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Opened 11 months ago
Closed 11 months ago
#16440 closed defect (limitation)
H-Bonds: acc_phi_psi() bad number of arguments
| 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: Windows-10-10.0.22631
ChimeraX Version: 1.9rc202412062357 (2024-12-06 23:57:32 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202412062357 (2024-12-06)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model20.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model19.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model18.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model17.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model16.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model15.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model14.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model13.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model12.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model11.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model10.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model9.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model8.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model7.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model6.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model5.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model4.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model3.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model2.1.pdb
> C:/Users/hp/Downloads/modelling_paper/target_ribosome_refined_model1.pdb
Chain information for target_ribosome_refined_model20.pdb #1
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model19.pdb #2
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model18.pdb #3
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model17.pdb #4
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model16.pdb #5
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model15.pdb #6
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model14.pdb #7
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model13.pdb #8
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model12.pdb #9
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model11.pdb #10
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model10.pdb #11
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model9.pdb #12
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model8.pdb #13
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model7.pdb #14
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model6.pdb #15
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model5.pdb #16
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model4.pdb #17
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model3.pdb #18
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model2.1.pdb #19
---
Chain | Description
A | No description available
Chain information for target_ribosome_refined_model1.pdb #20
---
Chain | Description
A | No description available
Computing secondary structure
[Repeated 19 time(s)]
> open C:/Users/hp/Downloads/modelling_paper/1j5e.pdb
1j5e.pdb title:
Structure of the thermus thermophilus 30S ribosomal subunit [more info...]
Chain information for 1j5e.pdb #21
---
Chain | Description | UniProt
A | 16S ribosomal RNA |
B | 30S ribosomal protein S2 |
C | 30S ribosomal protein S3 |
D | 30S ribosomal protein S4 | RS4_THETH 2-209
E | 30S ribosomal protein S5 | RS5_THETH 2-162
F | 30S ribosomal protein S6 | RS6_THETH 1-101
G | 30S ribosomal protein S7 | RS7_THETH 2-156
H | 30S ribosomal protein S8 | RS8_THETH 1-138
I | 30S ribosomal protein S9 |
J | 30S ribosomal protein S10 | RS10_THETH 2-105
K | 30S ribosomal protein S11 |
L | 30S ribosomal protein S12 | RS12_THETH 1-135
M | 30S ribosomal protein S13 |
N | 30S ribosomal protein S14 | RS14_THETH 2-61
O | 30S ribosomal protein S15 | RS15_THETH 2-89
P | 30S ribosomal protein S16 | RS16_THETH 1-88
Q | 30S ribosomal protein S17 | RS17_THETH 2-105
R | 30S ribosomal protein S18 |
S | 30S ribosomal protein S19 | RS19_THETH 2-93
T | 30S ribosomal protein S20 |
V | 30S ribosomal protein THX | RSHX_THETH 2-27
Non-standard residues in 1j5e.pdb #21
---
UNX — unknown atom or ion
ZN — zinc ion
> style stick
Changed 70515 atom styles
> ui tool show Matchmaker
> matchmaker #1-20 to #21
Computing secondary structure
[Repeated 20 time(s)] 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 1j5e.pdb, chain T (#21) with target_ribosome_refined_model20.pdb,
chain A (#1), sequence alignment score = 212.6
RMSD between 77 pruned atom pairs is 0.447 angstroms; (across all 85 pairs:
3.725)
Matchmaker 1j5e.pdb, chain S (#21) with target_ribosome_refined_model19.pdb,
chain A (#2), sequence alignment score = 313.5
RMSD between 79 pruned atom pairs is 0.367 angstroms; (across all 80 pairs:
0.573)
Matchmaker 1j5e.pdb, chain R (#21) with target_ribosome_refined_model18.pdb,
chain A (#3), sequence alignment score = 190.8
RMSD between 63 pruned atom pairs is 0.204 angstroms; (across all 71 pairs:
1.374)
Matchmaker 1j5e.pdb, chain Q (#21) with target_ribosome_refined_model17.pdb,
chain A (#4), sequence alignment score = 250.9
RMSD between 81 pruned atom pairs is 0.436 angstroms; (across all 81 pairs:
0.436)
Matchmaker 1j5e.pdb, chain P (#21) with target_ribosome_refined_model16.pdb,
chain A (#5), sequence alignment score = 173.8
RMSD between 41 pruned atom pairs is 0.316 angstroms; (across all 81 pairs:
2.678)
Matchmaker 1j5e.pdb, chain O (#21) with target_ribosome_refined_model15.pdb,
chain A (#6), sequence alignment score = 300.1
RMSD between 15 pruned atom pairs is 1.378 angstroms; (across all 88 pairs:
4.752)
Matchmaker 1j5e.pdb, chain N (#21) with target_ribosome_refined_model14.pdb,
chain A (#7), sequence alignment score = 112.4
RMSD between 34 pruned atom pairs is 0.396 angstroms; (across all 60 pairs:
15.120)
Matchmaker 1j5e.pdb, chain M (#21) with target_ribosome_refined_model13.pdb,
chain A (#8), sequence alignment score = 372.2
RMSD between 43 pruned atom pairs is 1.144 angstroms; (across all 117 pairs:
5.294)
Matchmaker 1j5e.pdb, chain L (#21) with target_ribosome_refined_model12.pdb,
chain A (#9), sequence alignment score = 491.3
RMSD between 96 pruned atom pairs is 0.273 angstroms; (across all 123 pairs:
9.170)
Matchmaker 1j5e.pdb, chain K (#21) with target_ribosome_refined_model11.pdb,
chain A (#10), sequence alignment score = 424.6
RMSD between 103 pruned atom pairs is 0.277 angstroms; (across all 117 pairs:
3.934)
Matchmaker 1j5e.pdb, chain J (#21) with target_ribosome_refined_model10.pdb,
chain A (#11), sequence alignment score = 299
RMSD between 97 pruned atom pairs is 0.688 angstroms; (across all 98 pairs:
0.748)
Matchmaker 1j5e.pdb, chain I (#21) with target_ribosome_refined_model9.pdb,
chain A (#12), sequence alignment score = 407.6
RMSD between 109 pruned atom pairs is 0.253 angstroms; (across all 127 pairs:
3.067)
Matchmaker 1j5e.pdb, chain H (#21) with target_ribosome_refined_model8.pdb,
chain A (#13), sequence alignment score = 356.7
RMSD between 124 pruned atom pairs is 0.404 angstroms; (across all 129 pairs:
1.683)
Matchmaker 1j5e.pdb, chain G (#21) with target_ribosome_refined_model7.pdb,
chain A (#14), sequence alignment score = 536.7
RMSD between 146 pruned atom pairs is 0.366 angstroms; (across all 155 pairs:
3.628)
Matchmaker 1j5e.pdb, chain F (#21) with target_ribosome_refined_model6.pdb,
chain A (#15), sequence alignment score = 183
RMSD between 85 pruned atom pairs is 0.367 angstroms; (across all 100 pairs:
5.747)
Matchmaker 1j5e.pdb, chain E (#21) with target_ribosome_refined_model5.pdb,
chain A (#16), sequence alignment score = 416.8
RMSD between 124 pruned atom pairs is 0.255 angstroms; (across all 131 pairs:
1.118)
Matchmaker 1j5e.pdb, chain D (#21) with target_ribosome_refined_model4.pdb,
chain A (#17), sequence alignment score = 453.6
RMSD between 131 pruned atom pairs is 0.424 angstroms; (across all 138 pairs:
0.873)
Matchmaker 1j5e.pdb, chain C (#21) with target_ribosome_refined_model3.pdb,
chain A (#18), sequence alignment score = 363.6
RMSD between 15 pruned atom pairs is 1.311 angstroms; (across all 139 pairs:
5.329)
Matchmaker 1j5e.pdb, chain C (#21) with target_ribosome_refined_model2.1.pdb,
chain A (#19), sequence alignment score = 403.9
RMSD between 136 pruned atom pairs is 0.419 angstroms; (across all 139 pairs:
0.905)
Matchmaker 1j5e.pdb, chain B (#21) with target_ribosome_refined_model1.pdb,
chain A (#20), sequence alignment score = 263
RMSD between 10 pruned atom pairs is 1.206 angstroms; (across all 135 pairs:
11.338)
> matchmaker #1-20 to #21
Computing secondary structure
[Repeated 20 time(s)] 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 1j5e.pdb, chain T (#21) with target_ribosome_refined_model20.pdb,
chain A (#1), sequence alignment score = 212.6
RMSD between 77 pruned atom pairs is 0.447 angstroms; (across all 85 pairs:
3.725)
Matchmaker 1j5e.pdb, chain S (#21) with target_ribosome_refined_model19.pdb,
chain A (#2), sequence alignment score = 313.5
RMSD between 79 pruned atom pairs is 0.367 angstroms; (across all 80 pairs:
0.573)
Matchmaker 1j5e.pdb, chain R (#21) with target_ribosome_refined_model18.pdb,
chain A (#3), sequence alignment score = 190.8
RMSD between 63 pruned atom pairs is 0.204 angstroms; (across all 71 pairs:
1.374)
Matchmaker 1j5e.pdb, chain Q (#21) with target_ribosome_refined_model17.pdb,
chain A (#4), sequence alignment score = 250.9
RMSD between 81 pruned atom pairs is 0.436 angstroms; (across all 81 pairs:
0.436)
Matchmaker 1j5e.pdb, chain P (#21) with target_ribosome_refined_model16.pdb,
chain A (#5), sequence alignment score = 173.8
RMSD between 41 pruned atom pairs is 0.316 angstroms; (across all 81 pairs:
2.678)
Matchmaker 1j5e.pdb, chain O (#21) with target_ribosome_refined_model15.pdb,
chain A (#6), sequence alignment score = 300.1
RMSD between 15 pruned atom pairs is 1.378 angstroms; (across all 88 pairs:
4.752)
Matchmaker 1j5e.pdb, chain N (#21) with target_ribosome_refined_model14.pdb,
chain A (#7), sequence alignment score = 112.4
RMSD between 34 pruned atom pairs is 0.396 angstroms; (across all 60 pairs:
15.120)
Matchmaker 1j5e.pdb, chain M (#21) with target_ribosome_refined_model13.pdb,
chain A (#8), sequence alignment score = 372.2
RMSD between 43 pruned atom pairs is 1.144 angstroms; (across all 117 pairs:
5.294)
Matchmaker 1j5e.pdb, chain L (#21) with target_ribosome_refined_model12.pdb,
chain A (#9), sequence alignment score = 491.3
RMSD between 96 pruned atom pairs is 0.273 angstroms; (across all 123 pairs:
9.170)
Matchmaker 1j5e.pdb, chain K (#21) with target_ribosome_refined_model11.pdb,
chain A (#10), sequence alignment score = 424.6
RMSD between 103 pruned atom pairs is 0.277 angstroms; (across all 117 pairs:
3.934)
Matchmaker 1j5e.pdb, chain J (#21) with target_ribosome_refined_model10.pdb,
chain A (#11), sequence alignment score = 299
RMSD between 97 pruned atom pairs is 0.688 angstroms; (across all 98 pairs:
0.748)
Matchmaker 1j5e.pdb, chain I (#21) with target_ribosome_refined_model9.pdb,
chain A (#12), sequence alignment score = 407.6
RMSD between 109 pruned atom pairs is 0.253 angstroms; (across all 127 pairs:
3.067)
Matchmaker 1j5e.pdb, chain H (#21) with target_ribosome_refined_model8.pdb,
chain A (#13), sequence alignment score = 356.7
RMSD between 124 pruned atom pairs is 0.404 angstroms; (across all 129 pairs:
1.683)
Matchmaker 1j5e.pdb, chain G (#21) with target_ribosome_refined_model7.pdb,
chain A (#14), sequence alignment score = 536.7
RMSD between 146 pruned atom pairs is 0.366 angstroms; (across all 155 pairs:
3.628)
Matchmaker 1j5e.pdb, chain F (#21) with target_ribosome_refined_model6.pdb,
chain A (#15), sequence alignment score = 183
RMSD between 85 pruned atom pairs is 0.367 angstroms; (across all 100 pairs:
5.747)
Matchmaker 1j5e.pdb, chain E (#21) with target_ribosome_refined_model5.pdb,
chain A (#16), sequence alignment score = 416.8
RMSD between 124 pruned atom pairs is 0.255 angstroms; (across all 131 pairs:
1.118)
Matchmaker 1j5e.pdb, chain D (#21) with target_ribosome_refined_model4.pdb,
chain A (#17), sequence alignment score = 453.6
RMSD between 131 pruned atom pairs is 0.424 angstroms; (across all 138 pairs:
0.873)
Matchmaker 1j5e.pdb, chain C (#21) with target_ribosome_refined_model3.pdb,
chain A (#18), sequence alignment score = 363.6
RMSD between 15 pruned atom pairs is 1.311 angstroms; (across all 139 pairs:
5.329)
Matchmaker 1j5e.pdb, chain C (#21) with target_ribosome_refined_model2.1.pdb,
chain A (#19), sequence alignment score = 403.9
RMSD between 136 pruned atom pairs is 0.419 angstroms; (across all 139 pairs:
0.905)
Matchmaker 1j5e.pdb, chain B (#21) with target_ribosome_refined_model1.pdb,
chain A (#20), sequence alignment score = 263
RMSD between 10 pruned atom pairs is 1.206 angstroms; (across all 135 pairs:
11.338)
> hide #21
> ui tool show Matchmaker
> combine
> #1,#2,#3,#4,#5,#6,#7,#8,#9,#10,#11,#12,#13,#14,#15,#16,#17,#18,#19,#20
Expected a keyword
> combine #1-20 modelId 21
Remapping chain ID 'A' in target_ribosome_refined_model19.pdb #2 to 'B'
Remapping chain ID 'A' in target_ribosome_refined_model18.pdb #3 to 'C'
Remapping chain ID 'A' in target_ribosome_refined_model17.pdb #4 to 'D'
Remapping chain ID 'A' in target_ribosome_refined_model16.pdb #5 to 'E'
Remapping chain ID 'A' in target_ribosome_refined_model15.pdb #6 to 'F'
Remapping chain ID 'A' in target_ribosome_refined_model14.pdb #7 to 'G'
Remapping chain ID 'A' in target_ribosome_refined_model13.pdb #8 to 'H'
Remapping chain ID 'A' in target_ribosome_refined_model12.pdb #9 to 'I'
Remapping chain ID 'A' in target_ribosome_refined_model11.pdb #10 to 'J'
Remapping chain ID 'A' in target_ribosome_refined_model10.pdb #11 to 'K'
Remapping chain ID 'A' in target_ribosome_refined_model9.pdb #12 to 'L'
Remapping chain ID 'A' in target_ribosome_refined_model8.pdb #13 to 'M'
Remapping chain ID 'A' in target_ribosome_refined_model7.pdb #14 to 'N'
Remapping chain ID 'A' in target_ribosome_refined_model6.pdb #15 to 'O'
Remapping chain ID 'A' in target_ribosome_refined_model5.pdb #16 to 'P'
Remapping chain ID 'A' in target_ribosome_refined_model4.pdb #17 to 'Q'
Remapping chain ID 'A' in target_ribosome_refined_model3.pdb #18 to 'R'
Remapping chain ID 'A' in target_ribosome_refined_model2.1.pdb #19 to 'S'
Remapping chain ID 'A' in target_ribosome_refined_model1.pdb #20 to 'T'
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\atomic\cmd.py", line 174, in combine_cmd
session.models.add([combination])
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\core\models.py", line 758, in add
p = self._parent_for_added_model(model, parent, root_model = root_model)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\core\models.py", line 828, in _parent_for_added_model
raise ValueError('Tried to add model %s with the same id as another model %s'
ValueError: Tried to add model combination #21 with the same id as another
model 1j5e.pdb #21
ValueError: Tried to add model combination #21 with the same id as another
model 1j5e.pdb #21
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\core\models.py", line 828, in _parent_for_added_model
raise ValueError('Tried to add model %s with the same id as another model %s'
See log for complete Python traceback.
> combine #1-20 modelId 22
Remapping chain ID 'A' in target_ribosome_refined_model19.pdb #2 to 'B'
Remapping chain ID 'A' in target_ribosome_refined_model18.pdb #3 to 'C'
Remapping chain ID 'A' in target_ribosome_refined_model17.pdb #4 to 'D'
Remapping chain ID 'A' in target_ribosome_refined_model16.pdb #5 to 'E'
Remapping chain ID 'A' in target_ribosome_refined_model15.pdb #6 to 'F'
Remapping chain ID 'A' in target_ribosome_refined_model14.pdb #7 to 'G'
Remapping chain ID 'A' in target_ribosome_refined_model13.pdb #8 to 'H'
Remapping chain ID 'A' in target_ribosome_refined_model12.pdb #9 to 'I'
Remapping chain ID 'A' in target_ribosome_refined_model11.pdb #10 to 'J'
Remapping chain ID 'A' in target_ribosome_refined_model10.pdb #11 to 'K'
Remapping chain ID 'A' in target_ribosome_refined_model9.pdb #12 to 'L'
Remapping chain ID 'A' in target_ribosome_refined_model8.pdb #13 to 'M'
Remapping chain ID 'A' in target_ribosome_refined_model7.pdb #14 to 'N'
Remapping chain ID 'A' in target_ribosome_refined_model6.pdb #15 to 'O'
Remapping chain ID 'A' in target_ribosome_refined_model5.pdb #16 to 'P'
Remapping chain ID 'A' in target_ribosome_refined_model4.pdb #17 to 'Q'
Remapping chain ID 'A' in target_ribosome_refined_model3.pdb #18 to 'R'
Remapping chain ID 'A' in target_ribosome_refined_model2.1.pdb #19 to 'S'
Remapping chain ID 'A' in target_ribosome_refined_model1.pdb #20 to 'T'
> focus #22
Unknown command: focus #22
> open C:/Users/hp/Downloads/modelling_paper/rna_only.cif
Summary of feedback from opening
C:/Users/hp/Downloads/modelling_paper/rna_only.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Skipping residue with duplicate label_seq_id 129 in chain A
Skipping residue with duplicate label_seq_id 190 in chain A
Skipping residue with duplicate label_seq_id 190 in chain A
Skipping residue with duplicate label_seq_id 1030 in chain A
Skipping residue with duplicate label_seq_id 1030 in chain A
1 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for rna_only.cif #23
---
Chain | Description
A | No description available
Computing secondary structure
> fitmap #2 into #23
Expected a keyword
> fitmap #2 map #23
Expected a keyword
Must specify one map, got 0
> ui tool show Matchmaker
> matchmaker #1-20 to #23
No matrix compatible with both reference structure and all match structures
> ui tool show Clashes
> clashes ignoreHiddenModels true
523324 clashes
> clashes ignoreHiddenModels true
523324 clashes
> clashes models #2 radius 0.4 ignoreHiddenModels true
Expected a keyword
> ui tool show "Renumber Residues"
> minimize
Unknown command: minimize
> hide #24 models
> show #24 models
> color #24 #ff5500ff models
> ui tool show Matchmaker
> combine #22, #23
Expected a keyword
> combine #22, #23 modelId 25
Expected a keyword
> combine #22-23 modelId 25
Remapping chain ID 'A' in rna_only.cif #23 to 'U'
> ui tool show "Add Charges"
> ui tool show "Add Hydrogens"
> addh #!25
Summary of feedback from adding hydrogens to combination #25
---
warnings | Not adding hydrogens to combination #25/U U 5 P because it is missing heavy-atom bond partners
Not adding hydrogens to combination #25/U C 190 P because it is missing heavy-
atom bond partners
Not adding hydrogens to combination #25/U C 190 P because it is missing heavy-
atom bond partners
Not adding hydrogens to combination #25/U C 190 P because it is missing heavy-
atom bond partners
Not adding hydrogens to combination #25/U G 1003 P because it is missing
heavy-atom bond partners
combination #25/U C 190 O4' has bad number of bonds (8)
combination #25/U C 190 O2' has bad number of bonds (4)
combination #25/U U 190D O4' has bad number of bonds (4)
combination #25/U G 190F O4' has bad number of bonds (8)
combination #25/U G 190F O3' has bad number of bonds (4)
combination #25/U G 190F O2' has bad number of bonds (4)
combination #25/U G 1003 O4' has bad number of bonds (4)
notes | No usable SEQRES records for combination (#25) chain A; guessing termini instead
No usable SEQRES records for combination (#25) chain B; guessing termini
instead
No usable SEQRES records for combination (#25) chain C; guessing termini
instead
No usable SEQRES records for combination (#25) chain D; guessing termini
instead
No usable SEQRES records for combination (#25) chain E; guessing termini
instead
16 messages similar to the above omitted
Chain-initial residues that are actual N termini: combination #25/A MET 1,
combination #25/B MET 1, combination #25/C MET 1, combination #25/D MET 1,
combination #25/E MET 1, combination #25/F MET 1, combination #25/G MET 1,
combination #25/H MET 1, combination #25/I MET 1, combination #25/J MET 1,
combination #25/K MET 1, combination #25/L MET 1, combination #25/M MET 1,
combination #25/N MET 1, combination #25/O MET 1, combination #25/P MET 1,
combination #25/Q MET 1, combination #25/R MET 1, combination #25/S GLY 1,
combination #25/T MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: combination #25/A ALA 87,
combination #25/B LYS 92, combination #25/C GLN 75, combination #25/D LEU 84,
combination #25/E ALA 82, combination #25/F ARG 89, combination #25/G TRP 101,
combination #25/H LYS 118, combination #25/I ALA 124, combination #25/J VAL
129, combination #25/K GLY 103, combination #25/L ARG 130, combination #25/M
ALA 130, combination #25/N ASN 179, combination #25/O GLU 131, combination
#25/P THR 140, combination #25/Q ASN 140, combination #25/R ASN 140,
combination #25/S ASN 139, combination #25/T GLU 140
Chain-final residues that are not actual C termini:
Skipping possible acceptor with bad geometry: combination #25/U C 190 O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U C 190
O2
Skipping possible acceptor with bad geometry: combination #25/U C 190 O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U C 190
O2
Skipping possible acceptor with bad geometry: combination #25/U C 190 O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U C 190
O2
donor: combination #25/U U 190D O2' acceptor: combination #25/U G 190F N7
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\tool.py", line 184, in add_h
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 259, in add_hydrogens
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 14 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 14 were given
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> save #25
Cannot determine format for '#25'
> select backbone
105741 atoms, 110252 bonds, 236562 pseudobonds, 13956 residues, 28 models
selected
> select #25/U
46556 atoms, 50590 bonds, 1 pseudobond, 1499 residues, 2 models selected
> select clear
> select #25/U
46556 atoms, 50590 bonds, 1 pseudobond, 1499 residues, 2 models selected
> select clear
> save C:/Users/hp/Downloads/modelling_paper/combined_structure_chimeraX.pdb
> #25
> ui tool show "Add Hydrogens"
> addh #!25
Summary of feedback from adding hydrogens to combination #25
---
warnings | Not adding hydrogens to combination #25/U U 5 P because it is missing heavy-atom bond partners
Not adding hydrogens to combination #25/U C 190 P because it is missing heavy-
atom bond partners
Not adding hydrogens to combination #25/U C 190 P because it is missing heavy-
atom bond partners
Not adding hydrogens to combination #25/U C 190 P because it is missing heavy-
atom bond partners
Not adding hydrogens to combination #25/U G 1003 P because it is missing
heavy-atom bond partners
combination #25/U C 190 O4' has bad number of bonds (8)
combination #25/U C 190 O2' has bad number of bonds (4)
combination #25/U U 190D O4' has bad number of bonds (4)
combination #25/U G 190F O4' has bad number of bonds (8)
combination #25/U G 190F O3' has bad number of bonds (4)
combination #25/U G 190F O2' has bad number of bonds (4)
combination #25/U G 1003 O4' has bad number of bonds (4)
notes | No usable SEQRES records for combination (#25) chain A; guessing termini instead
No usable SEQRES records for combination (#25) chain B; guessing termini
instead
No usable SEQRES records for combination (#25) chain C; guessing termini
instead
No usable SEQRES records for combination (#25) chain D; guessing termini
instead
No usable SEQRES records for combination (#25) chain E; guessing termini
instead
16 messages similar to the above omitted
Chain-initial residues that are actual N termini: combination #25/A MET 1,
combination #25/B MET 1, combination #25/C MET 1, combination #25/D MET 1,
combination #25/E MET 1, combination #25/F MET 1, combination #25/G MET 1,
combination #25/H MET 1, combination #25/I MET 1, combination #25/J MET 1,
combination #25/K MET 1, combination #25/L MET 1, combination #25/M MET 1,
combination #25/N MET 1, combination #25/O MET 1, combination #25/P MET 1,
combination #25/Q MET 1, combination #25/R MET 1, combination #25/S GLY 1,
combination #25/T MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: combination #25/A ALA 87,
combination #25/B LYS 92, combination #25/C GLN 75, combination #25/D LEU 84,
combination #25/E ALA 82, combination #25/F ARG 89, combination #25/G TRP 101,
combination #25/H LYS 118, combination #25/I ALA 124, combination #25/J VAL
129, combination #25/K GLY 103, combination #25/L ARG 130, combination #25/M
ALA 130, combination #25/N ASN 179, combination #25/O GLU 131, combination
#25/P THR 140, combination #25/Q ASN 140, combination #25/R ASN 140,
combination #25/S ASN 139, combination #25/T GLU 140
Chain-final residues that are not actual C termini:
Skipping possible acceptor with bad geometry: combination #25/U C 190 O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U C 190
O2
Skipping possible acceptor with bad geometry: combination #25/U C 190 O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U C 190
O2
Skipping possible acceptor with bad geometry: combination #25/U C 190 O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U C 190
O2
donor: combination #25/U U 190D O2' acceptor: combination #25/U G 190F N7
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\tool.py", line 184, in add_h
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 259, in add_hydrogens
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 14 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 14 were given
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> hbonds #25 suppress-warnings true
Expected a keyword
> ui tool show "Add Charges"
Closest equivalent command: addcharge #25 standardizeResidues 5BU,CSL,MSE,UMS
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen combination #25/U U 190D H bonded to atom that should not have
hydrogens (combination #25/U U 190D P)
> ui tool show H-Bonds
> hbonds reveal true
rna_only.cif #23/A C 190 O4' has bad number of bonds (8)
rna_only.cif #23/A C 190 O2' has bad number of bonds (4)
rna_only.cif #23/A U 190D O4' has bad number of bonds (4)
rna_only.cif #23/A G 190F O4' has bad number of bonds (8)
rna_only.cif #23/A G 190F O3' has bad number of bonds (4)
rna_only.cif #23/A G 190F O2' has bad number of bonds (4)
rna_only.cif #23/A G 1003 O4' has bad number of bonds (4)
combination #25/U C 190 O4' has bad number of bonds (8)
combination #25/U C 190 O2' has bad number of bonds (4)
combination #25/U U 190D O4' has bad number of bonds (4)
combination #25/U G 190F O4' has bad number of bonds (8)
combination #25/U G 190F O3' has bad number of bonds (4)
combination #25/U G 190F O2' has bad number of bonds (4)
combination #25/U G 1003 O4' has bad number of bonds (4)
Skipping possible acceptor with bad geometry: rna_only.cif #23/A U 190D O4
Wrong number of grandchild atoms for phi/psi acceptor rna_only.cif #23/A U
190D O4
Skipping possible acceptor with bad geometry: combination #25/U U 190D O4
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U U 190D
O4
Skipping possible acceptor with bad geometry: rna_only.cif #23/A U 190D O4
Wrong number of grandchild atoms for phi/psi acceptor rna_only.cif #23/A U
190D O4
Skipping possible acceptor with bad geometry: combination #25/U U 190D O4
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U U 190D
O4
Skipping possible acceptor with bad geometry: rna_only.cif #23/A U 190D O2
Wrong number of grandchild atoms for phi/psi acceptor rna_only.cif #23/A U
190D O2
Skipping possible acceptor with bad geometry: combination #25/U U 190D O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U U 190D
O2
Skipping possible acceptor with bad geometry: rna_only.cif #23/A U 190D O2
Wrong number of grandchild atoms for phi/psi acceptor rna_only.cif #23/A U
190D O2
Skipping possible acceptor with bad geometry: combination #25/U U 190D O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U U 190D
O2
donor: 1j5e.pdb #21/Q ARG 63 NH2 acceptor: rna_only.cif #23/A G 190F N7
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\hbonds\tool.py", line 52, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\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 "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 14 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 14 were given
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Closest equivalent command: addcharge #25 standardizeResidues 5BU,CSL,MSE,UMS
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen combination #25/U U 190D H bonded to atom that should not have
hydrogens (combination #25/U U 190D P)
Closest equivalent command: addcharge #25 standardizeResidues 5BU,CSL,MSE,UMS
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen combination #25/U U 190D H bonded to atom that should not have
hydrogens (combination #25/U U 190D P)
> validate #25
Unknown command: validate #25
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to combination #25
---
warnings | Not adding hydrogens to combination #25/U U 5 P because it is missing heavy-atom bond partners
Not adding hydrogens to combination #25/U C 190 P because it is missing heavy-
atom bond partners
Not adding hydrogens to combination #25/U C 190 P because it is missing heavy-
atom bond partners
Not adding hydrogens to combination #25/U C 190 P because it is missing heavy-
atom bond partners
Not adding hydrogens to combination #25/U G 1003 P because it is missing
heavy-atom bond partners
combination #25/U C 190 O4' has bad number of bonds (8)
combination #25/U C 190 O2' has bad number of bonds (4)
combination #25/U U 190D O4' has bad number of bonds (4)
combination #25/U G 190F O4' has bad number of bonds (8)
combination #25/U G 190F O3' has bad number of bonds (4)
combination #25/U G 190F O2' has bad number of bonds (4)
combination #25/U G 1003 O4' has bad number of bonds (4)
notes | No usable SEQRES records for combination (#25) chain A; guessing termini instead
No usable SEQRES records for combination (#25) chain B; guessing termini
instead
No usable SEQRES records for combination (#25) chain C; guessing termini
instead
No usable SEQRES records for combination (#25) chain D; guessing termini
instead
No usable SEQRES records for combination (#25) chain E; guessing termini
instead
16 messages similar to the above omitted
Chain-initial residues that are actual N termini: combination #25/A MET 1,
combination #25/B MET 1, combination #25/C MET 1, combination #25/D MET 1,
combination #25/E MET 1, combination #25/F MET 1, combination #25/G MET 1,
combination #25/H MET 1, combination #25/I MET 1, combination #25/J MET 1,
combination #25/K MET 1, combination #25/L MET 1, combination #25/M MET 1,
combination #25/N MET 1, combination #25/O MET 1, combination #25/P MET 1,
combination #25/Q MET 1, combination #25/R MET 1, combination #25/S GLY 1,
combination #25/T MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: combination #25/A ALA 87,
combination #25/B LYS 92, combination #25/C GLN 75, combination #25/D LEU 84,
combination #25/E ALA 82, combination #25/F ARG 89, combination #25/G TRP 101,
combination #25/H LYS 118, combination #25/I ALA 124, combination #25/J VAL
129, combination #25/K GLY 103, combination #25/L ARG 130, combination #25/M
ALA 130, combination #25/N ASN 179, combination #25/O GLU 131, combination
#25/P THR 140, combination #25/Q ASN 140, combination #25/R ASN 140,
combination #25/S ASN 139, combination #25/T GLU 140
Chain-final residues that are not actual C termini:
Skipping possible acceptor with bad geometry: combination #25/U C 190 O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U C 190
O2
Skipping possible acceptor with bad geometry: combination #25/U C 190 O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U C 190
O2
Skipping possible acceptor with bad geometry: combination #25/U C 190 O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U C 190
O2
donor: combination #25/U U 190D O2' acceptor: combination #25/U G 190F N7
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\tool.py", line 206, in add_h
cb(*tuple(args), **kw)
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\dock_prep.py", line 48, in <lambda>
memo_name), keywords=keywords: run_for_dock_prep(*(args1 + (structures,
keywords)),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\dock_prep.py", line 55, in run_for_dock_prep
cmd_addh(session, structures, **active_settings)
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 259, in add_hydrogens
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 14 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 14 were given
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> select #25
79242 atoms, 83544 bonds, 1 pseudobond, 3852 residues, 2 models selected
> addh #25 excludeResidues 190D
Expected a keyword
> addh #25:A
Summary of feedback from adding hydrogens to combination #25
---
warnings | Not adding hydrogens to combination #25/U U 5 P because it is missing heavy-atom bond partners
Not adding hydrogens to combination #25/U C 190 P because it is missing heavy-
atom bond partners
Not adding hydrogens to combination #25/U C 190 P because it is missing heavy-
atom bond partners
Not adding hydrogens to combination #25/U C 190 P because it is missing heavy-
atom bond partners
Not adding hydrogens to combination #25/U G 1003 P because it is missing
heavy-atom bond partners
combination #25/U C 190 O4' has bad number of bonds (8)
combination #25/U C 190 O2' has bad number of bonds (4)
combination #25/U U 190D O4' has bad number of bonds (4)
combination #25/U G 190F O4' has bad number of bonds (8)
combination #25/U G 190F O3' has bad number of bonds (4)
combination #25/U G 190F O2' has bad number of bonds (4)
combination #25/U G 1003 O4' has bad number of bonds (4)
notes | No usable SEQRES records for combination (#25) chain A; guessing termini instead
No usable SEQRES records for combination (#25) chain B; guessing termini
instead
No usable SEQRES records for combination (#25) chain C; guessing termini
instead
No usable SEQRES records for combination (#25) chain D; guessing termini
instead
No usable SEQRES records for combination (#25) chain E; guessing termini
instead
16 messages similar to the above omitted
Chain-initial residues that are actual N termini: combination #25/A MET 1,
combination #25/B MET 1, combination #25/C MET 1, combination #25/D MET 1,
combination #25/E MET 1, combination #25/F MET 1, combination #25/G MET 1,
combination #25/H MET 1, combination #25/I MET 1, combination #25/J MET 1,
combination #25/K MET 1, combination #25/L MET 1, combination #25/M MET 1,
combination #25/N MET 1, combination #25/O MET 1, combination #25/P MET 1,
combination #25/Q MET 1, combination #25/R MET 1, combination #25/S GLY 1,
combination #25/T MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: combination #25/A ALA 87,
combination #25/B LYS 92, combination #25/C GLN 75, combination #25/D LEU 84,
combination #25/E ALA 82, combination #25/F ARG 89, combination #25/G TRP 101,
combination #25/H LYS 118, combination #25/I ALA 124, combination #25/J VAL
129, combination #25/K GLY 103, combination #25/L ARG 130, combination #25/M
ALA 130, combination #25/N ASN 179, combination #25/O GLU 131, combination
#25/P THR 140, combination #25/Q ASN 140, combination #25/R ASN 140,
combination #25/S ASN 139, combination #25/T GLU 140
Chain-final residues that are not actual C termini:
Skipping possible acceptor with bad geometry: combination #25/U C 190 O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U C 190
O2
Skipping possible acceptor with bad geometry: combination #25/U C 190 O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U C 190
O2
Skipping possible acceptor with bad geometry: combination #25/U C 190 O2
Wrong number of grandchild atoms for phi/psi acceptor combination #25/U C 190
O2
donor: combination #25/U U 190D O2' acceptor: combination #25/U G 190F N7
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 259, in add_hydrogens
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 14 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 14 were given
File "C:\Program Files\ChimeraX 1.9rc202412062357\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.14761 Core Profile Forward-Compatible Context 21.30.44 30.0.13044.0
OpenGL renderer: AMD Radeon(TM) Vega 8 Graphics
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_IN.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: HP
Model: HP Laptop 15s-eq0xxx
OS: Microsoft Windows 11 Home Single Language (Build 22631)
Memory: 6,355,427,328
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD Ryzen 5 3500U with Radeon Vega Mobile Gfx
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9rc202412062357
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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
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: 1.2.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
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
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.2
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (2)
comment:1 by , 11 months ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → H-Bonds: acc_phi_psi() bad number of arguments |
comment:2 by , 11 months ago
| Resolution: | → limitation |
|---|---|
| Status: | accepted → closed |
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