id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
7196	Crash during drag/drop	ichcharisma@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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    ""name"" : ""libqcocoa.dylib""
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    ""size"" : 5226496,
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    ""name"" : ""QtCore""
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    ""size"" : 2818048,
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    ""path"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtWidgets.abi3.so"",
    ""name"" : ""QtWidgets.abi3.so""
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    ""arch"" : ""x86_64"",
    ""base"" : 4533698560,
    ""CFBundleShortVersionString"" : ""3.9.11, (c) 2001-2021 Python Software Foundation."",
    ""CFBundleIdentifier"" : ""org.python.python"",
    ""size"" : 2527232,
    ""uuid"" : ""ef9cc1f4-5991-3213-9a9e-e68c578b6c1b"",
    ""path"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python"",
    ""name"" : ""Python"",
    ""CFBundleVersion"" : ""3.9.11""
  },
  {
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    ""arch"" : ""x86_64"",
    ""base"" : 4528877568,
    ""CFBundleShortVersionString"" : ""1.4.0"",
    ""CFBundleIdentifier"" : ""edu.ucsf.cgl.ChimeraX"",
    ""size"" : 4096,
    ""uuid"" : ""9596eff5-d2be-396c-9c4e-6177235c3dae"",
    ""path"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX"",
    ""name"" : ""ChimeraX"",
    ""CFBundleVersion"" : ""1.4.0.0""
  },
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    ""size"" : 442368,
    ""uuid"" : ""b70ce1ec-b902-3852-8268-05de00bfa8d5"",
    ""path"" : ""\/usr\/lib\/dyld"",
    ""name"" : ""dyld""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 5151870976,
    ""size"" : 165068800,
    ""uuid"" : ""c9795830-14cd-3b40-983d-a3143cd9cbd9"",
    ""path"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore"",
    ""name"" : ""QtWebEngineCore""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 4616671232,
    ""size"" : 8192,
    ""uuid"" : ""1eae6074-8612-3bc6-b16b-c173a995e90c"",
    ""path"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/_queue.cpython-39-darwin.so"",
    ""name"" : ""_queue.cpython-39-darwin.so""
  },
  {
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    ""arch"" : ""x86_64"",
    ""base"" : 4531412992,
    ""size"" : 20480,
    ""uuid"" : ""2f042ce6-bef0-3ad9-97f5-2da7655122a4"",
    ""path"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/select.cpython-39-darwin.so"",
    ""name"" : ""select.cpython-39-darwin.so""
  },
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    ""size"" : 63488000,
    ""uuid"" : ""10431d8f-5e3b-3bbc-abd5-81f6a73a5269"",
    ""path"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib"",
    ""name"" : ""libopenblas64_.0.dylib""
  }
],
  ""sharedCache"" : {
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  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=6.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=6.1G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework              1152K        9 \nActivity Tracing                   256K        1 \nCG backing stores                 18.9M       11 \nCG image                          1128K      101 \nColorSync                          236K       28 \nCoreAnimation                     3472K      208 \nCoreGraphics                        16K        3 \nCoreImage                           40K       10 \nCoreServices                       624K        2 \nCoreUI image data                 5360K       61 \nFoundation                          40K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             5.1G     2284 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            256K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        16K        3 \nObjC additional data                15K        1 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        200K       50 \nStack                            485.9M       51 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      241.7M      278 \nVM_ALLOCATE (reserved)           128.0M        1         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            57.5M      693 \n__DATA_CONST                      33.1M      355 \n__DATA_DIRTY                      1659K      217 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       678.7M      150 \n__TEXT                           825.9M      688 \n__UNICODE                          592K        1 \ndyld private memory               1184K        3 \nmapped file                      562.5M       94 \nshared memory                     2996K       32 \n===========                     =======  ======= \nTOTAL                              8.3G     5356 \nTOTAL, minus reserved VM space     8.0G     5356 \n"",
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===== Log before crash start =====
Startup Messages  
---  
warning | No presets found in custom preset folder
/Users/ich/Charisma/S-PRED/ep2_ab  
  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/ich/Downloads/7cx2.pdb format pdb

No such file/path: /Users/ich/Downloads/7cx2.pdb  

> open /Users/ich/Charisma/S-PRED/ep2_ab/ep2_alphafold.pdb
> /Users/ich/Charisma/S-PRED/ep2_ab/ep2_blast.pdb
> /Users/ich/Charisma/S-PRED/ep2_ab/ep2_7cx2.pdb format pdb

Chain information for ep2_alphafold.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for ep2_blast.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for ep2_7cx2.pdb #3  
---  
Chain | Description  
R | No description available  
  

> set bgColor white

> hide #!3 models

> hide #2 models

> color #1 ocean

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

> color name

Missing or invalid ""name"" argument: Expected a text string  

> name frozen af #1

> select af

5630 atoms, 5688 bonds, 358 residues, 1 model selected  

> color sel #0066cc

> view

> 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 cornflowerblue

> ligth soft

Unknown command: ligth soft  

> lighting soft

> select clear

> graphics silhouettes true

> lighting soft

> graphics silhouettes true width 1

> surface af

> color af cornflowerblue

> transparency 95 target s

> show ions : graphics silhouettes grey true width 1

Expected true or false or a keyword  

> graphics silhouettes true width 1 color grey

> open
> /Users/ich/Charisma/S-PRED/ep2_ab/7cx2_rabgn_ab0_method3/7cx2_rabgn_ab0_55e8a_unrelaxed_rank_1_model_4.pdb

Chain information for 7cx2_rabgn_ab0_55e8a_unrelaxed_rank_1_model_4.pdb #4  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> hide #!1 models

> view

> select #4/F:1-128

973 atoms, 993 bonds, 128 residues, 1 model selected  

> select #4/F:1-128

973 atoms, 993 bonds, 128 residues, 1 model selected  

> select #4/E:1-71

547 atoms, 555 bonds, 71 residues, 1 model selected  

> select #4/D:1-358

2762 atoms, 2817 bonds, 358 residues, 1 model selected  

> select #4/C:1-394

3210 atoms, 3272 bonds, 394 residues, 1 model selected  

> select #4/B:1-505

3806 atoms, 3885 bonds, 505 residues, 1 model selected  

> delete #4 /c/d/e/f

> view

> show sel target c

> hide sel target a

> color sel maroon

> view

Alignment identifier is 4/B  

> select #4/B:1

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:1-117

900 atoms, 920 bonds, 117 residues, 1 model selected  

> select ~sel

13350 atoms, 13573 bonds, 2 pseudobonds, 1370 residues, 5 models selected  

> delete sel

> select clear

Drag select of 117 residues  

> view

> rename #4 ab0

> open
> /Users/ich/Charisma/S-PRED/ep2_ab/7cx2_rabgn_ab1_method3/7cx2_rabgn_ab1_fe4cf_unrelaxed_rank_1_model_2.pdb

Chain information for 7cx2_rabgn_ab1_fe4cf_unrelaxed_rank_1_model_2.pdb #1  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> rename #1 ab1

> rename #1 #2

No name or id option specified for renaming  

> rename #1 id #2

> rename #4 id #1

> hide #1 models

> select add #1

900 atoms, 920 bonds, 117 residues, 1 model selected  

> select subtract #1

Nothing selected  

> delete #2 /c/d/e/f

Alignment identifier is 2/B  
Alignment identifier is 1/B  

> select #2/B:115

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

> select #2/B:115-502

2906 atoms, 2964 bonds, 388 residues, 1 model selected  

> delete sel

Drag select of 846 atoms  

> view

> show sel target c

> hide sel target a

> color #2 #005493 transparency 0

> show #1 models

> open
> /Users/ich/Charisma/S-PRED/ep2_ab/7cx2_rabgn_ab2_method3/7cx2_rabgn_ab2_0feb1_unrelaxed_rank_1_model_4.pdb

Chain information for 7cx2_rabgn_ab2_0feb1_unrelaxed_rank_1_model_4.pdb #3  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> color #3 #941751 transparency 0

> rename #3 ab3

> delete #3 /c/d/e/f

Alignment identifier is 2/B  

> select add #3

4697 atoms, 3936 bonds, 626 residues, 2 models selected  

> select add #2

4697 atoms, 4800 bonds, 626 residues, 2 models selected  

> select subtract #2

3851 atoms, 3936 bonds, 512 residues, 1 model selected  
Alignment identifier is 3/B  

> select #3/B:125

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

> select #3/B:125-512

2906 atoms, 2964 bonds, 388 residues, 1 model selected  

> delete sel

Drag select of 945 atoms  

> show sel target c

> hide sel target a

> select add #3

945 atoms, 971 bonds, 124 residues, 1 model selected  

> select subtract #3

Nothing selected  

> open
> /Users/ich/Charisma/S-PRED/ep2_ab/7cx2_rabgn_ab3_method3/7cx2_rabgn_ab3_5df0d_unrelaxed_rank_1_model_2.pdb

Chain information for 7cx2_rabgn_ab3_5df0d_unrelaxed_rank_1_model_2.pdb #4  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> hide #3 models

> hide #2 models

> hide #1 models

> delete #4 /c/d/e/f

> color #4 #008f00 transparency 0

> color #4 #009051 transparency 0

Alignment identifier is 2/B  
Alignment identifier is 1/B  
Alignment identifier is 3/B  
Alignment identifier is 4/B  

> select #4/B:128

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

> select #4/B:128-270

963 atoms, 978 bonds, 143 residues, 1 model selected  

> select #4/B:128-515

2906 atoms, 2964 bonds, 388 residues, 1 model selected  

> delete sel

Drag select of 963 atoms  

> view

> show sel target c

> hide sel target a

> rename #4 ab4

> open
> /Users/ich/Charisma/S-PRED/ep2_ab/7cx2_rabgn_ab4_method3/7cx2_rabgn_ab3_c9300_unrelaxed_rank_1_model_4.pdb

Chain information for 7cx2_rabgn_ab3_c9300_unrelaxed_rank_1_model_4.pdb #5  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> select add #4

963 atoms, 985 bonds, 127 residues, 1 model selected  

> select subtract #4

Nothing selected  

> hide #4 models

> color #5 #945200 transparency 0

> delete #5 /c/d/e/f

> select add #5

3786 atoms, 3866 bonds, 505 residues, 1 model selected  
Alignment identifier is 5/B  

> select #5/B:118

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

> select #5/B:118-505

2906 atoms, 2964 bonds, 388 residues, 1 model selected  

> delete sel

> select add #5

880 atoms, 901 bonds, 117 residues, 1 model selected  

> view

> show sel target c

> hide sel target a

> mmaker #2-5 to 1

> matchmaker #2-5 to 1

Invalid ""to"" argument: invalid atoms specifier  

> mmaker #2-5 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 ab0, chain B (#1) with ab1, chain B (#2), sequence alignment score
= 1881.4  
RMSD between 104 pruned atom pairs is 0.429 angstroms; (across all 113 pairs:
2.078)  
  
Matchmaker ab0, chain B (#1) with ab3, chain B (#3), sequence alignment score
= 1911.2  
RMSD between 109 pruned atom pairs is 0.429 angstroms; (across all 117 pairs:
1.746)  
  
Matchmaker ab0, chain B (#1) with ab4, chain B (#4), sequence alignment score
= 1913.2  
RMSD between 113 pruned atom pairs is 0.325 angstroms; (across all 117 pairs:
1.541)  
  
Matchmaker ab0, chain B (#1) with
7cx2_rabgn_ab3_c9300_unrelaxed_rank_1_model_4.pdb, chain B (#5), sequence
alignment score = 1930  
RMSD between 111 pruned atom pairs is 0.454 angstroms; (across all 117 pairs:
1.369)  
  

> view

> show #4 models

> show #3 models

> show #2 models

> show #1 models

> select clear

> pwd

Current working directory is: /Users/ich/Desktop  

> chdir ~/Charisma/S-PRED/ep2_ab/

Unknown command: chdir ~/Charisma/S-PRED/ep2_ab/  

> cd /Users/ich/Charisma/S-PRED/ep2_ab/

Current working directory is: /Users/ich/Charisma/S-PRED/ep2_ab  

> save ab_af.cxs

> save ab_af.png

> rename #5 ab5

> save ab_af.cxs

> hide #5 models

> hide #3 models

> hide #2 models

> hide #1 models

> surface #4

> color #4 #009051 transparency 0

> transparency 95 target s

> lighting soft

> graphics sillhouettes true color gre width 1

Expected a keyword  

> graphics silhouettes true color grey width 1

> save ab_af.cxs

> rename #3 ab2

> rename #4 ab3

> rename #5 ab4

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #3 models

> show #5 models

> show #2 models

> show #1 models

Populating font family aliases took 373 ms. Replace uses of missing font
family "".AppleSystemUIFont"" with one that exists to avoid this cost.  

> save /Users/ich/Charisma/S-PRED/ep2_ab/ab0.pdb models #1

> save ab1.pdb models #2

> save ab2.pdb models #3

> save ab3.pdb models #4

> save ab4.pdb models #5

> mmaker

> matchmaker

Missing or invalid ""matchAtoms"" argument: empty atom specifier  

> save ab_af.cxs

> close #1-3,5#4

> set silhouettes true

> open ltag

'ltag' has no suffix  

> open 1tag

Summary of feedback from opening 1tag fetched from pdb  
---  
warnings | Unknown polymer entity '3' near line 3513  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
1tag title:  
Structural determinants for activation of the α-subunit of A heterotrimeric G
protein [more info...]  
  
Chain information for 1tag #1  
---  
Chain | Description | UniProt  
A | transducin-α | GNAT1_BOVIN  
  
Non-standard residues in 1tag #1  
---  
MG — magnesium ion  
  

> open 1tnd

Summary of feedback from opening 1tnd fetched from pdb  
---  
notes | Fetching compressed mmCIF 1tnd from
http://files.rcsb.org/download/1tnd.cif  
Fetching CCD CAC from http://ligand-expo.rcsb.org/reports/C/CAC/CAC.cif  
Fetching CCD GSP from http://ligand-expo.rcsb.org/reports/G/GSP/GSP.cif  
  
1tnd title:  
The 2.2 angstroms crystal structure of transducin-α complexed with GTP γ S
[more info...]  
  
Chain information for 1tnd #2  
---  
Chain | Description | UniProt  
A B C | transducin | GNAT1_BOVIN  
  
Non-standard residues in 1tnd #2  
---  
CAC — cacodylate ion (dimethylarsinate)  
GSP — 5'-guanosine-diphosphate-monothiophosphate  
MG — magnesium ion  
  
1tnd mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
  

> delete ~/a

> hide

> show

> hide

> mmaker #2 to #1 compute f

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 1tag, chain A (#1) with 1tnd, chain A (#2), sequence alignment
score = 1667.6  
RMSD between 290 pruned atom pairs is 0.544 angstroms; (across all 314 pairs:
1.253)  
  

> view

> cartoon style model tube side 24

Expected an atoms specifier or a keyword  

> cartoon style modeHelix tube sides 24

> transparency (protein & ~:173-182,196-211,228-237) 100 target c

> hide (#1 & protein & ~:173-182,196-211,228-237) cartoons

> show #2 & ligand

> style ligand sphere

Changed 60 atom styles  

> 2dlabels text ""Switch 1"" xpos .05 ypos .38

> 2dlabels text ""Switch 2"" xpos .22 ypos .07

> 2dlabels text ""Switch 3"" xpos .65 ypos .48

> 2dlabels text GDP-bound color tan xpos .73 ypos .08

> 2dlabels text GTP-bound color deepskyblue xpos .73 ypos .04

> 2dlabels text ""Transducin α-Subunit"" xpos .04 ypos .93 size 30

> windowsize 600 800

> ui mousemode right ""move label""

> 2dlabels #3.1 xpos 0.238 ypos 0.339

> 2dlabels #3.2 xpos 0.327 ypos 0.052

> 2dlabels #3.3 xpos 0.574 ypos 0.458

> 2dlabels #3.6 xpos 0.237 ypos 0.943

> 2dlabels #3.4 xpos 0.668 ypos 0.110

> 2dlabels #3.5 xpos 0.670 ypos 0.068

> close #1-3

> open 5vms

Summary of feedback from opening 5vms fetched from pdb  
---  
notes | Fetching compressed mmCIF 5vms from
http://files.rcsb.org/download/5vms.cif  
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif  
  
5vms title:  
CryoEM structure of Xenopus KCNQ1 channel [more info...]  
  
Chain information for 5vms #1  
---  
Chain | Description | UniProt  
A | Potassium voltage-gated channel subfamily KQT member 1 | KCNQ1_XENLA  
B | Calmodulin | CALM_HUMAN  
  
Non-standard residues in 5vms #1  
---  
CA — calcium ion  
  
5vms mmCIF Assemblies  
---  
1| complete point assembly  
2| point asymmetric unit  
3| point asymmetric unit, std point frame  
  

> view

> sym #1 assembly 1 copies true

> close #1

> view

> zomm 1.1; turn x180

Unknown command: zomm 1.1; turn x180  

> zoom 1.1

> turn x180

Expected an axis vector or a keyword  

> zoom 1.1

> turn x 180

Fetching compressed palette paste12-4 from
http://www.colourlovers.com/api/palettes?keywords=paste12-4&format=json&numResults=100  
Could not find palette paste12-4 at COLOURlovers.com using keyword search  

> rainbow #2 structures palette pastel2-4

> surface /a

> color fromatoms target s

> hide /a target ac

> hide /b

> show Ca

> color modify /b whiteness -50

> color modify /b blackness -50

> color modify /b whiteness -50

> cartoon style modeHelix tube sides 20

> lighting gentle

> set silhouettes true

> set silhouettes depth 0.02

Invalid ""silhouettes"" argument: Expected true or false (or 1 or 0)  

> set sildepth 0.02

Expected a keyword  

> set silhouetteDepthJump 0.02

> size ions atomRadius 1.6

Changed 12 atom radii  

> color modify ions hue +45

> close

> open 1eys

Summary of feedback from opening 1eys fetched from pdb  
---  
notes | Fetching compressed mmCIF 1eys from
http://files.rcsb.org/download/1eys.cif  
Fetching CCD HEM from http://ligand-expo.rcsb.org/reports/H/HEM/HEM.cif  
Fetching CCD BGL from http://ligand-expo.rcsb.org/reports/B/BGL/BGL.cif  
Fetching CCD BCL from http://ligand-expo.rcsb.org/reports/B/BCL/BCL.cif  
Fetching CCD BPH from http://ligand-expo.rcsb.org/reports/B/BPH/BPH.cif  
Fetching CCD LDA from http://ligand-expo.rcsb.org/reports/L/LDA/LDA.cif  
Fetching CCD FE from http://ligand-expo.rcsb.org/reports/F/FE/FE.cif  
Fetching CCD MQ8 from http://ligand-expo.rcsb.org/reports/M/MQ8/MQ8.cif  
Fetching CCD CRT from http://ligand-expo.rcsb.org/reports/C/CRT/CRT.cif  
Fetching CCD PEF from http://ligand-expo.rcsb.org/reports/P/PEF/PEF.cif  
  
1eys title:  
Crystal structure of photosynthetic reaction center from A thermophilic
bacterium, thermochromatium tepidum [more info...]  
  
Chain information for 1eys #1  
---  
Chain | Description | UniProt  
C | photosynthetic reaction center |  
H | photosynthetic reaction center | Q93RD8_THETI  
L | photosynthetic reaction center |  
M | photosynthetic reaction center |  
  
Non-standard residues in 1eys #1  
---  
BCL — bacteriochlorophyll A  
BGL — 2-O-octyl-beta-D-glucopyranose  
BPH — bacteriopheophytin A  
CRT — spirilloxanthin (rhodoviolascin)  
FE — Fe (III) ion  
HEM — protoporphyrin IX containing Fe (HEME)  
LDA — lauryl dimethylamine-N-oxide  
MQ8 — menaquinone 8 (2-methyl-3-(3,7,11,15,19,23,27,31-octamethyl-
dotriaconta-2,6,10,14,18,22,26,30-octaenyl)-[1,4]napthoquinone)  
PEF — di-palmitoyl-3-Sn-phosphatidylethanolamine
(3-[aminoethylphosphoryl]-[1,2-di-palmitoyl]-Sn-glycerol)  
  

> view

> zoom 1.1

> turn x180

Expected an axis vector or a keyword  

> turn x 180

> ui mousemode right zoom

> hide

> cartoon style #1 modeHelix tube sides 24

> rainbow #1 structures palette pastel2-4

> rainbow #1 chains palette pastel2-4

> close

> open /Users/ich/Downloads/prc.cxs

restore_snapshot for ""Labels"" returned None  

opened ChimeraX session  

> view

> select ligand

835 atoms, 879 bonds, 20 residues, 1 model selected  

> select clear

> select /?:4567@O

1 atom, 1 residue, 1 model selected  

> select /?:4320@O

1 atom, 1 residue, 1 model selected  

> select /M:82

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /?:4650@O

1 atom, 1 residue, 1 model selected  

> select clear

> clip

> clip off

> close #1

> clsoe

Unknown command: clsoe  

> close

> open 6 ddf

'6' has no suffix  

> open 6ddf

Summary of feedback from opening 6ddf fetched from pdb  
---  
notes | Fetching compressed mmCIF 6ddf from
http://files.rcsb.org/download/6ddf.cif  
Fetching CCD DAL from http://ligand-expo.rcsb.org/reports/D/DAL/DAL.cif  
Fetching CCD MEA from http://ligand-expo.rcsb.org/reports/M/MEA/MEA.cif  
Fetching CCD ETA from http://ligand-expo.rcsb.org/reports/E/ETA/ETA.cif  
  
6ddf title:  
μ Opioid Receptor-Gi Protein Complex [more info...]  
  
Chain information for 6ddf #1  
---  
Chain | Description | UniProt  
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_HUMAN  
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_HUMAN  
D | DAMGO |  
R | Mu-type opioid receptor | OPRM_MOUSE  
  
Non-standard residues in 6ddf #1  
---  
ETA — ethanolamine  
  

> set bgColor white

> close

> open 4n6h

Summary of feedback from opening 4n6h fetched from pdb  
---  
notes | Fetching compressed mmCIF 4n6h from
http://files.rcsb.org/download/4n6h.cif  
Fetching CCD OLA from http://ligand-expo.rcsb.org/reports/O/OLA/OLA.cif  
Fetching CCD OLC from http://ligand-expo.rcsb.org/reports/O/OLC/OLC.cif  
Fetching CCD PGE from http://ligand-expo.rcsb.org/reports/P/PGE/PGE.cif  
Fetching CCD TLA from http://ligand-expo.rcsb.org/reports/T/TLA/TLA.cif  
Fetching CCD EJ4 from http://ligand-expo.rcsb.org/reports/E/EJ4/EJ4.cif  
  
4n6h title:  
1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target)
[more info...]  
  
Chain information for 4n6h #1  
---  
Chain | Description | UniProt  
A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein |
OPRD_HUMAN  
  
Non-standard residues in 4n6h #1  
---  
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)  
NA — sodium ion  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
PGE — triethylene glycol  
TLA — L(+)-tartaric acid  
  

> surface

> mlp

Map values for surface ""4n6h_A SES surface"": minimum -26.77, mean -0.8566,
maximum 23.81  

> lighting soft

> lighting simple

> hide surfaces

> delete :1002-1106

> hbonds

582 hydrogen bonds found  

> hbonds :ej4

10 hydrogen bonds found  

> :ej4

Unknown command: :ej4  

> view:ej4

Unknown command: view:ej4  

> view :ej4

> clip

> color :ej4 orange

> color byhetero

> hide cartoons

> clip off

> hide cartoons

> hide atoms

> show :ej4 : view

> addh

Summary of feedback from adding hydrogens to 4n6h #1  
---  
warnings | Not adding hydrogens to /A ARG 41 CD because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A VAL 154 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LEU 157 CG because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 166 CE because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 192 CD because it is missing heavy-atom bond
partners  
10 messages similar to the above omitted  
notes | Termini for 4n6h (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLY 36  
Chain-final residues that are actual C termini: /A GLY 338  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A GLY 338  
581 hydrogen bonds  
Adding 'H' to /A GLY 36  
3076 hydrogens added  
  

> open 4n6h fromDatabase eds

Summary of feedback from opening 4n6h fetched from eds  
---  
note | Fetching map 4n6h from
http://www.ebi.ac.uk/pdbe/coordinates/files/4n6h.ccp4  
  
Opened eds 4n6h as #2, grid size 114,100,190, pixel 0.599,0.607,0.603, shown
at level 0.799, step 1, values float32  

> hide #!1 models

> show #!1 models

> set bgColor black

> clip

> clip off

> volume zone #2 nearAtoms :ej4 range 6 newMap false

> delete H

> volume #2 style image region all imageMode ""tilted slab"" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 67.28 tiltedSlabSpacing 0.5988 tiltedSlabPlaneCount
> 10

> mousemode rightMode ""rotate slab""

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

> mousemode rightMode ""move planes""

> volume #2 orthoplanes xyz positionPlanes 57,50,95 style image region all

> mousemode rightMode ""move planes""

> volume #2 orthoplanes xyz positionPlanes 57,50,95 style image region all

> mousemode rightMode ""move planes""

> volume showOutlineBox false

> volume showOutlineBox true

> volume showOutlineBox false

> volume showOutlineBox true

> undo

> close

> open 4n6h

4n6h title:  
1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target)
[more info...]  
  
Chain information for 4n6h #1  
---  
Chain | Description | UniProt  
A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein |
OPRD_HUMAN  
  
Non-standard residues in 4n6h #1  
---  
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)  
NA — sodium ion  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
PGE — triethylene glycol  
TLA — L(+)-tartaric acid  
  

> surface

> mlp

Map values for surface ""4n6h_A SES surface"": minimum -26.77, mean -0.8566,
maximum 23.81  

> hide surfaces

> hide

> delete :1002-1106

> hbonds :ej4

10 hydrogen bonds found  

> show

> close

> open 4n6h

4n6h title:  
1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target)
[more info...]  
  
Chain information for 4n6h #1  
---  
Chain | Description | UniProt  
A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein |
OPRD_HUMAN  
  
Non-standard residues in 4n6h #1  
---  
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)  
NA — sodium ion  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
PGE — triethylene glycol  
TLA — L(+)-tartaric acid  
  

> surface

> mlp

Map values for surface ""4n6h_A SES surface"": minimum -26.77, mean -0.8566,
maximum 23.81  

> hide surfaces

> lighting gentle

> show surfaces

> hide surfaces

> lighting simple

> delete :1002-1106

> hbonds

582 hydrogen bonds found  

> hbonds :ej4

10 hydrogen bonds found  

> view side

Expected an objects specifier or a view name or a keyword  

> ui tool show ""Side View""

> sideview

Unknown command: sideview  

> view :ej4

> clip

> clip front 0 position :ej4

> ui mousemode right clip

> view ligand

> ui mousemode right zoom

> color :ej4 orange

> color byhetero

> hide cartoons

> clip off

> hide atoms

> show :ej4 : addh sel

Summary of feedback from adding hydrogens to 4n6h #1  
---  
warnings | Not adding hydrogens to /A ARG 41 CD because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A VAL 154 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LEU 157 CG because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 166 CE because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 192 CD because it is missing heavy-atom bond
partners  
10 messages similar to the above omitted  
notes | Termini for 4n6h (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLY 36  
Chain-final residues that are actual C termini: /A GLY 338  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A GLY 338  
581 hydrogen bonds  
Adding 'H' to /A GLY 36  
3076 hydrogens added  
  

> select clear

> open 4n6h fromDatabase eds

Opened eds 4n6h as #2, grid size 114,100,190, pixel 0.599,0.607,0.603, shown
at level 0.799, step 1, values float32  

> volume none #2 near :ej4 range 6 newmap false

Expected a density maps specifier or a keyword  

> volume zone #2 nearAtoms :ej4 range 6 newMap false

> delete h

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

> delete H

> view

> ui tool show ""Side View""

> clip off

> volume level .5

> ui mousemode right select

> ui mousemode right zoom

> select /A:132@CA

1 atom, 1 residue, 1 model selected  

> select /A:132@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select /A:132@C

1 atom, 1 residue, 1 model selected  

> select /A:132@CA

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 2 models selected  

> select /A:129@CB

1 atom, 1 residue, 1 model selected  

> close #2

Window position QRect(0,1145 575x178) outside any known screen, using primary
screen  

> style :ej4 sphere

Changed 31 atom styles  

> surface :ej4 : transparency 50


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

Log:
Startup Messages  
---  
warning | No presets found in custom preset folder
/Users/ich/Charisma/S-PRED/ep2_ab  
  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/ich/Downloads/7cx2_rabgn_ab0_8d82b.result/7cx2_rabgn_ab0_8d82b_unrelaxed_rank_3_model_1.pdb
> format pdb

No such file/path:
/Users/ich/Downloads/7cx2_rabgn_ab0_8d82b.result/7cx2_rabgn_ab0_8d82b_unrelaxed_rank_3_model_1.pdb  




OpenGL version: 4.1 ATI-4.8.54
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0)
      OS Loader Version: 540.120.3~6

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 1 minute

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        LG HDR WQHD:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 100.00Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: 111NTJJ17772
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.1
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

}}}
"	defect	feedback	normal		Window Toolkit				Tom Goddard				all	ChimeraX