0.038418,-0.96589,-0.2561,-14.966,#22,0.9267,-0.073688,-0.36852,467.59,-0.37571,-0.20418,-0.90396,-171.48,-0.0086324,0.97616,-0.2169,-12.673,#50,-0.56976,0.81706,-0.088269,467.56,-0.21281,-0.042943,0.97615,-173.7,0.79378,0.57495,0.19835,-13.631,#59,-0.79105,0.35074,-0.50122,467.79,-0.29626,0.4972,0.81549,-172.34,0.53523,0.79359,-0.2894,-14.242
> show #4 models
> hide #5 models
> hide #2 models
> hide #22 models
> hide #50 models
> hide #59 models
> view #50 clip false
> select add #4
10196 atoms, 4250 bonds, 1247 residues, 6 models selected
> view #50 clip false
> select subtract #4
6023 atoms, 730 residues, 5 models selected
> color bfactor range 50,90 palette ^rainbow
146029 atoms, 18064 residues, atom bfactor range 18.4 to 98.9
> close #4
> close
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/Fig4C/VNE6912_196/7plo_c.pdb
Summary of feedback from opening
/Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/Fig4C/VNE6912_196/7plo_c.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU Q 284
SER Q 300 1 17
Start residue of secondary structure not found: HELIX 2 2 THR Q 313 LYS Q 319
1 7
Start residue of secondary structure not found: HELIX 3 3 ARG Q 526 ALA Q 539
1 14
Start residue of secondary structure not found: HELIX 4 4 LYS Q 593 ALA Q 618
1 26
Start residue of secondary structure not found: HELIX 5 5 SER 2 181 SER 2 187
1 7
678 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (2158 )
Cannot find LINK/SSBOND residue CYS (2158 )
Cannot find LINK/SSBOND residue CYS (2161 )
Cannot find LINK/SSBOND residue CYS (2161 )
Cannot find LINK/SSBOND residue CYS (2187 )
36 messages similar to the above omitted
Chain information for 7plo_c.pdb #1
---
Chain | Description
C | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/Fig4C/VNE6912_196/VNE69_12196.pdb
Chain information for VNE69_12196.pdb #2
---
Chain | Description
A | No description available
> hide pbonds
> set bgColor white
> graphics silhouettes true
> set silhouetteWidth 5
> cartoon style width 3 thickness 1.5
> cartoon style modeHelix wrap
> color #1 lightgrey transparency 0
> color #1 & strand orchid transparency 0
> color #1 & helix medium violet red transparency 0
> color #2 lightgrey transparency 0
> color #2 & strand gold transparency 0
> color #2 & helix goldenrod transparency 0
> tile columns 2 spacingFactor 1
2 models tiled
> lighting flat
> tile columns 2 spacingFactor 1.5
2 models tiled
> tile columns 2 spacingFactor 1
2 models tiled
> lighting flat
> mmaker #1 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 VNE69_12196.pdb, chain A (#2) with 7plo_c.pdb, chain C (#1),
sequence alignment score = 274.1
RMSD between 100 pruned atom pairs is 1.209 angstroms; (across all 391 pairs:
12.197)
> tile columns 2 spacingFactor 1
2 models tiled
> lighting flat
> view matrix
view matrix camera 1,0,0,387.58,0,1,0,216.74,0,0,1,636.64
view matrix models
#1,0.60041,-0.69448,-0.39649,413.82,-0.17325,0.37106,-0.9123,378.8,0.7807,0.61645,0.10247,-142.24,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.95287,-0.022244,0.30258,430.73,0.2613,0.44661,0.85572,221.82,-0.15417,0.89445,-0.41975,216.43
> view matrix
view matrix camera 1,0,0,387.58,0,1,0,216.74,0,0,1,636.64
view matrix models
#1,-0.53403,0.74583,0.39819,234.45,-0.13931,0.38691,-0.91153,366.47,-0.83391,-0.54226,-0.10272,566.19,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.93818,0.099668,-0.33149,430.1,0.24688,0.4786,0.84261,221.95,0.24263,-0.87236,0.42441,209.46
> view matrix camera 1,0,0,387.58,0,1,0,216.74,0,0,1,636.64
> save /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/Fig4C/12_196_7plo-
> c_view01.png width 3000 height 3000 transparentBackground true
> view matrix camera 1,0,0,387.58,0,1,0,216.74,0,0,1,636.64
> save /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/Fig4C/12_196_7plo-
> c_view02.png width 3000 height 3000 transparentBackground true
> view matrix camera 1,0,0,387.58,0,1,0,216.74,0,0,1,636.64
> view matrix models
> #1,0.60041,-0.69448,-0.39649,413.82,-0.17325,0.37106,-0.9123,378.8,0.7807,0.61645,0.10247,-142.24,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.95287,-0.022244,0.30258,430.73,0.2613,0.44661,0.85572,221.82,-0.15417,0.89445,-0.41975,216.43
> save /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/Fig4C/12_196_7plo-
> c_view01.png width 3000 height 3000 transparentBackground true
> view matrix models
> #1,-0.53403,0.74583,0.39819,234.45,-0.13931,0.38691,-0.91153,366.47,-0.83391,-0.54226,-0.10272,566.19,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.93818,0.099668,-0.33149,430.1,0.24688,0.4786,0.84261,221.95,0.24263,-0.87236,0.42441,209.46
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Could not find tool "Structural Screening"
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/ColabFold_&_proteinFASTA/AF_models/v_necatrix_alphafold/VNE6909_017.pdb
Chain information for VNE6909_017.pdb #1
---
Chain | Description
A | No description available
> color bfactor range 50,90 palette ^rainbow
3781 atoms, 460 residues, atom bfactor range 18.8 to 59.8
> set bgColor white
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/ColabFold_&_proteinFASTA/AF_models/v_necatrix_alphafold/VNE6903_368.pdb
Chain information for VNE6903_368.pdb #2
---
Chain | Description
A | No description available
> view matrix models
> #1,-0.53403,0.74583,0.39819,234.45,-0.13931,0.38691,-0.91153,366.47,-0.83391,-0.54226,-0.10272,566.19,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.93818,0.099668,-0.33149,430.1,0.24688,0.4786,0.84261,221.95,0.24263,-0.87236,0.42441,209.46
Invalid "models" argument: No models specified by "#1.1"
> color bfactor range 50,90 palette ^rainbow
5261 atoms, 641 residues, atom bfactor range 18.8 to 95.5
> hide #1 models
> close #1
> close
> devel build
> /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX-
> main/ANNOTEX/
running build
running build_py
creating build
creating build/lib
creating build/lib/chimerax
creating build/lib/chimerax/annotex
copying src/proteome.py -> build/lib/chimerax/annotex
copying src/__init__.py -> build/lib/chimerax/annotex
copying src/tool.py -> build/lib/chimerax/annotex
running bdist_wheel
installing to build/bdist.macosx-10.9-universal2/wheel
running install
running install_lib
creating build/bdist.macosx-10.9-universal2
creating build/bdist.macosx-10.9-universal2/wheel
creating build/bdist.macosx-10.9-universal2/wheel/chimerax
creating build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex
copying build/lib/chimerax/annotex/proteome.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex
copying build/lib/chimerax/annotex/__init__.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex
copying build/lib/chimerax/annotex/tool.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex
running install_egg_info
running egg_info
creating ChimeraX_ANNOTEX.egg-info
writing ChimeraX_ANNOTEX.egg-info/PKG-INFO
writing dependency_links to ChimeraX_ANNOTEX.egg-info/dependency_links.txt
writing requirements to ChimeraX_ANNOTEX.egg-info/requires.txt
writing top-level names to ChimeraX_ANNOTEX.egg-info/top_level.txt
writing manifest file 'ChimeraX_ANNOTEX.egg-info/SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file 'ChimeraX_ANNOTEX.egg-info/SOURCES.txt'
writing manifest file 'ChimeraX_ANNOTEX.egg-info/SOURCES.txt'
Copying ChimeraX_ANNOTEX.egg-info to
build/bdist.macosx-10.9-universal2/wheel/ChimeraX_ANNOTEX-1.0-py3.9.egg-info
running install_scripts
creating build/bdist.macosx-10.9-universal2/wheel/ChimeraX_ANNOTEX-1.0.dist-
info/WHEEL
creating 'dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl' and adding
'build/bdist.macosx-10.9-universal2/wheel' to it
adding 'chimerax/annotex/__init__.py'
adding 'chimerax/annotex/proteome.py'
adding 'chimerax/annotex/tool.py'
adding 'ChimeraX_ANNOTEX-1.0.dist-info/METADATA'
adding 'ChimeraX_ANNOTEX-1.0.dist-info/WHEEL'
adding 'ChimeraX_ANNOTEX-1.0.dist-info/top_level.txt'
adding 'ChimeraX_ANNOTEX-1.0.dist-info/RECORD'
removing build/bdist.macosx-10.9-universal2/wheel
Distribution is in
/Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX-
main/ANNOTEX/dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl
> devel install
> /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX-
> main/ANNOTEX/
running build
running build_py
running bdist_wheel
installing to build/bdist.macosx-10.9-universal2/wheel
running install
running install_lib
creating build/bdist.macosx-10.9-universal2/wheel
creating build/bdist.macosx-10.9-universal2/wheel/chimerax
creating build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex
copying build/lib/chimerax/annotex/proteome.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex
copying build/lib/chimerax/annotex/__init__.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex
copying build/lib/chimerax/annotex/tool.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex
running install_egg_info
running egg_info
writing ChimeraX_ANNOTEX.egg-info/PKG-INFO
writing dependency_links to ChimeraX_ANNOTEX.egg-info/dependency_links.txt
writing requirements to ChimeraX_ANNOTEX.egg-info/requires.txt
writing top-level names to ChimeraX_ANNOTEX.egg-info/top_level.txt
listing git files failed - pretending there aren't any
reading manifest file 'ChimeraX_ANNOTEX.egg-info/SOURCES.txt'
writing manifest file 'ChimeraX_ANNOTEX.egg-info/SOURCES.txt'
Copying ChimeraX_ANNOTEX.egg-info to
build/bdist.macosx-10.9-universal2/wheel/ChimeraX_ANNOTEX-1.0-py3.9.egg-info
running install_scripts
creating build/bdist.macosx-10.9-universal2/wheel/ChimeraX_ANNOTEX-1.0.dist-
info/WHEEL
creating 'dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl' and adding
'build/bdist.macosx-10.9-universal2/wheel' to it
adding 'chimerax/annotex/__init__.py'
adding 'chimerax/annotex/proteome.py'
adding 'chimerax/annotex/tool.py'
adding 'ChimeraX_ANNOTEX-1.0.dist-info/METADATA'
adding 'ChimeraX_ANNOTEX-1.0.dist-info/WHEEL'
adding 'ChimeraX_ANNOTEX-1.0.dist-info/top_level.txt'
adding 'ChimeraX_ANNOTEX-1.0.dist-info/RECORD'
removing build/bdist.macosx-10.9-universal2/wheel
Distribution is in
/Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX-
main/ANNOTEX/dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl
[toolshed install](help:user/commands/toolshed.html#install)
/Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX-
main/ANNOTEX/dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl
[toolshed install
/Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX-
main/ANNOTEX/dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl](cxcmd:toolshed
install
/Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX-
main/ANNOTEX/dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl)
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip is available: 23.0 -> 23.3.1
[notice] To update, run:
/Applications/ChimeraX-1.6.1.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing ./Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX-
main/ANNOTEX/dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl
Requirement already satisfied: ChimeraX-Core~=1.2 in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ANNOTEX==1.0) (1.6.1)
Requirement already satisfied: ChimeraX-UI~=1.0 in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ANNOTEX==1.0) (1.28.4)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-ANNOTEX==1.0) (1.0)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-ANNOTEX==1.0) (1.2)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-ANNOTEX==1.0) (1.1.1)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-
ANNOTEX==1.0) (1.1)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-
ANNOTEX==1.0) (1.3)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-
ANNOTEX==1.0) (1.0.1)
Installing collected packages: ChimeraX-ANNOTEX
Successfully installed ChimeraX-ANNOTEX-1.0
\---
Successfully installed ChimeraX-ANNOTEX-1.0
Installed ChimeraX-ANNOTEX (1.0)
> devel clean
> /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX-
> main/ANNOTEX/
> ui tool show ANNOTEX
> close
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/pdbs/g1.t1.pdb
Chain information for g1.t1.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g1.t1_domain_1.pdb
Chain information for g1.t1_domain_1.pdb #2
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g1.t1_domain_2.pdb
Chain information for g1.t1_domain_2.pdb #3
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g1.t1_domain_3.pdb
Chain information for g1.t1_domain_3.pdb #4
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g1.t1_domain_4.pdb
Chain information for g1.t1_domain_4.pdb #5
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g1.t1_domain_5.pdb
Chain information for g1.t1_domain_5.pdb #6
---
Chain | Description
A | No description available
> color bfactor #1 range 50,90 palette ^rainbow
9047 atoms, 1121 residues, atom bfactor range 23 to 97.7
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/afdb_needed/AF-E7F1X4-F1-model_v2.pdb
AF-E7F1X4-F1-model_v2.pdb title:
Alphafold monomer V2.0 prediction for reverse transcriptase (E7F1X4) [more
info...]
Chain information for AF-E7F1X4-F1-model_v2.pdb #7
---
Chain | Description | UniProt
A | reverse transcriptase | E7F1X4_DANRE 1-1344
> mmaker #7 to #1
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 g1.t1.pdb, chain A (#1) with AF-E7F1X4-F1-model_v2.pdb, chain A
(#7), sequence alignment score = 1773
RMSD between 13 pruned atom pairs is 1.481 angstroms; (across all 1104 pairs:
43.841)
> close #7
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/afdb_needed/AF-A0A2R8QA15-F1-model_v2.pdb
Summary of feedback from opening
/Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/afdb_needed/AF-A0A2R8QA15-F1-model_v2.pdb
---
warning | Ignored bad PDB record found on line 38
DBREF XXXX A 1 1429 UNP A0A2R8QA15 A0A2R8QA15_DANRE 1 1429
AF-A0A2R8QA15-F1-model_v2.pdb title:
Alphafold monomer V2.0 prediction for reverse transcriptase (A0A2R8QA15) [more
info...]
Chain information for AF-A0A2R8QA15-F1-model_v2.pdb #7
---
Chain | Description
A | reverse transcriptase
> mmaker #7 to #1
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 g1.t1.pdb, chain A (#1) with AF-A0A2R8QA15-F1-model_v2.pdb, chain A
(#7), sequence alignment score = 1704.4
RMSD between 13 pruned atom pairs is 1.189 angstroms; (across all 1083 pairs:
43.479)
> close
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/pdbs/g30.t1.pdb
Chain information for g30.t1.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g30.t1_domain_1.pdb
Chain information for g30.t1_domain_1.pdb #2
---
Chain | Description
A | No description available
> color bfactor #1 range 50,90 palette ^rainbow
1381 atoms, 165 residues, atom bfactor range 39.5 to 94.8
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/afdb_needed/AF-Q99MU0-F1-model_v2.pdb
AF-Q99MU0-F1-model_v2.pdb title:
Alphafold monomer V2.0 prediction for protein DBF4 homolog A (Q99Μ0) [more
info...]
Chain information for AF-Q99MU0-F1-model_v2.pdb #3
---
Chain | Description | UniProt
A | protein DBF4 homolog A | DBF4A_CRIGR 1-676
> mmaker #3 to #1
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 g30.t1.pdb, chain A (#1) with AF-Q99MU0-F1-model_v2.pdb, chain A
(#3), sequence alignment score = 226.8
RMSD between 25 pruned atom pairs is 0.884 angstroms; (across all 144 pairs:
47.262)
> close
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/pdbs/g51.t1.pdb
Chain information for g51.t1.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g51.t1_domain_1.pdb
Chain information for g51.t1_domain_1.pdb #2
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g51.t1_domain_2.pdb
Chain information for g51.t1_domain_2.pdb #3
---
Chain | Description
A | No description available
> color bfactor #1 range 50,90 palette ^rainbow
3005 atoms, 356 residues, atom bfactor range 37.6 to 90.8
> open 7a6h
7a6h title:
Cryo-EM structure of human apo RNA Polymerase III [more info...]
Chain information for 7a6h #4
---
Chain | Description | UniProt
A | DNA-directed RNA polymerase III subunit RPC1 | RPC1_HUMAN 1-1390
B | DNA-directed RNA polymerase III subunit RPC2 | RPC2_HUMAN 1-1133
C | DNA-directed RNA polymerases I and III subunit RPAC1 | RPAC1_HUMAN 1-346
D | DNA-directed RNA polymerase III subunit RPC9 | RPC9_HUMAN 1-148
E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | RPAB1_HUMAN
1-210
F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | RPAB2_HUMAN
1-127
G | DNA-directed RNA polymerase III subunit RPC8 | RPC8_HUMAN 1-204
H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | RPAB3_HUMAN
1-150
I | DNA-directed RNA polymerase III subunit RPC10 | RPC10_HUMAN 1-108
J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | RPAB5_HUMAN
1-67
K | DNA-directed RNA polymerases I and III subunit RPAC2 | RPAC2_HUMAN 1-133
L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | RPAB4_HUMAN
1-58
M | DNA-directed RNA polymerase III subunit RPC5 | RPC5_HUMAN 1-708
N | DNA-directed RNA polymerase III subunit RPC4 | RPC4_HUMAN 1-398
O | DNA-directed RNA polymerase III subunit RPC3 | RPC3_HUMAN 1-534
P | DNA-directed RNA polymerase III subunit RPC6 | RPC6_HUMAN 1-316
Q | DNA-directed RNA polymerase III subunit RPC7 | RPC7_HUMAN 1-223
Non-standard residues in 7a6h #4
---
MG — magnesium ion
SF4 — iron/sulfur cluster
ZN — zinc ion
> mmaker #4/O to #1
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 g51.t1.pdb, chain A (#1) with 7a6h, chain O (#4), sequence
alignment score = 281.1
RMSD between 93 pruned atom pairs is 1.329 angstroms; (across all 339 pairs:
10.872)
> hide #4 atoms
> show #4 cartoons
> color #4/O green
> hide #1 models
> show #1 models
> close
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/pdbs/g86.t1.pdb
Chain information for g86.t1.pdb #1
---
Chain | Description
A | No description available
> color bfactor #1 range 50,90 palette ^rainbow
1493 atoms, 177 residues, atom bfactor range 27.8 to 73.6
> close
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/pdbs/g137.t1.pdb
Chain information for g137.t1.pdb #1
---
Chain | Description
A | No description available
> color bfactor #1 range 50,90 palette ^rainbow
1686 atoms, 199 residues, atom bfactor range 36.4 to 69.9
> close
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/pdbs/g213.t1.pdb
Chain information for g213.t1.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g213.t1_domain_1.pdb
Chain information for g213.t1_domain_1.pdb #2
---
Chain | Description
A | No description available
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g213.t1_domain_2.pdb
Chain information for g213.t1_domain_2.pdb #3
---
Chain | Description
A | No description available
> color bfactor #1 range 50,90 palette ^rainbow
3492 atoms, 418 residues, atom bfactor range 39.3 to 98.1
> open
> /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/afdb_needed/AF-Q6C3V4-F1-model_v2.pdb
AF-Q6C3V4-F1-model_v2.pdb title:
Alphafold monomer V2.0 prediction for probable kinetochore protein NUF2
(Q6C3V4) [more info...]
Chain information for AF-Q6C3V4-F1-model_v2.pdb #4
---
Chain | Description | UniProt
A | probable kinetochore protein NUF2 | NUF2_YARLI 1-452
> mmaker #4 to #1
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 g213.t1.pdb, chain A (#1) with AF-Q6C3V4-F1-model_v2.pdb, chain A
(#4), sequence alignment score = 795.1
RMSD between 29 pruned atom pairs is 1.304 angstroms; (across all 418 pairs:
65.526)
OpenGL version: 4.1 INTEL-20.6.4
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Macmini8,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 3,2 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0)
OS Loader Version: 577.140.2~15
Software:
System Software Overview:
System Version: macOS 13.6.1 (22G313)
Kernel Version: Darwin 22.6.0
Time since boot: 5 days, 7 hours, 42 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Metal Support: Metal 3
Displays:
LG Ultra HD:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
S27H85x:
Resolution: 2048 x 1152
UI Looks like: 2048 x 1152 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: H1AK500000
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Adapter Firmware Version: 2,19
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Platform |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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