Sorting error for chains in same structure with same ID

[sebastian.guettler@…]

The following bug report has been submitted:
Platform:        macOS-13.4.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/sguettler/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_Activation/PARP1_activation_HD-
> ART.cxs

Log from Thu Aug 31 15:18:04 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/sguettler/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_Activation/PARP1_activation.cxs

Log from Thu Aug 31 14:51:06 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/sguettler/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_Activation/PARP1_activation.cxs

Log from Thu Aug 31 14:29:35 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/sguettler/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_Activation/PARP1-DNA_complexes.cxs

Log from Wed Aug 30 10:46:54 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/sguettler/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_PARP2_DNA/PARP1_dV687-E688_DNA_7s6m.pdb

PARP1_dV687-E688_DNA_7s6m.pdb title:  
Human PARP1 DELTAV687-E688 bound to A DNA double strand break. [more info...]  
  
Chain information for PARP1_dV687-E688_DNA_7s6m.pdb #1  
---  
Chain | Description | UniProt  
A C | fusion of human PARP1 zinc fingers 1 and 3 (ZN1, ZN3) | PARP1_HUMAN
1-205 206-366  
B D | poly [adp-ribose] polymerase 1 | PARP1_HUMAN 518-1014  
M P | DNA (5'-D(*CP*GP*TP*CP*G)-3') |  
N O | DNA (5'-D(*CP*GP*ap*CP*G)-3') |  
  
Non-standard residues in PARP1_dV687-E688_DNA_7s6m.pdb #1  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
ZN — zinc ion  
  

> show cartoons

> style stick

Changed 22401 atom styles  

> hide atoms

> select /A:66

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select add /B:757

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select up

477 atoms, 478 bonds, 31 residues, 1 model selected  

> select up

3266 atoms, 3299 bonds, 203 residues, 1 model selected  

> select up

3379 atoms, 3410 bonds, 211 residues, 1 model selected  

> select up

10823 atoms, 10943 bonds, 686 residues, 1 model selected  

> select up

10846 atoms, 10959 bonds, 693 residues, 1 model selected  

> select up

22401 atoms, 22674 bonds, 1412 residues, 1 model selected  

> select down

10846 atoms, 10959 bonds, 693 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /N:2

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select add /M:23

66 atoms, 70 bonds, 2 residues, 1 model selected  

> select up

314 atoms, 337 bonds, 10 residues, 1 model selected  

> select up

11555 atoms, 11715 bonds, 719 residues, 1 model selected  

> select down

314 atoms, 337 bonds, 10 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> set bgColor white

> save "/Users/sguettler/OneDrive - The Institute of Cancer
> Research/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_PARP2_DNA/PARP1-DNA_complexes.cxs"

> open /Users/sguettler/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_PARP2_DNA/PARP1-DNA_4dqy.pdb

PARP1-DNA_4dqy.pdb title:  
Structure of human parp-1 bound to A DNA double strand break [more info...]  
  
Chain information for PARP1-DNA_4dqy.pdb #2  
---  
Chain | Description | UniProt  
A D | poly [adp-ribose] polymerase 1 | PARP1_HUMAN 1-96  
B E | poly [adp-ribose] polymerase 1 | PARP1_HUMAN 216-366  
C F | poly [adp-ribose] polymerase 1 | PARP1_HUMAN 518-1014  
M N | DNA (26-mer) |  
  
Non-standard residues in PARP1-DNA_4dqy.pdb #2  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
ZN — zinc ion  
  

> style stick

Changed 22975 atom styles  

> show cartoons

> hide atoms

> select #2/F:895

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

> select up

31 atoms, 32 bonds, 3 residues, 1 model selected  

> select up

2735 atoms, 2787 bonds, 350 residues, 1 model selected  

> select up

2760 atoms, 2811 bonds, 353 residues, 1 model selected  

> select up

3252 atoms, 3321 bonds, 411 residues, 1 model selected  

> select up

3268 atoms, 3336 bonds, 413 residues, 1 model selected  

> select up

3586 atoms, 3660 bonds, 456 residues, 1 model selected  

> select up

11734 atoms, 12079 bonds, 1413 residues, 1 model selected  

> select down

3586 atoms, 3660 bonds, 456 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/D:11

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

> select add #2/E:233

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select up

316 atoms, 318 bonds, 37 residues, 1 model selected  

> select up

1747 atoms, 1784 bonds, 222 residues, 1 model selected  

> select up

1749 atoms, 1784 bonds, 224 residues, 1 model selected  

> select up

8148 atoms, 8419 bonds, 957 residues, 1 model selected  

> select down

1749 atoms, 1784 bonds, 224 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/D:819

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

254 atoms, 255 bonds, 15 residues, 1 model selected  

> select up

3721 atoms, 3765 bonds, 236 residues, 1 model selected  

> select up

3728 atoms, 3771 bonds, 237 residues, 1 model selected  

> select up

5622 atoms, 5679 bonds, 355 residues, 1 model selected  

> select up

5715 atoms, 5772 bonds, 361 residues, 1 model selected  

> select up

7479 atoms, 7561 bonds, 471 residues, 1 model selected  

> select up

7490 atoms, 7569 bonds, 474 residues, 1 model selected  

> select up

11241 atoms, 11378 bonds, 709 residues, 1 model selected  

> select up

17640 atoms, 18013 bonds, 1442 residues, 2 models selected  

> select down

11241 atoms, 11378 bonds, 709 residues, 1 model selected  

> color sel lime

> select clear

> graphics silhouettes true

> select clear

> select #2/A:39

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

> select up

64 atoms, 63 bonds, 8 residues, 1 model selected  

> select up

704 atoms, 724 bonds, 86 residues, 1 model selected  

> select up

705 atoms, 724 bonds, 87 residues, 1 model selected  

> select up

6399 atoms, 6635 bonds, 733 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark red

> color sel light coral

> color sel purple

> select clear

> 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 PARP1_dV687-E688_DNA_7s6m.pdb, chain D (#1) with
PARP1-DNA_4dqy.pdb, chain C (#2), sequence alignment score = 2398.9  
RMSD between 238 pruned atom pairs is 0.701 angstroms; (across all 450 pairs:
6.069)  
  

> 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 PARP1_dV687-E688_DNA_7s6m.pdb, chain D (#1) with
PARP1-DNA_4dqy.pdb, chain C (#2), sequence alignment score = 2398.9  
RMSD between 238 pruned atom pairs is 0.701 angstroms; (across all 450 pairs:
6.069)  
  

> select clear

[Repeated 1 time(s)]

> ui tool show "Show Sequence Viewer"

[Repeated 1 time(s)]

> sequence chain #1/C

Alignment identifier is 1/C  

> ui tool show Matchmaker

> matchmaker #!2 to #1/C pairing bs

Parameters  
---  
Chain pairing | bs  
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 PARP1_dV687-E688_DNA_7s6m.pdb, chain C (#1) with
PARP1-DNA_4dqy.pdb, chain B (#2), sequence alignment score = 719.1  
RMSD between 124 pruned atom pairs is 0.617 angstroms; (across all 136 pairs:
1.370)  
  

> select clear

[Repeated 1 time(s)]

> select #2/B:349

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

> select up

95 atoms, 97 bonds, 13 residues, 1 model selected  

> select up

1043 atoms, 1060 bonds, 136 residues, 1 model selected  

> select up

1044 atoms, 1060 bonds, 137 residues, 1 model selected  

> select down

1043 atoms, 1060 bonds, 136 residues, 1 model selected  

> select down

95 atoms, 97 bonds, 13 residues, 1 model selected  

> select up

1043 atoms, 1060 bonds, 136 residues, 1 model selected  

> select clear

> ui tool show Matchmaker

Drag select of 34 residues  

> select clear

> select #1/C:347

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

> select up

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

> select up

2048 atoms, 2066 bonds, 136 residues, 1 model selected  

> select up

2073 atoms, 2090 bonds, 138 residues, 1 model selected  

> select up

3434 atoms, 3472 bonds, 222 residues, 1 model selected  

> select #1/D:613

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select up

293 atoms, 295 bonds, 18 residues, 1 model selected  

> select up

1857 atoms, 1882 bonds, 116 residues, 1 model selected  

> select up

1951 atoms, 1975 bonds, 122 residues, 1 model selected  

> select up

3758 atoms, 3796 bonds, 235 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #1/D:937

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select up

230 atoms, 233 bonds, 14 residues, 1 model selected  

> select up

3721 atoms, 3765 bonds, 236 residues, 1 model selected  

> select up

3728 atoms, 3771 bonds, 237 residues, 1 model selected  

> select up

5622 atoms, 5679 bonds, 355 residues, 1 model selected  

> select down

3728 atoms, 3771 bonds, 237 residues, 1 model selected  

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #1/D

Alignment identifier is 1/D  

> select #1/D:531-712

2708 atoms, 2738 bonds, 1 pseudobond, 167 residues, 2 models selected  

> select clear

> select #1/D:713

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/D:713-771

908 atoms, 914 bonds, 59 residues, 1 model selected  

> select
> #1/D:543-545,547-548,551-552,554-561,566-577,583-591,597-604,639-640,799-802,829-841,857-862,895-897,916-925,929-932,947-950,952-956,962-963,968-969,974-976,984-986,988-991,997-1009

2069 atoms, 2072 bonds, 122 residues, 1 model selected  

> select #1/D:641

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/D:640

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

> select #1/D:640

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

> select #1/D:633

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/D:633-634

43 atoms, 43 bonds, 2 residues, 1 model selected  

> select #1/D:638

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #1/D:638

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #1/D:639

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/D:531-639

1750 atoms, 1773 bonds, 109 residues, 1 model selected  

> color sel magenta

> select #1/C,D:517-638

1729 atoms, 1751 bonds, 108 residues, 1 model selected  

> select clear

> select #1/C,D:517-638

1729 atoms, 1751 bonds, 108 residues, 1 model selected  

> select #1/C, D:517-638

1729 atoms, 1751 bonds, 108 residues, 1 model selected  

> select #1/C

3437 atoms, 3472 bonds, 9 pseudobonds, 225 residues, 3 models selected  

> select #1/C,#1/D:517-638

Expected an objects specifier or a keyword  

> select #1/C,D:517-638

1729 atoms, 1751 bonds, 108 residues, 1 model selected  

> select #1/C,D:start-638

5166 atoms, 5223 bonds, 9 pseudobonds, 333 residues, 3 models selected  

> select clear

> select #1/C,D:start-638

5166 atoms, 5223 bonds, 9 pseudobonds, 333 residues, 3 models selected  

> color (#!1 & sel) lime

> select #1/D:789-833

737 atoms, 742 bonds, 45 residues, 1 model selected  

> select #1/D:789-833

737 atoms, 742 bonds, 45 residues, 1 model selected  

> hide #!1 models

> select #2/C:760

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

> select up

201 atoms, 201 bonds, 26 residues, 1 model selected  

> select up

2735 atoms, 2787 bonds, 350 residues, 1 model selected  

> select clear

> select #2/C,D

3590 atoms, 3663 bonds, 2 pseudobonds, 457 residues, 2 models selected  

> select clear

> select #2/C,D:start-644

851 atoms, 873 bonds, 1 pseudobond, 106 residues, 2 models selected  

> select #2/B,D:start-644

1044 atoms, 1060 bonds, 4 pseudobonds, 137 residues, 2 models selected  

> select clear

> select #2/B,C:start-644

1895 atoms, 1933 bonds, 5 pseudobonds, 243 residues, 3 models selected  

> select #2/A,B,C:start-644

2600 atoms, 2657 bonds, 9 pseudobonds, 330 residues, 3 models selected  

> ui tool show "Renumber Residues"

> ui tool show "Change Chain IDs"

> changechains sel A

Cannot reassign chain ID to only part of polymeric chain (PARP1-DNA_4dqy.pdb
#2/C)  

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 5 time(s)]

> save "/Users/sguettler/OneDrive - The Institute of Cancer
> Research/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_PARP2_DNA/PARP1-DNA_complexes.cxs"

——— End of log from Wed Aug 30 10:46:54 2023 ———

opened ChimeraX session  

> select clear

> show #!1 models

> open /Users/sguettler/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_Activation/PARP1_HD-
> ART_apo_7aaa.pdb

PARP1_HD-ART_apo_7aaa.pdb title:  
Crystal structure of the catalytic domain of human PARP1 (apo) [more info...]  
  
Chain information for PARP1_HD-ART_apo_7aaa.pdb #3  
---  
Chain | Description | UniProt  
A B | poly [adp-ribose] polymerase 1 | PARP1_HUMAN 662-1011  
  
Non-standard residues in PARP1_HD-ART_apo_7aaa.pdb #3  
---  
DMS — dimethyl sulfoxide  
EDO — 1,2-ethanediol (ethylene glycol)  
SO4 — sulfate ion  
  

> save "/Users/sguettler/OneDrive - The Institute of Cancer
> Research/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_Activation/PARP1-DNA_complexes.cxs"

——— End of log from Thu Aug 31 14:29:35 2023 ———

opened ChimeraX session  

> select #3/A:802

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

> select up

39 atoms, 38 bonds, 5 residues, 1 model selected  

> select up

2730 atoms, 2782 bonds, 350 residues, 1 model selected  

> select up

2971 atoms, 2793 bonds, 580 residues, 1 model selected  

> select up

5841 atoms, 5581 bonds, 1064 residues, 1 model selected  

> select down

2971 atoms, 2793 bonds, 580 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select #3/B:712

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

> select clear

> ui tool show Matchmaker

> matchmaker #!1 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 PARP1_HD-ART_apo_7aaa.pdb, chain B (#3) with
PARP1_dV687-E688_DNA_7s6m.pdb, chain D (#1), sequence alignment score = 1707.4  
RMSD between 242 pruned atom pairs is 0.724 angstroms; (across all 344 pairs:
3.189)  
  

> 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 PARP1_HD-ART_apo_7aaa.pdb, chain B (#3) with PARP1-DNA_4dqy.pdb,
chain C (#2), sequence alignment score = 1679.7  
RMSD between 273 pruned atom pairs is 0.857 angstroms; (across all 350 pairs:
1.840)  
  

> 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 PARP1_HD-ART_apo_7aaa.pdb, chain B (#3) with PARP1-DNA_4dqy.pdb,
chain C (#2), sequence alignment score = 1679.7  
RMSD between 273 pruned atom pairs is 0.857 angstroms; (across all 350 pairs:
1.840)  
  
Drag select of 1 residues  

> select clear

> open /Users/sguettler/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_Activation/PARP1_dV687-E688-DNA-
> EB47_7s6h.pdb

PARP1_dV687-E688-DNA-EB47_7s6h.pdb title:  
Human PARP1 DELTAV687-E688 bound to nad+ analog eb-47 and to A DNA double
strand break. [more info...]  
  
Chain information for PARP1_dV687-E688-DNA-EB47_7s6h.pdb #4  
---  
Chain | Description | UniProt  
A C | fusion of human PARP1 zinc fingers 1 and 3 (ZN1, ZN3) | PARP1_HUMAN
1-205 206-366  
B D | poly [adp-ribose] polymerase 1 | PARP1_HUMAN 518-1014  
E M | DNA (5'-D(*CP*GP*ap*CP*G)-3') |  
F N | DNA (5'-D(*CP*GP*TP*CP*G)-3') |  
  
Non-standard residues in PARP1_dV687-E688-DNA-EB47_7s6h.pdb #4  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
UHB —
2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide  
ZN — zinc ion  
  

> select #4/A:59@CA

1 atom, 1 residue, 1 model selected  

> select up

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

116 atoms, 116 bonds, 7 residues, 1 model selected  

> select up

1386 atoms, 1406 bonds, 86 residues, 1 model selected  

> select up

1407 atoms, 1426 bonds, 87 residues, 1 model selected  

> select up

3456 atoms, 3494 bonds, 223 residues, 1 model selected  

> select up

3458 atoms, 3494 bonds, 225 residues, 1 model selected  

> select up

22607 atoms, 22887 bonds, 1422 residues, 1 model selected  

> select clear

> select #4/A:230@CB

1 atom, 1 residue, 1 model selected  

> select up

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

565 atoms, 566 bonds, 33 residues, 1 model selected  

> select up

2070 atoms, 2088 bonds, 137 residues, 1 model selected  

> select up

2095 atoms, 2112 bonds, 139 residues, 1 model selected  

> select up

3456 atoms, 3494 bonds, 223 residues, 1 model selected  

> select up

3458 atoms, 3494 bonds, 225 residues, 1 model selected  

> select up

22607 atoms, 22887 bonds, 1422 residues, 1 model selected  

> select down

3458 atoms, 3494 bonds, 225 residues, 1 model selected  

> select clear

> hide #!2 models

> hide #3 models

> hide #!4 models

> hide #!1 models

> show #!4 models

> style #!4 stick

Changed 22607 atom styles  

> show #!4 cartoons

> hide #!4 atoms

> select #4/B:760

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

> select add #4/A:88

24 atoms, 22 bonds, 2 residues, 1 model selected  

> select up

615 atoms, 616 bonds, 38 residues, 1 model selected  

> select up

3294 atoms, 3327 bonds, 206 residues, 1 model selected  

> select up

3395 atoms, 3426 bonds, 213 residues, 1 model selected  

> select up

10916 atoms, 11036 bonds, 692 residues, 1 model selected  

> select up

10996 atoms, 11114 bonds, 700 residues, 1 model selected  

> select up

22607 atoms, 22887 bonds, 1422 residues, 1 model selected  

> select down

10996 atoms, 11114 bonds, 700 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #!4 models

> show #3 models

> color #3 white

> hide #3 models

> show #!2 models

> color #2 dim gray

> show #3 models

> hide #!2 models

> ui tool show "Color Actions"

> color floral white

[Repeated 1 time(s)]

> color cornsilk

> color seashell

> color lavender blush

> hide #3 models

> show #!2 models

> color light pink

> hide #!2 models

> show #3 models

> show #!4 models

> show #!1 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> hide #!4 models

> select add #3

2870 atoms, 2788 bonds, 484 residues, 1 model selected  

> color sel lavender blush

> select subtract #3

Nothing selected  

> hide #3 models

> show #!2 models

> select add #2

6399 atoms, 6635 bonds, 10 pseudobonds, 733 residues, 3 models selected  

> color sel pink

[Repeated 1 time(s)]

> color sel plum

> show #3 models

> hide #3 models

> hide #!2 models

> select subtract #2

Nothing selected  

> show #!1 models

> select add #1

11241 atoms, 11378 bonds, 11 pseudobonds, 709 residues, 3 models selected  

> color sel orchid

> select subtract #1

Nothing selected  

> hide #!1 models

> show #!4 models

> show #!1 models

> select add #1

11241 atoms, 11378 bonds, 11 pseudobonds, 709 residues, 3 models selected  

> hide #!4 models

> color sel dark orchid

> hide #!1 models

> select subtract #1

Nothing selected  

> select add #4

11611 atoms, 11773 bonds, 11 pseudobonds, 722 residues, 3 models selected  

> show #!4 models

> color sel dark violet

> color sel indigo

> show #!1 models

> show #!2 models

> show #3 models

> select clear

> ui tool show Matchmaker

> matchmaker #!4 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 PARP1_HD-ART_apo_7aaa.pdb, chain B (#3) with PARP1_dV687-E688-DNA-
EB47_7s6h.pdb, chain D (#4), sequence alignment score = 1734.8  
RMSD between 243 pruned atom pairs is 0.671 angstroms; (across all 345 pairs:
3.304)  
  

> matchmaker #!4 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 PARP1_HD-ART_apo_7aaa.pdb, chain B (#3) with PARP1_dV687-E688-DNA-
EB47_7s6h.pdb, chain D (#4), sequence alignment score = 1734.8  
RMSD between 243 pruned atom pairs is 0.671 angstroms; (across all 345 pairs:
3.304)  
  

> select clear

[Repeated 1 time(s)]

> hide target a

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> graphics silhouettes false

> graphics silhouettes true

> select add #4

11611 atoms, 11773 bonds, 11 pseudobonds, 722 residues, 3 models selected  

> show (#!4 & sel) target ab

> hide sel atoms

> select clear

> show #4 UHB

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

> show #4/UHB

> show #4.UHB

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

> show #4/D UHB

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

> show #4/D

> hide atoms

> show #4/D:1102

> show #4/D:763,766,770,1102

> save "/Users/sguettler/OneDrive - The Institute of Cancer
> Research/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_Activation/PARP1_activation.cxs"

——— End of log from Thu Aug 31 14:51:06 2023 ———

opened ChimeraX session  

> transparency #1,2,3 50 cartoons

> select add #1

11241 atoms, 11378 bonds, 11 pseudobonds, 709 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select add #4

11611 atoms, 11773 bonds, 11 pseudobonds, 722 residues, 3 models selected  

> select clear

> delete element.H

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete #4 element.H

Expected a keyword  

> delete #4@h

[Repeated 1 time(s)]

> delete atoms #4@h

> delete atoms #4@h**

> select clear

> color byhetero

> save "/Users/sguettler/OneDrive - The Institute of Cancer
> Research/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_Activation/PARP1_activation.cxs"

Drag select of 604 residues  

> select up

8238 atoms, 8530 bonds, 698 residues, 3 models selected  

> select up

11500 atoms, 11860 bonds, 980 residues, 3 models selected  

> select up

11626 atoms, 11984 bonds, 990 residues, 3 models selected  

> select up

14322 atoms, 14708 bonds, 1216 residues, 3 models selected  

> select down

11626 atoms, 11984 bonds, 990 residues, 3 models selected  

> select clear

> hide #!1 models

> hide #!2 models

> hide #!4 models

> show #!1 models

> select #1/D:646

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

> select up

187 atoms, 186 bonds, 12 residues, 1 model selected  

> select down

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

> select clear

Drag select of 7 residues  

> select up

607 atoms, 632 bonds, 28 residues, 1 model selected  

> select up

2171 atoms, 2219 bonds, 126 residues, 1 model selected  

> hide sel target a

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

Drag select of 46 residues  

> select up

1728 atoms, 1736 bonds, 115 residues, 1 model selected  

> select up

3434 atoms, 3472 bonds, 222 residues, 1 model selected  

> hide sel cartoons

> hide #3 models

> show #!2 models

> hide #!1 models

> select clear

> select #2/C:644

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

> select up

57 atoms, 55 bonds, 7 residues, 1 model selected  

> select clear

Drag select of 17 residues  

> select up

313 atoms, 319 bonds, 37 residues, 1 model selected  

> select up

851 atoms, 873 bonds, 106 residues, 1 model selected  

> hide sel cartoons

Drag select of 77 residues  

> select up

1905 atoms, 2041 bonds, 159 residues, 1 model selected  

> select up

2807 atoms, 2972 bonds, 274 residues, 1 model selected  

> hide sel cartoons

> hide #!2 models

> show #!4 models

Drag select of 7 residues  

> select up

286 atoms, 293 bonds, 32 residues, 1 model selected  

> select up

950 atoms, 975 bonds, 117 residues, 1 model selected  

> hide sel cartoons

Drag select of 64 residues  

> select up

952 atoms, 968 bonds, 119 residues, 1 model selected  

> select up

1740 atoms, 1778 bonds, 221 residues, 1 model selected  

> select up

1744 atoms, 1778 bonds, 225 residues, 1 model selected  

> select up

5929 atoms, 6091 bonds, 722 residues, 1 model selected  

> select down

1744 atoms, 1778 bonds, 225 residues, 1 model selected  

> select down

1740 atoms, 1778 bonds, 221 residues, 1 model selected  

> hide sel cartoons

Drag select of 20 residues  

> select up

5929 atoms, 6091 bonds, 722 residues, 1 model selected  

> select down

398 atoms, 20 residues, 1 model selected  

> hide sel cartoons

> show #3 models

> show #!2 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> hide #!4 models

> show #!2 models

> show #!1 models

> show #!4 models

> ui tool show "Side View"

> hide #!1 models

> hide #!2 models

> hide #3 models

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

39 atoms, 44 bonds, 1 residue, 1 model selected  

> color sel orange

> color sel byhetero

> show sel surfaces

> select up

3787 atoms, 3869 bonds, 477 residues, 2 models selected  

> select up

5929 atoms, 6091 bonds, 722 residues, 2 models selected  

> select down

3787 atoms, 3869 bonds, 477 residues, 2 models selected  

> select down

39 atoms, 44 bonds, 1 residue, 2 models selected  

> select clear

> transparency #4:1102 59 surfaces

> show #!1 models

> show #!2 models

> show #3 models

> save "/Users/sguettler/OneDrive - The Institute of Cancer
> Research/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_Activation/PARP1_activation.cxs"

——— End of log from Thu Aug 31 15:18:04 2023 ———

opened ChimeraX session  

> close #3#4

> show cartoons

> ui tool show "Show Sequence Viewer"

> save "/Users/sguettler/OneDrive - The Institute of Cancer
> Research/Guettler_Sebastian/Manuscripts/2023_Biochemical_Journal_Perspective/Structures/PARP1_Activation/PARP1_activation_Zn1_Zn3_WGR-
> HD-ART.cxs"

> hide #!1 models

> ui tool show "Side View"

Drag select of 115 residues  
Drag select of 40 residues, 1 pseudobonds  
Drag select of 103 residues  

> select up

1478 atoms, 1505 bonds, 1 pseudobond, 183 residues, 2 models selected  

> select up

2598 atoms, 2657 bonds, 1 pseudobond, 328 residues, 2 models selected  

> select up

2630 atoms, 2688 bonds, 1 pseudobond, 332 residues, 2 models selected  

> select up

5333 atoms, 5444 bonds, 1 pseudobond, 678 residues, 2 models selected  

> select down

2630 atoms, 2688 bonds, 1 pseudobond, 332 residues, 2 models selected  

> select down

2598 atoms, 2657 bonds, 1 pseudobond, 328 residues, 2 models selected  

> ui tool show "Change Chain IDs"

> changechains sel C

Cannot reassign chain ID to only part of polymeric chain (PARP1-DNA_4dqy.pdb
#2/C)  

> select clear

Drag select of 83 residues  

> select up

904 atoms, 915 bonds, 114 residues, 1 model selected  

> select up

1747 atoms, 1784 bonds, 222 residues, 1 model selected  

> select up

1749 atoms, 1784 bonds, 224 residues, 1 model selected  

> select up

6399 atoms, 6635 bonds, 733 residues, 1 model selected  

> select down

1749 atoms, 1784 bonds, 224 residues, 1 model selected  

> changechains sel C

Chain IDs of 224 residues changed  

> changechains sel C

Chain IDs of 0 residues changed  

> changechains sel C

Chain IDs of 0 residues changed  

> select clear

> ui tool show "Show Sequence Viewer"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 560, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1269, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/show_sequences/__init__.py", line 21, in start_tool  
return Sequences(session, tool_name)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/show_sequences/tool.py", line 55, in __init__  
self._update_show_button()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/show_sequences/tool.py", line 71, in _update_show_button  
self._show_button.setEnabled(bool(self.chain_list.value))  
AttributeError: 'ChainListWidget' object has no attribute 'value'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1656, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 567, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Show
Sequence Viewer in bundle ChimeraX-ShowSequences:  
'ChainListWidget' object has no attribute 'value'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Show
Sequence Viewer in bundle ChimeraX-ShowSequences:  
'ChainListWidget' object has no attribute 'value'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 567, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> ui tool show Matchmaker

> hide #!2 models

> show #!1 models

Drag select of 116 residues, 1 pseudobonds  

> select up

2395 atoms, 2409 bonds, 1 pseudobond, 157 residues, 2 models selected  

> select up

3434 atoms, 3472 bonds, 1 pseudobond, 222 residues, 2 models selected  

> select up

3437 atoms, 3472 bonds, 1 pseudobond, 225 residues, 2 models selected  

> select up

11241 atoms, 11378 bonds, 3 pseudobonds, 709 residues, 2 models selected  

> select down

3437 atoms, 3472 bonds, 1 pseudobond, 225 residues, 2 models selected  

> ui tool show "Change Chain IDs"

> changechains sel D

Chain IDs of 225 residues changed  

> select clear

> hide #!1 models

> show #!2 models

> show #!1 models

> ui tool show Matchmaker

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 79, in showEvent  
self._items_change()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 169, in _items_change  
item_names = self._item_names()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 48, in _item_names  
values.sort(key=self.key_func)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1061, in __lt__  
return self.residues < other.residues  
File "atomic_cpp/cymol.pyx", line 975, in
chimerax.atomic.cymol.CyResidue.__lt__  
AttributeError: 'NoneType' object has no attribute 'structure'  
  
AttributeError: 'NoneType' object has no attribute 'structure'  
  
File "atomic_cpp/cymol.pyx", line 975, in
chimerax.atomic.cymol.CyResidue.__lt__  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

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: Mac14,9
      Model Number: Z17G001SLB/A
      Chip: Apple M2 Pro
      Total Number of Cores: 10 (6 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 8422.121.1

Software:

    System Software Overview:

      System Version: macOS 13.4.1 (22F82)
      Kernel Version: Darwin 22.5.0
      Time since boot: 8 days, 10 hours, 59 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL G2410:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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

[Eric Pettersen]

Hi Sebastian,

Thanks for reporting this problem. I have committed a fix and that fix will be in the next daily build.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab