id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15360	Problems with the display of cyclic peptides	srettie@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-12.0.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
When drawing cartoon for a cyclic peptide the ""termini"" are drawn incorrectly. According to an earlier ticket this is a known issue. Is there any chance this could be fixed? We are submitting a paper where we are using Chimera for all figures and while using the shape tube option works well for peptides without secondary structure it becomes a bit unwieldy if there is a helix or sheet portion. 
Thank you very much.

Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/stephenrettie/Desktop/mcb_d2_alignzoom.cxs

Log from Thu May 16 12:45:06 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/stephenrettie/Desktop/mcl1_align.cxs

Log from Fri May 3 14:10:47 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/stephenrettie/Desktop/mcl1_surface.cxs

Log from Fri May 3 13:53:46 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/stephenrettie/Desktop/MCB_D2_figures_fixed_termini.cxs

Log from Tue Apr 30 14:54:36 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/stephenrettie/Downloads/MCB_D2_figures_sidechains.cxs

Log from Fri Apr 26 16:37:40 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/gauravbhardwaj/MCB_D2_figures.cxs

Log from Fri Apr 26 16:32:15 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/gauravbhardwaj/Downloads/MCB_D2_AF2.pdb

Chain information for MCB_D2_AF2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open ""/Users/gauravbhardwaj/Downloads/MCL1_2_refine_016 (1).pdb""

Chain information for MCL1_2_refine_016 (1).pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> 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 MCB_D2_AF2.pdb, chain A (#1) with MCL1_2_refine_016 (1).pdb, chain
A (#2), sequence alignment score = 784.7  
RMSD between 145 pruned atom pairs is 0.570 angstroms; (across all 149 pairs:
0.724)  
  

> set bgColor white

> lighting soft

> graphics silhouettes true width 5

> color /A rgn(200,200,200)

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

> color /A rgb(200,200,200)

> hide #2 models

> show #2 models

> bond /B:1@N/B:16@C reasonable false

Created 1 bond  

> cartoon /B suppressBackboneDisplay false

> show /B:1@N,CA/B:16@CA,C bonds

> size stickRadius 0.3

Changed 2701 bond radii  

> hide #2 models

> show #2 models

> hide #1 models

> show #2/B:1@N,CA/#2B:16@CA,C bonds

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

> bond #2/B:1@N#2/B:16@C reasonable false

Must specify two or more atoms  

> bond #2/B:152@N#2/B:167@C reasonable false

Created 0 bonds  

> show /B:152@N,CA/B:1667@CA,C bonds

> show /B:152@N,CA/B:167@CA,C bonds

> artoon style width 2 thick 0.6

Unknown command: artoon style width 2 thick 0.6  

> cartoon tether /B shape cone sides 4 scale 0 opacity 0

[Repeated 1 time(s)]

> cartoon style width 2 thickness 0.6

> color name coco_red rgb(255,0,0)

Color 'coco_red' is opaque: rgb(100%, 0%, 0%) hex: #ff0000

  

> color name coco_blue rgb(0,157,246)

Color 'coco_blue' is opaque: rgb(0%, 61.6%, 96.5%) hex: #009df6

  

> color name coco_orange rgb(255,156,0)

Color 'coco_orange' is opaque: rgb(100%, 61.2%, 0%) hex: #ff9c00

  

> color name coco_magenta rgb(255,0,148)

Color 'coco_magenta' is opaque: rgb(100%, 0%, 58%) hex: #ff0094

  

> color name coco_magenta2 rgb(206,0,119)

Color 'coco_magenta2' is opaque: rgb(80.8%, 0%, 46.7%) hex: #ce0077

  

> color name xkcd_green rgb(21,176,26)

Color 'xkcd_green' is opaque: rgb(8.24%, 69%, 10.2%) hex: #15b01a

  

> color name xkcd_pink rgb(255,129,192)

Color 'xkcd_pink' is opaque: rgb(100%, 50.6%, 75.3%) hex: #ff81c0

  

> color name xkcd_violet rgb(154,14,234)

Color 'xkcd_violet' is opaque: rgb(60.4%, 5.49%, 91.8%) hex: #9a0eea

  

> color name xkcd_periwinkle rgb(142,130,254)

Color 'xkcd_periwinkle' is opaque: rgb(55.7%, 51%, 99.6%) hex: #8e82fe

  

> color name xkcd_gold rgb(219,180,12)

Color 'xkcd_gold' is opaque: rgb(85.9%, 70.6%, 4.71%) hex: #dbb40c

  

> color name xkcd_bluegreen rgb(19,126,109)

Color 'xkcd_bluegreen' is opaque: rgb(7.45%, 49.4%, 42.7%) hex: #137e6d

  

> color name xkcd_cerulean rgb(4,133,209)

Color 'xkcd_cerulean' is opaque: rgb(1.57%, 52.2%, 82%) hex: #0485d1

  

> color name xkcd_marigold rgb(252,192,6)

Color 'xkcd_marigold' is opaque: rgb(98.8%, 75.3%, 2.35%) hex: #fcc006

  

> color name tomato2 rgb(245,96,42)

Color 'tomato2' is opaque: rgb(96.1%, 37.6%, 16.5%) hex: #f5602a

  

> color name hblue rgb(54,175,178)

Color 'hblue' is opaque: rgb(21.2%, 68.6%, 69.8%) hex: #36afb2

  

> color name hgreen rgb(139,194,70)

Color 'hgreen' is opaque: rgb(54.5%, 76.1%, 27.5%) hex: #8bc246

  

> color name hblue2 rgb(83,155,186)

Color 'hblue2' is opaque: rgb(32.5%, 60.8%, 72.9%) hex: #539bba

  

> color name light_red rgb(249,128,111)

Color 'light_red' is opaque: rgb(97.6%, 50.2%, 43.5%) hex: #f9806f

  

> color name yelloworange rgb(250,181,96)

Color 'yelloworange' is opaque: rgb(98%, 71%, 37.6%) hex: #fab560

  

> color name brightyellow rgb(255,202,3)

Color 'brightyellow' is opaque: rgb(100%, 79.2%, 1.18%) hex: #ffca03

  

> color name new_gray rgb(200,200,200)

Color 'new_gray' is opaque: gray(78.4%) hex: #c8c8c8

  

> color #/B xkcd_marigold

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

> color #2/B xkcd_marigold

> color #1/B coco_blue

> show #1 models

> color #1/B cotnflower blue

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

> color #1/B cornflower blue

> color #1/B xkcd_cerulean

> hide #2/A cartoons

> save /Users/gauravbhardwaj/mcb_D2_model_xray_chimeraX.png supersample 10

> color #1/B xkcd_violet

> color #1/B xkcd_periwinkle

> color #1/B xkcd_violet

> color #1/B coco_blue

> color #1/B coco_orange

> color #1/B coco_blue

> color #2/B coco_oramge

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

> color #2/B coco_orange

> color #2/B xkcd_marigold

> color #2/B xkcd_violet

> color #1/B xkcd_violet

> save /Users/gauravbhardwaj/mcb_D2_model_xray_chimeraX.png supersample 10

> hide #2 models

> show #1/a surfaces

> show #1/b and sidechain bonds

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

> show #1/a & sidechain bonds

> show #1/a & sidechain atoms

> show #1/b & sidechain atoms

> show #1/b:2@N atoms

> color #1 byhetero

> color #1/b byhetero

> hide #1/a atoms

> hide #1/a bonds

> save /Users/gauravbhardwaj/mcb_D2_model_surface_chimeraX.png supersample 10

> save /Users/gauravbhardwaj/mcb_D2_model_surface_no_sticks_chimeraX.png
> supersample 10

> save /Users/gauravbhardwaj/MCB_D2_figures.cxs

——— End of log from Fri Apr 26 16:32:15 2024 ———

opened ChimeraX session  

> hide #1/a surfaces

> hide #1/a bonds

> hide #1/a stoms

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

> hide #1/a atoms

> show #2 models

> hide /b atoms

> show /b atoms

> show /b and sidechain atoms

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

> show /b & sidechain atoms

> show #1/b:2@N atoms

> show #2/b:153@N atoms

> color /b byhetero

> save /Users/gauravbhardwaj/MCB_D2_figures_sidechains.cxs

——— End of log from Fri Apr 26 16:37:40 2024 ———

opened ChimeraX session  

> select #1/B:1@CA

1 atom, 1 residue, 1 model selected  

> hide sel cartoons

> select #2/B:152

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

> hide sel cartoons

[Repeated 1 time(s)]

> select #1/B:16

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

> hide sel cartoons

> shape tube #2/B@ca radius 0.3

> hide #!1 target m

> hide #3 target m

> shape tube #2/B:152-162@ca radius 0.3

> close #4

> shape tube #2/B:162-152@ca radius 0.3

No atoms specified  

> shape tube #2/B:166-167@ca radius 0.3

> shape tube #2/B:162-167@ca radius 0.3

> close #4

> show sel cartoons

> select #5

1 model selected  

> show #3 target m

> close #3

> hide #5 target m

> select #2/B:166

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

> hide sel cartoons

> show #5 target m

> color tube gold

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

> color #3 gold

> color #5 gold

> select #2/B:165

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

> hide sel cartoons

> select #2/B:164

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

> hide sel cartoons

> select #2/B:163

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

> hide sel cartoons

> select #2/B:162

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

> hide sel cartoons

> show sel cartoons

> select clear

> select #5

1 model selected  

> color #5 rgb(219,180,12)

> select #2/B:157

14 atoms, 15 bonds, 1 residue, 1 model selected  

> color #5 rgb(252,192,6)

> select #5

1 model selected  

> hide #5 target m

> select #2/B:163@CA

1 atom, 1 residue, 1 model selected  

> show sel cartoons

> show #5 models

> hide #5 models

> select #2/B:164@CA

1 atom, 1 residue, 1 model selected  

> show sel cartoons

> show #5 models

> show #1/B:152@c

> hide #1/B:152@c

> show #2/B:152@c

> hide pseudobonds

> select #2/B:153

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

> hide sel cartoons

> show sel cartoons

> show #!1 models

> hide #!2 models

> hide #5 models

> shape tube #1/B:1-12@ca radius 0.3

> hide #5 models

> close #3

> shape tube #1/B:11-16@ca radius 0.3

> select #1/A:17

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

> select #1/B:1@CA

1 atom, 1 residue, 1 model selected  

> show sel cartoons

> hide sel cartoons

> show #1/B:1@c

> show #!2 models

> hide #!2 models

> color #3 rgb(154,14,234)

> save MCB_D2_figures_fixed_termini.csx

No known data format for file suffix '.csx'  

> save MCB_D2_figures_fixed_termini.cxs

——— End of log from Tue Apr 30 14:54:36 2024 ———

opened ChimeraX session  

> select #2/A

1202 atoms, 1222 bonds, 150 residues, 1 model selected  

> select #1/A

1217 atoms, 1237 bonds, 151 residues, 1 model selected  

> show sel surfaces

> hide #1/B:3 * sidechain

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

> hide #1/B:3 & sidechain

> show #1/B:3@ca

> hide #1/B:3@ca

> hide #1/B:9 & sidechain

> undo

> hide #1/B:9 & sidechain

> hide #1/B:5 & sidechain

> hide #1/B:14 & sidechain

> hide #1/B:15 & sidechain

> ~select

Nothing selected  

> hide #1/B:2 & sidechain

> show #1/B:2@ca

> select #1/B:2@N

1 atom, 1 residue, 1 model selected  

> select #1/B:2@N

1 atom, 1 residue, 1 model selected  

> select #1/B:2@N

1 atom, 1 residue, 1 model selected  

> color #1/B:2@n rgb(154,14,234)

> ~select

Nothing selected  

> save mcl1_surface.cxs

——— End of log from Fri May 3 13:53:46 2024 ———

opened ChimeraX session  

> save mcl1_surface.png supersample 20 transparentBackground true

> show #!2 models

> hide /B & sidechain

> color #1/B rgb(154,14,234)

> color #2/B rgb(252,192,6)

> show /B:2@ca

> hide #2/B:2@ca

> show /B:153@ca

> show /B:167@ca

> show /B:167@c

> show #5 models

> show #1/B:1@ca

> show #1/B:2@ca

> show #1/B:2@n

> show #1/B:16@c

[Repeated 1 time(s)]

> show #1/B:16@ca

> show #2/B:152@ca

> select /A

2419 atoms, 2459 bonds, 301 residues, 2 models selected  

> hide sel surfaces

> ~select

Nothing selected  

> save mcl1_align.cxs

——— End of log from Fri May 3 14:10:47 2024 ———

opened ChimeraX session  

> show cartoons #2/A

Expected ',' or a keyword  

> show #2/A cartoons

> hide #1/A cartoons

> save mcbd2_xtal_align.png supersample 20 transparentBackground true

[Repeated 1 time(s)]

> show /B sidechain

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

> show /B & sidechain

> hide pbonds

> color sidechain byhetero

> color /B:pro@n byhetero

> save mcbd2_xtal_align_zoom.png supersample 20 transparentBackground true

> save mcb_d2_alignzoom.cxs

——— End of log from Thu May 16 12:45:06 2024 ———

opened ChimeraX session  

> open
> /Users/stephenrettie/Downloads/fold_2024_05_31_16_16/fold_2024_05_31_16_16_model_0.cif

Chain information for fold_2024_05_31_16_16_model_0.cif #4  
---  
Chain | Description  
A | .  
B | .  
  




OpenGL version: 4.1 Metal - 76.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 7429.41.5
      OS Loader Version: 7429.41.5

Software:

    System Software Overview:

      System Version: macOS 12.0.1 (21A559)
      Kernel Version: Darwin 21.1.0
      Time since boot: 10 days 17:24

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        BenQ PD2700U:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 30.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    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: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    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: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
}}}
"	defect	closed	normal		Depiction		duplicate		Eric Pettersen				all	ChimeraX