![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#16017 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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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{
"uptime" : 780000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,6",
"coalitionID" : 147449,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-09-24 17:23:33.8680 +0200",
"codeSigningMonitor" : 1,
"incident" : "14C40107-E6FF-4962-94E0-1D08CDDD6CE2",
"pid" : 53712,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-18 16:44:21.7792 +0200",
"procStartAbsTime" : 15890914783322,
"procExitAbsTime" : 18946669698621,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4AAB6390-76F2-0A24-A7A7-7A75AB52E181",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"IAAg1AAAINQAAEDUIAAg1AAAINQAAEDUIAAg1AAAINQAAEDUIAAg1A==","atPC":"AAAg1AAAQNQgACDUAAAg1AAAQNQgACDUAAAg1AAAQNQgACDUAAAg1A=="},
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"sleepWakeUUID" : "BB668DBD-C55E-4C87-9158-3F4D34237D05",
"sip" : "enabled",
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"os_fault" : {"process":"ChimeraX"},
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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
Change History (2)
comment:1 by , 13 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Crash in Mac Qt in _NSViewHierarchyDidChangeBackingProperties probably waking from sleep or connecting or disconnecting an external display.