id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15398	Crash destroying main window	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 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: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open ""/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh 7.1-AvrPikC.cxs""

Log from Sat Jun 8 15:14:22 2024UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh-AvrPikC_7a8x.pdb""

Pikh-AvrPikC_7a8x.pdb title:  
Complex of rice blast (magnaporthe oryzae) effector protein avr-pikc with the
hma domain of pikh-1 from rice (oryza sativa) [more info...]  
  
Chain information for Pikh-AvrPikC_7a8x.pdb #1  
---  
Chain | Description  
A B D E | NBS-LRR class disease resistance protein PIKH-1  
C F | avr-pik protein  
  

> ui tool show ""Show Sequence Viewer""

> sequence chain /A

Alignment identifier is 1/A  

> sequence chain /B

Alignment identifier is 1/B  

> sequence chain /C

Alignment identifier is 1/C  

> sequence chain /D

Alignment identifier is 1/D  

> sequence chain /E

Alignment identifier is 1/E  

> sequence chain /F

Alignment identifier is 1/F  

> select /E:186

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

> select /E:186-262

544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected  

> hide sel atoms

> select /B:186

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

> select /B:186-262

544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected  

> select /B:186

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

> select /B:186-262

544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected  

> hide sel atoms

> select /A:188-259

530 atoms, 531 bonds, 72 residues, 1 model selected  

> select /A:188-259

530 atoms, 531 bonds, 72 residues, 1 model selected  

> select /D:187-259

522 atoms, 522 bonds, 1 pseudobond, 71 residues, 2 models selected  

> select /A:188-259

530 atoms, 531 bonds, 72 residues, 1 model selected  

> select /F:32-113

668 atoms, 693 bonds, 82 residues, 1 model selected  

> select /C:33-112

651 atoms, 675 bonds, 80 residues, 1 model selected  

> select /F:32-113

668 atoms, 693 bonds, 82 residues, 1 model selected  

> select /A:188-259

530 atoms, 531 bonds, 72 residues, 1 model selected  

> select /C:33-112

651 atoms, 675 bonds, 80 residues, 1 model selected  

> select /F:32-113

668 atoms, 693 bonds, 82 residues, 1 model selected  

> select /A:188-259

530 atoms, 531 bonds, 72 residues, 1 model selected  

> select /D:187-259

522 atoms, 522 bonds, 1 pseudobond, 71 residues, 2 models selected  

> hide sel atoms

> select /A:188-259

530 atoms, 531 bonds, 72 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select /C:109-112

31 atoms, 31 bonds, 4 residues, 1 model selected  

> select /C:33-112

651 atoms, 675 bonds, 80 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show sel atoms

> show sel cartoons

> hide sel atoms

> select /F:60-113

431 atoms, 444 bonds, 54 residues, 1 model selected  

> select /F:32-113

668 atoms, 693 bonds, 82 residues, 1 model selected  

> show sel cartoons

> show sel cartoons

> hide sel atoms

> select /A:188-259

530 atoms, 531 bonds, 72 residues, 1 model selected  

> select /A:188-191

35 atoms, 34 bonds, 4 residues, 1 model selected  

> select /A:188-199

92 atoms, 91 bonds, 12 residues, 1 model selected  

> select /A:251-259

69 atoms, 68 bonds, 9 residues, 1 model selected  

> ui tool show ""Show Sequence Viewer""

> sequence chain /F

Alignment identifier is 1/F  

> sequence chain /A

Alignment identifier is 1/A  

> sequence chain /B

Alignment identifier is 1/B  

> sequence chain /C

Alignment identifier is 1/C  

> sequence chain /D

Alignment identifier is 1/D  

> sequence chain /E

Alignment identifier is 1/E  

> select /F:95

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

> select /F:32-95

528 atoms, 546 bonds, 64 residues, 1 model selected  

> select /B:186

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

> select /B:186-262

544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected  

> show sel atoms

> show sel cartoons

> hide sel atoms

> select /C:33-112

651 atoms, 675 bonds, 80 residues, 1 model selected  

> select /B:186

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

> select /B:186

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

> select /B:202-212,237-249

179 atoms, 178 bonds, 24 residues, 1 model selected  

> select /B:197

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

> select /B:186-197

91 atoms, 90 bonds, 12 residues, 1 model selected  

> select /B:186

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

> select /B:186-262

544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected  

> select /E:261

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

> select /E:261-262

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /E:186-262

544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected  

> select /E:186

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

> select /E:186-262

544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected  

> show sel cartoons

> select /D:187

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

> select /D:187-259

522 atoms, 522 bonds, 1 pseudobond, 71 residues, 2 models selected  

> show sel cartoons

> select /F:32-46

127 atoms, 129 bonds, 15 residues, 1 model selected  

> select /F:32-113

668 atoms, 693 bonds, 82 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> select /D:199

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

> select /D:197-199

21 atoms, 20 bonds, 3 residues, 1 model selected  

> select /D:197

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

> select /D:197-198

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /D:198-199

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /D:198-199

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /D:187-259

522 atoms, 522 bonds, 1 pseudobond, 71 residues, 2 models selected  

> hide sel cartoons

> select /A:188-259

530 atoms, 531 bonds, 72 residues, 1 model selected  

> select /F:35

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

> select /F:35-41

60 atoms, 60 bonds, 7 residues, 1 model selected  

> select /A:188-259

530 atoms, 531 bonds, 72 residues, 1 model selected  

> select /A:188-259

530 atoms, 531 bonds, 72 residues, 1 model selected  

> select /A:198

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

> select /A:198-199

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:188-259

530 atoms, 531 bonds, 72 residues, 1 model selected  

> hide sel cartoons

> select /B:196-197

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /B:195

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

> select /B:195-207

73 atoms, 71 bonds, 1 pseudobond, 10 residues, 2 models selected  

> select /E:195-196

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select /E:195-204

51 atoms, 49 bonds, 1 pseudobond, 7 residues, 2 models selected  

> select /E:202-212,237-249

179 atoms, 178 bonds, 24 residues, 1 model selected  

> select /E:189-195,216-222,228-233,252-259

210 atoms, 206 bonds, 28 residues, 1 model selected  

> select /E:195-204

51 atoms, 49 bonds, 1 pseudobond, 7 residues, 2 models selected  

> select /F:32-109

634 atoms, 657 bonds, 78 residues, 1 model selected  

> select /D:187-259

522 atoms, 522 bonds, 1 pseudobond, 71 residues, 2 models selected  

> select /E:224

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

> select /E:224-225

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /C:33-112

651 atoms, 675 bonds, 80 residues, 1 model selected  

> select /B:215

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

> select /B:213-215

15 atoms, 14 bonds, 3 residues, 1 model selected  

> select /A:213-259

346 atoms, 347 bonds, 47 residues, 1 model selected  

> select /A:213-259

346 atoms, 347 bonds, 47 residues, 1 model selected  

> select /A:198

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

> select /A:193-198

46 atoms, 45 bonds, 6 residues, 1 model selected  

> select /A:189-195,216-222,228-233,252-258

201 atoms, 197 bonds, 27 residues, 1 model selected  

> select /A:189

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

> select /A:188-189

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select solvent

116 atoms, 116 residues, 1 model selected  

> hide sel atoms

> select /E:197

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

> select /E:197

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

> select /F:32-113

668 atoms, 693 bonds, 82 residues, 1 model selected  

> hide sel cartoons

> select /E:186

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

> select /E:186-262

544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select /B:186

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

> select /B:186-262

544 atoms, 544 bonds, 1 pseudobond, 74 residues, 2 models selected  

> style sel sphere

Changed 544 atom styles  

> show sel atoms

> hide sel atoms

> style sel ball

Changed 544 atom styles  

> show sel atoms

> show sel atoms

> hide sel atoms

> select /B:189

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

> select /B:189

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

> select /B:190

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

> select /B:189-190

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /B:197

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

> select /B:197

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

> select /B:262

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

> select /B:262

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

> save ""/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh 7.1-AvrPikC.cxs""

> select /B:189

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

> select /B:189

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

> swapaa /B:189 arg

Using Dunbrack library  
/B GLN 189: phi -103.3, psi 148.2 trans  
Applying ARG rotamer (chi angles: -64.9 -179.8 -178.2 -87.3) to /B ARG 189  

> show sel atoms

> select /B:189

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

> select /B:189

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> select /B:190

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

> select /B:190

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

> swapaa /B:190 ile

Using Dunbrack library  
/B LYS 190: phi -119.0, psi 123.4 trans  
Applying ILE rotamer (chi angles: -59.9 171.3) to /B ILE 190  

> select /B:190

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

> select /B:190

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

> show sel atoms

> style sel stick

Changed 8 atom styles  

> select /B:197

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

> select /B:197

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

> swapaa /B:197 arg

Using Dunbrack library  
/B MET 197: phi -152.9, psi none trans  
Applying ARG rotamer (chi angles: 64.1 -175.8 68.0 -172.6) to /B ARG 197  

> show sel atoms

> style sel stick

Changed 4 atom styles  

> show sel atoms

> select /B:197

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

> select /B:197

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

> select /B:197

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

> show sel atoms

> show sel atoms

> style sel stick

Changed 11 atom styles  

> swapaa /B:198 gly

No amino acid residues specified for swapping  

> save ""/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh 7.1-AvrPikC.cxs""

> select /B:186

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

> select /B:186-262

548 atoms, 548 bonds, 1 pseudobond, 74 residues, 2 models selected  

> color (#!1 & sel) white

> select /C:33-112

651 atoms, 675 bonds, 80 residues, 1 model selected  

> color sel gray

> color sel byhetero

> undo

> color sel bychain

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for Pikh-AvrPikC_7a8x.pdb_C SES surface #1.2: minimum,
-14.58, mean -1.64, maximum 7.77  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp sel

Map values for surface ""Pikh-AvrPikC_7a8x.pdb_C SES surface"": minimum -26.66,
mean -5.066, maximum 23.1  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic sel

Coulombic values for Pikh-AvrPikC_7a8x.pdb_C SES surface #1.2: minimum,
-14.58, mean -1.64, maximum 7.77  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic sel

Coulombic values for Pikh-AvrPikC_7a8x.pdb_C SES surface #1.2: minimum,
-14.58, mean -1.64, maximum 7.77  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color sel bychain

> rainbow sel

> style sel stick

Changed 651 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 651 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel atoms

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> hide sel atoms

> show sel cartoons

> hide sel atoms

> hide sel surfaces

> coulombic sel

Coulombic values for Pikh-AvrPikC_7a8x.pdb_C SES surface #1.2: minimum,
-14.58, mean -1.64, maximum 7.77  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color sel byhetero

> color sel bychain

> hide sel surfaces

> show sel surfaces

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> coulombic sel

Coulombic values for Pikh-AvrPikC_7a8x.pdb_C SES surface #1.2: minimum,
-14.58, mean -1.64, maximum 7.77  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> show sel surfaces

> color sel bychain

> select /B:186-262

548 atoms, 548 bonds, 1 pseudobond, 74 residues, 2 models selected  

> select /C:33-112

651 atoms, 675 bonds, 80 residues, 1 model selected  

> select /B:189

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

> select /B:189-190

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select /B:191

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

> select /B:190-191

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /B:191

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

> select /B:190-191

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /B:189

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

> select /B:188-189

20 atoms, 19 bonds, 2 residues, 1 model selected  

> select /B:190

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

> select /B:189-190

19 atoms, 18 bonds, 2 residues, 1 model selected  

> color sel yellow

> select /B:197

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

> select /B:197

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

> color sel yellow

> lighting soft

> lighting full

> lighting simple

> select /B:189-195,216-222,228-233,252-259

211 atoms, 207 bonds, 28 residues, 1 model selected  

> select /B:186

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

> select /B:186

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

> select /B:186

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

> select /B:186

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

> save ""/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh 7.1-AvrPikC.cxs""

> select /B:186

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

> select /B:186-262

548 atoms, 548 bonds, 1 pseudobond, 74 residues, 2 models selected  

> hide sel surfaces

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> select /B:186-262

548 atoms, 548 bonds, 1 pseudobond, 74 residues, 2 models selected  

> ui mousemode right select

> ui mousemode right select

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000026141b0>
contents scale of 2 - updating layer to match.  

> undo

> view sel

> ui tool show ""Command Line Interface""

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 705 of 86524 triangles  
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 154 of 86524 triangles, 1
residues  
Drag select of 2 residues  

> select clear

> select clear

Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 44 of 86524 triangles  

> select clear

Drag select of 2 residues  

> select clear

> select clear

Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 722 of 86524 triangles  

> save ""/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh 7.1-AvrPikC.cxs""

Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 597 of 86524 triangles, 1
residues  
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 3328 of 86524 triangles, 6
residues  
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 81 of 86524 triangles  

> select clear

Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 346 of 86524 triangles  
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 465 of 86524 triangles  

> select clear

> select clear

Drag select of 3 residues  

> select clear

> select clear

Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 85 of 86524 triangles  
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 2742 of 86524 triangles, 5
atoms, 8 residues, 5 bonds  

> select clear

> select clear

> select clear

> set bgColor white

> set bgColor black

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting simple

Permission denied reading directory ""/Users/yrim/Desktop"" while trying to
determine next unused file name image#.png.  
Permission denied reading directory ""/Users/yrim/Desktop"" while trying to
determine next unused file name image#.png.  
Drag select of Pikh-AvrPikC_7a8x.pdb_C SES surface, 335 of 86524 triangles, 9
residues, 2 bonds  

> select clear

> select /C:33-112

651 atoms, 675 bonds, 80 residues, 1 model selected  

> ui tool show ""Color Actions""

> ui tool show ""Side View""

> transparency (#!1 & sel) 70

> cartoon hide (#!1 & sel)

> transparency (#!1 & sel) 20

> transparency (#!1 & sel) 40

> select clear

> select /C:60-112

419 atoms, 431 bonds, 53 residues, 1 model selected  

> select /C:33-112

651 atoms, 675 bonds, 80 residues, 1 model selected  

> select /C:33-36

30 atoms, 29 bonds, 4 residues, 1 model selected  

> select /C:33-112

651 atoms, 675 bonds, 80 residues, 1 model selected  

> transparency (#!1 & sel) 60

> select clear

Drag select of 8 residues  

> select clear

> select clear

> save ""/Users/yrim/Documents/UC Davis Ronald Lab/Crystal structures/AvrPik
> and other Magnaporthe effectors/Pikh 7.1-AvrPikC.cxs""

——— End of log from Sat Jun 8 15:14:22 2024 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Model Number: MJ123LL/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 8422.141.2.700.1

Software:

    System Software Overview:

      System Version: macOS 13.6.6 (22G630)
      Kernel Version: Darwin 22.6.0
      Time since boot: 58 days, 17 hours, 23 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL U2720Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
}}}
"	defect	closed	normal		Window Toolkit		can't reproduce						all	ChimeraX