id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16017	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar Lab/Research
> Data/SERT/structural comparison/ChimeraX - conformational
> comparisons/cysteine-acc-assay_outward_comparison_6DZZ-6DZV-6DZY-
> mystructure.cxs""

Log from Sun Sep 15 18:15:13 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar Lab/Research
> Data/SERT/ASH_SERT/SERT_J326-Cl-Na_IBL-revised-
> geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08.pdb""
> format pdb

Chain information for SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08.pdb
#1  
---  
Chain | Description  
D | No description available  
  

> set bgColor white

> surface

> ui tool show ""Side View""

> ui tool show ""Surface Color""

> color single #1.1.1

> ui tool show ""Show Volume Menu""

> ui tool show ""Color Zone""

No surface chosen for color zoning  

> volume planes z style image imageMode ""full region""

No volumes specified  

> select add #1

4601 atoms, 4737 bonds, 542 residues, 2 models selected  

> volume planes z style image imageMode ""full region""

No volumes specified  

> volume hide

No volumes specified  

> ui mousemode right ""color key""

> key borderColor default

[Repeated 9 time(s)]

> key borderColor white

> key borderColor default

> key borderColor white

> ui mousemode right translate

> ui mousemode right ""contour level""

> ui mousemode right ""color key""

> key colorTreatment distinct

> key colorTreatment blended

> key delete

> ui mousemode right ""contour level""

[Repeated 1 time(s)]

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> toolshed show

> ui tool show ""Surface Zone""

> ui tool show ""Surface Color""

No map chosen for coloring  

> color cylindrical #1.1.1 palette #ff0000:#ffffff:#0000ff

[Repeated 1 time(s)]

> color cylindrical #1.1.1 palette 127.6,#102714:156.9,#0b130b:186.1,#0e1b18

> hide #!1.1 models

> show #1.1 models

> hide #!1.1 models

> show #1.1 models

> hide #!1 models

> show #!1 models

> color cylindrical #1.1.1 palette #102714:#0b130b:#0e1b18

> select add #1.1

4601 atoms, 4737 bonds, 542 residues, 3 models selected  

> select subtract #1.1

40 atoms, 38 bonds, 5 residues, 2 models selected  

> select add #1

4601 atoms, 4737 bonds, 542 residues, 2 models selected  

> select subtract #1

1 model selected  

> hide cartoons

> hide

> preset ""initial styles"" ""original look""

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> rainbow

> view

> surface

> lighting soft

> hide #1.1 models

> show #1.1 models

> color #1.1 silver

> hide #1.1 models

> show #1.1 models

> transparency 50

> transparency 0

> transparency 50

> ui tool show ""Surface Color""

> color radial #1.1 palette #ff0000:#ffffff:#0000ff

> color radial #1.1 palette 144.7,#000000:187.3,#000000:229.8,#000000

> color single #1.1

> color cylindrical #1.1 palette 144.7,#000000:187.3,#000000:229.8,#000000

> color single #1.1

> color cylindrical #1.1 palette 144.7,#000000:187.3,#000000:229.8,#000000
> center 103.39,110.27,113.83

> color single #1.1

[Repeated 3 time(s)]

> color cylindrical #1.1 palette 144.7,#000000:187.3,#000000:229.8,#000000
> center 103.39,110.27,113.83

> color single #1.1.1

> color cylindrical #1.1.1 palette 144.7,#000000:187.3,#000000:229.8,#000000
> center 103.39,110.27,113.83

> color single #1.1.1

> color cylindrical #1.1.1 palette 144.7,#000000:187.3,#c0c0c0:229.8,#000000
> center 103.39,110.27,113.83

> color single #1.1.1

> color cylindrical #1.1.1 palette #000000:#c0c0c0:#000000 center
> 103.39,110.27,113.83

> color single #1.1.1

[Repeated 3 time(s)]

> transparency 0

> transparency 50

> transparency 0

> transparency 50

> transparency 0

> transparency 50

> transparency 0

> transparency 50

> color cylindrical #1.1.1 palette 0.7441,#000000:15.99,#c0c0c0:31.23,#000000
> center 103.39,110.27,113.83

> transparency 0

> transparency 50

> graphics silhouettes true

> color cylindrical #1.1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

> color single #1.1.1

> color cylindrical #1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

> color cylindrical #1.1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

[Repeated 1 time(s)]

> color single #1.1.1

[Repeated 2 time(s)]

> color cylindrical #1.1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

[Repeated 1 time(s)]

> color single #1.1.1

> transparency 0

> transparency 50

> color cylindrical #1.1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

[Repeated 1 time(s)]

> transparency 0

> transparency 50

> lighting full

> color cylindrical #1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

> color cylindrical #1.1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

> lighting soft

> lighting simple

> graphics silhouettes false

> graphics silhouettes true

> transparency 50

> transparency 0

> color single #1.1.1

[Repeated 2 time(s)]

> color cylindrical #1.1.1 palette 0.7441,#000000:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

> color cylindrical #1.1.1 palette 0.7441,#000000:15.99,#000000:31.23,#c0c0c0
> center 103.39,110.27,113.83

> color cylindrical #1.1.1 palette 0.7441,#000000:15.99,#000000:31.23,#000000
> center 103.39,110.27,113.83

> lighting soft

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> hide #!1 models

> hide #1.1 models

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar Lab/Research
> Data/SERT/ASH_SERT/SERT_J326-Cl-Na_IBL-revised-
> geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08.pdb""

Chain information for SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08.pdb
#3  
---  
Chain | Description  
D | No description available  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar Lab/Research
> Data/SERT/ASH_SERT/cryosparc_P132_J294_006_volume_map_sharp.mrc""

Opened cryosparc_P132_J294_006_volume_map_sharp.mrc as #4, grid size
300,300,300, pixel 0.725, shown at level 0.0232, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.08525

> volume #4 level 0.06879

> hide #!4 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> :556

Unknown command: :556  

> show :556

> show #!4 models

> volume #4 level 0.06023

> volume #4 level 0.04609

> volume #4 level 0.09101

> show :556,104,493

Drag select of 4 cryosparc_P132_J294_006_volume_map_sharp.mrc  

> volume #4 level 0.07249

> volume #4 level 0.08916

> volume #4 level 0.08885

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> volume #4 level 0.1479

> volume #4 level 0.06718

> close session

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/6DZV_-
> _IBG_occluded_-_prepared.pdb""

6DZV_-_IBG_occluded_-_prepared.pdb title:  
Wild type human serotonin transporter In complex with 15B8 fab bound to
ibogaine In occluded conformation [more info...]  
  
Chain information for 6DZV_-_IBG_occluded_-_prepared.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6DZV_-_IBG_occluded_-_prepared.pdb #1  
---  
HJM — (5Β)-12-methoxyibogamine  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/6DZY_-
> _IBG_outward-open_-_prepared.pdb""

6DZY_-_IBG_outward-open_-_prepared.pdb title:  
Cryo-em structure of the TS2-active human serotonin transporter In complex
with 15B8 fab and 8B6 SCFV bound to ibogaine [more info...]  
  
Chain information for 6DZY_-_IBG_outward-open_-_prepared.pdb #2  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6DZY_-_IBG_outward-open_-_prepared.pdb #2  
---  
HJM — (5Β)-12-methoxyibogamine  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/6DZZ_-
> _IBG_inward-open_prepared.pdb""

6DZZ_-_IBG_inward-open_prepared.pdb title:  
Cryo-em structure of the wild-type human serotonin transporter In complex with
ibogaine and 15B8 fab In the inward conformation [more info...]  
  
Chain information for 6DZZ_-_IBG_inward-open_prepared.pdb #3  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6DZZ_-_IBG_inward-open_prepared.pdb #3  
---  
HJM — (5Β)-12-methoxyibogamine  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational
> comparisons/9EO4_-_hDAT_cocaine_-_prepared.pdb""

9EO4_-_hDAT_cocaine_-_prepared.pdb title:  
Outward-open structure of human dopamine transporter bound to cocaine [more
info...]  
  
Chain information for 9EO4_-_hDAT_cocaine_-_prepared.pdb #4  
---  
Chain | Description  
B | No description available  
  
Non-standard residues in 9EO4_-_hDAT_cocaine_-_prepared.pdb #4  
---  
CL — chloride ion  
COC — cocaine  
NA — sodium ion  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/SERT_J326-Cl-
> Na_IBL-revised-
> geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb""

SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
title:  
SERT_J326-Cl-Na_IBL-revised-geometry_real_space_refined_010_
namdinator_real_space_refined_011-coot-4_ASH_21-08 - prepared [more info...]  
  
Chain information for SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
#5  
---  
Chain | Description  
D | No description available  
  
Non-standard residues in SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
#5  
---  
CL — (CL)  
IBL — (IBL)  
NA — (NA)  
  

> close #1-3,5#4

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/6DZV_-
> _IBG_occluded_-_prepared.pdb""

6DZV_-_IBG_occluded_-_prepared.pdb title:  
Wild type human serotonin transporter In complex with 15B8 fab bound to
ibogaine In occluded conformation [more info...]  
  
Chain information for 6DZV_-_IBG_occluded_-_prepared.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6DZV_-_IBG_occluded_-_prepared.pdb #1  
---  
HJM — (5Β)-12-methoxyibogamine  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/6DZY_-
> _IBG_outward-open_-_prepared.pdb""

6DZY_-_IBG_outward-open_-_prepared.pdb title:  
Cryo-em structure of the TS2-active human serotonin transporter In complex
with 15B8 fab and 8B6 SCFV bound to ibogaine [more info...]  
  
Chain information for 6DZY_-_IBG_outward-open_-_prepared.pdb #2  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6DZY_-_IBG_outward-open_-_prepared.pdb #2  
---  
HJM — (5Β)-12-methoxyibogamine  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/6DZZ_-
> _IBG_inward-open_prepared.pdb""

6DZZ_-_IBG_inward-open_prepared.pdb title:  
Cryo-em structure of the wild-type human serotonin transporter In complex with
ibogaine and 15B8 fab In the inward conformation [more info...]  
  
Chain information for 6DZZ_-_IBG_inward-open_prepared.pdb #3  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6DZZ_-_IBG_inward-open_prepared.pdb #3  
---  
HJM — (5Β)-12-methoxyibogamine  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational
> comparisons/9EO4_-_hDAT_cocaine_-_prepared.pdb""

9EO4_-_hDAT_cocaine_-_prepared.pdb title:  
Outward-open structure of human dopamine transporter bound to cocaine [more
info...]  
  
Chain information for 9EO4_-_hDAT_cocaine_-_prepared.pdb #4  
---  
Chain | Description  
B | No description available  
  
Non-standard residues in 9EO4_-_hDAT_cocaine_-_prepared.pdb #4  
---  
CL — chloride ion  
COC — cocaine  
NA — sodium ion  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/SERT_J326-Cl-
> Na_IBL-revised-
> geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb""

SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
title:  
SERT_J326-Cl-Na_IBL-revised-geometry_real_space_refined_010_
namdinator_real_space_refined_011-coot-4_ASH_21-08 - prepared [more info...]  
  
Chain information for SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
#5  
---  
Chain | Description  
D | No description available  
  
Non-standard residues in SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
#5  
---  
CL — (CL)  
IBL — (IBL)  
NA — (NA)  
  

> camera ortho

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting simple

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting soft

> hide cartoons

> show cartoons :79-112

Expected ',' or a keyword  

> show cartoons and :79-112

Expected ',' or a keyword  

> show cartoons @:79-112

Expected ',' or a keyword  

> show #1,2,3,5:79-112 cartoons

> show #1,2,3,5:323-352 cartoons

> view

> hide #3 models

> hide #!4 models

> hide #5 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> combine #1

> combine #2

> matchmaker #7:79-96,341-351 to #6:79-96,341-351

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 copy of 6DZV_-_IBG_occluded_-_prepared.pdb, chain A (#6) with copy
of 6DZY_-_IBG_outward-open_-_prepared.pdb, chain A (#7), sequence alignment
score = 151.8  
RMSD between 29 pruned atom pairs is 0.769 angstroms; (across all 29 pairs:
0.769)  
  

> hide #2 models

> hide #1 models

> show #!4 models

> hide #!4 models

> show #5 models

> combine #5

> matchmaker #8:79-96,341-351 to #6:79-96,341-351

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 copy of 6DZV_-_IBG_occluded_-_prepared.pdb, chain A (#6) with copy
of SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb,
chain D (#8), sequence alignment score = 148.2  
RMSD between 27 pruned atom pairs is 0.736 angstroms; (across all 29 pairs:
0.940)  
  

> hide #5 models

> show #6,7,8:101,368

> select Na

5 atoms, 5 residues, 3 models selected  

> show #6,7,8:NA

> select #6,7,8:NA

2 atoms, 2 residues, 1 model selected  

> style sel sphere

Changed 2 atom styles  

> hide #6 models

> show #6 models

> hide #7 models

> show #7 models

> hide #7 models

> hide #6 models

> hide #8 models

> show #7 models

> show #5 models

> hide #5 models

> show #8 models

> hide #8 models

> show #6 models

> hide #6 models

> show #8 models

> show #6 models

> select #6,7,8:CL

1 atom, 1 residue, 1 model selected  

> select #6,7,8:CL sphere

Expected a keyword  

> show #6,7,8:CL sphere

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> select #6,7,8:CL

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> show #6,7,8:CL

> show #3 models

> hide #3 models

> hide #8 models

> show #1,2,3,5:156-192 cartoons

> show #1 models

> hide #1 models

> show #6,7,8:156-192 cartoons

> hide #6,7,8:156-192 cartoons

> hide #6,7,8:275-302 cartoons

> show #6,7,8:275-302 cartoons

> show #8 models

> dssp

> select clear

Drag select of 33 atoms, 30 bonds  

> select clear

> select add #6/A:172@CA

1 atom, 1 bond, 1 residue, 2 models selected  

> select add #7/A:172@N

2 atoms, 1 bond, 2 residues, 2 models selected  

> select up

8 atoms, 3 bonds, 5 residues, 2 models selected  

> select up

78 atoms, 73 bonds, 5 residues, 2 models selected  

> hide sel target a

> select add #6/A:497@CA

79 atoms, 73 bonds, 6 residues, 2 models selected  

> select add #8/D:172@CA

80 atoms, 73 bonds, 7 residues, 3 models selected  

> select add #7/A:173@CB

81 atoms, 74 bonds, 8 residues, 3 models selected  

> select up

83 atoms, 74 bonds, 9 residues, 3 models selected  

> select up

131 atoms, 124 bonds, 9 residues, 3 models selected  

> hide sel target a

> select add #7/A:169@N

132 atoms, 125 bonds, 10 residues, 3 models selected  

> select up

134 atoms, 125 bonds, 11 residues, 3 models selected  

> select up

151 atoms, 142 bonds, 11 residues, 3 models selected  

> hide sel target a

> select add #8/D:173@O

152 atoms, 142 bonds, 12 residues, 3 models selected  

> select up

161 atoms, 152 bonds, 12 residues, 3 models selected  

> hide sel target a

> view

> hide #6 models

> hide #7 models

> select add #8/D:439@C

162 atoms, 154 bonds, 13 residues, 3 models selected  

> select clear

> show #6,7,8:437

> show #6 models

> show #7 models

> hide #6,7,8:437

> hide #6,7,8:443

> hide #6,7,8:439

> hide #6,7,8:442

> hide #6,7,8:434

> show #6,7,8:252-274 cartoons

> hide #6,7,8:252-274 cartoons

> show #6,7,8:277,107 sticks

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #6,7,8:277,107

> show #6,7,8:252-274 cartoons

> matchmaker #8:156-192,252-274,414-482 to #6:156-192,252-274,414-482

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 copy of 6DZV_-_IBG_occluded_-_prepared.pdb, chain A (#6) with copy
of SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb,
chain D (#8), sequence alignment score = 652.9  
RMSD between 118 pruned atom pairs is 1.027 angstroms; (across all 129 pairs:
1.301)  
  

> matchmaker #7:156-192,252-274,414-482 to #6:156-192,252-274,414-482

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 copy of 6DZV_-_IBG_occluded_-_prepared.pdb, chain A (#6) with copy
of 6DZY_-_IBG_outward-open_-_prepared.pdb, chain A (#7), sequence alignment
score = 676.5  
RMSD between 126 pruned atom pairs is 0.840 angstroms; (across all 129 pairs:
0.909)  
  

> ~display HC

> hide :252-302

> hide #6,7,8:252-302 cartoons

> view

> hide #6,7,8:176

> show #1 models

> hide #1 models

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.tif"" width 1218
> height 777 supersample 4 transparentBackground true

[Repeated 1 time(s)]

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.tif"" width 1218
> height 777 supersample 4

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/test.png"" width 1600 height 1021 supersample 3
> transparentBackground true

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/test.png"" width 1218 height 777 supersample 3

> save /Users/ctn700/Desktop/image5.png supersample 3

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.cxs"" includeMaps
> true

> lighting simple

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.tif"" width 1218
> height 777 supersample 4 transparentBackground true

> lighting soft

> show #6,7,8:104

> ~display HC

> show #6,7,8:493

> ~display HC

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.cxs"" includeMaps
> true

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.tif"" width 2000
> height 2000 supersample 4 transparentBackground true

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.png"" width 2000
> height 2000 supersample 4 transparentBackground true

> show #6,7,8:252-302 cartoons

> show #6,7,8:107,277

> ~display HC

> show #6,7,8:107,277 spheres

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #6,7,8:107,277 sphere

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show sphere #6,7,8:107,277

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #6,7,8:107,277 sphere

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> select #6,7,8:107,277

96 atoms, 93 bonds, 6 residues, 3 models selected  

> style sel sphere

Changed 96 atom styles  

> select clear

> show #6,7,8:414-456 cartoons

> show #6,7,8:275-302 cartoons

> show #6,7,8:353-392 cartoons

> undo

> caera ortho

Unknown command: caera ortho  

> camera ortho

> show #6,7,8:483-516 cartoons

> undo

> show #6,7,8:457-482 cartoons

> show #6,7,8:113-146 cartoons

> show #6,7,8:156-192 cartoons

> undo

> show #6,7,8:353-392 cartoons

> show #6,7,8:414-456 cartoons

> show #6,7,8:517-560 cartoons

> show #6,7,8:561-615 cartoons

> undo

> hide #6 models

> hide #7 models

> hide #8 models

> show #6 models

> show #7 models

> show #8 models

> hide #6 models

> hide #7 models

> hide #8 models

> show #5 models

> show #5 cartoons

> show #7 models

> hide #5 models

> show #6 models

> show #8 models

> show #6,7,8:193-251 cartoons

> undo

> show #6,7,8:147-155 cartoons

[Repeated 1 time(s)]

> undo

> show #6,7,8:303-322 cartoons

> undo

> show #6,7,8:393-143 cartoons

> undo

> show #6,7,8:393-413 cartoons

> show #6,7,8:303-322 cartoons

> lighting flat

> lighting soft

> lighting full

> lighting soft

> show #6,7,8:393-413 cartoons

> show #6,7,8:193-251 cartoons

> combine #3

> hide #6 models

> hide #7 models

> hide #8 models

> matchmaker #9:156-192,252-274,414-482 to #6:156-192,252-274,414-482

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 copy of 6DZV_-_IBG_occluded_-_prepared.pdb, chain A (#6) with copy
of 6DZZ_-_IBG_inward-open_prepared.pdb, chain A (#9), sequence alignment score
= 572.5  
RMSD between 116 pruned atom pairs is 0.987 angstroms; (across all 129 pairs:
1.287)  
  

> show #6 models

> hide #6 models

> show #6 models

> show #6,7,8,9:193-251 cartoons

[Repeated 1 time(s)]

> show #6,7,8,9:393-413 cartoons

> show #6,7,8,9:303-322 cartoons

> hide #6 models

> hide #9:156-192

> hide #9:156-192 cartoons

> show #9:252-302 cartoons

> show #9:277,107

> style #9:277,107 sphere

Changed 32 atom styles  

> ~display HC

> show #6 models

> hide #6 models

> show #8 models

> show #6,7,8,9:457-482 cartoons

> undo

> show #6,7,8,9:483-516 cartoons

> hide #9 models

> hide #6,7,8,9:438

> show #7 models

> show #6 models

> show #9 models

> hide #8 models

> hide #6 models

> hide #7 models

> hide #6,7,8,9:446,439,443,442

> show #6 models

> hide #6,7,8,9:414-456 cartoons

> hide #6,7,8,9:193-251 cartoons

> show #6,7,8,9:414-456 cartoons

> hide #6,7,8,9:414-456 cartoons

> view

> show #7 models

> show #8 models

> hide #7 models

> show #7 models

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/cysteine-acc-assay_outward_comparison_6DZZ-6DZV-6DZY-
> mystructure.cxs"" includeMaps true

——— End of log from Sun Sep 15 18:15:13 2024 ———

opened ChimeraX session  

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> camera ortho

> hide #6 models

> hide #7 models

> hide #9 models

> select #8/D:107@CE2

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select sel : show sel & #8 atoms

> ~display HC

> style sel & #8 sphere

Changed 316 atom styles  

> ~display C

> ~display H

> select clear

> select #8/D:107@OH

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> label sel

> label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> select clear

> ui mousemode right ""move label""

> select #8/D:107@CE2

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> color sel cyan

> color sel byhetero

> select clear

> hide #!8 models

> show #6 models

> select #6/A:107@OH

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select sel : select sel : undo

> show sel & #6 atoms

> style sel & #6 sphere

Changed 293 atom styles  

> ~display H

> select clear

> select #6/A:107@OH

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel cyan

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> color sel cyan

> color sel byhetero

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #7 models

> hide #6 models

> select #7/A:107@CE2

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select sel : select sel : undo

> show sel & #7 atoms

> style sel & #7 sphere

Changed 287 atom styles  

> ~display H

> select clear

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> show #6 models

> show #9 models

> hide #9 models

> hide #6 models

> hide #!8 models

> select #7/A:107@CE2

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> color sel cyan

> color sel byhetero

> select clear

> hide #7 models

> show #9 models

> select #9/A:107@OH

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select sel : select sel : undo

> show sel & #9 atoms

> style sel & #9 sphere

Changed 361 atom styles  

> ~display H

> select clear

> select #9/A:107@CE2

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> color sel cyan

> color sel byhetero

> select clear

> show #6 models

> show #7 models

> show #!8 models

> label #6,7,8,9:107

> delete label

Missing or invalid ""atoms"" argument: invalid atoms specifier  

> delete labels

Missing or invalid ""atoms"" argument: invalid atoms specifier  

> label #6-9 text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> close #6.1

> close #7.1

> close #8.1

> close #9.1

> show #6 models

> show #7 models

> show #8 models

> select clear

> label #6,7,8,9:107

> tile columns 4 spacinfFactor 1

Expected a keyword  

> tile columns 4 spacingFactor 1

4 models tiled  

> tile columns 2 spacingFactor 1

4 models tiled  

> tile columns 2 spacingFactor 1.2

4 models tiled  

> select #6,7,8,9:107

84 atoms, 84 bonds, 4 residues, 4 models selected  

> view sel

> rainbow sel

> undo

> color cartoon rainbow

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color rainbow cartoon

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> select up

478 atoms, 489 bonds, 27 residues, 4 models selected  

> select up

34379 atoms, 34932 bonds, 2151 residues, 4 models selected  

> rainbow sel

> undo

> select clear

> combine #6

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #9.1 models

> hide #8.1 models

> hide #7.1 models

> hide #6.1 models

> mutate #10:107 CYS

Unknown command: mutate #10:107 CYS  

> select #10/A:107@OH

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> swapaa #10:107 CYS

Using Dunbrack library  
copy of copy of 6DZV_-_IBG_occluded_-_prepared.pdb #10/A TYR 107: phi -65.2,
psi -44.1 trans  
Applying CYS rotamer (chi angles: -175.1) to copy of copy of 6DZV_-
_IBG_occluded_-_prepared.pdb #10/A CYS 107  

> hide #10 models

> show #!6 models

> show #!7 models

> show #!8 models

> show #!9 models

> view

> select add #10

8624 atoms, 8765 bonds, 538 residues, 1 model selected  

> select subtract #10

Nothing selected  

> swapaa #6,7,8,9:107 CYS

Command cancelled by user  

> combine #7

> combine #8

> combine #9

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> show #10 models

> swapaa #10,11,12,13:107 CYS

Using Dunbrack library  
copy of copy of 6DZV_-_IBG_occluded_-_prepared.pdb #10/A CYS 107: phi -65.2,
psi -44.1 trans  
copy of copy of 6DZY_-_IBG_outward-open_-_prepared.pdb #11/A TYR 107: phi
-62.6, psi -39.3 trans  
copy of copy of SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
#12/D TYR 107: phi -66.3, psi -44.0 trans  
copy of copy of 6DZZ_-_IBG_inward-open_prepared.pdb #13/A TYR 107: phi -83.6,
psi -28.2 trans  
Applying CYS rotamer (chi angles: 64.4) to copy of copy of 6DZV_-
_IBG_occluded_-_prepared.pdb #10/A CYS 107  
Applying CYS rotamer (chi angles: -70.0) to copy of copy of 6DZY_-
_IBG_outward-open_-_prepared.pdb #11/A CYS 107  
Applying CYS rotamer (chi angles: -69.5) to copy of copy of SERT_J326-Cl-
Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
#12/D CYS 107  
Applying CYS rotamer (chi angles: -68.1) to copy of copy of 6DZZ_-_IBG_inward-
open_prepared.pdb #13/A CYS 107  

> label #10,11,12,113:107,277

> label height 1

> label height 2

> label height 4

> label #10,11,12,13:107,277

> label height 4

> label height 5

> label height 4

> label #10-13 text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> ~label #10-13 residues

> label #10,11,12,13:107,277

> label height 4

> lighting soft

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> tile off

> select #10,11,12,13:107

32 atoms, 28 bonds, 4 residues, 4 models selected  

> view sel

> ui tool show ""Side View""

> view orient

> view sel

> tile columns 2 spacingFactor 1.2

4 models tiled  

> view sel

> select clear

> select #10,11,12,13:107

32 atoms, 28 bonds, 4 residues, 4 models selected  

> label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> select #10,11,12,13:277

44 atoms, 40 bonds, 4 residues, 4 models selected  

> label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> select #10,11,12,13:107

32 atoms, 28 bonds, 4 residues, 4 models selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select sel : show sel & #!10-13 atoms

> style sel & #!10-13 sphere

Changed 1257 atom styles  

> ~display H

> select clear

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/Research Data/SERT/structural comparison/ChimeraX -
> conformational comparisons/cysteine-acc-
> assay_outward_comparison_6DZZ-6DZV-6DZY-mystructure3.tif"" width 2000 height
> 2000 supersample 4 transparentBackground true

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/Research Data/SERT/structural comparison/ChimeraX -
> conformational comparisons/cysteine-acc-
> assay_outward_comparison_6DZZ-6DZV-6DZY-mystructure3.cxs"" includeMaps true

> rename #10 ""Y107C 6DZV_-_IBG_occluded_-_prepared.pdb""

> rename #11 ""Y107C 6DZY_-_IBG_outward-open_-_prepared.pdb""

> rename #12 ""Y107C SERT_J326-Cl-Na_IBL-revised-
> geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb""

> rename #13 ""Y107C 6DZZ_-_IBG_inward-open_prepared.pdb""

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/Research Data/SERT/structural comparison/ChimeraX -
> conformational comparisons/Y107C_accessibility_comparison_for_Gary.cxs""
> includeMaps true

> lighting soft

> select #10,11,12,13:104

96 atoms, 92 bonds, 4 residues, 4 models selected  

> select #10,11,12,13:103104

Nothing selected  

> label sel

> select #10,11,12,13:103,104

192 atoms, 196 bonds, 8 residues, 4 models selected  

> label sel

> label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> label height 4

> ui mousemode right ""move label""

> select clear

> select #10,11,12,13:103,104

192 atoms, 196 bonds, 8 residues, 4 models selected  

> delete sel label

Expected a keyword  

> delete label sel

Missing or invalid ""atoms"" argument: invalid atoms specifier  

> select delete label

Expected an objects specifier or a keyword  

> ~label sel residues

> select clear

Unsupported scale factor (0.000000) detected on Display0  

> select #10,11,12,13:482-492

684 atoms, 688 bonds, 44 residues, 4 models selected  

> show sel atoms

> show sel cartoons

> style sel ball

Changed 684 atom styles  

> ~display H

> show #10,11,12,13:275-302 cartoons

> dssp

> tile off

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Shared Data/SNAT1 templates & Gln
> bound/cryosparc_P162_J541_class_00_final_volume.mrc""

Opened cryosparc_P162_J541_class_00_final_volume.mrc as #14, grid size
256,256,256, pixel 0.854, shown at level 0.038, step 1, values float32  

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> view

> select add #10

9137 atoms, 9281 bonds, 571 residues, 5 models selected  

> select subtract #10

513 atoms, 516 bonds, 33 residues, 3 models selected  

> select add #11

8953 atoms, 9096 bonds, 560 residues, 4 models selected  

> select subtract #11

342 atoms, 344 bonds, 22 residues, 2 models selected  

> select add #12

8788 atoms, 8924 bonds, 553 residues, 3 models selected  

> select subtract #12

171 atoms, 172 bonds, 11 residues, 1 model selected  

> select add #13

8667 atoms, 8809 bonds, 541 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #14

2 models selected  

> view

> select clear

> volume #14 level 0.05507

> volume #14 level 0.03529

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Shared Data/SNAT1 templates & Gln
> bound/cryosparc_P162_J541_class_00_final_volume.mrc""

Opened cryosparc_P162_J541_class_00_final_volume.mrc as #15, grid size
256,256,256, pixel 0.854, shown at level 0.038, step 1, values float32  

> close session

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-Na_IBL-
> revised-geometry.pdb""

deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-Na_IBL-revised-geometry.pdb
title:  
deltaN72C13 hSERT - AF-P31645-F1-model_v4 - Cl-Na_IBL-revised-geometry [more
info...]  
  
Chain information for deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-Na_IBL-
revised-geometry.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-
Na_IBL-revised-geometry.pdb #1  
---  
CL — (CL)  
IBL — (IBL)  
NA — (NA)  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/ASH_SERT/cryosparc_P132_J294_006_volume_map_sharp.mrc""

Opened cryosparc_P132_J294_006_volume_map_sharp.mrc as #2, grid size
300,300,300, pixel 0.725, shown at level 0.0232, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.055

> transparency 50

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting full

> lighting soft

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 78 residues in model #1 to IUPAC-IUB
standards.  
deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-Na_IBL-revised-geometry.pdb
title:  
deltaN72C13 hSERT - AF-P31645-F1-model_v4 - Cl-Na_IBL-revised-geometry [more
info...]  
  
Chain information for deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-Na_IBL-
revised-geometry.pdb  
---  
Chain | Description  
1.2/A | No description available  
  
Non-standard residues in deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-
Na_IBL-revised-geometry.pdb #1.2  
---  
CL — (CL)  
IBL — (IBL)  
NA — (NA)  
  
ISOLDE: created disulfide bonds between the following residues:  
A200-A209  

> clipper associate #2 toModel #1

Opened cryosparc_P132_J294_006_volume_map_sharp.mrc as #1.1.1.1, grid size
300,300,300, pixel 0.725, shown at step 1, values float32  

> isolde sim start /A,C,B,E

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to deltaN72C13_hSERT_-
_AF-P31645-F1-model_v4_-_Cl-Na_IBL-revised-geometry.pdb #1.2  
---  
notes | No usable SEQRES records for deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-Na_IBL-revised-geometry.pdb (#1.2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 73  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A PRO 617  
Chain-final residues that are not actual C termini:  
574 hydrogen bonds  
4346 hydrogens added  
  
Fetching CCD SAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/SAC/SAC.cif  
Fetching CCD N7P from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/N7P/N7P.cif  

> isolde sim start /A:701

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start /A:701

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde parameterise sel override false

Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpsu9v_lfi/ante.in.mol2 -fi
mol2 -o
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpsu9v_lfi/ante.out.mol2 -fo
mol2 -c bcc -nc 1 -j 5 -s 2 -dr n  
(IBL) ``  
(IBL) `Welcome to antechamber 20.0: molecular input file processor.`  
(IBL) ``  
(IBL) `Info: Finished reading file
(/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpsu9v_lfi/ante.in.mol2);
atoms read (36), bonds read (38).`  
(IBL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(IBL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(IBL) ``  
(IBL) ``  
(IBL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(IBL) `Info: Total number of electrons: 124; net charge: 1`  
(IBL) ``  
(IBL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(IBL) ``  
(IBL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(IBL) ``  
(IBL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(IBL) ``  
Charges for residue IBL determined  
OpenMM ffXML file IBL written to the current working directory.  
New template added to forcefield as USER_IBL. This ligand should now work in
all remaining simulations for this session. To use in future sessions, load
the ffXML file with ISOLDE's Load Residue MD Definition(s) button.  

> select up

8740 atoms, 8882 bonds, 546 residues, 1 model selected  

> select up

8746 atoms, 8884 bonds, 550 residues, 2 models selected  

> select down

8740 atoms, 8882 bonds, 546 residues, 2 models selected  

> select up

8746 atoms, 8884 bonds, 550 residues, 2 models selected  

> select down

8740 atoms, 8882 bonds, 546 residues, 2 models selected  

> select down

36 atoms, 38 bonds, 1 residue, 2 models selected  

> select up

8740 atoms, 8882 bonds, 546 residues, 1 model selected  

> select up

8746 atoms, 8884 bonds, 550 residues, 2 models selected  

> select down

8740 atoms, 8882 bonds, 546 residues, 2 models selected  

> select up

8746 atoms, 8884 bonds, 550 residues, 2 models selected  

> select up

8746 atoms, 8884 bonds, 550 residues, 3 models selected  

> select down

8746 atoms, 8884 bonds, 550 residues, 2 models selected  

> isolde sim start /A,C,B,E

ISOLDE: started sim  
Traceback (most recent call last):  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/ui.py"", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 141, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
IndexError: No dihedral with that name is registered for this residue type!  
  
IndexError: No dihedral with that name is registered for this residue type!  
  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/ui.py"", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 141, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
IndexError: No dihedral with that name is registered for this residue type!  
  
IndexError: No dihedral with that name is registered for this residue type!  
  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  

> ui tool show ""Ramachandran Plot""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> ui tool show ""Volume Viewer""

> volume #1.1.1.1 level 0.055

> camera ortho

> camera mono

> camera ortho

> label height 1

> label height 1=0.8

Invalid ""height"" argument: Expected 'fixed' or a number  

> label height 0.8

> ui tool show ""Volume Viewer""

> volume #1.1.1.1 level 0.01

> volume #1.1.1.1 level 0.02

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 13 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

415 atoms, 422 bonds, 28 residues, 2 models selected  

> isolde sim start /A:199-226

ISOLDE: started sim  

> volume #1.1.1.1 style surface

> lighting soft

> transparency 50

> lighting simple

> transparency 0

> transparency 50

> volume #1.1.1.1 level 0.03

> volume #1.1.1.1 style mesh

> transparency 0

> transparency 50

> transparency 0

> volume #1.1.1.1 level 0.04

> volume #1.1.1.1 level 0.055

> volume #1.1.1.1 level 0.01

> volume #1.1.1.1 level 0.055

> select clear

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/ui.py"", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 141, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
IndexError: No dihedral with that name is registered for this residue type!  
  
IndexError: No dihedral with that name is registered for this residue type!  
  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Traceback (most recent call last):  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/ui.py"", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 141, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
IndexError: No dihedral with that name is registered for this residue type!  
  
IndexError: No dihedral with that name is registered for this residue type!  
  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  

> isolde sim start /A:157

ISOLDE: started sim  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> isolde pepflip /A:157

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:494

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /A:409

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

70 atoms, 70 bonds, 5 residues, 2 models selected  

> select up

8704 atoms, 8844 bonds, 545 residues, 2 models selected  

> isolde sim start /A:73-617

ISOLDE: started sim  

> select clear

> select up

12 atoms, 11 bonds, 1 residue, 2 models selected  

> view sel

> ui tool show ""Ramachandran Plot""

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

415 atoms, 422 bonds, 28 residues, 2 models selected  

> select down

21 atoms, 21 bonds, 1 residue, 2 models selected  

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> isolde pepflip /A:400

> isolde stepto next

> isolde pepflip /A:401

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /A:110

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> isolde sim start /E

ISOLDE: started sim  

> select up

8746 atoms, 8884 bonds, 550 residues, 1 model selected  

> select clear

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select ::name=""CL""::name=""HOH""::name=""IBL""::name=""NA""

42 atoms, 40 bonds, 5 residues, 1 model selected  

> view

> view sel

> save ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/ISOLDE-session.cxs"" includeMaps true

Taking snapshot of stepper: deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-
Na_IBL-revised-geometry.pdb  

> save ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/deltaN72C13 hSERT - AF-P31645-F1-model_v4 - Cl-Na_IBL-
> revised-geometry_ISOLDE.pdb""

> ui tool show ""Build Structure""

> build start atom #1.2 res UKN

> ui tool show ""Build Structure""

> build modify /het:1@He O 2 geometry tetrahedral name O resName HOH

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> isolde sim start /het

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> isolde sim start /het

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select up

8749 atoms, 8886 bonds, 551 residues, 1 model selected  

> isolde sim start /A,C,B,E-het

ISOLDE: started sim  

> select clear

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> isolde pepflip /A:136

> ui tool show ""Build Structure""

> build start atom #1.2

> build modify /het:2@He O 4 geometry tetrahedral name O resName HOH

> build modify /het:2@O O 2 geometry tetrahedral

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

6 atoms, 4 bonds, 2 residues, 1 model selected  

> select up

8752 atoms, 8888 bonds, 552 residues, 1 model selected  

> select down

6 atoms, 4 bonds, 2 residues, 2 models selected  

> select down

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select up

6 atoms, 4 bonds, 2 residues, 1 model selected  

> select down

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select up

6 atoms, 4 bonds, 2 residues, 1 model selected  

> select down

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select up

6 atoms, 4 bonds, 2 residues, 1 model selected  

> select up

8752 atoms, 8888 bonds, 552 residues, 1 model selected  

> select up

8752 atoms, 8888 bonds, 552 residues, 3 models selected  

> select down

8752 atoms, 8888 bonds, 552 residues, 2 models selected  

> isolde sim start /A,C,B,E-het

ISOLDE: started sim  

> isolde stepto prev

> isolde pepflip /A:517

> isolde stepto next

> isolde pepflip #!1.2/A:542

> isolde stepto next

> isolde pepflip /A:543

> isolde stepto prev

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/ui.py"", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 141, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
IndexError: No dihedral with that name is registered for this residue type!  
  
IndexError: No dihedral with that name is registered for this residue type!  
  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  

> rainbow sel

> select up

91 atoms, 90 bonds, 6 residues, 2 models selected  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> show sel atoms

> mutate sel Pro

Unknown command: mutate sel Pro  

> ui tool show ""Build Structure""

> swapaa PRO sel

Missing or invalid ""residues"" argument: invalid residues specifier  

> swapaa PRO :617

Missing or invalid ""residues"" argument: invalid residues specifier  

> swapaa pro :617

Missing or invalid ""residues"" argument: invalid residues specifier  

> swapaa pro #1:617

Missing or invalid ""residues"" argument: invalid residues specifier  

> swapaa pro #1.2:617

Missing or invalid ""residues"" argument: invalid residues specifier  

> swapaa pro #1.2:617

Missing or invalid ""residues"" argument: invalid residues specifier  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> ui tool show ""Ramachandran Plot""

> isolde sim start /A:400

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> isolde sim start /A:397-403

ISOLDE: started sim  

> ui tool show ""Volume Viewer""

> volume #1.1.1.1 level 0.02

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:400

ISOLDE: started sim  

> select clear

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> isolde pepflip /A:400

> volume #1.1.1.1 level 0.05

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:500

ISOLDE: started sim  

> select clear

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> isolde pepflip /A:500

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:543

ISOLDE: started sim  

> select clear

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> isolde pepflip /A:543

> isolde stepto next

> isolde pepflip /A:544

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> ui tool show ""Ramachandran Plot""

> isolde pepflip /A:408

ISOLDE: started sim  

> isolde pepflip /A:405-411

Unable to flip peptide bond after 50 rounds. Giving up.  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:405-411

ISOLDE: started sim  

> select clear

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> isolde pepflip /A:408

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select clear

> isolde sim start /B

ISOLDE: started sim  

> select clear

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> isolde pepflip #!1.2/A:332

Peptide bond must be mobile in the simulation!  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select up

15 atoms, 13 bonds, 2 residues, 1 model selected  

> isolde sim start /A:437/het:1

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select up

39 atoms, 37 bonds, 2 residues, 1 model selected  

> select up

766 atoms, 772 bonds, 48 residues, 2 models selected  

> select up

8598 atoms, 8735 bonds, 538 residues, 2 models selected  

> select up

8634 atoms, 8773 bonds, 539 residues, 2 models selected  

> select up

8646 atoms, 8779 bonds, 545 residues, 2 models selected  

> isolde sim start /A,C,B,E-het

ISOLDE: started sim  

> volume #1.1.1.1 level 0.055

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/deltaN72C13 hSERT - AF-P31645-F1-model_v4 - Cl-Na_IBL-
> revised-geometry_ISOLDE.pdb""

Chain IDs longer than 2 characters; truncating  

> save ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/ISOLDE-session.cxs"" includeMaps true

Taking snapshot of stepper: deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-
Na_IBL-revised-geometry.pdb  

> select up

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select up

523 atoms, 526 bonds, 35 residues, 2 models selected  

> select up

8599 atoms, 8735 bonds, 539 residues, 2 models selected  

> select up

8636 atoms, 8773 bonds, 541 residues, 2 models selected  

> select up

8646 atoms, 8779 bonds, 545 residues, 2 models selected  

> select up

8646 atoms, 8779 bonds, 545 residues, 3 models selected  

> select down

8646 atoms, 8779 bonds, 545 residues, 2 models selected  

> select clear

> save ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/deltaN72C13 hSERT - AF-P31645-F1-model_v4 - Cl-Na_IBL-
> revised-geometry_ISOLDE.pdb""

Chain IDs longer than 2 characters; truncating  

> save ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/deltaN72C13 hSERT - AF-P31645-F1-model_v4 - Cl-Na_IBL-
> revised-geometry_ISOLDE.cif"" relModel #1.2

Not saving entity_poly_seq for non-authoritative sequences  

Fetching CCD IBL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/IBL/IBL.cif  
Fetching CCD CL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/ISOLDE-session.cxs""

Opened cryosparc_P132_J294_006_volume_map_sharp.mrc as #1.1.1.1, grid size
300,300,300, pixel 0.725, shown at level 0.055, step 1, values float32  
Log from Tue Sep 24 14:58:41 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar Lab/Research
> Data/SERT/structural comparison/ChimeraX - conformational
> comparisons/cysteine-acc-assay_outward_comparison_6DZZ-6DZV-6DZY-
> mystructure.cxs""

Log from Sun Sep 15 18:15:13 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar Lab/Research
> Data/SERT/ASH_SERT/SERT_J326-Cl-Na_IBL-revised-
> geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08.pdb""
> format pdb

Chain information for SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08.pdb
#1  
---  
Chain | Description  
D | No description available  
  

> set bgColor white

> surface

> ui tool show ""Side View""

> ui tool show ""Surface Color""

> color single #1.1.1

> ui tool show ""Show Volume Menu""

> ui tool show ""Color Zone""

No surface chosen for color zoning  

> volume planes z style image imageMode ""full region""

No volumes specified  

> select add #1

4601 atoms, 4737 bonds, 542 residues, 2 models selected  

> volume planes z style image imageMode ""full region""

No volumes specified  

> volume hide

No volumes specified  

> ui mousemode right ""color key""

> key borderColor default

[Repeated 9 time(s)]

> key borderColor white

> key borderColor default

> key borderColor white

> ui mousemode right translate

> ui mousemode right ""contour level""

> ui mousemode right ""color key""

> key colorTreatment distinct

> key colorTreatment blended

> key delete

> ui mousemode right ""contour level""

[Repeated 1 time(s)]

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> toolshed show

> ui tool show ""Surface Zone""

> ui tool show ""Surface Color""

No map chosen for coloring  

> color cylindrical #1.1.1 palette #ff0000:#ffffff:#0000ff

[Repeated 1 time(s)]

> color cylindrical #1.1.1 palette 127.6,#102714:156.9,#0b130b:186.1,#0e1b18

> hide #!1.1 models

> show #1.1 models

> hide #!1.1 models

> show #1.1 models

> hide #!1 models

> show #!1 models

> color cylindrical #1.1.1 palette #102714:#0b130b:#0e1b18

> select add #1.1

4601 atoms, 4737 bonds, 542 residues, 3 models selected  

> select subtract #1.1

40 atoms, 38 bonds, 5 residues, 2 models selected  

> select add #1

4601 atoms, 4737 bonds, 542 residues, 2 models selected  

> select subtract #1

1 model selected  

> hide cartoons

> hide

> preset ""initial styles"" ""original look""

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> rainbow

> view

> surface

> lighting soft

> hide #1.1 models

> show #1.1 models

> color #1.1 silver

> hide #1.1 models

> show #1.1 models

> transparency 50

> transparency 0

> transparency 50

> ui tool show ""Surface Color""

> color radial #1.1 palette #ff0000:#ffffff:#0000ff

> color radial #1.1 palette 144.7,#000000:187.3,#000000:229.8,#000000

> color single #1.1

> color cylindrical #1.1 palette 144.7,#000000:187.3,#000000:229.8,#000000

> color single #1.1

> color cylindrical #1.1 palette 144.7,#000000:187.3,#000000:229.8,#000000
> center 103.39,110.27,113.83

> color single #1.1

[Repeated 3 time(s)]

> color cylindrical #1.1 palette 144.7,#000000:187.3,#000000:229.8,#000000
> center 103.39,110.27,113.83

> color single #1.1.1

> color cylindrical #1.1.1 palette 144.7,#000000:187.3,#000000:229.8,#000000
> center 103.39,110.27,113.83

> color single #1.1.1

> color cylindrical #1.1.1 palette 144.7,#000000:187.3,#c0c0c0:229.8,#000000
> center 103.39,110.27,113.83

> color single #1.1.1

> color cylindrical #1.1.1 palette #000000:#c0c0c0:#000000 center
> 103.39,110.27,113.83

> color single #1.1.1

[Repeated 3 time(s)]

> transparency 0

> transparency 50

> transparency 0

> transparency 50

> transparency 0

> transparency 50

> transparency 0

> transparency 50

> color cylindrical #1.1.1 palette 0.7441,#000000:15.99,#c0c0c0:31.23,#000000
> center 103.39,110.27,113.83

> transparency 0

> transparency 50

> graphics silhouettes true

> color cylindrical #1.1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

> color single #1.1.1

> color cylindrical #1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

> color cylindrical #1.1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

[Repeated 1 time(s)]

> color single #1.1.1

[Repeated 2 time(s)]

> color cylindrical #1.1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

[Repeated 1 time(s)]

> color single #1.1.1

> transparency 0

> transparency 50

> color cylindrical #1.1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

[Repeated 1 time(s)]

> transparency 0

> transparency 50

> lighting full

> color cylindrical #1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

> color cylindrical #1.1.1 palette 0.7441,#c0c0c0:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

> lighting soft

> lighting simple

> graphics silhouettes false

> graphics silhouettes true

> transparency 50

> transparency 0

> color single #1.1.1

[Repeated 2 time(s)]

> color cylindrical #1.1.1 palette 0.7441,#000000:15.99,#c0c0c0:31.23,#c0c0c0
> center 103.39,110.27,113.83

> color cylindrical #1.1.1 palette 0.7441,#000000:15.99,#000000:31.23,#c0c0c0
> center 103.39,110.27,113.83

> color cylindrical #1.1.1 palette 0.7441,#000000:15.99,#000000:31.23,#000000
> center 103.39,110.27,113.83

> lighting soft

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> hide #!1 models

> hide #1.1 models

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar Lab/Research
> Data/SERT/ASH_SERT/SERT_J326-Cl-Na_IBL-revised-
> geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08.pdb""

Chain information for SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08.pdb
#3  
---  
Chain | Description  
D | No description available  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar Lab/Research
> Data/SERT/ASH_SERT/cryosparc_P132_J294_006_volume_map_sharp.mrc""

Opened cryosparc_P132_J294_006_volume_map_sharp.mrc as #4, grid size
300,300,300, pixel 0.725, shown at level 0.0232, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.08525

> volume #4 level 0.06879

> hide #!4 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> :556

Unknown command: :556  

> show :556

> show #!4 models

> volume #4 level 0.06023

> volume #4 level 0.04609

> volume #4 level 0.09101

> show :556,104,493

Drag select of 4 cryosparc_P132_J294_006_volume_map_sharp.mrc  

> volume #4 level 0.07249

> volume #4 level 0.08916

> volume #4 level 0.08885

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> volume #4 level 0.1479

> volume #4 level 0.06718

> close session

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/6DZV_-
> _IBG_occluded_-_prepared.pdb""

6DZV_-_IBG_occluded_-_prepared.pdb title:  
Wild type human serotonin transporter In complex with 15B8 fab bound to
ibogaine In occluded conformation [more info...]  
  
Chain information for 6DZV_-_IBG_occluded_-_prepared.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6DZV_-_IBG_occluded_-_prepared.pdb #1  
---  
HJM — (5Β)-12-methoxyibogamine  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/6DZY_-
> _IBG_outward-open_-_prepared.pdb""

6DZY_-_IBG_outward-open_-_prepared.pdb title:  
Cryo-em structure of the TS2-active human serotonin transporter In complex
with 15B8 fab and 8B6 SCFV bound to ibogaine [more info...]  
  
Chain information for 6DZY_-_IBG_outward-open_-_prepared.pdb #2  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6DZY_-_IBG_outward-open_-_prepared.pdb #2  
---  
HJM — (5Β)-12-methoxyibogamine  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/6DZZ_-
> _IBG_inward-open_prepared.pdb""

6DZZ_-_IBG_inward-open_prepared.pdb title:  
Cryo-em structure of the wild-type human serotonin transporter In complex with
ibogaine and 15B8 fab In the inward conformation [more info...]  
  
Chain information for 6DZZ_-_IBG_inward-open_prepared.pdb #3  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6DZZ_-_IBG_inward-open_prepared.pdb #3  
---  
HJM — (5Β)-12-methoxyibogamine  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational
> comparisons/9EO4_-_hDAT_cocaine_-_prepared.pdb""

9EO4_-_hDAT_cocaine_-_prepared.pdb title:  
Outward-open structure of human dopamine transporter bound to cocaine [more
info...]  
  
Chain information for 9EO4_-_hDAT_cocaine_-_prepared.pdb #4  
---  
Chain | Description  
B | No description available  
  
Non-standard residues in 9EO4_-_hDAT_cocaine_-_prepared.pdb #4  
---  
CL — chloride ion  
COC — cocaine  
NA — sodium ion  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/SERT_J326-Cl-
> Na_IBL-revised-
> geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb""

SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
title:  
SERT_J326-Cl-Na_IBL-revised-geometry_real_space_refined_010_
namdinator_real_space_refined_011-coot-4_ASH_21-08 - prepared [more info...]  
  
Chain information for SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
#5  
---  
Chain | Description  
D | No description available  
  
Non-standard residues in SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
#5  
---  
CL — (CL)  
IBL — (IBL)  
NA — (NA)  
  

> close #1-3,5#4

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/6DZV_-
> _IBG_occluded_-_prepared.pdb""

6DZV_-_IBG_occluded_-_prepared.pdb title:  
Wild type human serotonin transporter In complex with 15B8 fab bound to
ibogaine In occluded conformation [more info...]  
  
Chain information for 6DZV_-_IBG_occluded_-_prepared.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6DZV_-_IBG_occluded_-_prepared.pdb #1  
---  
HJM — (5Β)-12-methoxyibogamine  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/6DZY_-
> _IBG_outward-open_-_prepared.pdb""

6DZY_-_IBG_outward-open_-_prepared.pdb title:  
Cryo-em structure of the TS2-active human serotonin transporter In complex
with 15B8 fab and 8B6 SCFV bound to ibogaine [more info...]  
  
Chain information for 6DZY_-_IBG_outward-open_-_prepared.pdb #2  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6DZY_-_IBG_outward-open_-_prepared.pdb #2  
---  
HJM — (5Β)-12-methoxyibogamine  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/6DZZ_-
> _IBG_inward-open_prepared.pdb""

6DZZ_-_IBG_inward-open_prepared.pdb title:  
Cryo-em structure of the wild-type human serotonin transporter In complex with
ibogaine and 15B8 fab In the inward conformation [more info...]  
  
Chain information for 6DZZ_-_IBG_inward-open_prepared.pdb #3  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 6DZZ_-_IBG_inward-open_prepared.pdb #3  
---  
HJM — (5Β)-12-methoxyibogamine  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational
> comparisons/9EO4_-_hDAT_cocaine_-_prepared.pdb""

9EO4_-_hDAT_cocaine_-_prepared.pdb title:  
Outward-open structure of human dopamine transporter bound to cocaine [more
info...]  
  
Chain information for 9EO4_-_hDAT_cocaine_-_prepared.pdb #4  
---  
Chain | Description  
B | No description available  
  
Non-standard residues in 9EO4_-_hDAT_cocaine_-_prepared.pdb #4  
---  
CL — chloride ion  
COC — cocaine  
NA — sodium ion  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris - Shahsavar
> Lab/presentations/structural biology section meetings/240916 - Kolokouris SB
> section meeting on SERT/ChimeraX - conformational comparisons/SERT_J326-Cl-
> Na_IBL-revised-
> geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb""

SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
title:  
SERT_J326-Cl-Na_IBL-revised-geometry_real_space_refined_010_
namdinator_real_space_refined_011-coot-4_ASH_21-08 - prepared [more info...]  
  
Chain information for SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
#5  
---  
Chain | Description  
D | No description available  
  
Non-standard residues in SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
#5  
---  
CL — (CL)  
IBL — (IBL)  
NA — (NA)  
  

> camera ortho

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting simple

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting soft

> hide cartoons

> show cartoons :79-112

Expected ',' or a keyword  

> show cartoons and :79-112

Expected ',' or a keyword  

> show cartoons @:79-112

Expected ',' or a keyword  

> show #1,2,3,5:79-112 cartoons

> show #1,2,3,5:323-352 cartoons

> view

> hide #3 models

> hide #!4 models

> hide #5 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> combine #1

> combine #2

> matchmaker #7:79-96,341-351 to #6:79-96,341-351

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 copy of 6DZV_-_IBG_occluded_-_prepared.pdb, chain A (#6) with copy
of 6DZY_-_IBG_outward-open_-_prepared.pdb, chain A (#7), sequence alignment
score = 151.8  
RMSD between 29 pruned atom pairs is 0.769 angstroms; (across all 29 pairs:
0.769)  
  

> hide #2 models

> hide #1 models

> show #!4 models

> hide #!4 models

> show #5 models

> combine #5

> matchmaker #8:79-96,341-351 to #6:79-96,341-351

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 copy of 6DZV_-_IBG_occluded_-_prepared.pdb, chain A (#6) with copy
of SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb,
chain D (#8), sequence alignment score = 148.2  
RMSD between 27 pruned atom pairs is 0.736 angstroms; (across all 29 pairs:
0.940)  
  

> hide #5 models

> show #6,7,8:101,368

> select Na

5 atoms, 5 residues, 3 models selected  

> show #6,7,8:NA

> select #6,7,8:NA

2 atoms, 2 residues, 1 model selected  

> style sel sphere

Changed 2 atom styles  

> hide #6 models

> show #6 models

> hide #7 models

> show #7 models

> hide #7 models

> hide #6 models

> hide #8 models

> show #7 models

> show #5 models

> hide #5 models

> show #8 models

> hide #8 models

> show #6 models

> hide #6 models

> show #8 models

> show #6 models

> select #6,7,8:CL

1 atom, 1 residue, 1 model selected  

> select #6,7,8:CL sphere

Expected a keyword  

> show #6,7,8:CL sphere

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> select #6,7,8:CL

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> show #6,7,8:CL

> show #3 models

> hide #3 models

> hide #8 models

> show #1,2,3,5:156-192 cartoons

> show #1 models

> hide #1 models

> show #6,7,8:156-192 cartoons

> hide #6,7,8:156-192 cartoons

> hide #6,7,8:275-302 cartoons

> show #6,7,8:275-302 cartoons

> show #8 models

> dssp

> select clear

Drag select of 33 atoms, 30 bonds  

> select clear

> select add #6/A:172@CA

1 atom, 1 bond, 1 residue, 2 models selected  

> select add #7/A:172@N

2 atoms, 1 bond, 2 residues, 2 models selected  

> select up

8 atoms, 3 bonds, 5 residues, 2 models selected  

> select up

78 atoms, 73 bonds, 5 residues, 2 models selected  

> hide sel target a

> select add #6/A:497@CA

79 atoms, 73 bonds, 6 residues, 2 models selected  

> select add #8/D:172@CA

80 atoms, 73 bonds, 7 residues, 3 models selected  

> select add #7/A:173@CB

81 atoms, 74 bonds, 8 residues, 3 models selected  

> select up

83 atoms, 74 bonds, 9 residues, 3 models selected  

> select up

131 atoms, 124 bonds, 9 residues, 3 models selected  

> hide sel target a

> select add #7/A:169@N

132 atoms, 125 bonds, 10 residues, 3 models selected  

> select up

134 atoms, 125 bonds, 11 residues, 3 models selected  

> select up

151 atoms, 142 bonds, 11 residues, 3 models selected  

> hide sel target a

> select add #8/D:173@O

152 atoms, 142 bonds, 12 residues, 3 models selected  

> select up

161 atoms, 152 bonds, 12 residues, 3 models selected  

> hide sel target a

> view

> hide #6 models

> hide #7 models

> select add #8/D:439@C

162 atoms, 154 bonds, 13 residues, 3 models selected  

> select clear

> show #6,7,8:437

> show #6 models

> show #7 models

> hide #6,7,8:437

> hide #6,7,8:443

> hide #6,7,8:439

> hide #6,7,8:442

> hide #6,7,8:434

> show #6,7,8:252-274 cartoons

> hide #6,7,8:252-274 cartoons

> show #6,7,8:277,107 sticks

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #6,7,8:277,107

> show #6,7,8:252-274 cartoons

> matchmaker #8:156-192,252-274,414-482 to #6:156-192,252-274,414-482

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 copy of 6DZV_-_IBG_occluded_-_prepared.pdb, chain A (#6) with copy
of SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb,
chain D (#8), sequence alignment score = 652.9  
RMSD between 118 pruned atom pairs is 1.027 angstroms; (across all 129 pairs:
1.301)  
  

> matchmaker #7:156-192,252-274,414-482 to #6:156-192,252-274,414-482

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 copy of 6DZV_-_IBG_occluded_-_prepared.pdb, chain A (#6) with copy
of 6DZY_-_IBG_outward-open_-_prepared.pdb, chain A (#7), sequence alignment
score = 676.5  
RMSD between 126 pruned atom pairs is 0.840 angstroms; (across all 129 pairs:
0.909)  
  

> ~display HC

> hide :252-302

> hide #6,7,8:252-302 cartoons

> view

> hide #6,7,8:176

> show #1 models

> hide #1 models

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.tif"" width 1218
> height 777 supersample 4 transparentBackground true

[Repeated 1 time(s)]

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.tif"" width 1218
> height 777 supersample 4

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/test.png"" width 1600 height 1021 supersample 3
> transparentBackground true

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/test.png"" width 1218 height 777 supersample 3

> save /Users/ctn700/Desktop/image5.png supersample 3

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.cxs"" includeMaps
> true

> lighting simple

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.tif"" width 1218
> height 777 supersample 4 transparentBackground true

> lighting soft

> show #6,7,8:104

> ~display HC

> show #6,7,8:493

> ~display HC

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.cxs"" includeMaps
> true

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.tif"" width 2000
> height 2000 supersample 4 transparentBackground true

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/TM1_6_outward_comparison_6DZV-6DZY-mystructure.png"" width 2000
> height 2000 supersample 4 transparentBackground true

> show #6,7,8:252-302 cartoons

> show #6,7,8:107,277

> ~display HC

> show #6,7,8:107,277 spheres

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #6,7,8:107,277 sphere

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show sphere #6,7,8:107,277

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #6,7,8:107,277 sphere

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> select #6,7,8:107,277

96 atoms, 93 bonds, 6 residues, 3 models selected  

> style sel sphere

Changed 96 atom styles  

> select clear

> show #6,7,8:414-456 cartoons

> show #6,7,8:275-302 cartoons

> show #6,7,8:353-392 cartoons

> undo

> caera ortho

Unknown command: caera ortho  

> camera ortho

> show #6,7,8:483-516 cartoons

> undo

> show #6,7,8:457-482 cartoons

> show #6,7,8:113-146 cartoons

> show #6,7,8:156-192 cartoons

> undo

> show #6,7,8:353-392 cartoons

> show #6,7,8:414-456 cartoons

> show #6,7,8:517-560 cartoons

> show #6,7,8:561-615 cartoons

> undo

> hide #6 models

> hide #7 models

> hide #8 models

> show #6 models

> show #7 models

> show #8 models

> hide #6 models

> hide #7 models

> hide #8 models

> show #5 models

> show #5 cartoons

> show #7 models

> hide #5 models

> show #6 models

> show #8 models

> show #6,7,8:193-251 cartoons

> undo

> show #6,7,8:147-155 cartoons

[Repeated 1 time(s)]

> undo

> show #6,7,8:303-322 cartoons

> undo

> show #6,7,8:393-143 cartoons

> undo

> show #6,7,8:393-413 cartoons

> show #6,7,8:303-322 cartoons

> lighting flat

> lighting soft

> lighting full

> lighting soft

> show #6,7,8:393-413 cartoons

> show #6,7,8:193-251 cartoons

> combine #3

> hide #6 models

> hide #7 models

> hide #8 models

> matchmaker #9:156-192,252-274,414-482 to #6:156-192,252-274,414-482

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 copy of 6DZV_-_IBG_occluded_-_prepared.pdb, chain A (#6) with copy
of 6DZZ_-_IBG_inward-open_prepared.pdb, chain A (#9), sequence alignment score
= 572.5  
RMSD between 116 pruned atom pairs is 0.987 angstroms; (across all 129 pairs:
1.287)  
  

> show #6 models

> hide #6 models

> show #6 models

> show #6,7,8,9:193-251 cartoons

[Repeated 1 time(s)]

> show #6,7,8,9:393-413 cartoons

> show #6,7,8,9:303-322 cartoons

> hide #6 models

> hide #9:156-192

> hide #9:156-192 cartoons

> show #9:252-302 cartoons

> show #9:277,107

> style #9:277,107 sphere

Changed 32 atom styles  

> ~display HC

> show #6 models

> hide #6 models

> show #8 models

> show #6,7,8,9:457-482 cartoons

> undo

> show #6,7,8,9:483-516 cartoons

> hide #9 models

> hide #6,7,8,9:438

> show #7 models

> show #6 models

> show #9 models

> hide #8 models

> hide #6 models

> hide #7 models

> hide #6,7,8,9:446,439,443,442

> show #6 models

> hide #6,7,8,9:414-456 cartoons

> hide #6,7,8,9:193-251 cartoons

> show #6,7,8,9:414-456 cartoons

> hide #6,7,8,9:414-456 cartoons

> view

> show #7 models

> show #8 models

> hide #7 models

> show #7 models

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/presentations/structural biology section meetings/240916 -
> Kolokouris SB section meeting on SERT/ChimeraX - conformational
> comparisons/cysteine-acc-assay_outward_comparison_6DZZ-6DZV-6DZY-
> mystructure.cxs"" includeMaps true

——— End of log from Sun Sep 15 18:15:13 2024 ———

opened ChimeraX session  

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> camera ortho

> hide #6 models

> hide #7 models

> hide #9 models

> select #8/D:107@CE2

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select sel :< 5

3110 atoms, 3116 bonds, 186 residues, 9 models selected  

> show sel & #8 atoms

> ~display HC

> style sel & #8 sphere

Changed 316 atom styles  

> ~display C

> ~display H

> select clear

> select #8/D:107@OH

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> label sel

> label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> select clear

> ui mousemode right ""move label""

> select #8/D:107@CE2

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> color sel cyan

> color sel byhetero

> select clear

> hide #!8 models

> show #6 models

> select #6/A:107@OH

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select sel :< 5

2600 atoms, 2611 bonds, 153 residues, 9 models selected  

> select sel :< 5

17212 atoms, 17251 bonds, 1052 residues, 9 models selected  

> undo

> show sel & #6 atoms

> style sel & #6 sphere

Changed 293 atom styles  

> ~display H

> select clear

> select #6/A:107@OH

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel cyan

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> color sel cyan

> color sel byhetero

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #7 models

> hide #6 models

> select #7/A:107@CE2

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select sel :< 5

2759 atoms, 2774 bonds, 166 residues, 9 models selected  

> select sel :< 5

17289 atoms, 17317 bonds, 1071 residues, 9 models selected  

> undo

> show sel & #7 atoms

> style sel & #7 sphere

Changed 287 atom styles  

> ~display H

> select clear

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> show #6 models

> show #9 models

> hide #9 models

> hide #6 models

> hide #!8 models

> select #7/A:107@CE2

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> color sel cyan

> color sel byhetero

> select clear

> hide #7 models

> show #9 models

> select #9/A:107@OH

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select sel :< 5

2622 atoms, 2619 bonds, 157 residues, 9 models selected  

> select sel :< 5

18064 atoms, 18123 bonds, 1106 residues, 9 models selected  

> undo

> show sel & #9 atoms

> style sel & #9 sphere

Changed 361 atom styles  

> ~display H

> select clear

> select #9/A:107@CE2

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> color sel cyan

> color sel byhetero

> select clear

> show #6 models

> show #7 models

> show #!8 models

> label #6,7,8,9:107

> delete label

Missing or invalid ""atoms"" argument: invalid atoms specifier  

> delete labels

Missing or invalid ""atoms"" argument: invalid atoms specifier  

> label #6-9 text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> close #6.1

> close #7.1

> close #8.1

> close #9.1

> show #6 models

> show #7 models

> show #8 models

> select clear

> label #6,7,8,9:107

> tile columns 4 spacinfFactor 1

Expected a keyword  

> tile columns 4 spacingFactor 1

4 models tiled  

> tile columns 2 spacingFactor 1

4 models tiled  

> tile columns 2 spacingFactor 1.2

4 models tiled  

> select #6,7,8,9:107

84 atoms, 84 bonds, 4 residues, 4 models selected  

> view sel

> rainbow sel

> undo

> color cartoon rainbow

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color rainbow cartoon

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> select up

478 atoms, 489 bonds, 27 residues, 4 models selected  

> select up

34379 atoms, 34932 bonds, 2151 residues, 4 models selected  

> rainbow sel

> undo

> select clear

> combine #6

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #9.1 models

> hide #8.1 models

> hide #7.1 models

> hide #6.1 models

> mutate #10:107 CYS

Unknown command: mutate #10:107 CYS  

> select #10/A:107@OH

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> swapaa #10:107 CYS

Using Dunbrack library  
copy of copy of 6DZV_-_IBG_occluded_-_prepared.pdb #10/A TYR 107: phi -65.2,
psi -44.1 trans  
Applying CYS rotamer (chi angles: -175.1) to copy of copy of 6DZV_-
_IBG_occluded_-_prepared.pdb #10/A CYS 107  

> hide #10 models

> show #!6 models

> show #!7 models

> show #!8 models

> show #!9 models

> view

> select add #10

8624 atoms, 8765 bonds, 538 residues, 1 model selected  

> select subtract #10

Nothing selected  

> swapaa #6,7,8,9:107 CYS

Command cancelled by user  

> combine #7

> combine #8

> combine #9

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> show #10 models

> swapaa #10,11,12,13:107 CYS

Using Dunbrack library  
copy of copy of 6DZV_-_IBG_occluded_-_prepared.pdb #10/A CYS 107: phi -65.2,
psi -44.1 trans  
copy of copy of 6DZY_-_IBG_outward-open_-_prepared.pdb #11/A TYR 107: phi
-62.6, psi -39.3 trans  
copy of copy of SERT_J326-Cl-Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
#12/D TYR 107: phi -66.3, psi -44.0 trans  
copy of copy of 6DZZ_-_IBG_inward-open_prepared.pdb #13/A TYR 107: phi -83.6,
psi -28.2 trans  
Applying CYS rotamer (chi angles: 64.4) to copy of copy of 6DZV_-
_IBG_occluded_-_prepared.pdb #10/A CYS 107  
Applying CYS rotamer (chi angles: -70.0) to copy of copy of 6DZY_-
_IBG_outward-open_-_prepared.pdb #11/A CYS 107  
Applying CYS rotamer (chi angles: -69.5) to copy of copy of SERT_J326-Cl-
Na_IBL-revised-
geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb
#12/D CYS 107  
Applying CYS rotamer (chi angles: -68.1) to copy of copy of 6DZZ_-_IBG_inward-
open_prepared.pdb #13/A CYS 107  

> label #10,11,12,113:107,277

> label height 1

> label height 2

> label height 4

> label #10,11,12,13:107,277

> label height 4

> label height 5

> label height 4

> label #10-13 text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> ~label #10-13 residues

> label #10,11,12,13:107,277

> label height 4

> lighting soft

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> tile off

> select #10,11,12,13:107

32 atoms, 28 bonds, 4 residues, 4 models selected  

> view sel

> ui tool show ""Side View""

> view orient

> view sel

> tile columns 2 spacingFactor 1.2

4 models tiled  

> view sel

> select clear

> select #10,11,12,13:107

32 atoms, 28 bonds, 4 residues, 4 models selected  

> label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> select #10,11,12,13:277

44 atoms, 40 bonds, 4 residues, 4 models selected  

> label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> select #10,11,12,13:107

32 atoms, 28 bonds, 4 residues, 4 models selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select sel :< 6

2724 atoms, 2708 bonds, 166 residues, 10 models selected  

> show sel & #!10-13 atoms

> style sel & #!10-13 sphere

Changed 1257 atom styles  

> ~display H

> select clear

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/Research Data/SERT/structural comparison/ChimeraX -
> conformational comparisons/cysteine-acc-
> assay_outward_comparison_6DZZ-6DZV-6DZY-mystructure3.tif"" width 2000 height
> 2000 supersample 4 transparentBackground true

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/Research Data/SERT/structural comparison/ChimeraX -
> conformational comparisons/cysteine-acc-
> assay_outward_comparison_6DZZ-6DZV-6DZY-mystructure3.cxs"" includeMaps true

> rename #10 ""Y107C 6DZV_-_IBG_occluded_-_prepared.pdb""

> rename #11 ""Y107C 6DZY_-_IBG_outward-open_-_prepared.pdb""

> rename #12 ""Y107C SERT_J326-Cl-Na_IBL-revised-
> geometry_real_space_refined_010_namdinator_real_space_refined_011-coot-4_ASH_21-08_-_prepared.pdb""

> rename #13 ""Y107C 6DZZ_-_IBG_inward-open_prepared.pdb""

> save ""/Users/ctn700/OneDrive - University of Copenhagen/ASH-Lab/Dimitris -
> Shahsavar Lab/Research Data/SERT/structural comparison/ChimeraX -
> conformational comparisons/Y107C_accessibility_comparison_for_Gary.cxs""
> includeMaps true

> lighting soft

> select #10,11,12,13:104

96 atoms, 92 bonds, 4 residues, 4 models selected  

> select #10,11,12,13:103104

Nothing selected  

> label sel

> select #10,11,12,13:103,104

192 atoms, 196 bonds, 8 residues, 4 models selected  

> label sel

> label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> label height 4

> ui mousemode right ""move label""

> select clear

> select #10,11,12,13:103,104

192 atoms, 196 bonds, 8 residues, 4 models selected  

> delete sel label

Expected a keyword  

> delete label sel

Missing or invalid ""atoms"" argument: invalid atoms specifier  

> select delete label

Expected an objects specifier or a keyword  

> ~label sel residues

> select clear

Unsupported scale factor (0.000000) detected on Display0  

[Repeated 7 time(s)]

> select #10,11,12,13:482-492

684 atoms, 688 bonds, 44 residues, 4 models selected  

> show sel atoms

> show sel cartoons

> style sel ball

Changed 684 atom styles  

> ~display H

> show #10,11,12,13:275-302 cartoons

> dssp

> tile off

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 3 time(s)]

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Shared Data/SNAT1 templates & Gln
> bound/cryosparc_P162_J541_class_00_final_volume.mrc""

Opened cryosparc_P162_J541_class_00_final_volume.mrc as #14, grid size
256,256,256, pixel 0.854, shown at level 0.038, step 1, values float32  

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> view

[Repeated 1 time(s)]

> select add #10

9137 atoms, 9281 bonds, 571 residues, 5 models selected  

> select subtract #10

513 atoms, 516 bonds, 33 residues, 3 models selected  

> select add #11

8953 atoms, 9096 bonds, 560 residues, 4 models selected  

> select subtract #11

342 atoms, 344 bonds, 22 residues, 2 models selected  

> select add #12

8788 atoms, 8924 bonds, 553 residues, 3 models selected  

> select subtract #12

171 atoms, 172 bonds, 11 residues, 1 model selected  

> select add #13

8667 atoms, 8809 bonds, 541 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #14

2 models selected  

> view

> select clear

> volume #14 level 0.05507

> volume #14 level 0.03529

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Shared Data/SNAT1 templates & Gln
> bound/cryosparc_P162_J541_class_00_final_volume.mrc""

Opened cryosparc_P162_J541_class_00_final_volume.mrc as #15, grid size
256,256,256, pixel 0.854, shown at level 0.038, step 1, values float32  

> close session

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-Na_IBL-
> revised-geometry.pdb""

deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-Na_IBL-revised-geometry.pdb
title:  
deltaN72C13 hSERT - AF-P31645-F1-model_v4 - Cl-Na_IBL-revised-geometry [more
info...]  
  
Chain information for deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-Na_IBL-
revised-geometry.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-
Na_IBL-revised-geometry.pdb #1  
---  
CL — (CL)  
IBL — (IBL)  
NA — (NA)  
  

> open ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/ASH_SERT/cryosparc_P132_J294_006_volume_map_sharp.mrc""

Opened cryosparc_P132_J294_006_volume_map_sharp.mrc as #2, grid size
300,300,300, pixel 0.725, shown at level 0.0232, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.055

> transparency 50

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting full

> lighting soft

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 78 residues in model #1 to IUPAC-IUB
standards.  
deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-Na_IBL-revised-geometry.pdb
title:  
deltaN72C13 hSERT - AF-P31645-F1-model_v4 - Cl-Na_IBL-revised-geometry [more
info...]  
  
Chain information for deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-Na_IBL-
revised-geometry.pdb  
---  
Chain | Description  
1.2/A | No description available  
  
Non-standard residues in deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-
Na_IBL-revised-geometry.pdb #1.2  
---  
CL — (CL)  
IBL — (IBL)  
NA — (NA)  
  
ISOLDE: created disulfide bonds between the following residues:  
A200-A209  

> clipper associate #2 toModel #1

Opened cryosparc_P132_J294_006_volume_map_sharp.mrc as #1.1.1.1, grid size
300,300,300, pixel 0.725, shown at step 1, values float32  

> isolde sim start /A,C,B,E

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to deltaN72C13_hSERT_-
_AF-P31645-F1-model_v4_-_Cl-Na_IBL-revised-geometry.pdb #1.2  
---  
notes | No usable SEQRES records for deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-Na_IBL-revised-geometry.pdb (#1.2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 73  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A PRO 617  
Chain-final residues that are not actual C termini:  
574 hydrogen bonds  
4346 hydrogens added  
  
Fetching CCD SAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/SAC/SAC.cif  
Fetching CCD N7P from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/N7P/N7P.cif  

> isolde sim start /A:701

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start /A:701

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde parameterise sel override false

Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpsu9v_lfi/ante.in.mol2 -fi
mol2 -o
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpsu9v_lfi/ante.out.mol2 -fo
mol2 -c bcc -nc 1 -j 5 -s 2 -dr n  
(IBL) ``  
(IBL) `Welcome to antechamber 20.0: molecular input file processor.`  
(IBL) ``  
(IBL) `Info: Finished reading file
(/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpsu9v_lfi/ante.in.mol2);
atoms read (36), bonds read (38).`  
(IBL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(IBL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(IBL) ``  
(IBL) ``  
(IBL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(IBL) `Info: Total number of electrons: 124; net charge: 1`  
(IBL) ``  
(IBL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(IBL) ``  
(IBL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(IBL) ``  
(IBL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(IBL) ``  
Charges for residue IBL determined  
OpenMM ffXML file IBL written to the current working directory.  
New template added to forcefield as USER_IBL. This ligand should now work in
all remaining simulations for this session. To use in future sessions, load
the ffXML file with ISOLDE's Load Residue MD Definition(s) button.  

> select up

8740 atoms, 8882 bonds, 546 residues, 1 model selected  

> select up

8746 atoms, 8884 bonds, 550 residues, 2 models selected  

> select down

8740 atoms, 8882 bonds, 546 residues, 2 models selected  

> select up

8746 atoms, 8884 bonds, 550 residues, 2 models selected  

> select down

8740 atoms, 8882 bonds, 546 residues, 2 models selected  

> select down

36 atoms, 38 bonds, 1 residue, 2 models selected  

> select up

8740 atoms, 8882 bonds, 546 residues, 1 model selected  

> select up

8746 atoms, 8884 bonds, 550 residues, 2 models selected  

> select down

8740 atoms, 8882 bonds, 546 residues, 2 models selected  

> select up

8746 atoms, 8884 bonds, 550 residues, 2 models selected  

> select up

8746 atoms, 8884 bonds, 550 residues, 3 models selected  

> select down

8746 atoms, 8884 bonds, 550 residues, 2 models selected  

> isolde sim start /A,C,B,E

ISOLDE: started sim  
Traceback (most recent call last):  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/ui.py"", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 141, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
IndexError: No dihedral with that name is registered for this residue type!  
  
IndexError: No dihedral with that name is registered for this residue type!  
  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/ui.py"", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 141, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
IndexError: No dihedral with that name is registered for this residue type!  
  
IndexError: No dihedral with that name is registered for this residue type!  
  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  

> ui tool show ""Ramachandran Plot""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 2 time(s)]

> ui tool show ""Volume Viewer""

> volume #1.1.1.1 level 0.055

> camera ortho

> camera mono

> camera ortho

> label height 1

> label height 1=0.8

Invalid ""height"" argument: Expected 'fixed' or a number  

> label height 0.8

> ui tool show ""Volume Viewer""

> volume #1.1.1.1 level 0.01

> volume #1.1.1.1 level 0.02

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 13 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

415 atoms, 422 bonds, 28 residues, 2 models selected  

> isolde sim start /A:199-226

ISOLDE: started sim  

> volume #1.1.1.1 style surface

> lighting soft

> transparency 50

> lighting simple

> transparency 0

> transparency 50

> volume #1.1.1.1 level 0.03

> volume #1.1.1.1 style mesh

> transparency 0

> transparency 50

> transparency 0

> volume #1.1.1.1 level 0.04

> volume #1.1.1.1 level 0.055

> volume #1.1.1.1 level 0.01

> volume #1.1.1.1 level 0.055

> select clear

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/ui.py"", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 141, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
IndexError: No dihedral with that name is registered for this residue type!  
  
IndexError: No dihedral with that name is registered for this residue type!  
  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Traceback (most recent call last):  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/ui.py"", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 141, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
IndexError: No dihedral with that name is registered for this residue type!  
  
IndexError: No dihedral with that name is registered for this residue type!  
  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  

> isolde sim start /A:157

ISOLDE: started sim  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> isolde pepflip /A:157

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:494

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /A:409

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

70 atoms, 70 bonds, 5 residues, 2 models selected  

> select up

8704 atoms, 8844 bonds, 545 residues, 2 models selected  

> isolde sim start /A:73-617

ISOLDE: started sim  

> select clear

> select up

12 atoms, 11 bonds, 1 residue, 2 models selected  

> view sel

> ui tool show ""Ramachandran Plot""

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

415 atoms, 422 bonds, 28 residues, 2 models selected  

> select down

21 atoms, 21 bonds, 1 residue, 2 models selected  

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> isolde pepflip /A:400

[Repeated 1 time(s)]

> isolde stepto next

> isolde pepflip /A:401

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /A:110

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> isolde sim start /E

ISOLDE: started sim  

> select up

8746 atoms, 8884 bonds, 550 residues, 1 model selected  

> select clear

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select ::name=""CL""::name=""HOH""::name=""IBL""::name=""NA""

42 atoms, 40 bonds, 5 residues, 1 model selected  

> view

> view sel

> save ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/ISOLDE-session.cxs"" includeMaps true

Taking snapshot of stepper: deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-
Na_IBL-revised-geometry.pdb  

> save ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/deltaN72C13 hSERT - AF-P31645-F1-model_v4 - Cl-Na_IBL-
> revised-geometry_ISOLDE.pdb""

> ui tool show ""Build Structure""

> build start atom #1.2 res UKN

> ui tool show ""Build Structure""

> build modify /het:1@He O 2 geometry tetrahedral name O resName HOH

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> isolde sim start /het

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> isolde sim start /het

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select up

8749 atoms, 8886 bonds, 551 residues, 1 model selected  

> isolde sim start /A,C,B,E-het

ISOLDE: started sim  

> select clear

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> isolde pepflip /A:136

[Repeated 1 time(s)]

> ui tool show ""Build Structure""

> build start atom #1.2

> build modify /het:2@He O 4 geometry tetrahedral name O resName HOH

> build modify /het:2@O O 2 geometry tetrahedral

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

6 atoms, 4 bonds, 2 residues, 1 model selected  

> select up

8752 atoms, 8888 bonds, 552 residues, 1 model selected  

> select down

6 atoms, 4 bonds, 2 residues, 2 models selected  

> select down

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select up

6 atoms, 4 bonds, 2 residues, 1 model selected  

> select down

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select up

6 atoms, 4 bonds, 2 residues, 1 model selected  

> select down

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select up

6 atoms, 4 bonds, 2 residues, 1 model selected  

> select up

8752 atoms, 8888 bonds, 552 residues, 1 model selected  

> select up

8752 atoms, 8888 bonds, 552 residues, 3 models selected  

> select down

8752 atoms, 8888 bonds, 552 residues, 2 models selected  

> isolde sim start /A,C,B,E-het

ISOLDE: started sim  

> isolde stepto prev

> isolde pepflip /A:517

[Repeated 3 time(s)]

> isolde stepto next

> isolde pepflip #!1.2/A:542

[Repeated 1 time(s)]

> isolde stepto next

> isolde pepflip /A:543

[Repeated 1 time(s)]

> isolde stepto prev

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/ui.py"", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/problem_regions/problems.py"", line 141, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
IndexError: No dihedral with that name is registered for this residue type!  
  
IndexError: No dihedral with that name is registered for this residue type!  
  
File ""/Users/ctn700/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  

> rainbow sel

> select up

91 atoms, 90 bonds, 6 residues, 2 models selected  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> show sel atoms

> mutate sel Pro

Unknown command: mutate sel Pro  

> ui tool show ""Build Structure""

> swapaa PRO sel

Missing or invalid ""residues"" argument: invalid residues specifier  

> swapaa PRO :617

Missing or invalid ""residues"" argument: invalid residues specifier  

> swapaa pro :617

Missing or invalid ""residues"" argument: invalid residues specifier  

> swapaa pro #1:617

Missing or invalid ""residues"" argument: invalid residues specifier  

> swapaa pro #1.2:617

Missing or invalid ""residues"" argument: invalid residues specifier  

> swapaa pro #1.2:617

Missing or invalid ""residues"" argument: invalid residues specifier  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> ui tool show ""Ramachandran Plot""

> isolde sim start /A:400

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> isolde sim start /A:397-403

ISOLDE: started sim  

> ui tool show ""Volume Viewer""

> volume #1.1.1.1 level 0.02

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:400

ISOLDE: started sim  

> select clear

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> isolde pepflip /A:400

[Repeated 1 time(s)]

> volume #1.1.1.1 level 0.05

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:500

ISOLDE: started sim  

> select clear

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> isolde pepflip /A:500

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:543

ISOLDE: started sim  

> select clear

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> isolde pepflip /A:543

[Repeated 3 time(s)]

> isolde stepto next

> isolde pepflip /A:544

[Repeated 1 time(s)]

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> ui tool show ""Ramachandran Plot""

> isolde pepflip /A:408

ISOLDE: started sim  

> isolde pepflip /A:405-411

Unable to flip peptide bond after 50 rounds. Giving up.  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:405-411

ISOLDE: started sim  

> select clear

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> isolde pepflip /A:408

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select clear

> isolde sim start /B

ISOLDE: started sim  

> select clear

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> isolde pepflip #!1.2/A:332

Peptide bond must be mobile in the simulation!  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select up

15 atoms, 13 bonds, 2 residues, 1 model selected  

> isolde sim start /A:437/het:1

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select up

39 atoms, 37 bonds, 2 residues, 1 model selected  

> select up

766 atoms, 772 bonds, 48 residues, 2 models selected  

> select up

8598 atoms, 8735 bonds, 538 residues, 2 models selected  

> select up

8634 atoms, 8773 bonds, 539 residues, 2 models selected  

> select up

8646 atoms, 8779 bonds, 545 residues, 2 models selected  

> isolde sim start /A,C,B,E-het

ISOLDE: started sim  

> volume #1.1.1.1 level 0.055

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/deltaN72C13 hSERT - AF-P31645-F1-model_v4 - Cl-Na_IBL-
> revised-geometry_ISOLDE.pdb""

Chain IDs longer than 2 characters; truncating  

> save ""/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/ISOLDE-session.cxs"" includeMaps true

Taking snapshot of stepper: deltaN72C13_hSERT_-_AF-P31645-F1-model_v4_-_Cl-
Na_IBL-revised-geometry.pdb  

——— End of log from Tue Sep 24 14:58:41 2024 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,6
      Model Number: MNWA3DK/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 27 days, 14 hours, 36 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 38
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        HP P34hc G4:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX