![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18698 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.6-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 4400,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir9,1",
"coalitionID" : 2170,
"osVersion" : {
"train" : "macOS 15.6",
"build" : "24G84",
"releaseType" : "User"
},
"captureTime" : "2025-09-03 11:00:25.5720 -0700",
"codeSigningMonitor" : 0,
"incident" : "4F7C6B67-6084-4486-A0FD-44DEB95B163C",
"pid" : 7138,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-03 10:30:04.7771 -0700",
"procStartAbsTime" : 2676386809351,
"procExitAbsTime" : 4497232075073,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"656AA428-3E01-51BC-BF6A-9D69E431F2D4","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4722C679-9B07-FC8F-BE85-64B724DE82D3",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["selectedLanguageDoesNotMatchSelectedSiriLanguage","deviceNotCapable"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"bootSessionUUID" : "023A2150-2552-4506-B73B-D156EC5B08B9",
"wakeTime" : 1989,
"bridgeVersion" : {"build":"22P6083","train":"9.6"},
"sleepWakeUUID" : "D1BABA23-EC89-413C-8F86-C322CCA71AB8",
"sip" : "enabled",
"vmRegionInfo" : "0x507 is not in any region. Bytes before following region: 4417010425\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 107464000-107468000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000507","rawCodes":[1,1287],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000507"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":7138},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x507 is not in any region. Bytes before following region: 4417010425\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 107464000-107468000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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changeWindow:toStatus:withConditionalGeneration:]_block_invoke","symbolLocation":44,"imageIndex":160},{"imageOffset":281004,"symbol":"___NSPersistentUIDispatchQueueAsync_block_invoke","symbolLocation":56,"imageIndex":160},{"imageOffset":5817,"symbol":"_dispatch_call_block_and_release","symbolLocation":12,"imageIndex":164},{"imageOffset":96764,"symbol":"_dispatch_client_callout","symbolLocation":6,"imageIndex":164},{"imageOffset":33631,"symbol":"_dispatch_lane_serial_drain","symbolLocation":779,"imageIndex":164},{"imageOffset":36269,"symbol":"_dispatch_lane_invoke","symbolLocation":382,"imageIndex":164},{"imageOffset":72598,"symbol":"_dispatch_root_queue_drain_deferred_wlh","symbolLocation":275,"imageIndex":164},{"imageOffset":70883,"symbol":"_dispatch_workloop_worker_thread","symbolLocation":688,"imageIndex":164},{"imageOffset":10421,"symbol":"_pthread_wqthread","symbolLocation":298,"imageIndex":154},{"imageOffset":6211,"symbol":"start_wqthread","symbolLocation":15,"imageIndex":154}]},{"id":107167,"frames":[{"imageOffset":6196,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":154}],"threadState":{"r13":{"value":0},"rax":{"value":33554800},"rflags":{"value":512},"cpu":{"value":0},"r14":{"value":1},"rsi":{"value":82031},"r8":{"value":409604},"cr2":{"value":0},"rdx":{"value":123145554358272},"r10":{"value":0},"r9":{"value":18446744073709551615},"r15":{"value":123145554881400},"rbx":{"value":123145554882560},"trap":{"value":133},"err":{"value":33554800},"r11":{"value":582},"rip":{"value":140703534143540},"rbp":{"value":0},"rsp":{"value":123145554882560},"r12":{"value":5193734},"rcx":{"value":0},"flavor":"x86_THREAD_STATE","rdi":{"value":123145554882560}}},{"id":107168,"frames":[{"imageOffset":6196,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":154}],"threadState":{"r13":{"value":0},"rax":{"value":33554800},"rflags":{"value":512},"cpu":{"value":0},"r14":{"value":1},"rsi":{"value":177907},"r8":{"value":409604},"cr2":{"value":0},"rdx":{"value":123145555968000},"r10":{"value":0},"r9":{"value":18446744073709551615},"r15":{"value":123145556491136},"rbx":{"value":123145556492288},"trap":{"value":133},"err":{"value":33554800},"r11":{"value":582},"rip":{"value":140703534143540},"rbp":{"value":0},"rsp":{"value":123145556492288},"r12":{"value":1982472},"rcx":{"value":0},"flavor":"x86_THREAD_STATE","rdi":{"value":123145556492288}}}],
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[deleted to fit within ticket limits]
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=2.7G written=552K(0%) resident=0K(0%) swapped_out=552K(0%) unallocated=2.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 264K 33 \nColorSync 264K 33 \nCoreAnimation 7908K 56 \nCoreGraphics 28K 4 \nCoreUI image data 4364K 34 \nFoundation 32K 2 \nIOKit 7940K 1 \nKernel Alloc Once 8K 1 \nMALLOC 2.2G 709 \nMALLOC guard page 48K 12 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 156K 39 \nStack 263.8M 40 \nStack Guard 56.0M 1 \nVM_ALLOCATE 215.6M 394 \n__CTF 824 1 \n__DATA 42.1M 1103 \n__DATA_CONST 110.7M 999 \n__DATA_DIRTY 2590K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 193.3M 155 \n__OBJC_RO 61.3M 1 \n__OBJC_RW 2396K 2 \n__TEXT 1.4G 1124 \n__TPRO_CONST 16 2 \ndyld private memory 532K 7 \nmapped file 552.0M 78 \nshared memory 2996K 28 \n=========== ======= ======= \nTOTAL 5.0G 5213 \nTOTAL, minus reserved VM space 5.0G 5213 \n",
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Log:
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/jeremyb/Desktop/Manuscript 1/Figures/Docking Figure/Docking
> Figure.cxs"
Log from Wed Jul 30 21:19:38 2025UCSF ChimeraX version: 1.8.dev202403220040
(2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/jeremyb/Desktop/Docking Data/Manuscript Figures 2.0.cxs" format
> session
Log from Wed Jul 30 20:30:24 2025UCSF ChimeraX version: 1.8.dev202403220040
(2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript
> 1/Figures/Docking Figure/Docking Figure.cxs"
Log from Fri Jun 20 16:16:52 2025UCSF ChimeraX version: 1.8.dev202403220040
(2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
Log from Fri Jun 20 14:58:38 2025UCSF ChimeraX version: 1.8.dev202403220040
(2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
Log from Fri Jun 20 11:25:34 2025UCSF ChimeraX version: 1.8.dev202403220040
(2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
Log from Thu Jun 19 20:47:46 2025UCSF ChimeraX version: 1.8.dev202403220040
(2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
Log from Thu Jun 19 09:37:09 2025UCSF ChimeraX version: 1.8.dev202403220040
(2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
Log from Wed Jun 18 14:04:06 2025UCSF ChimeraX version: 1.8.dev202403220040
(2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
Log from Wed Jun 18 13:11:23 2025UCSF ChimeraX version: 1.8.dev202403220040
(2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
Log from Wed Jun 18 10:39:40 2025UCSF ChimeraX version: 1.8.dev202403220040
(2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
Log from Sun Jun 8 21:16:38 2025UCSF ChimeraX version: 1.8.dev202403220040
(2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
Log from Sun Jun 8 21:03:10 2025UCSF ChimeraX version: 1.8.dev202403220040
(2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/CsTPS15CT_#14.pdb"
Summary of feedback from opening /Users/jeremyb/Desktop/Terpene Synthase
Project/Manuscript 1/Docking Figure/CsTPS15CT_#14.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
17 messages similar to the above omitted
Chain information for CsTPS15CT_#14.pdb
---
Chain | Description
1.1/A | No description available
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/CsTPS38FN_#6.pdb" "/Users/jeremyb/Desktop/Terpene Synthase
> Project/Manuscript 1/Docking Figure/CsTPS14CT_#3.pdb"
> "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/4xCsTPS38FN_LPP+_3.pdb" "/Users/jeremyb/Desktop/Terpene Synthase
> Project/Manuscript 1/Docking Figure/4xCsTPS14CT_#4.pdb"
Summary of feedback from opening /Users/jeremyb/Desktop/Terpene Synthase
Project/Manuscript 1/Docking Figure/CsTPS38FN_#6.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
17 messages similar to the above omitted
Summary of feedback from opening /Users/jeremyb/Desktop/Terpene Synthase
Project/Manuscript 1/Docking Figure/CsTPS14CT_#3.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
17 messages similar to the above omitted
Summary of feedback from opening /Users/jeremyb/Desktop/Terpene Synthase
Project/Manuscript 1/Docking Figure/4xCsTPS38FN_LPP+_3.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
17 messages similar to the above omitted
Summary of feedback from opening /Users/jeremyb/Desktop/Terpene Synthase
Project/Manuscript 1/Docking Figure/4xCsTPS14CT_#4.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
17 messages similar to the above omitted
Chain information for CsTPS38FN_#6.pdb
---
Chain | Description
2.1/A | No description available
Chain information for CsTPS14CT_#3.pdb
---
Chain | Description
3.1/A | No description available
Chain information for 4xCsTPS38FN_LPP+_3.pdb
---
Chain | Description
4.1/A | No description available
Chain information for 4xCsTPS14CT_#4.pdb
---
Chain | Description
5.1/A | No description available
> color #2.1 #d3b48cff
> color #3.1 #d4b48cff
> color #4.1 #d5b48cff
> color #5.1 #d6b48cff
> hide #5.2 models
> show #5.2 models
> color #5.2 #d7b48cff
> hide #4.2 models
> show #4.2 models
> hide #4.2 models
> show #4.2 models
> color #4.2 #d6b48cff
> color #3.2 #d5b48cff
> color #2.2 #d4b48cff
> color #1.2 #d3b48cff
> select #1.1/A:136
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
69 atoms, 71 bonds, 4 residues, 1 model selected
> select up
9366 atoms, 9470 bonds, 566 residues, 1 model selected
> select up
9378 atoms, 9478 bonds, 570 residues, 1 model selected
> select up
9405 atoms, 9504 bonds, 571 residues, 2 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 3 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> color sel byhetero
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> color sel byhetero
> color sel byelement
> select #4.1/A:638@MN
1 atom, 1 residue, 1 model selected
> select up
9189 atoms, 9292 bonds, 557 residues, 1 model selected
> select up
9216 atoms, 9318 bonds, 558 residues, 2 models selected
> select up
9216 atoms, 9318 bonds, 558 residues, 3 models selected
> select up
9216 atoms, 9318 bonds, 558 residues, 7 models selected
> select up
9216 atoms, 9318 bonds, 558 residues, 7 models selected
> select up
9216 atoms, 9318 bonds, 558 residues, 7 models selected
> select up
9216 atoms, 9318 bonds, 558 residues, 7 models selected
> select up
9216 atoms, 9318 bonds, 558 residues, 7 models selected
> color sel byhetero
> select #3.1/A:625@MN
1 atom, 1 residue, 1 model selected
> select up
9000 atoms, 9105 bonds, 552 residues, 1 model selected
> select up
9027 atoms, 9131 bonds, 553 residues, 2 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 3 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 7 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 7 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 7 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 7 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 7 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 7 models selected
> color #2.1.1 #9470dcff models
> color #3.1.1 #9470dcff models
> color #4.1.1 #9470dcff models
> color #5.1.1 #9470dcff models
> select #2.1/A:513
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #3.1/A:625@MN
1 atom, 1 residue, 1 model selected
> select up
9000 atoms, 9105 bonds, 552 residues, 1 model selected
> select up
9027 atoms, 9131 bonds, 553 residues, 2 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 3 models selected
> select down
9027 atoms, 9131 bonds, 553 residues, 2 models selected
> select down
9000 atoms, 9105 bonds, 552 residues, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
9000 atoms, 9105 bonds, 552 residues, 1 model selected
> color sel byelement
> select clear
> select #1.2//chain_id='>':1@C5
Nothing selected
> hide #2.2 models
> show #2.2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9027 atoms, 9131 bonds, 553 residues, 2 models selected
> select #4.1/A:488
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9405 atoms, 9504 bonds, 571 residues, 2 models selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9219 atoms, 9322 bonds, 558 residues, 2 models selected
> select down
27 atoms, 26 bonds, 1 residue, 1 model selected
> color sel byelement
> select up
9219 atoms, 9322 bonds, 558 residues, 2 models selected
> select up
9219 atoms, 9322 bonds, 558 residues, 3 models selected
> select up
9219 atoms, 9322 bonds, 558 residues, 7 models selected
> select down
9219 atoms, 9322 bonds, 558 residues, 3 models selected
> select down
9219 atoms, 9322 bonds, 558 residues, 2 models selected
> select down
27 atoms, 26 bonds, 1 residue, 1 model selected
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> undo
[Repeated 2 time(s)]
> color #2 #d3b48cff models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> color #1 #d3b48cff models
> color sel byhetero
> select #2.1/A:488
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2//chain_id='>':1@C3
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
432 atoms, 439 bonds, 24 residues, 1 model selected
> color #5 #d4b48cff models
> color #4 #d4b48cff models
> color #3 #d4b48cff models
> select #1.1/A:634@MN
1 atom, 1 residue, 1 model selected
> select up
9378 atoms, 9478 bonds, 570 residues, 1 model selected
> select up
9405 atoms, 9504 bonds, 571 residues, 2 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 3 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> color sel byhetero
> select #4.1/A:638@MN
1 atom, 1 residue, 1 model selected
> select up
9189 atoms, 9292 bonds, 557 residues, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #3.1/A:623@MN
1 atom, 1 residue, 1 model selected
> color #1.1.1 #aa85d9ff models
> color sel byelement
> hide #1.2#2.2#3.2#4.2#5.2#!2.1#!3.1#!4.1#!5.1 target m
> show #5.2 target m
> hide #!1.1 target m
> show #!5.1 target m
> hide #5.2 target m
> select #5.1/A:472
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
178 atoms, 180 bonds, 11 residues, 1 model selected
> select up
8985 atoms, 9094 bonds, 548 residues, 1 model selected
> select up
8997 atoms, 9102 bonds, 552 residues, 1 model selected
> select up
9024 atoms, 9128 bonds, 553 residues, 2 models selected
> select up
9024 atoms, 9128 bonds, 553 residues, 3 models selected
> select up
9024 atoms, 9128 bonds, 553 residues, 7 models selected
> select up
9024 atoms, 9128 bonds, 553 residues, 7 models selected
> select up
9024 atoms, 9128 bonds, 553 residues, 7 models selected
> show #!1.1 models
> show #1.2 models
> show #!2.1 models
> show #2.2 models
> show #!3.1 models
> show #3.2 models
> show #5.2 models
> show #!4.1 models
> show #4.2 models
> select clear
> select #2.1/A:560
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
252 atoms, 253 bonds, 14 residues, 1 model selected
> select up
9180 atoms, 9288 bonds, 553 residues, 1 model selected
> select up
9192 atoms, 9296 bonds, 557 residues, 1 model selected
> select up
9219 atoms, 9322 bonds, 558 residues, 2 models selected
> select up
9219 atoms, 9322 bonds, 558 residues, 3 models selected
> select up
9219 atoms, 9322 bonds, 558 residues, 7 models selected
> select up
9219 atoms, 9322 bonds, 558 residues, 7 models selected
> select up
9219 atoms, 9322 bonds, 558 residues, 7 models selected
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
397 atoms, 403 bonds, 23 residues, 1 model selected
> select up
9177 atoms, 9284 bonds, 553 residues, 1 model selected
> select up
9189 atoms, 9292 bonds, 557 residues, 1 model selected
> select up
9216 atoms, 9318 bonds, 558 residues, 2 models selected
> select up
9216 atoms, 9318 bonds, 558 residues, 3 models selected
> select up
9216 atoms, 9318 bonds, 558 residues, 7 models selected
> select up
9216 atoms, 9318 bonds, 558 residues, 7 models selected
> color sel byhetero
> select #3.1/A:625@MN
1 atom, 1 residue, 1 model selected
> select up
9000 atoms, 9105 bonds, 552 residues, 1 model selected
> select up
9027 atoms, 9131 bonds, 553 residues, 2 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 3 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 7 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 7 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 7 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 7 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 7 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 7 models selected
> color sel byhetero
> select clear
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> select clear
> select #5.1/A:565
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
378 atoms, 381 bonds, 23 residues, 1 model selected
> select up
8985 atoms, 9094 bonds, 548 residues, 1 model selected
> select up
8997 atoms, 9102 bonds, 552 residues, 1 model selected
> select up
9024 atoms, 9128 bonds, 553 residues, 2 models selected
> select up
9024 atoms, 9128 bonds, 553 residues, 3 models selected
> select up
9024 atoms, 9128 bonds, 553 residues, 7 models selected
> select up
9024 atoms, 9128 bonds, 553 residues, 7 models selected
> color sel byhetero
> hide #!5 models
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
> show #!1 models
> select #1.1/A:637@O1
1 atom, 1 residue, 1 model selected
> select add #1.2//chain_id='>':1@H17
1 atom, 1 residue, 1 model selected
> select add #1.2//chain_id='>':1@H17
1 atom, 1 residue, 1 model selected
> select #1.2//chain_id='>':1@H17
Nothing selected
> select #1.2//chain_id='>':1@H17
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9405 atoms, 9504 bonds, 571 residues, 2 models selected
> select down
27 atoms, 26 bonds, 1 residue, 1 model selected
> select sel @< 5
836 atoms, 746 bonds, 96 residues, 10 models selected
> show sel & #1.2#!1.1 atoms
> select up
1670 atoms, 1629 bonds, 96 residues, 10 models selected
> select up
8384 atoms, 8458 bonds, 495 residues, 10 models selected
> select up
45858 atoms, 46387 bonds, 2776 residues, 10 models selected
> select up
45891 atoms, 46403 bonds, 2793 residues, 10 models selected
> select up
45891 atoms, 46403 bonds, 2793 residues, 15 models selected
> select up
45891 atoms, 46403 bonds, 2793 residues, 15 models selected
> select clear
> select #1.1/A:373
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
425 atoms, 429 bonds, 24 residues, 1 model selected
> select up
9366 atoms, 9470 bonds, 566 residues, 1 model selected
> select up
9378 atoms, 9478 bonds, 570 residues, 1 model selected
> select up
9405 atoms, 9504 bonds, 571 residues, 2 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 3 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
Alignment identifier is 1.1/A
> select clear
> select
> #1.1/A:82-87,91-93,95-117,119-131,135-153,169-182,188-194,203-205,209-221,227-242,248-257,265-275,278-280,283-297,303-334,336-338,347-357,361-387,390-402,407-409,416-437,441-465,471-481,484-495,503-505,515-531,534-537,545-553,557-579,587-606,613-621
6728 atoms, 6770 bonds, 400 residues, 1 model selected
> select #1.1/A:346
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.1/A:346
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1.1/A:344
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.1/A:344
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #1.1/A:350
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.1/A:350
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #1.1/A:353
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #1.1/A:353
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1.1/A:371
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.1/A:371
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1.1/A:374
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.1/A:374
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select #1.1/A:377
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.1/A:377
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select
> #1.1/A:82-87,91-93,95-117,119-131,135-153,169-182,188-194,203-205,209-221,227-242,248-257,265-275,278-280,283-297,303-334,336-338,347-357,361-387,390-402,407-409,416-437,441-465,471-481,484-495,503-505,515-531,534-537,545-553,557-579,587-606,613-621
6728 atoms, 6770 bonds, 400 residues, 1 model selected
> select #1.1/A:374
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.1/A:374
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1.1/A:375
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.1/A:375-377
54 atoms, 53 bonds, 3 residues, 1 model selected
> select #1.1/A:374
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.1/A:374-375
36 atoms, 36 bonds, 2 residues, 1 model selected
> select #1.1/A:375
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.1/A:375-376
35 atoms, 34 bonds, 2 residues, 1 model selected
> show sel atoms
> select #1.1/A:378
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.1/A:378
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #1.1/A:381
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.1/A:381-382
24 atoms, 23 bonds, 2 residues, 1 model selected
> show sel atoms
> select #1.1/A:383
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.1/A:383-385
52 atoms, 52 bonds, 3 residues, 1 model selected
> show sel atoms
> select #1.1/A:385
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.1/A:383-385
52 atoms, 52 bonds, 3 residues, 1 model selected
> select
> #1.1/A:82-87,91-93,95-117,119-131,135-153,169-182,188-194,203-205,209-221,227-242,248-257,265-275,278-280,283-297,303-334,336-338,347-357,361-387,390-402,407-409,416-437,441-465,471-481,484-495,503-505,515-531,534-537,545-553,557-579,587-606,613-621
6728 atoms, 6770 bonds, 400 residues, 1 model selected
> select #1.1/A:385
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.1/A:383-385
52 atoms, 52 bonds, 3 residues, 1 model selected
> select #1.1/A:383
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.1/A:383-384
40 atoms, 40 bonds, 2 residues, 1 model selected
> select #1.1/A:456
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.1/A:456
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> color sel magenta
> color sel byhetero
> color sel byelement
> color sel #d4b48cff
> color sel byhetero
> select #1.1/A:482
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.1/A:481
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.1/A:481-487
93 atoms, 92 bonds, 7 residues, 1 model selected
> show sel atoms
> select #1.1/A:482
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.1/A:482
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select #1.1/A:528
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.1/A:528-532
64 atoms, 63 bonds, 5 residues, 1 model selected
> select #1.1/A:524
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.1/A:524-525
38 atoms, 37 bonds, 2 residues, 1 model selected
> show sel atoms
> select #1.1/A:524
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.1/A:524
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel magenta
> select #1.1/A:376
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
425 atoms, 429 bonds, 24 residues, 1 model selected
> select up
9366 atoms, 9470 bonds, 566 residues, 1 model selected
> select up
9378 atoms, 9478 bonds, 570 residues, 1 model selected
> select up
9405 atoms, 9504 bonds, 571 residues, 2 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 3 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select up
9405 atoms, 9504 bonds, 571 residues, 7 models selected
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #1.2#!1.1 atoms
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
> show #!2 models
> hide #!1 models
> select #2.2/6:1@C5
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9219 atoms, 9322 bonds, 558 residues, 2 models selected
> select down
27 atoms, 26 bonds, 1 residue, 1 model selected
> select sel @< 5
816 atoms, 675 bonds, 77 pseudobonds, 122 residues, 15 models selected
> show sel & #2.2#!2.1 atoms
> color #2.1.1 #ab85daff models
> show sel & #2.2#!2.1 atoms
> select up
1814 atoms, 1740 bonds, 77 pseudobonds, 122 residues, 15 models selected
> select down
816 atoms, 675 bonds, 77 pseudobonds, 122 residues, 15 models selected
> select down
790 atoms, 649 bonds, 77 pseudobonds, 122 residues, 15 models selected
> select down
790 atoms, 649 bonds, 77 pseudobonds, 122 residues, 15 models selected
> select up
1814 atoms, 1740 bonds, 77 pseudobonds, 122 residues, 15 models selected
> select up
8565 atoms, 8622 bonds, 77 pseudobonds, 519 residues, 15 models selected
> select down
1814 atoms, 1740 bonds, 77 pseudobonds, 122 residues, 15 models selected
> select up
8565 atoms, 8622 bonds, 77 pseudobonds, 519 residues, 15 models selected
> select down
1814 atoms, 1740 bonds, 77 pseudobonds, 122 residues, 15 models selected
> show sel & #2.2#!2.1 atoms
> hide #1.2#2.2#3.2#4.2#5.2#!2.1#!3.1#!4.1#!5.1 target m
> show #5.2 target m
> hide #!1.1 target m
> show #!5.1 target m
> hide #5.2 target m
> show #4.2 target m
> hide #!5.1 target m
> show #!5.1 target m
> hide #4.2 target m
> show #5.2 target m
> hide #!5.1 target m
> show #!1.1 target m
> hide #5.2 target m
> show #1.2 target m
> hide #!1.1 target m
> show #!2.1 target m
> hide #1.2 target m
> show #!3 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!1.1 models
> show #1.2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select sel @< 10
4118 atoms, 3800 bonds, 83 pseudobonds, 440 residues, 15 models selected
> select ~sel & ##selected
41773 atoms, 42603 bonds, 2640 residues, 5 models selected
> hide sel & #!1.1 atoms
> hide sel & #!1.1 cartoons
> hide #!1 models
> show #!2 models
> show #2.2 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select sel @< 10
4213 atoms, 3932 bonds, 83 pseudobonds, 425 residues, 15 models selected
> select ~sel & ##selected
41678 atoms, 42471 bonds, 2642 residues, 5 models selected
> hide sel & #!2.1 atoms
> hide sel & #!2.1 cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9219 atoms, 9322 bonds, 558 residues, 2 models selected
> select up
9219 atoms, 9322 bonds, 558 residues, 3 models selected
> select up
9219 atoms, 9322 bonds, 558 residues, 7 models selected
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #2.2#!2.1 atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!2 models
> show #!3 models
> show #!3.1 models
> show #3.2 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select sel @< 10
4135 atoms, 3817 bonds, 83 pseudobonds, 453 residues, 15 models selected
> show sel & #3.2#!3.1 atoms
> select ~sel & ##selected
41756 atoms, 42586 bonds, 2630 residues, 5 models selected
> hide sel & #!3.1 atoms
> hide sel & #!3.1 cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9027 atoms, 9131 bonds, 553 residues, 2 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 3 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 7 models selected
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #3.2#!3.1 atoms
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!3 models
> show #!4 models
> show #4.2 models
> show #!4.1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select sel @< 10
4246 atoms, 3950 bonds, 83 pseudobonds, 438 residues, 15 models selected
> show sel & #4.2#!4.1 atoms
> show sel & #4.2#!4.1 cartoons
> select ~sel & ##selected
41645 atoms, 42453 bonds, 2622 residues, 5 models selected
> hide sel & #!4.1 atoms
> hide sel & #!4.1 cartoons
> select #4.2/3:1@C4
1 atom, 1 residue, 1 model selected
> select #4.2/3:1@C4
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9216 atoms, 9318 bonds, 558 residues, 2 models selected
> select up
9216 atoms, 9318 bonds, 558 residues, 3 models selected
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #4.2#!4.1 atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select add #4.1
9216 atoms, 9318 bonds, 16 pseudobonds, 558 residues, 3 models selected
> select subtract #4.1
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!4 models
> ui tool show Matchmaker
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!2 models
> hide #!1 models
> show #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> color sel magenta
> color sel byhetero
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select #2.1/A:523
16 atoms, 15 bonds, 1 residue, 1 model selected
> color sel magenta
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 1 residue, 1 model selected
> color sel magenta
> select #2.1/A:378
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> show #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> select #3.1/A:474@CG2
1 atom, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 1 residue, 1 model selected
> color sel magenta
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> hide #!3 models
> show #!4 models
> select #4.1/A:375
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> show sel atoms
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #1.2#4.2#!1.1#!4.1 atoms
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select #4.1/A:378
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> hide #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!5 models
> hide #!4 models
> show #5.2 models
> show #!5.1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select sel @< 10
4277 atoms, 3958 bonds, 83 pseudobonds, 458 residues, 15 models selected
> show sel & #5.2#!5.1 atoms
> show sel & #5.2#!5.1 cartoons
> select ~sel & ##selected
41614 atoms, 42445 bonds, 2626 residues, 5 models selected
> hide sel & #!5.1 atoms
> hide sel & #!5.1 cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9024 atoms, 9128 bonds, 553 residues, 2 models selected
> select up
9024 atoms, 9128 bonds, 553 residues, 3 models selected
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #5.2#!5.1 atoms
> select #5.2/4:1@C6
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9024 atoms, 9128 bonds, 553 residues, 2 models selected
> select down
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> select #5.1/A:366
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel magenta
> select #5.1/A:514@CB
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> color sel byhetero
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #5.1/A:474@CG1
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
——— End of log from Sun Jun 8 21:03:10 2025 ———
opened ChimeraX session
> hide #!5 models
> show #!2 models
> hide #!2 models
> select clear
> select #1.2//chain_id='>':1@H17
Nothing selected
> show #!2 models
> hide #!1 models
> select #2.2/6:1@H4
1 atom, 1 residue, 1 model selected
> select add #2.1/A:639@O1
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #2.2/6:1@H4 #2.1/A:639@O1
Distance between CsTPS38FN_#6.pdb #2.2/6 1 H4 and CsTPS38FN_#6.pdb #2.1/A 0FV
639 O1: 2.556Å
> hide #!2 models
> show #!2 models
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
——— End of log from Sun Jun 8 21:16:38 2025 ———
opened ChimeraX session
> select #2.1/A:531
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> select #2.1/A:81
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2.1/A:80@C
1 atom, 1 residue, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> select #2.1/A:82
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2.1/A:606
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide #!6 models
> show #!1 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #1.2#!1.1 atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select #1.1/A:603@CG2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select #1.1/A:384@CB
1 atom, 1 residue, 1 model selected
> select #1.1/A:384@N
1 atom, 1 residue, 1 model selected
> select add #1.1/A:384@CB
2 atoms, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> undo
> show sel cartoons
> show sel atoms
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #1.2#!1.1 atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!2 models
> hide #!1 models
> select #2.1/A:383
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
423 atoms, 427 bonds, 24 residues, 1 model selected
> select up
9180 atoms, 9288 bonds, 553 residues, 1 model selected
> select up
9192 atoms, 9296 bonds, 557 residues, 1 model selected
> select up
9219 atoms, 9322 bonds, 558 residues, 2 models selected
> select up
9219 atoms, 9322 bonds, 558 residues, 3 models selected
> select clear
> show #!6 models
> hide #!6 models
> show #!1 models
> hide #!2 models
> show #!6 models
> hide #!6 models
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
——— End of log from Wed Jun 18 10:39:40 2025 ———
opened ChimeraX session
> hide #!1 models
> show #!3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.1/A:558@CG1
1 atom, 1 residue, 1 model selected
> select add #3.1/A:551@NH2
2 atoms, 2 residues, 1 model selected
> select add #3.1/A:558@CD1
3 atoms, 2 residues, 1 model selected
> select subtract #3.1/A:558@CG1
2 atoms, 2 residues, 1 model selected
> select up
43 atoms, 41 bonds, 2 residues, 1 model selected
> select add #3.1/A:532@CG1
44 atoms, 41 bonds, 3 residues, 1 model selected
> select add #3.1/A:377@N
45 atoms, 41 bonds, 4 residues, 1 model selected
> select add #3.1/A:376@CB
46 atoms, 41 bonds, 5 residues, 1 model selected
> select add #3.1/A:376@N
47 atoms, 41 bonds, 5 residues, 1 model selected
> select add #3.1/A:376@ND1
48 atoms, 41 bonds, 5 residues, 1 model selected
> select add #3.1/A:375@N
49 atoms, 41 bonds, 6 residues, 1 model selected
> hide sel atoms
> select up
51 atoms, 42 bonds, 7 residues, 1 model selected
> show sel atoms
> undo
> select down
49 atoms, 42 bonds, 6 residues, 1 model selected
> show sel atoms
> undo
> select clear
> select #3.1/A:363@O
1 atom, 1 residue, 1 model selected
> select add #3.1/A:362@O
2 atoms, 2 residues, 1 model selected
> select add #3.1/A:364@O
3 atoms, 3 residues, 1 model selected
> select add #3.1/A:362@OD1
4 atoms, 3 residues, 1 model selected
> select add #3.1/A:346@NE2
5 atoms, 4 residues, 1 model selected
> select add #3.1/A:510@O
6 atoms, 5 residues, 1 model selected
> hide sel atoms
> select add #3.1/A:274@CD1
7 atoms, 6 residues, 1 model selected
> select up
9 atoms, 1 bond, 7 residues, 1 model selected
> select up
11 atoms, 2 bonds, 7 residues, 1 model selected
> hide sel atoms
[Repeated 2 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:526@CA
1 atom, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:82@CZ
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
218 atoms, 222 bonds, 14 residues, 1 model selected
> select down
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3.1/A:336@CZ
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #3.2/3:1@H16
1 atom, 1 residue, 1 model selected
> show #!6 models
> select add #3.1/A:626@O1
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #3.2/3:1@H16 #3.1/A:626@O1
Distance between CsTPS14CT_#3.pdb #3.2/3 1 H16 and CsTPS14CT_#3.pdb #3.1/A 0FV
626 O1: 3.149Å
> select clear
[Repeated 1 time(s)]
> color #3.1.1 #ac85dbff models
> select #3.1/A:587@CG
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> hide sel cartoons
> select #3.1/A:531@CG
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
14 atoms, 12 bonds, 2 residues, 1 model selected
> select up
34 atoms, 32 bonds, 2 residues, 1 model selected
> select add #3.1/A:466@CZ
35 atoms, 32 bonds, 3 residues, 1 model selected
> select up
55 atoms, 53 bonds, 3 residues, 1 model selected
> select up
273 atoms, 275 bonds, 17 residues, 1 model selected
> select down
55 atoms, 53 bonds, 3 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:365@CA
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
416 atoms, 420 bonds, 24 residues, 1 model selected
> select down
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
56 atoms, 55 bonds, 4 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3.1/A:476@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:600
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
64 atoms, 65 bonds, 5 residues, 1 model selected
> select up
8988 atoms, 9097 bonds, 548 residues, 1 model selected
> select down
64 atoms, 65 bonds, 5 residues, 1 model selected
> select down
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
64 atoms, 65 bonds, 5 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #3.1/A:593@CG
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
272 atoms, 272 bonds, 17 residues, 1 model selected
> select down
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:588@C
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3.1/A:589@O
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 2 residues, 1 model selected
> select up
31 atoms, 32 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #3.1/A:444@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:521
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
18 atoms, 18 bonds, 1 residue, 1 model selected
> show sel cartoons
> show #!5 models
> hide #!3 models
> select #5.2/4:1@H17
1 atom, 1 residue, 1 model selected
> select add #5.1/A:626@O1
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #5.2/4:1@H17 #5.1/A:626@O1
Distance between 4xCsTPS14CT_#4.pdb #5.2/4 1 H17 and 4xCsTPS14CT_#4.pdb #5.1/A
0FV 626 O1: 3.233Å
> color #5.1.1 #ae85dcff models
> hide #!5 models
> show #!2 models
> show #!4 models
> hide #!2 models
> hide #!6 models
> show #!6 models
> select #4.2/3:1@H16
1 atom, 1 residue, 1 model selected
> select add #4.1/A:639@O1
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #4.2/3:1@H16 #4.1/A:639@O1
Distance between 4xCsTPS38FN_LPP+_3.pdb #4.2/3 1 H16 and
4xCsTPS38FN_LPP+_3.pdb #4.1/A 0FV 639 O1: 3.048Å
> show #!1 models
> hide #!4 models
> select #1.2//chain_id='>':1@H17
Nothing selected
> select #1.2//chain_id='>':1@H17
Nothing selected
> select #1.2//chain_id='>':1@H17
Nothing selected
> select #1.2//chain_id='>':1@H17
Nothing selected
> select add #1.1/A:637@O1
1 atom, 1 residue, 1 model selected
> select add #1.2//chain_id='>':1@H17
1 atom, 1 residue, 1 model selected
> select add #1.2//chain_id='>':1@H17
1 atom, 1 residue, 1 model selected
> show #!2 models
> hide #!1 models
> show #!4 models
> hide #!2 models
> select #4.1/A:382
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
411 atoms, 415 bonds, 23 residues, 1 model selected
> select up
9177 atoms, 9284 bonds, 553 residues, 1 model selected
> select up
9189 atoms, 9292 bonds, 557 residues, 1 model selected
> select up
9216 atoms, 9318 bonds, 558 residues, 2 models selected
Alignment identifier is 4.1/A
> select #4.1/A:486
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4.1/A:486
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #4.2#!4.1 atoms
> select #4.1/A:486
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4.1/A:486
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!4 models
> show #!2 models
> select #2.1/A:379
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
423 atoms, 427 bonds, 24 residues, 1 model selected
> select up
9180 atoms, 9288 bonds, 553 residues, 1 model selected
> select up
9192 atoms, 9296 bonds, 557 residues, 1 model selected
> select up
9219 atoms, 9322 bonds, 558 residues, 2 models selected
> select up
9219 atoms, 9322 bonds, 558 residues, 3 models selected
Alignment identifier is 2.1/A
> select #2.1/A:486
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #2.1/A:486
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> select up
176 atoms, 179 bonds, 11 residues, 1 model selected
> show sel cartoons
> select #2.1/A:489
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #2.1/A:488
38 atoms, 36 bonds, 2 residues, 1 model selected
> select add #2.1/A:490
54 atoms, 51 bonds, 3 residues, 1 model selected
> select add #2.1/A:492
64 atoms, 60 bonds, 4 residues, 1 model selected
> select add #2.1/A:493
85 atoms, 81 bonds, 5 residues, 1 model selected
> select add #2.1/A:491
102 atoms, 98 bonds, 6 residues, 1 model selected
> select add #2.1/A:494
122 atoms, 118 bonds, 7 residues, 1 model selected
> select add #2.1/A:495
133 atoms, 128 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select #2.1/A:487
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select add #2.1/A:485
29 atoms, 27 bonds, 2 residues, 1 model selected
> select #2.1/A:486
14 atoms, 14 bonds, 1 residue, 1 model selected
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #2.2#!2.1 atoms
> select clear
> select #2.1/A:486
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select #2.2/6:1@C5
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!4 models
> hide #!2 models
> select clear
> select #4.1/A:371@OG
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select up
6 atoms, 3 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #4.1/A:602@CD1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #4.1/A:475@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:546@OE1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #4.1/A:538@NH1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:533@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select #4.1/A:560@NE
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
[Repeated 4 time(s)]
> select #4.1/A:597@CE
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:604@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:607@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:599@N
1 atom, 1 residue, 1 model selected
> select #4.1/A:519@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
218 atoms, 220 bonds, 13 residues, 1 model selected
> select down
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> hide sel atoms
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #4.1/A:599@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:521@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #4.1/A:79@NH1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:83@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:384@N
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
40 atoms, 40 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #4.1/A:478@ND2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:345@NE
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
105 atoms, 105 bonds, 6 residues, 1 model selected
> show sel cartoons
> undo
> select down
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
173 atoms, 175 bonds, 11 residues, 1 model selected
> select down
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #4.1/A:487@CB
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:453@CG
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:374@CA
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
411 atoms, 415 bonds, 23 residues, 1 model selected
> select down
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel cartoons
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> select #4.1/A:532
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:544@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:475@CZ
1 atom, 1 residue, 1 model selected
> select #4.1/A:464@CG
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:535
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #4.1/A:460@CA
1 atom, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel cartoons
> show #!2 models
> hide #!2 models
> select #4.1/A:535
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #4.1/A:541@C
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> show sel cartoons
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
270 atoms, 275 bonds, 16 residues, 1 model selected
> select down
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select #2.1/A:601
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2.1/A:598
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2.1/A:530
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
274 atoms, 273 bonds, 17 residues, 1 model selected
> show sel cartoons
> select #2.1/A:529
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2.1/A:530
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
274 atoms, 273 bonds, 17 residues, 1 model selected
> select clear
> undo
> select clear
> select #2.1/A:523
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
274 atoms, 273 bonds, 17 residues, 1 model selected
> select up
9180 atoms, 9288 bonds, 553 residues, 1 model selected
Alignment identifier is 2.1/A
> select #2.1/A:523
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:524
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2.1/A:530@CA
1 atom, 1 residue, 1 model selected
> select #2.1/A:529
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2.1/A:530@CA
1 atom, 1 residue, 1 model selected
> select #2.1/A:531
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2.1/A:531-532
25 atoms, 24 bonds, 2 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> show sel atoms
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> select #2.1/A:532
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #2.1/A:522
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #2.1/A:521
36 atoms, 34 bonds, 2 residues, 1 model selected
> select add #2.1/A:520
46 atoms, 43 bonds, 3 residues, 2 models selected
> select add #2.1/A:519
57 atoms, 53 bonds, 4 residues, 2 models selected
> select add #2.1/A:518
74 atoms, 69 bonds, 5 residues, 2 models selected
> select add #2.1/A:516
93 atoms, 87 bonds, 6 residues, 2 models selected
> select add #2.1/A:517
117 atoms, 110 bonds, 7 residues, 2 models selected
> select add #2.1/A:514
131 atoms, 123 bonds, 8 residues, 2 models selected
> select add #2.1/A:515
150 atoms, 141 bonds, 9 residues, 2 models selected
> hide sel cartoons
> select up
274 atoms, 273 bonds, 17 residues, 2 models selected
> select up
9180 atoms, 9288 bonds, 553 residues, 2 models selected
> select up
9192 atoms, 9296 bonds, 557 residues, 2 models selected
> select up
9192 atoms, 9296 bonds, 16 pseudobonds, 557 residues, 3 models selected
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #2.2#!2.1 atoms
> select #2.2/6:1@C2
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #4.1/A:594
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select clear
> select #4.1/A:82
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #!2 models
> hide #!2 models
> select #4.1/A:81
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #!2 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
63 atoms, 65 bonds, 3 residues, 1 model selected
> select up
9177 atoms, 9284 bonds, 553 residues, 1 model selected
> select up
9189 atoms, 9292 bonds, 557 residues, 1 model selected
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #4.2#!4.1 atoms
> select clear
> show #!2 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #4.1/A:350@C
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> select #2.1/A:380
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:377@N
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 25 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!4 models
> select #2.1/A:354
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #2.1/A:354
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #2.2#!2.1 atoms
> select clear
> show #!4 models
> select #4.1/A:479
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #2.1/A:479
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #4.1/A:605
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
411 atoms, 415 bonds, 23 residues, 1 model selected
> select down
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:601
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #4.1/A:598
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #2.1/A:344
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
182 atoms, 185 bonds, 11 residues, 1 model selected
> select down
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
182 atoms, 185 bonds, 11 residues, 1 model selected
> select down
24 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> hide #!4 models
> select #2.2/6:1@C3
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9219 atoms, 9322 bonds, 558 residues, 2 models selected
> select down
27 atoms, 26 bonds, 1 residue, 2 models selected
> show sel atoms
> select clear
> select #2.1/A:527
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2.1/A:527
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide #!2 models
> show #!1 models
> select #1.1/A:485@OG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> select H
22767 atoms, 2773 residues, 10 models selected
> select H
22767 atoms, 2773 residues, 10 models selected
> hide sel & #1.2#!1.1 cartoons
> undo
> hide sel & #1.2#!1.1 atoms
> select clear
> select #1.1/A:607
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.1/A:608
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> select #1.1/A:603
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select #1.1/A:600
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #1.1/A:524
33 atoms, 31 bonds, 2 residues, 1 model selected
> select add #1.1/A:374
53 atoms, 51 bonds, 3 residues, 1 model selected
> select add #1.1/A:482
72 atoms, 69 bonds, 4 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select clear
> hide #!1 models
> show #!3 models
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
——— End of log from Wed Jun 18 13:11:23 2025 ———
opened ChimeraX session
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/4xCsTPS15CT_LPP+_14.pdb"
Summary of feedback from opening /Users/jeremyb/Desktop/Terpene Synthase
Project/Manuscript 1/Docking Figure/4xCsTPS15CT_LPP+_14.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
17 messages similar to the above omitted
Chain information for 4xCsTPS15CT_LPP+_14.pdb
---
Chain | Description
7.1/A | No description available
> color #7.1 #d4b48cff
> color #7.1.1 #ab85daff models
> hide #!3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select sel @< 10
4904 atoms, 4526 bonds, 100 pseudobonds, 522 residues, 19 models selected
> select ~sel & ##selected
50395 atoms, 51384 bonds, 3183 residues, 6 models selected
> hide sel & #!7.1 atoms
> hide sel & #!7.1 cartoons
> select #7.1/A:636@MN
1 atom, 1 residue, 1 model selected
> select up
9381 atoms, 9481 bonds, 570 residues, 1 model selected
> select up
9408 atoms, 9507 bonds, 571 residues, 2 models selected
> color sel byhetero
> select clear
> select #7.1/A:374
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
426 atoms, 430 bonds, 24 residues, 1 model selected
> select up
9369 atoms, 9473 bonds, 566 residues, 1 model selected
> select up
9381 atoms, 9481 bonds, 570 residues, 1 model selected
> show sel atoms
> undo
> select down
9369 atoms, 9473 bonds, 566 residues, 1 model selected
> show sel atoms
> undo
> select down
426 atoms, 430 bonds, 24 residues, 1 model selected
> select down
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
426 atoms, 430 bonds, 24 residues, 1 model selected
> select up
9369 atoms, 9473 bonds, 566 residues, 1 model selected
> select down
426 atoms, 430 bonds, 24 residues, 1 model selected
> show sel atoms
> undo
> select clear
> select #7.1/A:382
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:379
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:378
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:377
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:375
16 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:374
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:371
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:349
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:350
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:347
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:346
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:353
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:608
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:607
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:603
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #7.1/A:600
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:531
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #7.1/A:527
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:524
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:484
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:483
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7.1/A:481
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> select up
426 atoms, 430 bonds, 24 residues, 1 model selected
> select up
9369 atoms, 9473 bonds, 566 residues, 1 model selected
> select up
9381 atoms, 9481 bonds, 570 residues, 1 model selected
> select H
27442 atoms, 3340 residues, 12 models selected
> hide sel & #7.2#!7.1 atoms
> select clear
> select #7.2//chain_id='>':1@C3
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> color #7.2 #d5b48cff
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> show #!1 models
> select #7.1/A:374
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
426 atoms, 430 bonds, 24 residues, 1 model selected
> select down
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 1 residue, 1 model selected
> color sel magenta
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> hide sel cartoons
> hide sel atoms
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #7.1/A:484
10 atoms, 9 bonds, 1 residue, 1 model selected
Alignment identifier is 7.1/A
> select #7.1/A:485
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #7.1/A:485-486
27 atoms, 26 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select #7.1/A:485
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #7.1/A:485
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select #7.1/A:486
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> show #!1 models
> hide #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> show #!5 models
> show #!1 models
> hide #!1 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #7.1/A:607
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> select #7.1/A:525@CA
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1.1/A:486
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:483
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:483
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.1/A:486
16 atoms, 15 bonds, 1 residue, 1 model selected
Alignment identifier is 1.1/A
> select #7.1/A:486
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #7.1/A:486-487
35 atoms, 34 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select up
190 atoms, 192 bonds, 12 residues, 1 model selected
> select up
9369 atoms, 9473 bonds, 566 residues, 1 model selected
> select up
9381 atoms, 9481 bonds, 570 residues, 1 model selected
> select H
27442 atoms, 3340 residues, 12 models selected
> hide sel & #1.2#7.2#!1.1#!7.1 atoms
> select clear
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!7 models
> show #!1 models
> select #1.2//chain_id='>':1@C6
Nothing selected
> select #1.2//chain_id='>':1@C6
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9405 atoms, 9504 bonds, 571 residues, 2 models selected
> select down
27 atoms, 26 bonds, 1 residue, 2 models selected
> show sel atoms
> select clear
> select #1.2//chain_id='>':1@H17
Nothing selected
> select #1.2//chain_id='>':1@H17
Nothing selected
> show #!5 models
> hide #!6 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!6 models
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
——— End of log from Wed Jun 18 14:04:06 2025 ———
opened ChimeraX session
> hide #!5 models
> show #!1 models
> select #1.1/A:456@CG
1 atom, 1 residue, 1 model selected
> select #1.1/A:456@CG
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select H
27442 atoms, 3340 residues, 12 models selected
> hide sel & #1.2#!1.1 atoms
> select #1.2//chain_id='>':1@C3
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1.1/A:374
20 atoms, 20 bonds, 1 residue, 1 model selected
> select add #1.1/A:377
39 atoms, 38 bonds, 2 residues, 2 models selected
> select add #1.1/A:482
58 atoms, 56 bonds, 3 residues, 2 models selected
> select add #1.1/A:524
72 atoms, 69 bonds, 4 residues, 2 models selected
> show sel surfaces
> select up
718 atoms, 720 bonds, 43 residues, 2 models selected
> select up
9366 atoms, 9470 bonds, 566 residues, 2 models selected
> select up
9378 atoms, 9478 bonds, 570 residues, 2 models selected
> select up
9378 atoms, 9478 bonds, 13 pseudobonds, 570 residues, 3 models selected
> select up
9378 atoms, 9478 bonds, 13 pseudobonds, 570 residues, 3 models selected
> show sel surfaces
> hide sel surfaces
> select clear
> select #1.1/A:485
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1.1 & sel) magenta
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #1.1/A:607
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!1 models
> hide #!3 models
> select #1.1/A:482
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #1.1/A:524
33 atoms, 31 bonds, 2 residues, 2 models selected
> select add #1.1/A:377
52 atoms, 49 bonds, 3 residues, 2 models selected
> select add #1.1/A:374
72 atoms, 69 bonds, 4 residues, 2 models selected
> show sel surfaces
> show #!5 models
> hide #!1 models
> hide #!5 models
> show #!3 models
> select #3.1/A:366
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3.1/A:369
40 atoms, 39 bonds, 2 residues, 1 model selected
> select add #3.1/A:514
59 atoms, 57 bonds, 3 residues, 1 model selected
> select add #3.1/A:474
75 atoms, 72 bonds, 4 residues, 1 model selected
> show sel surfaces
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!5 models
> hide #!3 models
> show #!1 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!5 models
> select add #5.1/A:536@CD1
76 atoms, 72 bonds, 5 residues, 3 models selected
> select add #5.1/A:532@CG1
77 atoms, 72 bonds, 6 residues, 3 models selected
> select add #5.1/A:469@ND2
78 atoms, 72 bonds, 7 residues, 3 models selected
> select add #5.1/A:529@NH1
79 atoms, 72 bonds, 8 residues, 3 models selected
> select add #5.1/A:375@N
80 atoms, 72 bonds, 9 residues, 3 models selected
> select add #5.1/A:364@O
81 atoms, 72 bonds, 10 residues, 3 models selected
> select add #5.1/A:363@O
82 atoms, 72 bonds, 11 residues, 3 models selected
> select add #5.1/A:362@O
83 atoms, 72 bonds, 12 residues, 3 models selected
> select add #5.1/A:362@OD1
84 atoms, 72 bonds, 12 residues, 3 models selected
> select add #5.1/A:344@C
85 atoms, 72 bonds, 13 residues, 3 models selected
> select add #5.1/A:604@CB
86 atoms, 72 bonds, 14 residues, 3 models selected
> select add #5.1/A:558@CD1
87 atoms, 72 bonds, 15 residues, 3 models selected
> hide sel & #!5.1 atoms
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!5 models
> show #!3 models
> hide #!5 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!5 models
> hide #!3 models
> select add #5.1/A:474
106 atoms, 90 bonds, 16 residues, 3 models selected
> select add #5.1/A:514
120 atoms, 103 bonds, 17 residues, 3 models selected
> select add #5.1/A:366
140 atoms, 123 bonds, 18 residues, 3 models selected
> select add #5.1/A:369
159 atoms, 141 bonds, 19 residues, 3 models selected
> show sel & #!5.1 surfaces
> color (#!5.1 & sel) magenta
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!5 models
> show #!3 models
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
——— End of log from Thu Jun 19 09:37:09 2025 ———
opened ChimeraX session
> hide #!3 models
> show #!2 models
> show #!4 models
> hide #!6 models
> select #4.2/3:1@C7
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9216 atoms, 9318 bonds, 558 residues, 2 models selected
> select down
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!4 models
> select #2.1/A:483
16 atoms, 15 bonds, 1 residue, 1 model selected
> show sel surfaces
> select #2.1/A:378
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #2.1/A:375
40 atoms, 39 bonds, 2 residues, 2 models selected
> select add #2.1/A:486
54 atoms, 53 bonds, 3 residues, 2 models selected
> select subtract #2.1/A:486
40 atoms, 39 bonds, 2 residues, 2 models selected
> select add #2.1/A:523
56 atoms, 54 bonds, 3 residues, 2 models selected
> select add #2.1/A:483
72 atoms, 69 bonds, 4 residues, 2 models selected
> show sel surfaces
> select up
720 atoms, 722 bonds, 43 residues, 2 models selected
> show sel surfaces
> select up
9180 atoms, 9288 bonds, 553 residues, 2 models selected
> select up
9192 atoms, 9296 bonds, 557 residues, 2 models selected
> select up
9192 atoms, 9296 bonds, 16 pseudobonds, 557 residues, 3 models selected
> show sel surfaces
> undo
[Repeated 2 time(s)]
> hide sel surfaces
> select clear
> select add #2.1/A:523
16 atoms, 15 bonds, 1 residue, 1 model selected
> select add #2.1/A:483
32 atoms, 30 bonds, 2 residues, 1 model selected
> select add #2.1/A:378
51 atoms, 48 bonds, 3 residues, 2 models selected
> select add #2.1/A:375
72 atoms, 69 bonds, 4 residues, 2 models selected
> select add #2.1/A:486
86 atoms, 83 bonds, 5 residues, 2 models selected
Alignment identifier is 2.1/A
> select #2.1/A:376
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:376-377
35 atoms, 34 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel cartoons
> hide sel atoms
> select add #2.1/A:523
51 atoms, 49 bonds, 3 residues, 2 models selected
> select add #2.1/A:483
67 atoms, 64 bonds, 4 residues, 2 models selected
> select clear
> select #2.1/A:345
24 atoms, 23 bonds, 1 residue, 1 model selected
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel atoms
> select #4.1/A:525@C
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel atoms
> select #4.1/A:526
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #4.1/A:482
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #4.1/A:483
19 atoms, 18 bonds, 1 residue, 1 model selected
Alignment identifier is 4.1/A
> select #4.1/A:482-483
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #4.1/A:482-483
30 atoms, 29 bonds, 2 residues, 1 model selected
> show sel cartoons
> select #4.1/A:457
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #4.1/A:528
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select clear
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #4.1/A:375
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #4.1/A:376
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #4.1/A:376-378
54 atoms, 53 bonds, 3 residues, 1 model selected
> show sel cartoons
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #2.1/A:528@OD2
1 atom, 1 residue, 1 model selected
> select clear
> select #2.1/A:528@OD2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> select #4.1/A:379
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #4.1/A:380
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #4.1/A:380-382
50 atoms, 49 bonds, 3 residues, 1 model selected
> show sel cartoons
> hide #!2 models
> show #!2 models
> hide #!4 models
> select #2.1/A:379
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2.1/A:379-382
64 atoms, 63 bonds, 4 residues, 1 model selected
> show sel cartoons
> select clear
> show #!6 models
> hide #!6 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel cartoons
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> select clear
> set bgColor white
> select #2.1/A:639@O1
1 atom, 1 residue, 1 model selected
> select add #2.2/6:1@H4
2 atoms, 2 residues, 2 models selected
> select clear
> set bgColor black
> select #2.1/A:483
16 atoms, 15 bonds, 1 residue, 1 model selected
> select add #2.1/A:523
32 atoms, 30 bonds, 2 residues, 2 models selected
> select add #2.1/A:375
53 atoms, 51 bonds, 3 residues, 2 models selected
> select add #2.1/A:378
72 atoms, 69 bonds, 4 residues, 2 models selected
> show sel surfaces
> show #!4 models
> hide #!2 models
> select add #4.1/A:523
86 atoms, 82 bonds, 5 residues, 3 models selected
> select add #4.1/A:483
105 atoms, 100 bonds, 6 residues, 3 models selected
> select add #4.1/A:378
124 atoms, 118 bonds, 7 residues, 3 models selected
> select add #4.1/A:375
144 atoms, 138 bonds, 8 residues, 3 models selected
> show sel & #!4.1 surfaces
> hide sel & #!4.1 surfaces
> show #!2 models
> hide sel surfaces
> hide #!4 models
> hide #!2 models
> show #!4 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> hide #!4 models
> show #!2 models
> show #!1 models
> hide #!2 models
> select #1.1/A:377
19 atoms, 18 bonds, 1 residue, 1 model selected
Alignment identifier is 1.1/A
> select #1.1/A:378-379
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #1.1/A:378-381
64 atoms, 63 bonds, 4 residues, 1 model selected
> show sel cartoons
> select clear
> select #1.1/A:531
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1.1/A:377
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.1/A:377
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.1/A:377-382
95 atoms, 94 bonds, 6 residues, 1 model selected
> show sel cartoons
> select #1.1/A:376
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.1/A:372-376
98 atoms, 98 bonds, 5 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> select #1.1/A:371
10 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
> select #1.1/A:371
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
425 atoms, 429 bonds, 24 residues, 1 model selected
> select up
9366 atoms, 9470 bonds, 566 residues, 2 models selected
> select up
9378 atoms, 9478 bonds, 570 residues, 2 models selected
> hide sel surfaces
> select clear
> select #1.1/A:383@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
> select #1.1/A:600
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!7 models
> hide #!1 models
> select #7.1/A:378
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
426 atoms, 430 bonds, 24 residues, 1 model selected
> select up
9369 atoms, 9473 bonds, 566 residues, 1 model selected
> select up
9381 atoms, 9481 bonds, 570 residues, 1 model selected
> select up
9408 atoms, 9507 bonds, 571 residues, 2 models selected
> select up
9408 atoms, 9507 bonds, 571 residues, 3 models selected
> select up
9408 atoms, 9507 bonds, 4 pseudobonds, 571 residues, 9 models selected
> show sel surfaces
> hide sel surfaces
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
——— End of log from Thu Jun 19 20:47:46 2025 ———
opened ChimeraX session
> select clear
> select #7.1/A:484
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #7.1/A:486
16 atoms, 15 bonds, 1 residue, 1 model selected
> select add #7.1/A:487
35 atoms, 33 bonds, 2 residues, 2 models selected
> hide sel atoms
> select clear
> hide #!7 models
> show #!1 models
> select #1.1/A:486
16 atoms, 15 bonds, 1 residue, 1 model selected
> select add #1.1/A:487
35 atoms, 33 bonds, 2 residues, 2 models selected
> hide sel atoms
> select clear
> select #1.1/A:487
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #1.1/A:486
35 atoms, 33 bonds, 2 residues, 2 models selected
> hide sel cartoons
> select #1.1/A:481
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1.1/A:603
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show #!7 models
> hide #!1 models
> select #7.1/A:607
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #7.1/A:608
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #7.1/A:607
19 atoms, 17 bonds, 2 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> hide sel atoms
> select #7.1/A:603
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #7.1/A:600
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #7.1/A:487
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #7.1/A:486
35 atoms, 33 bonds, 2 residues, 2 models selected
> hide sel cartoons
> show #!1 models
> hide #!7 models
> select #1.1/A:349
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #1.1/A:350
25 atoms, 23 bonds, 2 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show #!7 models
> select #1.1/A:349
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #7.1/A:350
25 atoms, 23 bonds, 2 residues, 3 models selected
> hide sel atoms
> select #1.1/A:349
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide sel atoms
> hide #!1 models
> select #7.1/A:349
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel atoms
> select #7.1/A:371
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #7.1/A:531
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #7.1/A:382
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> hide #!7 models
> hide #!1 models
> show #!1 models
> select #1.1/A:382
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1.1/A:484
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!6 models
> hide #!6 models
> select #1.1/A:371
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!7 models
> hide #!1 models
> select #7.1/A:379
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #7.1/A:347
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #7.1/A:379
19 atoms, 18 bonds, 1 residue, 1 model selected
Alignment identifier is 7.1/A
> select #7.1/A:380
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #7.1/A:380-381
31 atoms, 30 bonds, 2 residues, 1 model selected
> show sel cartoons
> select clear
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #7.1/A:527
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> select #7.1/A:481
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #7.1/A:525
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #7.1/A:459
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel surfaces
> hide sel cartoons
> select #7.1/A:347
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #7.1/A:346
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #7.1/A:346
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #7.1/A:345-346
36 atoms, 35 bonds, 2 residues, 1 model selected
> select #7.1/A:347
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #7.1/A:349
34 atoms, 32 bonds, 2 residues, 2 models selected
> select #7.1/A:348-349
32 atoms, 31 bonds, 2 residues, 1 model selected
> select #7.1/A:346-349
75 atoms, 74 bonds, 4 residues, 1 model selected
> show sel cartoons
> select #7.1/A:346-347
43 atoms, 42 bonds, 2 residues, 1 model selected
> select #7.1/A:341-347
123 atoms, 123 bonds, 7 residues, 1 model selected
> select #7.1/A:353
24 atoms, 25 bonds, 1 residue, 1 model selected
> select add #7.1/A:350
34 atoms, 34 bonds, 2 residues, 2 models selected
> select #7.1/A:350-351
30 atoms, 30 bonds, 2 residues, 1 model selected
> select #7.1/A:350-353
73 atoms, 75 bonds, 4 residues, 1 model selected
> show sel cartoons
> select clear
> show #!1 models
> hide #!7 models
> select #1.1/A:349
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #1.1/A:353
39 atoms, 39 bonds, 2 residues, 2 models selected
Alignment identifier is 1.1/A
> select #1.1/A:353
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #1.1/A:350-353
73 atoms, 75 bonds, 4 residues, 1 model selected
> show sel cartoons
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> select #7.1/A:525
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1.1/A:459
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #7.1/A:525
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.1/A:525
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!7 models
> select #1.1/A:347
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #1.1/A:349
34 atoms, 32 bonds, 2 residues, 1 model selected
> select #1.1/A:348
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.1/A:348-349
32 atoms, 31 bonds, 2 residues, 1 model selected
> show sel cartoons
> select clear
> show #!7 models
> hide #!1 models
> show #!3 models
> hide #!7 models
> select #3.1/A:514@CD2
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> select up
272 atoms, 272 bonds, 17 residues, 2 models selected
> select up
8988 atoms, 9097 bonds, 548 residues, 2 models selected
> select up
9000 atoms, 9105 bonds, 552 residues, 2 models selected
> select up
9000 atoms, 9105 bonds, 19 pseudobonds, 552 residues, 3 models selected
> select up
9000 atoms, 9105 bonds, 19 pseudobonds, 552 residues, 3 models selected
> select up
9027 atoms, 9131 bonds, 19 pseudobonds, 553 residues, 4 models selected
> select up
9027 atoms, 9131 bonds, 19 pseudobonds, 553 residues, 5 models selected
> hide sel surfaces
> hide sel atoms
> undo
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
> select clear
> select #3.1/A:515
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:519
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:520
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:595
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.1/A:590
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add #3.1/A:591
21 atoms, 19 bonds, 2 residues, 2 models selected
> hide sel atoms
> select clear
> select #3.1/A:372
19 atoms, 18 bonds, 1 residue, 1 model selected
Alignment identifier is 3.1/A
> select add #3.1/A:373
31 atoms, 29 bonds, 2 residues, 2 models selected
> select #3.1/A:371
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3.1/A:370-371
33 atoms, 32 bonds, 2 residues, 1 model selected
> show sel cartoons
> select clear
> select #3.1/A:369
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #3.1/A:370
33 atoms, 31 bonds, 2 residues, 2 models selected
> select add #3.1/A:371
52 atoms, 49 bonds, 3 residues, 2 models selected
> select #3.1/A:368
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3.1/A:368
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select #3.1/A:368
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #3.1/A:371
38 atoms, 36 bonds, 2 residues, 2 models selected
> hide sel atoms
> select #3.1/A:372
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
21 atoms, 19 bonds, 2 residues, 2 models selected
> select up
31 atoms, 29 bonds, 2 residues, 2 models selected
> show sel cartoons
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select up
432 atoms, 439 bonds, 24 residues, 2 models selected
> select up
8988 atoms, 9097 bonds, 548 residues, 2 models selected
> select up
9000 atoms, 9105 bonds, 552 residues, 2 models selected
> select H
27442 atoms, 3340 residues, 12 models selected
> hide sel & #3.2#!3.1 atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #3.1/A:367
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!1 models
> hide #!7 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
> show #!2 models
> select add #2.1/A:84
23 atoms, 22 bonds, 2 residues, 3 models selected
> select add #2.1/A:345
47 atoms, 45 bonds, 3 residues, 4 models selected
> select add #2.1/A:347
71 atoms, 68 bonds, 4 residues, 4 models selected
Alignment identifier is 2.1/A
Alignment identifier is 3.1/A
> select #2.1/A:346
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2.1/A:346
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select #2.1/A:84
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #2.1/A:354
24 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #2.1/A:464
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #2.1/A:543
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #2.1/A:531@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> undo
> select up
14 atoms, 13 bonds, 1 residue, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #2.1/A:530
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2.1/A:387
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:382
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2.1/A:387
28 atoms, 26 bonds, 2 residues, 2 models selected
> select #2.1/A:383
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2.1/A:383-386
64 atoms, 64 bonds, 4 residues, 1 model selected
> show sel cartoons
> select clear
> select #2.1/A:80
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> select #4.1/A:543
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> select #4.1/A:354
24 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #4.1/A:80
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #4.1/A:383
36 atoms, 34 bonds, 2 residues, 2 models selected
> select add #4.1/A:386
48 atoms, 45 bonds, 3 residues, 2 models selected
> select #2.1/A:382-383
24 atoms, 23 bonds, 2 residues, 1 model selected
> select #2.1/A:382-386
76 atoms, 76 bonds, 5 residues, 1 model selected
> show #4.2#!4.1 cartoons
> undo
> show #4.2#!4.1 cartoons
> undo
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> select #4.1/A:383
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #4.1/A:386
24 atoms, 22 bonds, 2 residues, 2 models selected
Alignment identifier is 4.1/A
> select #4.1/A:386
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #4.1/A:383-386
64 atoms, 64 bonds, 4 residues, 1 model selected
> show sel cartoons
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> select #2.1/A:457
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #2.1/A:528
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> select #4.1/A:530
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #4.1/A:345
24 atoms, 23 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #4.1/A:345
24 atoms, 23 bonds, 1 residue, 1 model selected
> select add #4.1/A:347
48 atoms, 46 bonds, 2 residues, 2 models selected
Alignment identifier is 4.1/A
> select #4.1/A:346
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #4.1/A:346
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #4.1/A:464
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> select #2.1/A:530
10 atoms, 9 bonds, 1 residue, 1 model selected
Alignment identifier is 2.1/A
> select #2.1/A:531
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2.1/A:531
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> select H
27442 atoms, 3340 residues, 12 models selected
> hide sel & #2.2#!2.1 atoms
> select #2.2/6:1@C7
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
> hide #!4 models
> show #!1 models
> show #!7 models
> hide #!1 models
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
> show #!3 models
> hide #!7 models
> show #!5 models
> hide #!3 models
> select #5.1/A:517
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
267 atoms, 267 bonds, 17 residues, 2 models selected
> select up
8985 atoms, 9094 bonds, 548 residues, 2 models selected
> hide sel surfaces
> select clear
> select add #5.1/A:344@CD2
1 atom, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> select clear
> show #!3 models
> hide #!3 models
> select #5.1/A:370
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #5.1/A:367
30 atoms, 28 bonds, 2 residues, 2 models selected
Alignment identifier is 5.1/A
> select #5.1/A:368
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.1/A:368-370
52 atoms, 51 bonds, 3 residues, 1 model selected
> show sel cartoons
> select clear
> select #5.1/A:344@CG
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> select #5.1/A:479@N
1 atom, 1 residue, 1 model selected
> select add #5.1/A:478@N
2 atoms, 2 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> select #5.1/A:367
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5.1/A:368
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5.1/A:372
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> select #5.1/A:594
17 atoms, 16 bonds, 1 residue, 1 model selected
> select add #5.1/A:590
27 atoms, 25 bonds, 2 residues, 2 models selected
> select #5.1/A:591
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.1/A:591-594
65 atoms, 65 bonds, 4 residues, 1 model selected
> show sel cartoons
> select #5.1/A:592
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5.1/A:593
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 2 residues, 1 model selected
> select up
31 atoms, 30 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select #5.1/A:590
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 2 models selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel atoms
> select #5.1/A:470
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #5.1/A:600
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 2 models selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> select #5.1/A:523
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
56 atoms, 55 bonds, 4 residues, 2 models selected
> select up
8985 atoms, 9094 bonds, 548 residues, 2 models selected
> select down
56 atoms, 55 bonds, 4 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #5.1/A:600
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
64 atoms, 65 bonds, 5 residues, 2 models selected
> select up
8985 atoms, 9094 bonds, 548 residues, 2 models selected
> select down
64 atoms, 65 bonds, 5 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 2 models selected
> select up
218 atoms, 222 bonds, 14 residues, 2 models selected
> select up
8985 atoms, 9094 bonds, 548 residues, 2 models selected
> select down
218 atoms, 222 bonds, 14 residues, 2 models selected
> select down
21 atoms, 21 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #5.1/A:336@NE
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 2 models selected
> select up
129 atoms, 130 bonds, 7 residues, 2 models selected
> select down
24 atoms, 23 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #5.1/A:592
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
307 atoms, 309 bonds, 19 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #!5 models
> show #!3 models
> hide #!5 models
> hide #!3 models
> show #!3 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> select #5.1/A:595
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #5.1/A:595
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #5.1/A:552-594
687 atoms, 694 bonds, 43 residues, 1 model selected
> select #5.1/A:552-595
708 atoms, 716 bonds, 44 residues, 1 model selected
> select #5.1/A:596
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #5.1/A:590-596
113 atoms, 114 bonds, 7 residues, 1 model selected
> show sel cartoons
> select #5.1/A:597
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #5.1/A:597-598
28 atoms, 28 bonds, 2 residues, 1 model selected
> show sel cartoons
> select #5.1/A:595
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select #5.1/A:594
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5.1/A:591
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
307 atoms, 309 bonds, 19 residues, 2 models selected
> select up
8985 atoms, 9094 bonds, 548 residues, 2 models selected
> select H
27442 atoms, 3340 residues, 12 models selected
> hide sel & #5.2#!5.1 atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5.1/A:510@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5.1/A:477@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> show #!3 models
> hide #!5 models
> show #!5 models
> select #3.1/A:519
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
272 atoms, 272 bonds, 17 residues, 1 model selected
> select up
8988 atoms, 9097 bonds, 548 residues, 2 models selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> select #3.1/A:520
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
272 atoms, 272 bonds, 17 residues, 2 models selected
> select #3.1/A:520
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
272 atoms, 272 bonds, 17 residues, 2 models selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #5.1/A:520@CD2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #5.1/A:520@CD1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide #!3 models
> show #!3 models
> hide #!3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel cartoons
> show #!3 models
> hide #!3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 2 models selected
> show sel cartoons
> show #!3 models
> hide #!3 models
> select clear
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!3 models
> hide #!3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 2 models selected
> show sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 2 models selected
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> hide sel atoms
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #5.1/A:478@CG2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5.1/A:476
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #5.1/A:512
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5.1/A:513
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!5 models
> show #!5 models
> hide sel cartoons
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5.1/A:598
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #5.1/A:597
28 atoms, 27 bonds, 2 residues, 2 models selected
> select add #5.1/A:596
45 atoms, 43 bonds, 3 residues, 2 models selected
> hide sel cartoons
> hide #!5 models
> show #!5 models
> select #5.1/A:593
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #5.1/A:592
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select clear
[Repeated 1 time(s)]
> select #3.1/A:517
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add #3.1/A:515
34 atoms, 32 bonds, 2 residues, 2 models selected
Alignment identifier is 3.1/A
> select #3.1/A:516
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3.1/A:516
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #3.1/A:517@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3.1/A:594
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
307 atoms, 309 bonds, 19 residues, 2 models selected
> show sel cartoons
> undo
> select #3.1/A:581
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #3.1/A:581-586
95 atoms, 94 bonds, 6 residues, 1 model selected
> select #3.1/A:594
17 atoms, 16 bonds, 1 residue, 1 model selected
> select add #3.1/A:590
27 atoms, 25 bonds, 2 residues, 2 models selected
> select #3.1/A:591
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3.1/A:591-594
65 atoms, 65 bonds, 4 residues, 1 model selected
> show sel cartoons
> select #3.1/A:590
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #3.1/A:595
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> select #3.1/A:595
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select H
27442 atoms, 3340 residues, 12 models selected
> hide sel & #3.2#!3.1 atoms
> select clear
> select #3.1/A:517
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/A:521
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!5 models
> hide #!5 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!5 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 17 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
178 atoms, 180 bonds, 11 residues, 2 models selected
> select down
19 atoms, 18 bonds, 1 residue, 2 models selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:473
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select up
178 atoms, 180 bonds, 11 residues, 2 models selected
> select up
8988 atoms, 9097 bonds, 548 residues, 2 models selected
> select down
178 atoms, 180 bonds, 11 residues, 2 models selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:342
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
180 atoms, 182 bonds, 11 residues, 2 models selected
> select down
11 atoms, 10 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #5.1/A:342@CB
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:517
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
272 atoms, 272 bonds, 17 residues, 2 models selected
> select up
8988 atoms, 9097 bonds, 548 residues, 2 models selected
> select H
27442 atoms, 3340 residues, 12 models selected
> hide sel & #3.2#5.2#!3.1#!5.1 atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5.1/A:590
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #5.1/A:591
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #5.1/A:595
32 atoms, 31 bonds, 2 residues, 2 models selected
> select #5.1/A:592
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #5.1/A:592-595
75 atoms, 76 bonds, 4 residues, 1 model selected
> show sel cartoons
> show #!3 models
> hide #!5 models
> show #!5 models
> select #3.1/A:374
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #3.1/A:374
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide sel cartoons
> show sel cartoons
> hide #!3 models
> select #5.1/A:373
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #5.1/A:374
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #5.1/A:374
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel cartoons
> show #!3 models
> hide #!3 models
> show #!3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> hide sel atoms
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> hide sel atoms
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #5.1/A:591@OG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> hide #!5 models
> show #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!2 models
> hide #!2 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1.1/A:371
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide #!1 models
> show #!1 models
> hide #!7 models
> select #1.1/A:372
24 atoms, 23 bonds, 1 residue, 1 model selected
> select add #1.1/A:373
43 atoms, 41 bonds, 2 residues, 2 models selected
Alignment identifier is 1.1/A
> select #1.1/A:374
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.1/A:374
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #1.1/A:371
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.1/A:371-372
34 atoms, 33 bonds, 2 residues, 1 model selected
> show sel cartoons
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
> show #!3 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!7 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!4 models
> show #!4 models
> show #!2 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> hide #!2 models
> show #!4 models
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
[Repeated 1 time(s)]
——— End of log from Fri Jun 20 11:25:34 2025 ———
opened ChimeraX session
> show #!1 models
> hide #!4 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> select clear
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!1 models
> select #7.2//chain_id='>':1@C7
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> color sel #fff2ccff
> color sel byhetero
> select clear
> undo
> color sel yellow
> color sel byhetero
> color sel lime
> color sel purple
> color sel cyan
> color sel #d5b48cff
> color sel byhetero
> select clear
> show #!1 models
> hide #!7 models
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> hide #!1 models
> show #!3 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!2 models
> show #!4 models
> hide #!4 models
> select #2.1/A:531
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show #!6 models
> hide #!6 models
> show #!4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #4.1/A:531@OG1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!4 models
> show #!4 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> hide #1.2#2.2#3.2#4.2#5.2#7.2#!2.1#!3.1#!4.1#!5.1#!7.1 target m
> undo
> show #!4 models
> hide #!2 models
> show #!6 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
——— End of log from Fri Jun 20 14:58:38 2025 ———
opened ChimeraX session
> hide #!4 models
> show #!5 models
> open "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/CsTPS14CT_#5.pdb"
Summary of feedback from opening /Users/jeremyb/Desktop/Terpene Synthase
Project/Manuscript 1/Docking Figure/CsTPS14CT_#5.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
17 messages similar to the above omitted
Chain information for CsTPS14CT_#5.pdb
---
Chain | Description
8.1/A | No description available
> color #6 #d5b48cff models
> color #8.1 #d5b48cff
> color #4.1.1 #ae85dcff models
> color #8.1.1 #b085ddff models
> hide #4.1.2 models
> show #4.1.2 models
> hide #4.1.2 models
> show #4.1.2 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!8 models
> show #!8 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel #d6b48cff
> color sel byhetero
> select clear
> select #8.1/A:625@MN
1 atom, 1 residue, 1 model selected
> select up
9000 atoms, 9105 bonds, 552 residues, 1 model selected
> select up
9027 atoms, 9131 bonds, 553 residues, 2 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 3 models selected
> select up
9027 atoms, 9131 bonds, 4 pseudobonds, 553 residues, 10 models selected
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9027 atoms, 9131 bonds, 553 residues, 2 models selected
> select down
27 atoms, 26 bonds, 1 residue, 1 model selected
> select sel @< 5
933 atoms, 774 bonds, 20 pseudobonds, 146 residues, 20 models selected
> select ~sel & ##selected
63393 atoms, 64267 bonds, 99 pseudobonds, 3894 residues, 17 models selected
> hide sel & #!8.1 atoms
> hide sel & #!8.1 cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select sel @< 10
5447 atoms, 5059 bonds, 119 pseudobonds, 578 residues, 22 models selected
> hide sel & #8.2#!8.1 atoms
> show sel & #8.2#!8.1 atoms
> show sel & #8.2#!8.1 cartoons
> select clear
> show #!5 models
> select #5.1/A:371
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
415 atoms, 419 bonds, 24 residues, 2 models selected
> select up
8985 atoms, 9094 bonds, 548 residues, 2 models selected
> select up
8997 atoms, 9102 bonds, 552 residues, 2 models selected
> select clear
> hide #!5 models
> select #8.1/A:369
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> show #!5 models
> hide #!5 models
> select #8.1/A:366
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> show #!5 models
> hide #!5 models
> select #8.1/A:514
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> show #!5 models
> hide #!5 models
> select #8.1/A:474
16 atoms, 15 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select up
23 atoms, 22 bonds, 2 residues, 1 model selected
> select up
8988 atoms, 9097 bonds, 548 residues, 1 model selected
> select up
9000 atoms, 9105 bonds, 552 residues, 1 model selected
> select up
9027 atoms, 9131 bonds, 553 residues, 2 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 3 models selected
> select H
31914 atoms, 3889 residues, 14 models selected
> hide sel & #8.2#!8.1 atoms
> select clear
> select #8.1/A:536
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
139 atoms, 140 bonds, 9 residues, 1 model selected
> select up
8988 atoms, 9097 bonds, 548 residues, 1 model selected
> select down
139 atoms, 140 bonds, 9 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #8.1/A:551
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #8.1/A:527
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #8.1/A:526
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #8.1/A:525
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select #8.1/A:524
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #8.1/A:379@OH
1 atom, 1 residue, 1 model selected
> select add #8.1/A:379@CE1
2 atoms, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #8.1/A:558
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #8.1/A:532@CG1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!8 models
> select #8.1/A:522
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #8.1/A:466
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #8.1/A:523
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #8.1/A:532@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #8.1/A:531
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #8.1/A:336
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #8.1/A:596
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
307 atoms, 309 bonds, 19 residues, 1 model selected
> select up
8988 atoms, 9097 bonds, 548 residues, 1 model selected
> select down
307 atoms, 309 bonds, 19 residues, 1 model selected
> hide sel atoms
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #8.1/A:596
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #8.1/A:597
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #8.1/A:598
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #8.1/A:599
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #8.1/A:604
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #8.1/A:605
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #8.1/A:344@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #8.1/A:346@NE2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide #!8 models
> show #!8 models
> select #8.1/A:336
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #!8 models
> show #!8 models
> select #8.1/A:82
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #8.1/A:343
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #8.1/A:344
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #8.1/A:343
39 atoms, 38 bonds, 2 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #8.1/A:346
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #8.1/A:595
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #8.1/A:594
38 atoms, 37 bonds, 2 residues, 1 model selected
> show sel atoms
> select #8.1/A:529
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #8.1/A:451
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide sel atoms
> hide sel cartoons
> select #8.1/A:448
18 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8.1/A:377
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #5.1/A:473
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
178 atoms, 180 bonds, 11 residues, 2 models selected
> select up
8985 atoms, 9094 bonds, 548 residues, 2 models selected
> select up
8997 atoms, 9102 bonds, 552 residues, 2 models selected
> select down
8985 atoms, 9094 bonds, 548 residues, 2 models selected
> select down
178 atoms, 180 bonds, 11 residues, 2 models selected
> select down
11 atoms, 10 bonds, 1 residue, 2 models selected
> select #8.1/A:473@CB
1 atom, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #8.1/A:470
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #8.1/A:471
24 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select clear
> select #8.1/A:512
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #8.1/A:511
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #8.1/A:510
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #8.1/A:587
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #8.1/A:588
26 atoms, 24 bonds, 2 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #!8 models
> show #!8 models
> select #8.1/A:589
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide #!8 models
> show #!8 models
> select #8.1/A:590
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select clear
> select #8.1/A:600
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #5.1/A:367
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!8 models
> show #!8 models
> select #8.1/A:378
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select clear
> select #8.1/A:444@CD1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #5.1/A:516
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!5 models
> select #8.1/A:516
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #8.1/A:520
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #8.1/A:519
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #8.1/A:476
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #!8 models
> show #!8 models
> select #8.1/A:513
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #!8 models
> show #!8 models
> select #8.1/A:479
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #8.1/A:515@CD
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select clear
> select #5.1/A:473
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #!8 models
> show #!8 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!8 models
> select #8.1/A:472
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #5.1/A:595
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
307 atoms, 309 bonds, 19 residues, 2 models selected
> select up
8985 atoms, 9094 bonds, 548 residues, 2 models selected
> select up
8997 atoms, 9102 bonds, 552 residues, 2 models selected
> select up
8997 atoms, 9102 bonds, 19 pseudobonds, 552 residues, 3 models selected
> select H
31914 atoms, 3889 residues, 14 models selected
> hide sel & #5.2#8.2#!5.1#!8.1 atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!8 models
> show #!8 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #8.1/A:377
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 8.1/A
> select #8.1/A:374
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #8.1/A:374
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #8.1/A:376-377
29 atoms, 29 bonds, 2 residues, 1 model selected
> select #8.1/A:376-377
29 atoms, 29 bonds, 2 residues, 1 model selected
> select #8.1/A:377
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #8.1/A:377
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> show #!5 models
> hide #!5 models
> select #8.1/A:450
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #8.1/A:450-451
32 atoms, 31 bonds, 2 residues, 1 model selected
> select #8.1/A:450
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #8.1/A:450
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show #!5 models
> select #5.1/A:451
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide #!5 models
> select #8.1/A:377
12 atoms, 11 bonds, 1 residue, 1 model selected
Destroying pre-existing alignment with identifier 8.1/A
Alignment identifier is 8.1/A
> select #8.1/A:450
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #8.1/A:450
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> select #8.1/A:451
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #8.1/A:451
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> select up
432 atoms, 439 bonds, 24 residues, 1 model selected
> select up
8988 atoms, 9097 bonds, 548 residues, 1 model selected
> select up
9000 atoms, 9105 bonds, 552 residues, 1 model selected
> select up
9027 atoms, 9131 bonds, 553 residues, 2 models selected
> select up
9027 atoms, 9131 bonds, 553 residues, 3 models selected
> select H
31914 atoms, 3889 residues, 14 models selected
> hide sel & #8.2#!8.1 atoms
> select #8.2/5:1@C2
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
9027 atoms, 9131 bonds, 553 residues, 2 models selected
> select down
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!8 models
> hide #!3 models
> show #!8 models
> show #!3 models
> hide #!8 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!8 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select #5.1/A:338
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show #!8 models
> select #8.1/A:338
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #!8 models
> show #!8 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> select #5.1/A:514
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #5.1/A:342
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
180 atoms, 182 bonds, 11 residues, 2 models selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!5 models
> show #!5 models
> hide #!5 models
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript 1/Docking
> Figure/Docking Figure.cxs"
——— End of log from Fri Jun 20 16:16:52 2025 ———
opened ChimeraX session
> open "/Volumes/NO NAME/CsTPS15CT_LPP+_Docking/CsTPS15CT_LPP+_#14.pdb"
Summary of feedback from opening /Volumes/NO
NAME/CsTPS15CT_LPP+_Docking/CsTPS15CT_LPP+_#14.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
17 messages similar to the above omitted
Chain information for CsTPS15CT_LPP+_#14.pdb
---
Chain | Description
9.1/A | No description available
> hide #!8 models
> hide #!9 models
> show #!1 models
> show #!9 models
> hide #!1 models
> show #!1 models
> hide #!9 models
> open "/Users/jeremyb/Desktop/Research /Writing and
> Presentations/Presentations/MPS Seminar Documents/MPS Seminar/WT_14.pdb"
Summary of feedback from opening /Users/jeremyb/Desktop/Research /Writing and
Presentations/Presentations/MPS Seminar Documents/MPS Seminar/WT_14.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
15 messages similar to the above omitted
Chain information for WT_14.pdb
---
Chain | Description
10.1/A | No description available
> show #!8 models
> hide #!1 models
> hide #!8 models
> show #!3 models
> hide #!3 models
> select #10.2/1:1@C6
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 27 bonds, 1 residue, 1 model selected
> select sel @< 5
1621 atoms, 1413 bonds, 4 pseudobonds, 216 residues, 19 models selected
> show sel & #10.2#!10.1 atoms
> hide sel & #10.2#!10.1 cartoons
> show sel & #10.2#!10.1 cartoons
> select ~sel & ##selected
81139 atoms, 82266 bonds, 141 pseudobonds, 5003 residues, 27 models selected
> hide sel & #!10.1 atoms
> hide sel & #!10.1 cartoons
> select ~sel & ##selected
1593 atoms, 1386 bonds, 4 pseudobonds, 215 residues, 18 models selected
> show sel & #!10.1 cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
417 atoms, 421 bonds, 24 residues, 1 model selected
> select up
8990 atoms, 9099 bonds, 548 residues, 1 model selected
> select up
9001 atoms, 9107 bonds, 551 residues, 1 model selected
> select up
9029 atoms, 9134 bonds, 552 residues, 2 models selected
> select up
9029 atoms, 9134 bonds, 552 residues, 3 models selected
> color #10.1.1 #d6b48cff models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select sel @< 2
150 atoms, 82 bonds, 45 pseudobonds, 61 residues, 21 models selected
> show sel & #!10.1 atoms
> color #10.1 #d6b48cff
> color sel & #!10.1 byhetero
> select up
720 atoms, 664 bonds, 45 pseudobonds, 61 residues, 27 models selected
> select up
8513 atoms, 8546 bonds, 45 pseudobonds, 516 residues, 27 models selected
> select up
82587 atoms, 83522 bonds, 45 pseudobonds, 5024 residues, 27 models selected
> select up
82597 atoms, 83522 bonds, 45 pseudobonds, 5034 residues, 27 models selected
> select up
82597 atoms, 83522 bonds, 141 pseudobonds, 5034 residues, 27 models selected
> color sel & #!10.1 byhetero
> select H
41062 atoms, 5005 residues, 18 models selected
> hide sel & #10.2#!10.1 atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 27 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!3 models
> ui tool show Matchmaker
> hide #!3 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 27 bonds, 1 residue, 1 model selected
> select up
9029 atoms, 9134 bonds, 552 residues, 2 models selected
> select down
28 atoms, 27 bonds, 1 residue, 1 model selected
> show sel surfaces
> mlp sel
mlp: no amino acids specified
> mlp sel
mlp: no amino acids specified
> mlp sel
mlp: no amino acids specified
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue (net charge +0) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/jz/g0_x1x7j0214r651_6h13df80000gn/T/tmpse1_s0uq/ante.in.mol2 -fi
mol2 -o
/var/folders/jz/g0_x1x7j0214r651_6h13df80000gn/T/tmpse1_s0uq/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
() ``
() `Welcome to antechamber 20.0: molecular input file processor.`
() ``
() `Info: Finished reading file
(/var/folders/jz/g0_x1x7j0214r651_6h13df80000gn/T/tmpse1_s0uq/ante.in.mol2);
atoms read (28), bonds read (27).`
() `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
() `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
() ``
() ``
() `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
() `Info: Total number of electrons: 78; net charge: 0`
() ``
() `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
() ``
() `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
() ``
() `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
() ``
Charges for residue determined
Coulombic values for WT_14.pdb_1 SES surface #10.2.1: minimum, -0.72, mean
0.25, maximum 0.99
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select clear
> select #10.2/1:1@H3
1 atom, 1 residue, 1 model selected
> color #10.2 #d7b48cff
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 27 bonds, 1 residue, 2 models selected
> color sel byhetero
> select clear
> show #!1 models
> select #10.1/A:474
16 atoms, 15 bonds, 1 residue, 1 model selected
> color sel magenta
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select #10.1/A:369
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
417 atoms, 421 bonds, 24 residues, 1 model selected
> select down
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> select clear
> hide #!10 models
> select #1.1/A:528
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.1/A:482
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #1.1/A:524
33 atoms, 31 bonds, 2 residues, 2 models selected
> select add #1.1/A:374
53 atoms, 51 bonds, 3 residues, 2 models selected
> select add #1.1/A:377
72 atoms, 69 bonds, 4 residues, 2 models selected
> show sel surfaces
> show #!2 models
> hide #!1 models
> select #2.1/A:483
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:523
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:375
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #2.1/A:378
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #2.1/A:375
40 atoms, 39 bonds, 2 residues, 2 models selected
> select add #2.1/A:523
56 atoms, 54 bonds, 3 residues, 2 models selected
> select add #2.1/A:483
72 atoms, 69 bonds, 4 residues, 2 models selected
> show sel surfaces
> show #!10 models
> hide #!2 models
> select add #10.1/A:474
88 atoms, 84 bonds, 5 residues, 3 models selected
> select add #10.1/A:514
107 atoms, 102 bonds, 6 residues, 3 models selected
> select add #10.1/A:366
128 atoms, 123 bonds, 7 residues, 3 models selected
> select add #10.1/A:369
147 atoms, 141 bonds, 8 residues, 3 models selected
> show sel & #!10.1 surfaces
> select #10.1/A:479
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel surfaces
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> hide #!10 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!1 models
> save "/Users/jeremyb/Desktop/Docking Data/Manuscript Figures 2.0.cxs"
——— End of log from Wed Jul 30 20:30:24 2025 ———
opened ChimeraX session
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!10 models
> show #!3 models
> hide #!10 models
> select #3.1/A:474
16 atoms, 15 bonds, 1 residue, 1 model selected
> select add #3.1/A:514
35 atoms, 33 bonds, 2 residues, 2 models selected
> select add #3.1/A:366
56 atoms, 54 bonds, 3 residues, 2 models selected
> select add #3.1/A:369
75 atoms, 72 bonds, 4 residues, 2 models selected
> show sel cartoons
> show sel surfaces
> select clear
> hide #!3 models
> show #!1 models
> show #!10 models
> hide #!1 models
> select clear
> select #10.1/A:479
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select H
41062 atoms, 5005 residues, 18 models selected
> hide sel & #!10.1-2 atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 27 bonds, 1 residue, 2 models selected
> show sel atoms
> select clear
> select #10.1/A:514@CD1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> undo
> hide sel cartoons
> undo
> select clear
[Repeated 1 time(s)]
> save "/Users/jeremyb/Desktop/Terpene Synthase Project/Manuscript
> 1/Figures/Docking Figure/Docking Figure.cxs"
——— End of log from Wed Jul 30 21:19:38 2025 ———
opened ChimeraX session
OpenGL version: 4.1 INTEL-23.7.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine (1x6x8 (fused) LP
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir9,1
Processor Name: Dual-Core Intel Core i3
Processor Speed: 1.1 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 512 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 2075.140.4.0.0 (iBridge: 22.16.16083.0.0,0)
OS Loader Version: 583~2210
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 2 days, 12 hours, 20 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a5c
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403220040
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 3 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 3 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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