Opened 3 years ago

Closed 3 years ago

#6982 closed defect (fixed)

Segger session save: invalid literal for int() with base 10

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/ZIT-guanosine.cxs"

Log from Sat May 28 13:32:04 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/APO.cxs"

Log from Sat May 28 12:52:12 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/zhouyanxia/Desktop/MphE/figure/MODEL/XQJ_refine_196.pdb

Summary of feedback from opening
/Users/zhouyanxia/Desktop/MphE/figure/MODEL/XQJ_refine_196.pdb  
---  
warnings | Ignored bad PDB record found on line 4952  
TER  
  
Ignored bad PDB record found on line 9633  
TER  
  
Ignored bad PDB record found on line 10050  
END  
  
Chain information for XQJ_refine_196.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open /Users/zhouyanxia/Desktop/MphE/figure/MODEL/20210601_refine_72-ERY-
> GTP.pdb

Summary of feedback from opening
/Users/zhouyanxia/Desktop/MphE/figure/MODEL/20210601_refine_72-ERY-GTP.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2021-06-14 Time 12:10:41 EDT -0400 (1623687041.40 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name : /home/dengd/Documents/Dengd/QQQ/QQQ_deng7_B15_output.sca  
  
45 messages similar to the above omitted  
Duplicate atom serial number found: 5619  
Duplicate atom serial number found: 5620  
Duplicate atom serial number found: 5621  
Duplicate atom serial number found: 5622  
Duplicate atom serial number found: 5623  
13 messages similar to the above omitted  
  
Chain information for 20210601_refine_72-ERY-GTP.pdb #2  
---  
Chain | Description  
A B | No description available  
  

> open /Users/zhouyanxia/Desktop/MphE/figure/MODEL/20210601_refine_86-ZIT-
> GMP.pdb

Summary of feedback from opening
/Users/zhouyanxia/Desktop/MphE/figure/MODEL/20210601_refine_86-ZIT-GMP.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2021-08-24 Time 08:39:20 EDT -0400 (1629808760.96 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name : /home/dengd/Documents/Dengd/QQQ/QQQ_deng4_E16_output.sca  
  
25 messages similar to the above omitted  
  
Chain information for 20210601_refine_86-ZIT-GMP.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker XQJ_refine_196.pdb, chain A (#1) with 20210601_refine_72-ERY-
GTP.pdb, chain B (#2), sequence alignment score = 1490.5  
RMSD between 237 pruned atom pairs is 0.615 angstroms; (across all 293 pairs:
2.286)  
  

> matchmaker #!3 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 XQJ_refine_196.pdb, chain A (#1) with 20210601_refine_86-ZIT-
GMP.pdb, chain B (#3), sequence alignment score = 1420.7  
RMSD between 241 pruned atom pairs is 0.609 angstroms; (across all 286 pairs:
1.839)  
  

> select #1/B

2337 atoms, 2383 bonds, 292 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select #2/A

2358 atoms, 2405 bonds, 294 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #3/A

2193 atoms, 2238 bonds, 2 pseudobonds, 282 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> hide sel atoms

Drag select of 642 atoms, 864 residues, 556 bonds  

> hide sel atoms

> set bgColor white

> matchmaker #!3 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 XQJ_refine_196.pdb, chain A (#1) with 20210601_refine_86-ZIT-
GMP.pdb, chain B (#3), sequence alignment score = 1420.7  
RMSD between 241 pruned atom pairs is 0.609 angstroms; (across all 286 pairs:
1.839)  
  

> select clear

> graphics silhouettes true

> lighting soft

> hide #2 models

> hide #!3 models

> select #1/A: 96-119

193 atoms, 196 bonds, 24 residues, 1 model selected  

> select #1/A: 89-113

199 atoms, 201 bonds, 25 residues, 1 model selected  

> color sel #fd6666ff

> color sel #fd8880ff

> color sel #fd9990ff

> select #1/A: 1-99

809 atoms, 822 bonds, 99 residues, 1 model selected  

> select #1/A: 1-88

722 atoms, 734 bonds, 88 residues, 1 model selected  

> color sel #929b90ff

> color sel #929b90ff

> color sel #93b190ff

> color sel #93b190ff

> color sel #93adffff

> select #1/A: 114-185

597 atoms, 608 bonds, 72 residues, 1 model selected  

> select #1/A: 114-143

248 atoms, 252 bonds, 30 residues, 1 model selected  

> select #1/A: 114-140

223 atoms, 227 bonds, 27 residues, 1 model selected  

> select #1/A: 114-140, 187-252

729 atoms, 746 bonds, 93 residues, 1 model selected  

> color sel #9badffff

> color sel #9effffff

> color sel #9effa4ff

> select #1/A: 141-186， 253-293

Expected an objects specifier or a keyword  

> select #1/A: 141-186, 253-293

697 atoms, 707 bonds, 87 residues, 1 model selected  

> color sel #89ffeaff

> color sel #c3ffedff

> color sel #fea7ecff

> color sel #fec4efff

> color sel #fdb7ffff

> color sel #fec4d7ff

> color sel #fec0a8ff

> color sel #feb3bfff

> color sel #fffab3ff

> color sel #fea6a3ff

> color sel #feb3d1ff

> color sel #c4ffa8ff

> color sel #b0ff99ff

> color sel #bbffa3ff

> color sel #a3b7ffff

> color sel #95a8ffff

> color sel #8f9bffff

> color sel #8f9bffff

> color sel #929affff

> color sel #929affff

> color sel #93adffff

> select #1/A: 114-140, 187-252

729 atoms, 746 bonds, 93 residues, 1 model selected  

> color sel #f5daffff

> color sel #ffefd5ff

> color sel #fff8a6ff

> color sel #ddffc4ff

> color sel #d0ffd1ff

> color sel #ffd6b1ff

> color sel #fed3d4ff

> color sel #fbffb5ff

> color sel #b8ff94ff

> color sel #b8ff95ff

> color sel #b8ff95ff

> color sel #9eff94ff

> color sel #9effa4ff

> select clear

> select #1/A: 1-88

722 atoms, 734 bonds, 88 residues, 1 model selected  

> color sel #febda5ff

> color sel #fd9899ff

> color sel #fd9eb7ff

> color sel #feafa1ff

> color sel #c8ccffff

> color sel #bdfff6ff

> color sel #ffe9edff

> color sel #febae5ff

> color sel #fff8b1ff

> color sel #f1ffc3ff

> color sel #fffeabff

> color sel #ffe8a9ff

> color sel #ffdeaaff

> color sel #fecfa7ff

> color sel #fea6b4ff

> color sel #fda0c9ff

> color sel #fd9ad6ff

> color sel #fd97f7ff

> color sel #f79bffff

> color sel #f17fffff

> color sel #f1a8ffff

> color sel #febadfff

> color sel #fea4d5ff

> color sel #fd97d2ff

> select clear

> select #1/A: 1-88

722 atoms, 734 bonds, 88 residues, 1 model selected  

> color sel #febfd3ff

> color sel #66ccffff

> color sel #66ffffff

> color sel #66ccffff

> color sel #89d8ffff

> color sel #9ae0ffff

> color sel #afe7ffff

> select clear

> select #1/A: 1-88

722 atoms, 734 bonds, 88 residues, 1 model selected  

> color sel #ccff66ff

> color sel #cdff82ff

> color sel #c1ff99ff

> color sel #bbfde1ff

> color sel #fad9e3ff

> color sel #f7defbff

> color sel #e5d9fbff

> color sel #f9bfbeff

> color sel #dafbf9ff

> color sel #ccff66ff

> color sel #ddfe8fff

> color sel #fd66ffff

> color sel #fec0f7ff

> color sel #ffe1bfff

> color sel #fffcb7ff

> select clear

> select #1/A: 1-88

722 atoms, 734 bonds, 88 residues, 1 model selected  

> color sel #efff91ff

> select clear

> select #1/A: 1-88

722 atoms, 734 bonds, 88 residues, 1 model selected  

> color sel #efff91ff

> color sel #efff94ff

> color sel #efff96ff

> color sel #efff97ff

> color sel #efff9bff

> color sel #efff9dff

> color sel #efff9eff

> color sel #efffa3ff

> color sel #efffa3ff

> color sel #efffa4ff

> color sel #efffa8ff

> color sel #efffaaff

> color sel #efffacff

> color sel #efffaeff

> color sel #efffb0ff

> color sel #efffb0ff

> color sel #efffafff

> color sel #efffaeff

> color sel #efffaeff

> color sel #efffadff

> color sel #efffacff

> color sel #efffabff

> color sel #f3ffabff

> color sel #f5ffabff

> color sel #f6ffabff

> color sel #f6ffabff

> color sel #f6ffabff

> color sel #f6feabff

> color sel #f5fcabff

> color sel #f5f8abff

> color sel #f5f3abff

> color sel #f5f2abff

> select clear

> save "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/APO.png" width 779
> height 611 supersample 3

> save "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/APO.cxs"

> save "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/APO.cxs"

opened ChimeraX session  

> select #1/A: 1-88

722 atoms, 734 bonds, 88 residues, 1 model selected  

> color sel #f8ffb7ff

> color sel #fffcb1ff

> select clear

> save "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/APO.png" width 2400
> height 2016 supersample 3

> save "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/APO.cxs"

> hide #1 models

> show #2 models

> select #2/A: 1-88

723 atoms, 734 bonds, 88 residues, 1 model selected  

> select #2/B: 1-88

720 atoms, 731 bonds, 88 residues, 1 model selected  

> color sel #fffcb1ff

> select #2/B: 114-140, 187-252

724 atoms, 740 bonds, 93 residues, 1 model selected  

> show #1 models

> hide #1 models

> color sel #9efeb1ff

> color sel #9efeb1ff

> color sel #9effb1ff

> color sel #9effb1ff

> color sel #9effa4ff

> select #2/B: 141-186, 253-293

700 atoms, 711 bonds, 87 residues, 1 model selected  

> color sel #96ffa4ff

> color sel #93b0a4ff

> color sel #93adffff

> select clear

> show #1 models

> hide #2 models

> hide #1 models

> show #2 models

> select #2/B: 89-113

207 atoms, 211 bonds, 25 residues, 1 model selected  

> show #1 models

> select #2/B: 90-113

200 atoms, 203 bonds, 24 residues, 1 model selected  

> select #2/B: 89-113

207 atoms, 211 bonds, 25 residues, 1 model selected  

> color sel #feaaffff

> color sel #fd8effff

> color sel #fd938bff

> select clear

> hide #1 models

> select #2/B: 89

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

> color sel #fd818bff

> color sel #fd80b1ff

> color sel #fffdb1ff

> select clear

> show #1 models

> hide #2 models

> hide #1 models

> show #!3 models

> select #3/B: 89-113

180 atoms, 183 bonds, 2 pseudobonds, 22 residues, 2 models selected  

> select #3/B: 90-113

173 atoms, 175 bonds, 2 pseudobonds, 21 residues, 2 models selected  

> color (#!3 & sel) #fffdb1ff

> select #3/B: 1-89

720 atoms, 732 bonds, 89 residues, 1 model selected  

> color sel #fffdb1ff

> select #3/B: 90-113

173 atoms, 175 bonds, 2 pseudobonds, 21 residues, 2 models selected  

> color (#!3 & sel) #fd92b1ff

> color (#!3 & sel) #fd938bff

> select #3/B: 114-140， 187-252

Expected an objects specifier or a keyword  

> select #3/B: 114-140, 187-252

720 atoms, 736 bonds, 93 residues, 1 model selected  

> color sel #92968aff

> color sel #93b18aff

> color sel #93adffff

> select #3/B: 141-186, 253-293

664 atoms, 674 bonds, 2 pseudobonds, 84 residues, 2 models selected  

> show #1 models

> hide #1 models

> color (#!3 & sel) #93adffff

> select #3/B: 114-140, 187-252

720 atoms, 736 bonds, 93 residues, 1 model selected  

> color sel #9badffff

> color sel #9effffff

> color sel #9effa4ff

> select clear

> show #2 models

> select ::name="ERY"

102 atoms, 106 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 102 atom styles  

> style sel stick

Changed 102 atom styles  

> style sel sphere

Changed 102 atom styles  

> style sel ball

Changed 102 atom styles  

> color sel byelement

> style sel stick

Changed 102 atom styles  

> style sel ball

Changed 102 atom styles  
Drag select of 51 atoms, 53 bonds  

> hide sel atoms

> select ::name="GMP"

40 atoms, 44 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 40 atom styles  

> color sel byelement

> select clear

Drag select of 20 atoms, 22 bonds  

> hide sel atoms

> select ::name="GTP"

64 atoms, 68 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 64 atom styles  

> color sel byelement

> select clear

Drag select of 32 atoms, 34 bonds  

> hide sel atoms

> select ::name="ZIT"

104 atoms, 108 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 104 atom styles  

> color sel byelement

> select clear

Drag select of 52 atoms, 54 bonds  

> hide sel atoms

> select ::name="MG"

7 atoms, 7 residues, 2 models selected  

> show sel & #2 atoms

> style sel & #2 ball

Changed 6 atom styles  

> show sel & #2 atoms

> style sel & #2 sphere

Changed 6 atom styles  

> color (#2 & sel) byelement

> select clear

Drag select of 3 atoms  

> hide sel atoms

Drag select of 1 atoms  

> hide sel atoms

Drag select of 21 residues  

> show #1 models

> hide #1 models

> hide #2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #2 models

> select ::name="ERY"

102 atoms, 106 bonds, 2 residues, 1 model selected  

> select clear

> select #2/E:2@MG

1 atom, 1 residue, 1 model selected  

> select #2/E:1@MG

1 atom, 1 residue, 1 model selected  

> color sel #8000ffff

> color sel #6666ffff

> color sel #cc66ffff

> select clear

> style #2 stick

Changed 5754 atom styles  

> style #2 ball

Changed 5754 atom styles  

> style #2 sphere

Changed 5754 atom styles  

> undo

> undo

> undo

> select #2/B: 294

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

> color sel #cc66ffff

> color sel #9168ffff

> color sel #9168ffff

> color sel #93adffff

> color sel #93adffff

> select clear

> save "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/EYR-GTP.cxs"

> save "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/EYR-GTP.png" width 2400
> height 2049 supersample 3

> hide #2 models

> show #!3 models

> save "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/ZIT-guanosine.png" width
> 2400 height 2049 supersample 3

> save "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/ZIT-guanosine.cxs"

> show #2 models

> show #1 models

> select #3/B: 89-113

180 atoms, 183 bonds, 2 pseudobonds, 22 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> select clear

> save "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/ZIT-guanosine.cxs"

opened ChimeraX session  

> ui tool show Matchmaker

> matchmaker #!3 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 XQJ_refine_196.pdb, chain A (#1) with 20210601_refine_86-ZIT-
GMP.pdb, chain B (#3), sequence alignment score = 1420.7  
RMSD between 241 pruned atom pairs is 0.609 angstroms; (across all 286 pairs:
1.839)  
  

> matchmaker #!3 to #2

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 20210601_refine_72-ERY-GTP.pdb, chain B (#2) with
20210601_refine_86-ZIT-GMP.pdb, chain B (#3), sequence alignment score =
1434.4  
RMSD between 271 pruned atom pairs is 0.686 angstroms; (across all 287 pairs:
0.977)  
  

> matchmaker #2 to #3

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 20210601_refine_86-ZIT-GMP.pdb, chain B (#3) with
20210601_refine_72-ERY-GTP.pdb, chain B (#2), sequence alignment score =
1434.4  
RMSD between 271 pruned atom pairs is 0.686 angstroms; (across all 287 pairs:
0.977)  
  

> select #3/A

2193 atoms, 2238 bonds, 2 pseudobonds, 282 residues, 2 models selected  

> show sel cartoons

> matchmaker #3/A 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 XQJ_refine_196.pdb, chain A (#1) with 20210601_refine_86-ZIT-
GMP.pdb, chain A (#3), sequence alignment score = 1355.9  
RMSD between 222 pruned atom pairs is 0.621 angstroms; (across all 281 pairs:
1.765)  
  
Drag select of 20 residues  
Drag select of 17 residues  
Drag select of 21 residues  
Drag select of 72 atoms, 286 residues, 76 bonds  

> hide sel cartoons

> hide sel atoms

Drag select of 1 residues  

> hide sel cartoons

Drag select of 5 residues  

> hide #2 models

> hide #!3 models

> show #2 models

> hide #2 models

> hide #1 models

> show #!3 models

> select #3/A: 1-88

707 atoms, 718 bonds, 88 residues, 1 model selected  

> color sel #fffbffff

> color sel #fffbbeff

> select #3/A: 1-89

714 atoms, 726 bonds, 89 residues, 1 model selected  

> color sel #fffbbeff

> select #3/A: 90-113

189 atoms, 192 bonds, 24 residues, 1 model selected  

> color sel #ffa6beff

> color sel #ffa69cff

> select #3/A: 114-140, 187-252

724 atoms, 740 bonds, 93 residues, 1 model selected  

> color sel #aba69cff

> color sel #abff9cff

> color sel #abffb3ff

> select #3/A: 141-186, 253-293

566 atoms, 575 bonds, 2 pseudobonds, 76 residues, 2 models selected  

> color (#!3 & sel) #a3ffb3ff

> color (#!3 & sel) #a3bdb3ff

> color (#!3 & sel) #a3bdffff

> select ::name="ZIT"

104 atoms, 108 bonds, 2 residues, 1 model selected  

> style sel ball

Changed 104 atom styles  

> show sel atoms

> select ::name="GMP"

40 atoms, 44 bonds, 2 residues, 1 model selected  

> show sel atoms

Drag select of 72 atoms, 76 bonds  

> hide sel atoms

> show #2 models

> show #1 models

> save "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/APO.cxs"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/segment_dialog.py", line 3391, in take_snapshot  
data[attr] = getattr(self, attr).value  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/composite.py", line 145, in _get_value  
return self.string_to_value(self._line_edit.text())  
ValueError: invalid literal for int() with base 10: 'AAa'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x11e9b5dd0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x124ca7a10> 'segment map'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x11e9b5dd0> -> <chimerax.segger.segment_dialog.VolumeSegmentationDialog
object at 0x124ca7a10> 'segment map': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x11e9b5dd0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x124ca7a10> 'segment map'  
  
ValueError: error processing: 'tools' -> -> 'segment map': Error while saving
session data for 'tools' -> -> 'segment map'  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/segment_dialog.py", line 3391, in take_snapshot  
data[attr] = getattr(self, attr).value  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/composite.py", line 145, in _get_value  
return self.string_to_value(self._line_edit.text())  
ValueError: invalid literal for int() with base 10: 'AAa'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x11e9b5dd0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x124ca7a10> 'segment map'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x11e9b5dd0> -> <chimerax.segger.segment_dialog.VolumeSegmentationDialog
object at 0x124ca7a10> 'segment map': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x11e9b5dd0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x124ca7a10> 'segment map'  
  
ValueError: error processing: 'tools' -> -> 'segment map': Error while saving
session data for 'tools' -> -> 'segment map'  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "/Users/zhouyanxia/Desktop/MphE/figure/Fig 2/A/ZIT-guanosine.cxs"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/segment_dialog.py", line 3391, in take_snapshot  
data[attr] = getattr(self, attr).value  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/composite.py", line 145, in _get_value  
return self.string_to_value(self._line_edit.text())  
ValueError: invalid literal for int() with base 10: 'AAa'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x11e9b5dd0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x124ca7a10> 'segment map'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x11e9b5dd0> -> <chimerax.segger.segment_dialog.VolumeSegmentationDialog
object at 0x124ca7a10> 'segment map': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x11e9b5dd0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x124ca7a10> 'segment map'  
  
ValueError: error processing: 'tools' -> -> 'segment map': Error while saving
session data for 'tools' -> -> 'segment map'  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/segment_dialog.py", line 3391, in take_snapshot  
data[attr] = getattr(self, attr).value  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/composite.py", line 145, in _get_value  
return self.string_to_value(self._line_edit.text())  
ValueError: invalid literal for int() with base 10: 'AAa'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x11e9b5dd0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x124ca7a10> 'segment map'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x11e9b5dd0> -> <chimerax.segger.segment_dialog.VolumeSegmentationDialog
object at 0x124ca7a10> 'segment map': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x11e9b5dd0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x124ca7a10> 'segment map'  
  
ValueError: error processing: 'tools' -> -> 'segment map': Error while saving
session data for 'tools' -> -> 'segment map'  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir9,1
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 1.1 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      Boot ROM Version: 1554.120.19.0.0 (iBridge: 18.16.14663.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 5 days 4:48

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a51
      Revision ID: 0x0007
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    decorator: 4.4.2
    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: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Segger session save: invalid literal for int() with base 10

comment:2 by Tom Goddard, 3 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in ChimeraX 1.5, not in 1.4.

Saving session failed because Segger tried to save non-numeric value in its dialog and convert it to a numeric value. Made Segger not save invalid values in sessions.

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