﻿id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15776	Crash waking Mac up from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-13.6.7-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.
Fatal Python error: Segmentation fault

Current thread 0x00000001f6e7e100 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56)


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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.  
How to cite UCSF ChimeraX  

> open ""/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/Rilee EC MgtA Paper
> Structures/Paper PDB
> Structures/monomer_apo_Mg_C1nosymm_D_1000277101_model_annotate_P1.pdb""

monomer_apo_Mg_C1nosymm_D_1000277101_model_annotate_P1.pdb title:  
Magnesium transporter MGTA monomer from E. Coli In 5 MM MGCL2 [more info...]  
  
Chain information for
monomer_apo_Mg_C1nosymm_D_1000277101_model_annotate_P1.pdb #1  
---  
Chain | Description | UniProt  
A | magnesium-transporting atpase, P-type 1 | ATMA_ECOLI 1-898  
  
Non-standard residues in
monomer_apo_Mg_C1nosymm_D_1000277101_model_annotate_P1.pdb #1  
---  
MG — magnesium ion  
  

> set bgColor white

> lighting flat

> lighting shadows true intensity 0.5

> select #1/A:95-115

164 atoms, 167 bonds, 21 residues, 1 model selected  

> select #1/A:95-137

326 atoms, 331 bonds, 43 residues, 1 model selected  

> select #1/A:1-95

344 atoms, 353 bonds, 62 residues, 1 model selected  

> select #1/A:1-90

300 atoms, 306 bonds, 57 residues, 1 model selected  

> select #1/A:1-85

271 atoms, 275 bonds, 52 residues, 1 model selected  

> select #1/A:1-86

278 atoms, 283 bonds, 53 residues, 1 model selected  

> select #1/A:87-115

223 atoms, 230 bonds, 29 residues, 1 model selected  

> select #1/A:87-137

385 atoms, 394 bonds, 51 residues, 1 model selected  

> select #1/A:87-140

404 atoms, 413 bonds, 54 residues, 1 model selected  

> select #1/A:87-142

415 atoms, 424 bonds, 56 residues, 1 model selected  

> select #1/A:87-145

430 atoms, 439 bonds, 59 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel silver

> color sel gray

> select /A:279

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:146-278

675 atoms, 682 bonds, 133 residues, 1 model selected  

> select #1/A:279-388

844 atoms, 857 bonds, 110 residues, 1 model selected  

> select #1/A:279-335

441 atoms, 451 bonds, 57 residues, 1 model selected  

> color sel burly wood

> color sel goldenrod

> color sel sienna

> color sel chocolate

> color sel dark goldenrod

> color sel goldenrod

> color sel sandy brown

> color sel sienna

> color sel brown

> color sel chocolate

> color sel saddle brown

> color sel peru

> color sel dark goldenrod

> color sel dark khaki

> color sel dark salmon

> color sel dark red

> color sel maroon

> color sel sienna

> color sel indian red

> color sel goldenrod

> color sel dark goldenrod

> color sel peru

> color sel dark goldenrod

> select /A:349

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/A:279-349

539 atoms, 549 bonds, 71 residues, 1 model selected  

> color sel dark goldenrod

> select #1/A:279-350

548 atoms, 558 bonds, 72 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel dark goldenrod

> select #1/A:351-400

382 atoms, 384 bonds, 50 residues, 1 model selected  

> select #1/A:351-375

194 atoms, 195 bonds, 25 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel deep sky blue

> color sel medium turquoise

> color sel cornflower blue

> select #1/A:376-450

519 atoms, 527 bonds, 75 residues, 1 model selected  

> select #1/A:376-550

1201 atoms, 1216 bonds, 175 residues, 1 model selected  

> select #1/A:376-549

1194 atoms, 1209 bonds, 174 residues, 1 model selected  

> color sel crimson

> color sel dark red

> color sel fire brick

> color sel red

> color sel orange red

> color sel crimson

> select #1/A:550-600

355 atoms, 356 bonds, 51 residues, 1 model selected  

> select #1/A:550-650

746 atoms, 753 bonds, 101 residues, 1 model selected  

> select #1/A:550-700

1124 atoms, 1133 bonds, 151 residues, 1 model selected  

> select #1/A:550-765

1639 atoms, 1663 bonds, 216 residues, 1 model selected  

> select #1/A:550-665

842 atoms, 849 bonds, 116 residues, 1 model selected  

> select #1/A:550-675

921 atoms, 928 bonds, 126 residues, 1 model selected  

> color sel cornflower blue

> select #1/A:550-690

1039 atoms, 1046 bonds, 141 residues, 1 model selected  

> color sel cornflower blue

> select #1/A:690-745

440 atoms, 451 bonds, 56 residues, 1 model selected  

> select #1/A:690-748

467 atoms, 479 bonds, 59 residues, 1 model selected  

> color sel midnight blue

> color sel black

> color sel dim gray

> color sel black

> color sel dim gray

> select #1/A:87-145

430 atoms, 439 bonds, 59 residues, 1 model selected  

> color sel light gray

> color sel gray

> color sel dim gray

> color sel gray

> ui tool show ""Color Actions""

> color sel pale violet red

> color sel orchid

> color sel thistle

> color sel plum

> color sel light pink

> color sel thistle

> color sel pale violet red

> color sel orchid

> color sel plum

> color sel orchid

> color sel pale violet red

> color sel violet

> color sel plum

> color sel violet

> select #1/A:690-748

467 atoms, 479 bonds, 59 residues, 1 model selected  

> color sel gray

> select #1/A:749-886

1118 atoms, 1155 bonds, 138 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel dark gray

> color sel dim gray

> color sel dark gray

> color sel dim gray

> color sel dark gray

> color sel dim gray

> select #1/A:690-748

467 atoms, 479 bonds, 59 residues, 1 model selected  

> color sel dark gray

> select clear

> select #1/A:749-889

1138 atoms, 1175 bonds, 141 residues, 1 model selected  

> select #1/A:749-891

1161 atoms, 1200 bonds, 143 residues, 1 model selected  

> select #1/A:749-892

1167 atoms, 1206 bonds, 144 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel dim gray

> select clear

> save ""/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/monomer_apo_Mg_C2nosymm_colorcoded_fig.png"" width 1152
> height 765 supersample 3 transparentBackground true

> select #1/A:690-748

467 atoms, 479 bonds, 59 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel dim gray

> select #1/A:749-892

1167 atoms, 1206 bonds, 144 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel dark gray

> select clear

> save ""/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/monomer_apo_Mg_C2nosymm_colorcoded_fig.png"" width 1152
> height 765 supersample 3 transparentBackground true

> open ""/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/Rilee EC MgtA Paper
> Structures/Paper PDB
> Structures/dimer_apo_Mg_C2symm_D_1000274597_model_annotate_P1.pdb""

dimer_apo_Mg_C2symm_D_1000274597_model_annotate_P1.pdb title:  
Magnesium transporter MGTA dimer from E. Coli In 5 MM MGCL2 [more info...]  
  
Chain information for dimer_apo_Mg_C2symm_D_1000274597_model_annotate_P1.pdb
#2  
---  
Chain | Description | UniProt  
A B | magnesium-transporting atpase, P-type 1 | ATMA_ECOLI 1-898  
  
Non-standard residues in
dimer_apo_Mg_C2symm_D_1000274597_model_annotate_P1.pdb #2  
---  
MG — magnesium ion  
  

> hide #!1 models

> select #1/A:87-145 color sel violet

Expected a keyword  

> select #1/A:87-145, color sel violet

Expected a keyword  

> select #1/A:87-145

430 atoms, 439 bonds, 59 residues, 1 model selected  

> select #2/A:87-145

467 atoms, 480 bonds, 59 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel violet

> select #2/A:87-145 color sel red

Expected a keyword  

> select #2/A:87-145, color sel red

Expected a keyword  

> ui tool show ""Color Actions""

> color sel rebecca purple

> open /Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/ChimeraX/PType_ATPases_Color.cxc

> select #2/A:1-86

642 atoms, 659 bonds, 86 residues, 1 model selected  

> select #2/A:87-145 (violet)

Expected a keyword  

> open /Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/ChimeraX/PType_ATPases_Color.cxc

> select #2/A:1-86

642 atoms, 659 bonds, 86 residues, 1 model selected  

> select #2/A:87-145

467 atoms, 480 bonds, 59 residues, 1 model selected  

> color sel violet

> select #2/A:146-278

949 atoms, 963 bonds, 133 residues, 1 model selected  

> select #2/A:279-350

548 atoms, 558 bonds, 72 residues, 1 model selected  

> color sel dark goldenrod

> select #2/A:351-375

194 atoms, 195 bonds, 25 residues, 1 model selected  

> color sel cornflower blue

> select #2/A:376-549

1389 atoms, 1410 bonds, 174 residues, 1 model selected  

> color sel crimson

> select #2/A:550-690

1039 atoms, 1046 bonds, 141 residues, 1 model selected  

> color sel cornflower blue

> select #2/A:690-748

467 atoms, 479 bonds, 59 residues, 1 model selected  

> color sel dim gray

> select #2/A:749-892

1167 atoms, 1206 bonds, 144 residues, 1 model selected  

> color sel dark gray

executed PType_ATPases_Color.cxc  

> select #2/A:1-86

642 atoms, 659 bonds, 86 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel wheat

> color sel gold

> color sel dark orange

> color sel orange

> color sel goldenrod

> color sel sandy brown

> hide #!2 models

> show #!1 models

> select clear

> select #1/A:259

4 atoms, 3 bonds, 1 residue, 1 model selected  

> hide #!1 models

> show #!2 models

> color sel pale goldenrod

> color sel khaki

> select #2/A:1-86

642 atoms, 659 bonds, 86 residues, 1 model selected  

> color sel pale goldenrod

> color sel khaki

> color sel wheat

> color sel beige

> color sel antique white

> color sel light goldenrod yellow

> color sel old lace

> color sel peach puff

> color sel navajo white

> color sel moccasin

> color sel bisque

> color sel misty rose

> color sel blanched almond

> color sel papaya whip

> color sel lemon chiffon

> hide #!2 models

> show #!1 models

> select #1

5982 atoms, 6094 bonds, 1 pseudobond, 860 residues, 2 models selected  

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color sel list

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> select #1/A:259

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/A:259

4 atoms, 3 bonds, 1 residue, 1 model selected  

> view #2 clip false

Drag select of 168 residues  

> select clear

Drag select of 90 residues  

> ui tool show ""Color Actions""

> color sel tan

> color sel burly wood

> color sel light coral

> color sel tan

> color sel burly wood

> color sel tan

> select clear

> hide #!1 models

> show #!2 models

> open /Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/ChimeraX/PType_ATPases_Color.cxc

> select #2/A:1-86

642 atoms, 659 bonds, 86 residues, 1 model selected  

> color sel tan

> select #2/A:87-145

467 atoms, 480 bonds, 59 residues, 1 model selected  

> color sel violet

> select #2/A:146-278

949 atoms, 963 bonds, 133 residues, 1 model selected  

> color sel tan

> select #2/A:279-350

548 atoms, 558 bonds, 72 residues, 1 model selected  

> color sel dark goldenrod

> select #2/A:351-375

194 atoms, 195 bonds, 25 residues, 1 model selected  

> color sel cornflower blue

> select #2/A:376-549

1389 atoms, 1410 bonds, 174 residues, 1 model selected  

> color sel crimson

> select #2/A:550-690

1039 atoms, 1046 bonds, 141 residues, 1 model selected  

> color sel cornflower blue

> select #2/A:690-748

467 atoms, 479 bonds, 59 residues, 1 model selected  

> color sel dim gray

> select #2/A:749-892

1167 atoms, 1206 bonds, 144 residues, 1 model selected  

> color sel dark gray

executed PType_ATPases_Color.cxc  

> select #2/A:898

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:898

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/B

7018 atoms, 7060 bonds, 4 pseudobonds, 1001 residues, 2 models selected  

> select #2/B:899

Nothing selected  

> open /Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/ChimeraX/PType_ATPases_Color.cxc

> select #2/A:1-86

642 atoms, 659 bonds, 86 residues, 1 model selected  

> color sel tan

> select #2/A:87-145

467 atoms, 480 bonds, 59 residues, 1 model selected  

> color sel violet

> select #2/A:146-278

949 atoms, 963 bonds, 133 residues, 1 model selected  

> color sel tan

> select #2/A:279-350

548 atoms, 558 bonds, 72 residues, 1 model selected  

> color sel dark goldenrod

> select #2/A:351-375

194 atoms, 195 bonds, 25 residues, 1 model selected  

> color sel cornflower blue

> select #2/A:376-549

1389 atoms, 1410 bonds, 174 residues, 1 model selected  

> color sel crimson

> select #2/A:550-690

1039 atoms, 1046 bonds, 141 residues, 1 model selected  

> color sel cornflower blue

> select #2/A:690-748

467 atoms, 479 bonds, 59 residues, 1 model selected  

> color sel dim gray

> select #2/A:749-898

1228 atoms, 1270 bonds, 150 residues, 1 model selected  

> color sel dark gray

> select #2/B:1-86

642 atoms, 659 bonds, 86 residues, 1 model selected  

> color sel tan

> select #2/B:87-145

467 atoms, 480 bonds, 59 residues, 1 model selected  

> color sel violet

> select #2/B:146-278

952 atoms, 966 bonds, 133 residues, 1 model selected  

> color sel tan

> select #2/B:279-350

548 atoms, 558 bonds, 72 residues, 1 model selected  

> color sel dark goldenrod

> select #2/B:351-375

194 atoms, 195 bonds, 25 residues, 1 model selected  

> color sel cornflower blue

> select #2/B:376-549

1389 atoms, 1410 bonds, 174 residues, 1 model selected  

> color sel crimson

> select #2/B:550-690

1039 atoms, 1046 bonds, 141 residues, 1 model selected  

> color sel cornflower blue

> select #2/B:690-748

467 atoms, 479 bonds, 59 residues, 1 model selected  

> color sel dim gray

> select #2/B:749-898

1228 atoms, 1270 bonds, 150 residues, 1 model selected  

> color sel dark gray

executed PType_ATPases_Color.cxc  

> select ~sel & ##selected

12805 atoms, 12847 bonds, 9 pseudobonds, 1852 residues, 2 models selected  

> select clear

> view orient

> ui tool show ""Side View""

> toolshed show

> view

> orient

Unknown command: orient  

> view orient

> ui tool show ""Side View""

> view orient

> view initial #1

> view initial 0

Expected a models specifier or a keyword  

> view initial

> center

Unknown command: center  

> view center

Expected an objects specifier or a view name or a keyword  

> ui view

Missing or invalid ""layout"" argument: Expected one of 'default', 'fourup',
'overunder', or 'sidebyside'  

> ui view default

> ui view fourup

> ui view overunder

> ui view default

> view orient

> view matrix 1,0,0,0,0,1,0,0,0,0,1,0

Expected a keyword  

> view matrix

view matrix camera 1,0,0,159.32,0,1,0,159.32,0,0,1,515.15  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> view matrix models #1

Invalid ""models"" argument: Expected model id and 12 comma-separated numbers  

> view matrix #1,1,0,0,0,0,1,0,0,0,0,1,0

Expected a keyword  

> view matrix camera 1,0,0,0,0,1,0,0,0,0,1,0

> view orient

> turn

> turn y 90

> turn x 90

> turn y 90

> turn y 180

> turn y 90

> view orient

> turn

> turn x -90

> view orient

> turn x -90

> turn y 90

> view orient

> turn x 90

> view orient

> turn y 90

> turn x -90

> turn y -90

> turn z 90

> turn x -90

> save ""/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/dimer_apo_Mg_C2nosymm_colorcoded_fig.png"" width 1152
> height 765 supersample 3 transparentBackground true

> show #!1 models

> ui tool show Matchmaker

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker monomer_apo_Mg_C1nosymm_D_1000277101_model_annotate_P1.pdb, chain A
(#1) with dimer_apo_Mg_C2symm_D_1000274597_model_annotate_P1.pdb, chain A
(#2), sequence alignment score = 4390.5  
RMSD between 305 pruned atom pairs is 0.980 angstroms; (across all 859 pairs:
11.849)  
  

> select #2/B

7018 atoms, 7060 bonds, 4 pseudobonds, 1001 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select #2/A

7015 atoms, 7057 bonds, 5 pseudobonds, 1001 residues, 2 models selected  

> select #21A

Expected an objects specifier or a keyword  

> select #1/A

5982 atoms, 6094 bonds, 1 pseudobond, 860 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel alice blue

> color sel orange

> color sel tomato

> color sel chartreuse

> color sel lime green

> color sel medium sea green

> color sel medium orchid

> color sel dark orchid

> color sel medium violet red

> color sel dark orchid

> color sel dark magenta

> select #1/A:95-137,288-335,696-886

2231 atoms, 2294 bonds, 282 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #!2 to #1 & sel

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker monomer_apo_Mg_C1nosymm_D_1000277101_model_annotate_P1.pdb, chain A
(#1) with dimer_apo_Mg_C2symm_D_1000274597_model_annotate_P1.pdb, chain B
(#2), sequence alignment score = 1415.7  
RMSD between 190 pruned atom pairs is 0.645 angstroms; (across all 282 pairs:
3.427)  
  

> select #2/A

7015 atoms, 7057 bonds, 5 pseudobonds, 1001 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select #2/B

7018 atoms, 7060 bonds, 4 pseudobonds, 1001 residues, 2 models selected  

> show sel cartoons

> clear select

Unknown command: clear select  

> select clear

> rmsd

Missing or invalid ""atoms"" argument: empty atom specifier  

> ui tool show Matchmaker

> ui tool show ""Render/Select by Attribute""

> hide #!1 models

> show #!1 models

> ui tool show ""Render/Select by Attribute""

> align

Missing or invalid ""atoms"" argument: empty atom specifier  

> align #2 toAtoms #1

Unequal number of atoms to pair, 14033 and 5982  

> ui tool show ""Render/Select by Attribute""

> color byattribute a:bfactor #!1-2 target absc palette
> 12.23,blue:125.825,white:239.42,red

20015 atoms, 2862 residues, atom bfactor range 12.2 to 239  

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!1 models

> save ""/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/dimer_apo_matchmaker_to_monomer_RMSD.png"" width 1152
> height 765 supersample 3 transparentBackground true

> ui tool show ""Render/Select by Attribute""

> ui tool show ""Scale Bar""

> undo

> redo

> ui tool show ""Surface Color""

> key red-white-blue :0.0 :0.5 :1.0 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> save ""/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/dimer_apo_matchmaker_to_monomer_RMSD.png"" width 1152
> height 765 supersample 3 transparentBackground true

> ui tool show ""Surface Color""

> key red-white-blue :0.0 :0.5 :1.0 showTool true

> ui mousemode right ""color key""

> key blue-white-red :1.0 :0.5 :0.0

> key red-white-blue :0.0 :0.5 :1.0

> key blue-white-red :1.0 :0.5 :0.0

> key red-white-blue :0.0 :0.5 :1.0

> key red-white-blue :1 :0.5 :1.0

> key red-white-blue :1. :0.5 :1.0

> key red-white-blue :1.0 :0.5 :1.0

> key red-white-blue :1.0 :0.5 :0

> key blue-white-red :0 :0.5 :1.0

> ui mousemode right translate

> key red-white-blue :0.0 :0.5 :1.0 showTool true

> ui mousemode right ""color key""

> key red-white-blue :0.0 :0.5 :0

> key red-white-blue :1 :0.5 :0

> key red-white-blue :12 :0.5 :0

> key blue-white-red :0 :0.5 :12

> key blue-white-red :0 :6 :12

> key blue-white-red :0 :6 :>12

> ui mousemode right translate

> save ""/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/dimer_apo_matchmaker_to_monomer_RMSD.png"" width 1152
> height 765 supersample 3 transparentBackground true

> hide #3 models

> hide #!1 models

> open ""/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/MgtA/CHARMM-GUI
> Processed/dimer_apo_proteinOnly.pdb""

Chain information for dimer_apo_proteinOnly.pdb #4  
---  
Chain | Description  
P | No description available  
  

> open ""/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/MgtS AlphaFold3
> Prediction/MgtS_AF3_CHARMMGUI.pdb""

Chain information for MgtS_AF3_CHARMMGUI.pdb #5  
---  
Chain | Description  
L | No description available  
  

> hide #5 models

> view

> select #4

14109 atoms, 14255 bonds, 898 residues, 1 model selected  

> color sel dark gray

> ui tool show ""Color Actions""

> color sel light slate gray

> color sel silver

> color sel light gray

> color sel gray

> color sel dim gray

> color sel dark gray

> color sel medium purple

> color sel pale violet red

> color sel thistle

> color sel dark olive green

> color sel dark slate gray

> color sel wheat

> color sel linen

> color sel ghost white

> color sel rosy brown

> color sel tan

> color sel dark sea green

> color sel spring green

> color sel deep sky blue

> color sel royal blue

> color sel teal

> color sel medium turquoise

> color sel cornflower blue

> color sel orange

> color sel maroon

> color sel fire brick

> color sel dark gray

> select clear

> save ""/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/dimer_apo_proteinOnly.png"" width 1152 height 765
> supersample 3 transparentBackground true

> hide #4 models

> show #5 models

> view

> select #5

489 atoms, 496 bonds, 31 residues, 1 model selected  

> color sel light sea green

> ui tool show ""Color Actions""

> color sel dark orchid

> color sel light sea green

> color sel dark cyan

> color sel medium aquamarine

> color sel dark cyan

> color sel turquoise

> color sel dodger blue

> color sel medium spring green

> color sel dark turquoise

> color sel deep sky blue

> color sel olive drab

> color sel medium sea green

> color sel dark blue

> color sel navy

> color sel indigo

> color sel royal blue

> color sel cadet blue

> color sel steel blue

> color sel dark cyan

> color sel medium aquamarine

> color sel medium orchid

> view

> save ""/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/MgtS.png"" width 1152 height 765 supersample 3
> transparentBackground true


===== Log before crash end =====

Log:
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/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model1.pdb""

Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model1.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 5  
Duplicate atom serial number found: 7  
Duplicate atom serial number found: 13  
Duplicate atom serial number found: 20  
94 messages similar to the above omitted  
  
Chain information for model1.pdb #1  
---  
Chain | Description  
L | No description available  
P | No description available  
  

> open ""/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model2.pdb""

Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model2.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 5  
Duplicate atom serial number found: 7  
Duplicate atom serial number found: 13  
Duplicate atom serial number found: 20  
94 messages similar to the above omitted  
  
Chain information for model2.pdb #2  
---  
Chain | Description  
L | No description available  
P | No description available  
  

> open ""/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model3.pdb""

Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model3.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 5  
Duplicate atom serial number found: 7  
Duplicate atom serial number found: 13  
Duplicate atom serial number found: 20  
94 messages similar to the above omitted  
  
Chain information for model3.pdb #3  
---  
Chain | Description  
L | No description available  
P | No description available  
  

> open ""/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model4.pdb""

Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model4.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 5  
Duplicate atom serial number found: 7  
Duplicate atom serial number found: 13  
Duplicate atom serial number found: 20  
94 messages similar to the above omitted  
  
Chain information for model4.pdb #4  
---  
Chain | Description  
L | No description available  
P | No description available  
  

> open ""/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model5.pdb""

Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model5.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 5  
Duplicate atom serial number found: 7  
Duplicate atom serial number found: 13  
Duplicate atom serial number found: 20  
94 messages similar to the above omitted  
  
Chain information for model5.pdb #5  
---  
Chain | Description  
L | No description available  
P | No description available  
  

> open ""/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model6.pdb""

Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model6.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 5  
Duplicate atom serial number found: 7  
Duplicate atom serial number found: 13  
Duplicate atom serial number found: 20  
94 messages similar to the above omitted  
  
Chain information for model6.pdb #6  
---  
Chain | Description  
L | No description available  
P | No description available  
  

> open ""/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model7.pdb""

Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model7.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 5  
Duplicate atom serial number found: 7  
Duplicate atom serial number found: 13  
Duplicate atom serial number found: 20  
94 messages similar to the above omitted  
  
Chain information for model7.pdb #7  
---  
Chain | Description  
L | No description available  
P | No description available  
  

> open ""/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model8.pdb""

Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model8.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 5  
Duplicate atom serial number found: 7  
Duplicate atom serial number found: 13  
Duplicate atom serial number found: 20  
94 messages similar to the above omitted  
  
Chain information for model8.pdb #8  
---  
Chain | Description  
L | No description available  
P | No description available  
  

> open ""/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model9.pdb""

Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model9.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 5  
Duplicate atom serial number found: 7  
Duplicate atom serial number found: 13  
Duplicate atom serial number found: 20  
94 messages similar to the above omitted  
  
Chain information for model9.pdb #9  
---  
Chain | Description  
L | No description available  
P | No description available  
  

> open ""/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model10.pdb""

Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model10.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 5  
Duplicate atom serial number found: 7  
Duplicate atom serial number found: 13  
Duplicate atom serial number found: 20  
94 messages similar to the above omitted  
  
Chain information for model10.pdb #10  
---  
Chain | Description  
L | No description available  
P | No description available  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 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: MacBookPro18,2
      Model Number: Z14X000HRLL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 8422.141.2.700.1
      OS Loader Version: 8422.141.2.700.1

Software:

    System Software Overview:

      System Version: macOS 13.6.7 (22G720)
      Kernel Version: Darwin 22.6.0
      Time since boot: 17 days, 1 hour, 5 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL U2424H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 120.00Hz
          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-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-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX
