id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
9997	Crashed in QTabBar::paintEvent()	pkoduro@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-13.5.2-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00000001e68ca080 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in 
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main


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    ""uuid"" : ""c3d03419-8cdf-37bf-b4f9-3d996fb20813"",
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    ""name"" : ""libobjc.A.dylib""
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    ""name"" : ""libsystem_configuration.dylib""
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    ""path"" : ""\/usr\/lib\/libresolv.9.dylib"",
    ""name"" : ""libresolv.9.dylib""
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}
===== Log before crash start =====
Startup Messages  
---  
warnings | Unable to find icon for toolbar provider 'Dump Bead Data' in bundle
'ChimeraX-GenomeTools'  
Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Genome Distance' in bundle
'ChimeraX-GenomeTools'  
1 messages similar to the above omitted  
  

> camera ortho

> cofr centerOfView

> mousemode rightMode clip

> mousemode alt rightMode ""contour level""

> mousemode alt leftMode ""move picked models""

> alias cofron cofr centerofview showpivot true

> alias cofroff cofr centerofview showpivot false

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias cootmode surface cap false; surface style solid; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10
> position cofr; color ##~num_residues cornflower blue

> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000

> alias map_unsphere surface unzone ##~num_residues

> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft

> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000

> alias showmaps surface unzone ##~num_residues

> buttonpanel Shortcuts rows 3 columns 4

> buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'""

> buttonpanel Shortcuts add Model_Panel command ""tool show Models""

> buttonpanel Shortcuts add Log command ""tool show Log""

> buttonpanel Shortcuts add default_disp command default_mol_display

> buttonpanel Shortcuts add map_sphere command map_sphere_15

> buttonpanel Shortcuts add map_unsphere command map_unsphere

> buttonpanel Shortcuts add cofron command cofron

> buttonpanel Shortcuts add cofroff command cofroff

> buttonpanel Shortcuts add cootmode command cootmode

> buttonpanel Shortcuts add mark_cofr command ""marker #10000 position cofr""

> buttonpanel Shortcuts add hidemaps command hidemaps

> buttonpanel Shortcuts add showmaps command showmaps

UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/patrick/Documents/Research/scs7p/New/compact/compact_af/Production_162/run1/frame_30ns.pdb

frame_30ns.pdb title:  
MDANALYSIS FRAMES FROM 0, STEP 1: Created by PDBWriter [more info...]  
  
Chain information for frame_30ns.pdb #1  
---  
Chain | Description  
X | No description available  
  
Non-standard residues in frame_30ns.pdb #1  
---  
FE2P — (FE2P)  
HEME — (heme)  
HSD — (HSD)  
  

> set bgColor white

> cartoon style helix width 2.5 thickness 0.3

> show surfaces

> color silver target s

> transparency 80 target s

> graphics silhouettes true

> transparency 30 target c

> hide surfaces

> color light gray target a

> color byhetero target a

> lighting gentle

> hide H

> hide target c

> hide @c,n,o

> hide #1.4 models

> ui mousemode right coordinationbond

> select ::name=""HEME""

73 atoms, 76 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> hide sel

> select clear

> ui mousemode right select

Drag select of 26 atoms, 23 bonds  

> select clear

Drag select of 85 atoms, 73 bonds  

> hide sel

> select clear

> ui mousemode right coordinationbond

> ui tool show Distances

> ui mousemode right select

> select /X:349@NE2

1 atom, 1 residue, 1 model selected  

> select add /X:386@FE2P

2 atoms, 2 residues, 2 models selected  

> distance /X:349@NE2 /X:386@FE2P

Distance between /X HSD 349 NE2 and FE2P 386 FE2P: 2.132Å  

> distance style decimalPlaces 2

> distance style decimalPlaces 1

> select add /X:271@NE2

3 atoms, 3 residues, 2 models selected  

> select subtract /X:386@FE2P

2 atoms, 2 residues, 2 models selected  

> select clear

> select add /X:271@NE2

1 atom, 1 residue, 1 model selected  

> select add /X:386@FE2P

2 atoms, 2 residues, 2 models selected  

> distance /X:271@NE2 /X:386@FE2P

Distance between /X HSD 271 NE2 and FE2P 386 FE2P: 2.1Å  

> select clear

> select add /X:330@NE2

1 atom, 1 residue, 1 model selected  

> select add /X:386@FE2P

2 atoms, 2 residues, 1 model selected  

> distance /X:330@NE2 /X:386@FE2P

Distance between /X HSD 330 NE2 and FE2P 386 FE2P: 2.2Å  

> select clear

> select add /X:345@NE2

1 atom, 1 residue, 1 model selected  

> select add /X:386@FE2P

2 atoms, 2 residues, 2 models selected  

> distance /X:345@NE2 /X:386@FE2P

Distance between /X HSD 345 NE2 and FE2P 386 FE2P: 2.1Å  

> select clear

> select add /X:326@NE2

1 atom, 1 residue, 1 model selected  

> select add /X:386@FE2P

2 atoms, 2 residues, 2 models selected  

> distance /X:326@NE2 /X:386@FE2P

Distance between /X HSD 326 NE2 and FE2P 386 FE2P: 2.2Å  

> select clear

> select /X:268@NE2

1 atom, 1 residue, 1 model selected  

> select add /X:387@FE2P

2 atoms, 2 residues, 2 models selected  

> distance /X:268@NE2 /X:387@FE2P

Distance between /X HSD 268 NE2 and FE2P 387 FE2P: 2.1Å  

> select clear

> select /X:249@NE2

1 atom, 1 residue, 1 model selected  

> select add /X:387@FE2P

2 atoms, 2 residues, 1 model selected  

> distance /X:249@NE2 /X:387@FE2P

Distance between /X HSD 249 NE2 and FE2P 387 FE2P: 2.1Å  

> select clear

> select add /X:348@NE2

1 atom, 1 residue, 1 model selected  

> select add /X:387@FE2P

2 atoms, 2 residues, 2 models selected  

> distance /X:348@NE2 /X:387@FE2P

Distance between /X HSD 348 NE2 and FE2P 387 FE2P: 2.2Å  

> select clear

> select add /X:272@NE2

1 atom, 1 residue, 1 model selected  

> select add /X:387@FE2P

2 atoms, 2 residues, 2 models selected  

> distance /X:272@NE2 /X:387@FE2P

Distance between /X HSD 272 NE2 and FE2P 387 FE2P: 2.1Å  

> select clear

> select add /X:244@NE2

1 atom, 1 residue, 1 model selected  

> select add /X:387@FE2P

2 atoms, 2 residues, 2 models selected  

> distance /X:244@NE2 /X:387@FE2P

Distance between /X HSD 244 NE2 and FE2P 387 FE2P: 2.1Å  

> select clear

> 2dlabels text 2.1Å bold true size 24

> ui mousemode right ""move label""

> 2dlabels #3.1 xpos 0.547 ypos 0.536

> ~2dlabels #3.1

> 2dlabels text 2.1Å bold true size 20

> 2dlabels #4.1 xpos 0.556 ypos 0.545

> ~2dlabels #4.1

> 2dlabels text 2.1 bold true size 20

> 2dlabels #5.1 xpos 0.569 ypos 0.559

> ~distance /X:268@NE2 /X:387@FE2P

> 2dlabels text 2.1 bold true size 20

> 2dlabels #5.2 xpos 0.394 ypos 0.346

> ~distance /X:345@NE2 /X:386@FE2P

> 2dlabels text 2.2 bold true size 20

> ~distance /X:326@NE2 /X:386@FE2P

> 2dlabels #5.3 xpos 0.299 ypos 0.314

> 2dlabels text 2.2 bold true size 20

> ~distance /X:330@NE2 /X:386@FE2P

> 2dlabels #5.4 xpos 0.271 ypos 0.417

> 2dlabels text 2.1 bold true size 20

> ~distance /X:271@NE2 /X:386@FE2P

> 2dlabels #5.5 xpos 0.300 ypos 0.490

> 2dlabels text 2.1 bold true size 20

> ~distance /X:349@NE2 /X:386@FE2P

> 2dlabels #5.6 xpos 0.378 ypos 0.452

> 2dlabels text 2.1 bold true size 20

> 2dlabels #5.7 xpos 0.609 ypos 0.492

> ~distance /X:244@NE2 /X:387@FE2P

> 2dlabels text 2.2 bold true size 20

Exactly two atoms must be selected!  

> ~distance /X:348@NE2 /X:387@FE2P

> 2dlabels #5.8 xpos 0.682 ypos 0.574

> 2dlabels text 2.1 bold true size 20

> ~distance /X:272@NE2 /X:387@FE2P

> 2dlabels #5.9 xpos 0.626 ypos 0.669

> 2dlabels text 2.1 bold true size 20

> ~distance /X:249@NE2 /X:387@FE2P

> 2dlabels #5.10 xpos 0.694 ypos 0.622

> 2dlabels #5.9 xpos 0.582 ypos 0.646

> 2dlabels #5.10 xpos 0.659 ypos 0.654

> 2dlabels text H326 bold true size 25

> 2dlabels #5.11 xpos 0.270 ypos 0.103

> 2dlabels text H345 bold true size 25

> 2dlabels #5.12 xpos 0.507 ypos 0.272

> 2dlabels text H330 bold true size 25

> 2dlabels #5.13 xpos 0.108 ypos 0.282

> 2dlabels text H271 bold true size 25

> 2dlabels #5.14 xpos 0.154 ypos 0.668

> 2dlabels text H349 bold true size 25

> 2dlabels #5.15 xpos 0.324 ypos 0.650

> 2dlabels text H268 bold true size 25

> 2dlabels #5.16 xpos 0.358 ypos 0.807

> 2dlabels text H272 bold true size 25

> 2dlabels #5.17 xpos 0.564 ypos 0.818

> 2dlabels #5.17 xpos 0.548 ypos 0.851

> 2dlabels text H249 bold true size 25

> 2dlabels #5.18 xpos 0.809 ypos 0.659

> 2dlabels text H348 bold true size 25

> 2dlabels #5.19 xpos 0.778 ypos 0.435

> 2dlabels text H244 bold true size 25

> 2dlabels #5.20 xpos 0.598 ypos 0.353

> 2dlabels text ""Catalytic Competent"" bold true size 25 color #b22222

> 2dlabels #5.21 xpos 0.609 ypos 0.052

> 2dlabels text FE1 bold true size 22 color #e25822

> 2dlabels #5.22 xpos 0.388 ypos 0.404

> 2dlabels text FE2 bold true size 22 color #e25822

> 2dlabels #5.23 xpos 0.556 ypos 0.522

> 2dlabels #5.23 xpos 0.555 ypos 0.518

> 2dlabels #5.23 xpos 0.611 ypos 0.579

> ~2dlabels #5.23

> ~2dlabels #5.22

> 2dlabels text FE2 bold true size 22 color silver

> 2dlabels #5.22 xpos 0.612 ypos 0.579

> 2dlabels text FE1 bold true size 22 color white

> 2dlabels #5.23 xpos 0.319 ypos 0.399

> ~2dlabels #5.22

> 2dlabels text FE2 bold true size 22 color white

> 2dlabels #5.22 xpos 0.610 ypos 0.580

> save /Users/patrick/Desktop/image198.png supersample 3

> ~2dlabels #5.1-23

> open /Users/patrick/4zr1.cif

4zr1.cif title:  
Hydroxylase domain of scs7p [more info...]  
  
Chain information for 4zr1.cif #2  
---  
Chain | Description | UniProt  
A B | Ceramide very long chain fatty acid hydroxylase SCS7 | SCS7_YEAST 96-384  
  
Non-standard residues in 4zr1.cif #2  
---  
BOG — octyl beta-D-glucopyranoside  
TRD — tridecane (lipid fragment)  
ZN — zinc ion  
  
4zr1.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> hide #!1 models

> view #2

> select #2/B

2424 atoms, 2510 bonds, 10 pseudobonds, 285 residues, 2 models selected  

> delete sel

> select ::name=""BOG""

120 atoms, 120 bonds, 6 residues, 1 model selected  

> delete sel

> select ::name=""TRD""

26 atoms, 24 bonds, 2 residues, 1 model selected  

> delete sel

> hide #!2 cartoons

Drag select of 55 atoms, 51 bonds  

> hide sel

Drag select of 20 atoms, 16 bonds  

> hide sel

Drag select of 29 atoms, 31 bonds  

> hide sel

Drag select of 35 atoms, 34 bonds  

> hide sel

Drag select of 1 atoms  

> hide sel

Drag select of 6 atoms, 5 bonds  

> hide sel

Drag select of 19 atoms, 18 bonds  

> hide sel

Drag select of 15 atoms, 16 bonds  

> hide sel

> hide @c,n,o

> hide #2.2 models

Drag select of 5 atoms, 4 bonds  

> hide sel

> select clear

Drag select of 72 atoms, 10 pseudobonds, 70 bonds  

> select subtract #2/A:401@ZN

71 atoms, 70 bonds, 5 pseudobonds, 11 residues, 2 models selected  

> select subtract #2/A:402@ZN

70 atoms, 70 bonds, 10 residues, 1 model selected  

> name frozen exp sel

> select clear

> show #!1 models

> view #1

Drag select of 15 atoms, 3 pseudobonds, 19 bonds  

> select clear

Drag select of 72 atoms, 10 pseudobonds, 70 bonds  

> select subtract #1/X:386@FE2P

71 atoms, 70 bonds, 5 pseudobonds, 11 residues, 3 models selected  

> select subtract #1/X:387@FE2P

70 atoms, 70 bonds, 10 residues, 2 models selected  

> name frozen comp sel

> select clear

> matchmaker exp to comp

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 frame_30ns.pdb, chain X (#1) with 4zr1.cif, chain A (#2), sequence
alignment score = 6.8  
RMSD between 10 pruned atom pairs is 0.598 angstroms; (across all 10 pairs:
0.598)  
  

> lighting simple

> open
> /Users/patrick/Documents/Research/scs7p/New/open/Production_187/run1/frame_30nso.pdb

frame_30nso.pdb title:  
MDANALYSIS FRAMES FROM 0, STEP 1: Created by PDBWriter [more info...]  
  
Chain information for frame_30nso.pdb #3  
---  
Chain | Description  
X | No description available  
  
Non-standard residues in frame_30nso.pdb #3  
---  
FE2P — (FE2P)  
HEME — (heme)  
HSD — (HSD)  
  

> hide #!2 models

> hide #!1 models

> hide target c

Drag select of 210 atoms, 6 pseudobonds, 206 bonds  

> hide sel

> hide H

> hide @c,n,o

> hide #3.3 models

> ui mousemode right coordinationbond

> ui mousemode right select

Drag select of 72 atoms, 70 bonds  

> select clear

> ui mousemode right coordinationbond

Drag select of 12 atoms, 13 bonds  

> select clear

Drag select of 72 atoms, 10 pseudobonds, 70 bonds  

> select #3/X:386@FE2P

1 atom, 1 residue, 1 model selected  

> select clear

Drag select of 60 atoms, 10 pseudobonds, 58 bonds  

> select clear

Drag select of 72 atoms, 10 pseudobonds, 70 bonds  

> select subtract #3/X:386@FE2P

71 atoms, 70 bonds, 5 pseudobonds, 11 residues, 2 models selected  

> select subtract #3/X:387@FE2P

70 atoms, 70 bonds, 10 residues, 1 model selected  

> name frozen open sel

> select clear

> show #!2 models

> show #!1 models

> matchmaker open to exp

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 4zr1.cif, chain A (#2) with frame_30nso.pdb, chain X (#3), sequence
alignment score = 6.8  
RMSD between 10 pruned atom pairs is 0.723 angstroms; (across all 10 pairs:
0.723)  
  

> center #1

Unknown command: center #1  

> hide #!3 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> 2dlabels text H244 bold true size 25

> ui mousemode right ""move label""

> 2dlabels #4.1 xpos 0.700 ypos 0.236

> 2dlabels text H348 bold true size 25

> 2dlabels #4.2 xpos 0.814 ypos 0.408

> 2dlabels text H249 bold true size 25

> 2dlabels #4.3 xpos 0.808 ypos 0.619

> 2dlabels #4.3 xpos 0.852 ypos 0.616

> 2dlabels text H272 bold true size 25

> 2dlabels #4.4 xpos 0.603 ypos 0.855

> 2dlabels text H268 bold true size 25

> 2dlabels #4.5 xpos 0.429 ypos 0.736

> 2dlabels text H349 bold true size 25

> 2dlabels #4.6 xpos 0.442 ypos 0.478

> 2dlabels text H345 bold true size 25

> 2dlabels #4.7 xpos 0.400 ypos 0.204

> 2dlabels text H326 bold true size 25

> 2dlabels #4.8 xpos 0.173 ypos 0.207

> 2dlabels text H330 bold true size 25

> 2dlabels #4.9 xpos 0.094 ypos 0.456

> 2dlabels text H271 bold true size 25

> 2dlabels #4.10 xpos 0.202 ypos 0.748

> 2dlabels text 2.1 size 20

> 2dlabels #4.11 xpos 0.326 ypos 0.521

> 2dlabels text 2.1 size 20

> 2dlabels #4.12 xpos 0.391 ypos 0.474

> 2dlabels text 2.1 size 20

> 2dlabels #4.13 xpos 0.396 ypos 0.376

> 2dlabels text 2.2 size 20

> 2dlabels #4.14 xpos 0.314 ypos 0.356

> 2dlabels text 2.2 size 20

> 2dlabels #4.15 xpos 0.285 ypos 0.455

> 2dlabels text 2.2 size 20

> 2dlabels #4.16 xpos 0.710 ypos 0.557

> 2dlabels text 2.1 size 20

> 2dlabels #4.17 xpos 0.697 ypos 0.638

> 2dlabels text 2.1 size 20

> 2dlabels #4.18 xpos 0.626 ypos 0.498

> 2dlabels #4.18 xpos 0.640 ypos 0.491

> 2dlabels text 2.1 size 20

> 2dlabels #4.19 xpos 0.601 ypos 0.569

> 2dlabels text 2.1 size 20

> 2dlabels #4.20 xpos 0.662 ypos 0.665

> 2dlabels #4.17 xpos 0.708 ypos 0.643

> 2dlabels text FE2 bold true size 22 color #e25822

> 2dlabels #4.21 xpos 0.586 ypos 0.520

> 2dlabels text FE1 bold true size 22 color #e25822

> 2dlabels #4.22 xpos 0.391 ypos 0.425

> save /Users/patrick/Desktop/image199.png supersample 3

> ~2dlabels #4.11-20

> show #!2 models

> hide #!1 models

> 2dlabels #4.2 xpos 0.786 ypos 0.417

> 2dlabels #4.3 xpos 0.838 ypos 0.617

> 2dlabels #4.5 xpos 0.402 ypos 0.727

> 2dlabels #4.10 xpos 0.230 ypos 0.749

> 2dlabels #4.8 xpos 0.180 ypos 0.207

> 2dlabels #4.22 xpos 0.418 ypos 0.430

> 2dlabels #4.6 xpos 0.456 ypos 0.488

> 2dlabels #4.21 xpos 0.573 ypos 0.513

> hide #4.21 models

> hide #4.22 models

> ui tool show Distances

> ui mousemode right select

> select #2/A:345@NE2

1 atom, 1 residue, 1 model selected  

> select add #2/A:401@ZN

2 atoms, 2 residues, 1 model selected  

> distance #2/A:345@NE2 #2/A:401@ZN

Distance between 4zr1.cif #2/A HIS 345 NE2 and ZN 401 ZN: 2.2Å  

> select clear

> select #2/A:326@NE2

1 atom, 1 residue, 1 model selected  

> select add #2/A:401@ZN

2 atoms, 2 residues, 1 model selected  

> distance #2/A:326@NE2 #2/A:401@ZN

Distance between 4zr1.cif #2/A HIS 326 NE2 and ZN 401 ZN: 2.3Å  

> select clear

> select add #2/A:330@NE2

1 atom, 1 residue, 1 model selected  

> select add #2/A:401@ZN

2 atoms, 2 residues, 1 model selected  

> distance #2/A:330@NE2 #2/A:401@ZN

Distance between 4zr1.cif #2/A HIS 330 NE2 and ZN 401 ZN: 2.1Å  

> select clear

> select add #2/A:271@NE2

1 atom, 1 residue, 1 model selected  

> select add #2/A:401@ZN

2 atoms, 2 residues, 1 model selected  

> distance #2/A:271@NE2 #2/A:401@ZN

Distance between 4zr1.cif #2/A HIS 271 NE2 and ZN 401 ZN: 2.3Å  

> select clear

> select add #2/A:349@NE2

1 atom, 1 residue, 1 model selected  

> select add #2/A:401@ZN

2 atoms, 2 residues, 1 model selected  

> distance #2/A:349@NE2 #2/A:401@ZN

Distance between 4zr1.cif #2/A HIS 349 NE2 and ZN 401 ZN: 2.0Å  

> select clear

> select add #2/A:268@NE2

1 atom, 1 residue, 1 model selected  

> select add #2/A:402@ZN

2 atoms, 2 residues, 1 model selected  

> distance #2/A:268@NE2 #2/A:402@ZN

Distance between 4zr1.cif #2/A HIS 268 NE2 and ZN 402 ZN: 2.2Å  

> select clear

> select add #2/A:272@NE2

1 atom, 1 residue, 1 model selected  

> select add #2/A:402@ZN

2 atoms, 2 residues, 1 model selected  

> distance #2/A:272@NE2 #2/A:402@ZN

Distance between 4zr1.cif #2/A HIS 272 NE2 and ZN 402 ZN: 2.3Å  

> select clear

> select add #2/A:249@NE2

1 atom, 1 residue, 1 model selected  

> select add #2/A:402@ZN

2 atoms, 2 residues, 1 model selected  

> distance #2/A:249@NE2 #2/A:402@ZN

Distance between 4zr1.cif #2/A HIS 249 NE2 and ZN 402 ZN: 2.1Å  

> select clear

> select add #2/A:348@NE2

1 atom, 1 residue, 1 model selected  

> select add #2/A:402@ZN

2 atoms, 2 residues, 1 model selected  

> distance #2/A:348@NE2 #2/A:402@ZN

Distance between 4zr1.cif #2/A HIS 348 NE2 and ZN 402 ZN: 2.2Å  

> select clear

> select add #2/A:244@NE2

1 atom, 1 residue, 1 model selected  

> select add #2/A:402@ZN

2 atoms, 2 residues, 1 model selected  

> distance #2/A:244@NE2 #2/A:402@ZN

Distance between 4zr1.cif #2/A HIS 244 NE2 and ZN 402 ZN: 2.3Å  

> select clear

> 2dlabels text 2.3 size 20

> ui mousemode right ""move label""

> 2dlabels #4.11 xpos 0.367 ypos 0.583

> ~distance #2/A:271@NE2 #2/A:401@ZN

> 2dlabels #4.11 xpos 0.352 ypos 0.538

> 2dlabels text 2.3 size 20

> 2dlabels #4.12 xpos 0.350 ypos 0.377

> ~distance #2/A:326@NE2 #2/A:401@ZN

> 2dlabels text 2.1 size 20

> ~distance #2/A:330@NE2 #2/A:401@ZN

> 2dlabels #4.13 xpos 0.319 ypos 0.480

> 2dlabels text 2.2 size 20

> ~distance #2/A:345@NE2 #2/A:401@ZN

> 2dlabels #4.14 xpos 0.420 ypos 0.374

> 2dlabels text 2.1 size 20

> ~distance #2/A:249@NE2 #2/A:402@ZN

> 2dlabels #4.15 xpos 0.690 ypos 0.636

> 2dlabels text 2.2 size 20

> 2dlabels #4.16 xpos 0.570 ypos 0.560

> ~distance #2/A:268@NE2 #2/A:402@ZN

> 2dlabels text 2.0 size 20

> ~distance #2/A:349@NE2 #2/A:401@ZN

> 2dlabels #4.17 xpos 0.408 ypos 0.475

> 2dlabels #4.11 xpos 0.340 ypos 0.558

> 2dlabels text 2.3 size 20

> ~distance #2/A:272@NE2 #2/A:402@ZN

> 2dlabels #4.18 xpos 0.632 ypos 0.677

> 2dlabels text 2.3 size 20

> 2dlabels #4.19 xpos 0.617 ypos 0.445

> ~distance #2/A:244@NE2 #2/A:402@ZN

> 2dlabels text 2.2 size 20

> ~distance #2/A:348@NE2 #2/A:402@ZN

> 2dlabels #4.20 xpos 0.697 ypos 0.551

> 2dlabels text ZN1 bold true size 22 color #6082b6

> 2dlabels #4.23 xpos 0.417 ypos 0.431

> 2dlabels text ZN2 bold true size 22 color #6082b6

> 2dlabels #4.24 xpos 0.584 ypos 0.515

> save /Users/patrick/Desktop/image200.png supersample 3

> show #!3 models

> hide #!2 models

> hide #4.11 models

> hide #4.12 models

> hide #4.13 models

> hide #4.14 models

> hide #4.15 models

> hide #4.16 models

> hide #4.17 models

> hide #4.18 models

> hide #4.19 models

> hide #4.20 models

> hide #4.23 models

> hide #4.24 models

> 2dlabels #4.4 xpos 0.618 ypos 0.884

> 2dlabels #4.5 xpos 0.402 ypos 0.764

> 2dlabels #4.6 xpos 0.460 ypos 0.497

> 2dlabels #4.10 xpos 0.210 ypos 0.753

> 2dlabels #4.9 xpos 0.093 ypos 0.441

> 2dlabels #4.8 xpos 0.160 ypos 0.143

> 2dlabels #4.7 xpos 0.385 ypos 0.211

> 2dlabels #4.1 xpos 0.695 ypos 0.235

> 2dlabels #4.2 xpos 0.782 ypos 0.402

> ui mousemode right select

> select add #3/X:345@NE2

1 atom, 1 residue, 1 model selected  

> select add #3/X:386@FE2P

2 atoms, 2 residues, 1 model selected  

> distance #3/X:345@NE2 #3/X:386@FE2P

Distance between frame_30nso.pdb #3/X HSD 345 NE2 and FE2P 386 FE2P: 2.2Å  

> select add #3/X:349@NE2

3 atoms, 3 residues, 1 model selected  

> select clear

> select add #3/X:349@NE2

1 atom, 1 residue, 1 model selected  

> select add #3/X:386@FE2P

2 atoms, 2 residues, 1 model selected  

> distance #3/X:349@NE2 #3/X:386@FE2P

Distance between frame_30nso.pdb #3/X HSD 349 NE2 and FE2P 386 FE2P: 2.1Å  

> select clear

> select add #3/X:271@NE2

1 atom, 1 residue, 1 model selected  

> select add #3/X:386@FE2P

2 atoms, 2 residues, 1 model selected  

> distance #3/X:271@NE2 #3/X:386@FE2P

Distance between frame_30nso.pdb #3/X HSD 271 NE2 and FE2P 386 FE2P: 2.1Å  

> select clear

> select add #3/X:330@NE2

1 atom, 1 residue, 1 model selected  

> select add #3/X:386@FE2P

2 atoms, 2 residues, 1 model selected  

> distance #3/X:330@NE2 #3/X:386@FE2P

Distance between frame_30nso.pdb #3/X HSD 330 NE2 and FE2P 386 FE2P: 2.1Å  

> select clear

> select add #3/X:326@NE2

1 atom, 1 residue, 1 model selected  

> select add #3/X:386@FE2P

2 atoms, 2 residues, 1 model selected  

> distance #3/X:326@NE2 #3/X:386@FE2P

Distance between frame_30nso.pdb #3/X HSD 326 NE2 and FE2P 386 FE2P: 2.3Å  

> select clear

> select add #3/X:268@NE2

1 atom, 1 residue, 1 model selected  

> select add #3/X:387@FE2P

2 atoms, 2 residues, 1 model selected  

> distance #3/X:268@NE2 #3/X:387@FE2P

Distance between frame_30nso.pdb #3/X HSD 268 NE2 and FE2P 387 FE2P: 2.1Å  

> select clear

> select add #3/X:272@NE2

1 atom, 1 residue, 1 model selected  

> select add #3/X:387@FE2P

2 atoms, 2 residues, 1 model selected  

> distance #3/X:272@NE2 #3/X:387@FE2P

Distance between frame_30nso.pdb #3/X HSD 272 NE2 and FE2P 387 FE2P: 2.2Å  

> select clear

> select add #3/X:249@NE2

1 atom, 1 residue, 1 model selected  

> select add #3/X:387@FE2P

2 atoms, 2 residues, 1 model selected  

> distance #3/X:249@NE2 #3/X:387@FE2P

Distance between frame_30nso.pdb #3/X HSD 249 NE2 and FE2P 387 FE2P: 2.1Å  

> select clear

> select add #3/X:348@NE2

1 atom, 1 residue, 1 model selected  

> select add #3/X:387@FE2P

2 atoms, 2 residues, 1 model selected  

> distance #3/X:348@NE2 #3/X:387@FE2P

Distance between frame_30nso.pdb #3/X HSD 348 NE2 and FE2P 387 FE2P: 2.4Å  

> select clear

> select add #3/X:244@NE2

1 atom, 1 residue, 1 model selected  

> select add #3/X:387@FE2P

2 atoms, 2 residues, 1 model selected  

> distance #3/X:244@NE2 #3/X:387@FE2P

Distance between frame_30nso.pdb #3/X HSD 244 NE2 and FE2P 387 FE2P: 2.2Å  

> select clear

> 2dlabels text 2.2 size 20

> ui mousemode right ""move label""

> 2dlabels #4.25 xpos 0.417 ypos 0.358

> ~distance #3/X:345@NE2 #3/X:386@FE2P

> 2dlabels text 2.1 size 20

> 2dlabels #4.26 xpos 0.294 ypos 0.439

> ~distance #3/X:330@NE2 #3/X:386@FE2P

> 2dlabels text 2.1 size 20

> ~distance #3/X:271@NE2 #3/X:386@FE2P

> 2dlabels #4.6 xpos 0.484 ypos 0.539

> 2dlabels #4.27 xpos 0.307 ypos 0.533

> 2dlabels text 2.1 size 20

> 2dlabels #4.28 xpos 0.400 ypos 0.486

> ~distance #3/X:349@NE2 #3/X:386@FE2P

> 2dlabels #4.28 xpos 0.402 ypos 0.488

> 2dlabels text 2.1 size 20

> 2dlabels #4.29 xpos 0.567 ypos 0.465

> ~distance #3/X:249@NE2 #3/X:387@FE2P

> 2dlabels #4.25 xpos 0.417 ypos 0.358

> 2dlabels #4.29 xpos 0.733 ypos 0.661

> 2dlabels text 2.2 size 20

> 2dlabels #4.30 xpos 0.677 ypos 0.706

> ~distance #3/X:272@NE2 #3/X:387@FE2P

> 2dlabels text 2.1 size 20

> ~distance #3/X:268@NE2 #3/X:387@FE2P

> 2dlabels #4.31 xpos 0.617 ypos 0.581

> ~distance #3/X:326@NE2 #3/X:386@FE2P

> 2dlabels text 2.2 size 20

> 2dlabels #4.32 xpos 0.309 ypos 0.341

> 2dlabels #4.28 xpos 0.400 ypos 0.486

> 2dlabels #4.25 xpos 0.413 ypos 0.359

> 2dlabels text 2.2 size 20

> 2dlabels #4.33 xpos 0.659 ypos 0.474

> ~distance #3/X:244@NE2 #3/X:387@FE2P

> ~distance #3/X:348@NE2 #3/X:387@FE2P

> 2dlabels text 2.3 size 20

> 2dlabels #4.34 xpos 0.729 ypos 0.572

> show #4.21 models

> show #4.22 models

> 2dlabels #4.22 xpos 0.395 ypos 0.429

> 2dlabels #4.21 xpos 0.616 ypos 0.530

> 2dlabels #4.6 xpos 0.464 ypos 0.495

> 2dlabels #4.6 xpos 0.461 ypos 0.495

> 2dlabels #4.26 xpos 0.297 ypos 0.452

> save /Users/patrick/Desktop/image201.png supersample 3

> hide #4.34 models

> hide #4.33 models

> hide #4.32 models

> hide #4.31 models

> hide #4.30 models

> hide #4.29 models

> hide #4.28 models

> hide #4.27 models

> hide #4.26 models

> hide #4.25 models

> hide #4.22 models

> hide #4.21 models

> show #!1 models

> hide #!3 models

> show #!2 models

> matchmaker comp to exp

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 4zr1.cif, chain A (#2) with frame_30ns.pdb, chain X (#1), sequence
alignment score = 6.8  
RMSD between 10 pruned atom pairs is 0.598 angstroms; (across all 10 pairs:
0.598)  
  

> 2dlabels #4.5 xpos 0.375 ypos 0.753

> 2dlabels #4.4 xpos 0.583 ypos 0.889

> 2dlabels #4.3 xpos 0.833 ypos 0.597

> 2dlabels #4.2 xpos 0.783 ypos 0.396

> 2dlabels #4.3 xpos 0.840 ypos 0.614

> 2dlabels #4.1 xpos 0.687 ypos 0.223

> 2dlabels #4.7 xpos 0.397 ypos 0.200

> 2dlabels #4.8 xpos 0.160 ypos 0.152

> 2dlabels #4.9 xpos 0.087 ypos 0.454

> 2dlabels #4.10 xpos 0.197 ypos 0.736

> 2dlabels #4.5 xpos 0.383 ypos 0.753

> 2dlabels #4.6 xpos 0.456 ypos 0.477

> save /Users/patrick/Desktop/image202.png supersample 3

> hide #!1 models

> show #!3 models

> matchmaker open to exp

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 4zr1.cif, chain A (#2) with frame_30nso.pdb, chain X (#3), sequence
alignment score = 6.8  
RMSD between 10 pruned atom pairs is 0.723 angstroms; (across all 10 pairs:
0.723)  
  

> 2dlabels #4.4 xpos 0.598 ypos 0.915

> 2dlabels #4.2 xpos 0.785 ypos 0.401

> 2dlabels #4.7 xpos 0.401 ypos 0.200

> 2dlabels #4.8 xpos 0.160 ypos 0.176

> 2dlabels #4.9 xpos 0.097 ypos 0.458

> 2dlabels #4.10 xpos 0.192 ypos 0.719

> 2dlabels #4.5 xpos 0.389 ypos 0.749

> 2dlabels #4.6 xpos 0.443 ypos 0.478

> save /Users/patrick/Desktop/image203.png supersample 3

> show #!1 models

> matchmaker open to comp

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 frame_30ns.pdb, chain X (#1) with frame_30nso.pdb, chain X (#3),
sequence alignment score = 9.8  
RMSD between 10 pruned atom pairs is 0.397 angstroms; (across all 10 pairs:
0.397)  
  

> save /Users/patrick/Desktop/image204.png supersample 3

Unsupported scale factor (0.000000) detected on Display0  

QPainter::begin: Paint device returned engine == 0, type: 3  


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

Log:
Startup Messages  
---  
warnings | Unable to find icon for toolbar provider 'Dump Bead Data' in bundle
'ChimeraX-GenomeTools'  
Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Genome Distance' in bundle
'ChimeraX-GenomeTools'  
1 messages similar to the above omitted  
  

> camera ortho

> cofr centerOfView

> mousemode rightMode clip

> mousemode alt rightMode ""contour level""

> mousemode alt leftMode ""move picked models""

> alias cofron cofr centerofview showpivot true

> alias cofroff cofr centerofview showpivot false

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias cootmode surface cap false; surface style solid; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10
> position cofr; color ##~num_residues cornflower blue

> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000

> alias map_unsphere surface unzone ##~num_residues

> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft

> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000

> alias showmaps surface unzone ##~num_residues

> buttonpanel Shortcuts rows 3 columns 4

> buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'""

> buttonpanel Shortcuts add Model_Panel command ""tool show Models""

> buttonpanel Shortcuts add Log command ""tool show Log""

> buttonpanel Shortcuts add default_disp command default_mol_display

> buttonpanel Shortcuts add map_sphere command map_sphere_15

> buttonpanel Shortcuts add map_unsphere command map_unsphere

> buttonpanel Shortcuts add cofron command cofron

> buttonpanel Shortcuts add cofroff command cofroff

> buttonpanel Shortcuts add cootmode command cootmode

> buttonpanel Shortcuts add mark_cofr command ""marker #10000 position cofr""

> buttonpanel Shortcuts add hidemaps command hidemaps

> buttonpanel Shortcuts add showmaps command showmaps

UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/patrick/Documents/Research/scs7p/New/compact/compact_af/Production_162/run1/frame_0nsc.pdb

frame_0nsc.pdb title:  
MDANALYSIS FRAMES FROM 0, STEP 1: Created by PDBWriter [more info...]  
  
Chain information for frame_0nsc.pdb #1  
---  
Chain | Description  
X | No description available  
  
Non-standard residues in frame_0nsc.pdb #1  
---  
FE2P — (FE2P)  
HEME — (heme)  
HSD — (HSD)  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: Z160000AKLL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8422.141.2
      OS Loader Version: 8422.141.2

Software:

    System Software Overview:

      System Version: macOS 13.5.2 (22G91)
      Kernel Version: Darwin 22.6.0
      Time since boot: 3 days, 1 hour, 52 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2417H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-GenomeTools: 0.9
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-OpenCommands: 1.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.2
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.0
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RMF: 0.14
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    Send2Trash: 1.8.2
    SEQCROW: 1.8.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

}}}
"	defect	closed	normal		Window Toolkit		duplicate		Tom Goddard				all	ChimeraX