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Opened 11 days ago
Closed 10 days ago
#19855 closed defect (not a bug)
AddH: acc_phi_psi() takes N positional arguments
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26200
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
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5rc202211120143
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
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
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.3
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.0.0
ipykernel: 6.15.3
ipython: 8.4.0
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jedi: 0.18.1
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kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
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MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.3
prompt-toolkit: 3.0.32
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.0
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.12
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.10.0
Change History (2)
comment:1 by , 10 days ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → AddH: acc_phi_psi() takes N positional arguments |
comment:2 by , 10 days ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
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