id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
9893	Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics 645	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/aimeepickford/Desktop/152 mutation .cxs""

Log from Tue Oct 3 09:30:24 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/aimeepickford/Desktop/draft report full spike .cxs""

Log from Tue Oct 3 09:10:46 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/aimeepickford/Desktop/everything together w the 210 mt .cxs""
> format session

Log from Mon Oct 2 21:58:42 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/aimeepickford/Desktop/everything together .cxs""

Log from Mon Oct 2 16:41:54 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/aimeepickford/Desktop/THIS IS THE FIRST GOOD ONE .cxs"" format
> session

Log from Mon Oct 2 16:01:41 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/aimeepickford/Desktop/session 4 .cxs""

Log from Mon Oct 2 15:41:00 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/aimeepickford/Desktop/session 3.cxs""

Log from Mon Oct 2 15:22:51 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/aimeepickford/Desktop/session 2.cxs""

Log from Mon Oct 2 15:10:40 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/aimeepickford/Downloads/7wpa.pdb format pdb

7wpa.pdb title:  
Sars-cov-2 ο variant spike trimer complexed with ACE2 [more info...]  
  
Chain information for 7wpa.pdb #1  
---  
Chain | Description | UniProt  
A B C | spike glycoprotein | SPIKE_SARS2 1-1205  
D | angiotensin-converting enzyme 2 | ACE2_HUMAN 1-805  
  
Non-standard residues in 7wpa.pdb #1  
---  
CL — chloride ion  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
ZN — zinc ion  
  

> set bgColor white

> show surfaces

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> hide surfaces

> interfaces ~solvent

4 buried areas: B C 5847, A B 5699, A C 4985, A D 881  

> show surfaces

> hide surfaces

[Repeated 1 time(s)]

> show surfaces

> hide surfaces

> color bychain

> show surfaces

> select /D:593@CG2

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 2 models selected  

> select down

1 atom, 1 residue, 2 models selected  

> select down

1 atom, 1 residue, 2 models selected  

> save ""/Users/aimeepickford/Desktop/session 1 .cxs""

> color (#!1 & sel) lime

> undo

> color sel bychain

> color (#!1 & sel) cyan

> undo

> select /A:343@CG

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 2 models selected  

> select up

297 atoms, 306 bonds, 36 residues, 2 models selected  

> select up

3283 atoms, 3374 bonds, 416 residues, 2 models selected  

> select up

3311 atoms, 3400 bonds, 420 residues, 2 models selected  

> select down

3283 atoms, 3374 bonds, 416 residues, 2 models selected  

> select down

297 atoms, 306 bonds, 36 residues, 2 models selected  

> select up

3283 atoms, 3374 bonds, 416 residues, 2 models selected  

> select up

3311 atoms, 3400 bonds, 420 residues, 2 models selected  

> select up

4947 atoms, 5075 bonds, 626 residues, 2 models selected  

> select up

5017 atoms, 5145 bonds, 634 residues, 2 models selected  

> select up

7467 atoms, 7650 bonds, 951 residues, 2 models selected  

> select up

7563 atoms, 7749 bonds, 962 residues, 2 models selected  

> select up

7966 atoms, 8160 bonds, 1014 residues, 2 models selected  

> select up

7987 atoms, 8182 bonds, 1016 residues, 2 models selected  

> select up

8413 atoms, 8624 bonds, 1067 residues, 2 models selected  

> select down

7987 atoms, 8182 bonds, 1016 residues, 2 models selected  

> select down

7966 atoms, 8160 bonds, 1014 residues, 2 models selected  

> select down

7563 atoms, 7749 bonds, 962 residues, 2 models selected  

> select down

7467 atoms, 7650 bonds, 951 residues, 2 models selected  

> select down

5017 atoms, 5145 bonds, 634 residues, 2 models selected  

> select down

4947 atoms, 5075 bonds, 626 residues, 2 models selected  

> select down

3311 atoms, 3400 bonds, 420 residues, 2 models selected  

> select down

3283 atoms, 3374 bonds, 416 residues, 2 models selected  

> select down

297 atoms, 306 bonds, 36 residues, 2 models selected  

> select down

11 atoms, 10 bonds, 1 residue, 2 models selected  

> select up

297 atoms, 306 bonds, 36 residues, 2 models selected  

> select up

3283 atoms, 3374 bonds, 416 residues, 2 models selected  

> color (#!1 & sel) orange

> color (#!1 & sel) purple

> color (#!1 & sel) orange

> select clear

> select /A:483@CE2

1 atom, 1 residue, 1 model selected  
Alignment identifier is 1/A  

> select#1/B:152

Unknown command: select#1/B:152  

> select#1/B:40-400

Unknown command: select#1/B:40-400  

> select #1/B:40-400

2545 atoms, 2614 bonds, 4 pseudobonds, 312 residues, 2 models selected  

> select #1/B:152

11 atoms, 11 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) cyan

> undo

> select #1/A:152

11 atoms, 11 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) cyan

> select /A:531@CG2

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 2 models selected  

> select up

91 atoms, 91 bonds, 12 residues, 2 models selected  

> select up

3283 atoms, 3374 bonds, 416 residues, 2 models selected  

> select up

3311 atoms, 3400 bonds, 420 residues, 2 models selected  

> select up

4947 atoms, 5075 bonds, 626 residues, 2 models selected  

> select up

5017 atoms, 5145 bonds, 634 residues, 2 models selected  

> select up

7467 atoms, 7650 bonds, 951 residues, 2 models selected  

> select up

7563 atoms, 7749 bonds, 962 residues, 2 models selected  

> select up

7966 atoms, 8160 bonds, 1014 residues, 2 models selected  

> select up

7987 atoms, 8182 bonds, 1016 residues, 2 models selected  

> color (#!1 & sel) orange

> select up

8413 atoms, 8624 bonds, 1067 residues, 2 models selected  

> color (#!1 & sel) orange

> select up

30444 atoms, 31229 bonds, 3821 residues, 2 models selected  

> color (#!1 & sel) orange

> undo

> select clear

> select #1/A:152

11 atoms, 11 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) lime

> select #1/A:157

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

> color (#!1 & sel) lime

> select /A

8413 atoms, 8624 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> hide sel atoms

> hide #1/B-C

> hide #1/B,C

> hide #1/B

> hide sel atoms

> hide sel cartoons

[Repeated 1 time(s)]

> hide sel surfaces

> undo

[Repeated 1 time(s)]

> hide #1/B surfaces

> hide sel atoms

> hide #1/C surfaces

> hide

> Sel #1/B

Unknown command: Sel #1/B  

> Sel 1/B

Unknown command: Sel 1/B  

> select #1/B

8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> select #1/A

8413 atoms, 8624 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> show sel surfaces

> select #1/B

8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> cartoon hide (#!1 & sel)

> select #1/C

8381 atoms, 8585 bonds, 8 pseudobonds, 1063 residues, 2 models selected  

> cartoon hide (#!1 & sel)

> select #1/A:210

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

> color (#!1 & sel) lime

> select #1/A:257

Nothing selected  

> select #1/A:257

Nothing selected  

> select #1/A:257

Nothing selected  

> select #1/A:339

11 atoms, 11 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) lime

> select #1/A:446

12 atoms, 12 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) lime

> select #1/A:460

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

> color (#!1 & sel) lime

> select #1/A:460

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

> ui tool show Rotamers

[Repeated 1 time(s)]

> save ""/Users/aimeepickford/Desktop/session 2.cxs""

——— End of log from Mon Oct 2 15:10:40 2023 ———

opened ChimeraX session  

> select #1/A:460

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

> ui tool show Rotamers

> swapaa interactive sel LYS rotLib Dunbrack

/A PRO 460: phi -62.4, psi 149.8 trans  
Changed 438 bond radii  

> swapaa #!1/A:460 LYS criteria 1 rotLib Dunbrack

Using Dunbrack library  
7wpa.pdb #!1/A PRO 460: phi -62.4, psi 149.8 trans  
Applying LYS rotamer (chi angles: -67.1 -178.8 -179.7 179.2) to 7wpa.pdb #!1/A
LYS 460  

> color (#!1 & sel) lime

> show sel atoms

[Repeated 1 time(s)]

> style sel sphere

Changed 4 atom styles  

> hide sel surfaces

> style sel ball

Changed 4 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel atoms

> hide sel surfaces

> select #1/A

8415 atoms, 8625 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> show sel cartoons

> hide sel surfaces

> select #1/A:460

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

> color (#!1 & sel) yellow

> color (#!1 & sel) cyan

> select #1/A

8415 atoms, 8625 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> show sel cartoons

[Repeated 1 time(s)]

> show sel surfaces

[Repeated 1 time(s)]

> show sel cartoons

> show sel atoms

> select clear

> select #1/A

8415 atoms, 8625 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> show sel cartoons

> hide sel surfaces

> hide sel atoms

> show sel atoms

[Repeated 1 time(s)]

> show sel cartoons

> hide sel atoms

> show sel atoms

> hide sel cartoons

[Repeated 1 time(s)]

> show sel atoms

> hide sel atoms

> undo

> hide sel atoms

> show sel atoms

> show sel cartoons

> hide sel atoms

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

> show sel atoms

> select #1/A:446

12 atoms, 12 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) cyan

> ui tool show Rotamers

[Repeated 1 time(s)]

> swapaa interactive sel SER rotLib Dunbrack

/A TYR 446: phi -90.1, psi 15.1 trans  
Changed 9 bond radii  

> swapaa #!1/A:446 SER criteria 1 rotLib Dunbrack

Using Dunbrack library  
7wpa.pdb #!1/A TYR 446: phi -90.1, psi 15.1 trans  
Applying SER rotamer (chi angles: 62.6) to 7wpa.pdb #!1/A SER 446  

> select #1/A:339

11 atoms, 11 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) cyan

> ui tool show Rotamers

[Repeated 1 time(s)]

> swapaa interactive sel HIS rotLib Dunbrack

/A PHE 339: phi -78.6, psi -45.9 trans  
Changed 288 bond radii  

> swapaa #!1/A:339 HIS criteria 1 rotLib Dunbrack

Using Dunbrack library  
7wpa.pdb #!1/A PHE 339: phi -78.6, psi -45.9 trans  
Applying HIS rotamer (chi angles: -177.7 69.6) to 7wpa.pdb #!1/A HIS 339  

> select #1/A:257

Nothing selected  

> select #1/A:210

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

> color (#!1 & sel) cyan

> ui tool show Rotamers

> swapaa interactive sel VAL rotLib Dunbrack

/A PRO 210: phi -75.0, psi -169.9 trans  
Changed 12 bond radii  

> swapaa #!1/A:210 VAL criteria 1 rotLib Dunbrack

Using Dunbrack library  
7wpa.pdb #!1/A PRO 210: phi -75.0, psi -169.9 trans  
Applying VAL rotamer (chi angles: -60.8) to 7wpa.pdb #!1/A VAL 210  

> select #1/A:157

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

> color (#!1 & sel) cyan

> ui tool show Rotamers

> swapaa interactive sel LEU rotLib Dunbrack

/A SER 157: phi -138.3, psi 149.4 trans  
Changed 45 bond radii  

> swapaa #!1/A:157 LEU criteria 1 rotLib Dunbrack

Using Dunbrack library  
7wpa.pdb #!1/A SER 157: phi -138.3, psi 149.4 trans  
Applying LEU rotamer (chi angles: -63.7 170.4) to 7wpa.pdb #!1/A LEU 157  

> select #1/A:152

11 atoms, 11 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) cyan

> ui tool show Rotamers

> swapaa interactive sel ARG rotLib Dunbrack

/A PHE 152: phi -74.5, psi 77.5 trans  
Changed 600 bond radii  

> swapaa #!1/A:152 ARG criteria 1 rotLib Dunbrack

Using Dunbrack library  
7wpa.pdb #!1/A PHE 152: phi -74.5, psi 77.5 trans  
Applying ARG rotamer (chi angles: -65.6 179.9 -179.5 -179.9) to 7wpa.pdb #!1/A
ARG 152  

> save ""/Users/aimeepickford/Desktop/session 3.cxs""

——— End of log from Mon Oct 2 15:22:51 2023 ———

opened ChimeraX session  

> select #1/A:460

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

> color (#!1 & sel) red

> select #1/A:446

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

> color (#!1 & sel) red

> select #1/A:339

10 atoms, 10 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) red

> select #1/A:210

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

> color (#!1 & sel) red

> select #1/A:157

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

> color (#!1 & sel) red

> select #1/A:152

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) red

> select #1/A

8410 atoms, 8617 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> color (#!1 & sel) blue

> undo

> color (#!1 & sel) medium blue

> select #1/A:152

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) red

> select #1/A:157

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

> color (#!1 & sel) red

> select #1/A:210

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

> color (#!1 & sel) red

> select #1/A:257

Nothing selected  

> color red

> undo

> select #1/A:210

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

> color (#!1 & sel) red

> select #1/A:257

Nothing selected  

> color red

> undo

> select #1/A:339

10 atoms, 10 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) red

> select #1/A:446

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

> color (#!1 & sel) red

> select #1/A:460

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

> color (#!1 & sel) red

> save ""/Users/aimeepickford/Desktop/session 4 .cxs""

——— End of log from Mon Oct 2 15:41:00 2023 ———

opened ChimeraX session  

> select /D:573@CG1

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 2 models selected  

> select up

158 atoms, 160 bonds, 21 residues, 2 models selected  

> select up

4899 atoms, 5039 bonds, 598 residues, 2 models selected  

> hide sel surfaces

> select clear

> ui mousemode right distance

[Repeated 5 time(s)]

> select /D

4901 atoms, 5039 bonds, 600 residues, 1 model selected  

> select sel @< 5

4987 atoms, 5103 bonds, 621 residues, 1 model selected  

> color (#!1 & sel) purple

> undo

> select #1/A

8410 atoms, 8617 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> hide sel atoms

> select clear

> select #1/A:446

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

> show sel atoms

> select #1/A:460

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

> show sel atoms

> select #1/A:339

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:257

Nothing selected  

> select #1/A:210

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

> show sel atoms

> select #1/A:157

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

> show sel atoms

> select #1/A:152

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> save ""/Users/aimeepickford/Desktop/THIS IS THE FIRST GOOD ONE .cxs""

——— End of log from Mon Oct 2 16:01:41 2023 ———

opened ChimeraX session  

> transparency #1/B 50

> select #1/b

8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> show sel surfaces

> show sel cartoons

> hide sel surfaces

> transparency #1/B 50

> transparency #1/B 90

> transparency#1/B 90

Unknown command: transparency#1/B 90  

> transparency #1/B 90

> select clear

> select #1/B

8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> color (#!1 & sel) light gray

> transparency #1/B 50

> select #1/C

8381 atoms, 8585 bonds, 8 pseudobonds, 1063 residues, 2 models selected  

> show sel surfaces

> show sel cartoons

> hide sel surfaces

> transparency #1/C 90

> select clear

> save ""/Users/aimeepickford/Desktop/everything together .cxs""

——— End of log from Mon Oct 2 16:41:54 2023 ———

opened ChimeraX session  

> select #1/A:230-270

172 atoms, 175 bonds, 1 pseudobond, 20 residues, 2 models selected  

> color (#!1 & sel) red

> save ""/Users/aimeepickford/Desktop/everything together w the 210 mt .cxs""

——— End of log from Mon Oct 2 21:58:42 2023 ———

opened ChimeraX session  

> select clear

> save ""/Users/aimeepickford/Desktop/draft report full spike .cxs""

——— End of log from Tue Oct 3 09:10:46 2023 ———

opened ChimeraX session  

> select #1/B

8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> color (#!1 & sel) #f2aaffff

> select #1/D

4901 atoms, 5039 bonds, 600 residues, 1 model selected  

> select sel @< 5

4987 atoms, 5103 bonds, 621 residues, 1 model selected  

> color (#!1 & sel) orange

> select #1/A

8410 atoms, 8617 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> select clear

> save ""/Users/aimeepickford/Desktop/receptor interaction w A.cxs""

> select #1/D

4901 atoms, 5039 bonds, 600 residues, 1 model selected  

> hide sel cartoons

> select #1/152

Nothing selected  

> select #1/A:152

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

0 hydrogen bonds found  

> ui tool show ""Side View""

> select #1/C

8381 atoms, 8585 bonds, 8 pseudobonds, 1063 residues, 2 models selected  

> select #1/B

8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> select #1/B

8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected  

> select clear

> save ""/Users/aimeepickford/Desktop/152 mutation .cxs""

——— End of log from Tue Oct 3 09:30:24 2023 ———

opened ChimeraX session  




OpenGL version: 4.1 INTEL-20.2.50
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

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

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,3
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 1.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
      OS Loader Version: 564.40.4~66

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 17 days, 16 hours, 10 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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

}}}
"	defect	closed	normal		Graphics		nonchimerax						all	ChimeraX