![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 58 minutes ago
#20326 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-15.7.3-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026_GDP_Taxol_TSA.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/opt/sbgrid/i386-mac/chimerax/1.10.1/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore
obj = sm.restore_snapshot(self, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/opt/sbgrid/i386-mac/chimerax/1.10.1/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/cmd.py", line 153, in restore_snapshot
return cls(session, data['base residue'], data['rotamers'],
group=data.get('group', False))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/opt/sbgrid/i386-mac/chimerax/1.10.1/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/cmd.py", line 116, in __init__
self.rotamers = list(rotamers) # don't want auto-shrinking of a Collection
^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
Log from Wed May 13 16:31:51 2026UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026_GDP_Taxol_TSA.cxs
> format session
Log from Wed May 13 16:04:03 2026UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/bIII_vs_BIIITaxol.cxs
Log from Fri May 8 14:06:26 2026UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass14/Figure5/PanelA_2.cxs
Log from Wed Mar 4 15:56:44 2026UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass14/Figure5/PanelA.cxs
> format session
Log from Tue Dec 23 17:02:48 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass14/Figure5/PanelA.cxs
> format session
Log from Tue Dec 23 16:28:15 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass14/Figure5/PanelA.cxs
> format session
Log from Tue Dec 23 16:23:44 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC_v3.cxs
Log from Sun Nov 16 06:15:27 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC_v2.cxs
> format session
Log from Sun Nov 16 06:10:24 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC_v2.cxs
> format session
Log from Sun Nov 16 05:56:58 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_vs_Brain_v1.cxs
Log from Tue Aug 5 21:56:42 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_vs_Brain_v1.cxs
> format session
Log from Tue Aug 5 13:30:36 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_vs_Brain_v1.cxs
> format session
Log from Tue Aug 5 12:54:37 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_1.cxs
> format session
Log from Tue Aug 5 10:25:42 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_1.cxs
> format session
Log from Mon Aug 4 15:15:28 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_1.cxs
> format session
Log from Mon Aug 4 15:13:06 2025 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/zehrea/Desktop/MT_models/TSA-
> GDP_Taxol/new_map_refit/RealSpaceRefine_5/fix_phe/latersl_interdimer-
> coot-130.pdb
Chain information for latersl_interdimer-coot-130.pdb #1
---
Chain | Description
A C | No description available
B D | No description available
> color dark gray
> hide atoms
> select :TA1
124 atoms, 136 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel cyan
> color sel byhetero
> select clear
> lighting soft
> select
13591 atoms, 13915 bonds, 2 pseudobonds, 1726 residues, 2 models selected
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & backbone) target ab
> select
13591 atoms, 13915 bonds, 2 pseudobonds, 1726 residues, 2 models selected
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & backbone) target ab
> select
13591 atoms, 13915 bonds, 2 pseudobonds, 1726 residues, 2 models selected
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select :359
24 atoms, 22 bonds, 4 residues, 1 model selected
> show sel atoms
> select
13591 atoms, 13915 bonds, 1708 pseudobonds, 1726 residues, 3 models selected
> color (#!1 & sel) byhetero
> select clear
> select /B:359@N
1 atom, 1 residue, 1 model selected
> select
13591 atoms, 13915 bonds, 1708 pseudobonds, 1726 residues, 3 models selected
> select /B:359@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select
13591 atoms, 13915 bonds, 1709 pseudobonds, 1726 residues, 3 models selected
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & backbone) target ab
> select @O
1720 atoms, 1720 residues, 1 model selected
> hide sel atoms
> select :359
24 atoms, 22 bonds, 4 residues, 1 model selected
> select :359@O
4 atoms, 4 residues, 1 model selected
> show sel atoms
> select /K:503@O12
1 atom, 1 residue, 1 model selected
> select add /B:359@O
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance style color black
[Repeated 2 time(s)]
> distance /K:503@O12 /B:359@O
Distance between /K TA1 503 O12 and /B ARG 359 O: 3.770Å
> select /K:503@O13
1 atom, 1 residue, 1 model selected
> select add /B:359@O
2 atoms, 2 residues, 1 model selected
> distance /K:503@O13 /B:359@O
Distance between /K TA1 503 O13 and /B ARG 359 O: 2.823Å
> ~distance /K:503@O12 /B:359@O
> select :358
32 atoms, 30 bonds, 4 residues, 1 model selected
> show sel atoms
> select /B:358@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select :358
32 atoms, 30 bonds, 4 residues, 1 model selected
> color sel byhetero
> select :361
30 atoms, 26 bonds, 4 residues, 1 model selected
> show sel atoms
> select /B:361@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> ui tool show "Side View"
> ui mousemode right zoom
> graphics silhouettes true
> select :279
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> select /B:279@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:279@NE2
1 atom, 1 residue, 1 model selected
> select add /K:503@O08
2 atoms, 2 residues, 1 model selected
> distance /B:279@NE2 /K:503@O08
Distance between /B GLN 279 NE2 and /K TA1 503 O08: 3.026Å
> select /B:279@OE1
1 atom, 1 residue, 1 model selected
> select add /K:503@O08
2 atoms, 2 residues, 1 model selected
> distance /B:279@OE1 /K:503@O08
Distance between /B GLN 279 OE1 and /K TA1 503 O08: 3.193Å
> select /B:279@OE1
1 atom, 1 residue, 1 model selected
> select add /K:503@O07
2 atoms, 2 residues, 1 model selected
> distance /B:279@OE1 /K:503@O07
Distance between /B GLN 279 OE1 and /K TA1 503 O07: 2.859Å
> select :276
38 atoms, 34 bonds, 4 residues, 1 model selected
> show sel atoms
> select /B:276@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:276@NH2
1 atom, 1 residue, 1 model selected
> select add /K:503@O03
2 atoms, 2 residues, 1 model selected
> distance /B:276@NH2 /K:503@O03
Distance between /B ARG 276 NH2 and /K TA1 503 O03: 2.736Å
> select :215
38 atoms, 34 bonds, 4 residues, 1 model selected
> show sel atoms
> select /B:215@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA.cxs
> distance style radius 0.05
[Repeated 2 time(s)]
> select :227
36 atoms, 34 bonds, 4 residues, 1 model selected
> show sel atoms
> select /B:227@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select :23
30 atoms, 26 bonds, 4 residues, 1 model selected
> show sel atoms
> select /B:23@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select :361
30 atoms, 26 bonds, 4 residues, 1 model selected
> select :272
38 atoms, 38 bonds, 4 residues, 1 model selected
> show sel atoms
> select /B:272@O
1 atom, 1 residue, 1 model selected
> select add /K:503@O06
2 atoms, 2 residues, 1 model selected
> distance /B:272@O /K:503@O06
Distance between /B PRO 272 O and /K TA1 503 O06: 2.811Å
> select :279
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> select /B:279@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select :359
24 atoms, 22 bonds, 4 residues, 1 model selected
> hide #2.1 models
> select clear
> distance style radius 0.05
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA.cxs
> select
13591 atoms, 13915 bonds, 8 pseudobonds, 1726 residues, 4 models selected
> size sel pseudobondRadius 0.2
Changed 8 pseudobond radii
> size sel pseudobondRadius 0.05
Changed 8 pseudobond radii
> size sel stickRadius 0.2
Changed 13915 bond radii
> size sel atomRadius 0.2
Changed 13591 atom radii
> size sel stickRadius 0.1
Changed 13915 bond radii
> size sel stickRadius 0.2
Changed 13915 bond radii
> size sel stickRadius 0.15
Changed 13915 bond radii
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_1.cxs
——— End of log from Mon Aug 4 15:13:06 2025 ———
opened ChimeraX session
Drag select of 2 atoms, 3 bonds
> hide sel atoms
Drag select of 4 atoms, 4 bonds
> hide sel atoms
Drag select of 7 atoms, 8 bonds
> select clear
Drag select of 8 atoms, 8 bonds
> hide sel atoms
Drag select of 4 atoms, 4 bonds
> hide sel atoms
> select /B:365@N
1 atom, 1 residue, 1 model selected
> select add /B:364@CA
2 atoms, 2 residues, 1 model selected
> hide sel atoms
> select /B:316@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 3 atoms, 3 bonds
> hide sel atoms
Drag select of 1 atoms, 1 bonds
> hide sel atoms
> select /B:231@CA
1 atom, 1 residue, 1 model selected
> select add /B:231@C
2 atoms, 1 residue, 1 model selected
> hide sel atoms
> select /B:229@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:225@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 4 atoms, 4 bonds
> hide sel atoms
Drag select of 2 atoms, 4 bonds
> select clear
Drag select of 5 atoms, 5 bonds
> hide sel atoms
> select /B:364@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:19@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:20@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:20@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:20@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:21@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_1.cxs
——— End of log from Mon Aug 4 15:15:28 2025 ———
opened ChimeraX session
> select /B:227@NE2
1 atom, 1 residue, 1 model selected
> select add /K:503@O14
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /B:227@NE2 /K:503@O14
Distance between /B HIS 227 NE2 and /K TA1 503 O14: 2.804Å
> distance style radius 0.05
> show #2.1 models
> hide #2.1 models
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_1.cxs
——— End of log from Tue Aug 5 10:25:42 2025 ———
opened ChimeraX session
> open 5syf
5syf title:
High-resolution cryo-EM reconstruction of Taxol-stabilized microtubule [more
info...]
Chain information for 5syf #3
---
Chain | Description | UniProt
A | Tubulin alpha chain | B6A7R0_PIG 1-437
B | Tubulin beta chain | TBB_PIG 1-436
Non-standard residues in 5syf #3
---
GDP — guanosine-5'-diphosphate
GTP — guanosine-5'-triphosphate
MG — magnesium ion
TA1 — TAXOL
5syf mmCIF Assemblies
---
1| representative helical assembly
2| helical asymmetric unit
3| helical asymmetric unit, std helical frame
> ui tool show Matchmaker
> matchmaker #!3 to #1/B pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker latersl_interdimer-coot-130.pdb, chain B (#1) with 5syf, chain B
(#3), sequence alignment score = 2138.9
RMSD between 422 pruned atom pairs is 0.671 angstroms; (across all 426 pairs:
0.720)
Drag select of 320 atoms, 326 bonds, 7 pseudobonds, 58 residues
> ui tool show Matchmaker
> matchmaker #!3 & sel to #1/B & sel pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker latersl_interdimer-coot-130.pdb, chain B (#1) with 5syf, chain B
(#3), sequence alignment score = 250.8
RMSD between 50 pruned atom pairs is 0.658 angstroms; (across all 50 pairs:
0.658)
> select clear
> select add #3
6818 atoms, 6978 bonds, 4 pseudobonds, 856 residues, 3 models selected
> hide (#!3 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!3 & sel-residues)
> show (#!3 & sel-residues & backbone) target ab
> select #3 @O
852 atoms, 852 residues, 1 model selected
> hide sel atoms
> select #3/B:281@CA
1 atom, 1 residue, 1 model selected
> show sel atoms
> select #3 :281
14 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3 :278
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3 :369@O
2 atoms, 2 residues, 1 model selected
> show sel atoms
> select #3 :374@O
2 atoms, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #3 :374@O
2 atoms, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #3 :374@O
2 atoms, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #3 :274@O
2 atoms, 2 residues, 1 model selected
> show sel atoms
> select #3 :23
15 atoms, 13 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3/B:23@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_vs_Brain.cxs
> select #3 :229
21 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3/B:229@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3 :360
14 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3/B:360@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3 :217
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3/B:217@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3 :371
15 atoms, 13 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3/B:371@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1:217-220
124 atoms, 122 bonds, 16 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> select add #1/B:219@O
1 atom, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:218@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:220@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:217@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide #!3 models
> select #1:224
40 atoms, 38 bonds, 4 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> select #1:223-225
92 atoms, 90 bonds, 12 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> select #1/B:223@O
1 atom, 1 residue, 1 model selected
> select add #1/B:225@O
2 atoms, 2 residues, 1 model selected
> hide sel atoms
> select #1/B:224@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show #!3 models
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_vs_Brain.cxs
> select #3/B:281@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:278@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3 :374
11 atoms, 9 bonds, 2 residues, 1 model selected
> show sel atoms
> undo
> select #3 :274
14 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_vs_Brain.cxs
> select
20409 atoms, 20893 bonds, 13 pseudobonds, 2582 residues, 7 models selected
> size sel stickRadius 0.15
Changed 20893 bond radii
> select clear
> hide #!2 models
> select #1/B:272@O
1 atom, 1 residue, 1 model selected
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_vs_Brain.cxs
> cd /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/
Current working directory is:
/Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol
> save Taxol_binding_TSA_vs_Brain.tif supersample 4 transparentBackground true
[Repeated 5 time(s)]
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_vs_Brain.cxs
Drag select of 13 atoms, 14 bonds
> hide sel atoms
> select #3/B:236@CA
1 atom, 1 residue, 1 model selected
> select add #3/B:236@N
2 atoms, 1 residue, 1 model selected
> hide sel atoms
Drag select of 2 pseudobonds
> hide atoms
> undo
> select :237
36 atoms, 30 bonds, 6 residues, 2 models selected
> hide sel atoms
> select :239
40 atoms, 34 bonds, 6 residues, 2 models selected
> hide sel atoms
> select #3/B:235@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:226@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:224@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select add #3/B:374@C
1 atom, 1 bond, 1 residue, 1 model selected
> select #3/B:375@N
1 atom, 1 residue, 1 model selected
> select add #3/B:374@C
2 atoms, 2 residues, 1 model selected
> select add #3/B:375@CA
3 atoms, 2 residues, 1 model selected
> hide sel atoms
> select #3/B:374@CA
1 atom, 1 residue, 1 model selected
> select add #3/B:374@N
2 atoms, 1 residue, 1 model selected
> select add #3/B:373@C
3 atoms, 2 residues, 1 model selected
> hide sel atoms
> select #1/B:363@C
1 atom, 1 residue, 1 model selected
> select add #3/B:320@CA
2 atoms, 2 residues, 2 models selected
> hide sel atoms
> select #3/B:320@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:232@C
1 atom, 1 residue, 1 model selected
> select add #3/B:232@CA
2 atoms, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:233@N
1 atom, 1 residue, 1 model selected
> select add #3/B:233@CA
2 atoms, 1 residue, 1 model selected
> hide sel atoms
> save Taxol_binding_TSA_vs_Brain.tif supersample 4 transparentBackground true
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_vs_Brain_v1.cxs
——— End of log from Tue Aug 5 12:54:37 2025 ———
opened ChimeraX session
> select #1 :276
38 atoms, 34 bonds, 4 residues, 1 model selected
> ui tool show Rotamers
> select #1/B:276@CA
1 atom, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
latersl_interdimer-coot-130.pdb #1/B ARG 276: phi -49.6, psi -37.2 trans
Changed 600 bond radii
> swapaa #!1/B:276 ARG criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
latersl_interdimer-coot-130.pdb #!1/B ARG 276: phi -49.6, psi -37.2 trans
Applying ARG rotamer (chi angles: -71.0 177.7 -180.0 172.1) to
latersl_interdimer-coot-130.pdb #!1/B ARG 276
> swapaa interactive sel ARG rotLib Dunbrack
latersl_interdimer-coot-130.pdb #1/B ARG 276: phi -49.6, psi -37.2 trans
Changed 600 bond radii
> select
20409 atoms, 20893 bonds, 12 pseudobonds, 2582 residues, 7 models selected
> size sel stickRadius 0.15
Changed 20893 bond radii
> select clear
> save Taxol_binding_TSA_vs_Brain.tif supersample 4 transparentBackground true
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_vs_Brain_v1.cxs
——— End of log from Tue Aug 5 13:30:36 2025 ———
opened ChimeraX session
> select #1 :211-234,354-364,271-285
1554 atoms, 1578 bonds, 200 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!3 to #1 & sel showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker latersl_interdimer-coot-130.pdb, chain B (#1) with 5syf, chain B
(#3), sequence alignment score = 250.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: latersl_interdimer-
coot-130.pdb #1/B, 5syf #3/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 50 pruned atom pairs is 0.608 angstroms; (across all 50 pairs:
0.608)
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass11/Taxol/Taxol_binding_site_TSA_vs_Brain_v1.cxs
——— End of log from Tue Aug 5 21:56:42 2025 ———
opened ChimeraX session
> select add #3
6818 atoms, 6978 bonds, 4 pseudobonds, 856 residues, 3 models selected
> ui tool show "Color Actions"
> color sel plum
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC.cxs
> open /Users/zehrea/Desktop/MT_models/TSA-
> GDP_Taxol/DEPOSIT_final/pdb_extract_out_2724076469.cif
Summary of feedback from opening /Users/zehrea/Desktop/MT_models/TSA-
GDP_Taxol/DEPOSIT_final/pdb_extract_out_2724076469.cif
---
warnings | Unknown polymer entity '3' near line 13674
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for pdb_extract_out_2724076469.cif #4
---
Chain | Description
A C | No description available
B D | No description available
Associated pdb_extract_out_2724076469.cif chain B to latersl_interdimer-
coot-130.pdb, chain B with 0 mismatches
Associated pdb_extract_out_2724076469.cif chain D to latersl_interdimer-
coot-130.pdb, chain B with 0 mismatches
Chains used in RMSD evaluation for alignment 1: latersl_interdimer-
coot-130.pdb #1/B, 5syf #3/B, pdb_extract_out_2724076469.cif #4/B
> ui tool show Matchmaker
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker latersl_interdimer-coot-130.pdb, chain B (#1) with
pdb_extract_out_2724076469.cif, chain B (#4), sequence alignment score =
2245.1
RMSD between 430 pruned atom pairs is 0.220 angstroms; (across all 430 pairs:
0.220)
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker latersl_interdimer-coot-130.pdb, chain B (#1) with
pdb_extract_out_2724076469.cif, chain B (#4), sequence alignment score =
2245.1
RMSD between 430 pruned atom pairs is 0.220 angstroms; (across all 430 pairs:
0.220)
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker latersl_interdimer-coot-130.pdb, chain B (#1) with
pdb_extract_out_2724076469.cif, chain B (#4), sequence alignment score =
2245.1
RMSD between 430 pruned atom pairs is 0.220 angstroms; (across all 430 pairs:
0.220)
> select add #4
13564 atoms, 13888 bonds, 2 pseudobonds, 1726 residues, 2 models selected
> hide (#!4 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!4 & sel-residues)
> show (#!4 & sel-residues & backbone) target ab
> color (#!4 & sel) dark gray
> color (#!4 & sel) byhetero
> select #3 @O
852 atoms, 852 residues, 1 model selected
> hide sel target a
> select #3 @O
852 atoms, 852 residues, 1 model selected
> select #3
6818 atoms, 6978 bonds, 4 pseudobonds, 856 residues, 3 models selected
> select #3 @O
852 atoms, 852 residues, 1 model selected
> hide sel atoms
> select #4 @O
1720 atoms, 1720 residues, 1 model selected
> hide sel atoms
> select #4 :279,276,23
104 atoms, 92 bonds, 12 residues, 1 model selected
> show sel atoms
> select #4 :279,276,23,361
134 atoms, 118 bonds, 16 residues, 1 model selected
> select #4 :279,276,23,361,274
162 atoms, 144 bonds, 20 residues, 1 model selected
> show sel atoms
> select #4 :274
28 atoms, 26 bonds, 4 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> select #4 :272
38 atoms, 38 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select add #1
13629 atoms, 13953 bonds, 8 pseudobonds, 1730 residues, 4 models selected
> select subtract #1
38 atoms, 38 bonds, 4 residues, 1 model selected
> hide #!1 models
> select #4/B:361@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:279@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:276@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4 :23
30 atoms, 26 bonds, 4 residues, 1 model selected
> select #4 :23@O
4 atoms, 4 residues, 1 model selected
> hide sel atoms
> select #4 :229
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC.cxs
> close #1
Chains used in RMSD evaluation for alignment 1: 5syf #3/B,
pdb_extract_out_2724076469.cif #4/B
> select #4 :234-238
132 atoms, 128 bonds, 20 residues, 1 model selected
> hide sel atoms
> select #4/B:233@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4 :230-231
54 atoms, 50 bonds, 8 residues, 1 model selected
> hide sel atoms
> select #4 :264-36
Nothing selected
> select #4 :264-366
3158 atoms, 3240 bonds, 412 residues, 1 model selected
> select #4 :364-366
68 atoms, 66 bonds, 12 residues, 1 model selected
> hide sel atoms
> select #4/B:272@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC.cxs
> select
20382 atoms, 20866 bonds, 6 pseudobonds, 2582 residues, 5 models selected
> size
> size sel stickRadius 0.1
Changed 20866 bond radii
> size sel stickRadius 0.15
Changed 20866 bond radii
> size sel stickRadius 0.15
Changed 20866 bond radii
> size sel stickRadius 0.1
Changed 20866 bond radii
> select clear
Drag select of 7 atoms, 6 bonds
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC_v2.cxs
> select #4/B:279@OE1
1 atom, 1 residue, 1 model selected
> select add #4/K:503@O10
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance style color black
[Repeated 2 time(s)]
> distance style radius 0.03
[Repeated 2 time(s)]
> distance #4/B:279@OE1 #4/K:503@O10
Distance between pdb_extract_out_2724076469.cif #4/B GLN 279 OE1 and /K TA1
503 O10: 3.935Å
> distance #4/B:279@OE1 #4/K:503@O10
Distance already exists; modify distance properties with 'distance style'
> select clear
> select #4/K:503@O10
1 atom, 1 residue, 1 model selected
> select add #4/B:279@OE1
2 atoms, 2 residues, 1 model selected
> distance #4/K:503@O10 #4/B:279@OE1
Distance already exists; modify distance properties with 'distance style'
> show #!2 models
> distance style radius 0.03
> hide #!2 models
> select #4/K:503@O07
1 atom, 1 residue, 1 model selected
> select add #4/B:279@OE1
2 atoms, 2 residues, 1 model selected
> distance #4/K:503@O07 #4/B:279@OE1
Distance between pdb_extract_out_2724076469.cif #4/K TA1 503 O07 and /B GLN
279 OE1: 2.992Å
> show #!2 models
> hide sel
[Repeated 1 time(s)]
> select #4/B:279@OE1
1 atom, 1 residue, 1 model selected
> select add #4/K:503@O07
2 atoms, 2 residues, 1 model selected
> distance #4/B:279@OE1 #4/K:503@O07
Distance already exists; modify distance properties with 'distance style'
> show sel
> close #2
> distance #4/B:279@OE1 #4/K:503@O07
Distance between pdb_extract_out_2724076469.cif #4/B GLN 279 OE1 and /K TA1
503 O07: 2.992Å
> hide #1.1 models
> select #4/B:274@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4 :272
38 atoms, 38 bonds, 4 residues, 1 model selected
> show sel atoms
> select #4/K:503@O06
1 atom, 1 residue, 1 model selected
> select add #4/B:272@O
2 atoms, 2 residues, 1 model selected
> distance #4/K:503@O06 #4/B:272@O
Distance between pdb_extract_out_2724076469.cif #4/K TA1 503 O06 and /B PRO
272 O: 2.999Å
> show #1.1 models
> hide #1.1 models
> select #4 :359
24 atoms, 22 bonds, 4 residues, 1 model selected
> style sel stick
Changed 24 atom styles
> style sel stick
Changed 24 atom styles
> show sel atoms
> select #4/B:359@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:359@O
1 atom, 1 residue, 1 model selected
> select add #4/K:503@O13
2 atoms, 2 residues, 1 model selected
> show sel atoms
> distance #4/B:359@O #4/K:503@O13
Distance between pdb_extract_out_2724076469.cif #4/B ARG 359 O and /K TA1 503
O13: 2.967Å
> show #1.1 models
> hide #1.1 models
> select #4 :359
24 atoms, 22 bonds, 4 residues, 1 model selected
> show sel atoms
> select #4/B:359@CB
1 atom, 1 residue, 1 model selected
> ui tool show Rotamers
Populating font family aliases took 64 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> swapaa interactive sel ARG rotLib Dunbrack
pdb_extract_out_2724076469.cif #4/B ARG 359: phi -61.3, psi 138.7 trans
Changed 600 bond radii
> swapaa #!4/B:359 ARG criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
pdb_extract_out_2724076469.cif #!4/B ARG 359: phi -61.3, psi 138.7 trans
Applying ARG rotamer (chi angles: -69.3 178.0 -66.5 172.3) to
pdb_extract_out_2724076469.cif #!4/B ARG 359
> select
20388 atoms, 20872 bonds, 9 pseudobonds, 2582 residues, 7 models selected
> size sel stickRadius 0.1
Changed 20872 bond radii
> select clear
Drag select of 23 atoms, 21 bonds
> hide sel atoms
Drag select of 12 atoms, 9 bonds
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC_v2.cxs
> select #4 :227
36 atoms, 34 bonds, 4 residues, 1 model selected
> show sel atoms
> select #4/B:227@NE2
1 atom, 1 residue, 1 model selected
> select add #4/K:503@O14
2 atoms, 2 residues, 1 model selected
> distance #4/B:227@NE2 #4/K:503@O14
Distance between pdb_extract_out_2724076469.cif #4/B HIS 227 NE2 and /K TA1
503 O14: 2.776Å
> show #1.1 models
> hide #1.1 models
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC_v2.cxs
> cd /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/
Current working directory is:
/Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5
> save Taxol_pocket_TSa_vs_Brain.tif supersample 4 transparentBackground false
> hide #!4 models
> select #3 :369
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> show #!4 models
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC_v2.cxs
——— End of log from Sun Nov 16 05:56:58 2025 ———
opened ChimeraX session
> select #4:215
38 atoms, 34 bonds, 4 residues, 1 model selected
> show sel atoms
> select #4/B:215@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 17 atoms, 17 bonds
> hide sel atoms
Drag select of 2 atoms, 1 bonds
> hide sel atoms
Drag select of 2 atoms, 2 bonds
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC_v2.cxs
> select #4/B:227@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:227@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:229@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:226@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:228@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save Taxol_pocket_TSa_vs_Brain.tif supersample 4 transparentBackground true
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC_v2.cxs
> select :279
49 atoms, 43 bonds, 6 residues, 2 models selected
> select #4/K:503@O08
1 atom, 1 residue, 1 model selected
> select add #4/B:279@OE1
2 atoms, 2 residues, 1 model selected
> ui tool show Matchmaker
> ui tool show Distances
> distance #4/K:503@O08 #4/B:279@OE1
Distance between pdb_extract_out_2724076469.cif #4/K TA1 503 O08 and /B GLN
279 OE1: 2.970Å
> show #1.1 models
> hide #1.1 models
> select clear
> save Taxol_pocket_TSa_vs_Brain.tif supersample 4 transparentBackground true
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC_v2.cxs
> select #4 :227
36 atoms, 34 bonds, 4 residues, 1 model selected
> select #4 TA1
Expected a keyword
> select #4 :TA1
124 atoms, 136 bonds, 2 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC_v2.cxs
——— End of log from Sun Nov 16 06:10:24 2025 ———
opened ChimeraX session
> select clear
Drag select of 9 atoms, 8 bonds
> hide sel target a
Drag select of 4 atoms, 1 bonds, 1 pseudobonds
> hide (#!3-4 & sel) target a
> select clear
> save Taxol_pocket_TSa_vs_Brain.tif supersample 4 transparentBackground true
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC_v2.cxs
> select #4 :TA1
124 atoms, 136 bonds, 2 residues, 1 model selected
> color sel cyan
> color sel byhetero
> select clear
> save Taxol_pocket_TSa_vs_Brain.tif supersample 4 transparentBackground true
> select #4 :@N
Expected a keyword
> select #4 @N
1720 atoms, 1720 residues, 1 model selected
> hide sel atoms
> show sel atoms
> color sel dark gray
> select clear
> select #4/B:224@N
1 atom, 1 residue, 1 model selected
> select add #4/B:223@N
2 atoms, 2 residues, 1 model selected
> select add #4/B:217@N
3 atoms, 3 residues, 1 model selected
> select add #4/B:218@N
4 atoms, 4 residues, 1 model selected
> hide sel atoms
> select #4/B:238@N
1 atom, 1 residue, 1 model selected
> select add #4/B:234@N
2 atoms, 2 residues, 1 model selected
> select add #4/B:231@N
3 atoms, 3 residues, 1 model selected
> select add #4/B:235@N
4 atoms, 4 residues, 1 model selected
> hide sel atoms
> select #4/B:365@N
1 atom, 1 residue, 1 model selected
> select add #4/B:318@N
2 atoms, 2 residues, 1 model selected
Drag select of 4 atoms
> hide sel atoms
> save Taxol_pocket_TSa_vs_Brain.tif supersample 4 transparentBackground true
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass13/Figure5/PanelC_v3.cxs
——— End of log from Sun Nov 16 06:15:27 2025 ———
opened ChimeraX session
> hide #!3 models
> hide sel
> select #4/B:279@NE2
1 atom, 1 residue, 1 model selected
> select add #4/K:503@O07
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #4/B:279@NE2 #4/K:503@O07
Distance between pdb_extract_out_2724076469.cif #4/B GLN 279 NE2 and /K TA1
503 O07: 4.723Å
> show #1.1 models
> hide #1.1 models
> hide sel
> select #4/B:279@CA
1 atom, 1 residue, 1 model selected
> select #4/B:279@CA
1 atom, 1 residue, 1 model selected
> select #4/B:279@CA
1 atom, 1 residue, 1 model selected
> select #4/B:279@CA
1 atom, 1 residue, 1 model selected
> select #4/B:279@CA
1 atom, 1 residue, 1 model selected
> select #4/B:279@CA
1 atom, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel GLN rotLib Dunbrack
pdb_extract_out_2724076469.cif #4/B GLN 279: phi -83.4, psi -31.2 trans
Changed 648 bond radii
> swapaa #!4/B:279 GLN criteria 13 rotLib Dunbrack retain false
Using Dunbrack library
pdb_extract_out_2724076469.cif #!4/B GLN 279: phi -83.4, psi -31.2 trans
Applying GLN rotamer (chi angles: -174.7 175.7 6.5) to
pdb_extract_out_2724076469.cif #!4/B GLN 279
Chains used in RMSD evaluation for alignment 1: 5syf #3/B,
pdb_extract_out_2724076469.cif #!4/B
> select :279
49 atoms, 43 bonds, 6 residues, 2 models selected
> color (#!4 & sel) byhetero
> select #4/B:279@NE2
1 atom, 1 residue, 1 model selected
> select add #4/K:503@O10
2 atoms, 2 residues, 1 model selected
> distance #4/B:279@NE2 #4/K:503@O10
Distance between pdb_extract_out_2724076469.cif #4/B GLN 279 NE2 and /K TA1
503 O10: 4.749Å
> select #4/B:279@OE1
1 atom, 1 residue, 1 model selected
> select add #4/K:503@O07
2 atoms, 2 residues, 1 model selected
> distance #4/B:279@OE1 #4/K:503@O07
Distance between pdb_extract_out_2724076469.cif #4/B GLN 279 OE1 and /K TA1
503 O07: 2.717Å
> open /Users/zehrea/Desktop/MT_models/TSA-
> GDP_Taxol/DEPOSIT_final/latersl_interdimer-coot-229.pdb
Chain information for latersl_interdimer-coot-229.pdb #2
---
Chain | Description
A C | No description available
B D | No description available
Associated latersl_interdimer-coot-229.pdb chain B to latersl_interdimer-
coot-130.pdb, chain B with 0 mismatches
Associated latersl_interdimer-coot-229.pdb chain D to latersl_interdimer-
coot-130.pdb, chain B with 0 mismatches
Chains used in RMSD evaluation for alignment 1: latersl_interdimer-
coot-229.pdb #2/B, 5syf #3/B, pdb_extract_out_2724076469.cif #4/B
> select add #2
13558 atoms, 13880 bonds, 2 pseudobonds, 1728 residues, 3 models selected
> select add #4
27126 atoms, 27774 bonds, 9 pseudobonds, 3452 residues, 5 models selected
> color (#!2,4 & sel) dark gray
> hide (#!2,4 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!2,4 & sel-residues)
> show (#!2,4 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> size sel atomRadius 0.2
Changed 27126 atom radii
> size sel atomRadius 0.08
Changed 27126 atom radii
> size
> size sel pseudobondRadius 0.1
Changed 3437 pseudobond radii
> size sel stickRadius 0.1
Changed 27774 bond radii
> select :TA1
310 atoms, 340 bonds, 5 residues, 3 models selected
> color (#!2,4 & sel) cyan
> color (#!2,4 & sel) byhetero
> select clear
> select #2 :279
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #2/B:279@NE2
1 atom, 1 residue, 1 model selected
> select add #2/K:503@O10
2 atoms, 2 residues, 1 model selected
> ~distance #4/B:279@NE2 #4/K:503@O10
> ~distance #4/B:279@OE1 #4/K:503@O07
> ~distance #4/B:227@NE2 #4/K:503@O14
> ~distance #4/B:359@O #4/K:503@O13
> ~distance #4/K:503@O06 #4/B:272@O
> distance #2/B:279@NE2 #2/K:503@O10
Distance between latersl_interdimer-coot-229.pdb #2/B GLN 279 NE2 and /K TA1
503 O10: 3.770Å
> select #2/B:279@OE1
1 atom, 1 residue, 1 model selected
> select add #2/K:503@O07
2 atoms, 2 residues, 1 model selected
> distance #2/B:279@OE1 #2/K:503@O07
Distance between latersl_interdimer-coot-229.pdb #2/B GLN 279 OE1 and /K TA1
503 O07: 2.992Å
> select #2/B:279@OE1
1 atom, 1 residue, 1 model selected
> select add #2/K:503@O08
2 atoms, 2 residues, 1 model selected
> distance #2/B:279@OE1 #2/K:503@O08
Distance between latersl_interdimer-coot-229.pdb #2/B GLN 279 OE1 and /K TA1
503 O08: 2.970Å
> ~distance #2/B:279@OE1 #2/K:503@O07
> select #2/B:279@N
1 atom, 1 residue, 1 model selected
> select add #2/B:279@O
2 atoms, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:279@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2 :272
38 atoms, 38 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #4/K:503@O06
1 atom, 1 residue, 1 model selected
> select add #2/B:272@O
2 atoms, 2 residues, 2 models selected
> distance #4/K:503@O06 #2/B:272@O
Distance between pdb_extract_out_2724076469.cif #4/K TA1 503 O06 and
latersl_interdimer-coot-229.pdb #2/B PRO 272 O: 2.973Å
> select #2 :227
36 atoms, 34 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #2/K:503@O14
1 atom, 1 residue, 1 model selected
> select add #2/B:227@NE2
2 atoms, 2 residues, 1 model selected
> distance #2/K:503@O14 #2/B:227@NE2
Distance between latersl_interdimer-coot-229.pdb #2/K TA1 503 O14 and /B HIS
227 NE2: 2.776Å
> select #2/B:227@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:227@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:227@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2 :23
30 atoms, 26 bonds, 4 residues, 1 model selected
> show sel atoms
> select #2/B:23@O
1 atom, 1 residue, 1 model selected
> select add #2/B:23@N
2 atoms, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:23@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2 :359
24 atoms, 22 bonds, 4 residues, 1 model selected
> show sel atoms
> ui tool show Rotamers
> select #2/B:359@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #2/B:359@CA
1 atom, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
latersl_interdimer-coot-229.pdb #2/B ARG 359: phi -61.3, psi 138.7 trans
Changed 600 bond radii
> swapaa interactive sel ARG rotLib Dunbrack
latersl_interdimer-coot-229.pdb #!2/B ARG 359: phi -61.3, psi 138.7 trans
Changed 600 bond radii
> swapaa #!2/B:359 ARG criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
latersl_interdimer-coot-229.pdb #!2/B ARG 359: phi -61.3, psi 138.7 trans
Applying ARG rotamer (chi angles: -69.3 178.0 -66.5 172.3) to
latersl_interdimer-coot-229.pdb #!2/B ARG 359
> select #2 :359
30 atoms, 28 bonds, 4 residues, 1 model selected
> color sel byhetero
> size sel stickRadius 0.1
Changed 28 bond radii
> select #2/B:359@N
1 atom, 1 residue, 1 model selected
> select add #2/K:503@O13
2 atoms, 2 residues, 1 model selected
> distance #2/B:359@N #2/K:503@O13
Distance between latersl_interdimer-coot-229.pdb #2/B ARG 359 N and /K TA1 503
O13: 3.288Å
> select #2/B:359@O
1 atom, 1 residue, 1 model selected
> select add #2/K:503@O12
2 atoms, 2 residues, 1 model selected
> distance #2/B:359@O #2/K:503@O12
Distance between latersl_interdimer-coot-229.pdb #2/B ARG 359 O and /K TA1 503
O12: 3.186Å
> select #2 :361
30 atoms, 26 bonds, 4 residues, 1 model selected
> show sel atoms
> select #2/B:361@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:361@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:361@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2 :358
32 atoms, 30 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #2/B:358@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2 :276
38 atoms, 34 bonds, 4 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #2 :215
38 atoms, 34 bonds, 4 residues, 1 model selected
> show sel atoms
> select #2/B:215@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:215@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:215@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #2 :361
30 atoms, 26 bonds, 4 residues, 1 model selected
> select #2 :361,358,359,23,227,215,279,272
270 atoms, 252 bonds, 32 residues, 1 model selected
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass14/Figure5/PanelA.cxs
——— End of log from Tue Dec 23 16:23:44 2025 ———
opened ChimeraX session
> select clear
> zoom 1.1
moved plane near 5.612909121778821 [-0.03254057 0.92642164 0.37507862]
moved plane far 5.612909121778821 [-0.03254057 0.92642164 0.37507862]
> zoom 1.1
moved plane near 5.102644832270665 [-0.03254057 0.92642164 0.37507862]
moved plane far 5.102644832270665 [-0.03254057 0.92642164 0.37507862]
> hide #1.1 models
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass14/Figure5/PanelA.cxs
> select #2 :231
26 atoms, 22 bonds, 4 residues, 1 model selected
> show sel atoms
> select #2/B:231@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:231@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:231@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2 :215,217
70 atoms, 62 bonds, 8 residues, 1 model selected
> show sel atoms
> select #2/B:215@O
1 atom, 1 residue, 1 model selected
> select #2 :215,217
70 atoms, 62 bonds, 8 residues, 1 model selected
> color sel byhetero
> select #2/B:217@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:215@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:215@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass14/Figure5/PanelA.cxs
[Repeated 1 time(s)]
——— End of log from Tue Dec 23 16:28:15 2025 ———
opened ChimeraX session
> select #2 :270
32 atoms, 30 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> select #2/B:270@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:215@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save PanelA.tif supersample 4 transparentBackground true
> select :360
58 atoms, 54 bonds, 10 residues, 3 models selected
> show sel & #!2,4 atoms
> color (#!2,4 & sel) byhetero
> select :228,224
184 atoms, 170 bonds, 20 residues, 3 models selected
> show sel & #!2,4 atoms
> hide (#!2,4 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!2,4 & sel-residues)
> show (#!2,4 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select #2:228,224
72 atoms, 66 bonds, 8 residues, 1 model selected
> select #2:228,224
72 atoms, 66 bonds, 8 residues, 1 model selected
> select #2 :228,224
72 atoms, 66 bonds, 8 residues, 1 model selected
> show sel atoms
> select #2/B:224@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:224@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:224@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:228@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:228@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:228@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2 :228,224
72 atoms, 66 bonds, 8 residues, 1 model selected
> color sel byhetero
> select clear
> save PanelA.tif supersample 4 transparentBackground true
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass14/Figure5/PanelA.cxs
> select #2 :227
36 atoms, 34 bonds, 4 residues, 1 model selected
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass14/Figure5/PanelA.cxs
> select #2/B:207@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!2,4 atoms
> undo
> select #4/B:207@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select :209
80 atoms, 70 bonds, 10 residues, 3 models selected
> hide sel & #!2,4 atoms
> select #2/B:234@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:234@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:364@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:364@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:318@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:318@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:289@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:289@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:288@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:288@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save PanelA.tif supersample 4 transparentBackground true
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass14/Figure5/PanelA.cxs
——— End of log from Tue Dec 23 17:02:48 2025 ———
opened ChimeraX session
> select #2/K:503@O07
1 atom, 1 residue, 1 model selected
> select add #2/B:279@OE1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #2/K:503@O07 #2/B:279@OE1
Distance between latersl_interdimer-coot-229.pdb #2/K TA1 503 O07 and /B GLN
279 OE1: 2.992Å
> select clear
> cd /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass14/Figure5/
Current working directory is:
/Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass14/Figure5
> save PanelA.tif supersample 4 transparentBackground true
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass14/Figure5/PanelA_2.cxs
——— End of log from Wed Mar 4 15:56:44 2026 ———
opened ChimeraX session
> open 9WDA
Summary of feedback from opening 9WDA fetched from pdb
---
warnings | Atom H1 is not in the residue template for MET /a:1
Atom H1 is not in the residue template for MET /b:1
9wda title:
Paclitaxel/GMPCPP-stabilized human alpha1A/beta3 microtubule [more info...]
Chain information for 9wda #5
---
Chain | Description | UniProt
a | Tubulin alpha-1A chain | TBA1A_HUMAN 1-451
b | Tubulin beta-3 chain | TBB3_HUMAN 1-450
Non-standard residues in 9wda #5
---
G2P — phosphomethylphosphonic acid guanylate ester
GTP — guanosine-5'-triphosphate
MG — magnesium ion
TA1 — TAXOL
> ui tool show Matchmaker
> matchmaker #!5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker latersl_interdimer-coot-229.pdb, chain A (#2) with 9wda, chain a
(#5), sequence alignment score = 2080
RMSD between 414 pruned atom pairs is 0.653 angstroms; (across all 427 pairs:
0.905)
> select add #5
13462 atoms, 13622 bonds, 5 pseudobonds, 862 residues, 3 models selected
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select clear
Drag select of 343 atoms, 95 pseudobonds, 271 bonds
> ui tool show Matchmaker
> matchmaker #!5 & sel to #2 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker latersl_interdimer-coot-229.pdb, chain B (#2) with 9wda, chain b
(#5), sequence alignment score = 121.1
RMSD between 26 pruned atom pairs is 0.488 angstroms; (across all 26 pairs:
0.488)
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/bIII_vs_BIIITaxol.cxs
> select add #5
13462 atoms, 13622 bonds, 859 pseudobonds, 862 residues, 4 models selected
> size
> size sel stickRadius 0.15
Changed 13622 bond radii
> size sel stickRadius 0.1
Changed 13622 bond radii
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/bIII_vs_BIIITaxol.cxs
> select H
6611 atoms, 860 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #5/b:279@CA
1 atom, 1 residue, 1 model selected
> open 9WDA format mmcif fromDatabase pdb
Summary of feedback from opening 9WDA fetched from pdb
---
warnings | Atom H1 is not in the residue template for MET /a:1
Atom H1 is not in the residue template for MET /b:1
9wda title:
Paclitaxel/GMPCPP-stabilized human alpha1A/beta3 microtubule [more info...]
Chain information for 9wda #6
---
Chain | Description | UniProt
a | Tubulin alpha-1A chain | TBA1A_HUMAN 1-451
b | Tubulin beta-3 chain | TBB3_HUMAN 1-450
Non-standard residues in 9wda #6
---
G2P — phosphomethylphosphonic acid guanylate ester
GTP — guanosine-5'-triphosphate
MG — magnesium ion
TA1 — TAXOL
> ui tool show Matchmaker
> matchmaker #!6 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 9wda, chain a (#5) with 9wda, chain a (#6), sequence alignment
score = 2316
RMSD between 431 pruned atom pairs is 0.000 angstroms; (across all 431 pairs:
0.000)
> select add #6
13463 atoms, 13622 bonds, 5 pseudobonds, 863 residues, 4 models selected
> ui tool show "Color Actions"
> color sel salmon
> hide (#!5-6 & sel-residues & (protein|nucleic)) target ab
> cartoon hide (#!5-6 & sel-residues)
> show (#!5-6 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> size sel stickRadius 0.15
Changed 13622 bond radii
> size sel stickRadius 0.1
Changed 13622 bond radii
> color (#!5-6 & sel) byhetero
> select H
6611 atoms, 860 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #5 :279
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel target ab
> select #5/b:279@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:279@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:279@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5 :215
19 atoms, 17 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> select #5/b:215@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:215@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:215@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5 :229
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> undo
> select #5 :227
18 atoms, 17 bonds, 2 residues, 1 model selected
> show sel atoms
> select #5/b:227@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:227@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:227@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select add #5
6851 atoms, 7011 bonds, 853 pseudobonds, 862 residues, 4 models selected
> color (#!5 & sel) byhetero
> select clear
> select #5/b:227@NE2
1 atom, 1 residue, 1 model selected
> select add #5/b:501@O14
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #5/b:227@NE2 #5/b:501@O14
Distance between 9wda #5/b HIS 227 NE2 and TA1 501 O14: 2.773Å
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> select #5 :229
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel target ab
> undo
[Repeated 1 time(s)]
> select #5 :359
18 atoms, 17 bonds, 2 residues, 1 model selected
> show sel atoms
> select #5/b:359@O
1 atom, 1 residue, 1 model selected
> select add #5/b:501@O12
2 atoms, 2 residues, 1 model selected
> distance #5/b:359@O #5/b:501@O12
Distance between 9wda #5/b ARG 359 O and TA1 501 O12: 3.318Å
> select #5/b:501@O13
1 atom, 1 residue, 1 model selected
> select add #5/b:359@N
2 atoms, 2 residues, 1 model selected
> distance #5/b:501@O13 #5/b:359@N
Distance between 9wda #5/b TA1 501 O13 and ARG 359 N: 3.719Å
> ~distance #2/B:359@O #2/K:503@O12
> select #5 :361
15 atoms, 13 bonds, 2 residues, 1 model selected
> show sel atoms
> select #5/b:361@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:361@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:360@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:360@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5 :23
15 atoms, 13 bonds, 2 residues, 1 model selected
> show sel atoms
> select #5/b:23@CG1
1 atom, 1 residue, 1 model selected
> select add #5/b:501@C32
2 atoms, 2 residues, 1 model selected
> distance #5/b:23@CG1 #5/b:501@C32
Distance between 9wda #5/b VAL 23 CG1 and TA1 501 C32: 4.560Å
> select #2/B:23@CG1
1 atom, 1 residue, 1 model selected
> select add #2/K:503@C36
2 atoms, 2 residues, 1 model selected
> distance #2/B:23@CG1 #2/K:503@C36
Distance between latersl_interdimer-coot-229.pdb #2/B VAL 23 CG1 and /K TA1
503 C36: 4.036Å
> select #5/b:23@CG2
1 atom, 1 residue, 1 model selected
> select add #5/b:501@C35
2 atoms, 2 residues, 1 model selected
> distance #5/b:23@CG2 #5/b:501@C35
Distance between 9wda #5/b VAL 23 CG2 and TA1 501 C35: 4.912Å
> undo
[Repeated 2 time(s)]
> select clear
> select #5/b:23@CA
1 atom, 1 residue, 1 model selected
> select add #5/b:501@C32
2 atoms, 2 residues, 1 model selected
> distance #5/b:23@CA #5/b:501@C32
Distance between 9wda #5/b VAL 23 CA and TA1 501 C32: 4.191Å
> hide sel
> select #5 :270
16 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> select #5/b:270@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:270@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:270@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:270@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:270@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5 :272
19 atoms, 19 bonds, 2 residues, 1 model selected
> show sel atoms
> select #5/b:272@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5 :272
19 atoms, 19 bonds, 2 residues, 1 model selected
> show sel atoms
> select #5/b:272@O
1 atom, 1 residue, 1 model selected
> select add #5/b:501@O06
2 atoms, 2 residues, 1 model selected
> distance #5/b:272@O #5/b:501@O06
Distance between 9wda #5/b PRO 272 O and TA1 501 O06: 3.433Å
> select clear
[Repeated 1 time(s)]
> hide sel
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/bIII_vs_BIIITaxol.cxs
——— End of log from Fri May 8 14:06:26 2026 ———
opened ChimeraX session
> select #2/B:279@CA
1 atom, 1 residue, 1 model selected
> select #2/B:279@CA
1 atom, 1 residue, 1 model selected
> select #2,5 :274
42 atoms, 39 bonds, 6 residues, 2 models selected
> show sel atoms
> color sel byhetero
> select #5/b:274@O
1 atom, 1 residue, 1 model selected
> select add #5/b:501@O06
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #5/b:274@O #5/b:501@O06
Distance between 9wda #5/b THR 274 O and TA1 501 O06: 3.481Å
> hide sel
> select #5/b:274@N
1 atom, 1 residue, 1 model selected
> select add #5/b:501@O06
2 atoms, 2 residues, 1 model selected
> distance #5/b:274@N #5/b:501@O06
Distance between 9wda #5/b THR 274 N and TA1 501 O06: 3.200Å
> select #2/K:503@O06
1 atom, 1 residue, 1 model selected
> select add #2/B:274@N
2 atoms, 2 residues, 1 model selected
> distance #2/K:503@O06 #2/B:274@N
Distance between latersl_interdimer-coot-229.pdb #2/K TA1 503 O06 and /B THR
274 N: 3.892Å
> select #2/B:279@CA
1 atom, 1 residue, 1 model selected
> ui tool show Rotamers
Populating font family aliases took 64 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> swapaa interactive sel GLN rotLib Dunbrack
latersl_interdimer-coot-229.pdb #2/B GLN 279: phi -83.4, psi -31.2 trans
Changed 648 bond radii
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026.cxs
> select #5/b:501@O05
1 atom, 1 residue, 1 model selected
> select add #5/b:227@NE2
2 atoms, 2 residues, 1 model selected
> distance #5/b:501@O05 #5/b:227@NE2
Distance between 9wda #5/b TA1 501 O05 and HIS 227 NE2: 4.810Å
> hide sel
> hide #!5 models
> show #!5 models
> select #5/b:23@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:23@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> open /Users/zehrea/Desktop/MT_models/TSA-
> GDP_Taxol/DEPOSIT_final/Corrected_FINAL/latersl_interdimer-coot-231.pdb
Chain information for latersl_interdimer-coot-231.pdb #7
---
Chain | Description
A C | No description available
B D | No description available
> hide #!6 models
> show #!6 models
> ~distance #5/b:274@N #5/b:501@O06
> ~distance #5/b:23@CA #5/b:501@C32
> ~distance #5/b:227@NE2 #5/b:501@O14
> ~distance #5/b:272@O #5/b:501@O06
> ~distance #2/K:503@O14 #2/B:227@NE2
> ~distance #4/K:503@O06 #2/B:272@O
> ~distance #2/B:279@NE2 #2/K:503@O10
> ~distance #2/B:279@OE1 #2/K:503@O08
> ~distance #2/B:359@N #2/K:503@O13
> ~distance #2/K:503@O07 #2/B:279@OE1
> ~distance #2/B:23@CG1 #2/K:503@C36
> ~distance #5/b:501@O13 #5/b:359@N
> ~distance #5/b:359@O #5/b:501@O12
> ~distance #5/b:23@CG2 #5/b:501@C35
> ~distance #5/b:23@CG1 #5/b:501@C32
> ~distance #5/b:501@O05 #5/b:227@NE2
> ~distance #2/K:503@O06 #2/B:274@N
> ~distance #5/b:274@O #5/b:501@O06
> open /Users/zehrea/Desktop/MT_models/TSA-
> GDP_Taxol/DEPOSIT_final/Corrected_FINAL/latersl_interdimer-coot-231.pdb
> format pdb
Chain information for latersl_interdimer-coot-231.pdb #1
---
Chain | Description
A C | No description available
B D | No description available
> rename #1 TSA-taxol.pdb
> rename #2 TSA-Taxolpdb
> close #3
> close #4
> close #2
> hide #!7 models
> show #!7 models
> rename #7 TSa_taxol.pdb
> select add #7
13563 atoms, 13886 bonds, 2 pseudobonds, 1727 residues, 3 models selected
> select add #1
27125 atoms, 27772 bonds, 4 pseudobonds, 3453 residues, 5 models selected
> hide (#!1,5,7 & sel-residues & (protein|nucleic)) target ab
> cartoon hide (#!1,5,7 & sel-residues)
> show (#!1,5,7 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> color (#!1,5,7 & sel) dark gray
> select clear
> select :279
108 atoms, 96 bonds, 12 residues, 4 models selected
> select #1:279
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1 :279
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 36 atom styles
> style sel stick
Changed 36 atom styles
> show sel target ab
> show sel atoms
> style sel ball
Changed 36 atom styles
> style sel stick
Changed 36 atom styles
> color sel byhetero
> select #1 :359
30 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 30 atom styles
> show sel target ab
> select #1 :274
28 atoms, 26 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 28 atom styles
> show sel target ab
> select #1 :227
36 atoms, 34 bonds, 4 residues, 1 model selected
> show sel target ab
> select #1 :215
38 atoms, 34 bonds, 4 residues, 1 model selected
> show sel target ab
> select #1 :272
38 atoms, 38 bonds, 4 residues, 1 model selected
> show sel atoms
> show sel target ab
> select #1 :270
32 atoms, 30 bonds, 4 residues, 1 model selected
> show sel target ab
> select #1 :23
30 atoms, 26 bonds, 4 residues, 1 model selected
> show sel atoms
> show sel target ab
> select #5 :23
15 atoms, 13 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel target ab
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026.cxs
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/TSA-
> Taxol.pdb models #7
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/bIII_Luo.pdb
> models #5 relModel #1
> select
40826 atoms, 41794 bonds, 5059 pseudobonds, 5176 residues, 14 models selected
> show (#!1,5-7 & sel) target ab
> undo
> color (#!1,5-7 & sel) byhetero
> select #7/K:503@O14
1 atom, 1 residue, 1 model selected
> select add #1/B:227@NE2
2 atoms, 2 residues, 2 models selected
> distance style color black
[Repeated 2 time(s)]
> distance style color #929292
[Repeated 2 time(s)]
> distance #7/K:503@O14 #1/B:227@NE2
Distance between TSa_taxol.pdb #7/K TA1 503 O14 and TSA-taxol.pdb #1/B HIS 227
NE2: 2.776Å
> select #5/b:501@O14
1 atom, 1 residue, 1 model selected
> select add #5/b:227@NE2
2 atoms, 2 residues, 1 model selected
> distance style color #ff7e79
[Repeated 2 time(s)]
> distance #5/b:501@O14 #5/b:227@NE2
Distance between 9wda #5/b TA1 501 O14 and HIS 227 NE2: 2.773Å
> select add #2
2 pseudobonds, 2 models selected
> ui tool show "Color Actions"
> color sel salmon
No visible atoms or bonds selected
[Repeated 1 time(s)]
> select subtract #2
Nothing selected
> select add #2.1
1 model selected
> select add #2
2 pseudobonds, 2 models selected
> select subtract #2.1
2 pseudobonds, 1 model selected
> select add #2
2 pseudobonds, 2 models selected
> select subtract #2
Nothing selected
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026.cxs
> select #5,1 :359
48 atoms, 45 bonds, 6 residues, 2 models selected
> show sel atoms
> show sel target ab
> select #1/B:359@O
1 atom, 1 residue, 1 model selected
> select add #7/K:503@O13
2 atoms, 2 residues, 2 models selected
> distance #1/B:359@O #7/K:503@O13
Distance between TSA-taxol.pdb #1/B ARG 359 O and TSa_taxol.pdb #7/K TA1 503
O13: 3.146Å
> select #5/b:359@O
1 atom, 1 residue, 1 model selected
> select add #5/b:501@O13
2 atoms, 2 residues, 1 model selected
> distance #5/b:359@O #5/b:501@O13
Distance between 9wda #5/b ARG 359 O and TA1 501 O13: 2.987Å
> select #1/B:359@N
1 atom, 1 residue, 1 model selected
> select add #7/K:503@O13
2 atoms, 2 residues, 2 models selected
> distance #1/B:359@N #7/K:503@O13
Distance between TSA-taxol.pdb #1/B ARG 359 N and TSa_taxol.pdb #7/K TA1 503
O13: 3.040Å
> select #5,1 :279
54 atoms, 48 bonds, 6 residues, 2 models selected
> select #7/K:503@O08
1 atom, 1 residue, 1 model selected
> select add #1/B:279@NE2
2 atoms, 2 residues, 2 models selected
> distance #7/K:503@O08 #1/B:279@NE2
Distance between TSa_taxol.pdb #7/K TA1 503 O08 and TSA-taxol.pdb #1/B GLN 279
NE2: 2.993Å
> select #5,1 :23
45 atoms, 39 bonds, 6 residues, 2 models selected
> select #5,1 :358
48 atoms, 45 bonds, 6 residues, 2 models selected
> show sel atoms
> show sel target ab
> select #5,1 :274
42 atoms, 39 bonds, 6 residues, 2 models selected
> select #1/B:274@N
1 atom, 1 residue, 1 model selected
> select add #7/K:503@O06
2 atoms, 2 residues, 2 models selected
> distance #1/B:274@N #7/K:503@O06
Distance between TSA-taxol.pdb #1/B THR 274 N and TSa_taxol.pdb #7/K TA1 503
O06: 3.892Å
> ~distance #1/B:274@N #7/K:503@O06
> select #5/b:274@N
1 atom, 1 residue, 1 model selected
> select add #5/b:501@O06
2 atoms, 2 residues, 1 model selected
> distance #5/b:274@N #5/b:501@O06
Distance between 9wda #5/b THR 274 N and TA1 501 O06: 3.200Å
> select #5,1 :228
48 atoms, 42 bonds, 6 residues, 2 models selected
> show sel atoms
> show sel target ab
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026.cxs
> select add #2
48 atoms, 42 bonds, 7 pseudobonds, 6 residues, 4 models selected
> select add #1
13578 atoms, 13900 bonds, 1651 pseudobonds, 1728 residues, 6 models selected
> select subtract #2.1
13578 atoms, 13900 bonds, 1651 pseudobonds, 1728 residues, 5 models selected
> select add #7
27140 atoms, 27786 bonds, 3367 pseudobonds, 3454 residues, 8 models selected
> color (#!1,5,7 & sel) dark gray
> color (#!1,5,7 & sel) byhetero
> select subtract #7
13578 atoms, 13900 bonds, 1647 pseudobonds, 1728 residues, 5 models selected
> select add #6
20429 atoms, 20911 bonds, 2506 pseudobonds, 2590 residues, 9 models selected
> select add #5
27264 atoms, 27908 bonds, 3333 pseudobonds, 3450 residues, 12 models selected
> select subtract #1
13702 atoms, 14022 bonds, 1689 pseudobonds, 1724 residues, 9 models selected
> ui tool show "Color Actions"
> color sel salmon
> color (#!5-6 & sel) byhetero
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026.cxs
> select
40826 atoms, 41794 bonds, 5053 pseudobonds, 5176 residues, 16 models selected
> size
> size sel stickRadius 0.15
Changed 41794 bond radii
> size sel stickRadius 0.1
Changed 41794 bond radii
> hide #2.1 models
> select #5,1 :262
69 atoms, 66 bonds, 6 residues, 2 models selected
> show sel atoms
[Repeated 1 time(s)]
> show sel target ab
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> select #5,1 :262
69 atoms, 66 bonds, 6 residues, 2 models selected
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select #5,1 :362
48 atoms, 42 bonds, 6 residues, 2 models selected
> show (#!1 & sel) target ab
> show #!5 models
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select #5,1 :361
45 atoms, 39 bonds, 6 residues, 2 models selected
> show sel target ab
> select clear
> select #1/B:361@O
1 atom, 1 residue, 1 model selected
> select add #5/b:361@O
2 atoms, 2 residues, 2 models selected
> hide sel atoms
> select #5/b:361@C
1 atom, 1 residue, 1 model selected
> select add #1/B:361@C
2 atoms, 2 residues, 2 models selected
> hide sel atoms
> select #5/b:361@N
1 atom, 1 residue, 1 model selected
> select add #1/B:361@N
2 atoms, 2 residues, 2 models selected
> hide sel atoms
> select #5/b:358@O
1 atom, 1 residue, 1 model selected
> select add #1/B:358@O
2 atoms, 2 residues, 2 models selected
> hide sel atoms
> select #1/B:358@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:358@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:23@N
1 atom, 1 residue, 1 model selected
> select add #1/B:23@N
2 atoms, 2 residues, 2 models selected
> hide sel atoms
> select add #1/B:23@O
1 atom, 1 bond, 1 residue, 2 models selected
> hide sel atoms
> select #5/b:23@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:23@C
1 atom, 1 residue, 1 model selected
> select add #1/B:23@C
2 atoms, 2 residues, 2 models selected
> hide sel atoms
> select #1/B:228@O
1 atom, 1 residue, 1 model selected
> select add #5/b:228@O
2 atoms, 2 residues, 2 models selected
> hide sel atoms
> select #1/B:228@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:228@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:227@O
1 atom, 1 residue, 1 model selected
> select add #1/B:227@N
2 atoms, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:227@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:228@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:228@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5/b:274@O
1 atom, 1 residue, 1 model selected
> select add #1/B:274@O
2 atoms, 2 residues, 2 models selected
> hide sel atoms
> select #5/b:274@C
1 atom, 1 residue, 1 model selected
> select add #1/B:274@C
2 atoms, 2 residues, 2 models selected
> hide sel atoms
> select #5/b:272@O
1 atom, 1 residue, 1 model selected
> select add #1/B:272@O
2 atoms, 2 residues, 2 models selected
> hide sel atoms
> select #5/b:272@C
1 atom, 1 residue, 1 model selected
> select add #1/B:272@C
2 atoms, 2 residues, 2 models selected
> hide sel atoms
> select #1/B:270@O
1 atom, 1 residue, 1 model selected
> select add #1/B:270@N
2 atoms, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:270@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026.cxs
> ui tool show "Side View"
> ui mousemode right zoom
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026.cxs
> select #5,1 :361
45 atoms, 39 bonds, 6 residues, 2 models selected
> select #5,1 :20
51 atoms, 48 bonds, 6 residues, 2 models selected
> show sel atoms
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select #5,1 :231
39 atoms, 33 bonds, 6 residues, 2 models selected
> show sel atoms
> color sel byhetero
> show sel target ab
> select #5/b:231@O
1 atom, 1 residue, 1 model selected
> select add #1/B:231@O
2 atoms, 2 residues, 2 models selected
> hide sel atoms
> select #5/b:231@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:231@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:231@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #5/b:231@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026.cxs
> select #5 :TA1
62 atoms, 68 bonds, 1 residue, 1 model selected
> color sel cyan
> show sel atoms
[Repeated 1 time(s)]
> select #1 :TA1
124 atoms, 136 bonds, 2 residues, 1 model selected
> color sel cyan
> color sel byhetero
> select clear
> open /Users/zehrea/Desktop/MT_models/TSA-GDP/Deposition/TSA-GDP_FINAL-
> coot-89.pdb
Chain information for TSA-GDP_FINAL-coot-89.pdb #3
---
Chain | Description
A E G | No description available
B F | No description available
C | No description available
D H | No description available
> open /Users/zehrea/Desktop/MT_models/TSA-GDP/Deposition/TSA-GDP_FINAL-
> coot-89.pdb
Chain information for TSA-GDP_FINAL-coot-89.pdb #4
---
Chain | Description
A E G | No description available
B F | No description available
C | No description available
D H | No description available
> select add #3
27210 atoms, 27621 bonds, 4 pseudobonds, 3664 residues, 2 models selected
> select add #4
54420 atoms, 55242 bonds, 8 pseudobonds, 7328 residues, 4 models selected
> style sel stick
Changed 54420 atom styles
> hide (#!3-4 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!3-4 & sel-residues)
> show (#!3-4 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select
95246 atoms, 97036 bonds, 11921 pseudobonds, 12504 residues, 22 models
selected
> size sel stickRadius 0.1
Changed 97036 bond radii
> select subtract #1
81684 atoms, 83150 bonds, 10276 pseudobonds, 10778 residues, 19 models
selected
> select subtract #2.1
81684 atoms, 83150 bonds, 10276 pseudobonds, 10778 residues, 18 models
selected
> select subtract #5
74833 atoms, 76139 bonds, 9445 pseudobonds, 9916 residues, 13 models selected
> select subtract #6
67982 atoms, 69128 bonds, 8586 pseudobonds, 9054 residues, 9 models selected
> select subtract #7
54420 atoms, 55242 bonds, 6870 pseudobonds, 7328 residues, 6 models selected
> ui tool show "Color Actions"
> color sel medium purple
> select clear
Drag select of 579 atoms, 396 bonds, 215 pseudobonds
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026_GDP_Taxol_TSA.cxs
> hide #!2 models
> ui tool show Matchmaker
> matchmaker #!3-4 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker TSA-taxol.pdb, chain B (#1) with TSA-GDP_FINAL-coot-89.pdb, chain B
(#3), sequence alignment score = 162.6
RMSD between 33 pruned atom pairs is 0.561 angstroms; (across all 33 pairs:
0.561)
Matchmaker TSA-taxol.pdb, chain B (#1) with TSA-GDP_FINAL-coot-89.pdb, chain B
(#4), sequence alignment score = 162.6
RMSD between 33 pruned atom pairs is 0.561 angstroms; (across all 33 pairs:
0.561)
> ui mousemode right zoom
> select clear
> select #3 :358
64 atoms, 60 bonds, 8 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #3/B:358@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3 :359
54 atoms, 50 bonds, 8 residues, 1 model selected
> show sel atoms
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
TSA-GDP_FINAL-coot-89.pdb #3/D ARG 359: phi -62.7, psi 132.4 trans
Changed 600 bond radii
TSA-GDP_FINAL-coot-89.pdb #!3/H ARG 359: phi -65.8, psi 134.8 trans
Changed 600 bond radii
TSA-GDP_FINAL-coot-89.pdb #!3/A PRO 359: phi -71.7, psi 165.9 trans
Changed 600 bond radii
TSA-GDP_FINAL-coot-89.pdb #!3/C PRO 359: phi -71.1, psi 166.5 trans
Changed 600 bond radii
TSA-GDP_FINAL-coot-89.pdb #!3/B ARG 359: phi -63.7, psi 132.4 trans
Changed 600 bond radii
TSA-GDP_FINAL-coot-89.pdb #!3/E PRO 359: phi -72.8, psi 160.8 trans
Changed 600 bond radii
TSA-GDP_FINAL-coot-89.pdb #!3/G PRO 359: phi -74.1, psi 164.2 trans
Changed 600 bond radii
TSA-GDP_FINAL-coot-89.pdb #!3/F ARG 359: phi -63.7, psi 132.9 trans
Changed 600 bond radii
> select clear
> select #!3/B:359@CA
1 atom, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
TSA-GDP_FINAL-coot-89.pdb #!3/B ARG 359: phi -63.7, psi 132.4 trans
Changed 600 bond radii
> swapaa #!3/B:359 ARG criteria 2 rotLib Dunbrack retain false
Using Dunbrack library
TSA-GDP_FINAL-coot-89.pdb #!3/B ARG 359: phi -63.7, psi 132.4 trans
Applying ARG rotamer (chi angles: -173.8 -179.4 -65.0 -84.1) to TSA-GDP_FINAL-
coot-89.pdb #!3/B ARG 359
> select #3 :359
60 atoms, 56 bonds, 8 residues, 1 model selected
> size sel stickRadius 0.1
Changed 56 bond radii
> color sel byhetero
> select #3 :361
60 atoms, 52 bonds, 8 residues, 1 model selected
> show sel atoms
> show sel target ab
> select #!3/B:361@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #!3/B:361@O
1 atom, 1 residue, 1 model selected
> select #!3/B:361@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide atoms
> undo
> select #!3/B:361@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3 :272
77 atoms, 76 bonds, 9 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #!3/B:272@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #!3/B:272@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026_GDP_Taxol_TSA.cxs
> select #3 :23
60 atoms, 52 bonds, 8 residues, 1 model selected
> show sel atoms
> select #!3/B:23@O
1 atom, 1 residue, 1 model selected
> hide #!5 models
> hide #!6 models
> hide sel atoms
> select #!3/B:23@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #!3/B:23@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:279@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:279@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:279@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3 :279
69 atoms, 60 bonds, 9 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #!3/B:279@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #!3/B:279@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #!3/B:279@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:274@N
1 atom, 1 residue, 1 model selected
> show #!2 models
> show #!6 models
> show #!5 models
> select #3 :274
57 atoms, 52 bonds, 9 residues, 1 model selected
> show sel atoms
> show sel target ab
> color sel byhetero
> select #1/B:215@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:215@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3 :215
77 atoms, 68 bonds, 9 residues, 1 model selected
> show sel atoms
> select #!3/B:215@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #!3/B:215@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3 :227
73 atoms, 68 bonds, 9 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #!3/B:227@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #!3/B:227@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #!3/B:227@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3 :228
64 atoms, 56 bonds, 8 residues, 1 model selected
> show sel atoms
> select #!3/B:228@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #!3/B:228@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026_GDP_Taxol_TSA.cxs
——— End of log from Wed May 13 16:04:03 2026 ———
opened ChimeraX session
> hide #!2 models
> hide #!5 models
> hide #!6 models
> save TSA-Taxol_vsApo.tif supersample 4 transparentBackground true
> cd /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/
Current working directory is:
/Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6
> save TSA-Taxol_vsApo.tif supersample 4 transparentBackground true
> hide #!4 models
> hide #!3 models
> show #!5 models
> show #!6 models
> show #!2 models
> save TSA-Taxol_vs_b3_taxol.tif supersample 4 transparentBackground true
> select #3 :217
64 atoms, 56 bonds, 8 residues, 1 model selected
> show #!1,5-7 atoms
> undo
> show #!3 models
> show #!4 models
> select #3,1,5 :217
112 atoms, 98 bonds, 14 residues, 3 models selected
> show sel atoms
> select clear
> select #1/B:217@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select :HOH
418 atoms, 418 residues, 2 models selected
> select #3,1,5 :217
112 atoms, 98 bonds, 14 residues, 3 models selected
> show sel target ab
> select clear
> select #3,1,5 :217
112 atoms, 98 bonds, 14 residues, 3 models selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select clear
> select #3 :270
65 atoms, 60 bonds, 9 residues, 1 model selected
> show sel target ab
> select clear
> select #!3/B:270@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #!3/B:270@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026_GDP_Taxol_TSA.cxs
——— End of log from Wed May 13 16:31:51 2026 ———
Failed opening file
/Users/zehrea/Documents/Lab_work/Papers/2023/MboC/Figures/Pass17/Figure6/Luo_et_al_bIII_2026_GDP_Taxol_TSA.cxs:
'_RotamerStateManager' object has no attribute 'triggers'
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,10
Model Number: Z175000ZKLL/A
Chip: Apple M2 Pro
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 13822.61.10
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.7.3 (24G419)
Kernel Version: Darwin 24.6.0
Time since boot: 58 days, 23 hours, 50 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 19
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Note:
See TracTickets
for help on using tickets.
