ChimeraX bug report submission

[eruera@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.5rc202211120143 (2022-11-12 01:43:47 UTC)
Description
Trying to add hydrogens to a model using addh but I receive an error saying "8 positional arguments are required but 9 were given". I'm struggling to understand what positional arguments it's asking for as I'm just trying to add hydrogen atoms. 

Log:
UCSF ChimeraX version: 1.5rc202211120143 (2022-11-12)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> C:\\\Users\\\alice\\\Documents\\\PCH45_Refined_models\\\Assembled_pentamer_09082025.cxs

Opened PCH45_full_vertex_map.mrc as #3, grid size 356,356,356, pixel 1.37,
shown at level 0.449, step 1, values float32  
Log from Sat Aug 9 15:43:20 2025UCSF ChimeraX version: 1.5rc202211120143
(2022-11-12)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\alice\Downloads\8bfp (1).cif" format mmcif

8bfp (1).cif title:  
Jumbo Phage phi-kp24 empty capsid pentamer hexamers [more info...]  
  
Chain information for 8bfp (1).cif #1  
---  
Chain | Description | UniProt  
A B C D E G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j | Major
head protein | A0A7U0GBA8_9CAUD  
  

> hide atoms

> show cartoons

> open C:/Users/alice/Documents/Refined_models/PCH45_MCP_1.pdb

Chain information for PCH45_MCP_1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #2/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 8bfp (1).cif, chain A (#1) with PCH45_MCP_1.pdb, chain A (#2),
sequence alignment score = 1387.3  
RMSD between 451 pruned atom pairs is 0.966 angstroms; (across all 543 pairs:
2.853)  
  

> matchmaker #2/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 8bfp (1).cif, chain A (#1) with PCH45_MCP_1.pdb, chain A (#2),
sequence alignment score = 1387.3  
RMSD between 451 pruned atom pairs is 0.966 angstroms; (across all 543 pairs:
2.853)  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_full_vertex_map.mrc

Opened PCH45_full_vertex_map.mrc as #3, grid size 356,356,356, pixel 1.37,
shown at level 0.449, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.5304

> select add #1

156905 atoms, 159565 bonds, 19950 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-33.911,0,1,0,7.1589,0,0,1,-308.79

> view matrix models #1,1,0,0,-47.549,0,1,0,15.697,0,0,1,-375.1

> view matrix models #1,1,0,0,-88.962,0,1,0,-7.7932,0,0,1,-398.4

> view matrix models
> #1,0.68958,-0.51576,0.5084,-205.38,-0.33561,0.3945,0.85542,-371.61,-0.64175,-0.7605,0.098946,880.13

> view matrix models
> #1,0.68958,-0.51576,0.5084,-156.98,-0.33561,0.3945,0.85542,-391,-0.64175,-0.7605,0.098946,878.59

> view matrix models
> #1,0.68958,-0.51576,0.5084,-273.78,-0.33561,0.3945,0.85542,-380.28,-0.64175,-0.7605,0.098946,860.14

> view matrix models
> #1,0.63942,-0.63179,0.43816,-157.38,-0.4181,0.19253,0.88776,-307.45,-0.64524,-0.75085,-0.14104,1056.8

> view matrix models
> #1,0.41772,-0.80437,0.42249,14.165,-0.30959,0.31116,0.89852,-403.99,-0.8542,-0.50613,-0.11904,1068.5

> view matrix models
> #1,0.41772,-0.80437,0.42249,-57.467,-0.30959,0.31116,0.89852,-467.6,-0.8542,-0.50613,-0.11904,977.35

> view matrix models
> #1,0.41772,-0.80437,0.42249,-46.107,-0.30959,0.31116,0.89852,-448.49,-0.8542,-0.50613,-0.11904,977.46

> view matrix models
> #1,0.55339,-0.7617,0.337,-54.223,-0.3982,0.11343,0.91026,-356.94,-0.73157,-0.63792,-0.24053,1056.6

> view matrix models
> #1,0.55339,-0.7617,0.337,-94.134,-0.3982,0.11343,0.91026,-381.75,-0.73157,-0.63792,-0.24053,1083

> view matrix models
> #1,0.55339,-0.7617,0.337,-54.799,-0.3982,0.11343,0.91026,-350.19,-0.73157,-0.63792,-0.24053,1050.9

> view matrix models
> #1,0.63136,-0.67,0.3905,-163.79,-0.30617,0.24728,0.9193,-441.77,-0.71249,-0.69997,-0.049011,901.95

> view matrix models
> #1,0.63136,-0.67,0.3905,-168.84,-0.30617,0.24728,0.9193,-433.55,-0.71249,-0.69997,-0.049011,853.95

> view matrix models
> #1,0.63136,-0.67,0.3905,-164.52,-0.30617,0.24728,0.9193,-435.94,-0.71249,-0.69997,-0.049011,852.72

> select subtract #1

Nothing selected  

> hide #1 models

> show #1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #1 models

> show #1 models

> select add #3

2 models selected  

> view matrix models #3,1,0,0,1.725,0,1,0,-6.2475,0,0,1,-0.093705

> undo

> select add #1

156905 atoms, 159565 bonds, 19950 residues, 3 models selected  

> view matrix models
> #1,0.63136,-0.67,0.3905,-165.28,-0.30617,0.24728,0.9193,-435.6,-0.71249,-0.69997,-0.049011,852.74,#3,1,0,0,-0.7559,0,1,0,0.34231,0,0,1,0.014814

> select subtract #3

156905 atoms, 159565 bonds, 19950 residues, 1 model selected  

> view matrix models
> #1,0.63136,-0.67,0.3905,-222.01,-0.30617,0.24728,0.9193,-445.81,-0.71249,-0.69997,-0.049011,853.45

> hide #1 models

> show #1 models

> view matrix models
> #1,0.63136,-0.67,0.3905,-216.94,-0.30617,0.24728,0.9193,-432.61,-0.71249,-0.69997,-0.049011,853.52

> view matrix models
> #1,0.63136,-0.67,0.3905,-212.91,-0.30617,0.24728,0.9193,-429.34,-0.71249,-0.69997,-0.049011,853.5

> view matrix models
> #1,0.63136,-0.67,0.3905,-206.56,-0.30617,0.24728,0.9193,-421.96,-0.71249,-0.69997,-0.049011,846.53

> view matrix models
> #1,0.63136,-0.67,0.3905,-207.7,-0.30617,0.24728,0.9193,-425.22,-0.71249,-0.69997,-0.049011,836.3

> fitmap #1 inMap #3

Fit molecule 8bfp (1).cif (#1) to map PCH45_full_vertex_map.mrc (#3) using
156905 atoms  
average map value = 0.3523, steps = 228  
shifted from previous position = 19  
rotated from previous position = 15.6 degrees  
atoms outside contour = 110337, contour level = 0.53044  
  
Position of 8bfp (1).cif (#1) relative to PCH45_full_vertex_map.mrc (#3)
coordinates:  
Matrix rotation and translation  
0.81551618 -0.50506999 0.28255558 -244.82931907  
-0.24061821 0.14812517 0.95925065 -469.61762319  
-0.52634232 -0.85027245 -0.00073056 730.83769017  
Axis -0.90491716 0.40451851 0.13224863  
Axis point 0.00000000 97.66520941 630.37641717  
Rotation angle (degrees) 91.06258839  
Shift along axis 128.23351597  
  

> select subtract #1

Nothing selected  

> hide #!2 models

> select #1/A

4483 atoms, 4559 bonds, 570 residues, 1 model selected  

> select ~sel

157142 atoms, 159825 bonds, 1 pseudobond, 19979 residues, 5 models selected  

> delete atoms (#1 & sel)

> delete bonds (#1 & sel)

> volume zone #3 nearAtoms #1 newMap true

Opened PCH45_full_vertex_map.mrc zone as #4, grid size 356,356,356, pixel
1.37, shown at step 1, values float32  

> show #!2 models

> hide #!2 models

> show #!2 models

> select subtract #2

2 models selected  

> select subtract #3

Nothing selected  

> ui tool show Matchmaker

> matchmaker #2/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 8bfp (1).cif, chain A (#1) with PCH45_MCP_1.pdb, chain A (#2),
sequence alignment score = 1387.3  
RMSD between 451 pruned atom pairs is 0.966 angstroms; (across all 543 pairs:
2.853)  
  

> matchmaker #2/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 8bfp (1).cif, chain A (#1) with PCH45_MCP_1.pdb, chain A (#2),
sequence alignment score = 1387.3  
RMSD between 451 pruned atom pairs is 0.966 angstroms; (across all 543 pairs:
2.853)  
  

> transparency #4.1 50

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> hide #!2 models

> show #!2 models

> show #1 models

> hide #1 models

> show #1 models

> volume zone #2 nearAtoms #1 newMap true

> hide #1 models

> volume zone #3 nearAtoms #2 newMap true

Opened PCH45_full_vertex_map.mrc zone as #5, grid size 356,356,356, pixel
1.37, shown at step 1, values float32  

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> set bgColor white

> hide #!3 models

> color #2 #eb17cfff

> lighting soft

> graphics silhouettes true

> surface dust #5 size 13.7

> transparency #5.1 50

> volume #5 level 0.6552

> hide #!5 models

Drag select of 17 residues  
Drag select of 34 residues  

> select ~sel

8924 atoms, 9093 bonds, 1 pseudobond, 1135 residues, 9 models selected  

> hide sel & #!2 cartoons

Drag select of 2 residues  

> hide sel cartoons

Drag select of 10 residues  

> hide sel cartoons

Drag select of 22 residues  

> save sel

Cannot determine format for 'sel'  

> combine

Remapping chain ID 'A' in PCH45_MCP_1.pdb #2 to 'B'  

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!2 models

> show #!2 models

> select add #2

4720 atoms, 4819 bonds, 1 pseudobond, 599 residues, 2 models selected  

> select subtract #2

Nothing selected  

> show #!6 models

> close #6

> select add #2

4720 atoms, 4819 bonds, 1 pseudobond, 599 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select add #2

4720 atoms, 4819 bonds, 1 pseudobond, 599 residues, 2 models selected  
Drag select of 22 residues  

> select ~sel

9023 atoms, 9195 bonds, 1 pseudobond, 1147 residues, 9 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> undo

Undo failed, probably because structures have been modified.  

> show #!2 cartoons

> close #2

> open C:/Users/alice/Documents/Refined_models/PCH45_MCP_1.pdb

Chain information for PCH45_MCP_1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> show #!3 models

> show #1 models

> ui tool show Matchmaker

> matchmaker #2/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 8bfp (1).cif, chain A (#1) with PCH45_MCP_1.pdb, chain A (#2),
sequence alignment score = 1387.3  
RMSD between 451 pruned atom pairs is 0.966 angstroms; (across all 543 pairs:
2.853)  
  

> matchmaker #2/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 8bfp (1).cif, chain A (#1) with PCH45_MCP_1.pdb, chain A (#2),
sequence alignment score = 1387.3  
RMSD between 451 pruned atom pairs is 0.966 angstroms; (across all 543 pairs:
2.853)  
  

> view matrix models
> #1,0.81552,-0.50507,0.28256,-239.8,-0.24062,0.14813,0.95925,-465.85,-0.52634,-0.85027,-0.00073056,726.19,#3,1,0,0,5.0301,0,1,0,3.7652,0,0,1,-4.6444,#4,1,0,0,5.0301,0,1,0,3.7652,0,0,1,-4.6444,#5,1,0,0,5.0301,0,1,0,3.7652,0,0,1,-4.6444

> undo

> select subtract #5

4483 atoms, 4559 bonds, 570 residues, 5 models selected  

> select subtract #4

4483 atoms, 4559 bonds, 570 residues, 3 models selected  

> select subtract #3

4483 atoms, 4559 bonds, 570 residues, 1 model selected  

> select subtract #1

Nothing selected  

> show #!5 models

> hide #!3 models

> hide #1 models

> hide #!5 models

Drag select of 20 residues  

> select ~sel

9038 atoms, 9209 bonds, 1 pseudobond, 1149 residues, 9 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 1 residues, 1 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 1 pseudobonds  

> show #!2 atoms

Drag select of 5 atoms, 4 bonds  

> delete atoms sel

> delete bonds sel

> show #!2 surfaces

> hide #!2 surfaces

> show #!2 atoms

Drag select of 95 atoms, 18 residues, 1 pseudobonds, 79 bonds  

> show sel atoms

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> show sel atoms

> hide sel atoms

[Repeated 1 time(s)]

> show sel atoms

> hide sel cartoons

> show sel cartoons

> select clear

> volume zone #3 nearAtoms #2 newMap true

Opened PCH45_full_vertex_map.mrc zone as #6, grid size 356,356,356, pixel
1.37, shown at step 1, values float32  

> surface dust #6 size 13.7

> transparency #2.2#6.1 50

> volume #6 level 0.6456

> save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png  

> snapshot ~/user/alice/Documents

Unknown command: snapshot ~/user/alice/Documents  

> snapshot

Unknown command: snapshot  

> save snapshot ~/user/alice/Document

Cannot determine format for 'snapshot'  

> save snapshot ~/user/alice/Document/image/png

Cannot determine format for 'snapshot'  

> save snapshot ~/user/alice/Document/image.png

Cannot determine format for 'snapshot'  

> save C:\Users\alice/user/alice/Document/image.png

Directory "C:\Users\alice/user/alice/Document" does not exist  

> save C:\Users\\\Users\alice\Documents\Refined_models\

Cannot determine format for 'C:\Users\\\Users\alice\Documents\Refined_models\'  

> save C:\Users\\\Users\alice\Documents\Refined_models\MCP1.png

Directory "C:\Users\\\Users\alice\Documents\Refined_models" does not exist  

> save C:\Users\alice\Documents\Refined_models\MCP1.png

> open C:/Users/alice/Documents/Refined_models/PCH45_MCP_1.pdb

Chain information for PCH45_MCP_1.pdb #7  
---  
Chain | Description  
A | No description available  
  

> hide #!2 models

> hide #!6 models

> show #!3 models

> show #1 models

> hide #!7 models

> close #1

> open "C:/Users/alice/Downloads/8bfp (1).cif"

8bfp (1).cif title:  
Jumbo Phage phi-kp24 empty capsid pentamer hexamers [more info...]  
  
Chain information for 8bfp (1).cif #1  
---  
Chain | Description | UniProt  
A B C D E G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j | Major
head protein | A0A7U0GBA8_9CAUD  
  

> select add #1

156905 atoms, 159565 bonds, 19950 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> view matrix models #1,1,0,0,17.699,0,1,0,12.177,0,0,1,-3.5778

> view matrix models
> #1,0.71156,-0.44618,0.54277,-158.19,-0.18164,0.62942,0.75554,-413.28,-0.67874,-0.6362,0.36683,1035.6

> view matrix models
> #1,0.64944,-0.58433,0.4866,-41.061,-0.40222,0.27909,0.87197,-298.95,-0.64532,-0.76202,-0.053779,1403

> view matrix models
> #1,0.64323,-0.60075,0.47472,-23.418,-0.43229,0.2268,0.87275,-269.59,-0.63197,-0.76659,-0.11382,1447.4

> view matrix models
> #1,0.64323,-0.60075,0.47472,-203.4,-0.43229,0.2268,0.87275,-331.57,-0.63197,-0.76659,-0.11382,919.12

> view matrix models
> #1,0.64323,-0.60075,0.47472,-235.22,-0.43229,0.2268,0.87275,-303.41,-0.63197,-0.76659,-0.11382,858.65

> view matrix models
> #1,0.64323,-0.60075,0.47472,-251.81,-0.43229,0.2268,0.87275,-311.41,-0.63197,-0.76659,-0.11382,862.79

> hide #1 models

> show #1 models

> hide #!3 models

> view matrix models
> #1,0.64323,-0.60075,0.47472,-289.54,-0.43229,0.2268,0.87275,-332.05,-0.63197,-0.76659,-0.11382,861.75

> show #!3 models

> view matrix models
> #1,0.64323,-0.60075,0.47472,-301.83,-0.43229,0.2268,0.87275,-330.86,-0.63197,-0.76659,-0.11382,860.21

> view matrix models
> #1,0.64323,-0.60075,0.47472,-304.47,-0.43229,0.2268,0.87275,-330.39,-0.63197,-0.76659,-0.11382,854.41

> view matrix models
> #1,0.70113,-0.64079,0.31275,-187.39,-0.31346,0.11697,0.94237,-413.36,-0.64044,-0.75876,-0.11885,860.38

> fitmap #1 inMap #3

Fit molecule 8bfp (1).cif (#1) to map PCH45_full_vertex_map.mrc (#3) using
156905 atoms  
average map value = 0.3523, steps = 164  
shifted from previous position = 8.82  
rotated from previous position = 11 degrees  
atoms outside contour = 110191, contour level = 0.53044  
  
Position of 8bfp (1).cif (#1) relative to PCH45_full_vertex_map.mrc (#3)
coordinates:  
Matrix rotation and translation  
0.81515411 -0.50564647 0.28256933 -244.53792081  
-0.24040076 0.14850305 0.95924675 -469.80294142  
-0.52700214 -0.84986381 -0.00050492 730.86070466  
Axis -0.90470884 0.40485445 0.13264537  
Axis point 0.00000000 97.71882076 630.51881913  
Rotation angle (degrees) 91.05567026  
Shift along axis 127.97909599  
  

> select subtract #1

Nothing selected  

> close #7

> open C:/Users/alice/Documents/Refined_models/PCH45_MCP_2.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_MCP_2.pdb  
---  
warning | CONECT record for nonexistent atom: 4407  
  
Chain information for PCH45_MCP_2.pdb #7  
---  
Chain | Description  
A | No description available  
  

> hide #!3 models

> hide #1 models

> show #1 models

> show #!3 models

> hide #1 models

> volume zone #3 nearAtoms 2\\#7 newMap true

Invalid "nearAtoms" argument: invalid atoms specifier  

> volume zone #3 nearAtoms #7 newMap true

Opened PCH45_full_vertex_map.mrc zone as #8, grid size 356,356,356, pixel
1.37, shown at step 1, values float32  

> surface dust #8 size 13.7

> transparency #8.1 50

> hide #!8 models

> show #!8 models

> color #8 #b2b2ffff models

> transparency #8.1 50

> hide #!8 models

Drag select of 27 residues  

> select ~sel

161137 atoms, 163877 bonds, 16 pseudobonds, 20491 residues, 15 models selected  

> delete atoms (#!7 & sel)

> delete bonds (#!7 & sel)

> show #!7 atoms

Drag select of 3 atoms, 2 bonds  

> delete atoms sel

> delete bonds sel

> show #!8 models

> hide #!8 models

> select add #7

214 atoms, 213 bonds, 1 pseudobond, 27 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> select subtract #7

Nothing selected  

> show #!8 models

> hide #!8 models

> volume zone #3 nearAtoms #7 newMap true

Opened PCH45_full_vertex_map.mrc zone as #9, grid size 356,356,356, pixel
1.37, shown at step 1, values float32  

> surface dust #9 size 13.7

> color #9 #b2b2ffff models

> transparency #9.1 50

> hide #!9 models

Drag select of 99 atoms, 20 residues, 83 bonds  

> select ~sel

157108 atoms, 159763 bonds, 2 pseudobonds, 19976 residues, 17 models selected  

> delete atoms (#!7 & sel)

> delete bonds (#!7 & sel)

> volume zone #3 nearAtoms #7 newMap true

Opened PCH45_full_vertex_map.mrc zone as #10, grid size 356,356,356, pixel
1.37, shown at step 1, values float32  

> surface dust #10 size 13.7

> color #10 #b2b2ffff models

> transparency #10.1 0

[Repeated 1 time(s)]

> select add #10

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 18 models selected  

> select subtract #9

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 16 models selected  

> select subtract #8

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 14 models selected  

> select subtract #6

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 12 models selected  

> transparency sel & #10.1 0

> select subtract #1

152 atoms, 151 bonds, 1 pseudobond, 19 residues, 11 models selected  

> select subtract #2

9 models selected  

> select subtract #4

6 models selected  

> select subtract #5

4 models selected  

> select subtract #3

2 models selected  

> select subtract #10

Nothing selected  

> select add #10

2 models selected  

> transparency sel 50

> select subtract #10

Nothing selected  

> select add #7

163 atoms, 164 bonds, 20 residues, 1 model selected  

> color sel hot pink

> select subtract #7

Nothing selected  

> hide #!7 models

> show #!7 models

> select clear

> select add #7

163 atoms, 164 bonds, 20 residues, 1 model selected  

> color sel byhetero

> select subtract #7

Nothing selected  

> save C:\Users\alice\Documents\Refined_models\MCP2.png

> hide #!7 models

> close #7

> close #6,8-10

> open C:/Users/alice/Documents/Refined_models/PCH45_MCP_3.pdb

Chain information for PCH45_MCP_3.pdb #6  
---  
Chain | Description  
A | No description available  
  

> show #!2 models

> hide #!2 models

> show #!3 models

> show #1 models

> hide #!3 models

> hide #1 models

> show #1 models

> show #!2 models

> hide #1 models

> hide #!2 models

> volume zone #3 nearAtoms #6 newMap true

Opened PCH45_full_vertex_map.mrc zone as #7, grid size 356,356,356, pixel
1.37, shown at step 1, values float32  

> color #7 #86cce5ff models

> transparency #7.1 50

> select add #6

4297 atoms, 4390 bonds, 1 pseudobond, 549 residues, 2 models selected  

> color (#!6 & sel) orange

> select subtract #6

Nothing selected  

> color #7 #a5afe580 models

> color #7 #a6b0e580 models

> color #7 #d8d8ffff models

> color #7 #e7e7ffff models

> transparency #7.1 50

> color #7 #c9ccffff models

> transparency #7.1 50

> color #7 #bdbeffff models

> volume #!7 showOutlineBox true

> volume #!7 showOutlineBox false

> transparency #7.1 50

> hide #!7 models

Drag select of 31 residues  

> select ~sel

161107 atoms, 163854 bonds, 2 pseudobonds, 20487 residues, 13 models selected  

> delete atoms (#!6 & sel)

> delete bonds (#!6 & sel)

Drag select of 6 residues, 2 pseudobonds  

> delete atoms (#!6 & sel)

> delete bonds (#!6 & sel)

Drag select of 25 residues  

> show sel atoms

Drag select of 5 atoms, 3 residues, 5 bonds  
Drag select of 7 atoms, 2 residues, 6 bonds  

> delete atoms sel

> delete bonds sel

Drag select of 22 atoms, 5 residues, 16 bonds  

> delete atoms sel

> delete bonds sel

Drag select of 95 atoms, 18 residues, 79 bonds  

> color sel byhetero

> select clear

> volume zone #3 nearAtoms #6 newMap true

Opened PCH45_full_vertex_map.mrc zone as #8, grid size 356,356,356, pixel
1.37, shown at step 1, values float32  

> color #8 #b8b9f8ff models

> transparency #8.1 50

> surface dust #8 size 13.7

> save C:\Users\alice\Documents\Refined_models\MCP3.png

> hide #!8 models

> hide #!6 models

> show #!3 models

> open C:/Users/alice/Documents/Refined_models/PCH45_gp13.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_gp13.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 12 12 ILE A 137
GLU A 146 1 10  
Start residue of secondary structure not found: HELIX 13 13 SER B 108 PHE B
111 1 4  
Start residue of secondary structure not found: HELIX 14 14 GLU B 119 LYS B
170 1 52  
Start residue of secondary structure not found: HELIX 15 15 GLY B 184 ALA B
187 1 4  
Start residue of secondary structure not found: HELIX 16 16 GLY B 188 LEU B
190 1 3  
Start residue of secondary structure not found: HELIX 17 17 TYR B 200 SER B
236 1 37  
138 messages similar to the above omitted  
  
Chain information for PCH45_gp13.pdb #9  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp13_seg_map.mrc

Opened PCH45_gp13_seg_map.mrc as #10, grid size 356,356,356, pixel 1.37, shown
at level 0.000149, step 2, values float32  

> hide #!3 models

> surface dust #10 size 13.7

> volume #10 step 1

> volume #10 level 0.1795

> volume #10 level 0.2051

> hide #!10 models

Drag select of 19 residues  

> select ~sel

158207 atoms, 160883 bonds, 1 pseudobond, 20113 residues, 17 models selected  

> delete atoms (#9 & sel)

> delete bonds (#9 & sel)

Drag select of 19 residues  

> show sel atoms

> show #!10 models

> volume zone #3 nearAtoms #9 newMap true

Opened PCH45_full_vertex_map.mrc zone as #11, grid size 356,356,356, pixel
1.37, shown at step 1, values float32  

> hide #!10 models

> select add #9

136 atoms, 136 bonds, 19 residues, 1 model selected  

> select subtract #9

Nothing selected  

> volume #11 level 0.5136

> volume #11 level 0.3791

> surface dust #11 size 13.7

> volume #11 level 0.2823

> volume #11 level 0.337

> transparency #11.1 50

> save C:\Users\alice\Documents\Refined_models\gp13.png

> close #9

> close #10

> close #6

> close #4-5,7

> close #11

> open C:/Users/alice/Documents/Refined_models/PCH45_gp20.pdb

Chain information for PCH45_gp20.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp20_seg_map.mrc

Opened PCH45_gp20_seg_map.mrc as #5, grid size 356,356,356, pixel 1.37, shown
at level 0.00021, step 2, values float32  

> volume #5 step 1

> volume #5 level 0.2473

> surface dust #5 size 13.7

> transparency #5.1 50

> show #4 atoms

> hide #!5 models

> select #4/A:88

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

> select up

137 atoms, 139 bonds, 16 residues, 1 model selected  

> select ~sel

158270 atoms, 160959 bonds, 1 pseudobond, 20122 residues, 10 models selected  

> hide sel & #4 cartoons

> hide sel & #4 atoms

> delete atoms (#4 & sel)

> delete bonds (#4 & sel)

> volume zone #5 nearAtoms #4 newMap true

Opened PCH45_gp20_seg_map.mrc zone as #6, grid size 356,356,356, pixel 1.37,
shown at step 1, values float32  

> surface dust #6 size 13.7

> color #6 white models

> color #6 #b8b9f8ff models

> transparency #6.1 0

> select add #6

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 12 models selected  

> select subtract #8

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 10 models selected  

> select subtract #5

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 8 models selected  

> select subtract #3

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 6 models selected  

> transparency sel & #6.1 0

> select subtract #6

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 4 models selected  

> hide #!6 models

> show #!6 models

> select add #6

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 6 models selected  

> transparency sel & #6.1 0

> show #!3 models

> hide #!3 models

> hide #!6 models

> show #!6 models

> show #!8 models

> select subtract #6

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 4 models selected  

> hide #!6 models

> select add #8

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 6 models selected  

> transparency sel & #8.1 0

> volume sel show

> close #8

> show #!6 models

> select add #6

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 6 models selected  

> transparency sel & #6.1 0

> volume sel step 1

> volume sel showOutlineBox true

> volume sel showOutlineBox false

> close #6

> show #!5 models

> select add #5

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 6 models selected  

> transparency sel & #5.1 0

> volume zone #5 nearAtoms #4 newMap true

Opened PCH45_gp20_seg_map.mrc zone as #6, grid size 356,356,356, pixel 1.37,
shown at step 1, values float32  

> select subtract #5

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 4 models selected  

> select subtract #2

156905 atoms, 159565 bonds, 19950 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select add #6

2 models selected  

> transparency sel 50

> surface dust #6 size 13.7

> select subtract #6

Nothing selected  

> hide #!6 models

> select #4/A:85

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #4/A:85

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #4/A:85

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> show #!6 models

> save C:\Users\alice\Documents\Refined_models\gp20.png

> hide #!6 models

> close #4

> close #5

> close #6

> open C:/Users/alice/Documents/Refined_models/PCH45_gp21.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_gp21.pdb  
---  
warnings | CONECT record for nonexistent atom: 2777  
Start residue of secondary structure not found: HELIX 1 1 ARG C 123 ARG C 181
1 59  
Start residue of secondary structure not found: HELIX 11 11 MET C 323 GLN C
325 1 3  
Start residue of secondary structure not found: HELIX 12 12 GLY C 332 THR C
344 1 13  
  
Chain information for PCH45_gp21.pdb #4  
---  
Chain | Description  
C | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp21_seg_map.mrc

Opened PCH45_gp21_seg_map.mrc as #5, grid size 356,356,356, pixel 1.37, shown
at level 1.76e-05, step 2, values float32  

> volume #5 step 1

> volume #5 level 0.2143

> surface dust #5 size 13.7

> volume #5 level 0.2596

> volume #5 level 0.2225

> show #!4 atoms

> transparency #5.1 50

> color #5 #bec2ffff models

> transparency #5.1 50

> color #5 #bbc2ffff models

> transparency #5.1 50

> hide #!5 models

> hide #!4 atoms

> show #!5 models

> hide #!5 models

Drag select of 14 residues  
Drag select of 16 residues  

> show sel atoms

> show #!5 models

> hide #!5 models

Drag select of 24 atoms, 16 residues, 15 bonds  
Drag select of 54 atoms, 17 residues, 46 bonds  

> show sel atoms

> select ~sel

159427 atoms, 162126 bonds, 2 pseudobonds, 20271 residues, 9 models selected  

> delete atoms (#!4 & sel)

> delete bonds (#!4 & sel)

> select subtract #3

157057 atoms, 159716 bonds, 1 pseudobond, 19969 residues, 6 models selected  

> select subtract #2

156905 atoms, 159565 bonds, 19950 residues, 4 models selected  

> select subtract #1

2 models selected  

> select subtract #5

Nothing selected  

> volume zone #5 nearAtoms #4 newMap true

Opened PCH45_gp21_seg_map.mrc zone as #6, grid size 356,356,356, pixel 1.37,
shown at step 1, values float32  

> surface dust #6 size 13.7

> volume #6 level 0.2562

> transparency #6.1 50

> color #6 #bbc2ffff models

> transparency #6.1 50

> save C:\Users\alice\Documents\Refined_models\gp21.png

> select add #4

125 atoms, 129 bonds, 17 residues, 1 model selected  

> color sel cyan

> color sel byhetero

> select subtract #4

Nothing selected  

> save C:\Users\alice\Documents\Refined_models\gp21.png

> open C:/Users/alice/Downloads/model_01.pdb

model_01.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) PCH45_MCP1 [more info...]  
  
Chain information for model_01.pdb #7  
---  
Chain | Description  
A | No description available  
  

> hide #!4 models

> hide #!6 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #1 models

> hide #!3 models

> hide #1 models

> show #!3 models

> volume zone #3 nearAtoms #7 newMap true

Opened PCH45_full_vertex_map.mrc zone as #8, grid size 356,356,356, pixel
1.37, shown at step 1, values float32  

> transparency #8.1 50

> show #7 atoms

> show #!2 models

> hide #!2 models

> close #2

> open C:/Users/alice/Documents/Refined_models/PCH45_MCP_1.pdb

Chain information for PCH45_MCP_1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> show #1 models

> open C:/Users/alice/Documents/Refined_models/PCH45_MCP_2.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_MCP_2.pdb  
---  
warning | CONECT record for nonexistent atom: 4407  
  
Chain information for PCH45_MCP_2.pdb #9  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_MCP_3.pdb

Chain information for PCH45_MCP_3.pdb #10  
---  
Chain | Description  
A | No description available  
  

> measure center #3

Center of mass grid index for PCH45_full_vertex_map.mrc = (178.00, 177.83,
179.38)  
Center of mass xyz coordinates for PCH45_full_vertex_map.mrc = (242.44,
243.31, 245.10)  

> sym C5 #2 around 242.44, 243.31, 245.10

Missing or invalid "structures" argument: invalid atomic structures specifier  

> sym #2 C5 around 242.44, 243.31, 245.10

Expected a keyword  

> sym #2 C5 center 242.44, 243.31, 245.10

> sym #9 C5 center 242.44, 243.31, 245.10

> sym #10 C5 center 242.44, 243.31, 245.10

> hide #1 models

> show #1 models

> show #!3 models

> volume zone #3 nearAtoms #1 newMap true

Opened PCH45_full_vertex_map.mrc zone as #14, grid size 356,356,356, pixel
1.37, shown at step 1, values float32  

> hide #!8 models

> show #!8 models

> hide #!11 models

> hide #!12 models

> show #!11 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!14 models

> hide #!11 models

> hide #!12 models

> hide #!12.1 models

> hide #!12.2 models

> hide #!12.3 models

> hide #!12.4 models

> hide #!12.5 models

> hide #!13 models

> hide #!13.1 models

> hide #!13.2 models

> hide #!13.3 models

> hide #!13.4 models

> hide #!13.5 models

> hide #!8 models

> show #!8 models

> hide #1 models

> close #7

> open C:/Users/alice/Documents/PCH45_MCP_1-coot-4.pdb

Chain information for PCH45_MCP_1-coot-4.pdb #7  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_MCP_2.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_MCP_2.pdb  
---  
warning | CONECT record for nonexistent atom: 4407  
  
Chain information for PCH45_MCP_2.pdb #15  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #15/A to #7/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 PCH45_MCP_1-coot-4.pdb, chain A (#7) with PCH45_MCP_2.pdb, chain A
(#15), sequence alignment score = 2971.1  
RMSD between 261 pruned atom pairs is 0.666 angstroms; (across all 549 pairs:
7.007)  
  

> matchmaker #15/A to #7/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 PCH45_MCP_1-coot-4.pdb, chain A (#7) with PCH45_MCP_2.pdb, chain A
(#15), sequence alignment score = 2971.1  
RMSD between 261 pruned atom pairs is 0.666 angstroms; (across all 549 pairs:
7.007)  
  

> hide #!15 models

> show #!15 models

> select add #15

4297 atoms, 4382 bonds, 15 pseudobonds, 549 residues, 2 models selected  

> view matrix models
> #15,-0.93239,0.2274,-0.28096,438.02,0.012947,-0.7558,-0.65468,511.14,-0.36122,-0.61405,0.70175,285.97

> view matrix models
> #15,-0.9159,0.042375,-0.39917,499.05,0.2342,-0.75121,-0.61712,459.63,-0.32601,-0.65871,0.6781,293.66

> view matrix models
> #15,-0.82746,0.11688,-0.54922,509.06,0.27932,-0.76282,-0.58317,444.42,-0.48712,-0.63596,0.59856,340.29

> fitmap #15 inMap #8

Fit molecule PCH45_MCP_2.pdb (#15) to map PCH45_full_vertex_map.mrc zone (#8)
using 4297 atoms  
average map value = 0.4435, steps = 192  
shifted from previous position = 1.24  
rotated from previous position = 12.8 degrees  
atoms outside contour = 2603, contour level = 0.53044  
  
Position of PCH45_MCP_2.pdb (#15) relative to PCH45_full_vertex_map.mrc zone
(#8) coordinates:  
Matrix rotation and translation  
-0.81332654 0.27320263 -0.51367330 468.79667664  
0.25086734 -0.63192306 -0.73330678 465.62656199  
-0.52494334 -0.72528172 0.44542217 403.91119562  
Axis 0.30544658 0.42895602 -0.85011712  
Axis point 308.76047686 332.90532123 0.00000000  
Rotation angle (degrees) 179.24730685  
Shift along axis -0.44616736  
  

> select clear

> hide #!15 models

> show #!15 models

> select add #7

4573 atoms, 4667 bonds, 1 pseudobond, 579 residues, 2 models selected  
Alignment identifier is 7/A  

> hide #!8 models

> select #7/A:170

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

> select #7/A:170-200

257 atoms, 265 bonds, 31 residues, 1 model selected  

> select #7/A:170

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

> select #7/A:170-194

206 atoms, 211 bonds, 25 residues, 1 model selected  

> select #7/A:191

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

> select #7/A:170-191

184 atoms, 188 bonds, 22 residues, 1 model selected  

> hide #!7 models

> show #!7 models

> hide #!7 models

> select add #7

4573 atoms, 4667 bonds, 1 pseudobond, 579 residues, 2 models selected  

> hide #!15 models

> open C:/Users/alice/Documents/Refined_models/PCH45_gp22.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_gp22.pdb  
---  
warning | Start residue of secondary structure not found: HELIX 1 1 GLU D 119
LYS D 170 1 52  
  
Chain information for PCH45_gp22.pdb #16  
---  
Chain | Description  
D | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_Gp22_seg_map.mrc

Opened PCH45_Gp22_seg_map.mrc as #17, grid size 356,356,356, pixel 1.37, shown
at level 1.47e-05, step 2, values float32  

> close #3

> close #5

> close #6

> close #8

> close #14

> select subtract #7

Nothing selected  

> select add #17

2 models selected  

> volume #17 step 1

> volume #17 level 0.2523

> view matrix models #17,1,0,0,1.5054,0,1,0,-4.2681,0,0,1,1.0495

> undo

> select subtract #17

Nothing selected  

> transparency 50

> select add #16

2320 atoms, 2346 bonds, 317 residues, 1 model selected  

> color sel orange

> color sel byhetero

> select subtract #16

Nothing selected  

> select add #16

2320 atoms, 2346 bonds, 317 residues, 1 model selected  

> show sel atoms

> hide #!17 models

Alignment identifier is 16/D  

> select #16/D:171

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

> select #16/D:171-180

66 atoms, 65 bonds, 10 residues, 1 model selected  

> select #16/D:171-172

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

> select #16/D:161-172

96 atoms, 95 bonds, 12 residues, 1 model selected  

> show #!17 models

> select #16/D:359@OH

1 atom, 1 residue, 1 model selected  

> select #16/D:351-352

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

> select #16/D:351-360

80 atoms, 81 bonds, 10 residues, 1 model selected  

> select #16/D:347

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

> select #16/D:347-360

105 atoms, 106 bonds, 14 residues, 1 model selected  

> select ~sel

247999 atoms, 252527 bonds, 118 pseudobonds, 31580 residues, 48 models
selected  

> delete atoms (#16 & sel)

> delete bonds (#16 & sel)

> select subtract #17

245784 atoms, 250289 bonds, 118 pseudobonds, 31277 residues, 45 models
selected  

> select subtract #15

241487 atoms, 245907 bonds, 103 pseudobonds, 30728 residues, 43 models
selected  

> select subtract #13.5

237190 atoms, 241517 bonds, 102 pseudobonds, 30179 residues, 41 models
selected  

> select subtract #13.4

232893 atoms, 237127 bonds, 101 pseudobonds, 29630 residues, 39 models
selected  

> show #!13.4 models

> hide #!13.4 models

> select subtract #13.3

228596 atoms, 232737 bonds, 100 pseudobonds, 29081 residues, 37 models
selected  

> select subtract #1

71691 atoms, 73172 bonds, 100 pseudobonds, 9131 residues, 36 models selected  

> select subtract #2

66971 atoms, 68353 bonds, 99 pseudobonds, 8532 residues, 34 models selected  

> select subtract #4

66846 atoms, 68224 bonds, 99 pseudobonds, 8515 residues, 33 models selected  

> select clear

> volume zone #17 nearAtoms #16 newMap true

Opened PCH45_Gp22_seg_map.mrc zone as #3, grid size 356,356,356, pixel 1.37,
shown at step 1, values float32  

> surface dust #3 size 13.7

> color #3 #99bfe5ff models

> transparency #3.1 50

> volume #17 level 0.2493

> volume #3 level 0.1928

> volume #3 level 0.2052

> save C:\Users\alice\Documents\Refined_models\gp22.png

> close #16

> close #3

> open C:/Users/alice/Documents/Refined_models/PCH45_gp30.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_gp30.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ARG A 3
LEU A 17 1 15  
Start residue of secondary structure not found: HELIX 2 2 LYS A 21 SER A 35 1
15  
Start residue of secondary structure not found: HELIX 3 3 PRO A 49 HIS A 56 1
8  
Start residue of secondary structure not found: HELIX 4 4 MET A 58 ASN A 69 1
12  
Start residue of secondary structure not found: HELIX 5 5 VAL A 76 TYR A 95 1
20  
105 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 119 119 GLN H 107 LEU H
126 1 20  
Start residue of secondary structure not found: HELIX 120 120 GLU H 127 SER H
129 1 3  
Start residue of secondary structure not found: SHEET 1 1 1 LYS B 179 VAL B
182 0  
Start residue of secondary structure not found: SHEET 2 2 2 THR B 269 THR B
271 0  
Start residue of secondary structure not found: SHEET 3 3 3 VAL B 281 SER B
285 0  
Start residue of secondary structure not found: SHEET 4 4 4 LYS B 293 ARG B
300 0  
23 messages similar to the above omitted  
  
Chain information for PCH45_gp30.pdb #3  
---  
Chain | Description  
H | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp30_seg_map.mrc

Opened PCH45_gp30_seg_map.mrc as #5, grid size 356,356,356, pixel 1.37, shown
at level 0.00015, step 2, values float32  

> volume #5 step 1

> close #17

> surface dust #5 size 13.7

> volume #5 level 0.4472

> hide #!13 models

> hide #!5 models

Drag select of 17 residues  

> select ~sel

246952 atoms, 251479 bonds, 119 pseudobonds, 31422 residues, 49 models
selected  

> delete atoms (#!3 & sel)

> delete bonds (#!3 & sel)

> show #!3 atoms

Drag select of 6 atoms, 7 bonds  

> delete atoms sel

> delete bonds sel

> select #3/H:205@CE1

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select add #3

130 atoms, 130 bonds, 1 pseudobond, 17 residues, 2 models selected  
Alignment identifier is 3/H  

> select #3/H:172

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

> select #3/H:172-187

127 atoms, 129 bonds, 16 residues, 1 model selected  

> select ~sel

245787 atoms, 250290 bonds, 118 pseudobonds, 31278 residues, 48 models
selected  

> delete atoms (#!3 & sel)

> delete bonds (#!3 & sel)

> select clear

> volume zone #5 nearAtoms #3 newMap true

Opened PCH45_gp30_seg_map.mrc zone as #6, grid size 356,356,356, pixel 1.37,
shown at step 1, values float32  

> surface dust #6 size 13.7

> color #6 skyblue models

> color #6 #a9c3ebff models

> transparency #6.1 50

> select add #3

127 atoms, 129 bonds, 16 residues, 1 model selected  

> color sel forest green

> color sel byhetero

> select subtract #3

Nothing selected  

> close #3

> close #15

> close #6

> close #5

> close #7,9-13

> show #1 models

> hide #1 models

> open C:/Users/alice/Documents/Refined_models/PCH45_gp30_seg_map.mrc

Opened PCH45_gp30_seg_map.mrc as #3, grid size 356,356,356, pixel 1.37, shown
at level 0.00015, step 2, values float32  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp30-coot-0.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_gp30-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ARG A 3
LEU A 17 1 15  
Start residue of secondary structure not found: HELIX 2 2 LYS A 21 SER A 35 1
15  
Start residue of secondary structure not found: HELIX 3 3 PRO A 49 HIS A 56 1
8  
Start residue of secondary structure not found: HELIX 4 4 MET A 58 ASN A 69 1
12  
Start residue of secondary structure not found: HELIX 5 5 VAL A 76 TYR A 95 1
20  
105 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 119 119 GLN H 107 LEU H
126 1 20  
Start residue of secondary structure not found: HELIX 120 120 GLU H 127 SER H
129 1 3  
Start residue of secondary structure not found: SHEET 1 1 1 LYS B 179 VAL B
182 0  
Start residue of secondary structure not found: SHEET 2 2 2 THR B 269 THR B
271 0  
Start residue of secondary structure not found: SHEET 3 3 3 VAL B 281 SER B
285 0  
Start residue of secondary structure not found: SHEET 4 4 4 LYS B 293 ARG B
300 0  
23 messages similar to the above omitted  
  
Chain information for PCH45_gp30-coot-0.pdb #5  
---  
Chain | Description  
H | No description available  
  

> volume #3 step 1

> close #3

> open C:/Users/alice/Documents/Refined_models/PCH45_full_vertex_map.mrc

Opened PCH45_full_vertex_map.mrc as #3, grid size 356,356,356, pixel 1.37,
shown at level 0.449, step 2, values float32  

> volume zone #3 nearAtoms #5 newMap true

Opened PCH45_full_vertex_map.mrc zone as #6, grid size 356,356,356, pixel
1.37, shown at step 1, values float32  

> volume #6 step 1

> surface dust #6 size 13.7

> select add #6

2 models selected  

> color #6.1 cornflower blue

> transparency sel 50

> select subtract #6

Nothing selected  

> select add #6

2 models selected  

> color #6.1 light gray

> select subtract #6

Nothing selected  

> select add #6

2 models selected  

> color #6.1 dark gray

> select subtract #6

Nothing selected  

> transparency #6.1 0

> hide #!5 models

> show #!3 models

> color #6 #9b34a980 models

> volume #3 step 1

> show #!5 models

> hide #!6 models

> hide #!3 models

> show #!3 models

> save C:/Users/alice/Documents/Refined_models/PCH45_gp30_seg_map.mrc models
> #6

> open C:/Users/alice/Documents/Refined_models/PCH45_gp13.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_gp13.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 12 12 ILE A 137
GLU A 146 1 10  
Start residue of secondary structure not found: HELIX 13 13 SER B 108 PHE B
111 1 4  
Start residue of secondary structure not found: HELIX 14 14 GLU B 119 LYS B
170 1 52  
Start residue of secondary structure not found: HELIX 15 15 GLY B 184 ALA B
187 1 4  
Start residue of secondary structure not found: HELIX 16 16 GLY B 188 LEU B
190 1 3  
Start residue of secondary structure not found: HELIX 17 17 TYR B 200 SER B
236 1 37  
138 messages similar to the above omitted  
  
Chain information for PCH45_gp13.pdb #7  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp20.pdb

Chain information for PCH45_gp20.pdb #8  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp21.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_gp21.pdb  
---  
warnings | CONECT record for nonexistent atom: 2777  
Start residue of secondary structure not found: HELIX 1 1 ARG C 123 ARG C 181
1 59  
Start residue of secondary structure not found: HELIX 11 11 MET C 323 GLN C
325 1 3  
Start residue of secondary structure not found: HELIX 12 12 GLY C 332 THR C
344 1 13  
  
Chain information for PCH45_gp21.pdb #9  
---  
Chain | Description  
C | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp22.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_gp22.pdb  
---  
warning | Start residue of secondary structure not found: HELIX 1 1 GLU D 119
LYS D 170 1 52  
  
Chain information for PCH45_gp22.pdb #10  
---  
Chain | Description  
D | No description available  
  

> close #7-8,10#4-6,9

> open C:/Users/alice/Documents/Refined_models/PCH45_MCP_2_final.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_MCP_2_final.pdb  
---  
warning | CONECT record for nonexistent atom: 4685  
  
Chain information for PCH45_MCP_2_final.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_MCP_3_final-coot-3.pdb

Chain information for PCH45_MCP_3_final-coot-3.pdb #5  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_MCP_1_final.pdb

Chain information for PCH45_MCP_1_final.pdb #6  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp30-coot-0.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_gp30-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ARG A 3
LEU A 17 1 15  
Start residue of secondary structure not found: HELIX 2 2 LYS A 21 SER A 35 1
15  
Start residue of secondary structure not found: HELIX 3 3 PRO A 49 HIS A 56 1
8  
Start residue of secondary structure not found: HELIX 4 4 MET A 58 ASN A 69 1
12  
Start residue of secondary structure not found: HELIX 5 5 VAL A 76 TYR A 95 1
20  
105 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 119 119 GLN H 107 LEU H
126 1 20  
Start residue of secondary structure not found: HELIX 120 120 GLU H 127 SER H
129 1 3  
Start residue of secondary structure not found: SHEET 1 1 1 LYS B 179 VAL B
182 0  
Start residue of secondary structure not found: SHEET 2 2 2 THR B 269 THR B
271 0  
Start residue of secondary structure not found: SHEET 3 3 3 VAL B 281 SER B
285 0  
Start residue of secondary structure not found: SHEET 4 4 4 LYS B 293 ARG B
300 0  
23 messages similar to the above omitted  
  
Chain information for PCH45_gp30-coot-0.pdb #7  
---  
Chain | Description  
H | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp30.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_gp30.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ARG A 3
LEU A 17 1 15  
Start residue of secondary structure not found: HELIX 2 2 LYS A 21 SER A 35 1
15  
Start residue of secondary structure not found: HELIX 3 3 PRO A 49 HIS A 56 1
8  
Start residue of secondary structure not found: HELIX 4 4 MET A 58 ASN A 69 1
12  
Start residue of secondary structure not found: HELIX 5 5 VAL A 76 TYR A 95 1
20  
105 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 119 119 GLN H 107 LEU H
126 1 20  
Start residue of secondary structure not found: HELIX 120 120 GLU H 127 SER H
129 1 3  
Start residue of secondary structure not found: SHEET 1 1 1 LYS B 179 VAL B
182 0  
Start residue of secondary structure not found: SHEET 2 2 2 THR B 269 THR B
271 0  
Start residue of secondary structure not found: SHEET 3 3 3 VAL B 281 SER B
285 0  
Start residue of secondary structure not found: SHEET 4 4 4 LYS B 293 ARG B
300 0  
23 messages similar to the above omitted  
  
Chain information for PCH45_gp30.pdb #8  
---  
Chain | Description  
H | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp22.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_gp22.pdb  
---  
warning | Start residue of secondary structure not found: HELIX 1 1 GLU D 119
LYS D 170 1 52  
  
Chain information for PCH45_gp22.pdb #9  
---  
Chain | Description  
D | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp21.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_gp21.pdb  
---  
warnings | CONECT record for nonexistent atom: 2777  
Start residue of secondary structure not found: HELIX 1 1 ARG C 123 ARG C 181
1 59  
Start residue of secondary structure not found: HELIX 11 11 MET C 323 GLN C
325 1 3  
Start residue of secondary structure not found: HELIX 12 12 GLY C 332 THR C
344 1 13  
  
Chain information for PCH45_gp21.pdb #10  
---  
Chain | Description  
C | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp20.pdb

Chain information for PCH45_gp20.pdb #11  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/alice/Documents/Refined_models/PCH45_gp13.pdb

Summary of feedback from opening
C:/Users/alice/Documents/Refined_models/PCH45_gp13.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 12 12 ILE A 137
GLU A 146 1 10  
Start residue of secondary structure not found: HELIX 13 13 SER B 108 PHE B
111 1 4  
Start residue of secondary structure not found: HELIX 14 14 GLU B 119 LYS B
170 1 52  
Start residue of secondary structure not found: HELIX 15 15 GLY B 184 ALA B
187 1 4  
Start residue of secondary structure not found: HELIX 16 16 GLY B 188 LEU B
190 1 3  
Start residue of secondary structure not found: HELIX 17 17 TYR B 200 SER B
236 1 37  
138 messages similar to the above omitted  
  
Chain information for PCH45_gp13.pdb #12  
---  
Chain | Description  
A | No description available  
  

> hide #!3 models

> show #!3 models

> measure center #3

Center of mass grid index for PCH45_full_vertex_map.mrc = (178.00, 177.81,
178.10)  
Center of mass xyz coordinates for PCH45_full_vertex_map.mrc = (243.20,
242.94, 243.33)  

> sym #4 C5 center 243.20, 242.94, 243.33

> sym #5 C5 center 243.20, 242.94, 243.33

> sym #6 C5 center 243.20, 242.94, 243.33

> sym #7 C5 center 243.20, 242.94, 243.33

> sym #8 C5 center 243.20, 242.94, 243.33

> sym #9 C5 center 243.20, 242.94, 243.33

> sym #10 C5 center 243.20, 242.94, 243.33

> sym #11 C5 center 243.20, 242.94, 243.33

> sym #12 C5 center 243.20, 242.94, 243.33

> hide #!3 models

> select add #10

2495 atoms, 2541 bonds, 1 pseudobond, 319 residues, 2 models selected  

> select subtract #10

Nothing selected  

> select add #19

12475 atoms, 12705 bonds, 5 pseudobonds, 1595 residues, 11 models selected  

> color (#!19.1-5 & sel) orange

> color (#!19.1-5 & sel) orange red

> select add #18

24075 atoms, 24435 bonds, 5 pseudobonds, 3180 residues, 17 models selected  

> select subtract #19

11600 atoms, 11730 bonds, 1585 residues, 6 models selected  

> color sel cyan

> select add #20

18350 atoms, 18650 bonds, 2430 residues, 12 models selected  

> select subtract #18

6750 atoms, 6920 bonds, 845 residues, 6 models selected  

> color sel purple

> select subtract #20

Nothing selected  

> select add #21

5685 atoms, 5775 bonds, 725 residues, 6 models selected  

> color sel hot pink

> select subtract #21

Nothing selected  

> select add #17

6510 atoms, 6655 bonds, 5 pseudobonds, 830 residues, 11 models selected  

> color (#!17.1-5 & sel) forest green

> select subtract #17

Nothing selected  

> hide #!13 models

> hide #!14 models

> hide #!15 models

> cartoon style #16-21 modeHelix tube sides 20

> select clear

> select add #16

6510 atoms, 6655 bonds, 5 pseudobonds, 830 residues, 11 models selected  

> select subtract #16

Nothing selected  

> save C:/Users/alice/Documents/Refined_models/Assembled_pentamer_09082025.cxs
> includeMaps true

——— End of log from Sat Aug 9 15:43:20 2025 ———

opened ChimeraX session  

> cartoon style #16-21 xsection oval modeHelix default

> lighting soft

> lighting shadows true intensity 0.5

> show #!2 models

> color #2 black

> show #!4 models

> show #!5 models

> show #!6 models

> hide #!6 models

> color #5 #0d0706ff

> color #4 #020302ff

> show #!13 models

> hide #!5 models

> hide #!4 models

> hide #!2 models

> show #!14 models

> show #!15 models

> select add #14

21405 atoms, 21800 bonds, 230 pseudobonds, 2745 residues, 11 models selected  

> color (#!14.1-5 & sel) dim gray

> select add #13

43740 atoms, 44590 bonds, 320 pseudobonds, 5600 residues, 22 models selected  

> select subtract #14

22335 atoms, 22790 bonds, 90 pseudobonds, 2855 residues, 11 models selected  

> color (#!13.1-5 & sel) dark gray

> show sel surfaces

> select subtract #13

5 models selected  

> select add #13

22335 atoms, 22790 bonds, 90 pseudobonds, 2855 residues, 11 models selected  

> color #13 #b5b5b5ff models

> color #13 #8d8d8dff models

> select add #14

43740 atoms, 44590 bonds, 320 pseudobonds, 5600 residues, 27 models selected  

> show sel surfaces

> color #14 #b6b6b6ff models

> select add #15

66605 atoms, 67925 bonds, 325 pseudobonds, 8495 residues, 43 models selected  

> show sel surfaces

> color #15 #b9b9b9ff models

> select subtract #15

43740 atoms, 44590 bonds, 320 pseudobonds, 5600 residues, 37 models selected  

> select subtract #14

22335 atoms, 22790 bonds, 90 pseudobonds, 2855 residues, 21 models selected  

> select subtract #13

5 models selected  

> hide #!18 models

> hide #!19 models

> color #13 #b6b6b6ff models

> color #13 #cececeff models

> color #14 #dfdfdfff models

> color #15 #e2e2e2ff models

> hide #!16 models

> show #!16 models

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

> lighting simple

> lighting flat

> lighting soft

> select add #13

22335 atoms, 22790 bonds, 90 pseudobonds, 2855 residues, 11 models selected  

> select add #14

43740 atoms, 44590 bonds, 320 pseudobonds, 5600 residues, 27 models selected  

> select subtract #14

22335 atoms, 22790 bonds, 90 pseudobonds, 2855 residues, 21 models selected  

> select subtract #13

5 models selected  

> hide #!13 models

> hide #!14 models

> hide #!15 models

> show #!3 models

> show #!4 models

> select add #4

4467 atoms, 4558 bonds, 18 pseudobonds, 571 residues, 2 models selected  

> transparency #3.1 50

> select subtract #4

Nothing selected  

> hide #!3 models

> hide #!4 models

> show #!13 models

> show #!14 models

> show #!15 models

> select add #14

21405 atoms, 21800 bonds, 230 pseudobonds, 2745 residues, 11 models selected  

> select add #13

43740 atoms, 44590 bonds, 320 pseudobonds, 5600 residues, 27 models selected  

> select add #15

66605 atoms, 67925 bonds, 325 pseudobonds, 8495 residues, 43 models selected  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
PCH45_MCP_2_final.pdb #13.1/A LYS 178  
PCH45_MCP_2_final.pdb #13.1/A MET 189  
PCH45_MCP_2_final.pdb #13.1/A LYS 192  
PCH45_MCP_2_final.pdb #13.1/A GLU 224  
PCH45_MCP_2_final.pdb #13.1/A GLU 361  
PCH45_MCP_2_final.pdb #13.1/A GLU 393  
PCH45_MCP_2_final.pdb #13.1/A GLU 421  
PCH45_MCP_2_final.pdb #13.1/A ARG 439  
PCH45_MCP_2_final.pdb #13.1/A LYS 455  
PCH45_MCP_2_final.pdb #13.1/A LYS 483  
PCH45_MCP_2_final.pdb #13.1/A ASP 512  
PCH45_MCP_2_final.pdb #13.1/A GLU 513  
PCH45_MCP_2_final.pdb #13.1/A LYS 594  
PCH45_MCP_2_final.pdb #13.1/A GLU 624  
PCH45_MCP_2_final.pdb #13.1/A GLU 625  
PCH45_MCP_2_final.pdb #13.1/A ARG 655  
PCH45_MCP_2_final.pdb #13.1/A PHE 661  
PCH45_MCP_2_final.pdb #13.1/A GLU 743  
PCH45_MCP_2_final.pdb #13.1/A GLU 744  
PCH45_MCP_2_final.pdb #13.2/A LYS 178  
PCH45_MCP_2_final.pdb #13.2/A MET 189  
PCH45_MCP_2_final.pdb #13.2/A LYS 192  
PCH45_MCP_2_final.pdb #13.2/A GLU 224  
PCH45_MCP_2_final.pdb #13.2/A GLU 361  
PCH45_MCP_2_final.pdb #13.2/A GLU 393  
PCH45_MCP_2_final.pdb #13.2/A GLU 421  
PCH45_MCP_2_final.pdb #13.2/A ARG 439  
PCH45_MCP_2_final.pdb #13.2/A LYS 455  
PCH45_MCP_2_final.pdb #13.2/A LYS 483  
PCH45_MCP_2_final.pdb #13.2/A ASP 512  
PCH45_MCP_2_final.pdb #13.2/A GLU 513  
PCH45_MCP_2_final.pdb #13.2/A LYS 594  
PCH45_MCP_2_final.pdb #13.2/A GLU 624  
PCH45_MCP_2_final.pdb #13.2/A GLU 625  
PCH45_MCP_2_final.pdb #13.2/A ARG 655  
PCH45_MCP_2_final.pdb #13.2/A PHE 661  
PCH45_MCP_2_final.pdb #13.2/A GLU 743  
PCH45_MCP_2_final.pdb #13.2/A GLU 744  
PCH45_MCP_2_final.pdb #13.3/A LYS 178  
PCH45_MCP_2_final.pdb #13.3/A MET 189  
PCH45_MCP_2_final.pdb #13.3/A LYS 192  
PCH45_MCP_2_final.pdb #13.3/A GLU 224  
PCH45_MCP_2_final.pdb #13.3/A GLU 361  
PCH45_MCP_2_final.pdb #13.3/A GLU 393  
PCH45_MCP_2_final.pdb #13.3/A GLU 421  
PCH45_MCP_2_final.pdb #13.3/A ARG 439  
PCH45_MCP_2_final.pdb #13.3/A LYS 455  
PCH45_MCP_2_final.pdb #13.3/A LYS 483  
PCH45_MCP_2_final.pdb #13.3/A ASP 512  
PCH45_MCP_2_final.pdb #13.3/A GLU 513  
PCH45_MCP_2_final.pdb #13.3/A LYS 594  
PCH45_MCP_2_final.pdb #13.3/A GLU 624  
PCH45_MCP_2_final.pdb #13.3/A GLU 625  
PCH45_MCP_2_final.pdb #13.3/A ARG 655  
PCH45_MCP_2_final.pdb #13.3/A PHE 661  
PCH45_MCP_2_final.pdb #13.3/A GLU 743  
PCH45_MCP_2_final.pdb #13.3/A GLU 744  
PCH45_MCP_2_final.pdb #13.4/A LYS 178  
PCH45_MCP_2_final.pdb #13.4/A MET 189  
PCH45_MCP_2_final.pdb #13.4/A LYS 192  
PCH45_MCP_2_final.pdb #13.4/A GLU 224  
PCH45_MCP_2_final.pdb #13.4/A GLU 361  
PCH45_MCP_2_final.pdb #13.4/A GLU 393  
PCH45_MCP_2_final.pdb #13.4/A GLU 421  
PCH45_MCP_2_final.pdb #13.4/A ARG 439  
PCH45_MCP_2_final.pdb #13.4/A LYS 455  
PCH45_MCP_2_final.pdb #13.4/A LYS 483  
PCH45_MCP_2_final.pdb #13.4/A ASP 512  
PCH45_MCP_2_final.pdb #13.4/A GLU 513  
PCH45_MCP_2_final.pdb #13.4/A LYS 594  
PCH45_MCP_2_final.pdb #13.4/A GLU 624  
PCH45_MCP_2_final.pdb #13.4/A GLU 625  
PCH45_MCP_2_final.pdb #13.4/A ARG 655  
PCH45_MCP_2_final.pdb #13.4/A PHE 661  
PCH45_MCP_2_final.pdb #13.4/A GLU 743  
PCH45_MCP_2_final.pdb #13.4/A GLU 744  
PCH45_MCP_2_final.pdb #13.5/A LYS 178  
PCH45_MCP_2_final.pdb #13.5/A MET 189  
PCH45_MCP_2_final.pdb #13.5/A LYS 192  
PCH45_MCP_2_final.pdb #13.5/A GLU 224  
PCH45_MCP_2_final.pdb #13.5/A GLU 361  
PCH45_MCP_2_final.pdb #13.5/A GLU 393  
PCH45_MCP_2_final.pdb #13.5/A GLU 421  
PCH45_MCP_2_final.pdb #13.5/A ARG 439  
PCH45_MCP_2_final.pdb #13.5/A LYS 455  
PCH45_MCP_2_final.pdb #13.5/A LYS 483  
PCH45_MCP_2_final.pdb #13.5/A ASP 512  
PCH45_MCP_2_final.pdb #13.5/A GLU 513  
PCH45_MCP_2_final.pdb #13.5/A LYS 594  
PCH45_MCP_2_final.pdb #13.5/A GLU 624  
PCH45_MCP_2_final.pdb #13.5/A GLU 625  
PCH45_MCP_2_final.pdb #13.5/A ARG 655  
PCH45_MCP_2_final.pdb #13.5/A PHE 661  
PCH45_MCP_2_final.pdb #13.5/A GLU 743  
PCH45_MCP_2_final.pdb #13.5/A GLU 744  
PCH45_MCP_3_final-coot-3.pdb #14.1/A MET 189  
PCH45_MCP_3_final-coot-3.pdb #14.1/A LYS 192  
PCH45_MCP_3_final-coot-3.pdb #14.1/A GLU 224  
PCH45_MCP_3_final-coot-3.pdb #14.1/A GLU 361  
PCH45_MCP_3_final-coot-3.pdb #14.1/A GLU 393  
PCH45_MCP_3_final-coot-3.pdb #14.1/A GLU 421  
PCH45_MCP_3_final-coot-3.pdb #14.1/A LYS 455  
PCH45_MCP_3_final-coot-3.pdb #14.1/A LYS 483  
PCH45_MCP_3_final-coot-3.pdb #14.1/A ASP 488  
PCH45_MCP_3_final-coot-3.pdb #14.1/A GLN 509  
PCH45_MCP_3_final-coot-3.pdb #14.1/A LYS 594  
PCH45_MCP_3_final-coot-3.pdb #14.1/A GLU 624  
PCH45_MCP_3_final-coot-3.pdb #14.1/A GLU 625  
PCH45_MCP_3_final-coot-3.pdb #14.1/A ARG 655  
PCH45_MCP_3_final-coot-3.pdb #14.1/A PHE 661  
PCH45_MCP_3_final-coot-3.pdb #14.1/A GLU 688  
PCH45_MCP_3_final-coot-3.pdb #14.1/A GLU 743  
PCH45_MCP_3_final-coot-3.pdb #14.1/A GLU 744  
PCH45_MCP_3_final-coot-3.pdb #14.2/A MET 189  
PCH45_MCP_3_final-coot-3.pdb #14.2/A LYS 192  
PCH45_MCP_3_final-coot-3.pdb #14.2/A GLU 224  
PCH45_MCP_3_final-coot-3.pdb #14.2/A GLU 361  
PCH45_MCP_3_final-coot-3.pdb #14.2/A GLU 393  
PCH45_MCP_3_final-coot-3.pdb #14.2/A GLU 421  
PCH45_MCP_3_final-coot-3.pdb #14.2/A LYS 455  
PCH45_MCP_3_final-coot-3.pdb #14.2/A LYS 483  
PCH45_MCP_3_final-coot-3.pdb #14.2/A ASP 488  
PCH45_MCP_3_final-coot-3.pdb #14.2/A GLN 509  
PCH45_MCP_3_final-coot-3.pdb #14.2/A LYS 594  
PCH45_MCP_3_final-coot-3.pdb #14.2/A GLU 624  
PCH45_MCP_3_final-coot-3.pdb #14.2/A GLU 625  
PCH45_MCP_3_final-coot-3.pdb #14.2/A ARG 655  
PCH45_MCP_3_final-coot-3.pdb #14.2/A PHE 661  
PCH45_MCP_3_final-coot-3.pdb #14.2/A GLU 688  
PCH45_MCP_3_final-coot-3.pdb #14.2/A GLU 743  
PCH45_MCP_3_final-coot-3.pdb #14.2/A GLU 744  
PCH45_MCP_3_final-coot-3.pdb #14.3/A MET 189  
PCH45_MCP_3_final-coot-3.pdb #14.3/A LYS 192  
PCH45_MCP_3_final-coot-3.pdb #14.3/A GLU 224  
PCH45_MCP_3_final-coot-3.pdb #14.3/A GLU 361  
PCH45_MCP_3_final-coot-3.pdb #14.3/A GLU 393  
PCH45_MCP_3_final-coot-3.pdb #14.3/A GLU 421  
PCH45_MCP_3_final-coot-3.pdb #14.3/A LYS 455  
PCH45_MCP_3_final-coot-3.pdb #14.3/A LYS 483  
PCH45_MCP_3_final-coot-3.pdb #14.3/A ASP 488  
PCH45_MCP_3_final-coot-3.pdb #14.3/A GLN 509  
PCH45_MCP_3_final-coot-3.pdb #14.3/A LYS 594  
PCH45_MCP_3_final-coot-3.pdb #14.3/A GLU 624  
PCH45_MCP_3_final-coot-3.pdb #14.3/A GLU 625  
PCH45_MCP_3_final-coot-3.pdb #14.3/A ARG 655  
PCH45_MCP_3_final-coot-3.pdb #14.3/A PHE 661  
PCH45_MCP_3_final-coot-3.pdb #14.3/A GLU 688  
PCH45_MCP_3_final-coot-3.pdb #14.3/A GLU 743  
PCH45_MCP_3_final-coot-3.pdb #14.3/A GLU 744  
PCH45_MCP_3_final-coot-3.pdb #14.4/A MET 189  
PCH45_MCP_3_final-coot-3.pdb #14.4/A LYS 192  
PCH45_MCP_3_final-coot-3.pdb #14.4/A GLU 224  
PCH45_MCP_3_final-coot-3.pdb #14.4/A GLU 361  
PCH45_MCP_3_final-coot-3.pdb #14.4/A GLU 393  
PCH45_MCP_3_final-coot-3.pdb #14.4/A GLU 421  
PCH45_MCP_3_final-coot-3.pdb #14.4/A LYS 455  
PCH45_MCP_3_final-coot-3.pdb #14.4/A LYS 483  
PCH45_MCP_3_final-coot-3.pdb #14.4/A ASP 488  
PCH45_MCP_3_final-coot-3.pdb #14.4/A GLN 509  
PCH45_MCP_3_final-coot-3.pdb #14.4/A LYS 594  
PCH45_MCP_3_final-coot-3.pdb #14.4/A GLU 624  
PCH45_MCP_3_final-coot-3.pdb #14.4/A GLU 625  
PCH45_MCP_3_final-coot-3.pdb #14.4/A ARG 655  
PCH45_MCP_3_final-coot-3.pdb #14.4/A PHE 661  
PCH45_MCP_3_final-coot-3.pdb #14.4/A GLU 688  
PCH45_MCP_3_final-coot-3.pdb #14.4/A GLU 743  
PCH45_MCP_3_final-coot-3.pdb #14.4/A GLU 744  
PCH45_MCP_3_final-coot-3.pdb #14.5/A MET 189  
PCH45_MCP_3_final-coot-3.pdb #14.5/A LYS 192  
PCH45_MCP_3_final-coot-3.pdb #14.5/A GLU 224  
PCH45_MCP_3_final-coot-3.pdb #14.5/A GLU 361  
PCH45_MCP_3_final-coot-3.pdb #14.5/A GLU 393  
PCH45_MCP_3_final-coot-3.pdb #14.5/A GLU 421  
PCH45_MCP_3_final-coot-3.pdb #14.5/A LYS 455  
PCH45_MCP_3_final-coot-3.pdb #14.5/A LYS 483  
PCH45_MCP_3_final-coot-3.pdb #14.5/A ASP 488  
PCH45_MCP_3_final-coot-3.pdb #14.5/A GLN 509  
PCH45_MCP_3_final-coot-3.pdb #14.5/A LYS 594  
PCH45_MCP_3_final-coot-3.pdb #14.5/A GLU 624  
PCH45_MCP_3_final-coot-3.pdb #14.5/A GLU 625  
PCH45_MCP_3_final-coot-3.pdb #14.5/A ARG 655  
PCH45_MCP_3_final-coot-3.pdb #14.5/A PHE 661  
PCH45_MCP_3_final-coot-3.pdb #14.5/A GLU 688  
PCH45_MCP_3_final-coot-3.pdb #14.5/A GLU 743  
PCH45_MCP_3_final-coot-3.pdb #14.5/A GLU 744  
PCH45_MCP_1_final.pdb #15.1/A LYS 192  
PCH45_MCP_1_final.pdb #15.1/A ARG 328  
PCH45_MCP_1_final.pdb #15.1/A GLU 361  
PCH45_MCP_1_final.pdb #15.1/A GLU 393  
PCH45_MCP_1_final.pdb #15.1/A GLU 421  
PCH45_MCP_1_final.pdb #15.1/A GLU 624  
PCH45_MCP_1_final.pdb #15.1/A GLU 625  
PCH45_MCP_1_final.pdb #15.1/A GLU 743  
PCH45_MCP_1_final.pdb #15.1/A GLU 744  
PCH45_MCP_1_final.pdb #15.2/A LYS 192  
PCH45_MCP_1_final.pdb #15.2/A ARG 328  
PCH45_MCP_1_final.pdb #15.2/A GLU 361  
PCH45_MCP_1_final.pdb #15.2/A GLU 393  
PCH45_MCP_1_final.pdb #15.2/A GLU 421  
PCH45_MCP_1_final.pdb #15.2/A GLU 624  
PCH45_MCP_1_final.pdb #15.2/A GLU 625  
PCH45_MCP_1_final.pdb #15.2/A GLU 743  
PCH45_MCP_1_final.pdb #15.2/A GLU 744  
PCH45_MCP_1_final.pdb #15.3/A LYS 192  
PCH45_MCP_1_final.pdb #15.3/A ARG 328  
PCH45_MCP_1_final.pdb #15.3/A GLU 361  
PCH45_MCP_1_final.pdb #15.3/A GLU 393  
PCH45_MCP_1_final.pdb #15.3/A GLU 421  
PCH45_MCP_1_final.pdb #15.3/A GLU 624  
PCH45_MCP_1_final.pdb #15.3/A GLU 625  
PCH45_MCP_1_final.pdb #15.3/A GLU 743  
PCH45_MCP_1_final.pdb #15.3/A GLU 744  
PCH45_MCP_1_final.pdb #15.4/A LYS 192  
PCH45_MCP_1_final.pdb #15.4/A ARG 328  
PCH45_MCP_1_final.pdb #15.4/A GLU 361  
PCH45_MCP_1_final.pdb #15.4/A GLU 393  
PCH45_MCP_1_final.pdb #15.4/A GLU 421  
PCH45_MCP_1_final.pdb #15.4/A GLU 624  
PCH45_MCP_1_final.pdb #15.4/A GLU 625  
PCH45_MCP_1_final.pdb #15.4/A GLU 743  
PCH45_MCP_1_final.pdb #15.4/A GLU 744  
PCH45_MCP_1_final.pdb #15.5/A LYS 192  
PCH45_MCP_1_final.pdb #15.5/A ARG 328  
PCH45_MCP_1_final.pdb #15.5/A GLU 361  
PCH45_MCP_1_final.pdb #15.5/A GLU 393  
PCH45_MCP_1_final.pdb #15.5/A GLU 421  
PCH45_MCP_1_final.pdb #15.5/A GLU 624  
PCH45_MCP_1_final.pdb #15.5/A GLU 625  
PCH45_MCP_1_final.pdb #15.5/A GLU 743  
PCH45_MCP_1_final.pdb #15.5/A GLU 744  

Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen copy of PCH45_MCP_1_final.pdb #/A ASN 706 H bonded to atom that
should not have hydrogens (copy of PCH45_MCP_1_final.pdb #/A ASN 706 C)  

> select subtract #15

43740 atoms, 44590 bonds, 320 pseudobonds, 5600 residues, 37 models selected  

> select subtract #14

22335 atoms, 22790 bonds, 90 pseudobonds, 2855 residues, 21 models selected  

> select subtract #13

5 models selected  

> select add #13.1

4467 atoms, 4558 bonds, 18 pseudobonds, 571 residues, 2 models selected  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
PCH45_MCP_2_final.pdb #13.1/A LYS 178  
PCH45_MCP_2_final.pdb #13.1/A MET 189  
PCH45_MCP_2_final.pdb #13.1/A LYS 192  
PCH45_MCP_2_final.pdb #13.1/A GLU 224  
PCH45_MCP_2_final.pdb #13.1/A GLU 361  
PCH45_MCP_2_final.pdb #13.1/A GLU 393  
PCH45_MCP_2_final.pdb #13.1/A GLU 421  
PCH45_MCP_2_final.pdb #13.1/A ARG 439  
PCH45_MCP_2_final.pdb #13.1/A LYS 455  
PCH45_MCP_2_final.pdb #13.1/A LYS 483  
PCH45_MCP_2_final.pdb #13.1/A ASP 512  
PCH45_MCP_2_final.pdb #13.1/A GLU 513  
PCH45_MCP_2_final.pdb #13.1/A LYS 594  
PCH45_MCP_2_final.pdb #13.1/A GLU 624  
PCH45_MCP_2_final.pdb #13.1/A GLU 625  
PCH45_MCP_2_final.pdb #13.1/A ARG 655  
PCH45_MCP_2_final.pdb #13.1/A PHE 661  
PCH45_MCP_2_final.pdb #13.1/A GLU 743  
PCH45_MCP_2_final.pdb #13.1/A GLU 744  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 327, in run  
f(s)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\coulombic\cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 84, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\hbond.py",
line 248, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  

> select subtract #13.1

1 model selected  

> select add #13.3

4467 atoms, 4558 bonds, 18 pseudobonds, 571 residues, 2 models selected  

> select subtract #13.3

1 model selected  

> show #!2 models

> select add #2

4720 atoms, 4819 bonds, 1 pseudobond, 599 residues, 2 models selected  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
PCH45_MCP_1.pdb #2/A LYS 192  
PCH45_MCP_1.pdb #2/A ARG 328  
PCH45_MCP_1.pdb #2/A GLU 361  
PCH45_MCP_1.pdb #2/A GLU 393  
PCH45_MCP_1.pdb #2/A GLU 421  
PCH45_MCP_1.pdb #2/A GLU 624  
PCH45_MCP_1.pdb #2/A GLU 625  
PCH45_MCP_1.pdb #2/A GLU 743  
PCH45_MCP_1.pdb #2/A GLU 744  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 327, in run  
f(s)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\coulombic\cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 84, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\hbond.py",
line 248, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  

> hide #!2 models

> select subtract #2

Nothing selected  

> show #!4 models

> select add #4

4467 atoms, 4558 bonds, 18 pseudobonds, 571 residues, 2 models selected  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
PCH45_MCP_2_final.pdb #4/A LYS 178  
PCH45_MCP_2_final.pdb #4/A MET 189  
PCH45_MCP_2_final.pdb #4/A LYS 192  
PCH45_MCP_2_final.pdb #4/A GLU 224  
PCH45_MCP_2_final.pdb #4/A GLU 361  
PCH45_MCP_2_final.pdb #4/A GLU 393  
PCH45_MCP_2_final.pdb #4/A GLU 421  
PCH45_MCP_2_final.pdb #4/A ARG 439  
PCH45_MCP_2_final.pdb #4/A LYS 455  
PCH45_MCP_2_final.pdb #4/A LYS 483  
PCH45_MCP_2_final.pdb #4/A ASP 512  
PCH45_MCP_2_final.pdb #4/A GLU 513  
PCH45_MCP_2_final.pdb #4/A LYS 594  
PCH45_MCP_2_final.pdb #4/A GLU 624  
PCH45_MCP_2_final.pdb #4/A GLU 625  
PCH45_MCP_2_final.pdb #4/A ARG 655  
PCH45_MCP_2_final.pdb #4/A PHE 661  
PCH45_MCP_2_final.pdb #4/A GLU 743  
PCH45_MCP_2_final.pdb #4/A GLU 744  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 327, in run  
f(s)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\coulombic\cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 84, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\hbond.py",
line 248, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  

> mlp sel

Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.24,
mean -4.853, maximum 23.99  
To also show corresponding color key, enter the above mlp command and add key
true  

> select add #5

8748 atoms, 8918 bonds, 64 pseudobonds, 1120 residues, 5 models selected  

> show #!5 models

> mlp sel

Map values for surface "PCH45_MCP_3_final-coot-3.pdb_A SES surface": minimum
-29.68, mean -4.778, maximum 23.14  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.24,
mean -4.853, maximum 23.99  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!13 models

> hide #!14 models

> hide #!15 models

> show #!2 models

> select add #2

13468 atoms, 13737 bonds, 65 pseudobonds, 1719 residues, 8 models selected  

> mlp sel

Map values for surface "PCH45_MCP_1.pdb_A SES surface": minimum -30.13, mean
-4.899, maximum 22.13  
Map values for surface "PCH45_MCP_3_final-coot-3.pdb_A SES surface": minimum
-29.68, mean -4.778, maximum 23.14  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.24,
mean -4.853, maximum 23.99  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!4 models

> show #!4 models

> hide #!2 models

> show #!2 models

> hide #!5 models

> show #!5 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select subtract #5

9187 atoms, 9377 bonds, 19 pseudobonds, 1170 residues, 7 models selected  

> select subtract #4

4720 atoms, 4819 bonds, 1 pseudobond, 599 residues, 4 models selected  

> select subtract #2

1 model selected  

> select add #2

4720 atoms, 4819 bonds, 1 pseudobond, 599 residues, 2 models selected  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
PCH45_MCP_1.pdb #2/A LYS 192  
PCH45_MCP_1.pdb #2/A ARG 328  
PCH45_MCP_1.pdb #2/A GLU 361  
PCH45_MCP_1.pdb #2/A GLU 393  
PCH45_MCP_1.pdb #2/A GLU 421  
PCH45_MCP_1.pdb #2/A GLU 624  
PCH45_MCP_1.pdb #2/A GLU 625  
PCH45_MCP_1.pdb #2/A GLU 743  
PCH45_MCP_1.pdb #2/A GLU 744  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 327, in run  
f(s)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\coulombic\cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 84, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\hbond.py",
line 248, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  

> select subtract #2

1 model selected  

> hide #!4 models

> hide #!2 models

> hide #!5 models

> show #!13 models

> show #!14 models

> show #!15 models

> select add #13

22335 atoms, 22790 bonds, 90 pseudobonds, 2855 residues, 11 models selected  

> mlp sel

Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.38,
mean -4.853, maximum 24.11  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.24,
mean -4.853, maximum 23.99  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.41,
mean -4.852, maximum 24.29  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.18,
mean -4.854, maximum 23.71  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.87,
mean -4.854, maximum 24.1  
To also show corresponding color key, enter the above mlp command and add key
true  

> select add #14

43740 atoms, 44590 bonds, 320 pseudobonds, 5600 residues, 27 models selected  

> mlp sel

Map values for surface "PCH45_MCP_3_final-coot-3.pdb_A SES surface": minimum
-28.91, mean -4.779, maximum 22.64  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.38,
mean -4.853, maximum 24.11  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.24,
mean -4.853, maximum 23.99  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.41,
mean -4.852, maximum 24.29  
Map values for surface "PCH45_MCP_3_final-coot-3.pdb_A SES surface": minimum
-29.68, mean -4.778, maximum 23.14  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.18,
mean -4.854, maximum 23.71  
Map values for surface "PCH45_MCP_3_final-coot-3.pdb_A SES surface": minimum
-29.28, mean -4.777, maximum 22.76  
Map values for surface "PCH45_MCP_3_final-coot-3.pdb_A SES surface": minimum
-29.25, mean -4.779, maximum 22.61  
Map values for surface "PCH45_MCP_3_final-coot-3.pdb_A SES surface": minimum
-29.2, mean -4.778, maximum 23.1  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.87,
mean -4.854, maximum 24.1  
To also show corresponding color key, enter the above mlp command and add key
true  

> select add #15

66605 atoms, 67925 bonds, 325 pseudobonds, 8495 residues, 43 models selected  

> mlp sel

Map values for surface "PCH45_MCP_1_final.pdb_A SES surface": minimum -29.32,
mean -4.854, maximum 23.84  
Map values for surface "PCH45_MCP_3_final-coot-3.pdb_A SES surface": minimum
-28.91, mean -4.779, maximum 22.64  
Map values for surface "PCH45_MCP_1_final.pdb_A SES surface": minimum -29.56,
mean -4.854, maximum 23.62  
Map values for surface "PCH45_MCP_1_final.pdb_A SES surface": minimum -29.7,
mean -4.853, maximum 23.67  
Map values for surface "PCH45_MCP_1_final.pdb_A SES surface": minimum -29.27,
mean -4.851, maximum 23.52  
Map values for surface "PCH45_MCP_1_final.pdb_A SES surface": minimum -29.33,
mean -4.853, maximum 23.39  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.38,
mean -4.853, maximum 24.11  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.24,
mean -4.853, maximum 23.99  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.41,
mean -4.852, maximum 24.29  
Map values for surface "PCH45_MCP_3_final-coot-3.pdb_A SES surface": minimum
-29.68, mean -4.778, maximum 23.14  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.18,
mean -4.854, maximum 23.71  
Map values for surface "PCH45_MCP_3_final-coot-3.pdb_A SES surface": minimum
-29.28, mean -4.777, maximum 22.76  
Map values for surface "PCH45_MCP_3_final-coot-3.pdb_A SES surface": minimum
-29.25, mean -4.779, maximum 22.61  
Map values for surface "PCH45_MCP_3_final-coot-3.pdb_A SES surface": minimum
-29.2, mean -4.778, maximum 23.1  
Map values for surface "PCH45_MCP_2_final.pdb_A SES surface": minimum -29.87,
mean -4.854, maximum 24.1  
To also show corresponding color key, enter the above mlp command and add key
true  

> select subtract #15

43740 atoms, 44590 bonds, 320 pseudobonds, 5600 residues, 37 models selected  

> select subtract #14

22335 atoms, 22790 bonds, 90 pseudobonds, 2855 residues, 21 models selected  

> select subtract #13

5 models selected  

> transparency cartoon 50

Missing or invalid "percent" argument: Expected a number  

> transparency cartoon 0.5

Missing or invalid "percent" argument: Expected a number  

> transparency cartoons 0.5

Missing or invalid "percent" argument: Expected a number  

> transparency cartoons 50

Missing or invalid "percent" argument: Expected a number  

> transparency 50 cartoons

> transparency 70 cartoons

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> transparency 95 cartoons

> transparency 85 cartoons

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!16 models

> show #!18 models

> hide #!18 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!21 models

> transparency105 cartoons

Unknown command: transparency105 cartoons  

> transparency 10 cartoons

> transparency 60 cartoons

> transparency 0 cartoons

> hide #!20 models

> hide #!21 models

> transparency 40 cartoons

> transparency 60 cartoons

> transparency 70 cartoons

> hide #!17.2 models

> hide #!17.4 models

> hide #!17.5 models

> ui tool show "Side View"

> lighting soft

> lighting simple

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting full

> lighting shadows false

> lighting shadows true

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting soft

> transparency 50 cartoons

> select add #17.3

1302 atoms, 1331 bonds, 1 pseudobond, 166 residues, 2 models selected  

> select subtract #17.3

Nothing selected  

> select add #17.1

1302 atoms, 1331 bonds, 1 pseudobond, 166 residues, 2 models selected  

> show sel surfaces

> select add #17

6510 atoms, 6655 bonds, 5 pseudobonds, 830 residues, 13 models selected  

> select subtract #17.1

5208 atoms, 5324 bonds, 4 pseudobonds, 664 residues, 10 models selected  

> select add #17.1

6510 atoms, 6655 bonds, 5 pseudobonds, 830 residues, 12 models selected  

> select subtract #17.1

5208 atoms, 5324 bonds, 4 pseudobonds, 664 residues, 10 models selected  

> select add #17

6510 atoms, 6655 bonds, 5 pseudobonds, 830 residues, 12 models selected  

> select subtract #17

1 model selected  

> select add #17

6510 atoms, 6655 bonds, 5 pseudobonds, 830 residues, 12 models selected  

> select subtract #17

1 model selected  

> lighting simple

> select add #17.3

1302 atoms, 1331 bonds, 1 pseudobond, 166 residues, 2 models selected  

> hide sel surfaces

> select subtract #17.3

Nothing selected  

> select add #17.1

1302 atoms, 1331 bonds, 1 pseudobond, 166 residues, 3 models selected  

> hide sel surfaces

> select subtract #17.1

1 model selected  

> select add #13

22335 atoms, 22790 bonds, 90 pseudobonds, 2855 residues, 21 models selected  

> hide sel surfaces

> select subtract #13

5 models selected  

> select add #14

21405 atoms, 21800 bonds, 230 pseudobonds, 2745 residues, 21 models selected  

> hide sel surfaces

> select subtract #14

5 models selected  

> select add #17.1

1302 atoms, 1331 bonds, 1 pseudobond, 166 residues, 3 models selected  

> hbonds sel reveal true

donor: 8bfp (1).cif #1/D ARG 548 NH1 acceptor: PCH45_MCP_1.pdb #2/A ASP 712 O  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 327, in run  
f(s)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\hbonds\cmd.py",
line 83, in cmd_hbonds  
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  

> addh #17.1

Summary of feedback from adding hydrogens to PCH45_gp30.pdb #17.1  
---  
warnings | Not adding hydrogens to PCH45_gp30.pdb #17.1/H GLN 19 CB because it
is missing heavy-atom bond partners  
Not adding hydrogens to PCH45_gp30.pdb #17.1/H LYS 21 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to PCH45_gp30.pdb #17.1/H GLU 42 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to PCH45_gp30.pdb #17.1/H LYS 43 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to PCH45_gp30.pdb #17.1/H GLU 60 CB because it is missing
heavy-atom bond partners  
7 messages similar to the above omitted  
notes | Termini for PCH45_gp30.pdb (#17.1) chain H determined from SEQRES
records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: PCH45_gp30.pdb #17.1/H
MET 18, PCH45_gp30.pdb #17.1/H PRO 142  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: PCH45_gp30.pdb #17.1/H LEU
117, PCH45_gp30.pdb #17.1/H VAL 207  
113 hydrogen bonds  
Adding 'H' to PCH45_gp30.pdb #17.1/H MET 18  
PCH45_gp30.pdb #17.1/H VAL 207 is not terminus, removing H atom from 'C'  
1303 hydrogens added  
  

> show sel atoms

> color sel byhetero

> select H

1303 atoms, 166 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> addh #13.5

Summary of feedback from adding hydrogens to PCH45_MCP_2_final.pdb #13.5  
---  
warnings | Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A LYS 178 CB
because it is missing heavy-atom bond partners  
Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A MET 189 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A LYS 192 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A GLU 224 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A VAL 348 CA because it is
missing heavy-atom bond partners  
22 messages similar to the above omitted  
notes | Termini for PCH45_MCP_2_final.pdb (#13.5) chain A determined from
SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: PCH45_MCP_2_final.pdb
#13.5/A SER 170, PCH45_MCP_2_final.pdb #13.5/A ARG 655  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: PCH45_MCP_2_final.pdb
#13.5/A GLN 646, PCH45_MCP_2_final.pdb #13.5/A GLN 748  
donor: PCH45_MCP_2_final.pdb #13.5/A VAL 348 N acceptor: PCH45_MCP_2_final.pdb
#13.5/A VAL 348 O  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\hbond.py",
line 248, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  

> addh #13.5

Summary of feedback from adding hydrogens to PCH45_MCP_2_final.pdb #13.5  
---  
warnings | Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A LYS 178 CB
because it is missing heavy-atom bond partners  
Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A MET 189 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A LYS 192 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A GLU 224 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A VAL 348 CA because it is
missing heavy-atom bond partners  
22 messages similar to the above omitted  
notes | Termini for PCH45_MCP_2_final.pdb (#13.5) chain A determined from
SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: PCH45_MCP_2_final.pdb
#13.5/A SER 170, PCH45_MCP_2_final.pdb #13.5/A ARG 655  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: PCH45_MCP_2_final.pdb
#13.5/A GLN 646, PCH45_MCP_2_final.pdb #13.5/A GLN 748  
donor: PCH45_MCP_2_final.pdb #13.5/A VAL 348 N acceptor: PCH45_MCP_2_final.pdb
#13.5/A VAL 348 O  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\hbond.py",
line 248, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  

> addh #13.5

Summary of feedback from adding hydrogens to PCH45_MCP_2_final.pdb #13.5  
---  
warnings | Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A LYS 178 CB
because it is missing heavy-atom bond partners  
Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A MET 189 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A LYS 192 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A GLU 224 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to PCH45_MCP_2_final.pdb #13.5/A VAL 348 CA because it is
missing heavy-atom bond partners  
22 messages similar to the above omitted  
notes | Termini for PCH45_MCP_2_final.pdb (#13.5) chain A determined from
SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: PCH45_MCP_2_final.pdb
#13.5/A SER 170, PCH45_MCP_2_final.pdb #13.5/A ARG 655  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: PCH45_MCP_2_final.pdb
#13.5/A GLN 646, PCH45_MCP_2_final.pdb #13.5/A GLN 748  
donor: PCH45_MCP_2_final.pdb #13.5/A VAL 348 N acceptor: PCH45_MCP_2_final.pdb
#13.5/A VAL 348 O  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\hbond.py",
line 248, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 581.32
OpenGL renderer: NVIDIA GeForce RTX 3050 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_NZ.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Dell G15 5520
OS: Microsoft Windows 11 Home (Build 26200)
Memory: 16,849,293,312
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700H
OSLanguage: en-US

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    ChimeraX-AddH: 2.2.1
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    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
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    ChimeraX-IMOD: 1.0
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    ChimeraX-PDB: 2.6.8
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