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Opened 23 months ago
Closed 23 months ago
#10303 closed defect (duplicate)
Unable to restore objects of NewerVersionQuery class
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.6.2-arm64-arm-64bit
ChimeraX Version: 1.7.dev202309222343 (2023-09-22 23:43:12 UTC)
Description
(Describe the actions that caused this problem to occur here)
Tried to save to OneDrive folder with structures and maps.
Log:
UCSF ChimeraX version: 1.7.dev202309222343 (2023-09-22)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/leightongo/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Projects/Sarita/Ara h 2/Arah2_FABs.cxs"
Opened cryosparc_P205_J69_003_volume_map_sharp.mrc as #16, grid size
110,110,110, pixel 2.68, shown at level 1.33, step 1, values float32
Opened BetV3.5.mrc as #22, grid size 120,74,86, pixel 1.17, shown at level
0.141, step 1, values float32
Opened cryosparc_P205_J80_007_volume_map_sharp.mrc as #23, grid size
440,440,440, pixel 0.67, shown at level 0.315, step 1, values float32
Opened cryosparc_P205_J81_003_volume_map_sharp.mrc as #25, grid size
440,440,440, pixel 0.67, shown at level 0.263, step 1, values float32
Opened cryosparc_P205_J94_004_volume_map_sharp.mrc as #28, grid size
440,440,440, pixel 0.67, shown at level 0.151, step 1, values float32
Opened Arah2P3415A1.pdb map 3.5 as #35, grid size 74,124,98, pixel 1.17, shown
at level 0.111, step 1, values float32
Opened cryosparc_P205_J117_006_volume_map_sharp.mrc as #1, grid size
420,420,420, pixel 0.67, shown at level 0.158, step 1, values float32
Opened cryosparc_P205_J122_004_volume_map_sharp.mrc as #5, grid size
420,420,420, pixel 0.67, shown at level 0.133, step 1, values float32
Opened map series J123_component_000_frame_000.mrc as #6, 20 images, grid size
440,440,440, pixel 0.67, shown at level 0.0467, step 1, values float32
Opened map series J123_component_001_frame_000.mrc as #7, 20 images, grid size
440,440,440, pixel 0.67, shown at level 0.0613, step 1, values float32
Opened map series J123_component_002_frame_000.mrc as #8, 20 images, grid size
440,440,440, pixel 0.67, shown at level 0.0569, step 1, values float32
Not registering illegal selector name "15A1"
Not registering illegal selector name "#21"
Log from Tue Nov 7 13:32:34 2023UCSF ChimeraX version: 1.7.dev202309222343
(2023-09-22)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/leightongo/Desktop/Arah2_FABs.cxs format session
Opened cryosparc_P205_J69_003_volume_map_sharp.mrc as #16, grid size
110,110,110, pixel 2.68, shown at level 1.33, step 1, values float32
Opened BetV3.5.mrc as #22, grid size 120,74,86, pixel 1.17, shown at level
0.141, step 1, values float32
Opened cryosparc_P205_J80_007_volume_map_sharp.mrc as #23, grid size
440,440,440, pixel 0.67, shown at level 0.315, step 1, values float32
Opened cryosparc_P205_J80_007_volume_map_sharp.mrc z flip as #24, grid size
440,440,440, pixel 0.67, shown at level 0.265, step 1, values float32
Opened cryosparc_P205_J81_003_volume_map_sharp.mrc as #25, grid size
440,440,440, pixel 0.67, shown at level 0.263, step 1, values float32
Opened cryosparc_P205_J94_004_volume_map_sharp.mrc as #28, grid size
440,440,440, pixel 0.67, shown at level 0.151, step 1, values float32
Opened Arah2P3415A1.pdb map 3.5 as #35, grid size 74,124,98, pixel 1.17, shown
at level 0.111, step 1, values float32
Not registering illegal selector name "15A1"
Not registering illegal selector name "#21"
Log from Fri Nov 3 18:29:31 2023UCSF ChimeraX version: 1.7.dev202309222343
(2023-09-22)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/leightongo/Desktop/Arah2_FABs.cxs
Opened cryosparc_P205_J69_003_volume_map_sharp.mrc as #16, grid size
110,110,110, pixel 2.68, shown at level 1.33, step 1, values float32
Opened BetV3.5.mrc as #22, grid size 120,74,86, pixel 1.17, shown at level
0.141, step 1, values float32
Not registering illegal selector name "15A1"
Not registering illegal selector name "#21"
Log from Sat Oct 28 16:20:26 2023UCSF ChimeraX version: 1.7.dev202309222343
(2023-09-22)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/leightongo/Desktop/VBPs.cxs format session
Not registering illegal selector name "15A1"
Log from Tue Oct 17 22:00:54 2023UCSF ChimeraX version: 1.7.dev202309222343
(2023-09-22)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/leightongo/Desktop/Arah2_FABs.cxs format session
Log from Mon Oct 16 11:07:31 2023UCSF ChimeraX version: 1.7.dev202309222343
(2023-09-22)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/leightongo/Downloads/AF-A0A7I4KRZ9-F1-model_v4.pdb
Summary of feedback from opening
/Users/leightongo/Downloads/AF-A0A7I4KRZ9-F1-model_v4.pdb
---
warning | Ignored bad PDB record found on line 37
DBREF XXXX A 1 461 UNP A0A7I4KRZ9 A0A7I4KRZ9_BRUMA 1 461
AF-A0A7I4KRZ9-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for bma-abu-10 (A0A7I4KRZ9) [more info...]
Chain information for AF-A0A7I4KRZ9-F1-model_v4.pdb #1
---
Chain | Description
A | bma-abu-10
> set bgColor white
> lighting flat
> lighting shadows true intensity 0.5
> select #1:cys
216 atoms, 181 bonds, 36 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select add #1
3533 atoms, 3613 bonds, 461 residues, 1 model selected
> color sel cornflower blue
> select #1:cys
216 atoms, 181 bonds, 36 residues, 1 model selected
> color sel byhetero
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:96-97
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /A:73-97
187 atoms, 186 bonds, 25 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for AF-A0A7I4KRZ9-F1-model_v4.pdb_A SES surface #1.1:
minimum, -13.66, mean -0.60, maximum 15.17
To also show corresponding color key, enter the above coulombic command and
add key true
> open
> /Users/leightongo/Downloads/JR21_dd2eb/JR21_dd2eb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
JR21_dd2eb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #2
---
Chain | Description
A | No description available
> hide #!1 models
> select add #1
3533 atoms, 3613 bonds, 461 residues, 2 models selected
> select subtract #1
1 model selected
> select add #2
441 atoms, 445 bonds, 51 residues, 1 model selected
> color sel white
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> select subtract #2
Nothing selected
> hide #2 models
> show #2 models
> lighting simple
> lighting flat
> select #2:cys
24 atoms, 20 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> rename JR03 #2
Missing or invalid "models" argument: invalid models specifier
> rename #2 JR03
> select #2:trp
Nothing selected
> select #2:tyr
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2:his
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right select
> select #2/A:25
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2:ile
Nothing selected
> select #2:asp
32 atoms, 30 bonds, 4 residues, 1 model selected
> open /Users/leightongo/Downloads/JR02_fd66b/JR02.pdb
Chain information for JR02.pdb #3
---
Chain | Description
A | No description available
> open /Users/leightongo/Downloads/JR01_3cfa8/JR01.pdb
Chain information for JR01.pdb #4
---
Chain | Description
A | No description available
> mmaker #3-4 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 JR03, chain A (#2) with JR02.pdb, chain A (#3), sequence alignment
score = 157.9
RMSD between 37 pruned atom pairs is 0.454 angstroms; (across all 43 pairs:
1.764)
Matchmaker JR03, chain A (#2) with JR01.pdb, chain A (#4), sequence alignment
score = 159.5
RMSD between 40 pruned atom pairs is 0.731 angstroms; (across all 45 pairs:
3.013)
> select#3-4:cys
Unknown command: select#3-4:cys
> show sel atoms
> hide #2 models
> show #2 models
> select #3-4:cys
48 atoms, 40 bonds, 8 residues, 2 models selected
> show sel atoms
> select add #3
444 atoms, 445 bonds, 51 residues, 2 models selected
> select add #4
857 atoms, 864 bonds, 96 residues, 2 models selected
> color sel white
> select #3-4:cys
48 atoms, 40 bonds, 8 residues, 2 models selected
> color sel byhetero
> select clear
> select #4/A:5
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:5
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> show sel cartoons
> undo
[Repeated 1 time(s)]
> hide #3 models
> hide #4 models
> select #2/A:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 15 atoms, 6 residues, 12 bonds
> hide sel atoms
> show #3 models
> show #4 models
> select add #2
441 atoms, 445 bonds, 51 residues, 1 model selected
> select subtract #2
Nothing selected
> open /Users/leightongo/Downloads/Cora164/Cora164.pdb
Chain information for Cora164.pdb #5
---
Chain | Description
A | No description available
> close #1
> open /Users/leightongo/Downloads/Cora168_0ed1a/Cora168.pdb
Chain information for Cora168.pdb #1
---
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 JR03, chain A (#2) with Cora168.pdb, chain A (#1), sequence
alignment score = 165.9
RMSD between 37 pruned atom pairs is 0.433 angstroms; (across all 39 pairs:
1.222)
> mmaker #5 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 JR03, chain A (#2) with Cora164.pdb, chain A (#5), sequence
alignment score = 147.5
RMSD between 34 pruned atom pairs is 0.379 angstroms; (across all 36 pairs:
0.762)
> select add #1
343 atoms, 346 bonds, 39 residues, 1 model selected
> select add #5
665 atoms, 670 bonds, 75 residues, 2 models selected
> color sel white
> select #1,5:cys
48 atoms, 40 bonds, 8 residues, 2 models selected
> show sel atoms
> color sel byhetero
> select add #1
367 atoms, 366 bonds, 43 residues, 2 models selected
> select subtract #1
24 atoms, 20 bonds, 4 residues, 1 model selected
> select add #5
322 atoms, 324 bonds, 36 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #1
343 atoms, 346 bonds, 39 residues, 1 model selected
> hide #3 models
> hide #4 models
> hide #5 models
> select subtract #1
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> save /Users/leightongo/Desktop/VBPs.cxs
> rename #1 id #6
> rename #4 id #1
> rename #2 id #4
> rename #3 id #2
> rename #4 id #3
> rename #5 id #4
> rename #6 id #5
> save /Users/leightongo/Desktop/VBPs.cxs
> ui mousemode right select
> select clear
> ui mousemode right translate
> save /Users/leightongo/Desktop/VBPs.cxs
> select #1,5:asp-glu
451 atoms, 427 bonds, 53 residues, 2 models selected
> select #1,5:asp,glu
178 atoms, 163 bonds, 20 residues, 2 models selected
> show sel & #5 atoms
> open /Users/leightongo/Downloads/Maci/Maci.pdb
Chain information for Maci.pdb #6
---
Chain | Description
A | No description available
> open /Users/leightongo/Downloads/Sesi_7b035/Sesi.pdb
Chain information for Sesi.pdb #7
---
Chain | Description
A | No description available
> open /Users/leightongo/Downloads/Zeam5_fc676/Zeam5.pdb
Chain information for Zeam5.pdb #8
---
Chain | Description
A | No description available
> mmaker #6-8 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 JR03, chain A (#3) with Maci.pdb, chain A (#6), sequence alignment
score = 101
RMSD between 32 pruned atom pairs is 0.918 angstroms; (across all 38 pairs:
2.415)
Matchmaker JR03, chain A (#3) with Sesi.pdb, chain A (#7), sequence alignment
score = 108.3
RMSD between 36 pruned atom pairs is 0.699 angstroms; (across all 39 pairs:
1.331)
Matchmaker JR03, chain A (#3) with Zeam5.pdb, chain A (#8), sequence alignment
score = 147.5
RMSD between 34 pruned atom pairs is 0.379 angstroms; (across all 36 pairs:
0.762)
> color #6 white
> color #7 white
> color #8 white
> select add #5
468 atoms, 460 bonds, 53 residues, 2 models selected
> select subtract #5
125 atoms, 114 bonds, 14 residues, 1 model selected
> select #6-8:cys
72 atoms, 60 bonds, 12 residues, 3 models selected
> show sel atoms
> color sel byhetero
> ui mousemode right select
> select clear
> hide #8 models
> hide #7 models
> hide #6 models
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> hide #5 models
> show #2 models
> hide #2 models
> select #3:asn
8 atoms, 7 bonds, 1 residue, 1 model selected
> open /Users/leightongo/Downloads/Orys2.1/Orys2.1.pdb
Chain information for Orys2.1.pdb #9
---
Chain | Description
A | No description available
> color #9 white
> open /Users/leightongo/Downloads/8db4.pdb
8db4.pdb title:
Crystal structure of the peanut allergen ara H 2 bound by two neutralizing
antibodies 22S1 and 13T1 [more info...]
Chain information for 8db4.pdb #10
---
Chain | Description
A G | 13T1 heavy chain
B H | 13T1 light chain
C I | 22S1 heavy chain
D J | 22S1 light chain
E F | ara H 2 allergen
Non-standard residues in 8db4.pdb #10
---
EDO — 1,2-ethanediol (ethylene glycol)
ZN — zinc ion
> hide #3 models
> select add #3
441 atoms, 445 bonds, 51 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #9 models
> select add #10
14409 atoms, 14425 bonds, 32 pseudobonds, 2220 residues, 3 models selected
> hide sel atoms
> show sel cartoons
Drag select of 414 residues, 1 pseudobonds
> select up
3250 atoms, 3327 bonds, 1 pseudobond, 438 residues, 2 models selected
> select up
3901 atoms, 3987 bonds, 1 pseudobond, 521 residues, 2 models selected
> select up
3973 atoms, 3987 bonds, 1 pseudobond, 593 residues, 2 models selected
> select up
14409 atoms, 14425 bonds, 8 pseudobonds, 2220 residues, 2 models selected
> select down
3973 atoms, 3987 bonds, 1 pseudobond, 593 residues, 2 models selected
> delete sel
Drag select of 200 residues, 1 pseudobonds
> select up
1967 atoms, 2006 bonds, 1 pseudobond, 265 residues, 2 models selected
> select up
3188 atoms, 3269 bonds, 1 pseudobond, 431 residues, 2 models selected
> select up
3302 atoms, 3272 bonds, 1 pseudobond, 542 residues, 2 models selected
> select up
10436 atoms, 10438 bonds, 6 pseudobonds, 1627 residues, 2 models selected
> select down
3302 atoms, 3272 bonds, 1 pseudobond, 542 residues, 2 models selected
> delete sel
> ui tool show "Show Sequence Viewer"
> sequence chain #10/F
Alignment identifier is 10/F
> select #10/F:121-122
9 atoms, 8 bonds, 2 residues, 1 model selected
> select #10/F:121-128
47 atoms, 46 bonds, 8 residues, 1 model selected
> color sel white
> select #10/F:31
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/F:31-39
70 atoms, 69 bonds, 9 residues, 1 model selected
> color sel light gray
> select #10/H:22
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
Drag select of 210 residues, 1 pseudobonds
> select up
1579 atoms, 1614 bonds, 1 pseudobond, 219 residues, 2 models selected
> select up
3194 atoms, 3271 bonds, 1 pseudobond, 431 residues, 2 models selected
> select up
3291 atoms, 3271 bonds, 1 pseudobond, 528 residues, 2 models selected
> select up
7134 atoms, 7166 bonds, 4 pseudobonds, 1085 residues, 2 models selected
> select down
3291 atoms, 3271 bonds, 1 pseudobond, 528 residues, 2 models selected
> ui tool show "Color Actions"
> color sel tomato
Drag select of 140 residues
> select up
1244 atoms, 1267 bonds, 171 residues, 1 model selected
> select up
3102 atoms, 3183 bonds, 427 residues, 1 model selected
> select up
3128 atoms, 3183 bonds, 453 residues, 1 model selected
> select up
7134 atoms, 7166 bonds, 1085 residues, 1 model selected
> select down
3128 atoms, 3183 bonds, 453 residues, 1 model selected
> color sel deep sky blue
> color sel dodger blue
> color sel cornflower blue
Drag select of 13 residues, 1 pseudobonds
> select up
279 atoms, 281 bonds, 1 pseudobond, 36 residues, 2 models selected
> select up
704 atoms, 712 bonds, 1 pseudobond, 93 residues, 2 models selected
> select up
715 atoms, 712 bonds, 1 pseudobond, 104 residues, 2 models selected
> select up
7134 atoms, 7166 bonds, 4 pseudobonds, 1085 residues, 2 models selected
> select down
715 atoms, 712 bonds, 1 pseudobond, 104 residues, 2 models selected
> color (#!10 & sel) white
> select clear
> select #10/F:31
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/F:31-39
70 atoms, 69 bonds, 9 residues, 1 model selected
> color sel medium orchid
> color sel medium purple
> color sel orchid
> color sel medium orchid
> select #10/F:124
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #10/F:124-133
81 atoms, 81 bonds, 10 residues, 1 model selected
> select #10/F:121-122
9 atoms, 8 bonds, 2 residues, 1 model selected
> select #10/F:121-128
47 atoms, 46 bonds, 8 residues, 1 model selected
> color sel pale violet red
> select clear
[Repeated 1 time(s)]
> open /Users/leightongo/Downloads/T1T5.pdb
Chain information for T1T5.pdb #11
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> select add #11
15431 atoms, 15369 bonds, 3 pseudobonds, 1288 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ui mousemode right translate
> mmaker #11 to #10
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 8db4.pdb, chain G (#10) with T1T5.pdb, chain C (#11), sequence
alignment score = 1093.3
RMSD between 216 pruned atom pairs is 0.646 angstroms; (across all 218 pairs:
0.674)
> hide #!10 models
> ui mousemode right select
Drag select of 73 residues
> select up
1363 atoms, 1376 bonds, 94 residues, 1 model selected
> select up
6156 atoms, 6235 bonds, 437 residues, 1 model selected
> select up
6196 atoms, 6271 bonds, 441 residues, 1 model selected
> select up
15431 atoms, 15369 bonds, 1288 residues, 1 model selected
> select down
6196 atoms, 6271 bonds, 441 residues, 1 model selected
> delete sel
Drag select of 44 residues
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!10 models
> show #!11 models
> delete sel
Drag select of 18 residues
> select up
404 atoms, 400 bonds, 34 residues, 1 model selected
> select up
1234 atoms, 1236 bonds, 94 residues, 1 model selected
> select up
2016 atoms, 2016 bonds, 146 residues, 1 model selected
> select up
8693 atoms, 8548 bonds, 803 residues, 1 model selected
> select down
2016 atoms, 2016 bonds, 146 residues, 1 model selected
> delete sel
> rename #11 T5
> show #!10 models
Drag select of 188 residues, 1 pseudobonds
> select up
2915 atoms, 2946 bonds, 1 pseudobond, 205 residues, 2 models selected
> select up
6383 atoms, 6460 bonds, 1 pseudobond, 435 residues, 2 models selected
> select up
6463 atoms, 6532 bonds, 1 pseudobond, 443 residues, 2 models selected
> select up
6677 atoms, 6532 bonds, 1 pseudobond, 657 residues, 2 models selected
> select up
6677 atoms, 6532 bonds, 1 pseudobond, 657 residues, 2 models selected
> select up
17197 atoms, 17114 bonds, 1 pseudobond, 2128 residues, 12 models selected
> select down
6677 atoms, 6532 bonds, 1 pseudobond, 657 residues, 2 models selected
> color sel dark orange
> color sel sandy brown
> color sel coral
> color sel orange
> color sel dark orange
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> save /Users/leightongo/Desktop/Arah2_FABs.cxs
——— End of log from Mon Oct 16 11:07:31 2023 ———
opened ChimeraX session
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> ui tool show "Show Sequence Viewer"
> sequence chain #10/F
Alignment identifier is 10/F
> select #10/F:31
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/F:31-39
70 atoms, 69 bonds, 9 residues, 1 model selected
> open /Users/leightongo/Downloads/Arah2_P34.pdb
Chain information for Arah2_P34.pdb #12
---
Chain | Description
E | No description available
P | No description available
Q | No description available
R | No description available
T | No description available
V | No description available
> select add #12
14780 atoms, 14937 bonds, 4 pseudobonds, 1058 residues, 3 models selected
> select add #10
21844 atoms, 22034 bonds, 17 pseudobonds, 2134 residues, 5 models selected
> select subtract #10
14710 atoms, 14868 bonds, 4 pseudobonds, 1049 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> mmaker #12 to #10
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 8db4.pdb, chain J (#10) with Arah2_P34.pdb, chain V (#12), sequence
alignment score = 1085.5
RMSD between 213 pruned atom pairs is 0.512 angstroms; (across all 213 pairs:
0.512)
> hide #!10 models
> ui mousemode right select
Drag select of 18 residues
> select up
298 atoms, 298 bonds, 24 residues, 1 model selected
> select up
1098 atoms, 1112 bonds, 81 residues, 1 model selected
> select up
1133 atoms, 1147 bonds, 84 residues, 1 model selected
> select up
3061 atoms, 3098 bonds, 216 residues, 1 model selected
> select up
14710 atoms, 14868 bonds, 1049 residues, 1 model selected
> select down
3061 atoms, 3098 bonds, 216 residues, 1 model selected
Drag select of 126 residues
> select up
2172 atoms, 2194 bonds, 155 residues, 1 model selected
> select up
6111 atoms, 6184 bonds, 429 residues, 1 model selected
> select up
14710 atoms, 14868 bonds, 1049 residues, 1 model selected
> select down
6111 atoms, 6184 bonds, 429 residues, 1 model selected
> delete sel
> select #12/P:94
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide #!11 models
> select clear
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!12 models
> show #!12 models
> select clear
Drag select of 25 residues
> select up
928 atoms, 928 bonds, 67 residues, 1 model selected
> select up
2304 atoms, 2313 bonds, 162 residues, 1 model selected
> select up
2311 atoms, 2319 bonds, 163 residues, 1 model selected
> select up
2702 atoms, 2712 bonds, 189 residues, 1 model selected
> select up
2712 atoms, 2721 bonds, 190 residues, 1 model selected
> select up
8599 atoms, 8684 bonds, 620 residues, 1 model selected
> select down
2712 atoms, 2721 bonds, 190 residues, 1 model selected
> select up
8599 atoms, 8684 bonds, 620 residues, 1 model selected
> select down
2712 atoms, 2721 bonds, 190 residues, 1 model selected
> delete sel
Drag select of 261 residues
> select up
4235 atoms, 4287 bonds, 299 residues, 1 model selected
> select up
5887 atoms, 5963 bonds, 430 residues, 1 model selected
> select up
23084 atoms, 23077 bonds, 2558 residues, 12 models selected
> select down
5887 atoms, 5963 bonds, 430 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> show #!10 models
> hide #!12 models
> select add #12
5887 atoms, 5963 bonds, 1 pseudobond, 430 residues, 2 models selected
> select subtract #12
Nothing selected
Drag select of 111 residues, 1 pseudobonds
> select clear
> show #!12 models
> show #!11 models
> select #10/F:122-123
9 atoms, 8 bonds, 2 residues, 1 model selected
> select #10/F:122-128
42 atoms, 41 bonds, 7 residues, 1 model selected
> hide #!11 models
> select #10/G:192
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/P:81
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> show #!11 models
> hide #!11 models
> select #10/F:122
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #10/F:122-128
42 atoms, 41 bonds, 7 residues, 1 model selected
> select #10/G:180
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #10/I:21
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #10/I:68
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> show #!11 models
> hide #!12 models
> show #!12 models
> ui mousemode right translate
> ui mousemode right select
Drag select of 33 residues
> select up
496 atoms, 500 bonds, 67 residues, 1 model selected
> select up
2101 atoms, 2155 bonds, 289 residues, 1 model selected
> select up
2119 atoms, 2173 bonds, 292 residues, 1 model selected
> select up
3102 atoms, 3183 bonds, 427 residues, 1 model selected
> select up
3128 atoms, 3183 bonds, 453 residues, 1 model selected
> select up
7134 atoms, 7166 bonds, 1085 residues, 1 model selected
> select down
3128 atoms, 3183 bonds, 453 residues, 1 model selected
> hide sel cartoons
Drag select of 9 residues
> select up
241 atoms, 240 bonds, 31 residues, 1 model selected
> select up
704 atoms, 712 bonds, 93 residues, 1 model selected
> select up
715 atoms, 712 bonds, 104 residues, 1 model selected
> select up
7134 atoms, 7166 bonds, 1085 residues, 1 model selected
> select down
715 atoms, 712 bonds, 104 residues, 1 model selected
> color sel white
> select clear
> save /Users/leightongo/Desktop/image1.png supersample 3
> open
> /Users/leightongo/Downloads/arah9F10antiFab_230714_SB1PN16_refine_13.pdb
Chain information for arah9F10antiFab_230714_SB1PN16_refine_13.pdb #13
---
Chain | Description
A | No description available
H | No description available
K | No description available
L | No description available
> hide #!10 models
> hide #!11 models
> hide #!12 models
> select #13/K:3
17 atoms, 16 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #13/K
Alignment identifier is 13/K
> select #13/K:118-120
41 atoms, 40 bonds, 3 residues, 1 model selected
> select #13/K
1733 atoms, 1752 bonds, 120 residues, 1 model selected
> show #!10 models
> show #!11 models
> show #!12 models
> select add #13
9248 atoms, 9164 bonds, 3 pseudobonds, 823 residues, 2 models selected
> select subtract #13
Nothing selected
> mmaker #13 to #10
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 8db4.pdb, chain J (#10) with
arah9F10antiFab_230714_SB1PN16_refine_13.pdb, chain L (#13), sequence
alignment score = 937.9
RMSD between 204 pruned atom pairs is 0.966 angstroms; (across all 209 pairs:
1.019)
> select #13/A:54
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
221 atoms, 220 bonds, 17 residues, 1 model selected
> select up
1227 atoms, 1238 bonds, 93 residues, 1 model selected
> select up
9248 atoms, 9164 bonds, 823 residues, 1 model selected
> select down
1227 atoms, 1238 bonds, 93 residues, 1 model selected
> delete sel
> open
> /Users/leightongo/Downloads/arah9F10antiFab_230714_SB1PN16_refine_13.pdb
Chain information for arah9F10antiFab_230714_SB1PN16_refine_13.pdb #14
---
Chain | Description
A | No description available
H | No description available
K | No description available
L | No description available
> mmaker #14 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 T5, chain B (#11) with
arah9F10antiFab_230714_SB1PN16_refine_13.pdb, chain L (#14), sequence
alignment score = 926.1
RMSD between 58 pruned atom pairs is 0.361 angstroms; (across all 209 pairs:
13.632)
> mmaker #14/H to #11/B
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 T5, chain B (#11) with
arah9F10antiFab_230714_SB1PN16_refine_13.pdb, chain H (#14), sequence
alignment score = 298.3
RMSD between 76 pruned atom pairs is 1.126 angstroms; (across all 196 pairs:
6.938)
> mmaker #14/L to #11/A
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 T5, chain A (#11) with
arah9F10antiFab_230714_SB1PN16_refine_13.pdb, chain L (#14), sequence
alignment score = 281.3
RMSD between 63 pruned atom pairs is 1.034 angstroms; (across all 195 pairs:
7.390)
> select #14/A:8
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
74 atoms, 74 bonds, 6 residues, 1 model selected
> select up
1227 atoms, 1238 bonds, 93 residues, 1 model selected
> select up
9248 atoms, 9164 bonds, 823 residues, 1 model selected
> select down
1227 atoms, 1238 bonds, 93 residues, 1 model selected
> delete sel
> open
> /Users/leightongo/Downloads/arah9F10antiFab_230714_SB1PN16_refine_13.pdb
Chain information for arah9F10antiFab_230714_SB1PN16_refine_13.pdb #15
---
Chain | Description
A | No description available
H | No description available
K | No description available
L | No description available
> mmaker #15/L 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 Arah2_P34.pdb, chain Q (#12) with
arah9F10antiFab_230714_SB1PN16_refine_13.pdb, chain L (#15), sequence
alignment score = 843.9
RMSD between 203 pruned atom pairs is 1.059 angstroms; (across all 208 pairs:
1.193)
> select #12/Q:20
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> hide #!10 models
> hide #!11 models
> hide #!12 models
> select #15/H:151
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
146 atoms, 146 bonds, 10 residues, 1 model selected
> select up
1107 atoms, 1121 bonds, 77 residues, 1 model selected
> select up
1131 atoms, 1145 bonds, 79 residues, 1 model selected
> select up
3075 atoms, 3115 bonds, 211 residues, 1 model selected
> select up
9248 atoms, 9164 bonds, 823 residues, 1 model selected
> select down
3075 atoms, 3115 bonds, 211 residues, 1 model selected
> delete sel
> select #15/L:135
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
129 atoms, 128 bonds, 9 residues, 1 model selected
> select up
3023 atoms, 3059 bonds, 209 residues, 1 model selected
> select up
6173 atoms, 6049 bonds, 612 residues, 1 model selected
> select down
3023 atoms, 3059 bonds, 209 residues, 1 model selected
> delete sel
> select #15/A:49
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
221 atoms, 220 bonds, 17 residues, 1 model selected
> select up
1227 atoms, 1238 bonds, 93 residues, 1 model selected
> select up
3150 atoms, 2990 bonds, 403 residues, 1 model selected
> select down
1227 atoms, 1238 bonds, 93 residues, 1 model selected
> delete sel
Drag select of 43 residues, 1 pseudobonds
> select up
1174 atoms, 1173 bonds, 1 pseudobond, 82 residues, 2 models selected
> select up
6098 atoms, 6174 bonds, 1 pseudobond, 420 residues, 2 models selected
> select up
8021 atoms, 7926 bonds, 3 pseudobonds, 730 residues, 2 models selected
> select down
6098 atoms, 6174 bonds, 1 pseudobond, 420 residues, 2 models selected
> delete sel
Drag select of 133 residues, 2 pseudobonds
> select up
2777 atoms, 2804 bonds, 2 pseudobonds, 188 residues, 2 models selected
> select up
6098 atoms, 6174 bonds, 2 pseudobonds, 420 residues, 2 models selected
> select up
8021 atoms, 7926 bonds, 3 pseudobonds, 730 residues, 2 models selected
> select down
6098 atoms, 6174 bonds, 2 pseudobonds, 420 residues, 2 models selected
> delete sel
Drag select of 360 residues
> select up
5769 atoms, 5256 bonds, 930 residues, 3 models selected
> select up
28853 atoms, 28333 bonds, 3488 residues, 15 models selected
> select up
28853 atoms, 28333 bonds, 3488 residues, 15 models selected
> select down
5769 atoms, 5256 bonds, 930 residues, 3 models selected
> color sel dim gray
> color sel dark gray
> color sel black
> color sel dim gray
> color sel gray
> combine #13-15
Remapping chain ID 'K' in arah9F10antiFab_230714_SB1PN16_refine_13.pdb #14 to
'L'
Remapping chain ID 'S' in arah9F10antiFab_230714_SB1PN16_refine_13.pdb #14 to
'T'
Remapping chain ID 'K' in arah9F10antiFab_230714_SB1PN16_refine_13.pdb #15 to
'M'
Remapping chain ID 'S' in arah9F10antiFab_230714_SB1PN16_refine_13.pdb #15 to
'U'
> hide #!13 models
> hide #!14 models
> hide #!15 models
> select subtract #15
3846 atoms, 3504 bonds, 620 residues, 2 models selected
> select subtract #14
1923 atoms, 1752 bonds, 310 residues, 1 model selected
> select subtract #13
Nothing selected
> hide #!16 models
> show #!16 models
> show #!12 models
> show #!11 models
> show #!10 models
> select #12/P:22
10 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
> open /Users/leightongo/Downloads/Arah2_P34.pdb
Chain information for Arah2_P34.pdb #17
---
Chain | Description
E | No description available
P | No description available
Q | No description available
R | No description available
T | No description available
V | No description available
> hide #!16 models
> hide #!12 models
> hide #!11 models
> select add #17
14710 atoms, 14868 bonds, 4 pseudobonds, 1049 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #17,1,0,0,-38.323,0,1,0,-30.016,0,0,1,-53.207
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.40591,0.82423,0.39483,-2.6033,-0.14261,-0.48385,0.86345,-75.685,0.90272,0.29417,0.31394,-50.249
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.40591,0.82423,0.39483,1.1038,-0.14261,-0.48385,0.86345,-90.727,0.90272,0.29417,0.31394,2.6867
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.31526,0.91661,0.24584,-10.604,-0.29874,-0.15003,0.94247,-83.944,0.90076,-0.37057,0.22653,-5.2588
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.31526,0.91661,0.24584,-18.791,-0.29874,-0.15003,0.94247,-34.435,0.90076,-0.37057,0.22653,-69.96
> view matrix models
> #17,0.31526,0.91661,0.24584,-26.132,-0.29874,-0.15003,0.94247,-33.412,0.90076,-0.37057,0.22653,-70.941
> view matrix models
> #17,0.31526,0.91661,0.24584,-26.989,-0.29874,-0.15003,0.94247,-35.985,0.90076,-0.37057,0.22653,-70.542
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.2049,0.94533,0.25372,-24.074,-0.27566,-0.19299,0.94168,-37.208,0.93916,-0.26289,0.22105,-69.603
> view matrix models
> #17,0.3035,0.89928,0.31494,-29.021,-0.23566,-0.24942,0.93928,-39.011,0.92323,-0.35929,0.13622,-68.24
> hide #!10 models
> ui mousemode right select
> select clear
Drag select of 456 residues, 1 pseudobonds
> select up
7788 atoms, 7862 bonds, 1 pseudobond, 546 residues, 2 models selected
> select up
8813 atoms, 8896 bonds, 1 pseudobond, 618 residues, 2 models selected
> select up
8823 atoms, 8905 bonds, 1 pseudobond, 619 residues, 2 models selected
> select up
14710 atoms, 14868 bonds, 4 pseudobonds, 1049 residues, 2 models selected
> select down
8823 atoms, 8905 bonds, 1 pseudobond, 619 residues, 2 models selected
> delete sel
> name #17 15A1
"15A1": invalid atom specifier
> name #17 Arah215A1
"Arah215A1": invalid atom specifier
> name Arah215A1 #17
> name 15A1 #17
Not registering illegal selector name "15A1"
> rename 15A1 #17
Missing or invalid "models" argument: invalid models specifier
> rename #17 15A1
> close #15
> close #13
> close #14
> select add #17
5887 atoms, 5963 bonds, 1 pseudobond, 430 residues, 2 models selected
> color sel orchid
> show #!10 models
> show #!11 models
> show #!12 models
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.3035,0.89928,0.31494,-29.152,-0.23566,-0.24942,0.93928,-39.559,0.92323,-0.35929,0.13622,-70.849
> view matrix models
> #17,0.3035,0.89928,0.31494,-29.485,-0.23566,-0.24942,0.93928,-39.92,0.92323,-0.35929,0.13622,-70.896
> color sel medium purple
> color sel plum
> color sel violet
> color sel thistle
> color sel orchid
> show #!16 models
> open
> /Users/leightongo/Downloads/arah9F10antiFab_230714_SB1PN16_refine_13.pdb
Chain information for arah9F10antiFab_230714_SB1PN16_refine_13.pdb #13
---
Chain | Description
A | No description available
H | No description available
K | No description available
L | No description available
> mmaker #13 to #17
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 15A1, chain Q (#17) with
arah9F10antiFab_230714_SB1PN16_refine_13.pdb, chain L (#13), sequence
alignment score = 843.9
RMSD between 203 pruned atom pairs is 1.059 angstroms; (across all 208 pairs:
1.193)
> hide #!16 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> show #!13 models
> hide #!17 models
> select subtract #17
Nothing selected
> ui mousemode right select
Drag select of 395 residues, 1 pseudobonds
> select clear
Drag select of 341 residues
> select up
5647 atoms, 5705 bonds, 394 residues, 1 model selected
> select up
7325 atoms, 7412 bonds, 513 residues, 1 model selected
> select up
9248 atoms, 9164 bonds, 823 residues, 1 model selected
> select down
7325 atoms, 7412 bonds, 513 residues, 1 model selected
> delete sel
> combine #13,16
Remapping chain ID 'K' in combination #16 to 'N'
Remapping chain ID 'S' in combination #16 to 'V'
> close #16
> close #13
> select add #14
7692 atoms, 7008 bonds, 1240 residues, 1 model selected
> color sel gray
> select subtract #14
Nothing selected
> hide #!14 models
> show #!17 models
> show #!12 models
> show #!11 models
> show #!10 models
> save /Users/leightongo/Desktop/Arah2_FABs.cxs
> show #!14 models
> save /Users/leightongo/Desktop/Arah2_FABs.cxs
> hide #!14 models
> show #!14 models
> show #3 models
> open 1WQE
Summary of feedback from opening 1WQE fetched from pdb
---
note | Fetching compressed mmCIF 1wqe from
http://files.rcsb.org/download/1wqe.cif
1wqe title:
An unusual fold for potassium channel blockers: NMR structure of three toxins
from the scorpion Opisthacanthus madagascariensis [more info...]
Chain information for 1wqe
---
Chain | Description
13.1/A 13.2/A 13.3/A 13.4/A 13.5/A 13.6/A 13.7/A 13.8/A 13.9/A 13.10/A 13.11/A
13.12/A 13.13/A 13.14/A 13.15/A 13.16/A 13.17/A 13.18/A 13.19/A 13.20/A
13.21/A 13.22/A 13.23/A 13.24/A 13.25/A 13.26/A 13.27/A 13.28/A 13.29/A
13.30/A | OmTx3
> hide #!10-14,17 target m
> show #!13 models
> select #13:cys
1200 atoms, 1140 bonds, 120 residues, 30 models selected
> show sel atoms
> open /Users/leightongo/Downloads/A1PRO_18182/A1Pro.pdb
Chain information for A1Pro.pdb #15
---
Chain | Description
A | No description available
> mmaker #13,15 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 JR03, chain A (#3) with 1wqe, chain A (#13.1), sequence alignment
score = 41.1
RMSD between 18 pruned atom pairs is 1.089 angstroms; (across all 23 pairs:
4.245)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.2), sequence alignment
score = 41.1
RMSD between 18 pruned atom pairs is 1.086 angstroms; (across all 23 pairs:
4.207)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.3), sequence alignment
score = 36.3
RMSD between 15 pruned atom pairs is 1.112 angstroms; (across all 23 pairs:
4.724)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.4), sequence alignment
score = 41.1
RMSD between 17 pruned atom pairs is 1.023 angstroms; (across all 23 pairs:
4.205)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.5), sequence alignment
score = 32.7
RMSD between 14 pruned atom pairs is 1.071 angstroms; (across all 23 pairs:
5.042)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.6), sequence alignment
score = 36.3
RMSD between 14 pruned atom pairs is 1.043 angstroms; (across all 23 pairs:
5.307)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.7), sequence alignment
score = 32.7
RMSD between 15 pruned atom pairs is 1.104 angstroms; (across all 23 pairs:
4.714)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.8), sequence alignment
score = 37.5
RMSD between 18 pruned atom pairs is 1.146 angstroms; (across all 23 pairs:
4.293)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.9), sequence alignment
score = 41.1
RMSD between 18 pruned atom pairs is 1.130 angstroms; (across all 23 pairs:
4.249)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.10), sequence alignment
score = 41.1
RMSD between 18 pruned atom pairs is 1.141 angstroms; (across all 23 pairs:
4.368)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.11), sequence alignment
score = 41.1
RMSD between 18 pruned atom pairs is 1.109 angstroms; (across all 23 pairs:
4.268)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.12), sequence alignment
score = 32.7
RMSD between 13 pruned atom pairs is 0.992 angstroms; (across all 23 pairs:
5.152)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.13), sequence alignment
score = 36.3
RMSD between 14 pruned atom pairs is 1.104 angstroms; (across all 23 pairs:
5.137)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.14), sequence alignment
score = 32.7
RMSD between 15 pruned atom pairs is 1.127 angstroms; (across all 23 pairs:
4.748)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.15), sequence alignment
score = 36.3
RMSD between 14 pruned atom pairs is 1.018 angstroms; (across all 23 pairs:
5.240)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.16), sequence alignment
score = 41.1
RMSD between 16 pruned atom pairs is 0.961 angstroms; (across all 23 pairs:
4.383)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.17), sequence alignment
score = 36.1
RMSD between 7 pruned atom pairs is 1.362 angstroms; (across all 22 pairs:
6.377)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.18), sequence alignment
score = 41.1
RMSD between 18 pruned atom pairs is 1.111 angstroms; (across all 23 pairs:
4.190)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.19), sequence alignment
score = 39.7
RMSD between 8 pruned atom pairs is 1.196 angstroms; (across all 22 pairs:
5.590)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.20), sequence alignment
score = 37.5
RMSD between 18 pruned atom pairs is 1.109 angstroms; (across all 23 pairs:
4.287)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.21), sequence alignment
score = 41.1
RMSD between 16 pruned atom pairs is 1.274 angstroms; (across all 23 pairs:
4.538)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.22), sequence alignment
score = 41.1
RMSD between 17 pruned atom pairs is 1.049 angstroms; (across all 23 pairs:
4.276)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.23), sequence alignment
score = 37.5
RMSD between 16 pruned atom pairs is 0.969 angstroms; (across all 23 pairs:
4.332)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.24), sequence alignment
score = 37.5
RMSD between 18 pruned atom pairs is 1.172 angstroms; (across all 23 pairs:
4.366)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.25), sequence alignment
score = 41.1
RMSD between 18 pruned atom pairs is 1.236 angstroms; (across all 23 pairs:
4.419)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.26), sequence alignment
score = 36.3
RMSD between 14 pruned atom pairs is 1.107 angstroms; (across all 23 pairs:
5.029)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.27), sequence alignment
score = 41.1
RMSD between 17 pruned atom pairs is 1.036 angstroms; (across all 23 pairs:
4.223)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.28), sequence alignment
score = 37.5
RMSD between 16 pruned atom pairs is 1.276 angstroms; (across all 23 pairs:
4.619)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.29), sequence alignment
score = 41.1
RMSD between 18 pruned atom pairs is 1.093 angstroms; (across all 23 pairs:
4.328)
Matchmaker JR03, chain A (#3) with 1wqe, chain A (#13.30), sequence alignment
score = 36.1
RMSD between 8 pruned atom pairs is 1.139 angstroms; (across all 22 pairs:
5.650)
Matchmaker JR03, chain A (#3) with A1Pro.pdb, chain A (#15), sequence
alignment score = 72.2
RMSD between 23 pruned atom pairs is 0.593 angstroms; (across all 44 pairs:
8.662)
> hide #13.2-30 target m
> select add #13
9630 atoms, 9720 bonds, 690 residues, 31 models selected
> select subtract #13
Nothing selected
> color #15 white
> color #13 white models
> select #13:cys
1200 atoms, 1140 bonds, 120 residues, 30 models selected
> color sel byhetero
> select add #13
9630 atoms, 9720 bonds, 690 residues, 31 models selected
> select subtract #13
Nothing selected
> save /Users/leightongo/Desktop/Arah2_FABs.cxs
> save /Users/leightongo/Desktop/VBPs.cxs
> hide #!13 models
> hide #3 models
> show #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #15/A
Alignment identifier is 15/A
> select #15:trp
Nothing selected
> select #15:tyr
36 atoms, 36 bonds, 3 residues, 1 model selected
> select #15:his
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #15:cys
36 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #15:ile
Nothing selected
> select #15:asp
32 atoms, 29 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel black
> color sel byhetero
> select #15:glm
Nothing selected
> select #15:thr
35 atoms, 31 bonds, 5 residues, 1 model selected
> hide #3 models
> open
> /Users/leightongo/Downloads/A1PRO_18182/A1PRO_18182_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
A1PRO_18182_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb #16
---
Chain | Description
A | No description available
> open
> /Users/leightongo/Downloads/A1PRO_18182/A1PRO_18182_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb
Chain information for
A1PRO_18182_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb #18
---
Chain | Description
A | No description available
> open
> /Users/leightongo/Downloads/A1PRO_18182/A1PRO_18182_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
A1PRO_18182_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb #19
---
Chain | Description
A | No description available
> open
> /Users/leightongo/Downloads/A1PRO_18182/A1PRO_18182_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb
Chain information for
A1PRO_18182_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb #20
---
Chain | Description
A | No description available
> mmaker #18-20 to #15
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 A1Pro.pdb, chain A (#15) with
A1PRO_18182_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#18), sequence alignment score = 305.5
RMSD between 41 pruned atom pairs is 0.661 angstroms; (across all 59 pairs:
2.465)
Matchmaker A1Pro.pdb, chain A (#15) with
A1PRO_18182_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#19), sequence alignment score = 305.5
RMSD between 46 pruned atom pairs is 0.861 angstroms; (across all 59 pairs:
4.017)
Matchmaker A1Pro.pdb, chain A (#15) with
A1PRO_18182_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#20), sequence alignment score = 305.5
RMSD between 38 pruned atom pairs is 0.465 angstroms; (across all 59 pairs:
2.452)
> hide #19 models
> hide #20 models
> mmaker #16 to #15
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 A1Pro.pdb, chain A (#15) with
A1PRO_18182_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#16), sequence alignment score = 327.1
RMSD between 49 pruned atom pairs is 0.658 angstroms; (across all 59 pairs:
3.810)
> hide #16 models
> hide #18 models
> show #19 models
> hide #19 models
> show #20 models
> hide #20 models
> show #16 models
> close #16
> select down
35 atoms, 31 bonds, 5 residues, 1 model selected
> select down
35 atoms, 31 bonds, 5 residues, 1 model selected
> close #18-20
> select clear
> select #15/A:39
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel black
> color sel byhetero
> select #15:glu
36 atoms, 32 bonds, 4 residues, 1 model selected
> select clear
> select #15/A:25
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel black
> color sel byhetero
> select #15:glu
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #15/A:35
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:35
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> color sel black
> color sel byhetero
> select #15/A:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel black
> color sel byhetero
> show sel atoms
> save /Users/leightongo/Desktop/VBPs.cxs
——— End of log from Tue Oct 17 22:00:54 2023 ———
opened ChimeraX session
> ui mousemode right select
> select clear
> hide #15 models
> show #5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5:trp
Nothing selected
> select #5:tyr
24 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> select #5:his
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #4 models
> select #4:his
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4:tyr
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #4:trp
Nothing selected
> select #4:glu
54 atoms, 50 bonds, 6 residues, 1 model selected
> show sel atoms
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> select clear
> show #4 models
> hide #4 models
> hide #5 models
> show #!11 models
> hide #!11 models
> show #!12 models
> show #!10 models
> save /Users/leightongo/Desktop/image2.png supersample 3
> open /Users/leightongo/Downloads/cryosparc_P205_J69_003_volume_map_sharp.mrc
Opened cryosparc_P205_J69_003_volume_map_sharp.mrc as #16, grid size
110,110,110, pixel 2.68, shown at level 0.229, step 1, values float32
> select add #16
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #16,1,0,0,-4.1444,0,1,0,-108.59,0,0,1,-109.82
> view matrix models #16,1,0,0,-61.943,0,1,0,-124.92,0,0,1,-145
> volume #16 level 1.252
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.92468,0.32375,-0.20036,201.09,-0.22334,-0.88743,-0.40323,248.03,-0.30835,-0.32811,0.89289,-35.266
> select add #10
7134 atoms, 7166 bonds, 13 pseudobonds, 1085 residues, 5 models selected
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!14 models
> show #!11 models
> show #!17 models
> hide #!11 models
> hide #!14 models
> hide #!10 models
> show #!10 models
> combine #10/J,I close false
> hide #!18 models
> show #!18 models
> hide #!10 models
> select subtract #10
2 models selected
> hide #!18 models
> show #!18 models
> ui mousemode right select
> select #18/F:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
128 atoms, 127 bonds, 17 residues, 1 model selected
> select up
704 atoms, 712 bonds, 93 residues, 1 model selected
> select up
715 atoms, 712 bonds, 104 residues, 1 model selected
> select up
7134 atoms, 7166 bonds, 1085 residues, 1 model selected
> select down
715 atoms, 712 bonds, 104 residues, 1 model selected
> delete sel
> rename #18 S1
> hide #!18 models
> show #!10 models
> select #10/I:38
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
56 atoms, 57 bonds, 6 residues, 1 model selected
> select up
1014 atoms, 1038 bonds, 137 residues, 1 model selected
> select up
1018 atoms, 1041 bonds, 138 residues, 1 model selected
> select up
1596 atoms, 1635 bonds, 218 residues, 1 model selected
> select up
1636 atoms, 1635 bonds, 258 residues, 1 model selected
> select up
7134 atoms, 7166 bonds, 1085 residues, 1 model selected
> select down
1636 atoms, 1635 bonds, 258 residues, 1 model selected
Drag select of 90 residues
> select up
1114 atoms, 1134 bonds, 152 residues, 1 model selected
> select up
3194 atoms, 3271 bonds, 431 residues, 1 model selected
> select up
3291 atoms, 3271 bonds, 528 residues, 1 model selected
> select up
7134 atoms, 7166 bonds, 1085 residues, 1 model selected
> select down
3291 atoms, 3271 bonds, 528 residues, 1 model selected
> delete sel
> rename #10 Arah2
> select add #16
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.92468,0.32375,-0.20036,154.02,-0.22334,-0.88743,-0.40323,223.27,-0.30835,-0.32811,0.89289,-50.675
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.70127,0.57344,-0.42354,119.75,-0.61559,-0.18745,0.76545,-5.3063,0.35955,0.79751,0.48446,-249.32
> view matrix models
> #16,0.78951,0.54864,-0.2751,-116.16,-0.48884,0.83315,0.25865,-94.605,0.3711,-0.06973,0.92597,-192.45
> view matrix models
> #16,-0.90656,0.37657,-0.19064,142.11,0.4217,0.78906,-0.44672,-110.07,-0.017791,-0.48537,-0.87413,206.33
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.90656,0.37657,-0.19064,94.344,0.4217,0.78906,-0.44672,-158.52,-0.017791,-0.48537,-0.87413,206.74
> view matrix models
> #16,-0.90656,0.37657,-0.19064,76.559,0.4217,0.78906,-0.44672,-139.08,-0.017791,-0.48537,-0.87413,207.48
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.80827,0.58446,-0.071406,13.096,0.48933,0.59931,-0.63355,-91.803,-0.32749,-0.54703,-0.7704,245.29
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.80827,0.58446,-0.071406,12.193,0.48933,0.59931,-0.63355,-94.513,-0.32749,-0.54703,-0.7704,242.59
> view matrix models
> #16,-0.80827,0.58446,-0.071406,12.356,0.48933,0.59931,-0.63355,-94.163,-0.32749,-0.54703,-0.7704,241.09
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.77201,0.63164,-0.070943,0.083239,0.55079,0.60911,-0.57062,-114.36,-0.31721,-0.4796,-0.81814,237.14
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.77201,0.63164,-0.070943,-1.0079,0.55079,0.60911,-0.57062,-115.8,-0.31721,-0.4796,-0.81814,235.88
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.78436,0.61302,-0.094784,7.2453,0.52412,0.57321,-0.62987,-97.389,-0.33179,-0.54372,-0.7709,240.04
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.78436,0.61302,-0.094784,8.9107,0.52412,0.57321,-0.62987,-96.232,-0.33179,-0.54372,-0.7709,241.27
> transparency #16.1 30
> view matrix models
> #16,-0.78436,0.61302,-0.094784,9.5299,0.52412,0.57321,-0.62987,-95.57,-0.33179,-0.54372,-0.7709,239.85
> view matrix models
> #16,-0.78436,0.61302,-0.094784,7.5643,0.52412,0.57321,-0.62987,-93.796,-0.33179,-0.54372,-0.7709,240.73
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.76314,0.63978,-0.091073,-0.030036,0.54148,0.55613,-0.63049,-93.708,-0.35273,-0.53046,-0.77084,241.81
> view matrix models
> #16,-0.69686,0.71115,-0.09302,-19.84,0.57226,0.47315,-0.66981,-79.83,-0.43232,-0.51999,-0.73668,246.49
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.69686,0.71115,-0.09302,-22.189,0.57226,0.47315,-0.66981,-79.019,-0.43232,-0.51999,-0.73668,246.56
> select subtract #16
Nothing selected
> ui tool show "Fit in Map"
> fitmap #17 inMap #16
Fit molecule 15A1 (#17) to map cryosparc_P205_J69_003_volume_map_sharp.mrc
(#16) using 5887 atoms
average map value = 0.9836, steps = 104
shifted from previous position = 7.26
rotated from previous position = 54.3 degrees
atoms outside contour = 3801, contour level = 1.2516
Position of 15A1 (#17) relative to cryosparc_P205_J69_003_volume_map_sharp.mrc
(#16) coordinates:
Matrix rotation and translation
0.08525285 -0.97772477 0.19179738 129.29329023
-0.56170130 0.11182980 0.81974737 171.25126215
-0.82293597 -0.17761864 -0.53965546 205.49591376
Axis -0.67280668 0.68452240 0.28064258
Axis point 207.38355012 0.00000000 6.60026166
Rotation angle (degrees) 132.16642790
Shift along axis 87.90683953
> save Arah2P3415A1.pdb #12,10,17
> volume #16 level 2.617
> save Arah2P3415A1.pdb #12,#10,#17
Expected a models specifier or a keyword
> save Arah2P3415A1.pdb displayedOnly true
> save Arah2P3415A1.pdb #10,12,17
> ui mousemode right select
> select #17/Q:184
14 atoms, 13 bonds, 1 residue, 1 model selected
> open
> /Users/leightongo/Downloads/test_f61f1_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
test_f61f1_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb #19
---
Chain | Description
A | No description available
B | No description available
> mmaker #19 to #17
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 15A1, chain Q (#17) with
test_f61f1_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B
(#19), sequence alignment score = 886.2
RMSD between 81 pruned atom pairs is 0.422 angstroms; (across all 216 pairs:
7.617)
> hide #!17 models
> select add #17
5887 atoms, 5963 bonds, 1 pseudobond, 430 residues, 2 models selected
> select subtract #17
Nothing selected
> fitmap #19 inMap #16
Fit molecule test_f61f1_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
(#19) to map cryosparc_P205_J69_003_volume_map_sharp.mrc (#16) using 3611
atoms
average map value = 0.9275, steps = 88
shifted from previous position = 4.01
rotated from previous position = 13.9 degrees
atoms outside contour = 3382, contour level = 2.6167
Position of test_f61f1_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
(#19) relative to cryosparc_P205_J69_003_volume_map_sharp.mrc (#16)
coordinates:
Matrix rotation and translation
-0.81825762 -0.42284764 0.38942823 147.18375851
0.50124684 -0.85648586 0.12322172 144.71032751
0.28143576 0.29602677 0.91277712 191.44410738
Axis 0.18261221 0.11412134 0.97653935
Axis point 40.43986560 74.70750505 0.00000000
Rotation angle (degrees) 151.76119178
Shift along axis 230.34479208
> save Arah2P3415A1.pdb #10,12,19
> select add #19
3611 atoms, 3695 bonds, 1 pseudobond, 476 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.74925,-0.65818,0.073661,-29.206,0.39414,-0.53251,-0.74906,-61.53,0.53224,-0.5322,0.6584,-25.05
> ui mousemode right "translate selected models"
> view matrix models
> #19,-0.74925,-0.65818,0.073661,-36.528,0.39414,-0.53251,-0.74906,-56.361,0.53224,-0.5322,0.6584,-33.786
> view matrix models
> #19,-0.74925,-0.65818,0.073661,-38.619,0.39414,-0.53251,-0.74906,-53.803,0.53224,-0.5322,0.6584,-31.296
> fitmap #19 inMap #16
Fit molecule test_f61f1_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
(#19) to map cryosparc_P205_J69_003_volume_map_sharp.mrc (#16) using 3611
atoms
average map value = 1.068, steps = 132
shifted from previous position = 2.59
rotated from previous position = 28.6 degrees
atoms outside contour = 3352, contour level = 2.6167
Position of test_f61f1_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
(#19) relative to cryosparc_P205_J69_003_volume_map_sharp.mrc (#16)
coordinates:
Matrix rotation and translation
0.84285239 0.09823277 -0.52910318 147.41484496
-0.46506378 -0.36173751 -0.80799855 143.88501247
-0.27076841 0.92709023 -0.25920682 190.71315679
Axis 0.94173590 -0.14021365 -0.30573455
Axis point 0.00000000 9.26712587 172.92929277
Rotation angle (degrees) 112.89514992
Shift along axis 60.34360742
> save Arah2P3415A1.pdb #10,12,19
> save Ab15A1.pdb #119
No structures to save
> save /Users/leightongo/Desktop/Arah2P3415A1.pdb models #10,12,19
> volume #16 level 1.335
> open /Users/leightongo/Downloads/15A1_Fab/15A1.pdb
Chain information for 15A1.pdb #20
---
Chain | Description
A | No description available
B | No description available
> mmaker #20 to #19
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 test_f61f1_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#19) with 15A1.pdb, chain A (#20), sequence alignment score = 1223.2
RMSD between 218 pruned atom pairs is 0.508 angstroms; (across all 238 pairs:
1.819)
> close #19
Window position QRect(-646,313 488x902) outside any known screen, using
primary screen
> fitmap #20 inMap #16
Fit molecule 15A1.pdb (#20) to map cryosparc_P205_J69_003_volume_map_sharp.mrc
(#16) using 3611 atoms
average map value = 1.085, steps = 60
shifted from previous position = 0.17
rotated from previous position = 1.92 degrees
atoms outside contour = 2351, contour level = 1.3349
Position of 15A1.pdb (#20) relative to
cryosparc_P205_J69_003_volume_map_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.93727099 0.08047156 0.33918641 147.57578262
-0.34278964 0.38968435 0.85477563 144.79233034
-0.06339050 -0.91742599 0.39282465 189.85105194
Axis -0.94973826 0.21574447 -0.22682936
Axis point 0.00000000 208.38543607 -58.96418423
Rotation angle (degrees) 68.90655977
Shift along axis -151.98401533
> save /Users/leightongo/Desktop/15A1Test.pdb models #20
> save Arah2P3415A1.pdb #10,12,20
> fitmap #12 inMap #16
Fit molecule Arah2_P34.pdb (#12) to map
cryosparc_P205_J69_003_volume_map_sharp.mrc (#16) using 5887 atoms
average map value = 1.3, steps = 88
shifted from previous position = 7.4
rotated from previous position = 21.5 degrees
atoms outside contour = 3347, contour level = 1.3349
Position of Arah2_P34.pdb (#12) relative to
cryosparc_P205_J69_003_volume_map_sharp.mrc (#16) coordinates:
Matrix rotation and translation
-0.73962383 0.62449719 0.25091802 183.26378162
-0.15683468 -0.52248851 0.83809823 147.94256864
0.65449177 0.58052477 0.48438777 115.79561771
Axis -0.28108666 -0.44041494 -0.85265759
Axis point 80.09490548 26.61048138 0.00000000
Rotation angle (degrees) 152.73062850
Shift along axis -215.40313363
> fitmap #10 inMap #16
Fit molecule Arah2 (#10) to map cryosparc_P205_J69_003_volume_map_sharp.mrc
(#16) using 3843 atoms
average map value = 0.8811, steps = 272
shifted from previous position = 29
rotated from previous position = 72.4 degrees
atoms outside contour = 2704, contour level = 1.3349
Position of Arah2 (#10) relative to
cryosparc_P205_J69_003_volume_map_sharp.mrc (#16) coordinates:
Matrix rotation and translation
-0.34163397 0.88419162 0.31857717 163.07452906
-0.03084378 0.32824139 -0.94409017 154.68399204
-0.93932683 -0.33235940 -0.08486660 130.97632289
Axis 0.36598273 0.75257149 -0.54744206
Axis point 111.35455626 0.00000000 76.99211583
Rotation angle (degrees) 123.30731967
Shift along axis 104.39127502
> undo
[Repeated 1 time(s)]
> save Ab15A1.pdb #20
> show #!17 models
> select add #20
3611 atoms, 3695 bonds, 1 pseudobond, 476 residues, 2 models selected
> color #20 orchid
> hide #!17 models
> ui mousemode right translate
> ui mousemode right select
Drag select of 13 residues
> hide sel
> hide sel atoms
> hide sel cartoons
> select #20:1-20
292 atoms, 298 bonds, 40 residues, 1 model selected
> hide sel cartoons
> ui mousemode right translate
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/leightongo/Desktop/movie4.mp4
Movie saved to /Users/leightongo/Desktop/movie4.mp4
> hide #!16 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/leightongo/Desktop/movie5.mp4
Movie saved to /Users/leightongo/Desktop/movie5.mp4
> save /Users/leightongo/Desktop/image3.png supersample 3
> save /Users/leightongo/Desktop/image4.png supersample 3
> save /Users/leightongo/Desktop/image5.png supersample 3
> show #!17 models
> hide #!17 models
> show #!14 models
> show #!11 models
> show #!18 models
> ui mousemode right zoom
> hide #!14 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/leightongo/Desktop/movie6.mp4
Movie saved to /Users/leightongo/Desktop/movie6.mp4
> show #!14 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/leightongo/Desktop/movie7.mp4
Movie saved to /Users/leightongo/Desktop/movie7.mp4
> open /Users/leightongo/Downloads/cryosparc_P205_J69_003_volume_mask_fsc.mrc
Opened cryosparc_P205_J69_003_volume_mask_fsc.mrc as #19, grid size
110,110,110, pixel 2.68, shown at level 0.453, step 1, values float32
> open
> /Users/leightongo/Downloads/cryosparc_P205_J69_003_volume_mask_fsc_auto.mrc
Opened cryosparc_P205_J69_003_volume_mask_fsc_auto.mrc as #21, grid size
110,110,110, pixel 2.68, shown at level 0.807, step 1, values float32
> volume #21 level 0.9534
> select add #20
3611 atoms, 3695 bonds, 1 pseudobond, 476 residues, 2 models selected
> select subtract #20
Nothing selected
> select add #21
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #21,1,0,0,-4.0587,0,1,0,-132.96,0,0,1,-55.185
> view matrix models #21,1,0,0,-87.697,0,1,0,-180.08,0,0,1,-186.5
> close #21
> close #19
> open /Users/leightongo/Downloads/job.pdb-AF-I1KKA8-F1-model_v4.pdb
job.pdb-AF-I1KKA8-F1-model_v4.pdb title:
job.pdb - AF-I1KKA8-F1-model_v4 [more info...]
Chain information for job.pdb-AF-I1KKA8-F1-model_v4.pdb
---
Chain | Description
19.1/A | No description available
19.2/A | No description available
> hide #!14 models
> hide #!18 models
> hide #!19 models
> hide #19.1 models
> show #19.1 models
> hide #!19 models
> hide #!20 models
> show #!19 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> select #19:cys
224 atoms, 179 bonds, 45 residues, 2 models selected
> show sel atoms
> color sel yellow
> hide #19.1 models
> view matrix models
> #19.1,1,0,0,-12.138,0,1,0,8.7618,0,0,1,-24.477,#19.2,1,0,0,-12.138,0,1,0,8.7618,0,0,1,-24.477
> open 2k7h
Summary of feedback from opening 2k7h fetched from pdb
---
note | Fetching compressed mmCIF 2k7h from
http://files.rcsb.org/download/2k7h.cif
2k7h title:
NMR solution structure of soybean allergen Gly m 4 [more info...]
Chain information for 2k7h
---
Chain | Description | UniProt
21.1/A 21.2/A 21.3/A 21.4/A 21.5/A 21.6/A 21.7/A 21.8/A 21.9/A 21.10/A 21.11/A
21.12/A 21.13/A 21.14/A 21.15/A 21.16/A 21.17/A 21.18/A 21.19/A 21.20/A |
Stress-induced protein SAM22 | SAM22_SOYBN 1-157
> mmaker #21 to #10\
> matchmaker #21 to #10\
Invalid "to" argument: only initial part "#10" of atom specifier valid
> mmaker #21 to #10
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 Arah2, chain H (#10) with 2k7h, chain A (#21.1), sequence alignment
score = 37
RMSD between 7 pruned atom pairs is 1.266 angstroms; (across all 95 pairs:
17.750)
Matchmaker Arah2, chain G (#10) with 2k7h, chain A (#21.2), sequence alignment
score = 33.7
RMSD between 7 pruned atom pairs is 1.449 angstroms; (across all 79 pairs:
16.713)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.3), sequence alignment
score = 37
RMSD between 7 pruned atom pairs is 1.183 angstroms; (across all 95 pairs:
17.692)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.4), sequence alignment
score = 37
RMSD between 7 pruned atom pairs is 1.151 angstroms; (across all 95 pairs:
17.968)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.5), sequence alignment
score = 39.1
RMSD between 8 pruned atom pairs is 0.843 angstroms; (across all 95 pairs:
16.792)
Matchmaker Arah2, chain G (#10) with 2k7h, chain A (#21.6), sequence alignment
score = 32.3
RMSD between 8 pruned atom pairs is 1.234 angstroms; (across all 78 pairs:
11.868)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.7), sequence alignment
score = 34.6
RMSD between 7 pruned atom pairs is 1.121 angstroms; (across all 95 pairs:
17.970)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.8), sequence alignment
score = 31.3
RMSD between 8 pruned atom pairs is 1.090 angstroms; (across all 95 pairs:
18.168)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.9), sequence alignment
score = 34.6
RMSD between 7 pruned atom pairs is 1.235 angstroms; (across all 95 pairs:
17.877)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.10), sequence
alignment score = 32.8
RMSD between 8 pruned atom pairs is 0.974 angstroms; (across all 81 pairs:
14.571)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.11), sequence
alignment score = 37
RMSD between 7 pruned atom pairs is 0.563 angstroms; (across all 95 pairs:
22.354)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.12), sequence
alignment score = 33.4
RMSD between 9 pruned atom pairs is 1.368 angstroms; (across all 95 pairs:
19.953)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.13), sequence
alignment score = 33.4
RMSD between 7 pruned atom pairs is 1.198 angstroms; (across all 95 pairs:
17.597)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.14), sequence
alignment score = 37
RMSD between 6 pruned atom pairs is 1.159 angstroms; (across all 95 pairs:
18.490)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.15), sequence
alignment score = 37
RMSD between 8 pruned atom pairs is 1.273 angstroms; (across all 95 pairs:
18.012)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.16), sequence
alignment score = 37
RMSD between 7 pruned atom pairs is 1.242 angstroms; (across all 95 pairs:
18.003)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.17), sequence
alignment score = 37
RMSD between 8 pruned atom pairs is 1.225 angstroms; (across all 95 pairs:
18.072)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.18), sequence
alignment score = 37
RMSD between 6 pruned atom pairs is 1.245 angstroms; (across all 95 pairs:
16.962)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.19), sequence
alignment score = 37
RMSD between 8 pruned atom pairs is 1.149 angstroms; (across all 95 pairs:
17.973)
Matchmaker Arah2, chain H (#10) with 2k7h, chain A (#21.20), sequence
alignment score = 26.3
RMSD between 5 pruned atom pairs is 0.801 angstroms; (across all 89 pairs:
19.815)
> close #21.2-20
> show #!10 models
> mmaker #21 to #10
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 Arah2, chain H (#10) with 2k7h, chain A (#21.1), sequence alignment
score = 37
RMSD between 7 pruned atom pairs is 1.266 angstroms; (across all 95 pairs:
17.750)
> hide #!19 models
> select add #19
8296 atoms, 8413 bonds, 1396 residues, 3 models selected
> select subtract #19
Nothing selected
> open 4a88
Summary of feedback from opening 4a88 fetched from pdb
---
notes | Fetching compressed mmCIF 4a88 from
http://files.rcsb.org/download/4a88.cif
Fetching CCD SO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif
Fetching CCD MPD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MPD/MPD.cif
4a88 title:
Crystal Structure of native Major Birch Pollen Allergen Bet v 1 isoform a
[more info...]
Chain information for 4a88 #22
---
Chain | Description | UniProt
A | MAJOR POLLEN ALLERGEN BET V 1-A | BEV1A_BETPN 1-159
Non-standard residues in 4a88 #22
---
MPD — (4S)-2-methyl-2,4-pentanediol
SO4 — sulfate ion
> mmaker #21 to #22
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 4a88, chain A (#22) with 2k7h, chain A (#21.1), sequence alignment
score = 453.9
RMSD between 88 pruned atom pairs is 1.181 angstroms; (across all 157 pairs:
2.967)
> close #21
> close #22
> hide #!10 models
> open 6oy4
Summary of feedback from opening 6oy4 fetched from pdb
---
note | Fetching compressed mmCIF 6oy4 from
http://files.rcsb.org/download/6oy4.cif
6oy4 title:
Crystal structure of complex between recombinant Der p 2.0103 and Fab fragment
of 7A1 [more info...]
Chain information for 6oy4 #21
---
Chain | Description | UniProt
A | Der p 2 variant 3 | I2CMD6_DERPT 1-129
C | Fab fragment of IgG, LIGHT CHAIN |
D | Fab fragment of IgG, HEAVY CHAIN |
Non-standard residues in 6oy4 #21
---
SO4 — sulfate ion
> open 7mlh
Summary of feedback from opening 7mlh fetched from pdb
---
note | Fetching compressed mmCIF 7mlh from
http://files.rcsb.org/download/7mlh.cif
7mlh title:
Crystal structure of human IgE (2F10) in complex with Der p 2.0103 [more
info...]
Chain information for 7mlh #22
---
Chain | Description | UniProt
A D | IgE Light Chain |
B F | Der p 2 variant 3 | I2CMD6_DERPT 1-129
C E | IgE Heavy chain |
Non-standard residues in 7mlh #22
---
CL — chloride ion
SO4 — sulfate ion
7mlh mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> mmaker #21 to #22
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 7mlh, chain E (#22) with 6oy4, chain D (#21), sequence alignment
score = 692
RMSD between 162 pruned atom pairs is 1.185 angstroms; (across all 213 pairs:
2.191)
> select add #22
8927 atoms, 8530 bonds, 3 pseudobonds, 1699 residues, 2 models selected
> select add #21
13344 atoms, 12831 bonds, 7 pseudobonds, 2476 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> mmaker #21/A to #22/B
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 7mlh, chain B (#22) with 6oy4, chain A (#21), sequence alignment
score = 629.6
RMSD between 119 pruned atom pairs is 0.876 angstroms; (across all 122 pairs:
0.967)
> ui mousemode right select
Drag select of 315 residues, 2 pseudobonds
> select up
2856 atoms, 2916 bonds, 2 pseudobonds, 379 residues, 2 models selected
> select up
4095 atoms, 4196 bonds, 2 pseudobonds, 545 residues, 2 models selected
> select up
4312 atoms, 4216 bonds, 2 pseudobonds, 742 residues, 2 models selected
> select up
8927 atoms, 8530 bonds, 3 pseudobonds, 1699 residues, 2 models selected
> select down
4312 atoms, 4216 bonds, 2 pseudobonds, 742 residues, 2 models selected
> delete sel
Drag select of 203 residues, 1 pseudobonds
> delete sel
> hide #!22 models
> show #!22 models
> hide #!21 models
> select #22/B:75
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
49 atoms, 50 bonds, 6 residues, 1 model selected
> select up
988 atoms, 1010 bonds, 129 residues, 1 model selected
> select up
1102 atoms, 1022 bonds, 231 residues, 1 model selected
> select up
4615 atoms, 4314 bonds, 957 residues, 1 model selected
> select down
1102 atoms, 1022 bonds, 231 residues, 1 model selected
> delete sel
> show #!21 models
> select add #22
3513 atoms, 3292 bonds, 1 pseudobond, 726 residues, 2 models selected
> color (#!22 & sel) cornflower blue
> select #21/A:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
33 atoms, 32 bonds, 4 residues, 1 model selected
> select up
481 atoms, 490 bonds, 64 residues, 1 model selected
> select up
506 atoms, 513 bonds, 68 residues, 1 model selected
> select up
894 atoms, 909 bonds, 122 residues, 1 model selected
> select up
904 atoms, 909 bonds, 132 residues, 1 model selected
> select up
2897 atoms, 2739 bonds, 574 residues, 1 model selected
> select down
904 atoms, 909 bonds, 132 residues, 1 model selected
> color sel white
> select clear
Drag select of 144 residues
> select up
1273 atoms, 1298 bonds, 165 residues, 1 model selected
> select up
1777 atoms, 1826 bonds, 230 residues, 1 model selected
> select up
1993 atoms, 1830 bonds, 442 residues, 1 model selected
> select up
2897 atoms, 2739 bonds, 574 residues, 1 model selected
> select down
1993 atoms, 1830 bonds, 442 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> combine help
Expected a keyword
> help combine
> combine #21-22 close true
Remapping chain ID 'D' in 7mlh #22 to 'F'
> name BetV #21
> name #21 BetV
Not registering illegal selector name "#21"
> rename #21 BetV
> help molmap
> molmap #21 3.5
Opened BetV map 3.5 as #22, grid size 127,83,91, pixel 1.17, shown at level
0.0987, step 1, values float32
> select add #21.1
4 pseudobonds, 1 model selected
> hide #!22 models
> show #!21 atoms
> select add #21
6410 atoms, 6031 bonds, 4 pseudobonds, 1300 residues, 2 models selected
> select subtract #21
Nothing selected
> select add #21.1
4 pseudobonds, 1 model selected
> delete sel
> hide #!21 atoms
> show #!21 atoms
> style #!21 stick
Changed 6410 atom styles
> help molmap
> close #22
> select subtract #21.1
Nothing selected
> select #21:water
Nothing selected
> select #21:HOH
513 atoms, 513 residues, 1 model selected
> delete sel
> molmap #21 3.5
Opened BetV map 3.5 as #22, grid size 120,74,86, pixel 1.17, shown at level
0.102, step 1, values float32
> molmap #21 4.5
Opened BetV map 4.5 as #22, grid size 98,61,71, pixel 1.5, shown at level
0.103, step 1, values float32
> molmap #21 3.5
Opened BetV map 3.5 as #22, grid size 120,74,86, pixel 1.17, shown at level
0.102, step 1, values float32
> volume #22 level 0.1989
> ui tool show "Measure Volume and Area"
> volume #22 level 0.1891
> volume #22 level 0.143
> volume #22 level 0.146
> volume #22 level 0.142
> volume #22 level 0.141
> volume #22 level 0.1415
> select add #22
2 models selected
> transparency #22.1 50
> select subtract #22
Nothing selected
> select add #21
5897 atoms, 6031 bonds, 4 pseudobonds, 787 residues, 2 models selected
> hide sel atoms
> select subtract #21
Nothing selected
> save BetV3.5.mrc #22
> save /Users/leightongo/Desktop/Arah2_FABs.cxs includeMaps true
——— End of log from Sat Oct 28 16:20:26 2023 ———
opened ChimeraX session
> hide #!21 models
> hide #!22 models
> show #!18 models
> hide #!18 models
> show #!17 models
> show #!12 models
> hide #!12 models
> show #!11 models
> ui mousemode right translate
> hide #!11 models
> show #!10 models
> show #!12 models
> open /Users/leightongo/Downloads/cryosparc_P205_J80_007_volume_map_sharp.mrc
Opened cryosparc_P205_J80_007_volume_map_sharp.mrc as #23, grid size
440,440,440, pixel 0.67, shown at level 0.0548, step 2, values float32
> select add #23
2 models selected
> ui mousemode right "translate selected models"
> volume #23 level 0.2045
> view matrix models #23,1,0,0,-130.55,0,1,0,-176.52,0,0,1,-174.5
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.93027,-0.35198,-0.10349,230.67,0.23571,-0.78957,0.56659,-43.679,-0.28114,0.50268,0.81748,-175.38
> volume #23 level 0.3427
> view matrix models
> #23,0.43317,-0.89952,-0.056885,95.119,-0.69378,-0.29248,-0.65812,216.62,0.57535,0.32454,-0.75076,-35.702
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.43317,-0.89952,-0.056885,49,-0.69378,-0.29248,-0.65812,211.47,0.57535,0.32454,-0.75076,-10.982
> view matrix models
> #23,0.43317,-0.89952,-0.056885,44.952,-0.69378,-0.29248,-0.65812,212.59,0.57535,0.32454,-0.75076,-24.319
> view matrix models
> #23,0.43317,-0.89952,-0.056885,46.566,-0.69378,-0.29248,-0.65812,213.35,0.57535,0.32454,-0.75076,-24.329
> view matrix models
> #23,0.43317,-0.89952,-0.056885,46.37,-0.69378,-0.29248,-0.65812,215.97,0.57535,0.32454,-0.75076,-27.173
> ui mousemode right translate
> volume #23 step 1
> volume #23 level 0.265
> transparency #23.1 50
> combine #10,12,17 close false
Remapping chain ID 'P' in 15A1 #17 to 'R'
Remapping chain ID 'Q' in 15A1 #17 to 'S'
> hide #!17 models
> hide #!12 models
> hide #!10 models
> ui tool show "Fit in Map"
> fitmap #24 inMap #23
Fit molecule combination (#24) to map
cryosparc_P205_J80_007_volume_map_sharp.mrc (#23) using 15617 atoms
average map value = 0.1062, steps = 436
shifted from previous position = 4.18
rotated from previous position = 6.87 degrees
atoms outside contour = 12736, contour level = 0.26504
Position of combination (#24) relative to
cryosparc_P205_J80_007_volume_map_sharp.mrc (#23) coordinates:
Matrix rotation and translation
0.33061212 -0.74157918 0.58374304 141.63785768
-0.93792894 -0.18948703 0.29048918 113.32773957
-0.10480900 -0.64354874 -0.75819529 126.35492384
Axis -0.79364531 0.58505772 -0.16683698
Axis point 0.00000000 132.47326280 17.00183252
Rotation angle (degrees) 143.95305242
Shift along axis -67.18762673
> close #24
> show #!10 models
> fitmap #10 inMap #23
Fit molecule Arah2 (#10) to map cryosparc_P205_J80_007_volume_map_sharp.mrc
(#23) using 3843 atoms
average map value = 0.0426, steps = 172
shifted from previous position = 4.6
rotated from previous position = 5.48 degrees
atoms outside contour = 3485, contour level = 0.26504
Position of Arah2 (#10) relative to
cryosparc_P205_J80_007_volume_map_sharp.mrc (#23) coordinates:
Matrix rotation and translation
0.39442230 -0.71895246 0.57230971 144.24482770
-0.91886106 -0.31615478 0.23609426 109.93485431
0.01119790 -0.61899395 -0.78531592 124.37717323
Axis -0.82053829 0.53844003 -0.19183128
Axis point 0.00000000 120.87186535 18.83785502
Rotation angle (degrees) 148.59707539
Shift along axis -83.02450974
> ui mousemode right "translate selected models"
> select subtract #23
Nothing selected
> select add #10
3843 atoms, 3895 bonds, 7 pseudobonds, 557 residues, 3 models selected
> view matrix models
> #10,0.99674,0.0081709,0.080209,5.1108,-0.012268,0.99864,0.050725,-3.06,-0.079685,-0.051544,0.99549,-4.949
> fitmap #10 inMap #23
Fit molecule Arah2 (#10) to map cryosparc_P205_J80_007_volume_map_sharp.mrc
(#23) using 3843 atoms
average map value = 0.0394, steps = 96
shifted from previous position = 1.93
rotated from previous position = 2.74 degrees
atoms outside contour = 3482, contour level = 0.26504
Position of Arah2 (#10) relative to
cryosparc_P205_J80_007_volume_map_sharp.mrc (#23) coordinates:
Matrix rotation and translation
0.38929012 -0.72609774 0.56677621 145.16019474
-0.92044304 -0.28314374 0.26947028 110.54197952
-0.03518263 -0.62658734 -0.77855667 128.74796206
Axis -0.81694951 0.54881513 -0.17718760
Axis point 0.00000000 124.94886302 20.32632806
Rotation angle (degrees) 146.74153573
Shift along axis -80.73398144
> view matrix models
> #10,0.99858,-0.024186,0.047405,2.867,0.022279,0.99894,0.040354,-2.1907,-0.048331,-0.039241,0.99806,-2.3606
> fitmap #10 inMap #23
Fit molecule Arah2 (#10) to map cryosparc_P205_J80_007_volume_map_sharp.mrc
(#23) using 3843 atoms
average map value = 0.03941, steps = 104
shifted from previous position = 2.16
rotated from previous position = 0.0237 degrees
atoms outside contour = 3482, contour level = 0.26504
Position of Arah2 (#10) relative to
cryosparc_P205_J80_007_volume_map_sharp.mrc (#23) coordinates:
Matrix rotation and translation
0.38957424 -0.72617126 0.56648673 145.15896372
-0.92031741 -0.28334821 0.26968439 110.53725390
-0.03532405 -0.62640969 -0.77869321 128.75303671
Axis -0.81704736 0.54872354 -0.17702003
Axis point 0.00000000 124.93085834 20.35352577
Rotation angle (degrees) 146.74450743
Shift along axis -80.73922070
> select subtract #10
Nothing selected
> show #!12 models
> fitmap #12 inMap #23
Fit molecule Arah2_P34.pdb (#12) to map
cryosparc_P205_J80_007_volume_map_sharp.mrc (#23) using 5887 atoms
average map value = 0.1551, steps = 112
shifted from previous position = 3.02
rotated from previous position = 5.97 degrees
atoms outside contour = 4379, contour level = 0.26504
Position of Arah2_P34.pdb (#12) relative to
cryosparc_P205_J80_007_volume_map_sharp.mrc (#23) coordinates:
Matrix rotation and translation
0.68412898 -0.44818573 -0.57541036 112.49581533
-0.10797697 0.71799461 -0.68762251 160.73297640
0.72132414 0.53255355 0.44280719 111.76584589
Axis 0.67310473 -0.71533785 0.18767466
Axis point 5.50338601 0.00000000 213.86942763
Rotation angle (degrees) 65.00966391
Shift along axis -18.28129941
> select add #12
5887 atoms, 5963 bonds, 1 pseudobond, 430 residues, 2 models selected
> view matrix models
> #12,0.35244,-0.87028,0.34409,-53.406,-0.91778,-0.24954,0.3089,12.089,-0.18297,-0.42466,-0.88667,5.5556
> fitmap #12 inMap #23
Fit molecule Arah2_P34.pdb (#12) to map
cryosparc_P205_J80_007_volume_map_sharp.mrc (#23) using 5887 atoms
average map value = 0.2207, steps = 104
shifted from previous position = 3.28
rotated from previous position = 7.71 degrees
atoms outside contour = 3837, contour level = 0.26504
Position of Arah2_P34.pdb (#12) relative to
cryosparc_P205_J80_007_volume_map_sharp.mrc (#23) coordinates:
Matrix rotation and translation
0.71771905 -0.33938118 -0.60802943 116.45235670
-0.13293081 0.79035127 -0.59805875 160.18019974
0.68352671 0.51006400 0.52213595 115.15996858
Axis 0.64641599 -0.75342063 0.12043144
Axis point -12.60627863 0.00000000 230.90531558
Rotation angle (degrees) 58.99565104
Shift along axis -31.53752013
> hide #!10 models
> show #!10 models
> select subtract #12
Nothing selected
> show #!17 models
> fitmap #17 inMap #23
Fit molecule 15A1 (#17) to map cryosparc_P205_J80_007_volume_map_sharp.mrc
(#23) using 5887 atoms
average map value = 0.103, steps = 116
shifted from previous position = 2.28
rotated from previous position = 4.47 degrees
atoms outside contour = 4877, contour level = 0.26504
Position of 15A1 (#17) relative to cryosparc_P205_J80_007_volume_map_sharp.mrc
(#23) coordinates:
Matrix rotation and translation
0.07798930 0.91908153 -0.38627298 157.69663507
0.49788004 -0.37158377 -0.78360766 123.39698093
-0.86373210 -0.13120460 -0.48657191 203.72284388
Axis 0.71567110 0.52376163 -0.46204830
Axis point 0.00000000 -36.81881803 166.20108585
Rotation angle (degrees) 152.88370230
Shift along axis 83.35973321
> save /Users/leightongo/Desktop/Arah2_FABs.cxs includeMaps true
> ui mousemode right select
> select #10/F:131
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #10/F:131
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/F:130
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> vop zflip #23
> volume zflip #23
Expected a density maps specifier or a keyword
> vop #23 zflip
> volume #23 zflip
Expected a keyword
> volume flip #23
Opened cryosparc_P205_J80_007_volume_map_sharp.mrc z flip as #24, grid size
440,440,440, pixel 0.67, shown at step 1, values float32
> select add #10
3843 atoms, 3895 bonds, 7 pseudobonds, 557 residues, 3 models selected
> select subtract #10
Nothing selected
> select add #24
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.43317,-0.89952,-0.056885,45.746,-0.69378,-0.29248,-0.65812,206.79,0.57535,0.32454,-0.75076,-35.49
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.071352,-0.99084,-0.11462,143.78,0.59212,-0.13455,0.79453,-212.47,-0.80268,-0.011179,0.5963,37.001
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.071352,-0.99084,-0.11462,142.15,0.59212,-0.13455,0.79453,-215.74,-0.80268,-0.011179,0.5963,35.288
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.77825,-0.57491,-0.25261,208.71,0.38741,-0.75616,0.52739,-57.753,-0.49421,0.31257,0.81121,-88.2
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.77825,-0.57491,-0.25261,215.3,0.38741,-0.75616,0.52739,-52.884,-0.49421,0.31257,0.81121,-89.045
> view matrix models
> #24,-0.77825,-0.57491,-0.25261,208.14,0.38741,-0.75616,0.52739,-38.915,-0.49421,0.31257,0.81121,-86.021
> view matrix models
> #24,-0.77825,-0.57491,-0.25261,207.19,0.38741,-0.75616,0.52739,-42.297,-0.49421,0.31257,0.81121,-90.788
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.77872,-0.60535,-0.16475,199.53,0.48432,-0.74698,0.45547,-48.457,-0.39879,0.27489,0.87487,-108.66
> view matrix models
> #24,-0.72538,-0.68818,-0.015547,182.79,0.57335,-0.61654,0.53958,-92.501,-0.38091,0.38249,0.84179,-122.38
> view matrix models
> #24,-0.95175,-0.28451,0.11503,140.85,0.29998,-0.7834,0.54433,-27.378,-0.064749,0.55257,0.83095,-193.65
> view matrix models
> #24,0.97558,0.054013,-0.2129,-156.42,-0.082643,-0.8078,-0.58364,190.16,-0.20351,0.58698,-0.78361,45.416
> view matrix models
> #24,0.98559,-0.16869,-0.012425,-153.4,-0.092073,-0.47342,-0.87601,183.59,0.14189,0.86453,-0.48213,-88.966
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.98559,-0.16869,-0.012425,-146.95,-0.092073,-0.47342,-0.87601,175.92,0.14189,0.86453,-0.48213,-86.234
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.81628,-0.52806,-0.23415,-38.565,-0.52761,-0.51654,-0.6744,220.66,0.23517,0.67404,-0.70026,-42.773
> view matrix models
> #24,0.92268,-0.38442,-0.029858,-103.75,-0.31079,-0.69565,-0.64767,209.86,0.22821,0.60687,-0.76133,-23.563
> view matrix models
> #24,0.9194,-0.39226,-0.028806,-102.27,-0.3168,-0.69515,-0.64529,210.37,0.2331,0.60241,-0.7634,-23.377
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.9194,-0.39226,-0.028806,-101.87,-0.3168,-0.69515,-0.64529,210.02,0.2331,0.60241,-0.7634,-23.112
> view matrix models
> #24,0.9194,-0.39226,-0.028806,-96.613,-0.3168,-0.69515,-0.64529,208.21,0.2331,0.60241,-0.7634,-22.073
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.69121,-0.72008,-0.061016,-9.9862,-0.56207,-0.48262,-0.67168,218.47,0.45421,0.49856,-0.73833,-44.193
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.69121,-0.72008,-0.061016,-17.136,-0.56207,-0.48262,-0.67168,219.75,0.45421,0.49856,-0.73833,-46.575
> hide #!24 models
> show #!23 models
> select subtract #24
Nothing selected
> select add #23
2 models selected
> ui tool show "Hide Dust"
> surface dust #23 size 4.02
> surface dust #23 size 3.84
> surface dust #23 size 6.82
> fitmap #10 inMap #23
Fit molecule Arah2 (#10) to map cryosparc_P205_J80_007_volume_map_sharp.mrc
(#23) using 3843 atoms
average map value = 0.03942, steps = 44
shifted from previous position = 0.0219
rotated from previous position = 0.0642 degrees
atoms outside contour = 3482, contour level = 0.26504
Position of Arah2 (#10) relative to
cryosparc_P205_J80_007_volume_map_sharp.mrc (#23) coordinates:
Matrix rotation and translation
0.39029627 -0.72638307 0.56571765 145.15870769
-0.92001198 -0.28413486 0.26989876 110.52788999
-0.03530978 -0.62580750 -0.77917790 128.76332050
Axis -0.81731834 0.54842839 -0.17668344
Axis point 0.00000000 124.86337663 20.43154432
Rotation angle (degrees) 146.77321503
Shift along axis -80.77458639
> volume #23 level 0.7191
> volume #23 level 0.4622
> list name
Unknown command: list name
> list
Unknown command: list
> name list
Arah215A1 #17
BetV #21
> open /Users/leightongo/Downloads/cryosparc_P205_J81_003_volume_map_sharp.mrc
Opened cryosparc_P205_J81_003_volume_map_sharp.mrc as #25, grid size
440,440,440, pixel 0.67, shown at level 0.0379, step 2, values float32
> select subtract #23
Nothing selected
> select add #25
2 models selected
> hide #!23 models
> volume #25 level 0.1637
> view matrix models #25,1,0,0,-118.23,0,1,0,-67.869,0,0,1,-141.22
> view matrix models #25,1,0,0,-156.41,0,1,0,-90.361,0,0,1,-188.27
> view matrix models #25,1,0,0,-166.31,0,1,0,-102.97,0,0,1,-203.87
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.50725,0.85113,-0.13519,-40.781,0.84954,0.46748,-0.24443,-116.07,-0.14484,-0.23884,-0.9602,158.31
> view matrix models
> #25,0.71801,-0.5369,-0.44294,23.264,-0.69412,-0.50526,-0.51274,300.26,0.05149,0.67561,-0.73546,-39.053
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.71801,-0.5369,-0.44294,-4.3474,-0.69412,-0.50526,-0.51274,239.29,0.05149,0.67561,-0.73546,1.2935
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.70903,-0.6731,-0.21028,-19.511,-0.61634,-0.44662,-0.64858,240.2,0.34264,0.58947,-0.73152,-30.85
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.70903,-0.6731,-0.21028,-6.7275,-0.61634,-0.44662,-0.64858,231.69,0.34264,0.58947,-0.73152,-28.925
> view matrix models
> #25,0.70903,-0.6731,-0.21028,-3.5192,-0.61634,-0.44662,-0.64858,228.79,0.34264,0.58947,-0.73152,-32.164
> view matrix models
> #25,0.70903,-0.6731,-0.21028,-3.2875,-0.61634,-0.44662,-0.64858,227.22,0.34264,0.58947,-0.73152,-33.715
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.56975,-0.79565,-0.20571,34.834,-0.62316,-0.25509,-0.73932,214.62,0.53577,0.54942,-0.64116,-71.197
> transparency #25.1 50
> color #25 darkgrey models
> view matrix models
> #25,0.73227,-0.63874,-0.23619,-7.7447,-0.52489,-0.30839,-0.79334,215.91,0.4339,0.70491,-0.5611,-90.83
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.73227,-0.63874,-0.23619,-6.836,-0.52489,-0.30839,-0.79334,213.94,0.4339,0.70491,-0.5611,-85.373
> view matrix models
> #25,0.73227,-0.63874,-0.23619,-5.4528,-0.52489,-0.30839,-0.79334,213.48,0.4339,0.70491,-0.5611,-82.91
> volume #25 level 0.2788
> volume #25 step 1
> fitmap #10 inMap #25
Fit molecule Arah2 (#10) to map cryosparc_P205_J81_003_volume_map_sharp.mrc
(#25) using 3843 atoms
average map value = 0.05368, steps = 352
shifted from previous position = 7.15
rotated from previous position = 16.3 degrees
atoms outside contour = 3485, contour level = 0.2788
Position of Arah2 (#10) relative to
cryosparc_P205_J81_003_volume_map_sharp.mrc (#25) coordinates:
Matrix rotation and translation
0.52812868 -0.67750331 0.51192711 148.33821732
-0.73646517 -0.06532946 0.67331353 123.32766184
-0.42272822 -0.73261267 -0.53345995 120.89903615
Axis -0.83226085 0.55328440 -0.03490343
Axis point 0.00000000 150.24360281 5.70865057
Rotation angle (degrees) 122.36631886
Shift along axis -59.44061015
> volume #25 level 0.1566
> surface dust #25 size 4.02
> ui mousemode right "rotate selected models"
> volume #25 level 0.1322
> hide #!25 models
> show #!11 models
> show #!25 models
> hide #!11 models
> ui mousemode right select
> select clear
> select add #17
5887 atoms, 5963 bonds, 1 pseudobond, 430 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.55558,0.64733,0.52183,-4.7296,0.46488,-0.2785,0.84043,-63.098,0.68936,0.70951,-0.1462,-41.505
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.55558,0.64733,0.52183,-8.7873,0.46488,-0.2785,0.84043,-69.261,0.68936,0.70951,-0.1462,-31.829
> view matrix models
> #17,-0.55558,0.64733,0.52183,-8.7611,0.46488,-0.2785,0.84043,-70.807,0.68936,0.70951,-0.1462,-31.877
> fitmap #17 inMap #25
Fit molecule 15A1 (#17) to map cryosparc_P205_J81_003_volume_map_sharp.mrc
(#25) using 5887 atoms
average map value = 0.1033, steps = 232
shifted from previous position = 3.04
rotated from previous position = 23.6 degrees
atoms outside contour = 3744, contour level = 0.13216
Position of 15A1 (#17) relative to cryosparc_P205_J81_003_volume_map_sharp.mrc
(#25) coordinates:
Matrix rotation and translation
-0.09180213 0.95609527 -0.27830594 162.57104839
0.56048560 -0.18139661 -0.80805394 122.91470554
-0.82306030 -0.23016755 -0.51922504 204.80445020
Axis 0.65132122 0.61397895 -0.44588172
Axis point 0.00000000 -59.16057000 170.19599170
Rotation angle (degrees) 153.66451960
Shift along axis 90.03445553
> fitmap #10 inMap #25
Fit molecule Arah2 (#10) to map cryosparc_P205_J81_003_volume_map_sharp.mrc
(#25) using 3843 atoms
average map value = 0.05368, steps = 60
shifted from previous position = 0.00373
rotated from previous position = 0.0161 degrees
atoms outside contour = 3039, contour level = 0.13216
Position of Arah2 (#10) relative to
cryosparc_P205_J81_003_volume_map_sharp.mrc (#25) coordinates:
Matrix rotation and translation
0.52805134 -0.67738104 0.51216862 148.34224793
-0.73657526 -0.06518328 0.67320727 123.32972923
-0.42263301 -0.73273874 -0.53336224 120.90135323
Axis -0.83222057 0.55333643 -0.03503879
Axis point 0.00000000 150.25751914 5.68613292
Rotation angle (degrees) 122.36066964
Shift along axis -59.44687438
> fitmap #10 inMap #25
Fit molecule Arah2 (#10) to map cryosparc_P205_J81_003_volume_map_sharp.mrc
(#25) using 3843 atoms
average map value = 0.05368, steps = 84
shifted from previous position = 0.00379
rotated from previous position = 0.0149 degrees
atoms outside contour = 3038, contour level = 0.13216
Position of Arah2 (#10) relative to
cryosparc_P205_J81_003_volume_map_sharp.mrc (#25) coordinates:
Matrix rotation and translation
0.52814871 -0.67747082 0.51194943 148.34013834
-0.73647943 -0.06535712 0.67329525 123.32685280
-0.42267835 -0.73264024 -0.53346161 120.89952787
Axis -0.83226924 0.55327002 -0.03493123
Axis point 0.00000000 150.24092500 5.70627366
Rotation angle (degrees) 122.36663370
Shift along axis -59.44905303
> select subtract #17
Nothing selected
> hide #!10 models
> hide #!12 models
> hide #!17 models
> hide #!25 models
> show #1 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> show #8 models
> show #9 models
> hide #9 models
> hide #8 models
> show #15 models
> hide #1 models
> hide #15 models
> show #!10 models
> ui tool show "Show Sequence Viewer"
> sequence chain #10/F
Alignment identifier is 10/F
> select #10/F:121
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #10/F:121-128
47 atoms, 46 bonds, 8 residues, 1 model selected
> color sel tomato
> show #!11 models
> hide #!11 models
> show #!17 models
> show #!25 models
> select add #10
3843 atoms, 3895 bonds, 7 pseudobonds, 557 residues, 3 models selected
> select subtract #10
Nothing selected
> select add #25
2 models selected
> select subtract #25
Nothing selected
> select add #17
5887 atoms, 5963 bonds, 1 pseudobond, 430 residues, 2 models selected
> view matrix models
> #17,-0.23083,0.87035,0.43498,-12.233,0.5283,-0.26331,0.8072,-73.063,0.81708,0.41613,-0.39903,-39.338
> fitmap #17 inMap #25
Fit molecule 15A1 (#17) to map cryosparc_P205_J81_003_volume_map_sharp.mrc
(#25) using 5887 atoms
average map value = 0.1033, steps = 108
shifted from previous position = 1.87
rotated from previous position = 0.015 degrees
atoms outside contour = 3745, contour level = 0.13216
Position of 15A1 (#17) relative to cryosparc_P205_J81_003_volume_map_sharp.mrc
(#25) coordinates:
Matrix rotation and translation
-0.09180377 0.95609675 -0.27830033 162.57165334
0.56026963 -0.18145138 -0.80819140 122.91978945
-0.82320715 -0.23011824 -0.51901405 204.81423975
Axis 0.65130255 0.61393475 -0.44596987
Axis point 0.00000000 -59.17452144 170.22345678
Rotation angle (degrees) 153.65453925
Shift along axis 90.00708215
> select subtract #17
Nothing selected
> select add #25
2 models selected
> view matrix models
> #25,0.73227,-0.63874,-0.23619,-1.3328,-0.52489,-0.30839,-0.79334,218.04,0.4339,0.70491,-0.5611,-86.851
> view matrix models
> #25,0.73227,-0.63874,-0.23619,-0.60693,-0.52489,-0.30839,-0.79334,220.13,0.4339,0.70491,-0.5611,-87.011
> volume #25 level 0.2633
> open 6urs
Summary of feedback from opening 6urs fetched from pdb
---
note | Fetching compressed mmCIF 6urs from
http://files.rcsb.org/download/6urs.cif
6urs title:
Sleeping Beauty transposase PAI subdomain mutant - H19Y [more info...]
Chain information for 6urs
---
Chain | Description
26.1/A 26.2/A 26.3/A 26.4/A 26.5/A 26.6/A 26.7/A 26.8/A | Sleeping Beauty
transposase PAI subdomain
> close #26.2-8
> ui tool show "Show Sequence Viewer"
> sequence chain #26.1/A
Alignment identifier is 26.1/A
> select #26.1/A:14
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #26.1/A:14
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26.1/A:21
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #26.1/A:21
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cornflower blue
> color sel bynucleotide
> color sel byelement
> select #26.1/A:33
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #26.1/A:33
17 atoms, 16 bonds, 1 residue, 1 model selected
> open 2m8e
Summary of feedback from opening 2m8e fetched from pdb
---
note | Fetching compressed mmCIF 2m8e from
http://files.rcsb.org/download/2m8e.cif
2m8e title:
NMR structure of the PAI subdomain of Sleeping Beauty transposase [more
info...]
Chain information for 2m8e
---
Chain | Description
27.1/A 27.2/A 27.3/A 27.4/A 27.5/A 27.6/A 27.7/A 27.8/A 27.9/A 27.10/A 27.11/A
27.12/A 27.13/A 27.14/A | SLEEPING BEAUTY TRANSPOSASE
> close #27.2-14
> mmaker #26 to #27
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 2m8e, chain A (#27.1) with 6urs, chain A (#26.1), sequence
alignment score = 270.8
RMSD between 23 pruned atom pairs is 1.225 angstroms; (across all 57 pairs:
6.110)
> ui tool show "Show Sequence Viewer"
> sequence chain #27.1/A
Alignment identifier is 27.1/A
> select #27.1/A:16
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #27.1/A:16
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26.1/A:14
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #26.1/A:14
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #26.1/A:15
13 atoms, 12 bonds, 1 residue, 1 model selected
> select #26.1/A:15
13 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #26.1/A:16
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #26.1/A:16
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> select #27.1/A:21
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #27.1/A:21
17 atoms, 17 bonds, 1 residue, 1 model selected
> show sel atoms
> select #27.1/A:35
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #27.1/A:35
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26.1/A:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #26.1/A:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #26.1 models
> hide #!26 models
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x600003b99d50, name="Built-in Retina Display") screenTo: QScreen(0x0)
wdgScreen: QScreen(0x600003b99d50, name="Built-in Retina Display")
orgWdgScreen QScreen(0x600003b99d50, name="Built-in Retina Display")
[Repeated 9 time(s)]
Window position QRect(2447,1484 561x70) outside any known screen, using
primary screen
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x600003baf670, name="DELL P2723QE") screenTo: QScreen(0x600003baf670,
name="DELL P2723QE") wdgScreen: QScreen(0x600003baf670, name="DELL P2723QE")
orgWdgScreen QScreen(0x0)
[Repeated 88 time(s)]
Window position QRect(2447,1484 561x91) outside any known screen, using
primary screen
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x600003baf670, name="DELL P2723QE") screenTo: QScreen(0x600003baf670,
name="DELL P2723QE") wdgScreen: QScreen(0x600003baf670, name="DELL P2723QE")
orgWdgScreen QScreen(0x0)
[Repeated 55 time(s)]
Window position QRect(2447,1389 561x93) outside any known screen, using
primary screen
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x600003baf670, name="DELL P2723QE") screenTo: QScreen(0x600003baf670,
name="DELL P2723QE") wdgScreen: QScreen(0x600003baf670, name="DELL P2723QE")
orgWdgScreen QScreen(0x0)
[Repeated 60 time(s)]
> select #27.1/A:33
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #27.1/A:33
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide #!27 models
> select add #27
928 atoms, 934 bonds, 57 residues, 2 models selected
> select subtract #27
Nothing selected
> open /Users/leightongo/Downloads/cryosparc_P205_J94_004_volume_map_sharp.mrc
Opened cryosparc_P205_J94_004_volume_map_sharp.mrc as #28, grid size
440,440,440, pixel 0.67, shown at level 0.0357, step 2, values float32
> hide #!25 models
> select add #28
2 models selected
> volume #28 step 1
> volume #28 level 0.1844
> view matrix models #28,1,0,0,-161.49,0,1,0,-108.55,0,0,1,-63.777
> view matrix models #28,1,0,0,-174.45,0,1,0,-203.4,0,0,1,-192.77
> view matrix models #28,1,0,0,-143.08,0,1,0,-105.19,0,0,1,-216.56
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.94873,0.13859,0.2841,85.276,0.22707,-0.32645,0.91754,-89.526,0.2199,0.935,0.27824,-273
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.94873,0.13859,0.2841,79.255,0.22707,-0.32645,0.91754,-149.88,0.2199,0.935,0.27824,-166.53
> view matrix models
> #28,-0.94873,0.13859,0.2841,60.652,0.22707,-0.32645,0.91754,-148.46,0.2199,0.935,0.27824,-217.81
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.62086,0.45427,-0.63888,108.94,0.38602,-0.53216,-0.75352,116.78,-0.68229,-0.71445,0.15504,175.64
> view matrix models
> #28,0.59328,-0.6885,-0.41712,57.802,-0.47796,0.11567,-0.87073,170.82,0.64775,0.71595,-0.26045,-166.71
> view matrix models
> #28,0.15867,-0.97566,-0.15134,123.39,-0.55977,0.037374,-0.8278,187.78,0.81331,0.21607,-0.54022,-75.747
> view matrix models
> #28,0.5798,-0.68114,-0.44708,63.407,-0.81457,-0.47278,-0.33609,223.62,0.017556,0.55904,-0.82895,38.825
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.5798,-0.68114,-0.44708,61.28,-0.81457,-0.47278,-0.33609,212.99,0.017556,0.55904,-0.82895,29.223
> view matrix models
> #28,0.5798,-0.68114,-0.44708,54.023,-0.81457,-0.47278,-0.33609,206.96,0.017556,0.55904,-0.82895,34.292
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.84303,-0.49042,-0.22088,-48.213,-0.51724,-0.62657,-0.58298,222.92,0.14751,0.60572,-0.78189,0.72027
> view matrix models
> #28,0.15905,-0.98389,0.081682,78.981,-0.52067,-0.15388,-0.83978,194.82,0.83881,0.091034,-0.53675,-66.537
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.15905,-0.98389,0.081682,72.829,-0.52067,-0.15388,-0.83978,196.4,0.83881,0.091034,-0.53675,-68.468
> view matrix models
> #28,0.15905,-0.98389,0.081682,73.912,-0.52067,-0.15388,-0.83978,196.56,0.83881,0.091034,-0.53675,-58.149
Window position QRect(-665,861 402x98) outside any known screen, using primary
screen
> fitmap #17 inMap #28
Fit molecule 15A1 (#17) to map cryosparc_P205_J94_004_volume_map_sharp.mrc
(#28) using 5887 atoms
average map value = 0.1082, steps = 176
shifted from previous position = 5.35
rotated from previous position = 25.9 degrees
atoms outside contour = 4427, contour level = 0.18437
Position of 15A1 (#17) relative to cryosparc_P205_J94_004_volume_map_sharp.mrc
(#28) coordinates:
Matrix rotation and translation
0.08936067 0.85749024 -0.50668053 157.00941153
0.47476814 -0.48387396 -0.73516067 122.74149978
-0.87556261 -0.17486133 -0.45034834 208.32437215
Axis 0.72547116 0.47762560 -0.49554555
Axis point 0.00000000 -23.90903274 170.19669467
Rotation angle (degrees) 157.28407864
Shift along axis 69.29606660
Window position QRect(-531,-252 402x1028) outside any known screen, using
primary screen
> select subtract #28
Nothing selected
> select add #10
3843 atoms, 3895 bonds, 7 pseudobonds, 557 residues, 3 models selected
> view matrix models
> #10,0.957,-0.2813,0.070819,-0.55479,0.28523,0.95698,-0.053144,-5.9773,-0.052823,0.071059,0.99607,0.15864
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.93334,-0.35846,-0.019448,-4.1906,0.31869,0.85231,-0.41473,-15.402,0.16524,0.38088,0.90974,6.327
> view matrix models
> #10,0.52377,-0.30687,-0.79467,-28.449,0.399,0.91258,-0.089421,-5.5638,0.75264,-0.27024,0.60042,-0.55479
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.52377,-0.30687,-0.79467,-31.291,0.399,0.91258,-0.089421,-8.6392,0.75264,-0.27024,0.60042,13.678
> fitmap #10 inMap #28
Fit molecule Arah2 (#10) to map cryosparc_P205_J94_004_volume_map_sharp.mrc
(#28) using 3843 atoms
average map value = 0.07211, steps = 216
shifted from previous position = 7.21
rotated from previous position = 11.4 degrees
atoms outside contour = 3166, contour level = 0.18437
Position of Arah2 (#10) relative to
cryosparc_P205_J94_004_volume_map_sharp.mrc (#28) coordinates:
Matrix rotation and translation
0.54183642 -0.71675790 0.43894352 152.60294662
-0.37048892 0.26509006 0.89020516 147.23441884
-0.75442114 -0.64496928 -0.12191541 129.07445515
Axis -0.77728787 0.60422311 0.17532254
Axis point 0.00000000 204.44207430 -1.38413405
Rotation angle (degrees) 99.06149567
Shift along axis -7.02431998
> volume #28 level 0.2551
> show #!12 models
> select subtract #10
Nothing selected
> select add #12
5887 atoms, 5963 bonds, 1 pseudobond, 430 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.27613,-0.54595,0.79101,-37.724,-0.96087,-0.17539,0.21438,16.3,0.021695,-0.81926,-0.57302,-3.6445
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.27613,-0.54595,0.79101,-43.331,-0.96087,-0.17539,0.21438,23.411,0.021695,-0.81926,-0.57302,-6.0809
> fitmap #12 inMap #28
Fit molecule Arah2_P34.pdb (#12) to map
cryosparc_P205_J94_004_volume_map_sharp.mrc (#28) using 5887 atoms
average map value = 0.1133, steps = 84
shifted from previous position = 3.81
rotated from previous position = 6.72 degrees
atoms outside contour = 4693, contour level = 0.25507
Position of Arah2_P34.pdb (#12) relative to
cryosparc_P205_J94_004_volume_map_sharp.mrc (#28) coordinates:
Matrix rotation and translation
0.63301614 -0.60453441 -0.48355838 110.64032273
-0.18511376 0.48831409 -0.85280845 149.64832317
0.75168042 0.62935482 0.19720306 111.11339844
Axis 0.75066340 -0.62560487 0.21242176
Axis point 0.00000000 36.18717029 163.32757246
Rotation angle (degrees) 80.83566788
Shift along axis 13.03582501
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.58017,-0.52612,0.62177,-55.25,-0.70313,-0.70883,0.056303,6.6901,0.4111,-0.46985,-0.78118,-16.309
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.58017,-0.52612,0.62177,-59.062,-0.70313,-0.70883,0.056303,2.6119,0.4111,-0.46985,-0.78118,-14.422
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.3746,-0.718,0.58665,-57.13,-0.72087,-0.62346,-0.30274,0.17523,0.58312,-0.30949,-0.75112,-16.033
> fitmap #12 inMap #28
Fit molecule Arah2_P34.pdb (#12) to map
cryosparc_P205_J94_004_volume_map_sharp.mrc (#28) using 5887 atoms
average map value = 0.1134, steps = 92
shifted from previous position = 2.57
rotated from previous position = 6.62 degrees
atoms outside contour = 4544, contour level = 0.25507
Position of Arah2_P34.pdb (#12) relative to
cryosparc_P205_J94_004_volume_map_sharp.mrc (#28) coordinates:
Matrix rotation and translation
0.89308164 -0.14873980 -0.42459588 116.62162623
-0.15670002 0.78182937 -0.60347986 160.20609660
0.42172300 0.60549097 0.67492992 129.79700587
Axis 0.81920749 -0.57347187 -0.00539390
Axis point 0.00000000 -58.92172231 289.58807914
Rotation angle (degrees) 47.55202606
Shift along axis 2.96350768
> ui mousemode right translate
> select subtract #12
Nothing selected
> select add #10
3843 atoms, 3895 bonds, 7 pseudobonds, 557 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.70202,-0.022675,-0.7118,-22.528,0.21705,0.95875,0.18353,-5.4718,0.67828,-0.28334,0.67798,14.558
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.70202,-0.022675,-0.7118,-23.661,0.21705,0.95875,0.18353,-6.9138,0.67828,-0.28334,0.67798,14.202
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.82291,-0.36002,-0.43955,-20.19,0.41158,0.91105,0.024344,-8.0673,0.39169,-0.20095,0.89789,15.737
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.82291,-0.36002,-0.43955,-25.557,0.41158,0.91105,0.024344,-6.8769,0.39169,-0.20095,0.89789,7.2677
> view matrix models
> #10,0.82291,-0.36002,-0.43955,-26.614,0.41158,0.91105,0.024344,-3.9614,0.39169,-0.20095,0.89789,3.8515
> select subtract #10
Nothing selected
> select add #28
2 models selected
> transparency #28.1 50
> select subtract #28
Nothing selected
> select add #10
3843 atoms, 3895 bonds, 7 pseudobonds, 557 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.29704,-0.61341,0.73177,-21.725,0.12355,0.73523,0.66646,3.6531,-0.94684,0.28837,-0.14261,-35.819
> view matrix models
> #10,-0.8244,0.027054,0.56536,-25.118,0.41117,0.71508,0.56534,5.8236,-0.38898,0.69852,-0.60064,-31.173
> view matrix models
> #10,-0.40889,-0.1804,0.89457,-13.47,0.47683,0.79358,0.37798,3.6905,-0.7781,0.58111,-0.23846,-30.951
> view matrix models
> #10,0.15305,0.22121,-0.96314,-41.621,0.017264,0.97388,0.22642,-4.939,0.98807,-0.05128,0.14523,-1.5525
> view matrix models
> #10,0.78401,-0.3326,-0.52413,-28.845,0.53282,0.79377,0.2933,2.6529,0.31849,-0.50922,0.79954,-4.1814
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.78401,-0.3326,-0.52413,-21.505,0.53282,0.79377,0.2933,2.2772,0.31849,-0.50922,0.79954,-1.6802
> select subtract #10
Nothing selected
> select add #12
5887 atoms, 5963 bonds, 1 pseudobond, 430 residues, 2 models selected
> view matrix models
> #12,0.33066,-0.74343,0.58136,-54.879,-0.79504,-0.55134,-0.25285,3.694,0.5085,-0.37859,-0.77336,-17.47
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.45922,-0.66895,0.58448,-57.131,-0.77463,-0.62361,-0.10512,3.6663,0.43481,-0.40449,-0.80457,-16.245
> fitmap #12 inMap #28
Fit molecule Arah2_P34.pdb (#12) to map
cryosparc_P205_J94_004_volume_map_sharp.mrc (#28) using 5887 atoms
average map value = 0.1169, steps = 60
shifted from previous position = 2.13
rotated from previous position = 3.4 degrees
atoms outside contour = 4571, contour level = 0.25507
Position of Arah2_P34.pdb (#12) relative to
cryosparc_P205_J94_004_volume_map_sharp.mrc (#28) coordinates:
Matrix rotation and translation
0.82845917 -0.16565340 -0.53499005 113.57252926
-0.29100997 0.68884174 -0.66393543 159.61460002
0.47850663 0.70573084 0.52247047 127.63518939
Axis 0.80169094 -0.59321831 -0.07337351
Axis point 0.00000000 -18.74832320 237.57686634
Rotation angle (degrees) 58.67541599
Shift along axis -13.00127779
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> select subtract #12
Nothing selected
> select add #10
3843 atoms, 3895 bonds, 7 pseudobonds, 557 residues, 3 models selected
> view matrix models
> #10,0.80122,-0.45136,-0.39283,-19.88,0.56303,0.79095,0.23958,1.4866,0.20258,-0.41313,0.88785,-0.15748
> view matrix models
> #10,0.8242,-0.49522,-0.27467,-17.37,0.5398,0.83366,0.11673,-1.153,0.17117,-0.24448,0.95443,3.3359
> view matrix models
> #10,0.82459,-0.44473,-0.34968,-18.381,0.5071,0.85506,0.10832,-1.5866,0.25082,-0.26664,0.93059,3.7923
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.82459,-0.44473,-0.34968,-20.232,0.5071,0.85506,0.10832,-1.1459,0.25082,-0.26664,0.93059,4.3826
> volume #28 level 0.1394
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.82459,-0.44473,-0.34968,-20.506,0.5071,0.85506,0.10832,-1.5996,0.25082,-0.26664,0.93059,1.0105
> select subtract #10
Nothing selected
> select add #12
5887 atoms, 5963 bonds, 1 pseudobond, 430 residues, 2 models selected
> view matrix models
> #12,0.45717,-0.64644,0.61083,-56.784,-0.78841,-0.61241,-0.058037,5.3638,0.41159,-0.45505,-0.78964,-12.763
> view matrix models
> #12,0.45717,-0.64644,0.61083,-56.468,-0.78841,-0.61241,-0.058037,7.6405,0.41159,-0.45505,-0.78964,-12.319
> fitmap #12 inMap #28
Fit molecule Arah2_P34.pdb (#12) to map
cryosparc_P205_J94_004_volume_map_sharp.mrc (#28) using 5887 atoms
average map value = 0.1784, steps = 132
shifted from previous position = 1.93
rotated from previous position = 16.6 degrees
atoms outside contour = 2849, contour level = 0.1394
Position of Arah2_P34.pdb (#12) relative to
cryosparc_P205_J94_004_volume_map_sharp.mrc (#28) coordinates:
Matrix rotation and translation
0.71123463 -0.32467772 -0.62348190 117.09966466
-0.14915138 0.79704904 -0.58520654 161.06302541
0.68694917 0.50921234 0.51846275 115.02600943
Axis 0.63765028 -0.76350724 0.10226836
Axis point -11.34890209 -0.00000000 230.44290157
Rotation angle (degrees) 59.11122000
Shift along axis -36.54063140
> select subtract #12
Nothing selected
> fitmap #10 inMap #28
Fit molecule Arah2 (#10) to map cryosparc_P205_J94_004_volume_map_sharp.mrc
(#28) using 3843 atoms
average map value = 0.0436, steps = 276
shifted from previous position = 4.51
rotated from previous position = 12.9 degrees
atoms outside contour = 3176, contour level = 0.1394
Position of Arah2 (#10) relative to
cryosparc_P205_J94_004_volume_map_sharp.mrc (#28) coordinates:
Matrix rotation and translation
0.27238167 -0.77828360 0.56575866 141.28832755
-0.82269087 0.11655091 0.55641318 129.00401910
-0.49898694 -0.61700123 -0.60854048 125.35700304
Axis -0.74027570 0.67171946 -0.02801535
Axis point 0.00000000 170.08908261 12.31607676
Rotation angle (degrees) 127.57532863
Shift along axis -21.44972584
> fitmap #17 inMap #28
Fit molecule 15A1 (#17) to map cryosparc_P205_J94_004_volume_map_sharp.mrc
(#28) using 5887 atoms
average map value = 0.1082, steps = 44
shifted from previous position = 0.00719
rotated from previous position = 0.0417 degrees
atoms outside contour = 3848, contour level = 0.1394
Position of 15A1 (#17) relative to cryosparc_P205_J94_004_volume_map_sharp.mrc
(#28) coordinates:
Matrix rotation and translation
0.08878864 0.85776141 -0.50632197 157.03094507
0.47484803 -0.48329833 -0.73548765 122.75251395
-0.87557748 -0.17512304 -0.45021772 208.32149938
Axis 0.72525464 0.47791077 -0.49558753
Axis point 0.00000000 -23.98307430 170.23028367
Rotation angle (degrees) 157.27412290
Shift along axis 69.31063228
Window position QRect(-751,1171 402x98) outside any known screen, using
primary screen
> surface dust #28 size 4.02
> save /Users/leightongo/Desktop/Arah2_FABs.cxs includeMaps true
> ui mousemode right "tape measure"
> marker segment #29 position -39.61,-96.52,-11.61 toPosition
> -48.9,15.04,48.17 color yellow radius 0.1 label 126.9 labelHeight 12.69
> labelColor yellow
> marker delete #29
> ui mousemode right translate
> hide #!28 models
> show #!23 models
> select add #23
2 models selected
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view matrix models
> #23,0.43317,-0.89952,-0.056885,43.853,-0.69378,-0.29248,-0.65812,211.18,0.57535,0.32454,-0.75076,-26.995
> view matrix models
> #23,0.43317,-0.89952,-0.056885,47.534,-0.69378,-0.29248,-0.65812,206.92,0.57535,0.32454,-0.75076,-22.589
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.21495,-0.97491,-0.057846,90.299,-0.68036,-0.10699,-0.72502,188.02,0.70064,0.1952,-0.68629,-31.609
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.21495,-0.97491,-0.057846,92.25,-0.68036,-0.10699,-0.72502,191.86,0.70064,0.1952,-0.68629,-34.57
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.13926,-0.95901,-0.24678,128.82,-0.58026,0.12291,-0.8051,155.87,0.80244,0.25532,-0.53936,-79.727
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view matrix models
> #23,0.13926,-0.95901,-0.24678,130.27,-0.58026,0.12291,-0.8051,154.63,0.80244,0.25532,-0.53936,-77.544
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.071139,-0.96608,-0.24826,141.42,-0.55637,0.16815,-0.81374,145.89,0.82788,0.19601,-0.52553,-74.707
> view matrix models
> #23,-0.014058,-0.99618,-0.086137,134.25,-0.48391,0.082163,-0.87125,156.27,0.875,0.029434,-0.48322,-63.712
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.014058,-0.99618,-0.086137,133.64,-0.48391,0.082163,-0.87125,155.78,0.875,0.029434,-0.48322,-64.514
> view matrix models
> #23,-0.014058,-0.99618,-0.086137,136.28,-0.48391,0.082163,-0.87125,156.19,0.875,0.029434,-0.48322,-66.444
> select subtract #23
Nothing selected
> select add #23
2 models selected
> select subtract #23
Nothing selected
> hide #!23 models
> show #!23 models
> volume #23 level 0.4048
> volume #23 level 0.3147
> hide #!23 models
> show #!28 models
> volume #28 level 0.2204
> ui mousemode right translate
> open
> /Users/leightongo/Downloads/cryosparc_P205_J108_series_000/J108_series_000_frame_000.mrc
Opened J108_series_000_frame_000.mrc as #29, grid size 440,440,440, pixel
0.67, shown at level 0.000448, step 2, values float32
> select add #29
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #29,1,0,0,-105.45,0,1,0,-202.49,0,0,1,-136.33
> ui mousemode right "rotate selected models"
> view matrix models
> #29,-0.5158,-0.79186,0.32697,181.5,0.27345,0.20952,0.93879,-275.28,-0.8119,0.57364,0.10846,39.852
> volume #29 level 0.002694
> volume #29 step 1
> volume #29 level 0.002901
> view matrix models
> #29,0.24994,-0.96375,-0.093346,158.39,-0.014983,0.092544,-0.9956,87.074,0.96815,0.25024,0.0086909,-162.11
> view matrix models
> #29,0.11578,-0.98061,0.15813,141.43,-0.32337,-0.18774,-0.92746,162.82,0.93916,0.056252,-0.33883,-75.35
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.11578,-0.98061,0.15813,125.7,-0.32337,-0.18774,-0.92746,210.99,0.93916,0.056252,-0.33883,-117.41
> view matrix models
> #29,0.11578,-0.98061,0.15813,95.132,-0.32337,-0.18774,-0.92746,178.11,0.93916,0.056252,-0.33883,-83.883
> view matrix models
> #29,0.11578,-0.98061,0.15813,71.927,-0.32337,-0.18774,-0.92746,189.62,0.93916,0.056252,-0.33883,-99.385
> view matrix models
> #29,0.11578,-0.98061,0.15813,68.559,-0.32337,-0.18774,-0.92746,189,0.93916,0.056252,-0.33883,-97.725
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.64234,-0.7663,0.013394,-18.057,-0.46931,-0.40709,-0.7836,219.95,0.60592,0.49705,-0.62113,-67.916
> hide #!28 models
> view matrix models
> #29,0.68987,-0.60923,-0.39104,15.392,-0.68711,-0.38095,-0.61868,222.72,0.22796,0.6955,-0.68141,-31.086
> view matrix models
> #29,0.079184,-0.99329,0.08432,87.378,-0.59146,-0.1149,-0.7981,198.04,0.80244,0.013325,-0.59659,-30.88
> transparency #29.1 50
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.079184,-0.99329,0.08432,85.081,-0.59146,-0.1149,-0.7981,192.69,0.80244,0.013325,-0.59659,-32.259
> close #29
> open
> /Users/leightongo/Downloads/cryosparc_P205_J109_series_000/J109_series_000_frame_000.mrc
Opened J109_series_000_frame_000.mrc as #29, grid size 440,440,440, pixel
0.67, shown at level 0.00132, step 2, values float32
> open
> /Users/leightongo/Downloads/cryosparc_P205_J109_series_000/J109_series_000_frame_001.mrc
Opened J109_series_000_frame_001.mrc as #30, grid size 440,440,440, pixel
0.67, shown at level 0.00126, step 2, values float32
> open
> /Users/leightongo/Downloads/cryosparc_P205_J109_series_000/J109_series_000_frame_002.mrc
Opened J109_series_000_frame_002.mrc as #31, grid size 440,440,440, pixel
0.67, shown at level 0.00103, step 2, values float32
> open
> /Users/leightongo/Downloads/cryosparc_P205_J109_series_000/J109_series_000_frame_003.mrc
Opened J109_series_000_frame_003.mrc as #32, grid size 440,440,440, pixel
0.67, shown at level 0.000994, step 2, values float32
> open
> /Users/leightongo/Downloads/cryosparc_P205_J109_series_000/J109_series_000_frame_004.mrc
Opened J109_series_000_frame_004.mrc as #33, grid size 440,440,440, pixel
0.67, shown at level 0.00105, step 2, values float32
> open
> /Users/leightongo/Downloads/cryosparc_P205_J109_series_000/J109_series_000_frame_005.mrc
Opened J109_series_000_frame_005.mrc as #34, grid size 440,440,440, pixel
0.67, shown at level 0.000977, step 2, values float32
> open
> /Users/leightongo/Downloads/cryosparc_P205_J109_series_000/J109_series_000_frame_006.mrc
Opened J109_series_000_frame_006.mrc as #35, grid size 440,440,440, pixel
0.67, shown at level 0.000893, step 2, values float32
> open
> /Users/leightongo/Downloads/cryosparc_P205_J109_series_000/J109_series_000_frame_007.mrc
Opened J109_series_000_frame_007.mrc as #36, grid size 440,440,440, pixel
0.67, shown at level 0.000899, step 2, values float32
> open
> /Users/leightongo/Downloads/cryosparc_P205_J109_series_000/J109_series_000_frame_008.mrc
Opened J109_series_000_frame_008.mrc as #37, grid size 440,440,440, pixel
0.67, shown at level 0.000845, step 2, values float32
> open
> /Users/leightongo/Downloads/cryosparc_P205_J109_series_000/J109_series_000_frame_009.mrc
Opened J109_series_000_frame_009.mrc as #38, grid size 440,440,440, pixel
0.67, shown at level 0.000958, step 2, values float32
> select add #29
2 models selected
> select add #30
4 models selected
> select add #31
6 models selected
> select add #32
8 models selected
> select add #33
10 models selected
> select add #34
12 models selected
> select add #35
14 models selected
> select add #36
16 models selected
> select add #37
18 models selected
> select add #38
20 models selected
> view matrix models
> #29,1,0,0,-119.94,0,1,0,-154.65,0,0,1,-165.11,#30,1,0,0,-119.94,0,1,0,-154.65,0,0,1,-165.11,#31,1,0,0,-119.94,0,1,0,-154.65,0,0,1,-165.11,#32,1,0,0,-119.94,0,1,0,-154.65,0,0,1,-165.11,#33,1,0,0,-119.94,0,1,0,-154.65,0,0,1,-165.11,#34,1,0,0,-119.94,0,1,0,-154.65,0,0,1,-165.11,#35,1,0,0,-119.94,0,1,0,-154.65,0,0,1,-165.11,#36,1,0,0,-119.94,0,1,0,-154.65,0,0,1,-165.11,#37,1,0,0,-119.94,0,1,0,-154.65,0,0,1,-165.11,#38,1,0,0,-119.94,0,1,0,-154.65,0,0,1,-165.11
> ui mousemode right "rotate selected models"
> view matrix models
> #29,-0.94695,-0.2402,0.2135,167.47,0.29964,-0.41978,0.85674,-127.93,-0.11616,0.87526,0.46949,-191.35,#30,-0.94695,-0.2402,0.2135,167.47,0.29964,-0.41978,0.85674,-127.93,-0.11616,0.87526,0.46949,-191.35,#31,-0.94695,-0.2402,0.2135,167.47,0.29964,-0.41978,0.85674,-127.93,-0.11616,0.87526,0.46949,-191.35,#32,-0.94695,-0.2402,0.2135,167.47,0.29964,-0.41978,0.85674,-127.93,-0.11616,0.87526,0.46949,-191.35,#33,-0.94695,-0.2402,0.2135,167.47,0.29964,-0.41978,0.85674,-127.93,-0.11616,0.87526,0.46949,-191.35,#34,-0.94695,-0.2402,0.2135,167.47,0.29964,-0.41978,0.85674,-127.93,-0.11616,0.87526,0.46949,-191.35,#35,-0.94695,-0.2402,0.2135,167.47,0.29964,-0.41978,0.85674,-127.93,-0.11616,0.87526,0.46949,-191.35,#36,-0.94695,-0.2402,0.2135,167.47,0.29964,-0.41978,0.85674,-127.93,-0.11616,0.87526,0.46949,-191.35,#37,-0.94695,-0.2402,0.2135,167.47,0.29964,-0.41978,0.85674,-127.93,-0.11616,0.87526,0.46949,-191.35,#38,-0.94695,-0.2402,0.2135,167.47,0.29964,-0.41978,0.85674,-127.93,-0.11616,0.87526,0.46949,-191.35
> ui mousemode right "translate selected models"
> view matrix models
> #29,-0.94695,-0.2402,0.2135,165.98,0.29964,-0.41978,0.85674,-149.43,-0.11616,0.87526,0.46949,-240.74,#30,-0.94695,-0.2402,0.2135,165.98,0.29964,-0.41978,0.85674,-149.43,-0.11616,0.87526,0.46949,-240.74,#31,-0.94695,-0.2402,0.2135,165.98,0.29964,-0.41978,0.85674,-149.43,-0.11616,0.87526,0.46949,-240.74,#32,-0.94695,-0.2402,0.2135,165.98,0.29964,-0.41978,0.85674,-149.43,-0.11616,0.87526,0.46949,-240.74,#33,-0.94695,-0.2402,0.2135,165.98,0.29964,-0.41978,0.85674,-149.43,-0.11616,0.87526,0.46949,-240.74,#34,-0.94695,-0.2402,0.2135,165.98,0.29964,-0.41978,0.85674,-149.43,-0.11616,0.87526,0.46949,-240.74,#35,-0.94695,-0.2402,0.2135,165.98,0.29964,-0.41978,0.85674,-149.43,-0.11616,0.87526,0.46949,-240.74,#36,-0.94695,-0.2402,0.2135,165.98,0.29964,-0.41978,0.85674,-149.43,-0.11616,0.87526,0.46949,-240.74,#37,-0.94695,-0.2402,0.2135,165.98,0.29964,-0.41978,0.85674,-149.43,-0.11616,0.87526,0.46949,-240.74,#38,-0.94695,-0.2402,0.2135,165.98,0.29964,-0.41978,0.85674,-149.43,-0.11616,0.87526,0.46949,-240.74
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.59882,-0.76985,-0.2208,85.09,-0.50404,-0.14802,-0.8509,200.1,0.62238,0.62083,-0.47667,-162.69,#30,0.59882,-0.76985,-0.2208,85.09,-0.50404,-0.14802,-0.8509,200.1,0.62238,0.62083,-0.47667,-162.69,#31,0.59882,-0.76985,-0.2208,85.09,-0.50404,-0.14802,-0.8509,200.1,0.62238,0.62083,-0.47667,-162.69,#32,0.59882,-0.76985,-0.2208,85.09,-0.50404,-0.14802,-0.8509,200.1,0.62238,0.62083,-0.47667,-162.69,#33,0.59882,-0.76985,-0.2208,85.09,-0.50404,-0.14802,-0.8509,200.1,0.62238,0.62083,-0.47667,-162.69,#34,0.59882,-0.76985,-0.2208,85.09,-0.50404,-0.14802,-0.8509,200.1,0.62238,0.62083,-0.47667,-162.69,#35,0.59882,-0.76985,-0.2208,85.09,-0.50404,-0.14802,-0.8509,200.1,0.62238,0.62083,-0.47667,-162.69,#36,0.59882,-0.76985,-0.2208,85.09,-0.50404,-0.14802,-0.8509,200.1,0.62238,0.62083,-0.47667,-162.69,#37,0.59882,-0.76985,-0.2208,85.09,-0.50404,-0.14802,-0.8509,200.1,0.62238,0.62083,-0.47667,-162.69,#38,0.59882,-0.76985,-0.2208,85.09,-0.50404,-0.14802,-0.8509,200.1,0.62238,0.62083,-0.47667,-162.69
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.59882,-0.76985,-0.2208,16.358,-0.50404,-0.14802,-0.8509,199.01,0.62238,0.62083,-0.47667,-121.02,#30,0.59882,-0.76985,-0.2208,16.358,-0.50404,-0.14802,-0.8509,199.01,0.62238,0.62083,-0.47667,-121.02,#31,0.59882,-0.76985,-0.2208,16.358,-0.50404,-0.14802,-0.8509,199.01,0.62238,0.62083,-0.47667,-121.02,#32,0.59882,-0.76985,-0.2208,16.358,-0.50404,-0.14802,-0.8509,199.01,0.62238,0.62083,-0.47667,-121.02,#33,0.59882,-0.76985,-0.2208,16.358,-0.50404,-0.14802,-0.8509,199.01,0.62238,0.62083,-0.47667,-121.02,#34,0.59882,-0.76985,-0.2208,16.358,-0.50404,-0.14802,-0.8509,199.01,0.62238,0.62083,-0.47667,-121.02,#35,0.59882,-0.76985,-0.2208,16.358,-0.50404,-0.14802,-0.8509,199.01,0.62238,0.62083,-0.47667,-121.02,#36,0.59882,-0.76985,-0.2208,16.358,-0.50404,-0.14802,-0.8509,199.01,0.62238,0.62083,-0.47667,-121.02,#37,0.59882,-0.76985,-0.2208,16.358,-0.50404,-0.14802,-0.8509,199.01,0.62238,0.62083,-0.47667,-121.02,#38,0.59882,-0.76985,-0.2208,16.358,-0.50404,-0.14802,-0.8509,199.01,0.62238,0.62083,-0.47667,-121.02
> ui mousemode right "rotate selected models"
> view matrix models
> #29,-0.072008,-0.99576,0.057259,103.98,-0.39448,-0.024294,-0.91858,175.55,0.91608,-0.088733,-0.39106,-74.549,#30,-0.072008,-0.99576,0.057259,103.98,-0.39448,-0.024294,-0.91858,175.55,0.91608,-0.088733,-0.39106,-74.549,#31,-0.072008,-0.99576,0.057259,103.98,-0.39448,-0.024294,-0.91858,175.55,0.91608,-0.088733,-0.39106,-74.549,#32,-0.072008,-0.99576,0.057259,103.98,-0.39448,-0.024294,-0.91858,175.55,0.91608,-0.088733,-0.39106,-74.549,#33,-0.072008,-0.99576,0.057259,103.98,-0.39448,-0.024294,-0.91858,175.55,0.91608,-0.088733,-0.39106,-74.549,#34,-0.072008,-0.99576,0.057259,103.98,-0.39448,-0.024294,-0.91858,175.55,0.91608,-0.088733,-0.39106,-74.549,#35,-0.072008,-0.99576,0.057259,103.98,-0.39448,-0.024294,-0.91858,175.55,0.91608,-0.088733,-0.39106,-74.549,#36,-0.072008,-0.99576,0.057259,103.98,-0.39448,-0.024294,-0.91858,175.55,0.91608,-0.088733,-0.39106,-74.549,#37,-0.072008,-0.99576,0.057259,103.98,-0.39448,-0.024294,-0.91858,175.55,0.91608,-0.088733,-0.39106,-74.549,#38,-0.072008,-0.99576,0.057259,103.98,-0.39448,-0.024294,-0.91858,175.55,0.91608,-0.088733,-0.39106,-74.549
> view matrix models
> #29,0.48941,-0.87159,0.028525,7.7577,-0.38897,-0.24745,-0.8874,202.32,0.7805,0.4232,-0.46013,-118.27,#30,0.48941,-0.87159,0.028525,7.7577,-0.38897,-0.24745,-0.8874,202.32,0.7805,0.4232,-0.46013,-118.27,#31,0.48941,-0.87159,0.028525,7.7577,-0.38897,-0.24745,-0.8874,202.32,0.7805,0.4232,-0.46013,-118.27,#32,0.48941,-0.87159,0.028525,7.7577,-0.38897,-0.24745,-0.8874,202.32,0.7805,0.4232,-0.46013,-118.27,#33,0.48941,-0.87159,0.028525,7.7577,-0.38897,-0.24745,-0.8874,202.32,0.7805,0.4232,-0.46013,-118.27,#34,0.48941,-0.87159,0.028525,7.7577,-0.38897,-0.24745,-0.8874,202.32,0.7805,0.4232,-0.46013,-118.27,#35,0.48941,-0.87159,0.028525,7.7577,-0.38897,-0.24745,-0.8874,202.32,0.7805,0.4232,-0.46013,-118.27,#36,0.48941,-0.87159,0.028525,7.7577,-0.38897,-0.24745,-0.8874,202.32,0.7805,0.4232,-0.46013,-118.27,#37,0.48941,-0.87159,0.028525,7.7577,-0.38897,-0.24745,-0.8874,202.32,0.7805,0.4232,-0.46013,-118.27,#38,0.48941,-0.87159,0.028525,7.7577,-0.38897,-0.24745,-0.8874,202.32,0.7805,0.4232,-0.46013,-118.27
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.48941,-0.87159,0.028525,13.432,-0.38897,-0.24745,-0.8874,203.12,0.7805,0.4232,-0.46013,-111.15,#30,0.48941,-0.87159,0.028525,13.432,-0.38897,-0.24745,-0.8874,203.12,0.7805,0.4232,-0.46013,-111.15,#31,0.48941,-0.87159,0.028525,13.432,-0.38897,-0.24745,-0.8874,203.12,0.7805,0.4232,-0.46013,-111.15,#32,0.48941,-0.87159,0.028525,13.432,-0.38897,-0.24745,-0.8874,203.12,0.7805,0.4232,-0.46013,-111.15,#33,0.48941,-0.87159,0.028525,13.432,-0.38897,-0.24745,-0.8874,203.12,0.7805,0.4232,-0.46013,-111.15,#34,0.48941,-0.87159,0.028525,13.432,-0.38897,-0.24745,-0.8874,203.12,0.7805,0.4232,-0.46013,-111.15,#35,0.48941,-0.87159,0.028525,13.432,-0.38897,-0.24745,-0.8874,203.12,0.7805,0.4232,-0.46013,-111.15,#36,0.48941,-0.87159,0.028525,13.432,-0.38897,-0.24745,-0.8874,203.12,0.7805,0.4232,-0.46013,-111.15,#37,0.48941,-0.87159,0.028525,13.432,-0.38897,-0.24745,-0.8874,203.12,0.7805,0.4232,-0.46013,-111.15,#38,0.48941,-0.87159,0.028525,13.432,-0.38897,-0.24745,-0.8874,203.12,0.7805,0.4232,-0.46013,-111.15
> volume #38 step 1
> volume #37 step 1
> volume #36 step 1
> volume #35 step 1
> volume #34 step 1
> volume #33 step 1
> volume #32 step 1
> volume #31 step 1
> volume #30 step 1
> volume #29 step 1
> close #30-38
> volume #29 level 0.05947
> view matrix models
> #29,0.48941,-0.87159,0.028525,12.709,-0.38897,-0.24745,-0.8874,201.39,0.7805,0.4232,-0.46013,-110.26
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.33044,-0.94378,0.010017,49.467,-0.46628,-0.17246,-0.86766,198.88,0.8206,0.28203,-0.49706,-90.024
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.33044,-0.94378,0.010017,54.074,-0.46628,-0.17246,-0.86766,197.95,0.8206,0.28203,-0.49706,-88.49
> view matrix models
> #29,0.33044,-0.94378,0.010017,55.978,-0.46628,-0.17246,-0.86766,195.04,0.8206,0.28203,-0.49706,-89.087
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.3148,-0.94912,-0.0088411,61.988,-0.54675,-0.17372,-0.81908,199.53,0.77586,0.26268,-0.57362,-67.785
> view matrix models
> #29,0.16133,-0.98674,0.017962,85.891,-0.54149,-0.10372,-0.83428,191,0.82508,0.12487,-0.55104,-58.628
> open
> /Users/leightongo/Downloads/cryosparc_P205_J109_series_001/J109_series_001_frame_000.mrc
Opened J109_series_001_frame_000.mrc as #30, grid size 440,440,440, pixel
0.67, shown at level 7.31e-05, step 2, values float32
> select add #30
4 models selected
> select subtract #29
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #30,1,0,0,-144.95,0,1,0,-135.67,0,0,1,-45.582
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.13049,-0.84915,-0.51178,185.79,-0.74642,0.25561,-0.61442,177.93,0.65256,0.46218,-0.60047,42.68
> view matrix models
> #30,0.5295,-0.80095,-0.27949,83.842,-0.14585,0.23861,-0.9601,146.46,0.83568,0.54914,0.0095231,-92.409
> view matrix models
> #30,0.14536,-0.98044,-0.13272,143.18,-0.7202,-0.01288,-0.69365,225.37,0.67837,0.19642,-0.70798,94.218
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.14536,-0.98044,-0.13272,115.51,-0.7202,-0.01288,-0.69365,254.03,0.67837,0.19642,-0.70798,1.7384
> view matrix models
> #30,0.14536,-0.98044,-0.13272,88.548,-0.7202,-0.01288,-0.69365,187.19,0.67837,0.19642,-0.70798,-30.318
> view matrix models
> #30,0.14536,-0.98044,-0.13272,107.19,-0.7202,-0.01288,-0.69365,187.56,0.67837,0.19642,-0.70798,-34.316
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.089199,-0.99278,0.080183,83.84,-0.57241,-0.11698,-0.81158,199.43,0.8151,0.026494,-0.57871,-50.048
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.089199,-0.99278,0.080183,86.954,-0.57241,-0.11698,-0.81158,193.59,0.8151,0.026494,-0.57871,-38.319
> color #30 #24bde3ff models
> color #30 #fc7cbbff models
> color #30 #947cfcff models
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.048232,-0.99837,0.030428,101.58,-0.49209,-0.050261,-0.86909,181.17,0.86921,0.026945,-0.49371,-59.649
> view matrix models
> #30,0.19033,-0.98096,0.038514,76.937,-0.47725,-0.12674,-0.86958,190.14,0.85791,0.14713,-0.49229,-75.611
> hide #!29 models
> volume #30 step 1
> volume #30 level 0.04369
> transparency #30.1 50
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.19033,-0.98096,0.038514,75.704,-0.47725,-0.12674,-0.86958,191.14,0.85791,0.14713,-0.49229,-75.19
> fitmap #17 inMap #30
Fit molecule 15A1 (#17) to map J109_series_001_frame_000.mrc (#30) using 5887
atoms
average map value = 0.08952, steps = 56
shifted from previous position = 2.09
rotated from previous position = 4.9 degrees
atoms outside contour = 1774, contour level = 0.043694
Position of 15A1 (#17) relative to J109_series_001_frame_000.mrc (#30)
coordinates:
Matrix rotation and translation
0.13540395 0.84788724 -0.51259438 154.77069919
0.46980647 -0.51044374 -0.72022849 121.98797498
-0.87232314 -0.14329838 -0.46745901 209.14433309
Axis 0.74160798 0.46240906 -0.48599944
Axis point 0.00000000 -20.41899068 167.54706088
Rotation angle (degrees) 157.10942412
Shift along axis 69.54350131
> volume #30 level 0.1228
> fitmap #10 inMap #30
Fit molecule Arah2 (#10) to map J109_series_001_frame_000.mrc (#30) using 3843
atoms
average map value = 0.08009, steps = 324
shifted from previous position = 18.2
rotated from previous position = 46.6 degrees
atoms outside contour = 2800, contour level = 0.12276
Position of Arah2 (#10) relative to J109_series_001_frame_000.mrc (#30)
coordinates:
Matrix rotation and translation
0.33732500 -0.93720712 0.08862646 127.81177003
-0.15162623 0.03882475 0.98767511 145.80434559
-0.92909705 -0.34660560 -0.12900863 132.61520530
Axis -0.72010767 0.54926261 0.42397587
Axis point 0.00000000 174.85133650 47.15674436
Rotation angle (degrees) 112.11268844
Shift along axis 44.27228615
> undo
[Repeated 1 time(s)]
> redo
[Repeated 1 time(s)]
> hide #!29 models
> volume #30 level 0.1296
> select subtract #30
Nothing selected
> select add #10
3843 atoms, 3895 bonds, 7 pseudobonds, 557 residues, 3 models selected
> view matrix models
> #10,0.17716,-0.22981,-0.95697,-38.092,0.66615,0.74376,-0.05529,-4.1111,0.72447,-0.6277,0.28486,-9.497
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.70692,-0.68443,0.17834,-9.2788,0.69844,0.71529,-0.02343,-3.2397,-0.11153,0.14113,0.98369,4.0406
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.70692,-0.68443,0.17834,-11.711,0.69844,0.71529,-0.02343,-2.3421,-0.11153,0.14113,0.98369,2.7822
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.76107,-0.36193,-0.5383,-22.854,0.46713,0.88159,0.067696,-1.6658,0.45006,-0.30298,0.84003,2.3659
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.76107,-0.36193,-0.5383,-25.251,0.46713,0.88159,0.067696,-0.30697,0.45006,-0.30298,0.84003,3.6709
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.76122,-0.57814,-0.29376,-22.687,0.57327,0.81169,-0.11193,-3.7472,0.30315,-0.083204,0.9493,6.9701
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.76122,-0.57814,-0.29376,-21.028,0.57327,0.81169,-0.11193,-5.1148,0.30315,-0.083204,0.9493,9.3161
> view matrix models
> #10,0.76122,-0.57814,-0.29376,-23.55,0.57327,0.81169,-0.11193,-6.1872,0.30315,-0.083204,0.9493,9.3969
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.8854,-0.40906,-0.22078,-17.287,0.43348,0.89809,0.074413,-2.914,0.16784,-0.16159,0.97248,6.5216
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.8854,-0.40906,-0.22078,-14.769,0.43348,0.89809,0.074413,-1.3896,0.16784,-0.16159,0.97248,6.4275
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.90819,-0.37806,-0.17961,-12.97,0.4051,0.90188,0.15003,-0.042089,0.10527,-0.20901,0.97223,4.6781
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.90819,-0.37806,-0.17961,-11.507,0.4051,0.90188,0.15003,-0.15592,0.10527,-0.20901,0.97223,4.2949
> ui tool show "Show Sequence Viewer"
> sequence chain #10/F
Destroying pre-existing alignment with identifier 10/F
Alignment identifier is 10/F
> select subtract #10
Nothing selected
> select add #17
5887 atoms, 5963 bonds, 1 pseudobond, 430 residues, 2 models selected
> fitmap #17 inMap #30
Fit molecule 15A1 (#17) to map J109_series_001_frame_000.mrc (#30) using 5887
atoms
average map value = 0.08952, steps = 36
shifted from previous position = 0.00154
rotated from previous position = 0.0102 degrees
atoms outside contour = 4301, contour level = 0.12957
Position of 15A1 (#17) relative to J109_series_001_frame_000.mrc (#30)
coordinates:
Matrix rotation and translation
0.13555200 0.84781914 -0.51266789 154.76388235
0.46979006 -0.51057627 -0.72014525 121.98585557
-0.87230898 -0.14322915 -0.46750663 209.14552016
Axis 0.74166247 0.46234157 -0.48598051
Axis point 0.00000000 -20.40120409 167.53802400
Rotation angle (degrees) 157.11178883
Shift along axis 69.54104878
> fitmap #17 inMap #30
Fit molecule 15A1 (#17) to map J109_series_001_frame_000.mrc (#30) using 5887
atoms
average map value = 0.08952, steps = 28
shifted from previous position = 0.00837
rotated from previous position = 0.00836 degrees
atoms outside contour = 4302, contour level = 0.12957
Position of 15A1 (#17) relative to J109_series_001_frame_000.mrc (#30)
coordinates:
Matrix rotation and translation
0.13554681 0.84777091 -0.51274902 154.76559671
0.46987605 -0.51062869 -0.72005198 121.97589248
-0.87226347 -0.14332773 -0.46756133 209.13976086
Axis 0.74166951 0.46233692 -0.48597419
Axis point 0.00000000 -20.39239303 167.52849896
Rotation angle (degrees) 157.12006222
Shift along axis 69.54235771
> save Arah2P3415A1.pdb #10,12,17
> ui tool show "Show Sequence Viewer"
> sequence chain #20/A
Alignment identifier is 20/A
> sequence chain #20/B
Alignment identifier is 20/B
> open
> /Users/leightongo/Downloads/Arah2_8450d/Arah2_8450d_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
Arah2_8450d_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #31
---
Chain | Description
A | No description available
> open
> /Users/leightongo/Downloads/Arah2_8450d/Arah2_8450d_unrelaxed_rank_002_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
Arah2_8450d_unrelaxed_rank_002_alphafold2_ptm_model_2_seed_000.pdb #32
---
Chain | Description
A | No description available
> open
> /Users/leightongo/Downloads/Arah2_8450d/Arah2_8450d_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
Arah2_8450d_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb #33
---
Chain | Description
A | No description available
> open
> /Users/leightongo/Downloads/Arah2_8450d/Arah2_8450d_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb
Chain information for
Arah2_8450d_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb #34
---
Chain | Description
A | No description available
> open
> /Users/leightongo/Downloads/Arah2_8450d/Arah2_8450d_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
Chain information for
Arah2_8450d_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb #35
---
Chain | Description
A | No description available
> mmaker #31-35 to #10
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 Arah2, chain F (#10) with
Arah2_8450d_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#31), sequence alignment score = 623.9
RMSD between 83 pruned atom pairs is 1.071 angstroms; (across all 93 pairs:
1.651)
Matchmaker Arah2, chain F (#10) with
Arah2_8450d_unrelaxed_rank_002_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#32), sequence alignment score = 629.9
RMSD between 81 pruned atom pairs is 0.958 angstroms; (across all 93 pairs:
1.498)
Matchmaker Arah2, chain F (#10) with
Arah2_8450d_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#33), sequence alignment score = 626.9
RMSD between 68 pruned atom pairs is 1.003 angstroms; (across all 93 pairs:
1.964)
Matchmaker Arah2, chain F (#10) with
Arah2_8450d_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#34), sequence alignment score = 637.1
RMSD between 81 pruned atom pairs is 1.026 angstroms; (across all 93 pairs:
1.641)
Matchmaker Arah2, chain F (#10) with
Arah2_8450d_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#35), sequence alignment score = 626.9
RMSD between 60 pruned atom pairs is 1.151 angstroms; (across all 93 pairs:
2.453)
> close #32-35
> hide #31 models
> open /Users/leightongo/Downloads/Arah2P34.pdb
Chain information for Arah2P34.pdb #32
---
Chain | Description
A | No description available
B | No description available
C M | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I V | No description available
J | No description available
K | No description available
L Q | No description available
N | No description available
O | No description available
P | No description available
R | No description available
T | No description available
> select add #32
54770 atoms, 55408 bonds, 14 pseudobonds, 3947 residues, 4 models selected
> select subtract #17
48883 atoms, 49445 bonds, 13 pseudobonds, 3517 residues, 2 models selected
> view matrix models #32,1,0,0,89.417,0,1,0,-46.458,0,0,1,-11.153
> hide sel atoms
> show sel cartoons
> ui mousemode right select
> select clear
Drag select of 2205 residues, 8 pseudobonds
> select up
32479 atoms, 32844 bonds, 8 pseudobonds, 2338 residues, 2 models selected
> select up
35576 atoms, 35986 bonds, 8 pseudobonds, 2561 residues, 2 models selected
> select up
48883 atoms, 49445 bonds, 13 pseudobonds, 3517 residues, 2 models selected
> select down
35576 atoms, 35986 bonds, 8 pseudobonds, 2561 residues, 2 models selected
> select down
32479 atoms, 32844 bonds, 8 pseudobonds, 2338 residues, 2 models selected
> select up
35576 atoms, 35986 bonds, 8 pseudobonds, 2561 residues, 2 models selected
> delete sel
> mmaker #32 to #10
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 Arah2, chain H (#10) with Arah2P34.pdb, chain V (#32), sequence
alignment score = 914.8
RMSD between 83 pruned atom pairs is 0.334 angstroms; (across all 203 pairs:
8.431)
> select #32/T:88
17 atoms, 16 bonds, 1 residue, 1 model selected
> mmaker #32/T to #10
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 Arah2, chain F (#10) with Arah2P34.pdb, chain T (#32), sequence
alignment score = 448.8
RMSD between 89 pruned atom pairs is 0.570 angstroms; (across all 92 pairs:
0.854)
Drag select of 164 residues, 1 pseudobonds
> select up
2687 atoms, 2714 bonds, 1 pseudobond, 195 residues, 2 models selected
> select up
6111 atoms, 6184 bonds, 1 pseudobond, 429 residues, 2 models selected
> open
> /Users/leightongo/Downloads/P34_1a68d/P34_1a68d_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
Chain information for
P34_1a68d_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #33
---
Chain | Description
A | No description available
B | No description available
> mmaker #33 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 Arah2_P34.pdb, chain Q (#12) with
P34_1a68d_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#33), sequence alignment score = 886.2
RMSD between 74 pruned atom pairs is 0.611 angstroms; (across all 216 pairs:
5.293)
> select up
13307 atoms, 13459 bonds, 3 pseudobonds, 956 residues, 2 models selected
> select up
13307 atoms, 13459 bonds, 3 pseudobonds, 956 residues, 2 models selected
> select down
3 pseudobonds, 1 model selected
> select down
6111 atoms, 6184 bonds, 1 pseudobond, 429 residues, 2 models selected
> select up
13307 atoms, 13459 bonds, 3 pseudobonds, 956 residues, 2 models selected
> select clear
> save Arah2P3415A1.pdb #10,12,17
> save Arah2P3415A1.pdb #10,17,33
> hide #!32 models
> hide #!30 models
> show #!30 models
> hide #!12 models
> save Arah2P3415A1.pdb #10,17,33
> select add #33
3611 atoms, 3696 bonds, 476 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #33,0.6314,0.74788,0.20495,-50.705,0.67329,-0.65985,0.33359,-14.86,0.38472,-0.072641,-0.92017,8.7649
> ui mousemode right "translate selected models"
> view matrix models
> #33,0.6314,0.74788,0.20495,-33.772,0.67329,-0.65985,0.33359,-8.6918,0.38472,-0.072641,-0.92017,19.238
> view matrix models
> #33,0.6314,0.74788,0.20495,-34.179,0.67329,-0.65985,0.33359,-3.5929,0.38472,-0.072641,-0.92017,14.492
> fitmap #33 inMap #30
Fit molecule
P34_1a68d_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb (#33)
to map J109_series_001_frame_000.mrc (#30) using 3611 atoms
average map value = 0.1058, steps = 364
shifted from previous position = 5.67
rotated from previous position = 39.3 degrees
atoms outside contour = 2250, contour level = 0.12957
Position of
P34_1a68d_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb (#33)
relative to J109_series_001_frame_000.mrc (#30) coordinates:
Matrix rotation and translation
0.66579224 0.13017956 -0.73469312 146.32612127
-0.65867762 -0.36002900 -0.66069881 144.83748841
-0.35052031 0.92381405 -0.15395815 125.73059186
Axis 0.87482547 -0.21210567 -0.43553597
Axis point 0.00000000 37.72755041 155.21069154
Rotation angle (degrees) 115.09354841
Shift along axis 42.52876960
> help save
> save Arah2P3415A1.pdb models #10,17,33
> save Arah2P3415A1.pdb displayedOnly true
> open /Users/leightongo/Desktop/Arah2P3415A1.pdb
Summary of feedback from opening /Users/leightongo/Desktop/Arah2P3415A1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 3
GLU A 20 1 18
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1
25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1
25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
83 messages similar to the above omitted
Chain information for Arah2P3415A1.pdb
---
Chain | Description
34.1/A | No description available
34.2/A 34.6/A 34.7/A 34.8/A 34.10/A 34.11/A 34.12/A 34.13/A 34.14/A 34.15/A
34.16/A 34.17/A 34.18/A 34.19/A 34.20/A 34.21/A 34.22/A 34.23/A 34.24/A
34.25/A 34.26/A 34.27/A 34.28/A 34.29/A 34.30/A 34.31/A 34.32/A 34.33/A
34.34/A 34.35/A 34.36/A 34.37/A 34.38/A 34.39/A | No description available
34.3/A | No description available
34.4/A | No description available
34.5/A | No description available
34.40/A | No description available
34.41/A | No description available
34.42/A | No description available
34.43/A | No description available
34.44/A | No description available
34.9/F | No description available
> save Arah2P3415A1.pdb format pdb
> close #34
> open /Users/leightongo/Desktop/Arah2P3415A1.pdb
Summary of feedback from opening /Users/leightongo/Desktop/Arah2P3415A1.pdb
---
warnings | End residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU
A 20 1 18
End residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1 25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1
25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
End residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1 25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
End residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1 25
End residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1 18
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1
25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1
25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
End residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1 25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1
25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1
25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
38 messages similar to the above omitted
End residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1 25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1
25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1
25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
103 messages similar to the above omitted
Chain information for Arah2P3415A1.pdb
---
Chain | Description
34.1/A | No description available
34.2/A | No description available
34.3/A | No description available
34.4/A 34.8/A | No description available
34.5/A | No description available
34.6/A | No description available
34.7/A | No description available
34.9/A | No description available
34.11/A | No description available
34.15/A 34.16/A 34.17/A 34.18/A 34.19/A 34.20/A 34.21/A 34.22/A 34.23/A
34.24/A 34.25/A 34.26/A 34.27/A 34.28/A 34.29/A 34.30/A 34.31/A 34.32/A
34.33/A 34.34/A 34.35/A 34.36/A 34.37/A 34.38/A 34.39/A 34.40/A 34.41/A
34.42/A 34.43/A 34.44/A | No description available
34.45/A | No description available
34.47/A 34.55/A | No description available
34.48/A | No description available
34.49/A | No description available
34.50/A | No description available
34.51/A | No description available
34.52/A | No description available
34.53/A | No description available
34.56/A 34.57/A 34.61/A 34.62/A 34.63/A 34.65/A 34.66/A 34.67/A 34.68/A
34.69/A 34.70/A 34.71/A 34.72/A 34.73/A 34.74/A 34.75/A 34.76/A 34.77/A
34.78/A 34.79/A 34.80/A 34.81/A 34.82/A 34.83/A 34.84/A 34.85/A 34.86/A
34.87/A 34.88/A 34.89/A 34.90/A 34.91/A 34.92/A 34.93/A 34.94/A | No
description available
34.58/A | No description available
34.59/A | No description available
34.60/A | No description available
34.95/A | No description available
34.96/A | No description available
34.97/A | No description available
34.98/A | No description available
34.99/A | No description available
34.11/B | No description available
34.47/B 34.55/B | No description available
34.50/C | No description available
34.50/D | No description available
34.50/E | No description available
34.10/F | No description available
34.50/F | No description available
34.64/F | No description available
34.10/G 34.46/G | No description available
34.10/H 34.46/H | No description available
34.46/I | No description available
34.46/J 34.54/V | No description available
34.14/K 34.14/L 34.14/M 34.14/N | No description available
34.12/P 34.13/P 34.54/P | No description available
34.12/Q 34.13/Q 34.54/Q | No description available
34.54/R | No description available
34.54/T | No description available
> select subtract #33
Nothing selected
> select add #34
89204 atoms, 89183 bonds, 211 pseudobonds, 10004 residues, 153 models selected
> view matrix models #34,1,0,0,26.65,0,1,0,74.932,0,0,1,99.549
> close #34
> save Arah2P3415A1.pdb format pdb displayedOnly true
> open /Users/leightongo/Desktop/Arah2P3415A1.pdb
Summary of feedback from opening /Users/leightongo/Desktop/Arah2P3415A1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 3
GLU A 20 1 18
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1
25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1
25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
83 messages similar to the above omitted
Chain information for Arah2P3415A1.pdb
---
Chain | Description
34.1/A | No description available
34.2/A 34.6/A 34.7/A 34.8/A 34.10/A 34.11/A 34.12/A 34.13/A 34.14/A 34.15/A
34.16/A 34.17/A 34.18/A 34.19/A 34.20/A 34.21/A 34.22/A 34.23/A 34.24/A
34.25/A 34.26/A 34.27/A 34.28/A 34.29/A 34.30/A 34.31/A 34.32/A 34.33/A
34.34/A 34.35/A 34.36/A 34.37/A 34.38/A 34.39/A | No description available
34.3/A | No description available
34.4/A | No description available
34.5/A | No description available
34.40/A | No description available
34.41/A | No description available
34.42/A | No description available
34.43/A | No description available
34.44/A | No description available
34.9/F | No description available
> close #34
> select add #33
3611 atoms, 3696 bonds, 476 residues, 1 model selected
> select add #17
9498 atoms, 9659 bonds, 1 pseudobond, 906 residues, 3 models selected
> select add #10
13341 atoms, 13554 bonds, 8 pseudobonds, 1463 residues, 6 models selected
> save Arah2P3415A1.pdb format pdb selectedOnly true
> open /Users/leightongo/Desktop/Arah2P3415A1.pdb
Summary of feedback from opening /Users/leightongo/Desktop/Arah2P3415A1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 3
GLU A 20 1 18
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1
25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 GLU A 48 1
25
Start residue of secondary structure not found: HELIX 1 1 PRO A 3 GLU A 20 1
18
1 messages similar to the above omitted
Chain information for Arah2P3415A1.pdb
---
Chain | Description
34.3/A | No description available
34.3/B | No description available
34.1/F | No description available
34.1/G | No description available
34.1/H | No description available
34.2/P | No description available
34.2/Q | No description available
> hide #!34.1 models
> show #!34.1 models
> hide #!34.2 models
> show #!34.2 models
> hide #34.3 models
> show #34.3 models
> hide #!34 models
> show #!34 models
> select subtract #17
7454 atoms, 7591 bonds, 7 pseudobonds, 1033 residues, 4 models selected
> select subtract #10
3611 atoms, 3696 bonds, 476 residues, 1 model selected
> select subtract #33
Nothing selected
> select add #34
13341 atoms, 13554 bonds, 8 pseudobonds, 1463 residues, 7 models selected
> view matrix models #34,1,0,0,-34.668,0,1,0,-44.988,0,0,1,86.409
> select subtract #34.1
9498 atoms, 9659 bonds, 1 pseudobond, 906 residues, 4 models selected
> hide #!34.1 models
> show #!34.1 models
> ui mousemode right select
> select clear
Drag select of 70 residues, 1 pseudobonds
> select up
850 atoms, 863 bonds, 1 pseudobond, 116 residues, 2 models selected
> select up
3102 atoms, 3183 bonds, 1 pseudobond, 427 residues, 2 models selected
> select up
3128 atoms, 3183 bonds, 1 pseudobond, 453 residues, 2 models selected
> select up
3843 atoms, 3895 bonds, 3 pseudobonds, 557 residues, 2 models selected
> select down
3128 atoms, 3183 bonds, 1 pseudobond, 453 residues, 2 models selected
> delete sel
Drag select of 672 residues, 1 pseudobonds
> select up
7896 atoms, 8015 bonds, 1 pseudobond, 795 residues, 4 models selected
> save Arah2P3415A1.pdb format pdb models #34
> open /Users/leightongo/Desktop/Arah2P3415A1.pdb
Summary of feedback from opening /Users/leightongo/Desktop/Arah2P3415A1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 CYS F 33
GLU F 38 1 6
Start residue of secondary structure not found: HELIX 2 2 ARG F 43 ILE F 53 1
11
Start residue of secondary structure not found: HELIX 3 3 GLN F 88 GLU F 94 1
7
Start residue of secondary structure not found: HELIX 4 4 LEU F 95 PHE F 98 1
4
Start residue of secondary structure not found: HELIX 5 5 GLN F 102 GLN F 116
1 15
11 messages similar to the above omitted
Chain information for Arah2P3415A1.pdb
---
Chain | Description
35.3/A | No description available
35.3/B | No description available
35.1/F | No description available
35.2/P | No description available
35.2/Q | No description available
> hide #33 models
> hide #!35 models
> show #!35 models
> hide #!34 models
> show #!34 models
> show #33 models
> close #35
> close #34
> open /Users/leightongo/Desktop/Arah2P3415A1.pdb
Summary of feedback from opening /Users/leightongo/Desktop/Arah2P3415A1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 CYS F 33
GLU F 38 1 6
Start residue of secondary structure not found: HELIX 2 2 ARG F 43 ILE F 53 1
11
Start residue of secondary structure not found: HELIX 3 3 GLN F 88 GLU F 94 1
7
Start residue of secondary structure not found: HELIX 4 4 LEU F 95 PHE F 98 1
4
Start residue of secondary structure not found: HELIX 5 5 GLN F 102 GLN F 116
1 15
11 messages similar to the above omitted
Chain information for Arah2P3415A1.pdb
---
Chain | Description
34.3/A | No description available
34.3/B | No description available
34.1/F | No description available
34.2/P | No description available
34.2/Q | No description available
> close #34
> select add #33
3611 atoms, 3696 bonds, 476 residues, 1 model selected
> select add #17
9498 atoms, 9659 bonds, 1 pseudobond, 906 residues, 3 models selected
> select add #10
13341 atoms, 13554 bonds, 8 pseudobonds, 1463 residues, 6 models selected
> save Arah2P3415A1.cif models #33,17,10
Not saving entity_poly_seq for non-authoritative sequences
[Repeated 1 time(s)]
> open /Users/leightongo/Desktop/Arah2P3415A1.cif
Summary of feedback from opening /Users/leightongo/Desktop/Arah2P3415A1.cif
---
warnings | Unknown polymer entity '1' near line 121
Unknown polymer entity '2' near line 1898
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Unknown polymer entity '1' near line 7591
Unknown polymer entity '2' near line 10500
Atom 2HB is not in the residue template for SER /P:56
Atom 2HB is not in the residue template for ARG /P:57
Atom 2HB is not in the residue template for SER /Q:32
Atom 2HB is not in the residue template for LYS /Q:58
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for Arah2P3415A1.cif
---
Chain | Description
34.1/A | No description available
34.1/B | No description available
34.3/F | ara H 2 allergen
34.3/G | 13T1 heavy chain
34.3/H | 13T1 light chain
34.2/P | No description available
34.2/Q | No description available
> hide #!34.3 models
> show #!34.3 models
> hide #!34.2 models
> show #!34.2 models
> hide #34.1 models
> show #34.1 models
> open /Users/leightongo/Desktop/Arah2P3415A1.pdb
Chain information for Arah2P3415A1.pdb #35
---
Chain | Description
A | No description available
B | No description available
F | No description available
P | No description available
Q | No description available
> close #34
> select subtract #33
9730 atoms, 9858 bonds, 8 pseudobonds, 987 residues, 5 models selected
> select add #35
19700 atoms, 19987 bonds, 10 pseudobonds, 1954 residues, 7 models selected
> hide sel atoms
> show sel cartoons
> select clear
> close #35
> hide #!30 models
> hide #!17 models
> hide #!10 models
> hide #33 models
> open /Users/leightongo/Desktop/Arah2P3415A1.pdb
Chain information for Arah2P3415A1.pdb #34
---
Chain | Description
A | No description available
B | No description available
F | No description available
P | No description available
Q | No description available
> select add #34
9970 atoms, 10129 bonds, 2 pseudobonds, 967 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> lighting soft
> lighting simple
> lighting full
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> show #!28 models
> material transparentCastShadows true
> surface dust #28 size 4.02
> surface dust #28 size 4.07
> surface dust #28 size 8.76
> surface dust #28 size 8.92
> surface dust #28 size 9.33
> color #28 darkgrey models
Opened Arah2P3415A1.pdb map 3.5 as #35, grid size 74,124,98, pixel 1.17, shown
at level 0.111, step 1, values float32
> fitmap #34 inMap #30 resolution 3.5
You deleted or moved a volume file that is still open in ChimeraX.
/Users/leightongo/Downloads/cryosparc_P205_J109_series_001/J109_series_001_frame_000.mrc
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.
> select down
9970 atoms, 10129 bonds, 2 pseudobonds, 967 residues, 2 models selected
> close #29
> close #30
> show #!35 models
> hide #!35 models
> save /Users/leightongo/Desktop/Arah2_FABs.cxs includeMaps true
> open "/Users/leightongo/Downloads/last_frame_rsr (1).pdb"
Chain information for last_frame_rsr (1).pdb #29
---
Chain | Description
A | No description available
B | No description available
F | No description available
P | No description available
Q | No description available
> select subtract #34
Nothing selected
> show #!35 models
> hide #!35 models
> select add #29
7453 atoms, 7626 bonds, 2 pseudobonds, 967 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide #!34 models
> volume #28 level 0.2625
> volume #28 level 0.1514
> save /Users/leightongo/Desktop/Arah2_FABs.cxs includeMaps true
——— End of log from Fri Nov 3 18:29:31 2023 ———
opened ChimeraX session
> select down
7453 atoms, 7626 bonds, 2 pseudobonds, 967 residues, 2 models selected
> select down
7453 atoms, 7626 bonds, 2 pseudobonds, 967 residues, 2 models selected
Window position QRect(2433,653 575x176) outside any known screen, using
primary screen
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x600002148e30, name="DELL P2723QE") screenTo: QScreen(0x600002148e30,
name="DELL P2723QE") wdgScreen: QScreen(0x600002148e30, name="DELL P2723QE")
orgWdgScreen QScreen(0x0)
[Repeated 21 time(s)]
> close #1-9
> open
> /Users/leightongo/Downloads/cryosparc_P205_J117_006_volume_map_sharp.mrc
Opened cryosparc_P205_J117_006_volume_map_sharp.mrc as #1, grid size
420,420,420, pixel 0.67, shown at level 0.0537, step 2, values float32
> select add #1
7453 atoms, 7626 bonds, 2 pseudobonds, 967 residues, 4 models selected
> select subtract #29
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,3.6109,0,1,0,-200.24,0,0,1,-97.346
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.96092,0.2533,-0.11164,259.75,-0.12995,-0.056693,0.9899,-174.89,0.24441,0.96573,0.087394,-137.06
> volume #1 level 0.2504
> volume #1 step 1
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.96092,0.2533,-0.11164,208.94,-0.12995,-0.056693,0.9899,-153.16,0.24441,0.96573,0.087394,-195.07
> view matrix models
> #1,-0.96092,0.2533,-0.11164,88.595,-0.12995,-0.056693,0.9899,-142.18,0.24441,0.96573,0.087394,-175.43
> view matrix models
> #1,-0.96092,0.2533,-0.11164,143.95,-0.12995,-0.056693,0.9899,-148.83,0.24441,0.96573,0.087394,-144.04
> ui mousemode right "rotate selected models"
> hide #!29 models
> hide #!28 models
> show #!29 models
> view matrix models
> #1,-0.89327,-0.36431,0.26332,163.55,0.33662,-0.15392,0.92898,-194.21,-0.2979,0.91847,0.26013,-84.338
> view matrix models
> #1,0.6496,-0.68539,0.32902,-26.416,0.058746,-0.38622,-0.92053,153.98,0.758,0.61731,-0.21063,-126.23
> view matrix models
> #1,0.089586,-0.99266,0.081292,134.46,-0.29019,-0.10409,-0.95129,170.36,0.95277,0.061632,-0.29738,-64.869
> view matrix models
> #1,0.42882,-0.88375,0.18734,54.238,-0.2064,-0.29773,-0.93207,182.06,0.8795,0.36102,-0.31008,-93.679
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.42882,-0.88375,0.18734,9.0809,-0.2064,-0.29773,-0.93207,177.86,0.8795,0.36102,-0.31008,-133.42
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.40066,-0.87133,0.2833,-2.841,-0.40491,-0.44576,-0.79834,207.27,0.8219,0.20515,-0.53141,-70.512
> view matrix models
> #1,0.55277,-0.83323,0.013488,9.9726,-0.3695,-0.25957,-0.89224,190.38,0.74694,0.48822,-0.45135,-110.64
> view matrix models
> #1,0.58824,-0.80031,-0.1161,19.577,-0.41278,-0.17369,-0.89411,185.1,0.69541,0.57387,-0.43253,-117.79
> volume #1 level 0.158
> open "/Users/leightongo/Downloads/last_frame_rsr (2).pdb"
Chain information for last_frame_rsr (2).pdb #2
---
Chain | Description
A | No description available
B | No description available
F | No description available
P | No description available
Q | No description available
> select subtract #1
Nothing selected
> select add #2
7453 atoms, 7626 bonds, 2 pseudobonds, 967 residues, 2 models selected
> hide #!29 models
> hide sel atoms
> show sel cartoons
> open
> /Users/leightongo/Downloads/cryosparc_P202_J154_class_02_00418_volume.mrc
Opened cryosparc_P202_J154_class_02_00418_volume.mrc as #3, grid size
108,108,108, pixel 2.23, shown at level 0.539, step 1, values float32
> hide #!2 models
> hide #!1 models
> select subtract #2
Nothing selected
> select add #3
2 models selected
> open
> /Users/leightongo/Downloads/cryosparc_P202_J154_class_08_00418_volume.mrc
Opened cryosparc_P202_J154_class_08_00418_volume.mrc as #4, grid size
108,108,108, pixel 2.23, shown at level 0.539, step 1, values float32
> select add #4
4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,1,0,0,-162.72,0,1,0,-221.23,0,0,1,-81.126,#4,1,0,0,-162.72,0,1,0,-221.23,0,0,1,-81.126
> view matrix models
> #3,1,0,0,-146.07,0,1,0,-248.08,0,0,1,-70.854,#4,1,0,0,-146.07,0,1,0,-248.08,0,0,1,-70.854
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> close #3-4
> show #!1 models
> show #!2 models
> ui mousemode right translate
> ui tool show "Hide Dust"
> surface dust #1 size 4.02
> select add #1
2 models selected
> transparency #1.1 50
> hide #!2 models
> show #!34 models
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.58824,-0.80031,-0.1161,19.477,-0.41278,-0.17369,-0.89411,185.17,0.69541,0.57387,-0.43253,-118.41
> view matrix models
> #1,0.58824,-0.80031,-0.1161,16.677,-0.41278,-0.17369,-0.89411,183.04,0.69541,0.57387,-0.43253,-116.96
> view matrix models
> #1,0.58824,-0.80031,-0.1161,17.491,-0.41278,-0.17369,-0.89411,183.58,0.69541,0.57387,-0.43253,-117.12
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.27897,-0.95456,-0.1048,81.359,-0.47686,-0.042977,-0.87793,172.5,0.83353,0.29489,-0.46718,-93.636
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.27897,-0.95456,-0.1048,79.467,-0.47686,-0.042977,-0.87793,171.91,0.83353,0.29489,-0.46718,-93.282
> hide #!34 models
> show #!20 models
> view matrix models
> #1,0.27897,-0.95456,-0.1048,75.109,-0.47686,-0.042977,-0.87793,178.24,0.83353,0.29489,-0.46718,-100.4
> show #!10 models
> select #10/H
1528 atoms, 1555 bonds, 4 pseudobonds, 218 residues, 3 models selected
> delete sel
> select #10/G
1600 atoms, 1628 bonds, 1 pseudobond, 235 residues, 2 models selected
> delete sel
> color #10 black
> color #10 #0433ffff
> color #10 #fffb00ff
> select add #10
715 atoms, 712 bonds, 2 pseudobonds, 104 residues, 3 models selected
> view matrix models
> #10,0.90819,-0.37806,-0.17961,-10.588,0.4051,0.90188,0.15003,1.2788,0.10527,-0.20901,0.97223,-0.77995
> view matrix models
> #10,0.90819,-0.37806,-0.17961,-13.333,0.4051,0.90188,0.15003,3.9601,0.10527,-0.20901,0.97223,0.94623
> ui tool show "Fit in Map"
> fitmap #10 inMap #1
Fit molecule Arah2 (#10) to map cryosparc_P205_J117_006_volume_map_sharp.mrc
(#1) using 715 atoms
average map value = 0.1854, steps = 80
shifted from previous position = 3.12
rotated from previous position = 4.49 degrees
atoms outside contour = 382, contour level = 0.15799
Position of Arah2 (#10) relative to
cryosparc_P205_J117_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.15022938 -0.68901750 0.70900353 141.43662203
-0.88894174 0.21971687 0.40187943 119.06952868
-0.43268199 -0.69063693 -0.57948850 113.08616999
Axis -0.68590990 0.71677957 -0.12551758
Axis point 165.71358768 0.00000000 24.14638645
Rotation angle (degrees) 127.21237409
Shift along axis -25.86047635
> fitmap #20 inMap #1
Fit molecule 15A1.pdb (#20) to map
cryosparc_P205_J117_006_volume_map_sharp.mrc (#1) using 3611 atoms
average map value = 0.1633, steps = 392
shifted from previous position = 9.74
rotated from previous position = 23.5 degrees
atoms outside contour = 2228, contour level = 0.15799
Position of 15A1.pdb (#20) relative to
cryosparc_P205_J117_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.63189007 -0.27928105 -0.72299172 143.27071455
0.75919248 -0.41080778 -0.50484031 145.68046121
-0.15601829 -0.86789346 0.47161343 183.30644330
Axis -0.29334875 -0.45811735 0.83909177
Axis point 69.33126519 155.19593097 0.00000000
Rotation angle (degrees) 141.77085423
Shift along axis 45.04389703
> select subtract #10
Nothing selected
> select add #20
3611 atoms, 3695 bonds, 1 pseudobond, 476 residues, 2 models selected
> select subtract #20
Nothing selected
> show #!12 models
> select add #12
5887 atoms, 5963 bonds, 1 pseudobond, 430 residues, 2 models selected
> view matrix models
> #12,0.31598,-0.79425,0.51896,-60.336,-0.92425,-0.38123,-0.020712,21.728,0.21429,-0.47311,-0.85455,-13.699
> view matrix models
> #12,0.31598,-0.79425,0.51896,-57.898,-0.92425,-0.38123,-0.020712,25.985,0.21429,-0.47311,-0.85455,-14.731
> fitmap #12 inMap #1
Fit molecule Arah2_P34.pdb (#12) to map
cryosparc_P205_J117_006_volume_map_sharp.mrc (#1) using 5887 atoms
average map value = 0.1469, steps = 112
shifted from previous position = 4.44
rotated from previous position = 8.28 degrees
atoms outside contour = 3627, contour level = 0.15799
Position of Arah2_P34.pdb (#12) relative to
cryosparc_P205_J117_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.71551204 -0.39243118 -0.57796217 106.33570679
-0.13508955 0.73397722 -0.66560367 155.06117438
0.68541470 0.55432410 0.47215619 106.32436558
Axis 0.68728929 -0.71176788 0.14498247
Axis point 1.42474343 0.00000000 209.28828813
Rotation angle (degrees) 62.55979063
Shift along axis -21.86900065
> view matrix models
> #12,0.25673,-0.8682,0.42465,-46.662,-0.93714,-0.33106,-0.11031,25.72,0.23635,-0.36963,-0.89861,-13.539
> fitmap #12 inMap #1
Fit molecule Arah2_P34.pdb (#12) to map
cryosparc_P205_J117_006_volume_map_sharp.mrc (#1) using 5887 atoms
average map value = 0.209, steps = 124
shifted from previous position = 4.69
rotated from previous position = 5.22 degrees
atoms outside contour = 2995, contour level = 0.15799
Position of Arah2_P34.pdb (#12) relative to
cryosparc_P205_J117_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.71200485 -0.34014876 -0.61428650 110.12546796
-0.13568336 0.79169819 -0.59565426 153.58315192
0.68894057 0.50745718 0.51754043 108.18495931
Axis 0.64148897 -0.75786159 0.11890213
Axis point -9.87140984 0.00000000 218.24520382
Rotation angle (degrees) 59.29474793
Shift along axis -32.88707650
> view matrix models
> #12,0.25595,-0.9038,0.34299,-52.401,-0.93854,-0.31733,-0.13583,24.682,0.23161,-0.28714,-0.92947,-10.722
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.37102,0.68407,0.628,-2.9463,0.39813,0.72814,-0.55794,0.45297,-0.83895,0.04302,-0.54251,30.081
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.37102,0.68407,0.628,-6.8873,0.39813,0.72814,-0.55794,2.9661,-0.83895,0.04302,-0.54251,29.387
> fitmap #12 inMap #1
Fit molecule Arah2_P34.pdb (#12) to map
cryosparc_P205_J117_006_volume_map_sharp.mrc (#1) using 5887 atoms
average map value = 0.1406, steps = 224
shifted from previous position = 4.4
rotated from previous position = 4.45 degrees
atoms outside contour = 3650, contour level = 0.15799
Position of Arah2_P34.pdb (#12) relative to
cryosparc_P205_J117_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99578594 -0.09044421 0.01517243 168.83048055
0.05517988 -0.72304265 -0.68859603 120.49683163
0.07324984 -0.68485704 0.72498641 102.09849883
Axis 0.02384220 -0.37033817 0.92859097
Axis point 80.13241849 84.14997183 0.00000000
Rotation angle (degrees) 175.50274579
Shift along axis 54.20845675
> select subtract #12
Nothing selected
> save Arah2P3415A1.pdb format pdb models #10,12,20
> save Arah2P3415A1.cif models #10,12,20
Not saving entity_poly_seq for non-authoritative sequences
[Repeated 1 time(s)]
> open /Users/leightongo/Desktop/Arah2P3415A1.cif
Summary of feedback from opening /Users/leightongo/Desktop/Arah2P3415A1.cif
---
warnings | Unknown polymer entity '1' near line 1441
Unknown polymer entity '2' near line 4350
Atom 2HB is not in the residue template for SER /P:56
Atom 2HB is not in the residue template for ARG /P:57
Atom 2HB is not in the residue template for SER /Q:32
Atom 2HB is not in the residue template for LYS /Q:58
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Unknown polymer entity '1' near line 19600
Unknown polymer entity '2' near line 21377
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for Arah2P3415A1.cif
---
Chain | Description
3.3/A | No description available
3.3/B | No description available
3.1/F | ara H 2 allergen
3.2/P | No description available
3.2/Q | No description available
> hide #!3 models
> show #!3 models
> close #3
> open /Users/leightongo/Desktop/Arah2P3415A1.cif
Summary of feedback from opening /Users/leightongo/Desktop/Arah2P3415A1.cif
---
warnings | Unknown polymer entity '1' near line 1441
Unknown polymer entity '2' near line 4350
Atom 2HB is not in the residue template for SER /P:56
Atom 2HB is not in the residue template for ARG /P:57
Atom 2HB is not in the residue template for SER /Q:32
Atom 2HB is not in the residue template for LYS /Q:58
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Unknown polymer entity '1' near line 19600
Unknown polymer entity '2' near line 21377
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for Arah2P3415A1.cif
---
Chain | Description
3.3/A | No description available
3.3/B | No description available
3.1/F | ara H 2 allergen
3.2/P | No description available
3.2/Q | No description available
> save Arah2P3415A1.pdb models #3
> save Arah2P3415A1.cif models #3
Not saving entity_poly_seq for non-authoritative sequences
[Repeated 1 time(s)]
> close #3
> open /Users/leightongo/Desktop/Arah2P3415A1.pdb
Chain information for Arah2P3415A1.pdb #3
---
Chain | Description
A | No description available
B | No description available
F | No description available
P | No description available
Q | No description available
> close #3
> open "/Users/leightongo/Downloads/last_frame_rsr (3).pdb"
Chain information for last_frame_rsr (3).pdb #3
---
Chain | Description
A | No description available
B | No description available
F | No description available
P | No description available
Q | No description available
> select add #3
7686 atoms, 7864 bonds, 3 pseudobonds, 999 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide #!10 models
> hide #!12 models
> hide #!20 models
> hide #!3 models
> hide #!1 models
> select subtract #3
Nothing selected
> open /Users/leightongo/Downloads/cryosparc_P202_J161_map_sharp.mrc
Opened cryosparc_P202_J161_map_sharp.mrc as #4, grid size 260,260,260, pixel
0.67, shown at level 0.83, step 2, values float32
> select add #4
2 models selected
> view matrix models #4,1,0,0,17.996,0,1,0,-46.278,0,0,1,-83.45
> view matrix models #4,1,0,0,128.12,0,1,0,-77.08,0,0,1,-130.47
> volume #4 level 1.176
> volume #4 step 1
> close #4
> open "/Users/leightongo/Downloads/cryosparc_P202_J161_map_sharp (1).mrc"
Opened cryosparc_P202_J161_map_sharp (1).mrc as #4, grid size 260,260,260,
pixel 0.67, shown at level 0.115, step 2, values float32
> select add #4
2 models selected
> view matrix models #4,1,0,0,80.887,0,1,0,53.533,0,0,1,-61.808
> volume #4 level 0.04035
> volume #4 step 1
> show #!3 models
> view matrix models #4,1,0,0,-34.273,0,1,0,-15.999,0,0,1,-87.493
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-80.241,0,1,0,-87.839,0,0,1,-105.5
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.54217,0.79181,0.28122,-27.334,0.45443,-0.0052037,0.89077,-124.79,0.70678,0.61074,-0.35701,-102.8
> close #4
> open
> /Users/leightongo/Downloads/arah9F10antiFab_230714_SB1PN16_refine_13.pdb
Chain information for arah9F10antiFab_230714_SB1PN16_refine_13.pdb #4
---
Chain | Description
A | No description available
H | No description available
K | No description available
L | No description available
> ui tool show "Show Sequence Viewer"
> select add #4
9248 atoms, 9164 bonds, 3 pseudobonds, 823 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-59.618,0,1,0,61.809,0,0,1,56.518
> help sequence
> sequence chain #4/K
Alignment identifier is 4/K
> hide #!4 target m
> select subtract #4
Nothing selected
> select add #4
9248 atoms, 9164 bonds, 3 pseudobonds, 823 residues, 2 models selected
> select subtract #4
Nothing selected
> open
> /Users/leightongo/Downloads/cryosparc_P205_J122_004_volume_map_sharp.mrc
Opened cryosparc_P205_J122_004_volume_map_sharp.mrc as #5, grid size
420,420,420, pixel 0.67, shown at level 0.0402, step 2, values float32
> select add #5
2 models selected
> view matrix models #5,1,0,0,-219.53,0,1,0,51.704,0,0,1,-71.27
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.9025,0.39448,0.17288,-28.943,-0.12326,-0.62116,0.77393,187.12,0.41268,0.67716,0.60922,-169.61
> volume #5 level 0.1658
> volume #5 step 1
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.9025,0.39448,0.17288,-62.512,-0.12326,-0.62116,0.77393,-69.53,0.41268,0.67716,0.60922,-171.95
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.96064,-0.27629,-0.028935,-207.04,-0.10103,-0.25044,-0.96285,134.71,0.25878,0.92787,-0.2685,-53.804
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.96064,-0.27629,-0.028935,-187.58,-0.10103,-0.25044,-0.96285,185.64,0.25878,0.92787,-0.2685,-136.86
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.67108,-0.6387,-0.37645,-44.992,-0.54253,-0.076996,-0.8365,206.24,0.50529,0.76559,-0.39818,-130.62
> view matrix models
> #5,0.31446,-0.93472,-0.16559,15.119,-0.3001,0.067603,-0.95151,168.91,0.90058,0.34891,-0.25925,-150.77
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.31446,-0.93472,-0.16559,54.316,-0.3001,0.067603,-0.95151,150.97,0.90058,0.34891,-0.25925,-122.25
> view matrix models
> #5,0.31446,-0.93472,-0.16559,66.935,-0.3001,0.067603,-0.95151,149.75,0.90058,0.34891,-0.25925,-148.83
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.57486,-0.8082,0.12787,-31.193,-0.13455,-0.2475,-0.9595,170.38,0.80711,0.53437,-0.25102,-162.06
> view matrix models
> #5,0.47008,-0.85484,-0.21969,41.812,-0.38528,0.025198,-0.92246,163.41,0.79409,0.51827,-0.31751,-148.11
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.47008,-0.85484,-0.21969,48.155,-0.38528,0.025198,-0.92246,162.79,0.79409,0.51827,-0.31751,-143.32
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.47008,-0.85484,-0.21969,49.998,-0.38528,0.025198,-0.92246,166.9,0.79409,0.51827,-0.31751,-143.32
> view matrix models
> #5,0.47008,-0.85484,-0.21969,54.452,-0.38528,0.025198,-0.92246,166.57,0.79409,0.51827,-0.31751,-145.82
> hide #!3 models
> show #!10 models
> show #!17 models
> show #!13 models
> hide #!13 models
> show #!12 models
> select subtract #5
Nothing selected
> select add #10
715 atoms, 712 bonds, 2 pseudobonds, 104 residues, 3 models selected
> fitmap #12 inMap #5
Fit molecule Arah2_P34.pdb (#12) to map
cryosparc_P205_J122_004_volume_map_sharp.mrc (#5) using 5887 atoms
average map value = 0.1039, steps = 132
shifted from previous position = 3.79
rotated from previous position = 7.17 degrees
atoms outside contour = 4075, contour level = 0.1658
Position of Arah2_P34.pdb (#12) relative to
cryosparc_P205_J122_004_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.99035729 -0.00477427 0.13845446 170.13290758
-0.10875259 -0.59232425 -0.79832628 132.68023606
0.08582136 -0.80568553 0.58609343 102.36556725
Axis -0.06302199 0.45073073 -0.89043250
Axis point 83.93184242 89.50066454 0.00000000
Rotation angle (degrees) 176.65280129
Shift along axis -42.06868217
> select add #5
715 atoms, 712 bonds, 2 pseudobonds, 104 residues, 5 models selected
> select subtract #10
2 models selected
> transparency #5.1 50
> color #5 darkgrey models
> hide #!10 models
> select subtract #5
Nothing selected
> select add #17
5887 atoms, 5963 bonds, 1 pseudobond, 430 residues, 2 models selected
> view matrix models
> #17,-0.46873,0.65674,0.59075,-11.784,0.63426,-0.21525,0.74255,-72.274,0.61482,0.72274,-0.31566,-22.241
> view matrix models
> #17,-0.46873,0.65674,0.59075,-11.311,0.63426,-0.21525,0.74255,-70.788,0.61482,0.72274,-0.31566,-28.666
> fitmap #17 inMap #5
Fit molecule 15A1 (#17) to map cryosparc_P205_J122_004_volume_map_sharp.mrc
(#5) using 5887 atoms
average map value = 0.1054, steps = 160
shifted from previous position = 5.42
rotated from previous position = 23.9 degrees
atoms outside contour = 4261, contour level = 0.1658
Position of 15A1 (#17) relative to
cryosparc_P205_J122_004_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.08468570 0.86125540 -0.50106633 150.75468950
0.47218075 -0.47751139 -0.74096438 116.27363356
-0.87742445 -0.17384479 -0.44710660 201.57515149
Axis 0.72337086 0.48005130 -0.49627145
Axis point 0.00000000 -24.87350009 164.51723681
Rotation angle (degrees) 156.92113350
Shift along axis 64.83286421
> select subtract #17
Nothing selected
> select add #10
715 atoms, 712 bonds, 2 pseudobonds, 104 residues, 3 models selected
> show #!10 models
> view matrix models
> #10,0.93581,-0.32957,-0.1251,-11.836,0.34643,0.92545,0.15338,5.4371,0.065224,-0.18687,0.98022,-2.6158
> close #13.2-30
> show #!13 models
> hide #!13 models
> show #!32 models
> mmaker #32/T to #10
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 Arah2, chain F (#10) with Arah2P34.pdb, chain T (#32), sequence
alignment score = 448.8
RMSD between 89 pruned atom pairs is 0.570 angstroms; (across all 92 pairs:
0.854)
> ui mousemode right select
Drag select of 81 residues
> select up
1865 atoms, 1879 bonds, 132 residues, 1 model selected
> select up
6111 atoms, 6184 bonds, 429 residues, 1 model selected
> select up
13307 atoms, 13459 bonds, 956 residues, 1 model selected
> select down
6111 atoms, 6184 bonds, 429 residues, 1 model selected
> hide sel cartoons
Drag select of 5 residues
> select up
115 atoms, 112 bonds, 10 residues, 1 model selected
> select up
5847 atoms, 5923 bonds, 430 residues, 1 model selected
> color sel white
> select clear
> lighting flat
> color white #32/T
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #32/T white
> surface dust #5 size 4.02
> surface dust #5 size 3.84
> surface dust #5 size 4.95
> help vseries
> open
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_000.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_001.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_002.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_003.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_004.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_005.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_006.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_007.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_008.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_009.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_010.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_011.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_012.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_013.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_014.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_015.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_016.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_017.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_018.mrc
> /Users/leightongo/Downloads/cryosparc_P205_J123_component_000/J123_component_000_frame_019.mrc
Opened J123_component_000_frame_000.mrc as #6.1, grid size 440,440,440, pixel
0.67, shown at level 0.0211, step 2, values float32
Opened J123_component_000_frame_001.mrc as #6.2, grid size 440,440,440, pixel
0.67, shown at level 0.0216, step 2, values float32
Opened J123_component_000_frame_002.mrc as #6.3, grid size 440,440,440, pixel
0.67, shown at level 0.0219, step 2, values float32
Opened J123_component_000_frame_003.mrc as #6.4, grid size 440,440,440, pixel
0.67, shown at level 0.0224, step 2, values float32
Opened J123_component_000_frame_004.mrc as #6.5, grid size 440,440,440, pixel
0.67, shown at level 0.0229, step 2, values float32
Opened J123_component_000_frame_005.mrc as #6.6, grid size 440,440,440, pixel
0.67, shown at level 0.0235, step 2, values float32
Opened J123_component_000_frame_006.mrc as #6.7, grid size 440,440,440, pixel
0.67, shown at level 0.024, step 2, values float32
Opened J123_component_000_frame_007.mrc as #6.8, grid size 440,440,440, pixel
0.67, shown at level 0.0245, step 2, values float32
Opened J123_component_000_frame_008.mrc as #6.9, grid size 440,440,440, pixel
0.67, shown at level 0.0252, step 2, values float32
Opened J123_component_000_frame_009.mrc as #6.10, grid size 440,440,440, pixel
0.67, shown at level 0.0256, step 2, values float32
Opened J123_component_000_frame_010.mrc as #6.11, grid size 440,440,440, pixel
0.67, shown at level 0.0258, step 2, values float32
Opened J123_component_000_frame_011.mrc as #6.12, grid size 440,440,440, pixel
0.67, shown at level 0.0259, step 2, values float32
Opened J123_component_000_frame_012.mrc as #6.13, grid size 440,440,440, pixel
0.67, shown at level 0.026, step 2, values float32
Opened J123_component_000_frame_013.mrc as #6.14, grid size 440,440,440, pixel
0.67, shown at level 0.0258, step 2, values float32
Opened J123_component_000_frame_014.mrc as #6.15, grid size 440,440,440, pixel
0.67, shown at level 0.0256, step 2, values float32
Opened J123_component_000_frame_015.mrc as #6.16, grid size 440,440,440, pixel
0.67, shown at level 0.0254, step 2, values float32
Opened J123_component_000_frame_016.mrc as #6.17, grid size 440,440,440, pixel
0.67, shown at level 0.0255, step 2, values float32
Opened J123_component_000_frame_017.mrc as #6.18, grid size 440,440,440, pixel
0.67, shown at level 0.0258, step 2, values float32
Opened J123_component_000_frame_018.mrc as #6.19, grid size 440,440,440, pixel
0.67, shown at level 0.0262, step 2, values float32
Opened J123_component_000_frame_019.mrc as #6.20, grid size 440,440,440, pixel
0.67, shown at level 0.0267, step 2, values float32
> close #24
> select add #6
41 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-52.1,0,1,0,-237.08,0,0,1,-81.426
> view matrix models #6,1,0,0,-23.524,0,1,0,-208.56,0,0,1,-191.5
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.86881,-0.43317,-0.23985,96.5,-0.27219,-0.01317,-0.96215,130.45,0.41361,0.90122,-0.12934,-204.26
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.86881,-0.43317,-0.23985,34.05,-0.27219,-0.01317,-0.96215,199.32,0.41361,0.90122,-0.12934,-202.55
> view matrix models
> #6,0.86881,-0.43317,-0.23985,36.124,-0.27219,-0.01317,-0.96215,174.84,0.41361,0.90122,-0.12934,-218.77
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.54803,-0.8291,-0.11067,120.6,-0.53538,-0.24604,-0.80798,223.33,0.64267,0.50205,-0.57873,-124.22
> vseries play #6
No volume series specified
> pwd
Current working directory is: /Users/leightongo/Desktop
> close #6
> cd ../Downloads/
Current working directory is: /Users/leightongo/Downloads
> cd cryosparc_P205_J123_component_000
Current working directory is:
/Users/leightongo/Downloads/cryosparc_P205_J123_component_000
> open J123*.mrc vseries true
Opened map series J123_component_000_frame_000.mrc as #6, 20 images, grid size
440,440,440, pixel 0.67, shown at level 0.0211, step 2, values float32
> select add #6
22 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-44.294,0,1,0,-207.54,0,0,1,-207.19
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.77369,0.13805,0.61834,-127.29,-0.57829,0.55258,0.6002,-150.87,-0.25882,-0.82195,0.50735,26.974
> volume #6.1 step 1
> volume #6.1 level 0.07106
> vseries play #6
> vseries play #6 loop true
> top #6
Unknown command: vseries top #6
> vseries stop #6
> volume #6.1 level 0.02113
> volume #6.20 level 0.04665
> cd ../cryosparc_P205_J123_component_001
Current working directory is:
/Users/leightongo/Downloads/cryosparc_P205_J123_component_001
> open *.mrc vseries true
Opened map series J123_component_001_frame_000.mrc as #7, 20 images, grid size
440,440,440, pixel 0.67, shown at level 0.0255, step 2, values float32
> cd ../cryosparc_P205_J123_component_002
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> select add #6
41 models selected
> select subtract #6
Nothing selected
> select add #7
22 models selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,35.204,0,1,0,-55.458,0,0,1,-156.27
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.71941,-0.62635,0.30022,120.21,-0.2609,-0.64425,-0.71894,334.34,0.64373,0.43889,-0.62689,-59.192
> view matrix models
> #7,0.57146,-0.82062,-0.003891,218.33,-0.23914,-0.16199,-0.95738,299.07,0.78501,0.54803,-0.28882,-149.39
> cd ../cryosparc_P205_J123_component_002
Current working directory is:
/Users/leightongo/Downloads/cryosparc_P205_J123_component_002
> open *.mrc vseries true
Opened map series J123_component_002_frame_000.mrc as #8, 20 images, grid size
440,440,440, pixel 0.67, shown at level 0.0255, step 2, values float32
> vseries play #7
> volume #7.20 step 1
> volume #8.1 step 1
> volume #7.20 level 0.06134
> help vseries
> vseries slider #7
> vseries slider #8
> volume #8.1 level 0.05691
> hide #!6-8 target m
> select add #7
40 models selected
> select subtract #7
Nothing selected
> color #32 black
> color #32 #0433ffff
> color #32/T white
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/leightongo/Desktop/movie8.mp4
Movie saved to /Users/leightongo/Desktop/movie8.mp4
> hide #!32 models
> select add #10
715 atoms, 712 bonds, 2 pseudobonds, 104 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.93581,-0.32957,-0.1251,-12.566,0.34643,0.92545,0.15338,5.9459,0.065224,-0.18687,0.98022,-3.9177
> view matrix models
> #10,0.93581,-0.32957,-0.1251,-12.747,0.34643,0.92545,0.15338,5.8006,0.065224,-0.18687,0.98022,-4.3768
> fitmap #10 inMap #5 shift false
Fit molecule Arah2 (#10) to map cryosparc_P205_J122_004_volume_map_sharp.mrc
(#5) using 715 atoms
average map value = 0.07506, steps = 76
shifted from previous position = 2.93e-14
rotated from previous position = 12.7 degrees
atoms outside contour = 517, contour level = 0.1658
Position of Arah2 (#10) relative to
cryosparc_P205_J122_004_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.52259245 -0.53302100 0.66542148 147.39526372
-0.74848367 0.08689972 0.65743488 125.79465768
-0.40825154 -0.84162762 -0.35354437 120.06991684
Axis -0.80749113 0.57834910 -0.11606201
Axis point 0.00000000 163.05334262 -17.84021741
Rotation angle (degrees) 111.84062655
Shift along axis -60.20269739
> view matrix models
> #10,0.97519,-0.13995,-0.17153,-10.373,0.15639,0.98392,0.086322,1.6212,0.15669,-0.11101,0.98139,-0.40534
> fitmap #10 inMap #5 rotate false
Fit molecule Arah2 (#10) to map cryosparc_P205_J122_004_volume_map_sharp.mrc
(#5) using 715 atoms
average map value = 0.08978, steps = 56
shifted from previous position = 1.62
rotated from previous position = 0 degrees
atoms outside contour = 498, contour level = 0.1658
Position of Arah2 (#10) relative to
cryosparc_P205_J122_004_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.52259245 -0.53302100 0.66542148 149.29256739
-0.74848367 0.08689972 0.65743488 126.25521665
-0.40825154 -0.84162762 -0.35354437 118.83879479
Axis -0.80749113 0.57834910 -0.11606201
Axis point 0.00000000 163.39275359 -19.05709274
Rotation angle (degrees) 111.84062655
Shift along axis -61.32550292
> fitmap #10 inMap #5
Fit molecule Arah2 (#10) to map cryosparc_P205_J122_004_volume_map_sharp.mrc
(#5) using 715 atoms
average map value = 0.09651, steps = 96
shifted from previous position = 0.871
rotated from previous position = 4.39 degrees
atoms outside contour = 503, contour level = 0.1658
Position of Arah2 (#10) relative to
cryosparc_P205_J122_004_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.53670649 -0.48220629 0.69240395 151.55228541
-0.73535863 0.13508454 0.66407819 127.22060401
-0.41375575 -0.86558030 -0.28209381 119.37871458
Axis -0.80313573 0.58078086 -0.13291574
Axis point 0.00000000 168.78921809 -27.44592577
Rotation angle (degrees) 107.76727202
Shift along axis -63.69707314
> fitmap #10 inMap #5
Fit molecule Arah2 (#10) to map cryosparc_P205_J122_004_volume_map_sharp.mrc
(#5) using 715 atoms
average map value = 0.09652, steps = 68
shifted from previous position = 0.0024
rotated from previous position = 0.00867 degrees
atoms outside contour = 503, contour level = 0.1658
Position of Arah2 (#10) relative to
cryosparc_P205_J122_004_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.53678585 -0.48225320 0.69230975 151.55048233
-0.73525950 0.13508765 0.66418731 127.22396387
-0.41382896 -0.86555368 -0.28206811 119.38080525
Axis -0.80316443 0.58075927 -0.13283664
Axis point 0.00000000 168.79102362 -27.43806278
Rotation angle (degrees) 107.76401817
Shift along axis -63.69160526
> select subtract #10
Nothing selected
> volume #5 level 0.1325
> save /Users/leightongo/Desktop/image6.png supersample 3
> turn y 1 1 center #10/F:41
[Repeated 3 time(s)]
> save /Users/leightongo/Desktop/image7.png supersample 3
> turn y 1 1 center #10/F:41
[Repeated 1 time(s)]
> turn y 1 -1 center #10/F:41
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn y 1 -1 center #10/F:41
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn -y 1 1 center #10/F:41
[Repeated 7 time(s)]
> save /Users/leightongo/Desktop/image8.png supersample 3
> combine #10 close false
> select add #9
715 atoms, 712 bonds, 2 pseudobonds, 104 residues, 3 models selected
> ui mousemode right "rotate selected models"
> help rotate
No help found for 'rotate'
> help turn
> view matrix models
> #9,0.58127,0.75762,0.29687,8.6026,-0.57041,0.63958,-0.51534,-28.321,-0.5803,0.13021,0.80393,-11.893
> color #9 #f0f0f0ff
> color #9 #947cfcff
> view matrix models
> #9,-0.37393,0.72288,-0.58105,-28.482,0.92742,0.29665,-0.22778,-1.4492,0.0077084,-0.62406,-0.78134,-50.117
> view matrix models
> #9,0.10422,0.5093,-0.85425,-29.963,-0.50357,0.76771,0.39627,-4.0026,0.85765,0.38888,0.33648,5.1002
> view matrix models
> #9,0.95813,-0.15081,-0.24341,-10.977,-0.14637,0.47268,-0.86899,-31.91,0.24611,0.86823,0.43082,4.0391
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.95813,-0.15081,-0.24341,-11.885,-0.14637,0.47268,-0.86899,-32.573,0.24611,0.86823,0.43082,-4.1371
> view matrix models
> #9,0.95813,-0.15081,-0.24341,-10.166,-0.14637,0.47268,-0.86899,-33.456,0.24611,0.86823,0.43082,-7.6789
> view matrix models
> #9,0.95813,-0.15081,-0.24341,-8.2684,-0.14637,0.47268,-0.86899,-32.543,0.24611,0.86823,0.43082,-5.7414
> view matrix models
> #9,0.95813,-0.15081,-0.24341,-7.2918,-0.14637,0.47268,-0.86899,-32.891,0.24611,0.86823,0.43082,-7.4422
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.8938,-0.21804,-0.39189,-12.827,-0.15154,0.67561,-0.72152,-26.564,0.42209,0.70428,0.57082,-3.607
> select subtract #9
Nothing selected
> hide #!9 models
> show #!32 models
> mmaker #34 to #17
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 15A1, chain P (#17) with Arah2P3415A1.pdb, chain P (#34), sequence
alignment score = 1116.4
RMSD between 213 pruned atom pairs is 0.001 angstroms; (across all 213 pairs:
0.001)
> show #!34 models
> hide #!34 models
> mmaker #32 to #17
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 15A1, chain P (#17) with Arah2P34.pdb, chain P (#32), sequence
alignment score = 1116.4
RMSD between 213 pruned atom pairs is 0.003 angstroms; (across all 213 pairs:
0.003)
> show #!18 models
> show #!11 models
> show #!20 models
> hide #!20 models
> hide #!32 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/leightongo/Desktop/movie9.mp4
Movie saved to /Users/leightongo/Desktop/movie9.mp4
> ui mousemode right select
> select #12/Q:197
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #18/J:176
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> show #!4 models
> mmaker #4 to #18
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 S1, chain J (#18) with
arah9F10antiFab_230714_SB1PN16_refine_13.pdb, chain L (#4), sequence alignment
score = 937.9
RMSD between 204 pruned atom pairs is 0.966 angstroms; (across all 209 pairs:
1.019)
> select #4/A:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
221 atoms, 220 bonds, 17 residues, 1 model selected
> select up
1227 atoms, 1238 bonds, 93 residues, 1 model selected
> select up
9248 atoms, 9164 bonds, 823 residues, 1 model selected
> select down
1227 atoms, 1238 bonds, 93 residues, 1 model selected
> hide sel cartoons
> select #4/L:107
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
70 atoms, 70 bonds, 4 residues, 1 model selected
> select up
3023 atoms, 3059 bonds, 209 residues, 1 model selected
> hide sel cartoons
> select #4/H:198
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
33 atoms, 32 bonds, 3 residues, 1 model selected
> select up
1107 atoms, 1121 bonds, 77 residues, 1 model selected
> select up
1131 atoms, 1145 bonds, 79 residues, 1 model selected
> select up
3075 atoms, 3115 bonds, 211 residues, 1 model selected
> hide sel cartoons
> combine #4 close false
> mmaker #24 to #17
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 15A1, chain Q (#17) with copy of
arah9F10antiFab_230714_SB1PN16_refine_13.pdb, chain L (#24), sequence
alignment score = 843.9
RMSD between 203 pruned atom pairs is 1.059 angstroms; (across all 208 pairs:
1.193)
> hide #!5 models
> hide #!12 models
> hide #!11 models
> save /Users/leightongo/Desktop/image9.png supersample 3
> turn y 1 180
> save /Users/leightongo/Desktop/image10.png supersample 3
> turn x 1 90
> save /Users/leightongo/Desktop/image11.png supersample 3
> show #!26 models
> hide #!24 models
> show #!24 models
> hide #!26 models
> show #!21 models
> hide #!24 models
> hide #!18 models
> hide #!17 models
> hide #!10 models
> hide #!4 models
> select add #4
9248 atoms, 9164 bonds, 3 pseudobonds, 823 residues, 2 models selected
> select #21/D:24
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
Drag select of 57 residues
> select up
717 atoms, 725 bonds, 94 residues, 1 model selected
> select up
1777 atoms, 1826 bonds, 230 residues, 1 model selected
> color sel hot pink
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/leightongo/Desktop/movie10.mp4
Movie saved to /Users/leightongo/Desktop/movie10.mp4
> hide #!21 models
> show #!4 models
> hide #!4 models
> save /Users/leightongo/Desktop/Arah2_FABs.cxs includeMaps true
——— End of log from Tue Nov 7 13:32:34 2023 ———
opened ChimeraX session
> show #!10 models
> show #!11 models
> show #!12 models
> show #!17 models
> show #!18 models
> show #!4 models
> show #!14 models
> close #14
> show #!24 models
> show #!34 models
> hide #!34 models
> select add #24
9248 atoms, 9164 bonds, 3 pseudobonds, 823 residues, 2 models selected
> show sel cartoons
> undo
> help combine
> combine #24 modelName P34AntiFAB
Expected a keyword
> help combine
> combine #24 name P34AntiFAB
> mmaker #14 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 Arah2_P34.pdb, chain Q (#12) with P34AntiFAB, chain L (#14),
sequence alignment score = 843.9
RMSD between 203 pruned atom pairs is 1.059 angstroms; (across all 208 pairs:
1.193)
> select up
114585 atoms, 115531 bonds, 3 pseudobonds, 11961 residues, 43 models selected
> select down
9248 atoms, 9164 bonds, 3 pseudobonds, 823 residues, 2 models selected
> combine #24 name T5AntiFAB
> mmaker #30 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 T5, chain B (#11) with T5AntiFAB, chain L (#30), sequence alignment
score = 926.1
RMSD between 58 pruned atom pairs is 0.361 angstroms; (across all 209 pairs:
13.632)
> hide #!24 models
> show #!24 models
> rename #24 _15A1AntiFAB
> hide #!17 models
> hide #!18 models
> hide #!11 models
> hide #!12 models
> select add #4
18496 atoms, 18328 bonds, 6 pseudobonds, 1646 residues, 4 models selected
> select subtract #4
9248 atoms, 9164 bonds, 3 pseudobonds, 823 residues, 2 models selected
> combine #4 name S1AntiFAB
> hide #!4 models
> select add #36
18496 atoms, 18328 bonds, 6 pseudobonds, 1646 residues, 4 models selected
> select add #30
27744 atoms, 27492 bonds, 9 pseudobonds, 2469 residues, 6 models selected
> select add #14
36992 atoms, 36656 bonds, 12 pseudobonds, 3292 residues, 8 models selected
> show sel cartoons
> ui mousemode right select
> select clear
Drag select of 120 residues, 1 pseudobonds
> select up
2361 atoms, 2383 bonds, 1 pseudobond, 164 residues, 2 models selected
> select up
6098 atoms, 6174 bonds, 1 pseudobond, 420 residues, 2 models selected
> select up
9248 atoms, 9164 bonds, 3 pseudobonds, 823 residues, 2 models selected
> select down
6098 atoms, 6174 bonds, 1 pseudobond, 420 residues, 2 models selected
> delete sel
Drag select of 44 residues
> select up
1262 atoms, 1268 bonds, 86 residues, 1 model selected
> select up
6098 atoms, 6174 bonds, 420 residues, 1 model selected
> select up
9248 atoms, 9164 bonds, 823 residues, 1 model selected
> select down
6098 atoms, 6174 bonds, 420 residues, 1 model selected
> delete sel
Drag select of 108 residues, 2 pseudobonds
> select up
2221 atoms, 2241 bonds, 2 pseudobonds, 155 residues, 2 models selected
> select up
6098 atoms, 6174 bonds, 2 pseudobonds, 420 residues, 2 models selected
> select up
9248 atoms, 9164 bonds, 3 pseudobonds, 823 residues, 2 models selected
> select down
6098 atoms, 6174 bonds, 2 pseudobonds, 420 residues, 2 models selected
> delete sel
Drag select of 11 residues
> select up
514 atoms, 514 bonds, 36 residues, 1 model selected
> select up
1733 atoms, 1752 bonds, 120 residues, 1 model selected
> select up
3150 atoms, 2990 bonds, 403 residues, 1 model selected
> select up
114787 atoms, 115337 bonds, 12347 residues, 44 models selected
> select down
3150 atoms, 2990 bonds, 403 residues, 1 model selected
> select down
1733 atoms, 1752 bonds, 120 residues, 1 model selected
> delete sel
> hide #!10 models
Drag select of 329 residues
> select clear
Drag select of 49 residues
> select up
1382 atoms, 1391 bonds, 104 residues, 1 model selected
> select up
6218 atoms, 6291 bonds, 436 residues, 1 model selected
> select up
6239 atoms, 6311 bonds, 438 residues, 1 model selected
> select up
7325 atoms, 7412 bonds, 513 residues, 1 model selected
> select up
9248 atoms, 9164 bonds, 823 residues, 1 model selected
> select down
7325 atoms, 7412 bonds, 513 residues, 1 model selected
> delete sel
Drag select of 91 residues
> select up
1654 atoms, 1666 bonds, 127 residues, 2 models selected
> select up
2454 atoms, 2476 bonds, 186 residues, 2 models selected
> select up
4567 atoms, 4228 bonds, 686 residues, 2 models selected
> select down
2454 atoms, 2476 bonds, 186 residues, 2 models selected
> delete sel
> show #!10 models
> show #!11 models
> show #!12 models
> show #!17 models
> show #!18 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> hide #!18 models
> show #!18 models
> hide #!24 models
> show #!24 models
> hide #!30 models
> show #!30 models
Drag select of 44 residues
> select up
939 atoms, 943 bonds, 72 residues, 1 model selected
> select up
1227 atoms, 1238 bonds, 93 residues, 1 model selected
> select up
3150 atoms, 2990 bonds, 403 residues, 1 model selected
> select down
1227 atoms, 1238 bonds, 93 residues, 1 model selected
> delete sel
> show #!36 models
> hide #!36 models
> select add #36
190 atoms, 190 residues, 1 model selected
> show #!10-12,14,17-18,24,30 cartoons
> show #!36 models
> hide #!36 models
> show #!36 models
> close #36
> hide #!12 models
> show #!12 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> show #!18 models
Drag select of 5 residues
> select up
86 atoms, 85 bonds, 12 residues, 1 model selected
> select up
1516 atoms, 1555 bonds, 206 residues, 1 model selected
> select up
1528 atoms, 1555 bonds, 218 residues, 1 model selected
> select up
6419 atoms, 6454 bonds, 981 residues, 1 model selected
> select down
1528 atoms, 1555 bonds, 218 residues, 1 model selected
> delete sel
Drag select of 2 residues
> select up
27 atoms, 26 bonds, 4 residues, 1 model selected
> select up
1001 atoms, 1028 bonds, 138 residues, 1 model selected
> select up
1004 atoms, 1030 bonds, 139 residues, 1 model selected
> select up
1586 atoms, 1628 bonds, 221 residues, 1 model selected
> select up
1600 atoms, 1628 bonds, 235 residues, 1 model selected
> select up
4891 atoms, 4899 bonds, 763 residues, 1 model selected
> select down
1600 atoms, 1628 bonds, 235 residues, 1 model selected
> delete sel
> hide #!10 models
> show #!10 models
> show #!4 models
> select add #4
9248 atoms, 9164 bonds, 3 pseudobonds, 823 residues, 2 models selected
> show sel cartoons
> undo
> combine #4 name S1AntiFAB
> hide #!4 models
> select subtract #4
Nothing selected
> select add #36
9248 atoms, 9164 bonds, 3 pseudobonds, 823 residues, 2 models selected
> show sel cartoons
> hide #!18 models
> hide #!10 models
> select clear
Drag select of 17 residues
> select up
780 atoms, 785 bonds, 51 residues, 1 model selected
> select up
4991 atoms, 5053 bonds, 343 residues, 1 model selected
> select up
5012 atoms, 5073 bonds, 345 residues, 1 model selected
> select up
6098 atoms, 6174 bonds, 420 residues, 1 model selected
> select up
9248 atoms, 9164 bonds, 823 residues, 1 model selected
> select down
6098 atoms, 6174 bonds, 420 residues, 1 model selected
> delete sel
Drag select of 10 residues
> select up
576 atoms, 576 bonds, 43 residues, 1 model selected
> select up
1227 atoms, 1238 bonds, 93 residues, 1 model selected
> select up
3150 atoms, 2990 bonds, 403 residues, 1 model selected
> select down
1227 atoms, 1238 bonds, 93 residues, 1 model selected
> delete sel
> show #!18 models
> show #!10 models
> save Arah2_4FAB_AntiFAB.pdb #10-12,14,17-18,24,30,36
> help save
> save Arah2_4FAB_AntiFAB.cif #10-12,14,17-18,24,30,36
Not saving entity_poly_seq for non-authoritative sequences
[Repeated 6 time(s)]
> open /Users/leightongo/Desktop/Arah2_4FAB_AntiFAB.cif
Summary of feedback from opening
/Users/leightongo/Desktop/Arah2_4FAB_AntiFAB.cif
---
warnings | Unknown polymer entity '1' near line 1455
Unknown polymer entity '2' near line 4710
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Unknown polymer entity '1' near line 21644
Unknown polymer entity '2' near line 24553
Atom 2HB is not in the residue template for SER /P:56
Atom 2HB is not in the residue template for ARG /P:57
Atom 2HB is not in the residue template for SER /Q:32
Atom 2HB is not in the residue template for LYS /Q:58
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Unknown polymer entity '1' near line 39805
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Unknown polymer entity '1' near line 43853
Unknown polymer entity '2' near line 46762
Atom 2HB is not in the residue template for SER /P:56
Atom 2HB is not in the residue template for ARG /P:57
Atom 2HB is not in the residue template for SER /Q:32
Atom 2HB is not in the residue template for LYS /Q:58
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Unknown polymer entity '1' near line 66925
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Unknown polymer entity '1' near line 70973
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Unknown polymer entity '1' near line 75021
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for Arah2_4FAB_AntiFAB.cif
---
Chain | Description
37.2/A | No description available
37.2/B | No description available
37.1/F | ara H 2 allergen
37.6/I | 22S1 heavy chain
37.6/J | 22S1 light chain
37.4/K 37.7/K 37.8/K 37.9/K | No description available
37.3/P 37.5/P | No description available
37.3/Q 37.5/Q | No description available
> hide #!36 models
> hide #!30 models
> hide #!24 models
> hide #!18 models
> hide #!17 models
> hide #!14 models
> hide #!12 models
> hide #!10 models
> hide #!11 models
> save "/Users/leightongo/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Projects/Sarita/Ara h 2/Arah2_FABs.cxs"
> includeMaps true
Traceback (most recent call last):
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x10138e790>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x10138e790>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File
"/Users/leightongo/Desktop/Apps/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: MK1A3LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.41.12
OS Loader Version: 8422.141.2.700.1
Software:
System Software Overview:
System Version: macOS 13.6.2 (22G320)
Kernel Version: Darwin 22.6.0
Time since boot: 4 days, 1 hour, 9 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
DELL P2723QE:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.0
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.11
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.48
ChimeraX-AtomicLibrary: 10.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.3
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.4
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202309222343
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.12
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.10
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StarMap: 1.2.15
ChimeraX-StdCommands: 1.12.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.32.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.4
contourpy: 1.1.1
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.42.1
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.6
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.10.0
prompt-toolkit: 3.0.39
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
pyqtgraph: 0.13.3
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.0
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.2
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.0.5
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (3)
comment:1 by , 23 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Unable to restore objects of NewerVersionQuery class |
comment:2 by , 23 months ago
comment:3 by , 23 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hi Gage,
--Eric