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Opened 3 years ago
Closed 3 years ago
#8355 closed defect (duplicate)
alphafold pae: No module named 'jax'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202206100131 (2022-06-10 01:31:06 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5.dev202206100131 (2022-06-10)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/Bioinformatics/AlphaFold/Bacteriophages/P2VsPyocin.cxs
Log from Tue Mar 1 15:53:02 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/AlphaFold/Bacteriophages/P2/gpH_gpG
> multimer/Hexamer(trimer first)/ranked_0.pdb" format pdb
No such file/path: /Users/shj152/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Desktop/PhD/AlphaFold/Bacteriophages/P2/gpH_gpG
multimer/Hexamer(trimer first)/ranked_0.pdb
> open "/Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/AlphaFold/Bacteriophages/P2/gpH_gpG
> multimer/Hexamer(trimer first)/ranked_0.pdb" format pdb
No such file/path: /Users/shj152/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Desktop/PhD/AlphaFold/Bacteriophages/P2/gpH_gpG
multimer/Hexamer(trimer first)/ranked_0.pdb
> open "/Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/P2/gpH_gpG
> multimer/Hexamer(trimer first)/gpH_gpG_complex.pdb"
Chain information for gpH_gpG_complex.pdb #1
---
Chain | Description
B C D | No description available
E F G | No description available
> show cartoons
> hide atoms
> ui mousemode right select
> select /G:122
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
241 atoms, 241 bonds, 31 residues, 1 model selected
> select up
1429 atoms, 1459 bonds, 175 residues, 1 model selected
> select down
241 atoms, 241 bonds, 31 residues, 1 model selected
> select \--
Expected an objects specifier or a keyword
> select -
Expected an objects specifier or a keyword
> select clear
> select /G:61
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 5 residues, 1 model selected
> select up
1429 atoms, 1459 bonds, 175 residues, 1 model selected
> select down
35 atoms, 34 bonds, 5 residues, 1 model selected
> select clear
> select /B:29
12 atoms, 12 bonds, 1 residue, 1 model selected
> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/P2/gpG/ranked_0.pdb
Chain information for ranked_0.pdb #2
---
Chain | Description
A | No description available
> mmaker #1 to #2
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 ranked_0.pdb, chain A (#2) with gpH_gpG_complex.pdb, chain E (#1),
sequence alignment score = 897.5
RMSD between 125 pruned atom pairs is 0.723 angstroms; (across all 175 pairs:
2.633)
> hide #1 models
> select clear
Drag select of 107 residues
> delete sel
> show #1 models
> hide #1 models
> coulombic #2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for ranked_0.pdb_A SES surface #2.1: minimum, -14.58, mean
-3.43, maximum 9.27
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp #!2
Map values for surface "ranked_0.pdb_A SES surface": minimum -23.12, mean
-4.866, maximum 20.2
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!2 surfaces
> ui tool show "Show Sequence Viewer"
> sequence chain #1/E #1/F #1/G #2/A
Alignment identifier is 1
Drag select of 21 residues
> select clear
> select #2/A:162
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
51 atoms, 50 bonds, 3 residues, 2 models selected
> select up
1074 atoms, 1083 bonds, 68 residues, 2 models selected
> select down
51 atoms, 50 bonds, 3 residues, 2 models selected
> select #2/A:125
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
477 atoms, 477 bonds, 31 residues, 2 models selected
> select #2/A:148
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
275 atoms, 277 bonds, 16 residues, 2 models selected
> show #1 models
> select clear
> close session
> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/preliminer/complex_unrelaxed_model_2_multimer.pdb
> /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/preliminer/Pyocin_1_150ranked_0.pdb
> /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/preliminer/Pyocin_125_425ranked_0.pdb
> /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/preliminer/Pyocin_400_691ranked_0.pdb
> /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/preliminer/Pyocin_unrelaxed_model_1_multimer.pdb
> /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/preliminer/xeno_unrelaxed_model_1_multimer.pdb
Chain information for complex_unrelaxed_model_2_multimer.pdb #1
---
Chain | Description
B C D | No description available
E F G | No description available
Chain information for Pyocin_1_150ranked_0.pdb #2
---
Chain | Description
A B C | No description available
Chain information for Pyocin_125_425ranked_0.pdb #3
---
Chain | Description
A B C | No description available
Chain information for Pyocin_400_691ranked_0.pdb #4
---
Chain | Description
A B C | No description available
Chain information for Pyocin_unrelaxed_model_1_multimer.pdb #5
---
Chain | Description
B C D | No description available
Chain information for xeno_unrelaxed_model_1_multimer.pdb #6
---
Chain | Description
B C D | No description available
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #4 models
> show #3 models
> mmaker #4 to #3
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 Pyocin_125_425ranked_0.pdb, chain A (#3) with
Pyocin_400_691ranked_0.pdb, chain A (#4), sequence alignment score = 123.4
RMSD between 26 pruned atom pairs is 0.197 angstroms; (across all 26 pairs:
0.197)
> select clear
> show #2 models
> mmaker #2 to #3
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 Pyocin_125_425ranked_0.pdb, chain A (#3) with
Pyocin_1_150ranked_0.pdb, chain A (#2), sequence alignment score = 78.9
RMSD between 11 pruned atom pairs is 1.209 angstroms; (across all 25 pairs:
16.775)
> select clear
> ui mousemode right translate
> show #1 models
> mmaker #1 to #4
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 Pyocin_400_691ranked_0.pdb, chain A (#4) with
complex_unrelaxed_model_2_multimer.pdb, chain B (#1), sequence alignment score
= 518.1
RMSD between 99 pruned atom pairs is 0.452 angstroms; (across all 100 pairs:
0.510)
> select #1
5928 atoms, 6105 bonds, 756 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> ~select #1
Nothing selected
> hide #4 models
> show #4 models
> open "/Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/fastas/Pyocin
> tail fiber_trimer_1_150.fasta"
Summary of feedback from opening /Users/shj152/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/fastas/Pyocin tail
fiber_trimer_1_150.fasta
---
notes | Alignment identifier is Pyocin tail fiber_trimer_1_150.fasta
Associated Pyocin_1_150ranked_0.pdb chain A to Pyocin tail fiber with 0
mismatches
Associated Pyocin_1_150ranked_0.pdb chain B to Pyocin tail fiber with 0
mismatches
Associated Pyocin_1_150ranked_0.pdb chain C to Pyocin tail fiber with 0
mismatches
Associated Pyocin_unrelaxed_model_1_multimer.pdb chain B to Pyocin tail fiber
with 0 mismatches
Associated Pyocin_unrelaxed_model_1_multimer.pdb chain C to Pyocin tail fiber
with 0 mismatches
Associated Pyocin_unrelaxed_model_1_multimer.pdb chain D to Pyocin tail fiber
with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment Pyocin tail fiber_trimer_1_150.fasta
Opened 3 sequences from Pyocin tail fiber_trimer_1_150.fasta
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #3/B #3/C
Alignment identifier is 1
> ui mousemode right select
Drag select of 38 residues
> select clear
[Repeated 1 time(s)]Drag select of 107 residues
> select clear
> ui mousemode right translate
> show #5 models
> hide #5 models
> ui mousemode right select
Drag select of 2982 residues
> show sel atoms
> show sel surfaces
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> show #5 models
> select #5
15306 atoms, 15678 bonds, 2073 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,32.801,0,1,0,36.512,0,0,1,18.254
> view matrix models #5,1,0,0,52.104,0,1,0,115.45,0,0,1,18.69
> ui mousemode right translate
> show sel surfaces
> ~select #5
3 models selected
> ui mousemode right "translate selected models"
> select #5
15306 atoms, 15678 bonds, 2073 residues, 1 model selected
> view matrix models
> #5,-0.16022,0.77371,0.61294,22.305,0.97666,0.21425,-0.01515,139.85,-0.14305,0.59621,-0.78998,16.194
> ui mousemode right select
> select clear
> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/preliminer/ranked_0.pdb
Chain information for ranked_0.pdb #7
---
Chain | Description
B C D | No description available
Associated ranked_0.pdb chain B to Pyocin tail fiber with 0 mismatches
Associated ranked_0.pdb chain C to Pyocin tail fiber with 0 mismatches
Associated ranked_0.pdb chain D to Pyocin tail fiber with 0 mismatches
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> mmaker #7 to #3
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 Pyocin_125_425ranked_0.pdb, chain A (#3) with ranked_0.pdb, chain B
(#7), sequence alignment score = 340.6
RMSD between 40 pruned atom pairs is 1.029 angstroms; (across all 75 pairs:
13.669)
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> close session
> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/Pyocin/1_200.pdb
> /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/Pyocin/125_425.pdb
> /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/Pyocin/400_691.pdb
Chain information for 1_200.pdb #1
---
Chain | Description
B C D | No description available
Chain information for 125_425.pdb #2
---
Chain | Description
A B C | No description available
Chain information for 400_691.pdb #3
---
Chain | Description
A B C | No description available
> mmaker #2 to #3
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 400_691.pdb, chain A (#3) with 125_425.pdb, chain A (#2), sequence
alignment score = 123.4
RMSD between 26 pruned atom pairs is 0.197 angstroms; (across all 26 pairs:
0.197)
> mmaker #1 to #2
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 125_425.pdb, chain A (#2) with 1_200.pdb, chain B (#1), sequence
alignment score = 340.6
RMSD between 40 pruned atom pairs is 1.029 angstroms; (across all 75 pairs:
13.669)
> select clear
> ui mousemode right translate
> hide #1 models
> ui mousemode right select
Drag select of 199 residues
> delete sel
> show #1 models
> ui mousemode right translate
> color bfactor #1 palette alphafold
4383 atoms, 600 residues, atom bfactor range 42.2 to 96.6
> color bfactor #2 palette alphafold
9887 atoms, 701 residues, atom bfactor range 75.7 to 98
> color bfactor #3 palette alphafold
12900 atoms, 876 residues, atom bfactor range 85.1 to 98.6
> ui mousemode right select
> select #1/D:195
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
41 atoms, 41 bonds, 7 residues, 1 model selected
> select up
1461 atoms, 1485 bonds, 200 residues, 1 model selected
> select down
41 atoms, 41 bonds, 7 residues, 1 model selected
> delete sel
> select clear
> select #1/B:195
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
41 atoms, 41 bonds, 7 residues, 1 model selected
> delete sel
> select #1/C:195
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
41 atoms, 41 bonds, 7 residues, 1 model selected
> delete sel
> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/P2/gpH_trimer/401-669/ranked_0.pdb
Chain information for ranked_0.pdb #4
---
Chain | Description
A B C | No description available
> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/P2/gpH_trimer/301-669/ranked_1.pdb
Chain information for ranked_1.pdb #5
---
Chain | Description
A B C | No description available
> close #4
> close #5
> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/P2/gpH_trimer/301-669/gpH301_699trimer.pdb
Chain information for gpH301_699trimer.pdb #4
---
Chain | Description
A B C | No description available
> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/P2/gpH_trimer/200-400/gpH200-400trimer.pdb
Chain information for gpH200-400trimer.pdb #5
---
Chain | Description
A B C | No description available
> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/P2/gpH_trimer/1_250/gpH1_250trimer.pdb
Chain information for gpH1_250trimer.pdb #6
---
Chain | Description
B C D | No description available
> mmaker #4 to #5
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 gpH200-400trimer.pdb, chain A (#5) with gpH301_699trimer.pdb, chain
A (#4), sequence alignment score = 487.2
RMSD between 100 pruned atom pairs is 0.409 angstroms; (across all 100 pairs:
0.409)
> mmaker #6 to #5
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 gpH200-400trimer.pdb, chain A (#5) with gpH1_250trimer.pdb, chain B
(#6), sequence alignment score = 240.4
RMSD between 41 pruned atom pairs is 0.221 angstroms; (across all 51 pairs:
4.489)
> hide #3 models
> select #4/B:213
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide #!2 models
Drag select of 2460 residues
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.36339,-0.59371,-0.71795,197.48,-0.35927,-0.80033,0.47999,-89.525,-0.85958,0.083518,-0.50414,-223.28,#5,1,0,0,110.33,0,1,0,-36.299,0,0,1,-132.33,#6,0.52099,-0.58981,0.61701,15.748,-0.54135,-0.7872,-0.2954,19.821,0.65994,-0.18012,-0.72941,-36.542
> view matrix models
> #4,-0.39469,-0.61747,0.68041,56.057,-0.38266,-0.56278,-0.7327,-42.598,0.83534,-0.54955,-0.014158,-54.781,#5,-0.26533,0.96257,-0.055326,125.38,0.72112,0.23621,0.6513,-33.639,0.63999,0.13291,-0.7568,-172.32,#6,-0.69583,-0.59128,-0.4077,199.2,0.67764,-0.72858,-0.099908,-26.196,-0.23797,-0.34579,0.90763,-297.88
> view matrix models
> #4,-0.48978,-0.56677,0.66248,47.09,-0.45984,-0.47765,-0.7486,-51.834,0.74072,-0.67128,-0.026684,-63.238,#5,-0.31712,0.94756,0.039681,128.77,0.65394,0.18817,0.73277,-32.167,0.68688,0.25832,-0.67932,-171.14,#6,-0.65198,-0.56603,-0.50451,215.74,0.72241,-0.66581,-0.18659,-13.264,-0.2303,-0.48612,0.843,-286.68
> view matrix models
> #4,-0.35499,-0.63895,0.68244,61.807,-0.56242,-0.43714,-0.70184,-65.27,0.74677,-0.63297,-0.20418,-56.144,#5,-0.23962,0.96647,-0.092265,125.74,0.55905,0.21505,0.80076,-29.717,0.79376,0.14029,-0.59183,-171.69,#6,-0.70892,-0.60286,-0.36604,193.8,0.70329,-0.64325,-0.30267,6.1825,-0.052985,-0.472,0.88,-295.58
> view matrix models
> #4,-0.35499,-0.63895,0.68244,63.096,-0.56242,-0.43714,-0.70184,-91.718,0.74677,-0.63297,-0.20418,17.256,#5,-0.23962,0.96647,-0.092265,127.03,0.55905,0.21505,0.80076,-56.166,0.79376,0.14029,-0.59183,-98.289,#6,-0.70892,-0.60286,-0.36604,195.09,0.70329,-0.64325,-0.30267,-20.266,-0.052985,-0.472,0.88,-222.18
> show #3 models
> show #!2 models
> view matrix models
> #4,-0.17188,-0.73742,0.6532,84.169,-0.56773,-0.46773,-0.67742,-92.861,0.80507,-0.48728,-0.33827,26.778,#5,-0.093614,0.96546,-0.24315,121.6,0.55775,0.25316,0.79046,-56.103,0.82472,-0.061618,-0.56218,-99.515,#6,-0.73188,-0.661,-0.1656,161.34,0.67519,-0.67063,-0.30722,-18.928,0.092018,-0.33666,0.93712,-234.82
> view matrix models
> #4,-0.17188,-0.73742,0.6532,124.77,-0.56773,-0.46773,-0.67742,-90.832,0.80507,-0.48728,-0.33827,22.731,#5,-0.093614,0.96546,-0.24315,162.2,0.55775,0.25316,0.79046,-54.075,0.82472,-0.061618,-0.56218,-103.56,#6,-0.73188,-0.661,-0.1656,201.95,0.67519,-0.67063,-0.30722,-16.9,0.092018,-0.33666,0.93712,-238.87
> view matrix models
> #4,-0.17188,-0.73742,0.6532,131.63,-0.56773,-0.46773,-0.67742,-98.568,0.80507,-0.48728,-0.33827,24.935,#5,-0.093614,0.96546,-0.24315,169.06,0.55775,0.25316,0.79046,-61.81,0.82472,-0.061618,-0.56218,-101.36,#6,-0.73188,-0.661,-0.1656,208.81,0.67519,-0.67063,-0.30722,-24.635,0.092018,-0.33666,0.93712,-236.67
> view matrix models
> #4,-0.17212,-0.8561,0.4873,139.59,-0.46481,-0.36557,-0.80642,-84.307,0.86852,-0.3653,-0.33501,29.722,#5,0.095872,0.9809,-0.16922,168.06,0.6271,0.072502,0.77556,-64.566,0.77301,-0.18047,-0.60818,-102.57,#6,-0.59274,-0.79823,-0.10717,197.83,0.79928,-0.56663,-0.20019,-45.517,0.099068,-0.20432,0.97388,-244.07
> view matrix models
> #4,-0.17212,-0.8561,0.4873,155.56,-0.46481,-0.36557,-0.80642,-102.03,0.86852,-0.3653,-0.33501,30.01,#5,0.095872,0.9809,-0.16922,184.02,0.6271,0.072502,0.77556,-82.288,0.77301,-0.18047,-0.60818,-102.29,#6,-0.59274,-0.79823,-0.10717,213.79,0.79928,-0.56663,-0.20019,-63.239,0.099068,-0.20432,0.97388,-243.78
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select clear
> ui mousemode right translate
> color bfactor #4 palette alphafold
16722 atoms, 1107 residues, atom bfactor range 42.9 to 95.8
> color bfactor #5 palette alphafold
8673 atoms, 600 residues, atom bfactor range 27.6 to 97.5
> color bfactor #6 palette alphafold
5589 atoms, 753 residues, atom bfactor range 55 to 98.1
> open "/Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/P2/gpH_gpG
> multimer/Hexamer(trimer first)/gpH_gpG_complex.pdb"
Chain information for gpH_gpG_complex.pdb #7
---
Chain | Description
B C D | No description available
E F G | No description available
> mmaker #7 to #6
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 gpH1_250trimer.pdb, chain B (#6) with gpH_gpG_complex.pdb, chain B
(#7), sequence alignment score = 43.8
RMSD between 5 pruned atom pairs is 1.264 angstroms; (across all 60 pairs:
19.288)
> mmaker #7 to #4
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 gpH301_699trimer.pdb, chain B (#4) with gpH_gpG_complex.pdb, chain
B (#7), sequence alignment score = 352.4
RMSD between 63 pruned atom pairs is 0.797 angstroms; (across all 70 pairs:
1.534)
> color bfactor #7 palette alphafold
5979 atoms, 735 residues, atom bfactor range 45.9 to 97.8
> hide #6 models
> show #6 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/Pyocin/complex.pdb
Chain information for complex.pdb #8
---
Chain | Description
A B C | No description available
D E F | No description available
> color bfactor #8 palette alphafold
11559 atoms, 756 residues, atom bfactor range 39.2 to 97.1
> mmaker #8 to #3
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 400_691.pdb, chain A (#3) with complex.pdb, chain A (#8), sequence
alignment score = 521.1
RMSD between 99 pruned atom pairs is 0.466 angstroms; (across all 100 pairs:
0.580)
> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/Pyocin/ranked_1.pdb
> /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/Pyocin/ranked_2.pdb
> /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/Pyocin/ranked_3.pdb
> /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/Pyocin/ranked_4.pdb
Chain information for ranked_1.pdb #9
---
Chain | Description
A B C | No description available
Chain information for ranked_2.pdb #10
---
Chain | Description
A B C | No description available
Chain information for ranked_3.pdb #11
---
Chain | Description
A B C | No description available
Chain information for ranked_4.pdb #12
---
Chain | Description
A B C | No description available
> mmaker #9 to #3
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 400_691.pdb, chain A (#3) with ranked_1.pdb, chain A (#9), sequence
alignment score = 1544.2
RMSD between 292 pruned atom pairs is 0.990 angstroms; (across all 292 pairs:
0.990)
> mmaker #10 to #3
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 400_691.pdb, chain A (#3) with ranked_2.pdb, chain C (#10),
sequence alignment score = 1544.2
RMSD between 161 pruned atom pairs is 0.314 angstroms; (across all 292 pairs:
4.471)
> mmaker #11 to #3
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 400_691.pdb, chain A (#3) with ranked_3.pdb, chain B (#11),
sequence alignment score = 1544.2
RMSD between 160 pruned atom pairs is 0.418 angstroms; (across all 292 pairs:
11.209)
> mmaker #12 to #3
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 400_691.pdb, chain A (#3) with ranked_4.pdb, chain A (#12),
sequence alignment score = 1544.2
RMSD between 153 pruned atom pairs is 0.558 angstroms; (across all 292 pairs:
8.984)
> close #9-12
> ui mousemode right select
> select #7
5979 atoms, 6102 bonds, 735 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select #8
11559 atoms, 11736 bonds, 756 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select clear
> hide #7 models
> show #7 models
> hide #6 models
> show #6 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #6 models
> show #6 models
> hide #7 models
> show #7 models
> select clear
> ui mousemode right translate
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #5 models
> show #5 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #6 models
> show #6 models
> show #4 models
> hide #7 models
> ui mousemode right select
> select clear
Drag select of 214 residues
> delete sel
> show #7 models
> select clear
[Repeated 1 time(s)]Drag select of 2981 residues
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.1245,-0.82728,0.54783,157.97,-0.43612,-0.4503,-0.77912,-98.738,0.89124,-0.33592,-0.30473,30.902,#5,0.052604,0.96978,-0.23825,183.33,0.66824,0.14311,0.73005,-82.963,0.74208,-0.19761,-0.64051,-102.55,#6,-0.65481,-0.75152,-0.080228,209.95,0.75246,-0.63828,-0.16247,-68.2,0.070893,-0.16676,0.98345,-245.18,#7,-0.41835,-0.39632,-0.81726,136.53,0.15478,-0.91773,0.36581,-112.74,-0.895,0.02654,0.44528,133.73
> view matrix models
> #4,-0.067365,-0.79398,0.60421,161.2,-0.36393,-0.5443,-0.75584,-90.039,0.92899,-0.27081,-0.25229,33.391,#5,0.013118,0.94966,-0.31301,182.13,0.73356,0.20358,0.64841,-84.164,0.67949,-0.23812,-0.69396,-101.63,#6,-0.71383,-0.69893,-0.044121,204.2,0.69988,-0.70971,-0.080481,-80.006,0.024938,-0.088329,0.99578,-245.73,#7,-0.44994,-0.31728,-0.8348,143.33,0.040052,-0.94099,0.33605,-96.558,-0.89216,0.11777,0.43609,137.64
> view matrix models
> #4,-0.067365,-0.79398,0.60421,22.284,-0.36393,-0.5443,-0.75584,15.585,0.92899,-0.27081,-0.25229,-16.036,#5,0.013118,0.94966,-0.31301,43.217,0.73356,0.20358,0.64841,21.46,0.67949,-0.23812,-0.69396,-151.05,#6,-0.71383,-0.69893,-0.044121,65.288,0.69988,-0.70971,-0.080481,25.617,0.024938,-0.088329,0.99578,-295.15,#7,-0.44994,-0.31728,-0.8348,4.4216,0.040052,-0.94099,0.33605,9.0654,-0.89216,0.11777,0.43609,88.215
> view matrix models
> #4,-0.12917,-0.91654,0.37851,23.041,-0.45368,-0.28479,-0.84443,7.179,0.88175,-0.2808,-0.37903,-17.105,#5,0.22547,0.96163,-0.15633,40.353,0.61048,-0.014395,0.7919,25.23,0.75926,-0.27399,-0.5903,-151.55,#6,-0.50628,-0.86182,-0.030915,58.02,0.84845,-0.49137,-0.19669,42.54,0.15432,-0.12581,0.97998,-295.28,#7,-0.45302,-0.54683,-0.7041,7.5187,0.2696,-0.83684,0.47646,-8.2288,-0.84976,0.026016,0.52653,86.584
> view matrix models
> #4,-0.21134,-0.88325,0.41857,14.529,-0.49408,-0.27296,-0.82546,3.0697,0.84334,-0.38126,-0.37871,-19.148,#5,0.14708,0.98373,-0.10312,44.689,0.57515,-0.00023791,0.81805,27.332,0.80471,-0.17963,-0.56583,-150.31,#6,-0.52397,-0.84257,-0.12462,76.108,0.83963,-0.48639,-0.24175,51.282,0.14307,-0.23131,0.9623,-290.7,#7,-0.37009,-0.54171,-0.75471,-10.883,0.30781,-0.838,0.45056,-17.13,-0.87652,-0.065563,0.47688,81.728
> view matrix models
> #4,-0.20536,-0.89265,0.40126,15.52,-0.4465,-0.27939,-0.85005,7.8929,0.8709,-0.35373,-0.34119,-17.757,#5,0.16726,0.9808,-0.10032,44.02,0.61391,-0.023991,0.78901,24.872,0.77145,-0.19356,-0.60614,-150.43,#6,-0.51001,-0.85266,-0.11335,73.635,0.85352,-0.48532,-0.18964,41.042,0.10668,-0.19346,0.97529,-292.31,#7,-0.37904,-0.55424,-0.74104,-8.6361,0.26732,-0.83224,0.48572,-6.6703,-0.88593,-0.013989,0.46361,84.391
> view matrix models
> #4,-0.20547,-0.89249,0.40156,15.504,-0.44731,-0.27931,-0.84965,7.8579,0.87046,-0.3542,-0.34183,-17.738,#5,0.16691,0.98085,-0.10037,44.034,0.61329,-0.023575,0.78951,24.959,0.77202,-0.19333,-0.60548,-150.39,#6,-0.51026,-0.85249,-0.11355,73.68,0.8533,-0.48537,-0.19051,41.259,0.10729,-0.1941,0.9751,-292.25,#7,-0.37888,-0.55403,-0.74129,-8.6738,0.26799,-0.83237,0.48513,-6.7999,-0.88579,-0.01485,0.46384,84.391
> view matrix models
> #4,-0.20547,-0.89249,0.40156,13.396,-0.44731,-0.27931,-0.84965,3.081,0.87046,-0.3542,-0.34183,-15.307,#5,0.16691,0.98085,-0.10037,41.926,0.61329,-0.023575,0.78951,20.182,0.77202,-0.19333,-0.60548,-147.96,#6,-0.51026,-0.85249,-0.11355,71.572,0.8533,-0.48537,-0.19051,36.482,0.10729,-0.1941,0.9751,-289.82,#7,-0.37888,-0.55403,-0.74129,-10.782,0.26799,-0.83237,0.48513,-11.577,-0.88579,-0.01485,0.46384,86.822
> view matrix models
> #4,-0.20547,-0.89249,0.40156,201.39,-0.44731,-0.27931,-0.84965,27.213,0.87046,-0.3542,-0.34183,30.432,#5,0.16691,0.98085,-0.10037,229.92,0.61329,-0.023575,0.78951,44.314,0.77202,-0.19333,-0.60548,-102.22,#6,-0.51026,-0.85249,-0.11355,259.56,0.8533,-0.48537,-0.19051,60.614,0.10729,-0.1941,0.9751,-244.08,#7,-0.37888,-0.55403,-0.74129,177.21,0.26799,-0.83237,0.48513,12.555,-0.88579,-0.01485,0.46384,132.56
> ui mousemode right select
> select clear
> ui mousemode right translate
> save /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/P2VsPyocin.cxs
——— End of log from Tue Mar 1 15:53:02 2022 ———
opened ChimeraX session
> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/Bioinformatics/AlphaFold/Bacteriophages/Pyocin/complex.pdb
Chain information for complex.pdb #9
---
Chain | Description
A B C | No description available
D E F | No description available
> close session
> open /Users/shj152/relaxed_model_3_multimer_v3_pred_0.pdb
Chain information for relaxed_model_3_multimer_v3_pred_0.pdb #1
---
Chain | Description
A B C | No description available
> open /Users/shj152/relaxed_model_2_multimer_v3_pred_4.pdb
Chain information for relaxed_model_2_multimer_v3_pred_4.pdb #2
---
Chain | Description
A B C | No description available
> open /Users/shj152/relaxed_model_2_multimer_v3_pred_3.pdb
Chain information for relaxed_model_2_multimer_v3_pred_3.pdb #3
---
Chain | Description
A B C | No description available
> open /Users/shj152/relaxed_model_2_multimer_v3_pred_2.pdb
Chain information for relaxed_model_2_multimer_v3_pred_2.pdb #4
---
Chain | Description
A B C | No description available
> open /Users/shj152/relaxed_model_2_multimer_v3_pred_1.pdb
Chain information for relaxed_model_2_multimer_v3_pred_1.pdb #5
---
Chain | Description
A B C | No description available
> open /Users/shj152/relaxed_model_2_multimer_v3_pred_0.pdb
Chain information for relaxed_model_2_multimer_v3_pred_0.pdb #6
---
Chain | Description
A B C | No description available
> open /Users/shj152/relaxed_model_1_multimer_v3_pred_4.pdb
Chain information for relaxed_model_1_multimer_v3_pred_4.pdb #7
---
Chain | Description
A B C | No description available
> open /Users/shj152/relaxed_model_1_multimer_v3_pred_3.pdb
Chain information for relaxed_model_1_multimer_v3_pred_3.pdb #8
---
Chain | Description
A B C | No description available
> open /Users/shj152/relaxed_model_1_multimer_v3_pred_2.pdb
Chain information for relaxed_model_1_multimer_v3_pred_2.pdb #9
---
Chain | Description
A B C | No description available
> open /Users/shj152/relaxed_model_1_multimer_v3_pred_1.pdb
Chain information for relaxed_model_1_multimer_v3_pred_1.pdb #10
---
Chain | Description
A B C | No description available
> open /Users/shj152/relaxed_model_1_multimer_v3_pred_0.pdb
Chain information for relaxed_model_1_multimer_v3_pred_0.pdb #11
---
Chain | Description
A B C | No description available
> tile spacingFactor 01.
11 models tiled
> color bfactor #1-109 palette alphafold
330132 atoms, 22077 residues, atom bfactor range 3.5 to 98.4
> ui mousemode right distance
> ui mousemode right "tape measure"
> ui mousemode right distance
> ui mousemode right translate
> ui mousemode right distance
> select add #11
30012 atoms, 30273 bonds, 2007 residues, 1 model selected
> select subtract #11
Nothing selected
> select add #10
30012 atoms, 30273 bonds, 2007 residues, 1 model selected
> select subtract #10
Nothing selected
> select add #9
30012 atoms, 30273 bonds, 2007 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right distance
> ui mousemode right "pick blobs"
> ui mousemode right "tape measure"
> ui mousemode right select
> select clear
> select #9/A:643
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #9/C:301
34 atoms, 32 bonds, 2 residues, 1 model selected
> ui mousemode right distance
> ui tool show Distances
> ui mousemode right select
> select clear
> select add #9/A:643
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #9/C:301
34 atoms, 32 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> select add #9/A:643
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #9/C:301
34 atoms, 32 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #9/A:638
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #9/B:317
14 atoms, 13 bonds, 1 residue, 1 model selected
> distance #9/A:638 #9/A:317
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
33
> show sel atoms
> select #9/A:643
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> ui mousemode right translate
> ui mousemode right select
Exactly two atoms must be selected!
> select #9/B:317@CG2
1 atom, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select add #9/A:643
16 atoms, 14 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select add #9/A:643
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #9/A:643@CG2
16 atoms, 14 bonds, 2 residues, 1 model selected
> distance #9/A:638@CG2 #9/A:317@CG2
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
1
> select #9/A:669
17 atoms, 16 bonds, 1 residue, 1 model selected
> select down
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 17 atom styles
> style sel sphere
Changed 17 atom styles
> show sel atoms
> select #9/A:643
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 15 atom styles
> select #9/A:643@OE1
1 atom, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #9/A:300
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 14 atom styles
> show sel atoms
> select #9/A:300@OG1
1 atom, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select add #9/A:643@OE1
2 atoms, 2 residues, 1 model selected
> distance #9/A:300@OG1 #9/A:643@OE1
Distance between relaxed_model_1_multimer_v3_pred_2.pdb #9/A THR 300 OG1 and
GLU 643 OE1: 268.557Å
> ui mousemode right translate
> hide #11 models
> hide #10 models
> hide #9 models
> select add #8
30014 atoms, 30273 bonds, 2009 residues, 2 models selected
> hide #8 models
> select add #7
60026 atoms, 60546 bonds, 4016 residues, 3 models selected
> select subtract #8
30014 atoms, 30273 bonds, 2009 residues, 2 models selected
> select subtract #7
2 atoms, 2 residues, 1 model selected
> select add #2
30014 atoms, 30273 bonds, 2009 residues, 2 models selected
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.23676,0.85323,0.46469,532.02,0.33867,0.52077,-0.78365,-211.98,-0.91063,-0.028161,-0.41226,-8.2251,#9,-0.41442,0.90804,0.060979,183.81,-0.23051,-0.039913,-0.97225,-870.86,-0.88041,-0.41698,0.22585,-7.8884
> view matrix models
> #2,-0.58171,0.71814,0.38197,614.93,0.069316,0.51165,-0.85639,-212.39,-0.81044,-0.47169,-0.34741,-11.738,#9,-0.41442,0.90804,0.060979,266.08,-0.23051,-0.039913,-0.97225,-872.43,-0.88041,-0.41698,0.22585,-7.8884
> ui mousemode right translate
> ui mousemode right select
> select clear
> ui mousemode right translate
> preset pub
Multiple preset names match 'pub': publication 1 (silhouettes); publication 2
(depth-cued)
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_old/done/gpH_gp37_1.pdb
Chain information for gpH_gp37_1.pdb #13
---
Chain | Description
B C D | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_old/done/gpH_gp37_gp38_trimer.pdb
Chain information for gpH_gp37_gp38_trimer.pdb #14
---
Chain | Description
B C D | No description available
E F G | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_old/done/gpH_merged.pdb
Chain information for gpH_merged.pdb #15
---
Chain | Description
B C D | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_old/done/pyocin_merged.pdb
Chain information for pyocin_merged.pdb #16
---
Chain | Description
B C D | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_old/done/pyocinP2_merged.pdb
Chain information for pyocinP2_merged.pdb #17
---
Chain | Description
B C D | No description available
> close session
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_old/done/gpH_gp37_1.pdb
Chain information for gpH_gp37_1.pdb #1
---
Chain | Description
B C D | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_old/done/gpH_gp37_gp38_trimer.pdb
Chain information for gpH_gp37_gp38_trimer.pdb #2
---
Chain | Description
B C D | No description available
E F G | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_old/done/gpH_merged.pdb
Chain information for gpH_merged.pdb #3
---
Chain | Description
B C D | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_old/done/pyocin_merged.pdb
Chain information for pyocin_merged.pdb #4
---
Chain | Description
B C D | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_old/done/pyocinP2_merged.pdb
Chain information for pyocinP2_merged.pdb #5
---
Chain | Description
B C D | No description available
> hide atoms
> show cartoons
[Repeated 1 time(s)]
> hide #3 models
> show #3 models
> hide #5 models
> show #5 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #1 models
> show #2 models
> hide #2 models
> show #3 models
> color bfactor #1-109 palette alphafold
100944 atoms, 13425 residues, atom bfactor range 29.2 to 98.6
> hide #3 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/gpH_full.pdb
Chain information for gpH_full.pdb #6
---
Chain | Description
A B C | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/gpH_gp37_1.pdb
Chain information for gpH_gp37_1.pdb #7
---
Chain | Description
B C D | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/gpH_v231_merged.pdb
Chain information for gpH_v231_merged.pdb #8
---
Chain | Description
B C D | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/pyocin_v231_merged.pdb
Chain information for pyocin_v231_merged.pdb #9
---
Chain | Description
B C D | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/pyocinP2_v231_merged.pdb
Chain information for pyocinP2_v231_merged.pdb #10
---
Chain | Description
B C D | No description available
> hide #5 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> color bfactor #1-109 palette alphafold
218745 atoms, 27090 residues, atom bfactor range 3.5 to 99
> hide #6 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #9 models
> hide #9 models
> show #10 models
> show #8 models
> hide #10 models
> show #8 atoms
> show #8 surfaces
> color bfactor #1-109 palette alphafold
218745 atoms, 27090 residues, 3 surfaces, atom bfactor range 3.5 to 99
> hide #!8 atoms
> style #!8 sphere
Changed 15096 atom styles
> hide #!8 surfaces
> show #!8 atoms
> hide #!8 atoms
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_old/done/pyocin_merged.pdb
Chain information for pyocin_merged.pdb #11
---
Chain | Description
B C D | No description available
> color bfactor #1-109 palette alphafold
234051 atoms, 29163 residues, 3 surfaces, atom bfactor range 3.5 to 99
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/pyocin_v231_merged.pdb
Chain information for pyocin_v231_merged.pdb #12
---
Chain | Description
B C D | No description available
> color bfactor #1-109 palette alphafold
249357 atoms, 31236 residues, 3 surfaces, atom bfactor range 3.5 to 99
> mmaker #12 to #11
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 pyocin_merged.pdb, chain C (#11) with pyocin_v231_merged.pdb, chain
C (#12), sequence alignment score = 3455.4
RMSD between 386 pruned atom pairs is 1.146 angstroms; (across all 691 pairs:
12.188)
> hide #11 models
> show #11 models
> hide #11 models
> hide #12 models
> show #11 models
> hide #11 models
> show #12 models
> mmaker #8 to #11
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 pyocin_merged.pdb, chain C (#11) with gpH_v231_merged.pdb, chain C
(#8), sequence alignment score = 435.3
RMSD between 83 pruned atom pairs is 0.957 angstroms; (across all 544 pairs:
226.731)
> mmaker #8 to #12
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 pyocin_v231_merged.pdb, chain C (#12) with gpH_v231_merged.pdb,
chain D (#8), sequence alignment score = 427.9
RMSD between 21 pruned atom pairs is 0.965 angstroms; (across all 539 pairs:
131.215)
> show #1 models
> hide #1 models
> close session
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/ranked_5.pdb
Chain information for ranked_5.pdb #1
---
Chain | Description
A B C | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/ranked_4.pdb
Chain information for ranked_4.pdb #2
---
Chain | Description
A B C | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/ranked_3.pdb
Chain information for ranked_3.pdb #3
---
Chain | Description
A B C | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/ranked_2.pdb
Chain information for ranked_2.pdb #4
---
Chain | Description
A B C | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/ranked_1.pdb
Chain information for ranked_1.pdb #5
---
Chain | Description
A B C | No description available
> open
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/gpH_full.pdb
Chain information for gpH_full.pdb #6
---
Chain | Description
A B C | No description available
> color bfactor #1-109 palette alphafold
180072 atoms, 12042 residues, atom bfactor range 3.5 to 98.4
> mmaker #1-5 to #6
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 gpH_full.pdb, chain B (#6) with ranked_5.pdb, chain A (#1),
sequence alignment score = 3256.6
RMSD between 279 pruned atom pairs is 0.425 angstroms; (across all 669 pairs:
84.424)
Matchmaker gpH_full.pdb, chain B (#6) with ranked_4.pdb, chain B (#2),
sequence alignment score = 3264.4
RMSD between 355 pruned atom pairs is 0.379 angstroms; (across all 669 pairs:
46.802)
Matchmaker gpH_full.pdb, chain B (#6) with ranked_3.pdb, chain C (#3),
sequence alignment score = 3271.6
RMSD between 313 pruned atom pairs is 0.363 angstroms; (across all 669 pairs:
120.326)
Matchmaker gpH_full.pdb, chain B (#6) with ranked_2.pdb, chain B (#4),
sequence alignment score = 3236.8
RMSD between 327 pruned atom pairs is 0.561 angstroms; (across all 669 pairs:
37.278)
Matchmaker gpH_full.pdb, chain B (#6) with ranked_1.pdb, chain C (#5),
sequence alignment score = 3265.6
RMSD between 360 pruned atom pairs is 0.629 angstroms; (across all 669 pairs:
39.232)
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #1 models
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #4 models
> hide #4 models
> show #3 models
> hide #3 models
> show #2 models
> hide #2 models
> show #1 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/result_model_1_multimer_v3_pred_4.pkl
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 147, in _choose_pae_file
self._open_pae()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 160, in _open_pae
self._open_pae_from_file(s)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 184, in _open_pae_from_file
run(self.session, cmd)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 1006, in alphafold_pae
pae = AlphaFoldPAE(file, structure)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 739, in __init__
self._pae_matrix = read_pae_matrix(pae_path)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 833, in read_pae_matrix
return read_pickle_pae_matrix(path)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 880, in read_pickle_pae_matrix
p = pickle.load(f)
ModuleNotFoundError: No module named 'jax'
ModuleNotFoundError: No module named 'jax'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 880, in read_pickle_pae_matrix
p = pickle.load(f)
See log for complete Python traceback.
> alphafold pae #1 file
> /Users/shj152/Desktop/ERC/tailfibremodels/bestmodels/AF_v231/done/result_model_1_multimer_v3_pred_4.pkl
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 160, in _open_pae
self._open_pae_from_file(s)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 184, in _open_pae_from_file
run(self.session, cmd)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 1006, in alphafold_pae
pae = AlphaFoldPAE(file, structure)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 739, in __init__
self._pae_matrix = read_pae_matrix(pae_path)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 833, in read_pae_matrix
return read_pickle_pae_matrix(path)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 880, in read_pickle_pae_matrix
p = pickle.load(f)
ModuleNotFoundError: No module named 'jax'
ModuleNotFoundError: No module named 'jax'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 880, in read_pickle_pae_matrix
p = pickle.load(f)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: Z14V0004GDK/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 8419.60.44
OS Loader Version: 8419.60.44
Software:
System Software Overview:
System Version: macOS 13.1 (22C65)
Kernel Version: Darwin 22.2.0
Time since boot: 5 days, 21 hours, 37 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
P27q-20:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.7.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.2
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.5.dev202206100131
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.6
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.0
ChimeraX-ResidueFit: 1.0
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: 2.6.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.20.4
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.12.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
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
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → alphafold pae: No module named 'jax' |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #8032. Fixed in ChimeraX 1.5