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Opened 17 hours ago
Last modified 14 hours ago
#20140 feedback defect
H-Bonds: no bisectors
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
I wanted to display H-bonds in a nucleic acid helix
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/janpetrovsky/Downloads/custom.cif
Summary of feedback from opening /Users/janpetrovsky/Downloads/custom.cif
---
warnings | Unknown polymer entity '2' on line 97
Unknown polymer entity '2 1' on line 237
Unknown polymer entity '2 2' on line 367
Unknown polymer entity '2' on line 97
Unknown polymer entity '4' on line 13644
6 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom H61 is not in the residue template for DG /T:16
Atom P is not in the residue template for DRG /N:1
notes | Fetching CCD CTP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/CTP/CTP.cif
PDBx/mmCIF styling lost on line 391. Rereading mmCIF file from the beginning.
custom.cif title:
. [more info...]
Chain information for custom.cif #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
T | No description available
Non-standard residues in custom.cif #1
---
CTP — (CTP)
DRG — (DRG)
MG — (MG)
ZN — (ZN)
> select add #1
62827 atoms, 63496 bonds, 61 pseudobonds, 3920 residues, 3 models selected
> hide sel atoms
> show sel cartoons
Computing secondary structure
> hide #!1 models
> open
> /Users/janpetrovsky/Desktop/Ap4A_final/Final_AP4AG/final/final_Ap4AG_J3305_flip.mrc
Opened final_Ap4AG_J3305_flip.mrc as #2, grid size 512,512,512, pixel 0.76,
shown at level 0.0118, step 2, values float32
> volume #2 step 1
> volume #2 level 0.04128
> show #!1 models
> select /K:98
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /N:2
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
109 atoms, 118 bonds, 3 residues, 1 model selected
> select add /T:21
141 atoms, 152 bonds, 4 residues, 1 model selected
> select up
615 atoms, 664 bonds, 19 residues, 1 model selected
> select ~sel & ##selected
62212 atoms, 62832 bonds, 60 pseudobonds, 3901 residues, 3 models selected
> hide sel cartoons
Drag select of 18 residues
> vop zone #2 nearAtoms sel range 3
> show #!2 models
> surface dust #2 size 7.6
> vop zone #2 nearAtoms sel range 3 new true
Opened final_Ap4AG_J3305_flip.mrc zone as #3, grid size 512,512,512, pixel
0.76, shown at step 1, values float32
> surface dust #3 size 7.6
> show sel atoms
> hide sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 582 atom styles
> color sel byhetero
> hide H
> select clear
> select ::name="DRG"
53 atoms, 58 bonds, 1 residue, 1 model selected
> select ::name="CTP"
41 atoms, 42 bonds, 1 residue, 1 model selected
> show sel atoms
> save /Users/janpetrovsky/Desktop/final_final_finalAp4AG_Cppp_dnatco.pdb
> open /Users/janpetrovsky/Desktop/final_final_finalAp4AG_Cppp_dnatco.pdb
Chain information for final_final_finalAp4AG_Cppp_dnatco.pdb #4
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
T | No description available
> hide #!1 models
> hide #!3 models
> select add #4
62868 atoms, 63537 bonds, 53 pseudobonds, 3921 residues, 4 models selected
> hide sel & #!4 atoms
> show sel & #!4 cartoons
> select clear
> select ::name="CTP"
82 atoms, 84 bonds, 2 residues, 2 models selected
> show sel & #!4 atoms
> select #4/N:2
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
109 atoms, 118 bonds, 3 residues, 1 model selected
> show sel atoms
> hide #!4 models
> show #!1 models
> select clear
> show #!4 models
> hide #!1 models
> select #4/N:2
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
109 atoms, 118 bonds, 3 residues, 1 model selected
> select add #4/T:19
141 atoms, 152 bonds, 4 residues, 1 model selected
> select up
615 atoms, 664 bonds, 19 residues, 1 model selected
> select ~sel & ##selected
62212 atoms, 62831 bonds, 52 pseudobonds, 3901 residues, 3 models selected
> hide sel cartoons
> select clear
> select #4/N:2
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
109 atoms, 118 bonds, 3 residues, 1 model selected
> select up
62827 atoms, 63495 bonds, 3920 residues, 1 model selected
> show sel atoms
> hide #!4 models
> show #!4 models
> select add #4
62827 atoms, 63495 bonds, 53 pseudobonds, 3920 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select ~sel & ##selected
Nothing selected
> select #4/N:2
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
109 atoms, 118 bonds, 3 residues, 1 model selected
> select add #4/T:20
138 atoms, 148 bonds, 4 residues, 1 model selected
> select up
615 atoms, 664 bonds, 19 residues, 1 model selected
> select ~sel & ##selected
62212 atoms, 62831 bonds, 52 pseudobonds, 3901 residues, 3 models selected
> hide sel cartoons
Drag select of 18 residues
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 582 atom styles
> color sel byhetero
> select clear
> select ::name="CTP"
82 atoms, 84 bonds, 2 residues, 2 models selected
> show sel & #!4 atoms
> select add #1
62868 atoms, 63538 bonds, 61 pseudobonds, 3921 residues, 4 models selected
> select subtract #1
41 atoms, 42 bonds, 1 residue, 1 model selected
> open /Users/janpetrovsky/Downloads/custom.cif
Summary of feedback from opening /Users/janpetrovsky/Downloads/custom.cif
---
warnings | Unknown polymer entity '2' on line 109
Unknown polymer entity '3' on line 281
Unknown polymer entity '3 1' on line 421
Unknown polymer entity '3 2' on line 551
Unknown polymer entity '3 3' on line 713
10 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom P is not in the residue template for DRG /A:1
notes | PDBx/mmCIF styling lost on line 1104. Rereading mmCIF file from the beginning.
Fetching CCD UTP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/UTP/UTP.cif
custom.cif title:
. [more info...]
Chain information for custom.cif #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
T | No description available
Non-standard residues in custom.cif #5
---
DRG — (DRG)
MG — (MG)
UTP — (UTP)
ZN — (ZN)
> open /Users/janpetrovsky/Desktop/custom.cif
Summary of feedback from opening /Users/janpetrovsky/Desktop/custom.cif
---
warnings | Unknown polymer entity '2' on line 109
Unknown polymer entity '3' on line 281
Unknown polymer entity '3 1' on line 421
Unknown polymer entity '3 2' on line 551
Unknown polymer entity '3 3' on line 713
10 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom P is not in the residue template for DRG /A:1
note | PDBx/mmCIF styling lost on line 1104. Rereading mmCIF file from the beginning.
custom.cif title:
. [more info...]
Chain information for custom.cif #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
T | No description available
Non-standard residues in custom.cif #6
---
DRG — (DRG)
MG — (MG)
UTP — (UTP)
ZN — (ZN)
> hide #!4 models
> hide #!5 models
> select add #6
63302 atoms, 63996 bonds, 60 pseudobonds, 3937 residues, 4 models selected
> select add #4
126088 atoms, 127449 bonds, 113 pseudobonds, 7856 residues, 6 models selected
> select subtract #4
63261 atoms, 63954 bonds, 60 pseudobonds, 3936 residues, 3 models selected
> hide sel atoms
> show sel cartoons
Computing secondary structure
> select clear
> select #6/A:3
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
225 atoms, 250 bonds, 9 residues, 1 model selected
> select add #6/T:19
255 atoms, 281 bonds, 10 residues, 1 model selected
> select up
954 atoms, 1035 bonds, 32 residues, 1 model selected
> select ~sel & ##selected
62307 atoms, 62919 bonds, 60 pseudobonds, 3904 residues, 3 models selected
> hide sel cartoons
Drag select of 32 residues
> show sel atoms
> hide sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 954 atom styles
> color sel byhetero
> hide H
> select clear
> open
> /Users/janpetrovsky/Desktop/Ap4A_final/Final_GT/final/final_final_final_GT_mutant_Uppp_dnatco.cif
Summary of feedback from opening
/Users/janpetrovsky/Desktop/Ap4A_final/Final_GT/final/final_final_final_GT_mutant_Uppp_dnatco.cif
---
warnings | Unknown polymer entity '2' on line 109
Unknown polymer entity '3' on line 281
Unknown polymer entity '3 1' on line 421
Unknown polymer entity '3 2' on line 551
Unknown polymer entity '3 3' on line 713
10 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom P is not in the residue template for DRG /A:1
note | PDBx/mmCIF styling lost on line 1104. Rereading mmCIF file from the beginning.
final_final_final_GT_mutant_Uppp_dnatco.cif title:
. [more info...]
Chain information for final_final_final_GT_mutant_Uppp_dnatco.cif #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
T | No description available
Non-standard residues in final_final_final_GT_mutant_Uppp_dnatco.cif #7
---
DRG — (DRG)
MG — (MG)
UTP — (UTP)
ZN — (ZN)
> save
> /Users/janpetrovsky/Desktop/Ap4A_final/Final_GT/final/final_final_final_GT_mutant_Uppp_dnatco.pdb
> models #7
Computing secondary structure
> open
> /Users/janpetrovsky/Desktop/Ap4A_final/Final_GT/final/final_final_final_GT_mutant_Uppp_dnatco.pdb
Chain information for final_final_final_GT_mutant_Uppp_dnatco.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
T | No description available
> hide #!6 models
> hide #!7 models
> hide #!8 models
> show #!8 models
> select add #8
63261 atoms, 63954 bonds, 51 pseudobonds, 3936 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select #8/A:3
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
225 atoms, 250 bonds, 9 residues, 1 model selected
> select add #8/T:25
257 atoms, 283 bonds, 10 residues, 1 model selected
> select up
954 atoms, 1035 bonds, 32 residues, 1 model selected
> select ~sel & ##selected
62307 atoms, 62919 bonds, 51 pseudobonds, 3904 residues, 3 models selected
> hide sel cartoons
Drag select of 32 residues
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 954 atom styles
> color sel byhetero
> hide sel cartoons
> select ::name="CTP"
82 atoms, 84 bonds, 2 residues, 2 models selected
> select ::name="UTP"
160 atoms, 164 bonds, 4 residues, 4 models selected
> show sel & #!8 atoms
> select clear
Drag select of 994 atoms, 1076 bonds
> open
> /Users/janpetrovsky/Desktop/Ap4A_final/Final_GT/final/final_GT_J3048_flip.mrc
Opened final_GT_J3048_flip.mrc as #9, grid size 512,512,512, pixel 0.76, shown
at level 0.0215, step 2, values float32
> vop zone #9 nearAtoms sel range 3 new true
Opened final_GT_J3048_flip.mrc zone as #10, grid size 512,512,512, pixel 0.76,
shown at step 1, values float32
> surface dust #10 size 7.6
> volume #10 color #b2b2ff9b
> select clear
[Repeated 1 time(s)]
> volume #10 level 0.02146
> volume #10 step 1
> volume #10 level 0.04623
> volume #10 level 0.05736
Drag select of 5 atoms, 2 bonds
> select clear
Drag select of 698 atoms, 758 bonds
> hbonds sel reveal true
Skipping possible acceptor with bad geometry: custom.cif #1/I CYS 31 O
Wrong number of grandchild atoms for phi/psi acceptor custom.cif #1/I CYS 31 O
[Repeated 37 time(s)]
Skipped 38 atom(s) with bad connectivities; see log for details
380 hydrogen bonds found
> open
> /Users/janpetrovsky/Desktop/Ap4A_final/Final_GT/prefinal/final_final_final_GT_mutant_Uppp.pdb
Chain information for final_final_final_GT_mutant_Uppp.pdb #12
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
T | No description available
> hide #11 models
> hide #!8 models
> select add #8
63261 atoms, 63954 bonds, 103 pseudobonds, 3936 residues, 4 models selected
> select subtract #8
Nothing selected
> select add #12
63261 atoms, 63987 bonds, 41 pseudobonds, 3936 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select #12/M:663
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #12/A:3
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
225 atoms, 249 bonds, 9 residues, 1 model selected
> select add #12/T:25
257 atoms, 282 bonds, 10 residues, 1 model selected
> select up
954 atoms, 1034 bonds, 32 residues, 1 model selected
> select ~sel & ##selected
62307 atoms, 62953 bonds, 41 pseudobonds, 3904 residues, 2 models selected
> hide sel cartoons
Drag select of 32 residues
> show sel atoms
> hide sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 954 atom styles
> color sel byhetero
> hide H
> select clear
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!10 models
> show #!8 models
> hide #!12 models
> hide #!8 models
> show #!8 models
> show #!12 models
> hide #!12 models
> open /Users/janpetrovsky/Downloads/custom.cif
Summary of feedback from opening /Users/janpetrovsky/Downloads/custom.cif
---
warnings | Unknown polymer entity '2' on line 109
Unknown polymer entity '3' on line 281
Unknown polymer entity '3 1' on line 421
Unknown polymer entity '3 2' on line 551
Unknown polymer entity '3 3' on line 713
10 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom P is not in the residue template for DRG /A:1
note | PDBx/mmCIF styling lost on line 1104. Rereading mmCIF file from the beginning.
custom.cif title:
. [more info...]
Chain information for custom.cif #13
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
T | No description available
Non-standard residues in custom.cif #13
---
DRG — (DRG)
MG — (MG)
UTP — (UTP)
ZN — (ZN)
> hide #!8 models
> hide #!10 models
> select add #13
63261 atoms, 63954 bonds, 60 pseudobonds, 3936 residues, 3 models selected
> hide sel atoms
> show sel cartoons
Computing secondary structure
> select #13/A:3
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
225 atoms, 250 bonds, 9 residues, 1 model selected
> select add #13/T:25
257 atoms, 283 bonds, 10 residues, 1 model selected
> select up
954 atoms, 1035 bonds, 32 residues, 1 model selected
> select ~sel & ##selected
62307 atoms, 62919 bonds, 60 pseudobonds, 3904 residues, 3 models selected
> hide sel cartoons
Drag select of 32 residues
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 954 atom styles
> color sel byhetero
> hide sel cartoons
> select clear
> show #!12 models
> hide #!12 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #!13 models
> show #!13 models
> open "/Users/janpetrovsky/Downloads/custom (1).cif"
Summary of feedback from opening /Users/janpetrovsky/Downloads/custom (1).cif
---
warnings | Unknown polymer entity '2' on line 109
Unknown polymer entity '3' on line 281
Unknown polymer entity '3 1' on line 421
Unknown polymer entity '3 2' on line 551
Unknown polymer entity '3 3' on line 713
10 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom P is not in the residue template for DRG /A:1
note | PDBx/mmCIF styling lost on line 1104. Rereading mmCIF file from the beginning.
custom (1).cif title:
. [more info...]
Chain information for custom (1).cif #14
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
T | No description available
Non-standard residues in custom (1).cif #14
---
DRG — (DRG)
MG — (MG)
UTP — (UTP)
ZN — (ZN)
> hide #!13 models
> hide #!12 models
> select add #14
63261 atoms, 63954 bonds, 60 pseudobonds, 3936 residues, 3 models selected
> hide sel atoms
> show sel cartoons
Computing secondary structure
> select #14/A:3
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
225 atoms, 250 bonds, 9 residues, 1 model selected
> select add #14/T:25
257 atoms, 283 bonds, 10 residues, 1 model selected
> select up
954 atoms, 1035 bonds, 32 residues, 1 model selected
> select ~sel & ##selected
62307 atoms, 62919 bonds, 60 pseudobonds, 3904 residues, 3 models selected
> hide sel cartoons
Drag select of 32 residues
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 954 atom styles
> color sel byhetero
> hide sel cartoons
> hide H
> select clear
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #11 models
> hide #!14 models
> show #!8 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
225 atoms, 250 bonds, 9 residues, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select clear
> open /Users/janpetrovsky/Desktop/final_final_final_GT_mutant_Uppp_dnatco-
> coot-0.pdb
Chain information for final_final_final_GT_mutant_Uppp_dnatco-coot-0.pdb #15
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
T | No description available
> open "/Users/janpetrovsky/Downloads/custom (2).cif"
Summary of feedback from opening /Users/janpetrovsky/Downloads/custom (2).cif
---
warnings | Unknown polymer entity '2' on line 109
Unknown polymer entity '3' on line 281
Unknown polymer entity '3 1' on line 421
Unknown polymer entity '3 2' on line 551
Unknown polymer entity '3 3' on line 713
10 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom P is not in the residue template for DRG /A:1
note | PDBx/mmCIF styling lost on line 1104. Rereading mmCIF file from the beginning.
custom (2).cif title:
. [more info...]
Chain information for custom (2).cif #16
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
T | No description available
Non-standard residues in custom (2).cif #16
---
DRG — (DRG)
MG — (MG)
UTP — (UTP)
ZN — (ZN)
> hide #!15 models
> show #!15 models
> hide #!10 models
> hide #11 models
> hide #!8 models
> hide #!15 models
> show #!15 models
> hide #!15-16 atoms
> show #!15-16 cartoons
Computing secondary structure
> hide #!15 models
> select #16/A:5
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
225 atoms, 250 bonds, 9 residues, 1 model selected
> select add #16/T:25
257 atoms, 283 bonds, 10 residues, 1 model selected
> select up
954 atoms, 1035 bonds, 32 residues, 1 model selected
> select ~sel & ##selected
62307 atoms, 62919 bonds, 57 pseudobonds, 3904 residues, 3 models selected
> hide sel cartoons
> hide #!16 models
> show #!15 models
> select #15/T:25
32 atoms, 33 bonds, 1 residue, 1 model selected
> select up
729 atoms, 785 bonds, 23 residues, 1 model selected
> select add #15/A:5
749 atoms, 806 bonds, 24 residues, 1 model selected
> select up
954 atoms, 1035 bonds, 32 residues, 1 model selected
> select ~sel & ##selected
62307 atoms, 62919 bonds, 51 pseudobonds, 3904 residues, 3 models selected
> hide sel cartoons
> show #!16 models
> hide #!15 models
> show #!15 models
> select add #15
63261 atoms, 63954 bonds, 51 pseudobonds, 3936 residues, 3 models selected
> select subtract #15
Nothing selected
Drag select of 64 residues
> show sel atoms
> hide sel cartoons
> color sel byhetero
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1908 atom styles
> hide H
> hide #!15 models
> select clear
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!10 models
> volume #10 level 0.05233
Drag select of 669 atoms, 749 bonds
> hbonds sel reveal true
donor: custom.cif #1/B SER 472 OG acceptor:
final_final_final_GT_mutant_Uppp.pdb #12/B ASN 471 O
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run
f(s)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 594, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/cmd.py", line 94, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
IndexError: list index out of range
IndexError: list index out of range
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
See log for complete Python traceback.
> select clear
Drag select of 419 atoms, 466 bonds
> select clear
Drag select of 369 atoms, 410 bonds
> hbonds sel reveal true
donor: custom.cif #1/B SER 472 OG acceptor:
final_final_final_GT_mutant_Uppp.pdb #12/B ASN 471 O
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run
f(s)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 594, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/cmd.py", line 94, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
IndexError: list index out of range
IndexError: list index out of range
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
See log for complete Python traceback.
> select clear
> show #11 models
> show #!8 models
> hide #!16 models
> hide #11 models
> hide #!8 models
> show #!16 models
Drag select of 553 atoms, 617 bonds
> hbonds sel reveal true
donor: custom.cif #1/B SER 472 OG acceptor:
final_final_final_GT_mutant_Uppp.pdb #12/B ASN 471 O
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run
f(s)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 594, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/cmd.py", line 94, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
IndexError: list index out of range
IndexError: list index out of range
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
See log for complete Python traceback.
> hide #!16 models
> show #!15 models
> select add #16
63261 atoms, 63954 bonds, 57 pseudobonds, 3936 residues, 3 models selected
> select subtract #16
Nothing selected
Drag select of 537 atoms, 597 bonds
> hbonds sel reveal true
donor: custom.cif #1/B SER 472 OG acceptor:
final_final_final_GT_mutant_Uppp.pdb #12/B ASN 471 O
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run
f(s)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 594, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/cmd.py", line 94, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
IndexError: list index out of range
IndexError: list index out of range
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
See log for complete Python traceback.
> select clear
Drag select of 210 atoms, 235 bonds
> hbonds sel reveal true
donor: custom.cif #1/B SER 472 OG acceptor:
final_final_final_GT_mutant_Uppp.pdb #12/B ASN 471 O
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run
f(s)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 594, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/cmd.py", line 94, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
IndexError: list index out of range
IndexError: list index out of range
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
See log for complete Python traceback.
> close #15
> close #16
> open /Users/janpetrovsky/Desktop/final_final_final_GT_mutant_Uppp_dnatco-
> coot-0.pdb
Chain information for final_final_final_GT_mutant_Uppp_dnatco-coot-0.pdb #15
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
T | No description available
> select add #15
63261 atoms, 63954 bonds, 51 pseudobonds, 3936 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select clear
> select #15/A:3
20 atoms, 21 bonds, 1 residue, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
225 atoms, 250 bonds, 9 residues, 1 model selected
> select add #15/T:26
258 atoms, 285 bonds, 10 residues, 1 model selected
> select up
954 atoms, 1035 bonds, 32 residues, 1 model selected
> select ~sel & ##selected
62307 atoms, 62919 bonds, 51 pseudobonds, 3904 residues, 3 models selected
> hide sel cartoons
Drag select of 32 residues
> hbonds sel reveal true
donor: custom.cif #1/B SER 472 OG acceptor:
final_final_final_GT_mutant_Uppp.pdb #12/B ASN 471 O
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run
f(s)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 594, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/cmd.py", line 94, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
IndexError: list index out of range
IndexError: list index out of range
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
See log for complete Python traceback.
> hbonds sel reveal true
donor: custom.cif #1/B SER 472 OG acceptor:
final_final_final_GT_mutant_Uppp.pdb #12/B ASN 471 O
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run
f(s)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 594, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/cmd.py", line 94, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
IndexError: list index out of range
IndexError: list index out of range
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
~~~~~~~~~^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Mac14,3
Model Number: Z16L000FTCZ/A
Chip: Apple M2
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 16 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (a) (25D771280a)
Kernel Version: Darwin 25.3.0
Time since boot: 7 days, 5 hours, 25 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
U27P2G6B:
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
Rotation: Supported
U2790B:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 14 hours ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → H-Bonds: no bisectors |
comment:2 by , 14 hours ago
| Status: | accepted → feedback |
|---|
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Hi Jan,
--Eric