id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18698	ChimeraX bug report submission	chimerax-bug-report@…		"{{{
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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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
}}}
"	defect	new	normal		Unassigned