H-Bonds: acc_phi_psi() bad number of arguments

[chimerax-bug-report@…]

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

[pett]

Bad connectivity