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Opened 8 months ago
Closed 8 months ago
#17014 closed defect (fixed)
Coulombic of centroid
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface/Binding Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/keanadavis/Documents/Rotation/JT/hsTRIM5_wt_g330dup6_a331dup5_r332dup4.cxs
> format session
Log from Tue Feb 18 17:37:57 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/keanadavis/Documents/Rotation/JT/R332dup4_wt.cxs format session
Log from Tue Feb 18 14:49:12 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/keanadavis/Documents/Rotation/JT/A331dup5.cxs format session
Log from Sun Feb 16 16:08:42 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/keanadavis/Documents/Rotation/JT/R332dup4.cxs format session
Log from Fri Feb 14 14:34:16 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
> alphafold predict
> MASGILVNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPNRHVANIVEKLREVKLSPEGQKVDHCARHGEKLLLFCQEDGKVICWLCERSQEHRGHHTFLTEEVAREYQVKLQAALEMLRQKQQEAEELEADIREEKASWKTQIQYDKTNVLADFEQLRDILDWEESNELQNLEKEEEDILKSLTNSETEMVQQTQSLRELISDLEHRLQGSVMELLQGVDGVIKRTENVTLKKPETFPKNQRRVFRAPDLKGMLEVFRELTDVRRYWVDVTVAPNNISCAVISEDKRQVSSPKPQIIYGARGTRRGTRYQTFVNFNYCTGILGSQSITSGKHYWEVDVSKKTAWILGVCAGFQPDAMCNIEKNENYQPKYGYWVIGLEEGVKCSAFQDSSFHTPSVPFIVPLSVIICPDRVGVFLDYEACTVSFFNITNHGFLIYKFSHCSFSQPVFPYLNPRKCGVPMTLCSPSS
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/keanadavis/Downloads/ChimeraX/AlphaFold/prediction_4
> open
> /Users/keanadavis/Downloads/ChimeraX/AlphaFold/prediction_4/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> select clear
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> save /Users/keanadavis/Documents/Rotation/JT/R332dup6.png width 1344 height
> 903 supersample 3 transparentBackground true
> ui mousemode right select
> select /A:136
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
922 atoms, 929 bonds, 110 residues, 1 model selected
> select up
3983 atoms, 4066 bonds, 497 residues, 1 model selected
> color sel grey
> select clear
> undo
[Repeated 1 time(s)]Drag select of 4 residues
> select clear
[Repeated 1 time(s)]
> select /A:331
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select /A:332
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select /A:332
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:333
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:332
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:332-340
78 atoms, 78 bonds, 9 residues, 1 model selected
> select /A:332-339
66 atoms, 65 bonds, 8 residues, 1 model selected
> color sel blue
> select up
492 atoms, 501 bonds, 64 residues, 1 model selected
> select down
66 atoms, 65 bonds, 8 residues, 1 model selected
> select up
492 atoms, 501 bonds, 64 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> show sel atoms
> hide sel atoms
> select down
66 atoms, 65 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
[Repeated 1 time(s)]
> select /A:332
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
492 atoms, 501 bonds, 64 residues, 1 model selected
> select down
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:332-339
66 atoms, 65 bonds, 8 residues, 1 model selected
> color sel light blue
> color sel orange
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -19.52, mean
-1.95, maximum 11.02
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -19.52, mean
-1.95, maximum 11.02
To also show corresponding color key, enter the above coulombic command and
add key true
> style sel stick
Changed 66 atom styles
> hide sel surfaces
> hbonds sel reveal true
1 hydrogen bonds found
> select up
492 atoms, 501 bonds, 64 residues, 2 models selected
> select up
3983 atoms, 4066 bonds, 497 residues, 2 models selected
> select up
3983 atoms, 4066 bonds, 1 pseudobond, 497 residues, 3 models selected
> hbonds sel reveal true
393 hydrogen bonds found
> ~hbonds
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select down
3983 atoms, 4066 bonds, 497 residues, 2 models selected
> select down
492 atoms, 501 bonds, 64 residues, 2 models selected
> select down
66 atoms, 65 bonds, 8 residues, 2 models selected
> hbonds sel reveal true
1 hydrogen bonds found
> select clear
> select /A:339
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
492 atoms, 501 bonds, 64 residues, 2 models selected
> select down
11 atoms, 10 bonds, 1 residue, 2 models selected
> select /a:332-339
66 atoms, 65 bonds, 1 pseudobond, 8 residues, 2 models selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label height 1
[Repeated 1 time(s)]
> label color black
> select clear
> save /Users/keanadavis/Documents/Rotation/JT/R332dup4_label.png width 707
> height 606 supersample 3
> save /Users/keanadavis/Documents/Rotation/JT/R332dup4_label.png width 707
> height 606 supersample 3 transparentBackground true
> select /A:333
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
492 atoms, 501 bonds, 64 residues, 2 models selected
> select up
3983 atoms, 4066 bonds, 497 residues, 2 models selected
> color bfactor sel
3983 atoms, 497 residues, 1 surfaces, atom bfactor range 37.1 to 98.4
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/keanadavis/Downloads/ChimeraX/AlphaFold/prediction_4/best_model_pae.json
> color bfactor #1 palette alphafold
3983 atoms, 497 residues, 1 surfaces, atom bfactor range 37.1 to 98.4
> save /Users/keanadavis/Documents/Rotation/JT/R332dup4.cxs
——— End of log from Fri Feb 14 14:34:16 2025 ———
opened ChimeraX session
> ui tool show Contacts
> contacts ignoreHiddenModels true reveal true
2164 contacts
> color sel orange
> select clear
[Repeated 1 time(s)]
> contacts bondSeparation 3 ignoreHiddenModels true reveal true
3160 contacts
> contacts ignoreHiddenModels true reveal true
2164 contacts
> hbonds reveal true
393 hydrogen bonds found
> ui tool show Contacts
> contacts ignoreHiddenModels true
2164 contacts
> hide #1.3 models
> hide #1.2 models
> hide #1.4 models
> open
Missing or invalid "fileNames" argument: Expected a file name
Drag select of 5 atoms, 2 residues, 4 bonds
> open
> /Users/keanadavis/Downloads/ChimeraX/AlphaFold/prediction_5/best_model.pdb
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
Computing secondary structure
> rename #1 G330dup6
> rename #2 R332dup4
> color #2 magenta
> select #1
3983 atoms, 4066 bonds, 2557 pseudobonds, 497 residues, 4 models selected
> hide sel atoms
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker G330dup6, chain A (#1) with R332dup4, chain A (#2), sequence
alignment score = 2572.5
RMSD between 327 pruned atom pairs is 1.204 angstroms; (across all 497 pairs:
2.778)
> select clear
[Repeated 1 time(s)]
> save
> /Users/keanadavis/Downloads/ChimeraX/AlphaFold/prediction_5/hsTRIM5_indels.cxs
> close
> ui tool show AlphaFold
> alphafold predict
> MASGILVNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPNRHVANIVEKLREVKLSPEGQKVDHCARHGEKLLLFCQEDGKVICWLCERSQEHRGHHTFLTEEVAREYQVKLQAALEMLRQKQQEAEELEADIREEKASWKTQIQYDKTNVLADFEQLRDILDWEESNELQNLEKEEEDILKSLTNSETEMVQQTQSLRELISDLEHRLQGSVMELLQGVDGVIKRTENVTLKKPETFPKNQRRVFRAPDLKGMLEVFRELTDVRRYWVDVTVAPNNISCAVISEDKRQVSSPKPQIIYGARGTRARGTRYQTFVNFNYCTGILGSQSITSGKHYWEVDVSKKTAWILGVCAGFQPDAMCNIEKNENYQPKYGYWVIGLEEGVKCSAFQDSSFHTPSVPFIVPLSVIICPDRVGVFLDYEACTVSFFNITNHGFLIYKFSHCSFSQPVFPYLNPRKCGVPMTLCSPSS
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/keanadavis/Downloads/ChimeraX/AlphaFold/prediction_6
> open
> /Users/keanadavis/Downloads/ChimeraX/AlphaFold/prediction_6/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> save /Users/keanadavis/Documents/Rotation/JT/A331dup5.cxs
——— End of log from Sun Feb 16 16:08:42 2025 ———
opened ChimeraX session
> close
> open
> /Users/keanadavis/Documents/Wynton/AF2/output/a331dup5/unrelaxed_model_1_multimer_v3_pred_0.pdb
Chain information for unrelaxed_model_1_multimer_v3_pred_0.pdb #1
---
Chain | Description
B C | No description available
Computing secondary structure
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/keanadavis/Documents/Wynton/AF2/output/a331dup5/pae_model_1_multimer_v3_pred_0.json
> color bfactor #1 palette alphafold
7976 atoms, 996 residues, atom bfactor range 31.8 to 96.5
> open
> /Users/keanadavis/Documents/Rotation/JT/Structures/fold_2025_02_18_a331dup5_hstrim5a/fold_2025_02_18_a331dup5_hstrim5a_model_0.cif
Chain information for fold_2025_02_18_a331dup5_hstrim5a_model_0.cif #2
---
Chain | Description
A B | .
Computing secondary structure
> close
> open
> /Users/keanadavis/Documents/Rotation/JT/Structures/fold_2025_02_18_a331dup5_hstrim5a/fold_2025_02_18_a331dup5_hstrim5a_model_1.cif
Chain information for fold_2025_02_18_a331dup5_hstrim5a_model_1.cif #1
---
Chain | Description
A B | .
Computing secondary structure
> open
> /Users/keanadavis/Documents/Rotation/JT/Structures/fold_2025_02_18_a331dup5_hstrim5a/fold_2025_02_18_a331dup5_hstrim5a_model_2.cif
Chain information for fold_2025_02_18_a331dup5_hstrim5a_model_2.cif #2
---
Chain | Description
A B | .
Computing secondary structure
> close
> open /Users/keanadavis/Downloads/fold_hstrim5_wt_dimer_model_0.cif
Chain information for fold_hstrim5_wt_dimer_model_0.cif #1
---
Chain | Description
A B | .
Computing secondary structure
> select /A:330-341
96 atoms, 97 bonds, 12 residues, 1 model selected
> show sel atoms
> select /B:330-341
96 atoms, 97 bonds, 12 residues, 1 model selected
> show sel atoms
> save /Users/keanadavis/Documents/Rotation/JT/hsTRIM5_wt.cxs
> open
> /Users/keanadavis/Documents/Rotation/JT/Structures/fold_2025_02_18_r332dup4_hstrim5a/fold_2025_02_18_r332dup4_hstrim5a_model_0.cif
Chain information for fold_2025_02_18_r332dup4_hstrim5a_model_0.cif #2
---
Chain | Description
A B | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hstrim5_wt_dimer_model_0.cif, chain A (#1) with
fold_2025_02_18_r332dup4_hstrim5a_model_0.cif, chain A (#2), sequence
alignment score = 2561.2
RMSD between 355 pruned atom pairs is 1.037 angstroms; (across all 493 pairs:
1.972)
> select clear
> select 2/A:331-341
Expected an objects specifier or a keyword
> select /2A:331-341
Nothing selected
> select clear
[Repeated 1 time(s)]
> select #2/B:329
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:330-341
96 atoms, 96 bonds, 12 residues, 1 model selected
> show sel atoms
> select #2/B:330-341
96 atoms, 96 bonds, 12 residues, 1 model selected
> show sel atoms
> select clear
> hbonds reveal true
2624 hydrogen bonds found
> ~hbonds
> ui tool show Contacts
> contacts ignoreHiddenModels true
88538 contacts
> hide #1 models
> hide #2 models
> show #1 models
> show #2 models
> hide #3 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> save /Users/keanadavis/Documents/Rotation/JT/R332dup4_wt.cxs
> hide cartoons
> show cartoons
> hide atoms
> save /Users/keanadavis/Documents/Rotation/JT/R332dup4_wt.cxs
——— End of log from Tue Feb 18 14:49:12 2025 ———
opened ChimeraX session
> select add #3
88538 pseudobonds, 1 model selected
> hide #2 models
> hide #1 models
> close #2
> undo
[Repeated 1 time(s)]
> close
> open
> /Users/keanadavis/Documents/Rotation/JT/Structures/fold_2025_02_18_a331dup5_hstrim5a/fold_2025_02_18_a331dup5_hstrim5a_full_data_0.json
Failed opening file
/Users/keanadavis/Documents/Rotation/JT/Structures/fold_2025_02_18_a331dup5_hstrim5a/fold_2025_02_18_a331dup5_hstrim5a_full_data_0.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/keanadavis/Documents/Rotation/JT/Structures/fold_2025_02_18_a331dup5_hstrim5a/fold_2025_02_18_a331dup5_hstrim5a_full_data_0.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open
> /Users/keanadavis/Documents/Rotation/JT/Structures/fold_2025_02_18_a331dup5_hstrim5a/fold_2025_02_18_a331dup5_hstrim5a_summary_confidences_0.json
Failed opening file
/Users/keanadavis/Documents/Rotation/JT/Structures/fold_2025_02_18_a331dup5_hstrim5a/fold_2025_02_18_a331dup5_hstrim5a_summary_confidences_0.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/keanadavis/Documents/Rotation/JT/Structures/fold_2025_02_18_a331dup5_hstrim5a/fold_2025_02_18_a331dup5_hstrim5a_summary_confidences_0.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open
> /Users/keanadavis/Documents/Rotation/JT/Structures/fold_2025_02_18_a331dup5_hstrim5a/fold_2025_02_18_a331dup5_hstrim5a_model_0.cif
Chain information for fold_2025_02_18_a331dup5_hstrim5a_model_0.cif #1
---
Chain | Description
A B | .
Computing secondary structure
> open
> /Users/keanadavis/Documents/Rotation/JT/Structures/fold_2025_02_18_g330dup6_hstrim5/fold_2025_02_18_g330dup6_hstrim5_model_0.cif
Chain information for fold_2025_02_18_g330dup6_hstrim5_model_0.cif #2
---
Chain | Description
A B | .
Computing secondary structure
> open
> /Users/keanadavis/Documents/Rotation/JT/Structures/fold_2025_02_18_r332dup4_hstrim5a/fold_2025_02_18_r332dup4_hstrim5a_model_0.cif
Chain information for fold_2025_02_18_r332dup4_hstrim5a_model_0.cif #3
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/keanadavis/Downloads/fold_hstrim5_wt_dimer_model_0.cif
Chain information for fold_hstrim5_wt_dimer_model_0.cif #4
---
Chain | Description
A B | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2-4 to #1
Computing secondary structure
[Repeated 3 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_2025_02_18_a331dup5_hstrim5a_model_0.cif, chain B (#1) with
fold_2025_02_18_g330dup6_hstrim5_model_0.cif, chain B (#2), sequence alignment
score = 2593.1
RMSD between 359 pruned atom pairs is 0.766 angstroms; (across all 498 pairs:
3.187)
Matchmaker fold_2025_02_18_a331dup5_hstrim5a_model_0.cif, chain B (#1) with
fold_2025_02_18_r332dup4_hstrim5a_model_0.cif, chain B (#3), sequence
alignment score = 2610.7
RMSD between 352 pruned atom pairs is 0.549 angstroms; (across all 497 pairs:
4.685)
Matchmaker fold_2025_02_18_a331dup5_hstrim5a_model_0.cif, chain B (#1) with
fold_hstrim5_wt_dimer_model_0.cif, chain A (#4), sequence alignment score =
2551.2
RMSD between 327 pruned atom pairs is 0.759 angstroms; (across all 493 pairs:
3.730)
> color #4 #00fdffff
> color #3 #ff40ffff
> color #2 #00f900ff
> color #1 #ff9300ff
Unsupported scale factor (0.000000) detected on Display1
[Repeated 3 time(s)]
> select #2/A:330-341
84 atoms, 83 bonds, 12 residues, 1 model selected
> show sel atoms
> select #2/B:330-341
84 atoms, 83 bonds, 12 residues, 1 model selected
> show sel atoms
> select clear
> select #2/B:330-341, #2/A:330-341
Expected an objects specifier or a keyword
> select #2/B:330-341 and #2/A:330-341
Expected a keyword
> select #2/B:330-341 #2/A:330-341
168 atoms, 166 bonds, 24 residues, 1 model selected
> hbonds sel reveal true
16 hydrogen bonds found
> select clear
[Repeated 2 time(s)]
> select #2/B:330-341 #2/A:330-341
168 atoms, 166 bonds, 6 pseudobonds, 24 residues, 2 models selected
> ui tool show Contacts
> contacts ignoreHiddenModels true color #0433ff
467275 contacts
> select clear
> hide #1 models
> hide #2 models
> show #1 models
> show #2 models
> hide #2 models
> hide #1 models
> hide #3 models
> show #2 models
> hide #4 models
> select add #5
16 pseudobonds, 1 model selected
> close #5
> close #6
> save
> /Users/keanadavis/Documents/Rotation/JT/hsTRIM5_wt_g330dup6_a331dup5_r332dup4.cxs
——— End of log from Tue Feb 18 17:37:57 2025 ———
opened ChimeraX session
> hide #2 models
> show #1 models
> select #1/A:324-349 #1/B:324-349
436 atoms, 446 bonds, 52 residues, 1 model selected
> show sel atoms
> ui tool show Distances
> select aromatic-ring
2656 atoms, 2712 bonds, 432 residues, 4 models selected
> show (#1 & sel) target ab
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B phe 247 #1B/ TYR 349
Expected a keyword
> select #1/B PHE 247 #1B/ TYR 349
Expected a keyword
> select #1/B:247 #1/B:349
20 atoms, 19 bonds, 2 residues, 1 model selected
> select #1/B:347 #1/B:349
23 atoms, 23 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> surface sel
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_2025_02_18_a331dup5_hstrim5a_model_0.cif_B SES
surface #1.1: minimum, -17.83, mean -2.03, maximum 12.72
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> ui mousemode right distance
> ui mousemode right select
No items chosen in table
> select #1/B:347
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui tool show Axes/Planes/Centroids
> select down
2 atoms, 1 bond, 1 residue, 2 models selected
> select down
1 bond, 2 models selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 2 models selected
Need to select at least one atom
[Repeated 1 time(s)]Exactly two atoms must be selected!
No items chosen in table
Need to select at least one atom
> select down
6 bonds, 1 model selected
> select up
6 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
Exactly two atoms must be selected!
[Repeated 1 time(s)]
> select down
2 bonds, 1 model selected
> select clear
Exactly two atoms must be selected!
> hide sel cartoons
> show sel atoms
> show sel cartoons
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> select clear
> hide #!1 cartoons
> show #!1 atoms
> select clear
Exactly two atoms must be selected!
> ui mousemode right distance
> ui mousemode right select
> select clear
> ui mousemode right distance
> distance #1/B:347@CE2 #1/B:349@CE1
Distance between fold_2025_02_18_a331dup5_hstrim5a_model_0.cif #1/B PHE 347
CE2 and TYR 349 CE1: 4.937Å
> ui mousemode right distance
> undo
[Repeated 1 time(s)]
> ~distance #1/B:347@CE2 #1/B:349@CE1
> ui mousemode right select
> select clear
Need to select at least one atom
[Repeated 1 time(s)]
> select clear
> ui mousemode right distance
[Repeated 1 time(s)]
> select clear
> ui mousemode right distance
[Repeated 1 time(s)]
> select #1/B:347
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right distance
> ui mousemode right select
> select #1/B:349@CE1
1 atom, 1 residue, 1 model selected
> select #1/B:347@CZ
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> select add #1/B:349@CE1
2 atoms, 2 residues, 2 models selected
> ui mousemode right distance
> distance #1/B:347@CZ #1/B:349@CE1
Distance between fold_2025_02_18_a331dup5_hstrim5a_model_0.cif #1/B PHE 347 CZ
and TYR 349 CE1: 5.353Å
> distance #1/B:349@CE1 #1/B:347@CG
Distance between fold_2025_02_18_a331dup5_hstrim5a_model_0.cif #1/B TYR 349
CE1 and PHE 347 CG: 3.584Å
> distance #1/B:347@CD1 #1/B:347@CD2
Distance between fold_2025_02_18_a331dup5_hstrim5a_model_0.cif #1/B PHE 347
CD1 and CD2: 2.420Å
> distance #1/B:349@CE2 #1/B:347@CE2
Distance between fold_2025_02_18_a331dup5_hstrim5a_model_0.cif #1/B TYR 349
CE2 and PHE 347 CE2: 5.284Å
> distance #1/B:347@CE1 #1/B:349@CE1
Distance between fold_2025_02_18_a331dup5_hstrim5a_model_0.cif #1/B PHE 347
CE1 and TYR 349 CE1: 5.014Å
> ~distance #1/B:347@CD1 #1/B:347@CD2
Choose exactly one axis or plane in table
> ~distance #1/B:349@CE1 #1/B:347@CG
> ~distance #1/B:347@CZ #1/B:349@CE1
> ~distance #1/B:347@CE1 #1/B:349@CE1
> ~distance #1/B:349@CE2 #1/B:347@CE2
> select clear
> ui mousemode right distance
> ui mousemode right select
> select #1/B:347@CZ
1 atom, 1 residue, 1 model selected
> select add #1/B:347@CE1
2 atoms, 1 residue, 2 models selected
> select add #1/B:347@CD1
3 atoms, 1 residue, 2 models selected
> select add #1/B:347@CG
4 atoms, 1 residue, 2 models selected
> select add #1/B:347@CD2
5 atoms, 1 residue, 2 models selected
> select add #1/B:347@CE2
6 atoms, 1 residue, 2 models selected
> define centroid sel name C1 color #ff2600
Centroid 'C1' placed at [-21.08349991 -18.41616662 -41.6154995 ]
> close #1.2
> define centroid sel name C1 color #ff2600 radius 0.1
Centroid 'C1' placed at [-21.08349991 -18.41616662 -41.6154995 ]
> select clear
> select #!1/B:349@CD2
1 atom, 1 residue, 1 model selected
> select add #!1/B:349@CG
2 atoms, 1 residue, 2 models selected
> select add #!1/B:349@CD1
3 atoms, 1 residue, 2 models selected
> select add #!1/B:349@CE1
4 atoms, 1 residue, 2 models selected
> select add #!1/B:349@CE2
5 atoms, 1 residue, 2 models selected
> select add #!1/B:349@CZ
6 atoms, 1 residue, 2 models selected
> define centroid sel name C2 color #ff2600 radius 0.1
Centroid 'C2' placed at [-18.22083346 -15.42966668 -38.94766617]
> select #1.3
1 atom, 1 residue, 1 model selected
> select add #1.2
2 atoms, 2 residues, 2 models selected
> distance #1.3 #1.2
Distance between C2 #1.3 and C1 #1.2: 4.923Å
> select add #!1/B:340@CZ
3 atoms, 3 residues, 3 models selected
> select add #!1/B:340@NH1
4 atoms, 3 residues, 4 models selected
> select add #!1/B:340@NH2
5 atoms, 3 residues, 4 models selected
> select clear
> select #!1/B:340@NH2
1 atom, 1 residue, 1 model selected
> select #!1/B:340@CZ
1 atom, 1 residue, 1 model selected
> select add #!1/B:340@NH2
2 atoms, 1 residue, 2 models selected
> select add #!1/B:340@NH1
3 atoms, 1 residue, 2 models selected
> define centroid sel name C3 color #ff2600 radius 0.1
Centroid 'C3' placed at [-32.15566635 -7.01333332 -51.43966675]
> select #!1/B:329@CD1
1 atom, 1 residue, 1 model selected
> select add #!1/B:329@CG
2 atoms, 1 residue, 1 model selected
> select add #!1/B:329@CD2
3 atoms, 1 residue, 1 model selected
> select add #!1/B:329@CE2
4 atoms, 1 residue, 2 models selected
> select add #!1/B:329@CZ
5 atoms, 1 residue, 2 models selected
> select add #!1/B:329@CE1
6 atoms, 1 residue, 2 models selected
> define centroid sel name C4 color #ff2600 radius 0.1
Centroid 'C4' placed at [-29.82516638 -7.62150009 -46.31033262]
> select clear
[Repeated 1 time(s)]
> select #1.5
1 atom, 1 residue, 1 model selected
> select add #1.4
2 atoms, 2 residues, 2 models selected
> distance #1.5 #1.4
Distance between C4 #1.5 and C3 #1.4: 5.667Å
> save /Users/keanadavis/Documents/Rotation/JT/A331dup5.cxs
> hide #!1 models
> select #2 #3 #4
23856 atoms, 24354 bonds, 2978 residues, 3 models selected
> delete sel
> delete #5
> select #5
2 pseudobonds, 2 models selected
> delete sel
> clear
Unknown command: clear
> hide #!5 models
> select subtract #5
Nothing selected
> select add #5.1
1 model selected
> select subtract #5.1
Nothing selected
> show #!1 models
> hide #5.1 models
> show #!5 models
> show #5.1 models
> open "/Users/keanadavis/Library/CloudStorage/Box-Box/Tenthorey Lab
> Shared/Raw Data/Keana
> Data/Structures/2025_02_18_a331dup5_dimer/fold_2025_02_18_a331dup5_hstrim5a_model_1.cif"
Chain information for fold_2025_02_18_a331dup5_hstrim5a_model_1.cif #2
---
Chain | Description
A B | .
Computing secondary structure
> hide #!1 models
> show #!1 models
> open "/Users/keanadavis/Library/CloudStorage/Box-Box/Tenthorey Lab
> Shared/Raw Data/Keana
> Data/Structures/2025_02_18_a331dup5_dimer/fold_2025_02_18_a331dup5_hstrim5a_model_4.cif"
> "/Users/keanadavis/Library/CloudStorage/Box-Box/Tenthorey Lab Shared/Raw
> Data/Keana
> Data/Structures/2025_02_18_a331dup5_dimer/fold_2025_02_18_a331dup5_hstrim5a_model_2.cif"
> "/Users/keanadavis/Library/CloudStorage/Box-Box/Tenthorey Lab Shared/Raw
> Data/Keana
> Data/Structures/2025_02_18_a331dup5_dimer/fold_2025_02_18_a331dup5_hstrim5a_model_3.cif"
Chain information for fold_2025_02_18_a331dup5_hstrim5a_model_4.cif #3
---
Chain | Description
A B | .
Chain information for fold_2025_02_18_a331dup5_hstrim5a_model_2.cif #4
---
Chain | Description
A B | .
Chain information for fold_2025_02_18_a331dup5_hstrim5a_model_3.cif #6
---
Chain | Description
A B | .
Computing secondary structure
[Repeated 2 time(s)]
> ui tool show Matchmaker
> matchmaker #2-4,6 to #1
Specify a single 'to' model only
> matchmaker #2-4,6 to #1
Specify a single 'to' model only
> clear
Unknown command: clear
> matchmaker #2 to #1
Specify a single 'to' model only
> matchmaker #3 to #1
Specify a single 'to' model only
> matchmaker #3-4,6 to #1
Specify a single 'to' model only
> matchmaker #3 to #1
Specify a single 'to' model only
> ui tool show Matchmaker
> clear
Unknown command: clear
> matchmaker #3 & sel to #1
Specify a single 'to' model only
> matchmaker #3 & sel to #1
Specify a single 'to' model only
> clear
Unknown command: clear
> matchmaker #2 & sel to #1
Specify a single 'to' model only
> select #1
7982 atoms, 8144 bonds, 2 pseudobonds, 1000 residues, 6 models selected
> mmaker #2 to #1
Specify a single 'to' model only
> mmaker #2-4 to #1
Specify a single 'to' model only
> select add #2
15960 atoms, 16288 bonds, 2 pseudobonds, 1996 residues, 8 models selected
> select add #3
23938 atoms, 24432 bonds, 2 pseudobonds, 2992 residues, 9 models selected
> hide #3 target m
[Repeated 1 time(s)]
> show #3 target m
> select subtract #1
15956 atoms, 16288 bonds, 1992 residues, 3 models selected
> select subtract #2
7978 atoms, 8144 bonds, 996 residues, 1 model selected
> select subtract #3
Nothing selected
> mmaker #2-4 to #1
Specify a single 'to' model only
> mmaker #2-4 to #1.1
No 'to' model specified
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> close
> open
Missing or invalid "fileNames" argument: Expected a file name
> open "/Users/keanadavis/Library/CloudStorage/Box-Box/Tenthorey Lab
> Shared/Raw Data/Keana
> Data/Structures/2025_02_18_a331dup5_dimer/fold_2025_02_18_a331dup5_hstrim5a_model_1.cif"
> "/Users/keanadavis/Library/CloudStorage/Box-Box/Tenthorey Lab Shared/Raw
> Data/Keana
> Data/Structures/2025_02_18_a331dup5_dimer/fold_2025_02_18_a331dup5_hstrim5a_model_2.cif"
> "/Users/keanadavis/Library/CloudStorage/Box-Box/Tenthorey Lab Shared/Raw
> Data/Keana
> Data/Structures/2025_02_18_a331dup5_dimer/fold_2025_02_18_a331dup5_hstrim5a_model_3.cif"
> "/Users/keanadavis/Library/CloudStorage/Box-Box/Tenthorey Lab Shared/Raw
> Data/Keana
> Data/Structures/2025_02_18_a331dup5_dimer/fold_2025_02_18_a331dup5_hstrim5a_model_4.cif"
> "/Users/keanadavis/Library/CloudStorage/Box-Box/Tenthorey Lab Shared/Raw
> Data/Keana
> Data/Structures/2025_02_18_a331dup5_dimer/fold_2025_02_18_a331dup5_hstrim5a_model_0.cif"
Chain information for fold_2025_02_18_a331dup5_hstrim5a_model_1.cif #1
---
Chain | Description
A B | .
Chain information for fold_2025_02_18_a331dup5_hstrim5a_model_2.cif #2
---
Chain | Description
A B | .
Chain information for fold_2025_02_18_a331dup5_hstrim5a_model_3.cif #3
---
Chain | Description
A B | .
Chain information for fold_2025_02_18_a331dup5_hstrim5a_model_4.cif #4
---
Chain | Description
A B | .
Chain information for fold_2025_02_18_a331dup5_hstrim5a_model_0.cif #5
---
Chain | Description
A B | .
Computing secondary structure
[Repeated 4 time(s)]
> mmaker #1-4 to #5
Computing secondary structure
[Repeated 4 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_2025_02_18_a331dup5_hstrim5a_model_0.cif, chain B (#5) with
fold_2025_02_18_a331dup5_hstrim5a_model_1.cif, chain A (#1), sequence
alignment score = 2600.1
RMSD between 443 pruned atom pairs is 1.036 angstroms; (across all 498 pairs:
1.441)
Matchmaker fold_2025_02_18_a331dup5_hstrim5a_model_0.cif, chain B (#5) with
fold_2025_02_18_a331dup5_hstrim5a_model_2.cif, chain A (#2), sequence
alignment score = 2600.1
RMSD between 454 pruned atom pairs is 0.959 angstroms; (across all 498 pairs:
1.648)
Matchmaker fold_2025_02_18_a331dup5_hstrim5a_model_0.cif, chain B (#5) with
fold_2025_02_18_a331dup5_hstrim5a_model_3.cif, chain A (#3), sequence
alignment score = 2600.1
RMSD between 340 pruned atom pairs is 0.638 angstroms; (across all 498 pairs:
3.344)
Matchmaker fold_2025_02_18_a331dup5_hstrim5a_model_0.cif, chain B (#5) with
fold_2025_02_18_a331dup5_hstrim5a_model_4.cif, chain A (#4), sequence
alignment score = 2610.9
RMSD between 347 pruned atom pairs is 0.982 angstroms; (across all 498 pairs:
3.219)
> show atoms
[Repeated 1 time(s)]
> hide atoms
[Repeated 1 time(s)]
> select ::name="ARG"
2970 atoms, 2720 bonds, 270 residues, 5 models selected
> show sel atoms
> select aromatic-ring
3320 atoms, 3390 bonds, 540 residues, 5 models selected
> show sel atoms
> select clear
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #1 cartoons
> select all
39890 atoms, 40720 bonds, 4980 residues, 5 models selected
> show sel & #1 cartoons
[Repeated 1 time(s)]
> style sel & #1 stick
Changed 7978 atom styles
> show sel & #1 cartoons
> show sel & #1 atoms
> hide sel & #1 atoms
> undo
[Repeated 1 time(s)]
> show sel & #1 cartoons
> select clear
> select ::name="TYR"
1680 atoms, 1680 bonds, 140 residues, 5 models selected
> show sel & #1 atoms
> select ::name="PHE"
2200 atoms, 2210 bonds, 200 residues, 5 models selected
> show sel & #1 atoms
> select clear
> select add #1/A:329@CG
1 atom, 1 residue, 1 model selected
> select clear
> select #1/A:329@CG
1 atom, 1 residue, 1 model selected
> select clear
> select #1/A:329@CD1
1 atom, 1 residue, 1 model selected
> select #1/A:329
12 atoms, 12 bonds, 1 residue, 1 model selected
> select subtract #1/A:329
Nothing selected
> select phe
Expected an objects specifier or a keyword
> select F
Nothing selected
> select ::name="PHE"
2200 atoms, 2210 bonds, 200 residues, 5 models selected
> select clear
[Repeated 1 time(s)]
> show #1 atoms
> select ::name="PHE"
2200 atoms, 2210 bonds, 200 residues, 5 models selected
> show sel & #1 atoms
> select ::name="ARG"
2970 atoms, 2720 bonds, 270 residues, 5 models selected
> show sel & #1 atoms
> select ::name="TYR"
1680 atoms, 1680 bonds, 140 residues, 5 models selected
> show sel & #1 atoms
> select clear
[Repeated 1 time(s)]
> select #1/A:329@CD1
1 atom, 1 residue, 1 model selected
> select #1/A:329@CG
1 atom, 1 residue, 1 model selected
> select add #1/A:329@CD2
2 atoms, 1 residue, 1 model selected
> select add #1/A:329@CE2
3 atoms, 1 residue, 1 model selected
> select add #1/A:329@CZ
4 atoms, 1 residue, 1 model selected
> select add #1/A:329@CE1
5 atoms, 1 residue, 1 model selected
> select add #1/A:329@CD1
6 atoms, 1 residue, 1 model selected
> define centroid sel name C4 color #ff2600 radius 0.1
Centroid 'C4' placed at [ -0.15066667 -0.8485 -53.675 ]
> select clear
> select #!1/A:340@NH2
1 atom, 1 residue, 1 model selected
> select add #!1/A:340@CZ
2 atoms, 1 residue, 1 model selected
> select add #!1/A:340@NH1
3 atoms, 1 residue, 1 model selected
> define centroid sel name C3 color #ff2600 radius 0.1
Centroid 'C3' placed at [ -0.108 -4.39466667 -57.20133333]
> select clear
> select #!1/A:344@CG
1 atom, 1 residue, 1 model selected
> select add #!1/A:344@CD1
2 atoms, 1 residue, 1 model selected
> select add #!1/A:344@CE1
3 atoms, 1 residue, 1 model selected
> select add #!1/A:344@CZ
4 atoms, 1 residue, 1 model selected
> select add #!1/A:344@CE2
5 atoms, 1 residue, 1 model selected
> select add #!1/A:344@CD2
6 atoms, 1 residue, 1 model selected
> define centroid sel name C1 color #ff2600 radius 0.1
Centroid 'C1' placed at [ 4.6695 -0.15966667 -43.92533333]
> select clear
> select #!1/A:342@NE2
1 atom, 1 residue, 1 model selected
> select clear
> close #1.3
> select #!1/A:341@CZ
1 atom, 1 residue, 1 model selected
> select add #!1/A:341@CE1
2 atoms, 1 residue, 1 model selected
> select add #!1/A:341@CD1
3 atoms, 1 residue, 1 model selected
> select add #!1/A:341@CG
4 atoms, 1 residue, 1 model selected
> select add #!1/A:341@CD2
5 atoms, 1 residue, 1 model selected
> select add #!1/A:341@CE2
6 atoms, 1 residue, 1 model selected
> select #!1/A:341@CZ
1 atom, 1 residue, 1 model selected
> select add #!1/A:341@CE1
2 atoms, 1 residue, 1 model selected
> select add #!1/A:341@CD1
3 atoms, 1 residue, 1 model selected
> select add #!1/A:341@CG
4 atoms, 1 residue, 1 model selected
> select add #!1/A:341@CD2
5 atoms, 1 residue, 1 model selected
> select add #!1/A:341@CE2
6 atoms, 1 residue, 1 model selected
> define centroid sel name C1 color #ff2600 radius 0.1
Centroid 'C1' placed at [ 12.00183333 -2.74216667 -52.521 ]
> select clear
> select #!1/A:332@NH2
1 atom, 1 residue, 1 model selected
> select #!1/A:332@NH2
1 atom, 1 residue, 1 model selected
> select add #!1/A:332@NH1
2 atoms, 1 residue, 1 model selected
> select add #!1/A:332@CZ
3 atoms, 1 residue, 1 model selected
> define centroid sel name C2 color #ff2600 radius 0.1
Centroid 'C2' placed at [ 13.68833333 3.645 -56.299 ]
> select clear
> select #1.3
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #1.4
1 atom, 1 residue, 1 model selected
> select add #1.3
2 atoms, 2 residues, 2 models selected
> distance #1.4 #1.3
Distance between C2 #1.4 and C1 #1.3: 7.610Å
> select #1.1
1 atom, 1 residue, 1 model selected
> select add #1.2
2 atoms, 2 residues, 2 models selected
> distance #1.1 #1.2
Distance between C4 #1.1 and C3 #1.2: 5.001Å
> select clear
> select #!1/A:340@CZ
1 atom, 1 residue, 1 model selected
> sek #1/A:340 #1/A:329
Unknown command: sek #1/A:340 #1/A:329
> select #1/A:340 #1/A:329
23 atoms, 22 bonds, 2 residues, 1 model selected
> show sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_2025_02_18_a331dup5_hstrim5a_model_1.cif_A SES
surface #1.5: minimum, -18.01, mean -2.02, maximum 13.64
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
Either three or four atoms must be selected!
> select ::name="LYS"
2790 atoms, 2510 bonds, 310 residues, 5 models selected
> show sel & #!1 atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> show sel surfaces
> hide sel surfaces
> select add #1
7982 atoms, 8144 bonds, 2 pseudobonds, 1000 residues, 7 models selected
> show sel surfaces
> ~distance #1.4 #1.3
> select clear
> coulombic #1.1-4#!1
Using Amber 20 recommended default charges and atom types for standard
residues
[Repeated 1 time(s)]Assigning partial charges to residue centroid (net charge
+0) with am1-bcc method
Could not determine GAFF type for atom copy of C1 #/centroid centroid 1 C1
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue centroid (net charge +0) with am1-bcc
method
Could not determine GAFF type for atom copy of C3 #/centroid centroid 1 C3
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue centroid (net charge +0) with am1-bcc
method
Could not determine GAFF type for atom copy of C4 #/centroid centroid 1 C4
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue centroid (net charge +0) with am1-bcc
method
Could not determine GAFF type for atom copy of C2 #/centroid centroid 1 C2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 215, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 339, in run
f(s)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 536, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 134, in cmd_coulombic
color_vertices(session, target_surface, offset, charged_atoms, dist_dep,
dielectric, cmap,
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 214, in color_vertices
% (surface, amin(vertex_values), mean(vertex_values), amax(vertex_values)))
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 2970, in amin
return _wrapreduction(a, np.minimum, 'min', axis, None, out,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 88, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: zero-size array to reduction operation minimum which has no
identity
ValueError: zero-size array to reduction operation minimum which has no
identity
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 88, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> hide #1.2-4#!1#!1.1 surfaces
> hide #!1 models
> show #2 models
> select all
39894 atoms, 40720 bonds, 1 pseudobond, 4984 residues, 11 models selected
> show all
> show
> select ::name="LYS"
2790 atoms, 2510 bonds, 310 residues, 5 models selected
> show sel & #2 atoms
> select ::name="ARG"
2970 atoms, 2720 bonds, 270 residues, 5 models selected
> show sel & #2 atoms
> select ::name="PHE"
2200 atoms, 2210 bonds, 200 residues, 5 models selected
> show sel & #2 atoms
> select ::name="TYR"
1680 atoms, 1680 bonds, 140 residues, 5 models selected
> show sel & #2 atoms
> select ::name="TRP"
980 atoms, 1050 bonds, 70 residues, 5 models selected
> select add #1
8766 atoms, 8984 bonds, 1 pseudobond, 1056 residues, 12 models selected
> select add #1
8766 atoms, 8984 bonds, 1 pseudobond, 1056 residues, 12 models selected
> select clear
> show #2 surfaces
> coulombic #!2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_2025_02_18_a331dup5_hstrim5a_model_2.cif_A SES
surface #2.1: minimum, -18.76, mean -2.01, maximum 14.11
Coulombic values for fold_2025_02_18_a331dup5_hstrim5a_model_2.cif_B SES
surface #2.2: minimum, -20.15, mean -2.00, maximum 13.12
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2 surfaces
> select #2/A:347@CG
1 atom, 1 residue, 1 model selected
> select add #2/A:347@CD1
2 atoms, 1 residue, 1 model selected
> select add #2/A:347@CE1
3 atoms, 1 residue, 2 models selected
> select add #2/A:347@CZ
4 atoms, 1 residue, 2 models selected
> select add #2/A:347@CE2
5 atoms, 1 residue, 2 models selected
> select add #2/A:347@CD2
6 atoms, 1 residue, 2 models selected
> define centroid sel name 2/C1 color #ff2600 radius 0.1
Centroid '2/C1' placed at [ 11.09966667 -41.8585 16.85616667]
> select clear
> select add #!2/A:349@CD2
1 atom, 1 residue, 1 model selected
> select add #!2/A:349@CG
2 atoms, 1 residue, 2 models selected
> select add #!2/A:349@CD1
3 atoms, 1 bond, 1 residue, 2 models selected
> select #!2/A:349@CE1
1 atom, 1 residue, 1 model selected
> select add #!2/A:349@CD1
2 atoms, 1 residue, 2 models selected
> select add #!2/A:349@CG
3 atoms, 1 residue, 2 models selected
> select add #!2/A:349@CD2
4 atoms, 1 residue, 2 models selected
> select add #!2/A:349@CE2
5 atoms, 1 residue, 2 models selected
> select add #!2/A:349@CZ
6 atoms, 1 residue, 2 models selected
> define centroid sel name 2/C2 color #ff2600 radius 0.1
Centroid '2/C2' placed at [ 12.9845 -40.36866667 12.926 ]
> select add #!2/A:341@CZ
7 atoms, 2 residues, 2 models selected
> select clear
> select #!2/A:341@CE1
1 atom, 1 residue, 1 model selected
> select #!2/A:341@CD1
1 atom, 1 residue, 1 model selected
> select add #!2/A:341@CE1
2 atoms, 1 residue, 2 models selected
> select add #!2/A:341@CZ
3 atoms, 1 residue, 2 models selected
> select add #!2/A:341@CE2
4 atoms, 1 residue, 2 models selected
> select add #!2/A:341@CD2
5 atoms, 1 residue, 2 models selected
> select add #!2/A:341@CG
6 atoms, 1 residue, 2 models selected
> define centroid sel name 2/C3 color #ff2600 radius 0.1
Centroid '2/C3' placed at [ 2.80566667 -40.93833333 32.89016667]
> select clear
> select #!2/A:332@NH1
1 atom, 1 residue, 1 model selected
> select add #!2/A:332@CZ
2 atoms, 1 residue, 2 models selected
> select add #!2/A:332@NH2
3 atoms, 1 residue, 2 models selected
> define centroid sel name 2/C4 color #ff2600 radius 0.1
Centroid '2/C4' placed at [ 10.06366667 -46.42633333 32.07366667]
> select clear
[Repeated 1 time(s)]
> select add #!2/A:337@NH2
1 atom, 1 residue, 1 model selected
> select clear
> select #!2/A:337@NH1
1 atom, 1 residue, 1 model selected
> select add #!2/A:337@NH2
2 atoms, 1 residue, 2 models selected
> select add #!2/A:337@CZ
3 atoms, 1 residue, 2 models selected
> define centroid sel name 2/C5 color #ff2600 radius 0.1
Centroid '2/C5' placed at [ -6.21933333 -49.70466667 42.22766667]
> select clear
> select #!2/A:335@NH1
1 atom, 1 residue, 1 model selected
> select clear
> select #!2/A:335@NH1
1 atom, 1 residue, 1 model selected
> select add #!2/A:335@CZ
2 atoms, 1 residue, 2 models selected
> select add #!2/A:335@NH2
3 atoms, 1 residue, 2 models selected
> define centroid sel name 2/C6 color #ff2600 radius 0.1
Centroid '2/C6' placed at [ 6.401 -57.08766667 42.63433333]
> select clear
[Repeated 2 time(s)]
> select #2.8
1 atom, 1 residue, 1 model selected
> select add #2.7
2 atoms, 2 residues, 2 models selected
> distance #2.8 #2.7
Distance between 2/C6 #2.8 and 2/C5 #2.7: 14.627Å
> select #2.5
1 atom, 1 residue, 1 model selected
> select add #2.6
2 atoms, 2 residues, 2 models selected
> distance #2.5 #2.6
Distance between 2/C3 #2.5 and 2/C4 #2.6: 9.136Å
> select clear
[Repeated 1 time(s)]
> select #2.3
1 atom, 1 residue, 1 model selected
> select add #2.4
2 atoms, 2 residues, 2 models selected
> distance #2.3 #2.4
Distance between 2/C1 #2.3 and 2/C2 #2.4: 4.606Å
> hide #!2 models
> show #!1 models
> select clear
[Repeated 1 time(s)]
> select #1.3
1 atom, 1 residue, 1 model selected
> select add #1.4
2 atoms, 2 residues, 2 models selected
> distance #1.3 #1.4
Distance between C1 #1.3 and C2 #1.4: 7.610Å
> select clear
[Repeated 1 time(s)]
> select #!1/A:337@NH2
1 atom, 1 residue, 1 model selected
> select #!1/A:337@NH1
1 atom, 1 residue, 1 model selected
> select add #!1/A:337@NH2
2 atoms, 1 residue, 2 models selected
> select add #!1/A:337@CZ
3 atoms, 1 residue, 2 models selected
> define centroid sel name C5 color #ff2600 radius 0.1
Centroid 'C5' placed at [ 11.22966667 -13.80966667 -63.96833333]
> select clear
[Repeated 1 time(s)]
> select #!1/A:335@NH1
1 atom, 1 residue, 1 model selected
> select add #!1/A:335@CZ
2 atoms, 1 bond, 1 residue, 2 models selected
> select clear
> select #!1/A:335@NH2
1 atom, 1 residue, 1 model selected
> select add #!1/A:335@CZ
2 atoms, 1 residue, 2 models selected
> select add #!1/A:335@NH1
3 atoms, 1 residue, 2 models selected
> define centroid sel name C6 color #ff2600 radius 0.1
Centroid 'C6' placed at [ 16.945 -1.246 -70.17433333]
> select #!1/A:337@CZ
1 atom, 1 residue, 1 model selected
> select add #1.8
2 atoms, 2 residues, 3 models selected
> distance #!1/A:337@CZ #1.8
Distance between fold_2025_02_18_a331dup5_hstrim5a_model_1.cif #!1/A ARG 337
CZ and C6 #1.8: 14.834Å
> ~distance #!1/A:337@CZ #1.8
> select clear
> select #1.7
1 atom, 1 residue, 1 model selected
> select add #1.8
2 atoms, 2 residues, 2 models selected
> distance #1.7 #1.8
Distance between C5 #1.7 and C6 #1.8: 15.134Å
> hide #!1 models
> show #!2 models
> show #!1 models
> select clear
[Repeated 1 time(s)]
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select add #!2/A:331
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
[Repeated 4 time(s)]
> select #!2/A:329@CE2
1 atom, 1 residue, 1 model selected
> select add #!2/A:329@CD2
2 atoms, 1 residue, 2 models selected
> select add #!2/A:329@CG
3 atoms, 1 residue, 2 models selected
> select add #!2/A:329@CD1
4 atoms, 1 residue, 2 models selected
> select add #!2/A:329@CE1
5 atoms, 1 residue, 2 models selected
> select add #!2/A:329@CZ
6 atoms, 1 residue, 2 models selected
> define centroid sel name 2/C7 color #ff2600 radius 0.1
Centroid '2/C7' placed at [ -0.87566667 -46.07216667 22.10716667]
> select clear
> select #!2/A:344@CB
1 atom, 1 residue, 1 model selected
> select #!2/A:344@CG
1 atom, 1 residue, 1 model selected
> select add #!2/A:344@CD1
2 atoms, 1 residue, 2 models selected
> select add #!2/A:344@CE1
3 atoms, 1 residue, 2 models selected
> select add #!2/A:344@CZ
4 atoms, 1 residue, 2 models selected
> select add #!2/A:344@CE2
5 atoms, 1 residue, 2 models selected
> select add #!2/A:344@CD2
6 atoms, 1 residue, 2 models selected
> define centroid sel name 2/C8 color #ff2600 radius 0.1
Centroid '2/C8' placed at [ 2.34766667 -36.554 22.20933333]
> select clear
> show #2.3-10#!2 surfaces
> hide #2.3-10#!2 surfaces
> select #!2/A:340@CZ
1 atom, 1 residue, 1 model selected
> select add #!2/A:340@NH1
2 atoms, 1 residue, 2 models selected
> select add #!2/A:340@NH2
3 atoms, 1 residue, 2 models selected
> define centroid sel name 2/C9 color #ff2600 radius 0.1
Centroid '2/C9' placed at [ -3.83966667 -49.59133333 25.819 ]
> select clear
> select #2.11
1 atom, 1 residue, 1 model selected
> select clear
> select #2.9
1 atom, 1 residue, 1 model selected
> select add #2.11
2 atoms, 2 residues, 2 models selected
> distance #2.9 #2.11
Distance between 2/C7 #2.9 and 2/C9 #2.11: 5.912Å
> select clear
[Repeated 2 time(s)]
> select #2.9
1 atom, 1 residue, 1 model selected
> select add #2.10
2 atoms, 2 residues, 2 models selected
> distance #2.9 #2.10
Distance between 2/C7 #2.9 and 2/C8 #2.10: 10.050Å
> hide #!2 models
> show #!1 models
> show #1.2-4,7-8#!1#!1.1 surfaces
> hide #1.2-4,7-8#!1#!1.1 surfaces
[Repeated 1 time(s)]
> hide #!1 models
> show #3 models
> select #3/A:337@NH1
1 atom, 1 residue, 1 model selected
> select add #3/A:337@NH2
2 atoms, 1 bond, 1 pseudobond, 1 residue, 2 models selected
> select clear
> select #3/A:337@CZ
1 atom, 1 residue, 1 model selected
> select add #3/A:337@NH1
2 atoms, 1 residue, 1 model selected
> select add #3/A:337@NH2
3 atoms, 1 residue, 1 model selected
> define centroid sel name 3/C1 color #ff2600 radius 0.1
Centroid '3/C1' placed at [ 37.68233333 -43.26133333 -31.71 ]
> select clear
> select #!3/A:335@NH1
1 atom, 1 residue, 1 model selected
> select add #!3/A:335@CZ
2 atoms, 1 residue, 1 model selected
> select add #!3/A:335@NH2
3 atoms, 1 residue, 1 model selected
> define centroid sel name 3/C2 color #ff2600 radius 0.1
Centroid '3/C2' placed at [ 28.465 -49.61866667 -42.73833333]
> select clear
[Repeated 1 time(s)]
> select #!3/A:341@CZ
1 atom, 1 residue, 1 model selected
> select add #!3/A:341@CE1
2 atoms, 1 residue, 1 model selected
> select add #!3/A:341@CD1
3 atoms, 1 residue, 1 model selected
> select add #!3/A:341@CG
4 atoms, 1 residue, 1 model selected
> select add #!3/A:341@CD2
5 atoms, 1 residue, 1 model selected
> select add #!3/A:341@CE2
6 atoms, 1 residue, 1 model selected
> define centroid sel name 3/C3 color #ff2600 radius 0.1
Centroid '3/C3' placed at [ 22.50583333 -34.73433333 -34.07433333]
> select #!3/A:332@NH2
1 atom, 1 residue, 1 model selected
> select clear
> select #!3/A:332@NH1
1 atom, 1 residue, 1 model selected
> select add #!3/A:332@CZ
2 atoms, 1 residue, 1 model selected
> select add #!3/A:332@NH2
3 atoms, 1 residue, 1 model selected
> define centroid sel name 3/C4 color #ff2600 radius 0.1
Centroid '3/C4' placed at [ 19.63733333 -41.27066667 -36.31566667]
> select clear
> select #!3/A:340@NH2
1 atom, 1 residue, 1 model selected
> select add #!3/A:340@CZ
2 atoms, 1 residue, 1 model selected
> select add #!3/A:340@NH1
3 atoms, 1 residue, 1 model selected
> define centroid sel name 3/C5 color #ff2600 radius 0.1
Centroid '3/C5' placed at [ 26.67966667 -41.491 -23.715 ]
> select clear
> select #!3/A:329@CG
1 atom, 1 residue, 1 model selected
> select add #!3/A:329@CD2
2 atoms, 1 residue, 1 model selected
> select add #!3/A:329@CE2
3 atoms, 1 residue, 1 model selected
> select add #!3/A:329@CZ
4 atoms, 1 residue, 1 model selected
> select add #!3/A:329@CE1
5 atoms, 1 residue, 1 model selected
> select add #!3/A:329@CD1
6 atoms, 1 residue, 1 model selected
> define centroid sel name 3/C6 color #ff2600 radius 0.1
Centroid '3/C6' placed at [ 20.662 -41.377 -22.22716667]
> select #!3/A:347@CD2
1 atom, 1 residue, 1 model selected
> select add #!3/A:347@CG
2 atoms, 1 residue, 1 model selected
> select add #!3/A:347@CD1
3 atoms, 1 residue, 1 model selected
> select add #!3/A:347@CE1
4 atoms, 1 residue, 1 model selected
> select add #!3/A:347@CZ
5 atoms, 1 residue, 1 model selected
> select add #!3/A:347@CE2
6 atoms, 1 residue, 1 model selected
> define centroid sel name 3/C7 color #ff2600 radius 0.1
Centroid '3/C7' placed at [ 7.71666667 -38.5455 -25.43083333]
> select #!3/A:349@CD2
1 atom, 1 residue, 1 model selected
> select add #!3/A:349@CG
2 atoms, 1 residue, 1 model selected
> select add #!3/A:349@CD1
3 atoms, 1 residue, 1 model selected
> select add #!3/A:349@CE1
4 atoms, 1 residue, 1 model selected
> select add #!3/A:349@CZ
5 atoms, 1 residue, 1 model selected
> select add #!3/A:349@CE2
6 atoms, 1 residue, 1 model selected
> define centroid sel name 3/C8 color #ff2600 radius 0.1
Centroid '3/C8' placed at [ 5.244 -36.301 -21.976]
> select clear
> select #3.2
1 atom, 1 residue, 1 model selected
> select add #3.1
2 atoms, 2 residues, 2 models selected
> distance #3.2 #3.1
Distance between 3/C2 #3.2 and 3/C1 #3.1: 15.716Å
> select #3.5
1 atom, 1 residue, 1 model selected
> select add #3.6
2 atoms, 2 residues, 2 models selected
> distance #3.5 #3.6
Distance between 3/C5 #3.5 and 3/C6 #3.6: 6.200Å
> select #3.3
1 atom, 1 residue, 1 model selected
> select add #3.4
2 atoms, 2 residues, 2 models selected
> distance #3.3 #3.4
Distance between 3/C3 #3.3 and 3/C4 #3.4: 7.482Å
> select clear
> select #3.7
1 atom, 1 residue, 1 model selected
> select add #3.8
2 atoms, 2 residues, 2 models selected
> distance #3.7 #3.8
Distance between 3/C7 #3.7 and 3/C8 #3.8: 4.805Å
> select clear
> select #3.7
1 atom, 1 residue, 1 model selected
Need to select at least 3 atoms to define a plane
> select add #3.8
2 atoms, 2 residues, 2 models selected
> select add #!3/A:349@OH
3 atoms, 3 residues, 3 models selected
> select clear
> select #!3/A:349@OH
1 atom, 1 residue, 1 model selected
> select add #3.7
2 atoms, 2 residues, 2 models selected
> select add #!3/A:347@CD2
3 atoms, 3 residues, 2 models selected
> define plane sel name 3/A
Plane '3/A' placed at [-21.42683107 -15.80384532 -40.57095198] with normal [
0.42441851 -0.50833396 0.74931003] and radius 2.0
> select #3.9
1 model selected
> ~select #3.9
Nothing selected
> color #3.9 #00fdff
> hide #!3 models
> show #!3 models
ID must be one or more integers separated by '.' characters
> select clear
> select #3.7
1 atom, 1 residue, 1 model selected
> select add #3.8
2 atoms, 1 pseudobond, 2 residues, 3 models selected
> select #3.7
1 atom, 1 residue, 1 model selected
> select add #3.8
2 atoms, 1 pseudobond, 2 residues, 3 models selected
Either three or four atoms must be selected!
ID must be one or more integers separated by '.' characters
> close #3.9
> select #!3/A:349@CZ
1 atom, 1 residue, 1 model selected
> select clear
> select #!3/A:349@OH
1 atom, 1 residue, 1 model selected
> select add #3.8
2 atoms, 2 residues, 2 models selected
> select add #!3/A:349@CE2
3 atoms, 2 residues, 2 models selected
> select add #!3/A:349@CE1
4 atoms, 2 residues, 2 models selected
> select subtract #!3/A:349@OH
3 atoms, 2 residues, 2 models selected
> define plane sel name 3/A radius 10
Plane '3/A' placed at [-18.37655043 -15.35314812 -39.06437385] with normal
[-0.61265044 -0.74854438 0.2536548 ] and radius 10.0
> color #3.9 #ffffff
> color #3.9 #fffffff3
> color #3.9 #fffffff2
> color #3.9 #fffffff1
> color #3.9 #ffffffef
> color #3.9 #ffffffed
> color #3.9 #ffffffea
> color #3.9 #ffffffe8
> color #3.9 #ffffffe4
> color #3.9 #ffffffe0
> color #3.9 #ffffffde
> color #3.9 #ffffffdc
> color #3.9 #ffffffd9
> color #3.9 #ffffffd8
> color #3.9 #ffffffd7
> color #3.9 #ffffffd6
> color #3.9 #ffffffd4
> color #3.9 #ffffffd1
> color #3.9 #ffffffcd
> color #3.9 #ffffffc8
> color #3.9 #ffffffc1
> color #3.9 #ffffffbc
> color #3.9 #ffffffb6
> color #3.9 #ffffffb1
> color #3.9 #ffffffad
> color #3.9 #ffffffa9
> color #3.9 #ffffffa4
> color #3.9 #ffffffa1
> color #3.9 #ffffffa0
> color #3.9 #ffffff9f
> color #3.9 #ffffffad
> color #3.9 #ffffffb3
> color #3.9 #ffffffc1
> color #3.9 #ffffffcc
> color #3.9 #ffffffda
> color #3.9 #ffffffd9
> color #3.9 #ffffffd2
> color #3.9 #ffffffc7
> color #3.9 #ffffffc5
> color #3.9 #ffffffb4
> color #3.9 #ffffffb5
> color #3.9 #ffffffb6
> color #3.9 #ffffffbd
> color #3.9 #ffffffbc
> color #3.9 #ffffffb9
> color #3.9 #ffffffb8
> color #3.9 #ffffffb1
> color #3.9 #ff2600
> color #3.9 #ff2600fe
> color #3.9 #ff2600f7
> color #3.9 #ff2600cf
> color #3.9 #ff2600cd
> color #3.9 #ff2600cc
> color #3.9 #ff2600b6
> color #3.9 #ff2600b4
> color #3.9 #ff2600b2
> color #3.9 #ff2600b1
> color #3.9 #ff2600b0
> color #3.9 #ff2600af
> color #3.9 #ff2600ab
> select #3.9
1 model selected
> color #3.9 #ff2600ad
> color #3.9 #ff2600be
> color #3.9 #ff2600d2
> color #3.9 #ff2600
> color #3.9 #ffffff
> color #3.9 #aa7942
> color #3.9 #ffffff
> ui mousemode right "move picked models"
> view matrix models
> #3.9,1,2.2898e-16,-3.2483e-16,8.7521,-4.8572e-16,1,-2.2898e-16,2.9197,1.5613e-16,4.5797e-16,1,10.84
> view matrix models
> #3.9,1,2.0123e-16,-8.0665e-16,14.637,-3.1225e-16,1,-3.8858e-16,5.1471,1.5188e-15,4.3021e-16,1,15.117
> view matrix models
> #3.9,1,2.5674e-16,-4.1633e-16,12.953,-3.8164e-16,1,-2.8449e-16,3.8803,1.5318e-15,4.5103e-16,1,20.736
> view matrix models
> #3.9,1,2.4286e-16,-3.6993e-16,21.501,-3.5388e-16,1,-3.1225e-16,0.54059,1.507e-15,4.6491e-16,1,26.155
> view matrix models
> #3.9,1,2.4286e-16,-4.9656e-16,24.881,-3.8164e-16,1,-2.8449e-16,2.35,1.5443e-15,4.5797e-16,1,21.736
> view matrix models
> #3.9,1,2.6368e-16,-6.5919e-17,24.977,-2.7756e-16,1,-3.5388e-16,-11.048,2.0465e-15,4.7878e-16,1,10.63
> view matrix models
> #3.9,1,3.1225e-16,2.2777e-15,28.023,-3.1919e-16,1,-2.8449e-16,-10.547,1.8696e-15,4.7878e-16,1,12.573
> close #3.9
> view matrix models
> #3,-0.78841,-0.0030382,0.61514,-0.096322,0.61293,0.08092,0.78598,2.9783,-0.052165,0.99672,-0.061936,-0.88376
> view matrix models
> #3,-0.78841,-0.0030382,0.61514,0.26587,0.61293,0.08092,0.78598,4.0767,-0.052165,0.99672,-0.061936,1.2228
> view matrix models
> #3,-0.78841,-0.0030382,0.61514,0.2377,0.61293,0.08092,0.78598,5.4581,-0.052165,0.99672,-0.061936,2.7011
> view matrix models
> #3,-0.78841,-0.0030382,0.61514,0.16046,0.61293,0.08092,0.78598,6.9385,-0.052165,0.99672,-0.061936,4.1715
> show #4 models
> hide #!3 models
> view matrix models
> #4,-0.70038,0.70269,0.12528,-1.397,0.66106,0.70479,-0.25745,-0.90068,-0.2692,-0.097496,-0.95814,-3.4652
> ui mousemode right select
> select #4/A:335@CZ
1 atom, 1 residue, 1 model selected
> select add #4/A:335@NH1
2 atoms, 1 residue, 1 model selected
> select add #4/A:335@NH2
3 atoms, 1 residue, 1 model selected
> define centroid sel name 4/C1 color #ff2600 radius 0.1
Centroid '4/C1' placed at [ 33.774 -42.52366667 46.248 ]
> select clear
> select #!4/A:337@NH2
1 atom, 1 residue, 1 model selected
> select add #!4/A:337@CZ
2 atoms, 1 residue, 1 model selected
> select add #!4/A:337@NH1
3 atoms, 1 residue, 1 model selected
> define centroid sel name 4/C2 color #ff2600 radius 0.1
Centroid '4/C2' placed at [ 41.283 -35.18933333 36.386 ]
> select #!4/A:332@NH1
1 atom, 1 residue, 1 model selected
> select #!4/A:332@NH1
1 atom, 1 residue, 1 model selected
> select add #!4/A:332@CZ
2 atoms, 1 residue, 1 model selected
> select add #!4/A:332@NH2
3 atoms, 1 residue, 1 model selected
> define centroid sel name 4/C3 color #ff2600 radius 0.1
Centroid '4/C3' placed at [ 34.057 -25.17166667 46.67166667]
> select #!4/A:340@NH2
1 atom, 1 residue, 1 model selected
> select add #!4/A:340@CZ
2 atoms, 1 residue, 1 model selected
> select add #!4/A:340@NH1
3 atoms, 1 residue, 1 model selected
> define centroid sel name 4/C4 color #ff2600 radius 0.1
Centroid '4/C4' placed at [ 32.576 -20.18633333 40.504 ]
> select clear
> select #!4/A:329@CE1
1 atom, 1 residue, 1 model selected
> select add #!4/A:329@CE2
2 atoms, 1 residue, 1 model selected
> select add #!4/A:329@CD2
3 atoms, 1 residue, 1 model selected
> select add #!4/A:329@CD1
4 atoms, 1 residue, 1 model selected
> select add #!4/A:329@CG
5 atoms, 1 residue, 1 model selected
> define centroid sel name 4/C5 color #ff2600 radius 0.1
Centroid '4/C5' placed at [ 26.7664 -20.4188 40.2108]
> select #!4/A:347@CG
1 atom, 1 residue, 1 model selected
> select add #!4/A:347@CD1
2 atoms, 1 residue, 1 model selected
> select add #!4/A:347@CE1
3 atoms, 1 residue, 1 model selected
> select add #!4/A:347@CD2
4 atoms, 1 residue, 1 model selected
> select add #!4/A:347@CE2
5 atoms, 1 residue, 1 model selected
> select add #!4/A:347@CZ
6 atoms, 1 residue, 1 model selected
> define centroid sel name 4/C6 color #ff2600 radius 0.1
Centroid '4/C6' placed at [ 12.96533333 -22.4095 37.889 ]
> select #!4/A:349@CD2
1 atom, 1 residue, 1 model selected
> select add #!4/A:349@CG
2 atoms, 1 residue, 1 model selected
> select add #!4/A:349@CD1
3 atoms, 1 residue, 1 model selected
> select add #!4/A:349@CE1
4 atoms, 1 residue, 1 model selected
> select add #!4/A:349@CZ
5 atoms, 1 residue, 1 model selected
> select add #!4/A:349@CE2
6 atoms, 1 residue, 1 model selected
> define centroid sel name 4/C7 color #ff2600 radius 0.1
Centroid '4/C7' placed at [ 10.68683333 -18.887 36.601 ]
> select clear
> select #!4/A:326@OE1
1 atom, 1 residue, 1 model selected
> select add #!4/A:326@CD
2 atoms, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #4.7
1 atom, 1 residue, 1 model selected
> select clear
> select #4.6
1 atom, 1 residue, 1 model selected
> select add #4.7
2 atoms, 2 residues, 2 models selected
> distance #4.6 #4.7
Distance between 4/C6 #4.6 and 4/C7 #4.7: 4.388Å
> select clear
> select #4.5
1 atom, 1 residue, 1 model selected
> select add #!4/A:340@CZ
2 atoms, 2 residues, 2 models selected
> distance #4.5 #!4/A:340@CZ
Distance between fold_2025_02_18_a331dup5_hstrim5a_model_4.cif #!4/A ARG 340
CZ and 4/C5 #4.5: 5.713Å
> select clear
> select #!4/A:340@CZ
1 atom, 1 residue, 1 model selected
> select add #4.3
2 atoms, 2 residues, 2 models selected
> distance #!4/A:340@CZ #4.3
Distance between fold_2025_02_18_a331dup5_hstrim5a_model_4.cif #!4/A ARG 340
CZ and 4/C3 #4.3: 7.879Å
> select clear
> select #4.1
1 atom, 1 residue, 1 model selected
> select add #4.2
2 atoms, 2 residues, 2 models selected
> distance #4.1 #4.2
Distance between 4/C1 #4.1 and 4/C2 #4.2: 14.403Å
> ~distance #!4/A:340@CZ #4.5
> ~distance #!4/A:340@CZ #4.3
> select #4.3
1 atom, 1 residue, 1 model selected
> select clear
> select #4.4
1 atom, 1 residue, 1 model selected
> select add #4.5
2 atoms, 2 residues, 2 models selected
> distance #4.4 #4.5
Distance between 4/C4 #4.4 and 4/C5 #4.5: 5.822Å
> select #4/A:329
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #4/A:332
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/A:332 #4/A:337
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #4/A:332 #4/A:341
23 atoms, 22 bonds, 2 residues, 1 model selected
> show #!2 models
> hide #!4 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #5 models
> select clear
> select #5/B:335@CZ
1 atom, 1 residue, 1 model selected
> select add #5/B:335@NH2
2 atoms, 1 residue, 1 model selected
> select add #5/B:335@NH1
3 atoms, 1 residue, 1 model selected
> define centroid sel name 0/C1 color #ff2600 radius 0.1
Centroid '0/C1' placed at [-43.79366667 -19.16166667 -60.92833333]
> select clear
> select #!5/B:337@NH2
1 atom, 1 residue, 1 model selected
> select add #!5/B:337@CZ
2 atoms, 1 residue, 1 model selected
> select add #!5/B:337@NH1
3 atoms, 1 residue, 1 model selected
> define centroid sel name 0/C2 color #ff2600 radius 0.1
Centroid '0/C2' placed at [-46.47333333 -7.75333333 -56.06533333]
> select #!5/B:332@NH2
1 atom, 1 residue, 1 model selected
> select add #!5/B:332@NH1
2 atoms, 1 residue, 1 model selected
> select add #!5/B:332@CZ
3 atoms, 1 residue, 1 model selected
> define centroid sel name 0/C3 color #ff2600 radius 0.1
Centroid '0/C3' placed at [-37.08133333 -20.46966667 -43.96833333]
> select #!5/B:341@CZ
1 atom, 1 residue, 1 model selected
> select add #!5/B:341@CE1
2 atoms, 1 residue, 1 model selected
> select add #!5/B:341@CD1
3 atoms, 1 residue, 1 model selected
> select add #!5/B:341@CG
4 atoms, 1 residue, 1 model selected
> select add #!5/B:341@CD2
5 atoms, 1 residue, 1 model selected
> select add #!5/B:341@CE2
6 atoms, 1 residue, 1 model selected
> define centroid sel name 0/C4 color #ff2600 radius 0.1
Centroid '0/C4' placed at [-38.29966667 -13.99183333 -42.26533333]
> select #!5/B:329@CD1
1 atom, 1 residue, 1 model selected
> select add #!5/B:329@CG
2 atoms, 1 residue, 1 model selected
> select add #!5/B:329@CD2
3 atoms, 1 residue, 1 model selected
> select add #!5/B:329@CE2
4 atoms, 1 residue, 1 model selected
> select add #!5/B:329@CZ
5 atoms, 1 residue, 1 model selected
> select add #!5/B:329@CE1
6 atoms, 1 residue, 1 model selected
> define centroid sel name 0/C5 color #ff2600 radius 0.1
Centroid '0/C5' placed at [-29.82516667 -7.6215 -46.31033333]
> select #!5/B:340@NH1
1 atom, 1 residue, 1 model selected
> select #!5/B:340@NH2
1 atom, 1 residue, 1 model selected
> select add #!5/B:340@CZ
2 atoms, 1 residue, 1 model selected
> select add #!5/B:340@NH1
3 atoms, 1 residue, 1 model selected
> define centroid sel name 0/C6 color #ff2600 radius 0.1
Centroid '0/C6' placed at [-32.15566667 -7.01333333 -51.43966667]
> show sel surfaces
> hide sel surfaces
> select clear
> show #5.1-6#!5 surfaces
> coulombic #5.1-6#!5
Using Amber 20 recommended default charges and atom types for standard
residues
[Repeated 1 time(s)]Assigning partial charges to residue centroid (net charge
+0) with am1-bcc method
Could not determine GAFF type for atom copy of 0/C6 #/centroid centroid 1 0/C6
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue centroid (net charge +0) with am1-bcc
method
Could not determine GAFF type for atom copy of 0/C4 #/centroid centroid 1 0/C4
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue centroid (net charge +0) with am1-bcc
method
Could not determine GAFF type for atom copy of 0/C2 #/centroid centroid 1 0/C2
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue centroid (net charge +0) with am1-bcc
method
Could not determine GAFF type for atom copy of 0/C1 #/centroid centroid 1 0/C1
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue centroid (net charge +0) with am1-bcc
method
Could not determine GAFF type for atom copy of 0/C3 #/centroid centroid 1 0/C3
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue centroid (net charge +0) with am1-bcc
method
Could not determine GAFF type for atom copy of 0/C5 #/centroid centroid 1 0/C5
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 215, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 339, in run
f(s)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 536, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 134, in cmd_coulombic
color_vertices(session, target_surface, offset, charged_atoms, dist_dep,
dielectric, cmap,
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 214, in color_vertices
% (surface, amin(vertex_values), mean(vertex_values), amax(vertex_values)))
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 2970, in amin
return _wrapreduction(a, np.minimum, 'min', axis, None, out,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 88, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: zero-size array to reduction operation minimum which has no
identity
ValueError: zero-size array to reduction operation minimum which has no
identity
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 88, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> coulombic #5.2-6#!5#!5.1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 215, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 339, in run
f(s)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 536, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 134, in cmd_coulombic
color_vertices(session, target_surface, offset, charged_atoms, dist_dep,
dielectric, cmap,
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 214, in color_vertices
% (surface, amin(vertex_values), mean(vertex_values), amax(vertex_values)))
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 2970, in amin
return _wrapreduction(a, np.minimum, 'min', axis, None, out,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 88, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: zero-size array to reduction operation minimum which has no
identity
ValueError: zero-size array to reduction operation minimum which has no
identity
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 88, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: MLXW3LL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 38 days, 5 hours, 53 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2722HE:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
joblib: 1.4.2
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
llvmlite: 0.43.0
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numba: 0.60.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynndescent: 0.5.13
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scikit-learn: 1.6.0
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
threadpoolctl: 3.5.0
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
tqdm: 4.67.1
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
umap-learn: 0.5.7
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Surface/Binding Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Coulombic of centroid |
comment:2 by , 8 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Fix: https://github.com/RBVI/ChimeraX/commit/567bd4c9e84ba8dd8ecfe8ed33cc98fe12b8d65f