H-Bonds: acc_phi_psi() bad number of arguments

[bhogeba@…]

The following bug report has been submitted:
Platform:        macOS-26.5-arm64-arm-64bit
ChimeraX Version: 1.10rc202506100450 (2025-06-10 04:50:02 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10rc202506100450 (2025-06-10)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/bhogeba/T4_dimeric
> tRNA/Ecoli_M1RNP/3'CCA_T4_tRNA/5mM_Ca/Reextracted
> /5mM_Ca_3CCA_Ser_J2562/5mM_Ca-
> holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb" format pdb

Chain information for 5mM_Ca-holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open "/Users/bhogeba/T4_dimeric tRNA/Gst_RNP/10mM_Ca_GstRNaseP_T4
> complex_J635_P21/J635Pro-coot-0.pdb"

Summary of feedback from opening /Users/bhogeba/T4_dimeric
tRNA/Gst_RNP/10mM_Ca_GstRNaseP_T4 complex_J635_P21/J635Pro-coot-0.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1910 messages similar to the above omitted  
PDB SEQRES record for chain C is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for J635Pro-coot-0.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open "/Users/bhogeba/T4_dimeric tRNA/Gst_RNP/10mM_Ca_GstRNaseP_T4
> complex_J635_P21/GstRNaseP_T4 complex_J635_P21_1.mrc"

Opened GstRNaseP_T4 complex_J635_P21_1.mrc as #3, grid size 312,312,312, pixel
1.36, shown at level 0.0145, step 2, values float32  

> open "/Users/bhogeba/T4_dimeric tRNA/Gst_RNP/10mM_Ca_GstRNaseP_T4
> complex_J635_P21/GstRNP_T4_complex_J635REP.pdb"

Chain information for GstRNP_T4_complex_J635REP.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
F | No description available  
  

> hide #1 models

> volume #3 level 0.1461

> hide #!3 models

> show #!3 models

> hide #4 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #4 models

> volume #3 level 0.2752

> show #4 models

> hide #4 models

> hide #!3 models

> show #!3 models

> hide #2 models

> volume #3 level 0.08868

> show #4 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> color #4 bychain

> show #1 models

> hide #4 models

> color #1 bychain

> nucleotides #1 atoms

> style nucleic & #1 stick

Changed 11611 atom styles  

> select #1/B:43

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

> select up

37 atoms, 36 bonds, 5 residues, 1 model selected  

> select up

941 atoms, 956 bonds, 115 residues, 1 model selected  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel atoms

> select clear

> open "/Users/bhogeba/T4_dimeric tRNA/Ecoli_M1RNP/Published
> structure/Published_7uo1.pdb"

Chain information for Published_7uo1.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> hide #1 models

> color #!5 bychain

> nucleotides #!5 atoms

> style nucleic & #!5 stick

Changed 14693 atom styles  

> select #5/A:14

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

> select up

163 atoms, 166 bonds, 10 residues, 1 model selected  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel atoms

> select clear

> select add #5

16588 atoms, 17761 bonds, 20 pseudobonds, 577 residues, 2 models selected  

> select H

5894 atoms, 567 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/A#2/A#4/A#5/A

26894 atoms, 30029 bonds, 1320 residues, 4 models selected  

> ui tool show Matchmaker

> matchmaker #2,4#!5 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 5mM_Ca-holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb, chain A (#1)
with J635Pro-coot-0.pdb, chain A (#2), sequence alignment score = 1343.1  
RMSD between 39 pruned atom pairs is 1.150 angstroms; (across all 348 pairs:
36.851)  
  
Matchmaker 5mM_Ca-holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb, chain A (#1)
with GstRNP_T4_complex_J635REP.pdb, chain A (#4), sequence alignment score =
1343.1  
RMSD between 37 pruned atom pairs is 1.051 angstroms; (across all 348 pairs:
36.824)  
  
Matchmaker 5mM_Ca-holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb, chain A (#1)
with Published_7uo1.pdb, chain B (#5), sequence alignment score = 2219.3  
RMSD between 183 pruned atom pairs is 1.256 angstroms; (across all 373 pairs:
3.686)  
  

> show #2 models

> hide #2 models

> show #1 models

> hide sel & #1#!5 atoms

> select clear

> hide #1#!5 atoms

> color #1#!5 bychain

> select #5/C:-4

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

> select add #5/C:-3

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #5/C:-2

60 atoms, 63 bonds, 3 residues, 1 model selected  

> select add #5/C:-1

82 atoms, 87 bonds, 4 residues, 1 model selected  

> select add #1/C:76

102 atoms, 108 bonds, 5 residues, 2 models selected  

> select add #5/C:1

125 atoms, 133 bonds, 6 residues, 2 models selected  

> select add #5/C:0

145 atoms, 154 bonds, 7 residues, 2 models selected  

> select subtract #5/C:-1

123 atoms, 130 bonds, 6 residues, 2 models selected  

> select add #5/C:-1

145 atoms, 154 bonds, 7 residues, 2 models selected  

> select add #1/C:74

167 atoms, 178 bonds, 8 residues, 2 models selected  

> select add #1/C:73

190 atoms, 203 bonds, 9 residues, 2 models selected  

> select add #1/C:72

212 atoms, 227 bonds, 10 residues, 2 models selected  

> select add #1/C:71

235 atoms, 252 bonds, 11 residues, 2 models selected  

> select add #1/C:75

255 atoms, 273 bonds, 12 residues, 2 models selected  

> select add #1/C:77

278 atoms, 298 bonds, 13 residues, 2 models selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 278 atom styles  

> hbonds sel reveal true

141 hydrogen bonds found  

> select clear

[Repeated 1 time(s)]

> hide #1 models

> show #1 models

> hide #!5 models

> hide #6 models

> show #6 models

> show #!5 models

> hide #!5 models

> hide #1 models

> show #!5 models

> select #5/A:13

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

> select add #5/A:14

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

> select add #5/A:15

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

> select add #5/A:16

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

> select add #5/A:17

40 atoms, 37 bonds, 5 residues, 1 model selected  

> select add #5/A:18

51 atoms, 48 bonds, 6 residues, 1 model selected  

> select add #5/A:19

58 atoms, 54 bonds, 7 residues, 1 model selected  

> select add #5/A:20

69 atoms, 65 bonds, 8 residues, 1 model selected  

> select add #5/A:21

78 atoms, 73 bonds, 9 residues, 1 model selected  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel atoms

> select #5/B:352

22 atoms, 24 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #5/B:247

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

> show sel atoms

> select #5/B:248

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #5/B:247

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

> select #5/B:248

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #5/C:-1

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #5/B:333

44 atoms, 48 bonds, 2 residues, 1 model selected  

> select add #5/B:332

67 atoms, 73 bonds, 3 residues, 1 model selected  

> select clear

> show #1 models

> hide #6 models

> show #6 models

> hide #6 models

> hide #!5 models

> show #!5 models

> select add #1/B:11

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

> select add #1/B:10

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

> select add #1/B:13

28 atoms, 26 bonds, 3 residues, 1 model selected  

> select add #1/B:12

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

> select add #1/B:14

46 atoms, 42 bonds, 5 residues, 1 model selected  

> select add #1/B:15

55 atoms, 50 bonds, 6 residues, 1 model selected  

> select add #1/B:16

62 atoms, 56 bonds, 7 residues, 1 model selected  

> select add #1/B:17

73 atoms, 67 bonds, 8 residues, 1 model selected  

> select add #1/B:18

82 atoms, 75 bonds, 9 residues, 1 model selected  

> select add #1/B:19

91 atoms, 83 bonds, 10 residues, 1 model selected  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel atoms

> select clear

> hide #1 models

> hide #!5 models

> show #1 models

> open "/Users/bhogeba/T4_dimeric
> tRNA/Ecoli_M1RNP/3'CCA_T4_tRNA/5mM_Ca/Reextracted
> /5mM_Ca_3CCA_Ser_J2562/5mM_Ca-
> holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb"

Chain information for 5mM_Ca-holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> nucleotides #1,7 atoms

> style nucleic & #1,7 stick

Changed 23222 atom styles  

> color #1,7 bychain

> close #1

> select add #7

12594 atoms, 13953 bonds, 698 residues, 1 model selected  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 11611 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 11611 atom styles  

> show sel atoms

> select subtract #7

Nothing selected  

> hide #7 atoms

> select #7/C:76

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

> select add #7/C:75

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #7/C:74

62 atoms, 66 bonds, 3 residues, 1 model selected  

> select add #7/C:73

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select add #7/C:72

107 atoms, 115 bonds, 5 residues, 1 model selected  

> select add #7/C:71

130 atoms, 140 bonds, 6 residues, 1 model selected  

> show sel atoms

> hbonds sel reveal true

82 hydrogen bonds found  

> show #6 models

> select #7/C:75

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

> select #7/B:14

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

> select up

91 atoms, 92 bonds, 10 residues, 1 model selected  

> select up

941 atoms, 956 bonds, 115 residues, 1 model selected  

> show sel atoms

> select #7/A:352

22 atoms, 24 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> show sel atoms

> select #7/C:77

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #7/C:76

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

> select #7/C:77

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #7/C:76

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

> select #7/C:77

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

18 hydrogen bonds found  

> select #7/A:330

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select #7/A:353

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

> nucleotides sel atoms

> style nucleic & sel stick

Changed 20 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 20 atom styles  

> show sel atoms

> open "/Users/bhogeba/T4_dimeric tRNA/Gst_RNP/10mM_Ca_GstRNaseP_T4
> complex_J635_P21/J635Pro.pdb"

Summary of feedback from opening /Users/bhogeba/T4_dimeric
tRNA/Gst_RNP/10mM_Ca_GstRNaseP_T4 complex_J635_P21/J635Pro.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1910 messages similar to the above omitted  
PDB SEQRES record for chain C is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for J635Pro.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> hide #6 models

> hide #7 models

> show #7 models

> select add #7

12594 atoms, 13953 bonds, 6 pseudobonds, 698 residues, 2 models selected  

> select subtract #7

Nothing selected  

> hide #!1 models

> hide #7 models

> show #!1 models

> color #!1 bychain

> show #2 models

> color #2#!1 bychain

> hide #!1 models

> open "/Users/bhogeba/T4_dimeric
> tRNA/Ecoli_M1RNP/3'CCA_T4_tRNA/5mM_Ca/Reextracted
> /5mM_Ca_3CCA_Ser_J2562/J2562_no_Metals.pdb"

Chain information for J2562_no_Metals.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> hide #2 models

> color #8 bychain

> buriedArea #1/A,B #1/C

Unknown command: measure buriedArea #1/A,B #1/C  

> buriedArea #8/A,B #8/C

Unknown command: measure buriedArea #8/A,B #8/C  

> buriedArea #8/A #8/C

Unknown command: measure buriedArea #8/A #8/C  

> buriedArea #8/A with #8/C distance 4.0

Unknown command: measure buriedArea #8/A with #8/C distance 4.0  

> measure buriedarea #8/A withAtoms2 #8/B

Buried area between #8/A and #8/B = 1235.2  
area #8/A = 54424, area #8/B = 6440.1, area both = 58394  

> measure buriedarea #8/A,B withAtoms2 #8/C

Buried area between #8/A,B and #8/C = 2596.5  
area #8/A,B = 58394, area #8/C = 26800, area both = 80001  

> measure buriedarea #8/A,B withAtoms2 #8/C distance 4.0

Expected a keyword  

> surface #8

> measure buriedarea #8/A,B withAtoms2 #8/C select true cutoffArea 4

Buried area between #8/A,B and #8/C = 2596.5  
area #8/A,B = 58394, area #8/C = 26800, area both = 80001  

> color sel yellow target s

> hide sel surfaces

[Repeated 1 time(s)]

> show sel surfaces

> select clear

> hide #!8 surfaces

> show #!8 surfaces

> hide #!8 surfaces

> measure buriedarea #8/A,B withAtoms2 #8/C select true cutoffArea 4

Buried area between #8/A,B and #8/C = 2596.5  
area #8/A,B = 58394, area #8/C = 26800, area both = 80001  

> color sel yellow target s

> color (#!8 & sel) cyan

> show sel surfaces

> hide sel surfaces

> select clear

> nucleotides #!8 atoms

> style nucleic & #!8 stick

Changed 11611 atom styles  

> measure buriedarea #8/A,B withAtoms2 #8/C select true cutoffArea 4

Buried area between #8/A,B and #8/C = 2596.5  
area #8/A,B = 58394, area #8/C = 26800, area both = 80001  

> hbonds sel reveal true

Skipping possible acceptor with bad geometry: J635Pro.pdb #1/C U 155 O4  
Wrong number of grandchild atoms for phi/psi acceptor J635Pro.pdb #1/C U 155
O4  
  
donor: J635Pro.pdb #1/C A 139 N6 acceptor: J635Pro.pdb #1/C C 156 N3  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.10.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-rc2025.06.10.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):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File
"/Applications/ChimeraX-1.10-rc2025.06.10.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):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> hbonds sel reveal true

Skipping possible acceptor with bad geometry: J635Pro.pdb #1/C U 155 O4  
Wrong number of grandchild atoms for phi/psi acceptor J635Pro.pdb #1/C U 155
O4  
  
donor: J635Pro.pdb #1/C A 139 N6 acceptor: J635Pro.pdb #1/C C 156 N3  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.10.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-rc2025.06.10.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):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File
"/Applications/ChimeraX-1.10-rc2025.06.10.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):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> select clear

> select #8/C:145

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

> select add #8/C:144

40 atoms, 42 bonds, 2 residues, 2 models selected  

> select add #8/C:146

60 atoms, 63 bonds, 3 residues, 2 models selected  

> select add #8/C:143

83 atoms, 88 bonds, 4 residues, 2 models selected  

> select add #8/C:142

106 atoms, 113 bonds, 5 residues, 2 models selected  

> select add #8/C:151

126 atoms, 134 bonds, 6 residues, 2 models selected  

> select add #8/C:152

146 atoms, 155 bonds, 7 residues, 2 models selected  

> select add #8/C:153

166 atoms, 176 bonds, 8 residues, 2 models selected  

> select add #8/A:118

188 atoms, 200 bonds, 9 residues, 2 models selected  

> select add #8/A:233

210 atoms, 224 bonds, 10 residues, 3 models selected  

> select add #8/A:234

232 atoms, 248 bonds, 11 residues, 3 models selected  

> select add #8/A:5

252 atoms, 269 bonds, 12 residues, 3 models selected  

> select subtract #8/A:5

232 atoms, 248 bonds, 11 residues, 3 models selected  

> select add #8/C:154

254 atoms, 272 bonds, 12 residues, 3 models selected  

> select add #8/C:155

274 atoms, 293 bonds, 13 residues, 3 models selected  

> select add #8/C:156

294 atoms, 314 bonds, 14 residues, 3 models selected  

> select add #8/A:359

314 atoms, 335 bonds, 15 residues, 3 models selected  

> select add #8/A:70

334 atoms, 356 bonds, 16 residues, 3 models selected  

> select add #8/A:69

354 atoms, 377 bonds, 17 residues, 3 models selected  

> select add #8/A:360

374 atoms, 398 bonds, 18 residues, 3 models selected  

> hbonds sel reveal true

Skipping possible acceptor with bad geometry: J635Pro.pdb #1/C U 155 O4  
Wrong number of grandchild atoms for phi/psi acceptor J635Pro.pdb #1/C U 155
O4  
  
donor: J635Pro.pdb #1/C A 139 N6 acceptor: J635Pro.pdb #1/C C 156 N3  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.10.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-rc2025.06.10.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):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File
"/Applications/ChimeraX-1.10-rc2025.06.10.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):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3 Pro
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: MacBook Pro
      Model Identifier: Mac15,6
      Model Number: Z1AU00299LL/A
      Chip: Apple M3 Pro
      Total Number of Cores: 11 (5 Performance and 6 Efficiency)
      Memory: 18 GB
      System Firmware Version: 18000.120.36
      OS Loader Version: 18000.120.36

Software:

    System Software Overview:

      System Version: macOS 26.5 (25F71)
      Kernel Version: Darwin 25.5.0
      Time since boot: 6 hours, 13 minutes

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      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 P2715Q:
          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
        DELL P2715Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 30.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.4
    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: 14.1.18
    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-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: 1.10rc202506100450
    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-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: 2.2.1
    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: 1.1.2
    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: 1.45.1
    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: 7.8.2
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.2
    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: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    narwhals: 2.21.2
    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: 2.4.6
    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
    plotly: 6.7.0
    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
    pyelftools: 0.32
    Pygments: 2.18.0
    pyKVFinder: 0.9.2
    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: 8.4.0
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 26.4.0
    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
    tomlkit: 0.15.0
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.4.0
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[Eric Pettersen]

Hi Bapurao,

Thanks for reporting this problem. In order to find hydrogen bonds, ChimeraX requires that the normal bonds in your structure are correct. The bonds in your J635Pro-coot-0.pdb structure are not correct. This is undoubtedly because of incorrect CONECT records (which indicate bonds) in the PDB file. The simplest solution is just to use an editor to delete the CONECT records in the file. ChimeraX will then figure out the bond connectivity itself, which it usually does correctly. Then you should be able to find hydrogen bonds successfully.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab