![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8498 closed defect (duplicate)
Crash clearing aniso_u6
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | Eric Pettersen, Tom Goddard, Zach Pearson | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.2-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000102620580 (most recent call first):
File "/private/var/folders/57/lgvwg0s92qz_0_6q78v2dqp00000gn/T/AppTranslocation/FCBD6C9C-5CE4-48DD-B2AE-90A5BCB3E7AC/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 846 in _set_aniso_u6
File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/sanity_check.py", line 12 in remove_invalid_anisou
File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 667 in _anisou_sanity_check
File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 636 in add_model
File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 594 in __init__
File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 170 in _get_symmetry_handler
File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 159 in get_symmetry_handler
File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 814 in _change_selected_model
File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 771 in change_selected_model
File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 433 in selected_model
File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/ui/main_win.py", line 157 in _set_selected_model
File "/private/var/folders/57/lgvwg0s92qz_0_6q78v2dqp00000gn/T/AppTranslocation/FCBD6C9C-5CE4-48DD-B2AE-90A5BCB3E7AC/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/private/var/folders/57/lgvwg0s92qz_0_6q78v2dqp00000gn/T/AppTranslocation/FCBD6C9C-5CE4-48DD-B2AE-90A5BCB3E7AC/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/private/var/folders/57/lgvwg0s92qz_0_6q78v2dqp00000gn/T/AppTranslocation/FCBD6C9C-5CE4-48DD-B2AE-90A5BCB3E7AC/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/private/var/folders/57/lgvwg0s92qz_0_6q78v2dqp00000gn/T/AppTranslocation/FCBD6C9C-5CE4-48DD-B2AE-90A5BCB3E7AC/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/57/lgvwg0s92qz_0_6q78v2dqp00000gn/T/AppTranslocation/FCBD6C9C-5CE4-48DD-B2AE-90A5BCB3E7AC/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
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===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/zekecook/Downloads/cryosparc_P34_J150_000_volume_map_sharp.mrc
> format mrc
Opened cryosparc_P34_J150_000_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 1.05, shown at level 0.0805, step 2, values float32
> ui tool show Toolbar
> surface dust #1 size 10.5
> ui mousemode right zoom
> volume #1 step 1
> volume #1 level 0.1671
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> open /Users/zekecook/Downloads/cryosparc_P34_J150_002_volume_map_sharp.mrc
Opened cryosparc_P34_J150_002_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 1.05, shown at level 0.102, step 2, values float32
> volume #2 step 1
> volume #2 level 0.3059
> volume #2 level 0.1356
> volume #2 level 0.2718
> volume #2 color #ffffb282
> ui mousemode right zoom
> ui mousemode right translate
> open /Users/zekecook/Desktop/PI3k_Rab1a_Retry.pdb format pdb
Summary of feedback from opening /Users/zekecook/Desktop/PI3k_Rab1a_Retry.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 23
ASP A 34 1 12
Start residue of secondary structure not found: HELIX 2 2 GLN A 70 ARG A 74 1
5
Start residue of secondary structure not found: HELIX 3 3 ILE A 76 ARG A 82 1
7
Start residue of secondary structure not found: HELIX 4 4 ASP A 95 ASN A 100 1
6
Start residue of secondary structure not found: HELIX 5 5 ASN A 101 ALA A 113
1 13
18 messages similar to the above omitted
Chain information for PI3k_Rab1a_Retry.pdb
---
Chain | Description
3.1/A | No description available
3.2/A | No description available
3.1/B | No description available
3.2/B | No description available
3.2/C | No description available
3.2/D | No description available
> ui mousemode right zoom
> delete #3.1 B
Expected a keyword
> delete #3.1B
Missing or invalid "atoms" argument: only initial part "#3" of atom specifier
valid
> delete #3.1/B
> select add #3.1
1460 atoms, 1426 bonds, 6 pseudobonds, 231 residues, 2 models selected
> select add #3
32298 atoms, 32597 bonds, 17 pseudobonds, 2218 residues, 5 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.95645,-0.077047,0.28153,-30.271,0.18362,-0.59094,-0.78554,497.85,0.22689,0.80302,-0.55106,80.049
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.95645,-0.077047,0.28153,-12.561,0.18362,-0.59094,-0.78554,462.78,0.22689,0.80302,-0.55106,83.535
> view matrix models
> #3,0.95645,-0.077047,0.28153,-15.9,0.18362,-0.59094,-0.78554,457.83,0.22689,0.80302,-0.55106,79.222
> view matrix models
> #3,0.95645,-0.077047,0.28153,-13.994,0.18362,-0.59094,-0.78554,452.43,0.22689,0.80302,-0.55106,80.136
> view matrix models
> #3,0.95645,-0.077047,0.28153,-17.265,0.18362,-0.59094,-0.78554,449.09,0.22689,0.80302,-0.55106,81.536
> view matrix models
> #3,0.95645,-0.077047,0.28153,-19.919,0.18362,-0.59094,-0.78554,447.11,0.22689,0.80302,-0.55106,82.102
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
> surface dust #2 size 10.5
> hide #!3.1 models
> view matrix models
> #3,0.95645,-0.077047,0.28153,-23.871,0.18362,-0.59094,-0.78554,456.19,0.22689,0.80302,-0.55106,83.247
> view matrix models
> #3,0.95645,-0.077047,0.28153,-20.375,0.18362,-0.59094,-0.78554,448.69,0.22689,0.80302,-0.55106,81.709
> fitmap #3.2 inMap #2
Fit molecule PI3k_Rab1a_Retry.pdb (#3.2) to map
cryosparc_P34_J150_002_volume_map_sharp.mrc (#2) using 30838 atoms
average map value = 0.2937, steps = 216
shifted from previous position = 5.97
rotated from previous position = 9.32 degrees
atoms outside contour = 19077, contour level = 0.27185
Position of PI3k_Rab1a_Retry.pdb (#3.2) relative to
cryosparc_P34_J150_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99108833 0.10373670 -0.08356210 -2.80872555
-0.11104856 0.98989285 -0.08820641 47.76589675
0.07356729 0.09669979 0.99259106 -36.49490865
Axis 0.57059854 -0.48488261 -0.66280175
Axis point 422.14887768 60.18026385 0.00000000
Rotation angle (degrees) 9.32464443
Shift along axis -0.57461831
> show #!3.1 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
> hide #!3.2 models
> fitmap #3.1 inMap #2
Fit molecule PI3k_Rab1a_Retry.pdb (#3.1) to map
cryosparc_P34_J150_002_volume_map_sharp.mrc (#2) using 1460 atoms
average map value = 0.1937, steps = 92
shifted from previous position = 8.99
rotated from previous position = 13.7 degrees
atoms outside contour = 1026, contour level = 0.27185
Position of PI3k_Rab1a_Retry.pdb (#3.1) relative to
cryosparc_P34_J150_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.97168670 0.14264829 0.18835186 -51.75154598
-0.14339448 0.98961777 -0.00973061 44.02106028
-0.18778440 -0.01755352 0.98205341 49.58539580
Axis -0.01655257 0.79587040 -0.60524071
Axis point 253.16193821 0.00000000 312.29879124
Rotation angle (degrees) 13.66855856
Shift along axis 5.88057973
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.92038,-0.14978,0.36121,-13.42,0.14422,-0.72859,-0.6696,461.97,0.36346,0.66837,-0.64898,95.442
> view matrix models
> #3,0.96245,-0.18085,0.20245,13.208,0.0093915,-0.72315,-0.69063,495.22,0.2713,0.6666,-0.6943,125.09
> view matrix models
> #3,0.97773,-0.20292,0.05354,42.261,-0.066513,-0.54159,-0.83801,505.38,0.19905,0.81579,-0.54302,83.992
> view matrix models
> #3,0.9823,-0.18464,-0.031486,53.854,-0.1323,-0.56497,-0.81444,520.18,0.13258,0.80419,-0.5794,108.06
> view matrix models
> #3,0.98689,0.05585,-0.15144,29.413,-0.086854,-0.60707,-0.78989,513.39,-0.13605,0.79268,-0.59426,173.45
> view matrix models
> #3,0.98607,0.05477,-0.15707,30.873,-0.091515,-0.60988,-0.78719,514.47,-0.13891,0.7906,-0.59637,174.9
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98607,0.05477,-0.15707,29.491,-0.091515,-0.60988,-0.78719,513.01,-0.13891,0.7906,-0.59637,176.98
> fitmap #3.1 inMap #2
Fit molecule PI3k_Rab1a_Retry.pdb (#3.1) to map
cryosparc_P34_J150_002_volume_map_sharp.mrc (#2) using 1460 atoms
average map value = 0.2371, steps = 100
shifted from previous position = 5.24
rotated from previous position = 13.5 degrees
atoms outside contour = 940, contour level = 0.27185
Position of PI3k_Rab1a_Retry.pdb (#3.1) relative to
cryosparc_P34_J150_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.90872827 0.08759037 0.40809417 -73.59757847
-0.09315114 0.99563224 -0.00626993 31.94730578
-0.40686090 -0.03231678 0.91291831 113.62237350
Axis -0.03118774 0.97580329 -0.21641457
Axis point 234.31822995 0.00000000 232.07206660
Rotation angle (degrees) 24.68200011
Shift along axis 8.88009077
> ui mousemode right select
> select clear
> volume #2 level 0.1924
> ui mousemode right zoom
> ui mousemode right select
> select #3.1/A:137
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
95 atoms, 96 bonds, 12 residues, 1 model selected
> select up
1369 atoms, 1392 bonds, 171 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #3.1,0.90873,0.08759,0.40809,-68.025,-0.093151,0.99563,-0.0062699,31.495,-0.40686,-0.032317,0.91292,113.97
> fitmap #3.1 inMap #2
Fit molecule PI3k_Rab1a_Retry.pdb (#3.1) to map
cryosparc_P34_J150_002_volume_map_sharp.mrc (#2) using 1460 atoms
average map value = 0.3618, steps = 88
shifted from previous position = 1.57
rotated from previous position = 28.9 degrees
atoms outside contour = 511, contour level = 0.19239
Position of PI3k_Rab1a_Retry.pdb (#3.1) relative to
cryosparc_P34_J150_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.89450233 -0.18379227 0.40753648 -16.38621867
0.31327363 0.90803168 -0.27809729 7.05843205
-0.31894390 0.37642911 0.86981372 29.93132954
Axis 0.59668990 0.66228573 0.45314322
Axis point 54.58862409 0.00000000 66.72634213
Rotation angle (degrees) 33.26173235
Shift along axis 8.46038672
> show sel atoms
> view matrix models
> #3.1,0.8945,-0.18379,0.40754,-16.393,0.31327,0.90803,-0.2781,7.047,-0.31894,0.37643,0.86981,29.862
> undo
> ui mousemode right translate
> show #!3.2 models
> ui mousemode right select
> select #3.2/A:184
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
243 atoms, 243 bonds, 14 residues, 1 model selected
> show sel atoms
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #3.2,0.99109,0.10374,-0.083562,-2.3825,-0.11105,0.98989,-0.088206,48.291,0.073567,0.0967,0.99259,-36.296
> hide #!3.1 models
> fitmap #3.2 inMap #2
Fit molecule PI3k_Rab1a_Retry.pdb (#3.2) to map
cryosparc_P34_J150_002_volume_map_sharp.mrc (#2) using 30838 atoms
average map value = 0.2937, steps = 316
shifted from previous position = 8.51
rotated from previous position = 26.6 degrees
atoms outside contour = 13786, contour level = 0.19239
Position of PI3k_Rab1a_Retry.pdb (#3.2) relative to
cryosparc_P34_J150_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.93296280 0.00191752 0.35996770 -54.49951535
0.01315946 0.99913572 -0.03942895 6.11122621
-0.35973219 0.04152272 0.93213122 83.39566557
Axis 0.11176146 0.99361385 0.01552055
Axis point 196.23839018 0.00000000 188.34287444
Rotation angle (degrees) 21.23307877
Shift along axis 1.27560044
> ui mousemode right zoom
> show #!3.1 models
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right select
> select #3.2/A:185
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
96 atoms, 96 bonds, 6 residues, 1 model selected
> show sel atoms
> select #3.2/A:191
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
351 atoms, 353 bonds, 21 residues, 1 model selected
> show sel atoms
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> open /Users/zekecook/Downloads/DMF34_results/model1.pdb
Chain information for model1.pdb #4
---
Chain | Description
A | No description available
B | No description available
> hide #!3.1 models
> hide #!3 models
> color bfactor palette alphafold
50310 atoms, 3350 residues, atom bfactor range 13.1 to 151
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right select
> select clear
> select #4/A:343
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
366 atoms, 368 bonds, 21 residues, 1 model selected
> select up
7703 atoms, 7772 bonds, 492 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
Drag select of 15 atoms, 10 residues, 13 bonds
> select clear
> ui mousemode right translate
> open
> /Users/zekecook/Downloads/ATG13_150_230_WIPI4_52448.result/ATG13_150_230_WIPI4_52448_unrelaxed_rank_2_model_5.pdb
> format pdb
Chain information for ATG13_150_230_WIPI4_52448_unrelaxed_rank_2_model_5.pdb
#5
---
Chain | Description
B | No description available
C | No description available
> hide #5 models
> open
> /Users/zekecook/Downloads/ATG13_ATG101_WIPI3_7390a.result/ATG13_ATG101_WIPI3_7390a_unrelaxed_rank_1_model_1.pdb
Chain information for ATG13_ATG101_WIPI3_7390a_unrelaxed_rank_1_model_1.pdb #6
---
Chain | Description
B | No description available
C | No description available
D | No description available
> hide #4 models
> hide #!3.2 models
> view
> color bfactor palette alphafold
59900 atoms, 4572 residues, atom bfactor range 13.1 to 151
> ui mousemode right select
> select clear
> select #6/C:230
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
274 atoms, 284 bonds, 34 residues, 1 model selected
> show sel atoms
> color sel byhetero
> open
> /Users/zekecook/Downloads/ATG13_150_230_WIPI4_52448.result/ATG13_150_230_WIPI4_52448_unrelaxed_rank_1_model_3.pdb
Chain information for ATG13_150_230_WIPI4_52448_unrelaxed_rank_1_model_3.pdb
#7
---
Chain | Description
B | No description available
C | No description available
> ui tool show Matchmaker
> matchmaker #7 to #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ATG13_ATG101_WIPI3_7390a_unrelaxed_rank_1_model_1.pdb, chain D (#6)
with ATG13_150_230_WIPI4_52448_unrelaxed_rank_1_model_3.pdb, chain C (#7),
sequence alignment score = 1051.8
RMSD between 305 pruned atom pairs is 0.762 angstroms; (across all 340 pairs:
1.969)
> select #6/B:132
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #7/B:43
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
262 atoms, 269 bonds, 31 residues, 1 model selected
> show sel atoms
> color bfactor palette alphafold
63246 atoms, 5002 residues, atom bfactor range 13.1 to 151
> hide #6 models
> color sel byhetero
> open 6klr
6klr title:
Crystal structure of human WIPI3 in complex with the WIR-peptide from ATG2A
[more info...]
Chain information for 6klr #8
---
Chain | Description | UniProt
A B | chimera ATG2A and WIPI3 | WIPI3_HUMAN
> ui tool show Matchmaker
> matchmaker #!8 to #7
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 ATG13_150_230_WIPI4_52448_unrelaxed_rank_1_model_3.pdb, chain C
(#7) with 6klr, chain A (#8), sequence alignment score = 893.9
RMSD between 269 pruned atom pairs is 0.900 angstroms; (across all 297 pairs:
2.209)
> color #8 bychain
> select #8/B:1378
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 2 residues, 1 model selected
> select up
164 atoms, 170 bonds, 22 residues, 1 model selected
> show sel atoms
> color sel byhetero
> open
> /Users/zekecook/Downloads/ATG9_BECN1_ATG14_e3ff2.result/ATG9_BECN1_ATG14_e3ff2_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
ATG9_BECN1_ATG14_e3ff2_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#9
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!8 models
> hide #9 models
> show #9 models
> hide #7 models
> color bfactor palette alphafold
79897 atoms, 7120 residues, atom bfactor range 13.1 to 184
> open
> /Users/zekecook/Downloads/ATG13_FL_MSA000_f072e.result/ATG13_FL_MSA000_f072e.custom_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
ATG13_FL_MSA000_f072e.custom_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
#10
---
Chain | Description
A | No description available
> hide #9 models
> rainbow #10
> open
> /Users/zekecook/Downloads/ATG13HD_000_78f6e.result/ATG13HD_000_78f6e.custom_unrelaxed_rank_1_model_5_scores.json
Failed opening file
/Users/zekecook/Downloads/ATG13HD_000_78f6e.result/ATG13HD_000_78f6e.custom_unrelaxed_rank_1_model_5_scores.json:
'Channels'
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> open
> /Users/zekecook/Downloads/FIP200_1_640_ATG16L1_e8f76/FIP200_1_640_ATG16L1_e8f76_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
Chain information for
FIP200_1_640_ATG16L1_e8f76_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#11
---
Chain | Description
A | No description available
B | No description available
> hide #10 models
> color bfactor palette alphafold
93725 atoms, 8877 residues, atom bfactor range 13.1 to 184
> open
> /Users/zekecook/Downloads/FIP200_1_640_ATG16L1_309_end_7b85a/FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#12
---
Chain | Description
A | No description available
B | No description available
> hide #11 models
> color bfactor palette alphafold
101151 atoms, 9816 residues, atom bfactor range 13.1 to 184
> ui tool show "AlphaFold Error Plot"
> alphafold pae #12 file
> /Users/zekecook/Downloads/FIP200_1_640_ATG16L1_309_end_7b85a/FIP200_1_640_ATG16L1_309_end_7b85a_scores_rank_001_alphafold2_multimer_v3_model_5_seed_000.json
> show #11 models
> hide #12 models
> open
> /Users/zekecook/Downloads/ATG16L1_WIPI2_c6215.result/ATG16L1_WIPI2_c6215_unrelaxed_rank_1_model_1.pdb
Chain information for ATG16L1_WIPI2_c6215_unrelaxed_rank_1_model_1.pdb #13
---
Chain | Description
B | No description available
C | No description available
> ui mousemode right select
> select #13/B:102
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
1217 atoms, 1222 bonds, 148 residues, 1 model selected
> matchmaker sel 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
FIP200_1_640_ATG16L1_e8f76_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#11) with ATG16L1_WIPI2_c6215_unrelaxed_rank_1_model_1.pdb, chain B
(#13), sequence alignment score = 785.8
RMSD between 28 pruned atom pairs is 1.157 angstroms; (across all 148 pairs:
9.729)
> ui tool show "Show Sequence Viewer"
> sequence chain #12/B
Alignment identifier is 12/B
> select #12/B:229
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #12/B:229-241
107 atoms, 111 bonds, 13 residues, 1 model selected
> show #12 models
> hide #11 models
> hide #12 models
> ui tool show "Show Sequence Viewer"
> sequence chain #13/C
Alignment identifier is 13/C
> select #13/C:229
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #13/C:229-242
120 atoms, 123 bonds, 14 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #13/B
Alignment identifier is 13/B
> select #13/B:229
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/B:229-242
107 atoms, 107 bonds, 14 residues, 1 model selected
> hide #13 models
> show #12 models
> show #11 models
> matchmaker #12 to #11
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
FIP200_1_640_ATG16L1_e8f76_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain A (#11) with
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12), sequence alignment score = 3314.3
RMSD between 456 pruned atom pairs is 0.542 angstroms; (across all 640 pairs:
24.623)
> open
> /Users/zekecook/Downloads/FIP200_1_640_ATG16L1_309_end_38814/FIP200_1_640_ATG16L1_309_end_38814_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
FIP200_1_640_ATG16L1_309_end_38814_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#14
---
Chain | Description
A | No description available
B | No description available
> matchmaker #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
FIP200_1_640_ATG16L1_e8f76_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain A (#11) with
FIP200_1_640_ATG16L1_309_end_38814_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#14), sequence alignment score = 3323.3
RMSD between 505 pruned atom pairs is 0.748 angstroms; (across all 640 pairs:
22.411)
> color bfactor palette alphafold
114864 atoms, 11561 residues, atom bfactor range 13.1 to 184
> ui tool show "AlphaFold Error Plot"
> alphafold pae #12 file
> /Users/zekecook/Downloads/FIP200_1_640_ATG16L1_309_end_7b85a/FIP200_1_640_ATG16L1_309_end_7b85a_scores_rank_001_alphafold2_multimer_v3_model_5_seed_000.json
> alphafold contacts #14
Structure
FIP200_1_640_ATG16L1_309_end_38814_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#14 does not have PAE data opened
> alphafold contacts #12
> ui mousemode right zoom
> ui mousemode right translate
> hide #14 models
> ui mousemode right select
> select #12/A:366
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #11/B:409
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #12/A:366
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #12/B:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #12/B:97
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/B:406
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #11/A:144
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #11/B:406
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #11/A:144
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #11/A:147
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #11/A:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #12/B:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #11/B:388
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #12/A:48
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #12/B:56
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #11/A:49
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #12/B:58
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> ui mousemode right translate
> ui mousemode right select
> select #12/A:159
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #12/B:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> ui mousemode right zoom
> ui mousemode right select
> select #11/A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
546 atoms, 559 bonds, 67 residues, 1 model selected
> show sel atoms
> color sel byhetero
> open 4IWO
4iwo title:
Crystal structure and mechanism of activation of TBK1 [more info...]
Chain information for 4iwo #15
---
Chain | Description | UniProt
A | Serine/threonine-protein kinase TBK1 | TBK1_HUMAN
Non-standard residues in 4iwo #15
---
1H4 —
N-{3-[(5-cyclopropyl-2-{[3-(2-oxopyrrolidin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]propyl}cyclobutanecarboxamide
4iwo mmCIF Assemblies
---
1| author_defined_assembly
> ui tool show Matchmaker
> matchmaker #!15 to #14
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
FIP200_1_640_ATG16L1_309_end_38814_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#14) with 4iwo, chain A (#15), sequence alignment score = 238.5
RMSD between 42 pruned atom pairs is 1.037 angstroms; (across all 333 pairs:
40.203)
> select #15/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
598 atoms, 604 bonds, 75 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hide #11 models
> select clear
> select #15/A:452
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #15/A:355
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #12/B:55
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/B:56
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #12/A:49
4 atoms, 3 bonds, 1 residue, 1 model selected
> show #13 models
> hide #13 models
> show #14 models
> show #11 models
> hide #14 models
> show #14 models
> hide #14 models
> show #14 models
> hide #!15 models
> hide #14 models
> hide #!12 models
> select #11/B:399
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #11/B
Alignment identifier is 11/B
> select #11/B:428-476
399 atoms, 407 bonds, 49 residues, 1 model selected
> select #11/B:428-467
313 atoms, 318 bonds, 40 residues, 1 model selected
> select #11/B:490
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/B:490
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right zoom
> show #14 models
> show #13 models
> hide #13 models
> show #!12 models
> hide #14 models
> ui mousemode right translate
> ui mousemode right zoom
> show #13 models
> hide #13 models
> show #13 models
> hide #!12 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #13 models
> ui mousemode right select
> select #11/B:225
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
1192 atoms, 1197 bonds, 145 residues, 1 model selected
> show sel atoms
> hide #11 models
> show #14 models
> show #!12 models
> show #11 models
> hide #14 models
> hide #11 models
> select #12/A:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
546 atoms, 559 bonds, 67 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> ui mousemode right translate
> show #!15 models
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right select
> select #15/A:536
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #15/A:535
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #15/A:536
14 atoms, 15 bonds, 1 residue, 1 model selected
> ui mousemode right zoom
> ui mousemode right select
> select #15/A:455
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
598 atoms, 604 bonds, 75 residues, 1 model selected
> matchmaker sel 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
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12) with 4iwo, chain A (#15), sequence alignment score = 125.7
RMSD between 44 pruned atom pairs is 1.125 angstroms; (across all 75 pairs:
2.467)
> select clear
> select #15/A:539
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
64 atoms, 66 bonds, 8 residues, 1 model selected
> show sel atoms
> select #12/B:98
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right zoom
> ui mousemode right translate
> show sel atoms
> ui mousemode right zoom
> ui mousemode right select
> select #15/A:545
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
34 atoms, 35 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> select #12/B:139
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #12/A:374
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
310 atoms, 311 bonds, 39 residues, 1 model selected
> show sel atoms
> select #15/A:539
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
64 atoms, 66 bonds, 8 residues, 1 model selected
> select up
1373 atoms, 1398 bonds, 166 residues, 1 model selected
> select #15/A:550
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
234 atoms, 236 bonds, 27 residues, 1 model selected
> show sel atoms
> select #12/A:385
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
310 atoms, 311 bonds, 39 residues, 1 model selected
> color sel byhetero
> ui mousemode right zoom
> ui mousemode right translate
> hide pbonds
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select clear
> ui mousemode right zoom
> ui mousemode right translate
> select #11/B:490
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/B:490-499
77 atoms, 77 bonds, 10 residues, 1 model selected
> show #14 models
> show pbonds
> hide #14 models
> show #13 models
> hide #13 models
> show #11 models
> ui mousemode right zoom
> ui mousemode right translate
> select #11/B:490
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/B:490
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/B:490
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/B:490-494
37 atoms, 36 bonds, 5 residues, 1 model selected
> select #11/B:489
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #11/B:489-490
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #11/B:489
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #11/B:489-490
13 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> ui mousemode right select
> select clear
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right select
> select #11/A:61
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
20 atoms, 19 bonds, 3 residues, 1 model selected
> select up
5125 atoms, 5217 bonds, 640 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #15/A:521
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
266 atoms, 266 bonds, 35 residues, 1 model selected
> select up
1373 atoms, 1398 bonds, 166 residues, 1 model selected
> select up
1385 atoms, 1410 bonds, 167 residues, 1 model selected
> select up
3644 atoms, 3721 bonds, 450 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> open /Users/zekecook/Downloads/cryosparc_P34_J150_004_volume_map_sharp.mrc
Opened cryosparc_P34_J150_004_volume_map_sharp.mrc as #16, grid size
400,400,400, pixel 1.05, shown at level 0.141, step 2, values float32
> hide #!15 models
> hide #!12 models
> hide #11 models
> select add #16
1 pseudobond, 3 models selected
> view
> surface dust #16 size 10.5
> ui mousemode right zoom
> volume #16 step 1
> volume #16 level 0.4676
> ui mousemode right translate
> close #16
> show #!3 models
> open /Users/zekecook/Downloads/cryosparc_P34_J150_002_volume_map_sharp.mrc
> format mrc
Opened cryosparc_P34_J150_002_volume_map_sharp.mrc as #16, grid size
400,400,400, pixel 1.05, shown at level 0.102, step 2, values float32
> show #14 models
> view
> ui mousemode right zoom
> ui mousemode right translate
> show #13 models
> hide #14 models
> hide #13 models
> show #!12 models
> show #11 models
> hide #!12 models
> ui mousemode right select
> show #13 models
> hide #11 models
> open 7mu2
7mu2 title:
Crystal Structure of WIPI2 in complex with W2IR of ATG16L1 [more info...]
Chain information for 7mu2 #17
---
Chain | Description | UniProt
A C | WD repeat domain phosphoinositide-interacting protein 2 |
B D | Autophagy-related protein 16-1 | E7EVC7_HUMAN
7mu2 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> ui tool show Matchmaker
> matchmaker #!17 to #13
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 ATG16L1_WIPI2_c6215_unrelaxed_rank_1_model_1.pdb, chain C (#13)
with 7mu2, chain C (#17), sequence alignment score = 1505.4
RMSD between 303 pruned atom pairs is 0.633 angstroms; (across all 316 pairs:
1.297)
> select #17/D:222
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
63 atoms, 62 bonds, 9 residues, 1 model selected
> matchmaker sel to #13
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 ATG16L1_WIPI2_c6215_unrelaxed_rank_1_model_1.pdb, chain B (#13)
with 7mu2, chain D (#17), sequence alignment score = 40
RMSD between 9 pruned atom pairs is 0.230 angstroms; (across all 9 pairs:
0.230)
> ui mousemode right zoom
> select up
92 atoms, 91 bonds, 12 residues, 1 model selected
> select up
98 atoms, 91 bonds, 18 residues, 1 model selected
> select down
92 atoms, 91 bonds, 12 residues, 1 model selected
> select down
63 atoms, 62 bonds, 9 residues, 1 model selected
> ui mousemode right select
> select #13/B:54
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
1217 atoms, 1222 bonds, 148 residues, 1 model selected
> open
> /Users/zekecook/Downloads/FIP200_ATG16L1_dimer_72fde/FIP200_ATG16L1_dimer_72fde_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
FIP200_ATG16L1_dimer_72fde_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#18
---
Chain | Description
A B | No description available
C | No description available
> color bfactor palette alphafold
138834 atoms, 15153 residues, atom bfactor range 7.79 to 375
> hide #!17 models
> hide #13 models
> hide #18 models
> show #13 models
> show #11 models
> hide #11 models
> show #!16 models
> hide #!16 models
> show #!17 models
> open
> /Users/zekecook/Downloads/FIP200_ATG16L1_FBD_f15e8/FIP200_ATG16L1_FBD_f15e8_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
FIP200_ATG16L1_FBD_f15e8_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#19
---
Chain | Description
A | No description available
B | No description available
> hide #!17 models
> hide #13 models
> color bfactor palette alphafold
144359 atoms, 15843 residues, atom bfactor range 7.79 to 375
> select #19/B:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
148 atoms, 147 bonds, 18 residues, 1 model selected
> select up
400 atoms, 403 bonds, 50 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> ui mousemode right zoom
> show #18 models
> hide #19 models
> ui mousemode right select
> select #18/B:138
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 4 residues, 1 model selected
> select clear
> select #18/B:515
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #18/B:516
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/B:137
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 4 residues, 1 model selected
> select up
4038 atoms, 4101 bonds, 517 residues, 1 model selected
> show sel atoms
> ui mousemode right zoom
> ui mousemode right select
> select clear
> ui mousemode right zoom
> show #9 models
> hide #!3 models
> hide #18 models
> hide #9 models
> show #18 models
> ui tool show "Show Sequence Viewer"
> sequence chain #18/A #18/B
Alignment identifier is 1
> select #18/A-B:138-139
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #18/A-B:133-139
100 atoms, 98 bonds, 14 residues, 1 model selected
> select #18/A-B:1
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #18/A-B:1-17
286 atoms, 288 bonds, 34 residues, 1 model selected
> select #18/A-B:81
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #18/A-B:81-120
652 atoms, 656 bonds, 80 residues, 1 model selected
> open
> /Users/zekecook/Downloads/ATG16L1_WIPI2_c6215.result/ATG16L1_WIPI2_c6215_unrelaxed_rank_1_model_1.pdb
Chain information for ATG16L1_WIPI2_c6215_unrelaxed_rank_1_model_1.pdb #20
---
Chain | Description
B | No description available
C | No description available
> ui tool show Matchmaker
> matchmaker #20 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
FIP200_ATG16L1_dimer_72fde_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#18) with ATG16L1_WIPI2_c6215_unrelaxed_rank_1_model_1.pdb, chain B
(#20), sequence alignment score = 2537.2
RMSD between 292 pruned atom pairs is 0.283 angstroms; (across all 498 pairs:
49.389)
> ui mousemode right select
> select #20/B:172
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #20/B:171
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #20/B:169
19 atoms, 16 bonds, 3 residues, 1 model selected
> select add #20/B:170
28 atoms, 24 bonds, 4 residues, 1 model selected
> select add #20/B:168
36 atoms, 31 bonds, 5 residues, 1 model selected
> matchmaker sel 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
FIP200_ATG16L1_dimer_72fde_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#18) with ATG16L1_WIPI2_c6215_unrelaxed_rank_1_model_1.pdb, chain B
(#20), sequence alignment score = 25.1
RMSD between 5 pruned atom pairs is 0.242 angstroms; (across all 5 pairs:
0.242)
> select #18/A-B:50-81
522 atoms, 522 bonds, 64 residues, 1 model selected
> select #18/A-B:50-112
1026 atoms, 1032 bonds, 126 residues, 1 model selected
> select #18/A-B:80-81
34 atoms, 32 bonds, 4 residues, 1 model selected
> select #18/A-B:80-82
48 atoms, 46 bonds, 6 residues, 1 model selected
> select #18/A-B:81
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #18/A-B:81-138
948 atoms, 952 bonds, 116 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #18 to #9
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
ATG9_BECN1_ATG14_e3ff2_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#9) with
FIP200_ATG16L1_dimer_72fde_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain C (#18), sequence alignment score = 256.9
RMSD between 35 pruned atom pairs is 0.833 angstroms; (across all 368 pairs:
91.491)
> show #9 models
> hide #18 models
> select #9/C:234
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
78 atoms, 77 bonds, 10 residues, 1 model selected
> select up
3875 atoms, 3944 bonds, 492 residues, 1 model selected
> select down
78 atoms, 77 bonds, 10 residues, 1 model selected
> select add #9/C:243
85 atoms, 83 bonds, 11 residues, 1 model selected
> select add #9/C:232
91 atoms, 88 bonds, 12 residues, 1 model selected
> select add #9/C:231
97 atoms, 93 bonds, 13 residues, 1 model selected
> select add #9/C:230
104 atoms, 99 bonds, 14 residues, 1 model selected
> select add #9/C:244
111 atoms, 105 bonds, 15 residues, 1 model selected
> select add #9/C:245
123 atoms, 117 bonds, 16 residues, 1 model selected
> select add #9/C:246
131 atoms, 124 bonds, 17 residues, 1 model selected
> select add #9/C:248
135 atoms, 127 bonds, 18 residues, 1 model selected
> select add #9/C:249
146 atoms, 137 bonds, 19 residues, 1 model selected
> select add #9/C:250
160 atoms, 152 bonds, 20 residues, 1 model selected
> select add #9/C:251
167 atoms, 158 bonds, 21 residues, 1 model selected
> select add #9/C:252
173 atoms, 163 bonds, 22 residues, 1 model selected
> matchmaker sel 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
FIP200_ATG16L1_dimer_72fde_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain C (#18) with
ATG9_BECN1_ATG14_e3ff2_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain C (#9), sequence alignment score = 20.2
RMSD between 13 pruned atom pairs is 0.888 angstroms; (across all 13 pairs:
0.888)
> show #18 models
> ui mousemode right zoom
> ui mousemode right translate
> matchmaker sel 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
FIP200_ATG16L1_FBD_f15e8_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#19) with
ATG9_BECN1_ATG14_e3ff2_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain C (#9), sequence alignment score = 16.6
RMSD between 13 pruned atom pairs is 0.730 angstroms; (across all 13 pairs:
0.730)
> hide #18 models
> show #19 models
> hide #19 models
> matchmaker sel to #20
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 ATG16L1_WIPI2_c6215_unrelaxed_rank_1_model_1.pdb, chain C (#20)
with
ATG9_BECN1_ATG14_e3ff2_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain C (#9), sequence alignment score = 11.5
RMSD between 10 pruned atom pairs is 0.594 angstroms; (across all 22 pairs:
8.786)
> ui mousemode right zoom
> matchmaker sel to #20/A
No 'to' model specified
> matchmaker sel to #20:A
No 'to' model specified
> matchmaker sel to #20/A
No 'to' model specified
> color bfactor palette alphafold
152241 atoms, 16858 residues, atom bfactor range 7.79 to 375
> ui mousemode right select
> select #20/B:198
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right select
> select add #20/B:199
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #20/B:200
19 atoms, 16 bonds, 3 residues, 1 model selected
> select add #20/B:197
27 atoms, 23 bonds, 4 residues, 1 model selected
> select add #20/B:196
36 atoms, 31 bonds, 5 residues, 1 model selected
> select add #20/B:195
45 atoms, 39 bonds, 6 residues, 1 model selected
> select add #20/B:194
54 atoms, 47 bonds, 7 residues, 1 model selected
> select add #20/B:193
62 atoms, 54 bonds, 8 residues, 1 model selected
> select add #20/B:192
73 atoms, 64 bonds, 9 residues, 1 model selected
> select add #20/B:191
78 atoms, 68 bonds, 10 residues, 1 model selected
> select add #20/B:190
87 atoms, 76 bonds, 11 residues, 1 model selected
> select add #20/B:189
98 atoms, 86 bonds, 12 residues, 1 model selected
> select add #20/B:188
109 atoms, 96 bonds, 13 residues, 1 model selected
> select add #20/B:187
120 atoms, 106 bonds, 14 residues, 1 model selected
> select add #20/B:186
126 atoms, 111 bonds, 15 residues, 1 model selected
> matchmaker sel to #9
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
ATG9_BECN1_ATG14_e3ff2_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain C (#9) with ATG16L1_WIPI2_c6215_unrelaxed_rank_1_model_1.pdb, chain B
(#20), sequence alignment score = 44.5
RMSD between 15 pruned atom pairs is 0.462 angstroms; (across all 15 pairs:
0.462)
> ui mousemode right zoom
> open
> /Users/zekecook/Downloads/ATG9_522_770_ATG13_ATG101_18311.result/ATG9_522_770_ATG13_ATG101_18311_unrelaxed_rank_1_model_1.pdb
Chain information for
ATG9_522_770_ATG13_ATG101_18311_unrelaxed_rank_1_model_1.pdb #21
---
Chain | Description
B | No description available
C | No description available
D | No description available
> color bfactor palette alphafold
159833 atoms, 17841 residues, atom bfactor range 7.79 to 375
> hide #9 models
> hide #20 models
> open
> /Users/zekecook/Downloads/ATG13_1_200_ATG9_700_770_sample2_593c3.result/ATG13_1_200_ATG9_700_770_sample2_593c3_unrelaxed_rank_1_model_2.pdb
Chain information for
ATG13_1_200_ATG9_700_770_sample2_593c3_unrelaxed_rank_1_model_2.pdb #22
---
Chain | Description
B | No description available
C | No description available
> color bfactor palette alphafold
161958 atoms, 18112 residues, atom bfactor range 7.79 to 375
> hide #21 models
> open
> /Users/zekecook/Downloads/ATG9_700_770_ATG13HD_ATG101_7a466.result/ATG9_700_770_ATG13HD_ATG101_7a466_unrelaxed_rank_1_model_5.pdb
Chain information for
ATG9_700_770_ATG13HD_ATG101_7a466_unrelaxed_rank_1_model_5.pdb #23
---
Chain | Description
B | No description available
C | No description available
D | No description available
> color bfactor palette alphafold
165827 atoms, 18600 residues, atom bfactor range 7.79 to 375
> hide #22 models
> ui mousemode right select
> select clear
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_080_alphafold2_ptm_model_1_seed_005.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_080_alphafold2_ptm_model_1_seed_005.pdb #24
---
Chain | Description
A | No description available
> hide #23 models
> color bfactor palette alphafold
169797 atoms, 19117 residues, atom bfactor range 7.79 to 375
> ui mousemode right zoom
> ui mousemode right translate
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_079_alphafold2_ptm_model_1_seed_012.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_079_alphafold2_ptm_model_1_seed_012.pdb #25
---
Chain | Description
A | No description available
> color bfactor palette alphafold
173767 atoms, 19634 residues, atom bfactor range 7.79 to 375
> ui tool show Matchmaker
> matchmaker #25 to #24
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 ATG13_c6500_unrelaxed_rank_080_alphafold2_ptm_model_1_seed_005.pdb,
chain A (#24) with
ATG13_c6500_unrelaxed_rank_079_alphafold2_ptm_model_1_seed_012.pdb, chain A
(#25), sequence alignment score = 2498
RMSD between 31 pruned atom pairs is 0.625 angstroms; (across all 517 pairs:
35.495)
> hide #24 models
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_078_alphafold2_ptm_model_1_seed_007.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_078_alphafold2_ptm_model_1_seed_007.pdb #26
---
Chain | Description
A | No description available
> color bfactor palette alphafold
177737 atoms, 20151 residues, atom bfactor range 7.79 to 375
> hide #25 models
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_077_alphafold2_ptm_model_1_seed_004.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_077_alphafold2_ptm_model_1_seed_004.pdb #27
---
Chain | Description
A | No description available
> color bfactor palette alphafold
181707 atoms, 20668 residues, atom bfactor range 7.79 to 375
> hide #26 models
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_076_alphafold2_ptm_model_1_seed_011.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_076_alphafold2_ptm_model_1_seed_011.pdb #28
---
Chain | Description
A | No description available
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_075_alphafold2_ptm_model_1_seed_009.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_075_alphafold2_ptm_model_1_seed_009.pdb #29
---
Chain | Description
A | No description available
> hide #27 models
> hide #28 models
> color bfactor palette alphafold
189647 atoms, 21702 residues, atom bfactor range 7.79 to 375
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_074_alphafold2_ptm_model_4_seed_005.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_074_alphafold2_ptm_model_4_seed_005.pdb #30
---
Chain | Description
A | No description available
> color bfactor palette alphafold
193617 atoms, 22219 residues, atom bfactor range 7.79 to 375
> hide #29 models
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_073_alphafold2_ptm_model_2_seed_011.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_073_alphafold2_ptm_model_2_seed_011.pdb #31
---
Chain | Description
A | No description available
> color bfactor palette alphafold\
Fetching compressed palette alphafold\ from
http://www.colourlovers.com/api/palettes?keywords=alphafold%5C&format=json&numResults=100
Could not find palette alphafold\ at COLOURlovers.com using keyword search
> color bfactor palette alphafold
197587 atoms, 22736 residues, atom bfactor range 7.79 to 375
> hide #30 models
> show #24 models
> hide #24 models
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_001.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_001.pdb #32
---
Chain | Description
A | No description available
> color bfactor palette alphafold
201557 atoms, 23253 residues, atom bfactor range 7.79 to 375
> ui tool show Matchmaker
> matchmaker #32 to #31
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 ATG13_c6500_unrelaxed_rank_073_alphafold2_ptm_model_2_seed_011.pdb,
chain A (#31) with
ATG13_c6500_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_001.pdb, chain A
(#32), sequence alignment score = 2481.2
RMSD between 8 pruned atom pairs is 1.552 angstroms; (across all 517 pairs:
49.577)
> ui mousemode right select
> select #31/A:163
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
18 atoms, 17 bonds, 3 residues, 1 model selected
> matchmaker sel to #32
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 ATG13_c6500_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_001.pdb,
chain A (#32) with
ATG13_c6500_unrelaxed_rank_073_alphafold2_ptm_model_2_seed_011.pdb, chain A
(#31), sequence alignment score = 15.2
RMSD between 3 pruned atom pairs is 0.051 angstroms; (across all 3 pairs:
0.051)
> ui mousemode right translate
> ui mousemode right zoom
> hide #32 models
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_072_alphafold2_ptm_model_3_seed_009.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_072_alphafold2_ptm_model_3_seed_009.pdb #33
---
Chain | Description
A | No description available
> hide #31 models
> color bfactor palette alphafold
205527 atoms, 23770 residues, atom bfactor range 7.79 to 375
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_071_alphafold2_ptm_model_3_seed_010.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_071_alphafold2_ptm_model_3_seed_010.pdb #34
---
Chain | Description
A | No description available
> color bfactor palette alphafold
209497 atoms, 24287 residues, atom bfactor range 7.79 to 375
> hide #33 models
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_070_alphafold2_ptm_model_4_seed_015.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_070_alphafold2_ptm_model_4_seed_015.pdb #35
---
Chain | Description
A | No description available
> color bfactor palette alphafold
213467 atoms, 24804 residues, atom bfactor range 7.79 to 375
> hide #34 models
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_069_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_069_alphafold2_ptm_model_3_seed_000.pdb #36
---
Chain | Description
A | No description available
> color bfactor palette alphafold
217437 atoms, 25321 residues, atom bfactor range 7.79 to 375
> hide #35 models
> ui mousemode right select
> select #36/A:8
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
226 atoms, 228 bonds, 27 residues, 1 model selected
> show sel atoms
> color sel byhetero
> mlp sel
Map values for surface
"ATG13_c6500_unrelaxed_rank_069_alphafold2_ptm_model_3_seed_000.pdb_A SES
surface": minimum -28.93, mean -4.672, maximum 25.57
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_068_alphafold2_ptm_model_2_seed_004.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_068_alphafold2_ptm_model_2_seed_004.pdb #37
---
Chain | Description
A | No description available
> hide #!36 models
> color bfactor palette alphafold
221407 atoms, 25838 residues, 1 surfaces, atom bfactor range 7.79 to 375
> select #37/A:59
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
85 atoms, 86 bonds, 11 residues, 1 model selected
> select up
3970 atoms, 4057 bonds, 517 residues, 1 model selected
> select down
85 atoms, 86 bonds, 11 residues, 1 model selected
> select down
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #37/A:33
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
197 atoms, 200 bonds, 26 residues, 1 model selected
> show sel atoms
> color sel byhetero
> mlp sel
Map values for surface
"ATG13_c6500_unrelaxed_rank_068_alphafold2_ptm_model_2_seed_004.pdb_A SES
surface": minimum -27.3, mean -4.702, maximum 25.27
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
ATG13_c6500_unrelaxed_rank_068_alphafold2_ptm_model_2_seed_004.pdb_A SES
surface #37.1: minimum, -22.97, mean -1.52, maximum 11.65
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_067_alphafold2_ptm_model_1_seed_014.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_067_alphafold2_ptm_model_1_seed_014.pdb #38
---
Chain | Description
A | No description available
> color bfactor palette alphafold
225377 atoms, 26355 residues, 2 surfaces, atom bfactor range 7.79 to 375
> hide #!37 models
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_066_alphafold2_ptm_model_1_seed_013.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_066_alphafold2_ptm_model_1_seed_013.pdb #39
---
Chain | Description
A | No description available
> hide #38 models
> color bfactor palette alphafold
229347 atoms, 26872 residues, 2 surfaces, atom bfactor range 7.79 to 375
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_065_alphafold2_ptm_model_3_seed_004.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_065_alphafold2_ptm_model_3_seed_004.pdb #40
---
Chain | Description
A | No description available
> hide #39 models
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_064_alphafold2_ptm_model_1_seed_001.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_064_alphafold2_ptm_model_1_seed_001.pdb #41
---
Chain | Description
A | No description available
> hide #40 models
> color bfactor palette alphafold
237287 atoms, 27906 residues, 2 surfaces, atom bfactor range 7.79 to 375
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_063_alphafold2_ptm_model_3_seed_008.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_063_alphafold2_ptm_model_3_seed_008.pdb #42
---
Chain | Description
A | No description available
> hide #41 models
> color bfactor palette alphafold
241257 atoms, 28423 residues, 2 surfaces, atom bfactor range 7.79 to 375
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/ATG13_c6500/ATG13_c6500_unrelaxed_rank_062_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
ATG13_c6500_unrelaxed_rank_062_alphafold2_ptm_model_4_seed_000.pdb #43
---
Chain | Description
A | No description available
> hide #42 models
> color bfactor palette alphafold
245227 atoms, 28940 residues, 2 surfaces, atom bfactor range 7.79 to 375
> select #43/A:151
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #43/A:34
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
189 atoms, 192 bonds, 25 residues, 1 model selected
> show sel atoms
> color sel byhetero
> open
> /Users/zekecook/Downloads/ATG13_ATG101_WIPI3_7390a.result/ATG13_ATG101_WIPI3_7390a_unrelaxed_rank_3_model_4_scores.json
Failed opening file
/Users/zekecook/Downloads/ATG13_ATG101_WIPI3_7390a.result/ATG13_ATG101_WIPI3_7390a_unrelaxed_rank_3_model_4_scores.json:
'Channels'
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_002.pdb
Chain information for
ATG13_1_220_3dcd8_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_002.pdb #44
---
Chain | Description
A | No description available
> hide #43 models
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_unrelaxed_rank_080_alphafold2_ptm_model_2_seed_009.pdb
Chain information for
ATG13_1_220_3dcd8_unrelaxed_rank_080_alphafold2_ptm_model_2_seed_009.pdb #45
---
Chain | Description
A | No description available
> color bfactor palette alphafold
248713 atoms, 29380 residues, 2 surfaces, atom bfactor range 7.79 to 375
> matchmaker # 45 to #44
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
ATG13_1_220_3dcd8_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_002.pdb,
chain A (#44) with
ATG13_1_220_3dcd8_unrelaxed_rank_080_alphafold2_ptm_model_2_seed_009.pdb,
chain A (#45), sequence alignment score = 1079.4
RMSD between 80 pruned atom pairs is 0.674 angstroms; (across all 220 pairs:
9.190)
> select clear
> select #45/A:58
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
189 atoms, 192 bonds, 25 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #45/A:29
7 atoms, 6 bonds, 1 residue, 1 model selected
> select down
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
226 atoms, 228 bonds, 27 residues, 1 model selected
> show sel atoms
> color sel byhetero
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_unrelaxed_rank_079_alphafold2_ptm_model_2_seed_007.pdb
Chain information for
ATG13_1_220_3dcd8_unrelaxed_rank_079_alphafold2_ptm_model_2_seed_007.pdb #46
---
Chain | Description
A | No description available
> matchmaker # 46 to #45
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
ATG13_1_220_3dcd8_unrelaxed_rank_080_alphafold2_ptm_model_2_seed_009.pdb,
chain A (#45) with
ATG13_1_220_3dcd8_unrelaxed_rank_079_alphafold2_ptm_model_2_seed_007.pdb,
chain A (#46), sequence alignment score = 1081.2
RMSD between 85 pruned atom pairs is 0.579 angstroms; (across all 220 pairs:
10.361)
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_unrelaxed_rank_078_alphafold2_ptm_model_4_seed_009.pdb
Chain information for
ATG13_1_220_3dcd8_unrelaxed_rank_078_alphafold2_ptm_model_4_seed_009.pdb #47
---
Chain | Description
A | No description available
> matchmaker # 47 to #45
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
ATG13_1_220_3dcd8_unrelaxed_rank_080_alphafold2_ptm_model_2_seed_009.pdb,
chain A (#45) with
ATG13_1_220_3dcd8_unrelaxed_rank_078_alphafold2_ptm_model_4_seed_009.pdb,
chain A (#47), sequence alignment score = 1071.6
RMSD between 110 pruned atom pairs is 0.927 angstroms; (across all 220 pairs:
8.129)
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_unrelaxed_rank_077_alphafold2_ptm_model_1_seed_004.pdb
Chain information for
ATG13_1_220_3dcd8_unrelaxed_rank_077_alphafold2_ptm_model_1_seed_004.pdb #48
---
Chain | Description
A | No description available
> matchmaker # 48 to #45
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
ATG13_1_220_3dcd8_unrelaxed_rank_080_alphafold2_ptm_model_2_seed_009.pdb,
chain A (#45) with
ATG13_1_220_3dcd8_unrelaxed_rank_077_alphafold2_ptm_model_1_seed_004.pdb,
chain A (#48), sequence alignment score = 1108.2
RMSD between 82 pruned atom pairs is 0.660 angstroms; (across all 220 pairs:
10.312)
> hide #44 models
> hide #45 models
> hide #46 models
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_unrelaxed_rank_076_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
ATG13_1_220_3dcd8_unrelaxed_rank_076_alphafold2_ptm_model_2_seed_000.pdb #49
---
Chain | Description
A | No description available
> matchmaker # 49 to #45
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
ATG13_1_220_3dcd8_unrelaxed_rank_080_alphafold2_ptm_model_2_seed_009.pdb,
chain A (#45) with
ATG13_1_220_3dcd8_unrelaxed_rank_076_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#49), sequence alignment score = 1101
RMSD between 78 pruned atom pairs is 0.535 angstroms; (across all 220 pairs:
12.888)
> hide #47 models
> hide #48 models
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_unrelaxed_rank_075_alphafold2_ptm_model_1_seed_005.pdb
Chain information for
ATG13_1_220_3dcd8_unrelaxed_rank_075_alphafold2_ptm_model_1_seed_005.pdb #50
---
Chain | Description
A | No description available
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_unrelaxed_rank_074_alphafold2_ptm_model_1_seed_007.pdb
Chain information for
ATG13_1_220_3dcd8_unrelaxed_rank_074_alphafold2_ptm_model_1_seed_007.pdb #51
---
Chain | Description
A | No description available
> matchmaker #51 to #45
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
ATG13_1_220_3dcd8_unrelaxed_rank_080_alphafold2_ptm_model_2_seed_009.pdb,
chain A (#45) with
ATG13_1_220_3dcd8_unrelaxed_rank_074_alphafold2_ptm_model_1_seed_007.pdb,
chain A (#51), sequence alignment score = 1108.8
RMSD between 78 pruned atom pairs is 0.544 angstroms; (across all 220 pairs:
9.554)
> hide #51 models
> hide #50 models
> hide #49 models
> show #44 models
> hide #44 models
> show #45 models
> select #45/A:131
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
139 atoms, 140 bonds, 17 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #45/A:177
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #45/A:178
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
81 atoms, 81 bonds, 11 residues, 1 model selected
> show sel atoms
> color sel byhetero
> open /Users/zekecook/Downloads/test_aeef8/config.json
Failed opening file /Users/zekecook/Downloads/test_aeef8/config.json:
'Channels'
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_unrelaxed_rank_073_alphafold2_ptm_model_1_seed_001.pdb
Chain information for
ATG13_1_220_3dcd8_unrelaxed_rank_073_alphafold2_ptm_model_1_seed_001.pdb #52
---
Chain | Description
A | No description available
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_unrelaxed_rank_072_alphafold2_ptm_model_1_seed_003.pdb
Chain information for
ATG13_1_220_3dcd8_unrelaxed_rank_072_alphafold2_ptm_model_1_seed_003.pdb #53
---
Chain | Description
A | No description available
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_unrelaxed_rank_071_alphafold2_ptm_model_1_seed_000.pdb
Chain information for
ATG13_1_220_3dcd8_unrelaxed_rank_071_alphafold2_ptm_model_1_seed_000.pdb #54
---
Chain | Description
A | No description available
Drag select of 52 atoms, 169 residues, 42 bonds
> select clear
> ui mousemode right translate
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_unrelaxed_rank_070_alphafold2_ptm_model_4_seed_007.pdb
Chain information for
ATG13_1_220_3dcd8_unrelaxed_rank_070_alphafold2_ptm_model_4_seed_007.pdb #55
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #50-54 to #55
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
ATG13_1_220_3dcd8_unrelaxed_rank_070_alphafold2_ptm_model_4_seed_007.pdb,
chain A (#55) with
ATG13_1_220_3dcd8_unrelaxed_rank_075_alphafold2_ptm_model_1_seed_005.pdb,
chain A (#50), sequence alignment score = 1119
RMSD between 181 pruned atom pairs is 0.534 angstroms; (across all 220 pairs:
8.820)
Matchmaker
ATG13_1_220_3dcd8_unrelaxed_rank_070_alphafold2_ptm_model_4_seed_007.pdb,
chain A (#55) with
ATG13_1_220_3dcd8_unrelaxed_rank_074_alphafold2_ptm_model_1_seed_007.pdb,
chain A (#51), sequence alignment score = 1119
RMSD between 193 pruned atom pairs is 0.596 angstroms; (across all 220 pairs:
7.462)
Matchmaker
ATG13_1_220_3dcd8_unrelaxed_rank_070_alphafold2_ptm_model_4_seed_007.pdb,
chain A (#55) with
ATG13_1_220_3dcd8_unrelaxed_rank_073_alphafold2_ptm_model_1_seed_001.pdb,
chain A (#52), sequence alignment score = 1115.4
RMSD between 184 pruned atom pairs is 0.485 angstroms; (across all 220 pairs:
3.229)
Matchmaker
ATG13_1_220_3dcd8_unrelaxed_rank_070_alphafold2_ptm_model_4_seed_007.pdb,
chain A (#55) with
ATG13_1_220_3dcd8_unrelaxed_rank_072_alphafold2_ptm_model_1_seed_003.pdb,
chain A (#53), sequence alignment score = 1098
RMSD between 186 pruned atom pairs is 0.638 angstroms; (across all 220 pairs:
9.503)
Matchmaker
ATG13_1_220_3dcd8_unrelaxed_rank_070_alphafold2_ptm_model_4_seed_007.pdb,
chain A (#55) with
ATG13_1_220_3dcd8_unrelaxed_rank_071_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#54), sequence alignment score = 1115.4
RMSD between 182 pruned atom pairs is 0.640 angstroms; (across all 220 pairs:
7.387)
> hide #45 models
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_unrelaxed_rank_068_alphafold2_ptm_model_4_seed_005.pdb
Chain information for
ATG13_1_220_3dcd8_unrelaxed_rank_068_alphafold2_ptm_model_4_seed_005.pdb #56
---
Chain | Description
A | No description available
> hide #56 models
> show #56 models
> hide #55 models
> hide #54 models
> hide #53 models
> hide #52 models
> open
> /Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_scores_rank_001_alphafold2_ptm_model_5_seed_002.json
Failed opening file
/Users/zekecook/Documents/ATG13_1_220_3dcd8/ATG13_1_220_3dcd8_scores_rank_001_alphafold2_ptm_model_5_seed_002.json:
'Channels'
> color bfactor palette alphafold
267886 atoms, 31800 residues, 2 surfaces, atom bfactor range 7.79 to 375
> open 3gmh
3gmh title:
Crystal Structure of the Mad2 Dimer [more info...]
Chain information for 3gmh #57
---
Chain | Description | UniProt
A B C D E F G H I J K L | Mitotic spindle assembly checkpoint protein MAD2A |
MD2L1_HUMAN
Non-standard residues in 3gmh #57
---
SO4 — sulfate ion
3gmh mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
5| author_and_software_defined_assembly
6| author_and_software_defined_assembly
> delete #57/C,D,E,F,G,H,I
> ui mousemode right select
> select #57/J:83@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
76 atoms, 75 bonds, 10 residues, 1 model selected
> select up
819 atoms, 834 bonds, 101 residues, 1 model selected
> select up
1495 atoms, 1522 bonds, 185 residues, 1 model selected
> delete sel
> ui mousemode right zoom
> ui mousemode right select
Drag select of 2302 atoms, 1 pseudobonds, 4 bonds
> select up
2502 atoms, 2533 bonds, 1 pseudobond, 307 residues, 2 models selected
> select up
2945 atoms, 2993 bonds, 1 pseudobond, 363 residues, 2 models selected
> select up
3039 atoms, 3092 bonds, 1 pseudobond, 376 residues, 2 models selected
> delete sel
> select #57/B:142@CD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
64 atoms, 65 bonds, 8 residues, 1 model selected
> select up
676 atoms, 688 bonds, 84 residues, 1 model selected
> select up
1500 atoms, 1526 bonds, 186 residues, 1 model selected
> select up
3076 atoms, 3128 bonds, 382 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 3076 atom styles
> hide sel atoms
> matchmaker #56 to #57
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 3gmh, chain A (#57) with
ATG13_1_220_3dcd8_unrelaxed_rank_068_alphafold2_ptm_model_4_seed_005.pdb,
chain A (#56), sequence alignment score = 112.6
RMSD between 40 pruned atom pairs is 0.967 angstroms; (across all 169 pairs:
8.506)
> ui mousemode right translate
> ui mousemode right zoom
> open 5c50
5c50 title:
Crystal structure of the complex of human Atg101-Atg13 HORMA domain [more
info...]
Chain information for 5c50 #58
---
Chain | Description | UniProt
A | Autophagy-related protein 101 | ATGA1_HUMAN
B | Autophagy-related protein 13 | ATG13_HUMAN
Non-standard residues in 5c50 #58
---
BEN — benzamidine
> matchmaker #58 to #57
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 3gmh, chain A (#57) with 5c50, chain B (#58), sequence alignment
score = 137.1
RMSD between 51 pruned atom pairs is 0.980 angstroms; (across all 164 pairs:
9.056)
> color #58 bychain
> hide #56 models
> ui mousemode right select
> select clear
> hide #!57 models
> show #!57 models
> close #44-56
> show #6 models
> matchmaker #6 to #57
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 3gmh, chain B (#57) with
ATG13_ATG101_WIPI3_7390a_unrelaxed_rank_1_model_1.pdb, chain B (#6), sequence
alignment score = 127.4
RMSD between 69 pruned atom pairs is 1.252 angstroms; (across all 166 pairs:
17.301)
> hide #!57 models
> show #!57 models
> hide #58 models
> select #57/B:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
76 atoms, 75 bonds, 10 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #57/B:91
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
36 atoms, 35 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero
> show #58 models
> hide #!57 models
> hide #6 models
> show #6 models
> color #6,58 byhetero
> ui tool show "Show Sequence Viewer"
> sequence chain #6/B #21/D #23/C
Alignment identifier is 1
> sequence chain #6/C
Alignment identifier is 6/C
> sequence chain #6/D
Alignment identifier is 6/D
> select #6/B:218 #21/D:218 #23/C:218
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #6/B:209-218 #21/D:209-218 #23/C:209-218
249 atoms, 246 bonds, 30 residues, 3 models selected
1 [ID: 1] region chains B,C,D [209-218] RMSD: 104.812
> select #6/B:14-16,18-31,70-89,134-161,171-176,206-216
> #21/D:14-16,18-31,70-89,134-161,171-176,206-216
> #23/C:14-16,18-31,70-89,134-161,171-176,206-216
2010 atoms, 2001 bonds, 246 residues, 3 models selected
> select
> #6/B:4-13,33-35,37-41,44-47,52-56,63-67,95-106,115-129,185-187,190-197,203-209
> #21/D:4-13,33-35,37-41,44-47,52-56,63-67,95-106,115-129,185-187,190-197,203-209
> #23/C:4-13,33-35,37-41,44-47,52-56,63-67,95-106,115-129,185-187,190-197,203-209
1917 atoms, 1932 bonds, 231 residues, 3 models selected
> select #6/B:126-127 #21/D:126-127 #23/C:126-127
51 atoms, 51 bonds, 6 residues, 3 models selected
> select #6/B:126-128 #21/D:126-128 #23/C:126-128
72 atoms, 72 bonds, 9 residues, 3 models selected
1 [ID: 1] region chains B,C,D [126-128] RMSD: 83.535
> select #6/B:180 #21/D:180 #23/C:180
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #6/B:178-180 #21/D:178-180 #23/C:178-180
78 atoms, 78 bonds, 9 residues, 3 models selected
1 [ID: 1] region chains B,C,D [178-180] RMSD: 85.946
> hide #58 models
> select #6/B:191-192 #21/D:191-192 #23/C:191-192
51 atoms, 48 bonds, 6 residues, 3 models selected
> select #6/B:184-192 #21/D:184-192 #23/C:184-192
240 atoms, 246 bonds, 27 residues, 3 models selected
1 [ID: 1] region chains B,C,D [184-192] RMSD: 81.973
> select #6/B:125 #21/D:125 #23/C:125
27 atoms, 24 bonds, 3 residues, 3 models selected
> select #6/B:125-129 #21/D:125-129 #23/C:125-129
120 atoms, 120 bonds, 15 residues, 3 models selected
1 [ID: 1] region chains B,C,D [125-129] RMSD: 83.322
> select #6/B:103
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/B:190
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/B:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/B:116
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/B:115
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/B:106
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #6/B:108
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
72 atoms, 75 bonds, 8 residues, 1 model selected
> show sel atoms
> select #6/B:26 #21/D:26 #23/C:26
30 atoms, 30 bonds, 3 residues, 3 models selected
> select #6/B:26-27 #21/D:26-27 #23/C:26-27
51 atoms, 51 bonds, 6 residues, 3 models selected
1 [ID: 1] region chains B,C,D [26-27] RMSD: 68.172
> select #6/B:105 #21/D:105 #23/C:105
27 atoms, 24 bonds, 3 residues, 3 models selected
> select #6/B:105-112 #21/D:105-112 #23/C:105-112
228 atoms, 237 bonds, 24 residues, 3 models selected
1 [ID: 1] region chains B,C,D [105-112] RMSD: 107.834
> show sel & #6 atoms
> show #14 models
> ui mousemode right zoom
> show #13 models
> hide #14 models
> hide #13 models
> show #!12 models
> hide pbonds
> open 4IM2
Summary of feedback from opening 4IM2 fetched from pdb
---
notes | Fetching compressed mmCIF 4im2 from
http://files.rcsb.org/download/4im2.cif
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif
4im2 title:
Structure of Tank-Binding Kinase 1 [more info...]
Chain information for 4im2 #44
---
Chain | Description | UniProt
A | Serine/threonine-protein kinase TBK1 | TBK1_HUMAN
Non-standard residues in 4im2 #44
---
BX7 —
N-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide
CL — chloride ion
4im2 mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
> ui tool show Matchmaker
> matchmaker #!44 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
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12) with 4im2, chain A (#44), sequence alignment score = 260.1
RMSD between 42 pruned atom pairs is 1.064 angstroms; (across all 323 pairs:
45.637)
> ui mousemode right translate
> color sel & #6 byhetero
> ui mousemode right select
> select clear
> color #6#!12,44 byhetero
> select #44/A:577
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
241 atoms, 248 bonds, 28 residues, 1 model selected
> select up
1322 atoms, 1346 bonds, 162 residues, 1 model selected
> select up
1344 atoms, 1366 bonds, 165 residues, 1 model selected
> select up
3559 atoms, 3633 bonds, 443 residues, 1 model selected
> select up
3589 atoms, 3662 bonds, 449 residues, 1 model selected
> select up
5196 atoms, 5056 bonds, 860 residues, 1 model selected
> show sel atoms
> select clear
> hide #6#!12,44 atoms
> select #44/A:565
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
223 atoms, 225 bonds, 26 residues, 1 model selected
> show sel atoms
Drag select of 2 residues
> select up
310 atoms, 311 bonds, 39 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #44/A:572
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/A:573
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> show sel atoms
> select #12/A:404
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> select #44/A:576
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
241 atoms, 248 bonds, 28 residues, 1 model selected
> show sel atoms
> select #12/A:406
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
18 atoms, 17 bonds, 3 residues, 1 model selected
> select up
5125 atoms, 5217 bonds, 640 residues, 1 model selected
> select down
18 atoms, 17 bonds, 3 residues, 1 model selected
> show sel atoms
> select #12/A:409
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
647 atoms, 654 bonds, 80 residues, 1 model selected
> show sel atoms
> open matchmaker sel to #44
'matchmaker' has no suffix
> matchmaker sel to #44
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 4im2, chain A (#44) with
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12), sequence alignment score = 112
RMSD between 40 pruned atom pairs is 0.999 angstroms; (across all 80 pairs:
11.342)
> select #12/A:408
7 atoms, 6 bonds, 1 residue, 1 model selected
> select down
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
18 atoms, 17 bonds, 3 residues, 1 model selected
> matchmaker sel to #44
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 4im2, chain A (#44) with
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12), sequence alignment score = 11.7
RMSD between 3 pruned atom pairs is 0.039 angstroms; (across all 3 pairs:
0.039)
> select #12/A:114
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
647 atoms, 654 bonds, 80 residues, 1 model selected
> select #12/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> matchmaker sel to #44
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 4im2, chain A (#44) with
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12), sequence alignment score = 4.6
Fewer than 3 residues aligned; cannot match 4im2, chain A with
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A
> select #12/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
647 atoms, 654 bonds, 80 residues, 1 model selected
> matchmaker sel to #44
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 4im2, chain A (#44) with
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12), sequence alignment score = 112
RMSD between 40 pruned atom pairs is 0.999 angstroms; (across all 80 pairs:
11.342)
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select clear
> ui tool show Matchmaker
> matchmaker #!44 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
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12) with 4im2, chain A (#44), sequence alignment score = 260.1
RMSD between 42 pruned atom pairs is 1.064 angstroms; (across all 323 pairs:
45.637)
> select #44/A:417
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #44/A:500
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
230 atoms, 230 bonds, 31 residues, 1 model selected
> select up
1322 atoms, 1346 bonds, 162 residues, 1 model selected
> show sel atoms
> select clear
> ui mousemode right zoom
> select #12/A:350-430
636 atoms, 640 bonds, 238 pseudobonds, 81 residues, 2 models selected
> matchmaker sel to #44
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 4im2, chain A (#44) with
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12), sequence alignment score = 102.3
RMSD between 17 pruned atom pairs is 0.920 angstroms; (across all 81 pairs:
28.456)
> matchmaker sel to #44:545-608
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 4im2, chain A (#44) with
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12), sequence alignment score = 73.8
RMSD between 16 pruned atom pairs is 0.717 angstroms; (across all 62 pairs:
19.697)
> ui mousemode right select
> select clear
> matchmaker #12 to #44
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 4im2, chain A (#44) with
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12), sequence alignment score = 260.1
RMSD between 42 pruned atom pairs is 1.064 angstroms; (across all 323 pairs:
45.637)
> select #12/B:184
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
44 atoms, 43 bonds, 6 residues, 1 model selected
> select up
2301 atoms, 2347 bonds, 299 residues, 1 model selected
> select up
7426 atoms, 7564 bonds, 939 residues, 1 model selected
> select down
2301 atoms, 2347 bonds, 299 residues, 1 model selected
> hide sel cartoons
> select #6/B:65
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 106 residues
> select up
1797 atoms, 1819 bonds, 222 residues, 1 model selected
> select up
6244 atoms, 6374 bonds, 792 residues, 1 model selected
> select up
227562 atoms, 230760 bonds, 28549 residues, 49 models selected
> select up
227562 atoms, 230760 bonds, 28549 residues, 51 models selected
> select down
6244 atoms, 6374 bonds, 792 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> select #12/A:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
42 atoms, 41 bonds, 5 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #12/A:81
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
93 atoms, 96 bonds, 12 residues, 1 model selected
> show sel atoms
> select #44/A:386
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
199 atoms, 204 bonds, 24 residues, 1 model selected
> show sel atoms
> select #12/A:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:93
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
38 atoms, 37 bonds, 5 residues, 1 model selected
> show sel atoms
> select #12/A:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
5125 atoms, 5217 bonds, 640 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:99
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
51 atoms, 50 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #12/A:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!12 models
> show #!12 models
> ui tool show "Show Sequence Viewer"
> sequence chain #12/A
Alignment identifier is 12/A
> select #12/A:361
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/A:361-366
43 atoms, 42 bonds, 10 pseudobonds, 6 residues, 2 models selected
> select #12/A:362-363
17 atoms, 16 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select #12/A:362-365
29 atoms, 28 bonds, 6 pseudobonds, 4 residues, 2 models selected
> select #12/A:365
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:365-373
77 atoms, 77 bonds, 26 pseudobonds, 9 residues, 2 models selected
> select #12/A:367
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:367-368
19 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> color sel magenta
> select #12/A:374
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/A:374
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel magenta
> select #12/A:379
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/A:379
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel magenta
> select #12/A:383
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/A:383
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/A:386
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/A:386
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel magenta
> select #12/A:387
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/A:387
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel magenta
> select #12/A:390-391
14 atoms, 13 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select #12/A:390
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel magenta
> select #12/A:394
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:394-395
13 atoms, 12 bonds, 2 pseudobonds, 2 residues, 2 models selected
> color sel magenta
> select #12/A:405
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:405
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel magenta
> select #12/A:409
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:409
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel magenta
> select #12/A:416
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #12/A:416-418
23 atoms, 23 bonds, 4 pseudobonds, 3 residues, 2 models selected
> select #12/A:415-416
16 atoms, 16 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select #12/A:415-417
21 atoms, 21 bonds, 4 pseudobonds, 3 residues, 2 models selected
> select #12/A:416
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #12/A:416-417
15 atoms, 15 bonds, 2 pseudobonds, 2 residues, 2 models selected
> color sel magenta
> select #12/A:110
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
27 atoms, 27 bonds, 4 residues, 1 model selected
> show sel atoms
> select #44/A:408
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:421
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:421
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel magenta
Drag select of 65 atoms, 23 residues, 55 bonds
> select clear
> ui mousemode right translate
> ui mousemode right zoom
> select #12/A:387
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/A:387-389
26 atoms, 25 bonds, 4 pseudobonds, 3 residues, 2 models selected
> select #12/A:387
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/A:387-391
40 atoms, 39 bonds, 10 pseudobonds, 5 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #44/A
Alignment identifier is 44/A
> select #44/A:396
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/A:396-401
47 atoms, 47 bonds, 6 residues, 1 model selected
> select #12/A:387
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/A:387-391
40 atoms, 39 bonds, 10 pseudobonds, 5 residues, 2 models selected
> select #44/A:610
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/A:610-614
41 atoms, 41 bonds, 5 residues, 1 model selected
> select #44/A:553
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/A:553-570
157 atoms, 159 bonds, 18 residues, 1 model selected
> select #44/A:464
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #44/A:464-466
22 atoms, 21 bonds, 3 residues, 1 model selected
> select #44/A:176-236
419 atoms, 431 bonds, 2 pseudobonds, 55 residues, 2 models selected
> select #44/A:176-241
455 atoms, 467 bonds, 2 pseudobonds, 60 residues, 2 models selected
> select #44/A:307
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #44/A:307-657
2746 atoms, 2798 bonds, 2 pseudobonds, 336 residues, 2 models selected
> select #44/A:565
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/A:565-569
46 atoms, 46 bonds, 5 residues, 1 model selected
> select #12/A:413
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/A:413-414
14 atoms, 13 bonds, 2 pseudobonds, 2 residues, 2 models selected
> ui mousemode right select
> select #44/A:407
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
509 atoms, 515 bonds, 64 residues, 1 model selected
> show sel atoms
> select clear
> select #12/A:407
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.19549,-0.72487,0.66057,-23.57,0.89771,0.40346,0.17705,7.8521,-0.39485,0.55838,0.72959,14.628
> view matrix models
> #12,0.18272,-0.63741,0.74855,-21.414,0.9159,0.38714,0.1061,6.2693,-0.35742,0.66621,0.65453,13.314
> view matrix models
> #12,0.34661,-0.70639,0.61716,-24.997,0.91756,0.39198,-0.066668,2.7356,-0.19482,0.58938,0.78401,15.057
> view matrix models
> #12,0.2851,-0.72284,0.62945,-24.558,0.93083,0.36543,-0.0019575,3.9173,-0.22861,0.58648,0.77703,15.038
> view matrix models
> #12,0.3931,-0.72544,0.56498,-26.317,0.89877,0.43287,-0.069527,2.8929,-0.19413,0.53512,0.82217,15.649
> ui mousemode right zoom
> ui mousemode right select
> select #44/A:2
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
23 atoms, 22 bonds, 3 residues, 1 model selected
> select up
340 atoms, 346 bonds, 44 residues, 1 model selected
> hide sel cartoons
> select #44/A:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
42 atoms, 42 bonds, 5 residues, 1 model selected
> select up
893 atoms, 909 bonds, 113 residues, 1 model selected
> hide sel cartoons
Drag select of 47 residues, 2 pseudobonds
Drag select of 98 residues, 2 pseudobonds
> hide sel cartoons
Drag select of 20 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
Drag select of 2 residues, 8 atoms, 6 bonds
> select clear
> select #44/A:620
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
358 atoms, 363 bonds, 42 residues, 1 model selected
> select up
1322 atoms, 1346 bonds, 162 residues, 1 model selected
> select up
1344 atoms, 1366 bonds, 165 residues, 1 model selected
> select up
3559 atoms, 3633 bonds, 443 residues, 1 model selected
> matchmaker sel 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
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12) with 4im2, chain A (#44), sequence alignment score = 250.3
RMSD between 42 pruned atom pairs is 1.064 angstroms; (across all 323 pairs:
45.633)
> select clear
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> select #12/A:387
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/A:387-391
40 atoms, 39 bonds, 10 pseudobonds, 5 residues, 2 models selected
> matchmaker sel to #44
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 4im2, chain A (#44) with
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12), sequence alignment score = 16
RMSD between 5 pruned atom pairs is 0.109 angstroms; (across all 5 pairs:
0.109)
> select up
310 atoms, 311 bonds, 10 pseudobonds, 39 residues, 2 models selected
> matchmaker sel to #44
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 4im2, chain A (#44) with
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12), sequence alignment score = 81.4
RMSD between 28 pruned atom pairs is 1.044 angstroms; (across all 39 pairs:
2.683)
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.49283,0.56815,0.65904,-37.073,-0.86788,-0.26654,-0.41922,42.061,-0.062519,-0.77856,0.62444,31.164
> matchmaker #12 to #44
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 4im2, chain A (#44) with
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12), sequence alignment score = 260.1
RMSD between 42 pruned atom pairs is 1.064 angstroms; (across all 323 pairs:
45.637)
> hide #!44 models
> show #!44 models
> select add #44
5506 atoms, 5367 bonds, 16 pseudobonds, 899 residues, 4 models selected
> show sel cartoons
> select #44/A:193-194
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #44/A:193-202
29 atoms, 27 bonds, 1 pseudobond, 5 residues, 2 models selected
> select #44/A:394
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #44/A:394-401
68 atoms, 69 bonds, 8 residues, 1 model selected
> select #44/A:657
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #44/A:655-657
23 atoms, 22 bonds, 3 residues, 1 model selected
> open
> /Users/zekecook/Documents/AY_22_23/structure_prediction/TBK1_dimer_1ebbc/TBK1_dimer_1ebbc_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
TBK1_dimer_1ebbc_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#45
---
Chain | Description
A B | No description available
> view matrix models
> #44,-0.22162,0.80163,0.55522,-64.865,-0.77678,-0.48933,0.39644,123.62,0.58949,-0.34342,0.73114,-24.313
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right select
> select #45/A:728
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
95 atoms, 94 bonds, 13 residues, 1 model selected
> select up
5879 atoms, 5998 bonds, 729 residues, 1 model selected
> select down
95 atoms, 94 bonds, 13 residues, 1 model selected
> show sel atoms
> hide #!44 models
> color bfactor palette alphafold
271618 atoms, 32225 residues, 2 surfaces, atom bfactor range 7.79 to 375
> select #45/A:715
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
41 atoms, 41 bonds, 5 residues, 1 model selected
> select up
5879 atoms, 5998 bonds, 729 residues, 1 model selected
> select #45/A:685
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 3 residues, 1 model selected
> select up
5879 atoms, 5998 bonds, 729 residues, 1 model selected
> select down
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #45/A:689
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
190 atoms, 190 bonds, 24 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> ui mousemode right zoom
> ui mousemode right translate
> ui tool show "Show Sequence Viewer"
> sequence chain #45/B
Alignment identifier is 45/B
> select #45/B:729
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #45/B:543-729
1552 atoms, 1580 bonds, 187 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #45/A
Alignment identifier is 45/A
> select #45/A:729
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #45/A:664-729
503 atoms, 508 bonds, 66 residues, 1 model selected
> select #45/A:676-729
419 atoms, 422 bonds, 54 residues, 1 model selected
> select #45/A:702
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #45/A:702-707
48 atoms, 47 bonds, 6 residues, 1 model selected
> select up
190 atoms, 190 bonds, 24 residues, 1 model selected
> matchmaker sel 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
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12) with
TBK1_dimer_1ebbc_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#45), sequence alignment score = 60.7
RMSD between 24 pruned atom pairs is 0.671 angstroms; (across all 24 pairs:
0.671)
> ui mousemode right zoom
> select #45/A:637
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #45/A:637-639
25 atoms, 25 bonds, 3 residues, 1 model selected
> select #45/A:632
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #45/A:632-639
63 atoms, 63 bonds, 8 residues, 1 model selected
> matchmaker sel 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
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12) with
TBK1_dimer_1ebbc_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#45), sequence alignment score = 35.4
RMSD between 8 pruned atom pairs is 0.175 angstroms; (across all 8 pairs:
0.175)
> select #45/A:527-528
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #45/A:527-729
1663 atoms, 1695 bonds, 203 residues, 1 model selected
> ui mousemode right select
> select clear
> select #45/A:713
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
41 atoms, 41 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #45/A:668
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
135 atoms, 138 bonds, 18 residues, 1 model selected
> show sel atoms
> select #45/A:685
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> ui mousemode right zoom
> matchmaker #45 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
FIP200_1_640_ATG16L1_309_end_7b85a_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#12) with
TBK1_dimer_1ebbc_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#45), sequence alignment score = 365.3
RMSD between 40 pruned atom pairs is 0.914 angstroms; (across all 396 pairs:
41.550)
> ui mousemode right translate
> color #6,45#!12 byhetero
> select #45/A:527
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #45/A:527-729
1663 atoms, 1695 bonds, 203 residues, 1 model selected
> select #45/A:590-591
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #45/A:590-593
42 atoms, 44 bonds, 4 residues, 1 model selected
> select #45/A:566
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #45/A:566-568
29 atoms, 29 bonds, 3 residues, 1 model selected
> select #45/A:566
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #45/A:566-569
37 atoms, 37 bonds, 4 residues, 1 model selected
> select #45/A:566
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #45/A:566-574
82 atoms, 82 bonds, 9 residues, 1 model selected
> select #12/A:230-231
18 atoms, 17 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select #12/A:230-234
40 atoms, 39 bonds, 10 pseudobonds, 5 residues, 2 models selected
> select #12/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/A:231-233
23 atoms, 22 bonds, 4 pseudobonds, 3 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #12/A
Alignment identifier is 12/A
> select #12/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/A:231-233
23 atoms, 22 bonds, 4 pseudobonds, 3 residues, 2 models selected
> hide #!12 models
> show #!12 models
> select #45/A:570
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #45/A:570-573
34 atoms, 33 bonds, 4 residues, 1 model selected
> select #45/A:183
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #45/A:183
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select #45/A:677@CA
1 atom, 1 residue, 1 model selected
> select #45/A:676
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:502
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #12/A:502
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #45/A:672
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #45/A:729
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #45/A:710
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
190 atoms, 190 bonds, 24 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
TBK1_dimer_1ebbc_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb_A
SES surface #45.1: minimum, -20.74, mean -1.61, maximum 12.72
To also show corresponding color key, enter the above coulombic command and
add key true
> open /Users/zekecook/Downloads/DMF48_results/Final_ALL_MODELS/model_1.pdb
Chain information for model_1.pdb #46
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!45 models
> hide #!12 models
> hide #6 models
> color bfactor palette alphafold
296803 atoms, 33807 residues, 3 surfaces, atom bfactor range 7.79 to 375
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #46 models
> view
> open "/Users/zekecook/Downloads/cryosparc_P34_J129_006_volume_map_sharp
> (1).mrc"
Opened cryosparc_P34_J129_006_volume_map_sharp (1).mrc as #47, grid size
400,400,400, pixel 1.05, shown at level 0.0933, step 2, values float32
> hide #!2 models
> select clear
> surface dust #47 size 10.5
> volume #47 step 1
> volume #47 level 0.2635
> ui mousemode right zoom
> ui mousemode right translate
> volume #47 level 0.2558
> volume #47 color #b2ffb282
> show #!3 models
> ui mousemode right zoom
> show #!3.1 models
> show #!3.2 models
> ui mousemode right select
> select #47
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #47,-0.88954,0.24241,0.38725,265.14,-0.20135,-0.96888,0.14399,419.56,0.4101,0.050109,0.91066,-77.697
> view matrix models
> #47,-0.99463,0.10093,-0.023037,400.34,-0.10047,-0.99473,-0.020334,437.48,-0.024968,-0.01791,0.99953,9.0124
> hide #!3.1 models
> fitmap #3.2 inMap #47
Fit molecule PI3k_Rab1a_Retry.pdb (#3.2) to map
cryosparc_P34_J129_006_volume_map_sharp (1).mrc (#47) using 30838 atoms
average map value = 0.317, steps = 128
shifted from previous position = 2.68
rotated from previous position = 6.67 degrees
atoms outside contour = 13899, contour level = 0.25576
Position of PI3k_Rab1a_Retry.pdb (#3.2) relative to
cryosparc_P34_J129_006_volume_map_sharp (1).mrc (#47) coordinates:
Matrix rotation and translation
-0.93195857 0.00795635 -0.36247747 470.87803396
-0.02553126 -0.99871749 0.04372114 409.64640293
-0.36166473 0.05000080 0.93096646 83.37157440
Axis 0.18425682 -0.02384741 -0.98258879
Axis point 245.03169929 201.76585878 0.00000000
Rotation angle (degrees) 179.02360382
Shift along axis -4.92648877
> hide #!3.2 models
> show #!3.1 models
> fitmap #3.1 inMap #47
Fit molecule PI3k_Rab1a_Retry.pdb (#3.1) to map
cryosparc_P34_J129_006_volume_map_sharp (1).mrc (#47) using 1460 atoms
average map value = 0.297, steps = 60
shifted from previous position = 2.1
rotated from previous position = 1.62 degrees
atoms outside contour = 670, contour level = 0.25576
Position of PI3k_Rab1a_Retry.pdb (#3.1) relative to
cryosparc_P34_J129_006_volume_map_sharp (1).mrc (#47) coordinates:
Matrix rotation and translation
-0.90700932 0.10852650 -0.40688586 454.47504903
-0.24177104 -0.92531116 0.29214042 392.33093027
-0.34479104 0.36334730 0.86550441 38.27911918
Axis 0.19626235 -0.17114742 -0.96549969
Axis point 249.59016320 171.10776756 0.00000000
Rotation angle (degrees) 169.54825322
Shift along axis -14.90856171
> ui mousemode right zoom
> show #!3.2 models
> open "/Users/zekecook/Downloads/cryosparc_P34_J148_006_volume_map_sharp
> (1).mrc"
Opened cryosparc_P34_J148_006_volume_map_sharp (1).mrc as #48, grid size
400,400,400, pixel 1.05, shown at level 0.0959, step 2, values float32
> surface dust #48 size 10.5
> ui mousemode right translate
> volume #48 level 0.2053
> volume #48 step 1
> volume #48 color #e5bf994f
> volume #48 level 0.1641
> volume #48 level -0.04603
> volume #48 level 0.1682
> ui mousemode right zoom
> view
> hide #!3.1 models
> hide #!3.2 models
> ui mousemode right translate
> show #!3.1 models
> fitmap #3.1 inMap #48
Fit molecule PI3k_Rab1a_Retry.pdb (#3.1) to map
cryosparc_P34_J148_006_volume_map_sharp (1).mrc (#48) using 1460 atoms
average map value = 0.31, steps = 68
shifted from previous position = 1.6
rotated from previous position = 3.02 degrees
atoms outside contour = 407, contour level = 0.16822
Position of PI3k_Rab1a_Retry.pdb (#3.1) relative to
cryosparc_P34_J148_006_volume_map_sharp (1).mrc (#48) coordinates:
Matrix rotation and translation
0.90131162 -0.16270221 0.40145406 -21.56249221
0.28890283 0.91633480 -0.27724663 10.02518840
-0.32275768 0.36586682 0.87290833 32.12466019
Axis 0.60179677 0.67768491 0.42259178
Axis point 58.65970950 0.00000000 79.21401316
Rotation angle (degrees) 32.29833402
Shift along axis 7.39329793
> volume #48 level 0.2341
> show #!3.2 models
> ui mousemode right select
> select #48
2 models selected
Drag select of 2 residues
> select #3.2/A:184
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
243 atoms, 243 bonds, 14 residues, 1 model selected
> color sel byhetero
> select #3.1/A:78
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
62 atoms, 63 bonds, 7 residues, 1 model selected
> color sel byhetero
> select #3.1/A:78
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.1/A:77
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.1/A:75
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel byhetero
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right select
> ui mousemode right zoom
> ui mousemode right translate
> volume #48 level 0.3124
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
32 atoms, 34 bonds, 1 residue, 1 model selected
> ui mousemode right zoom
> color sel byhetero
> ui mousemode right select
> select #3.2/C:138
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
1769 atoms, 1778 bonds, 103 residues, 1 model selected
> ui mousemode right translate
> volume #48 level 0.2754
> ui mousemode right zoom
> show sel atoms
> ui mousemode right select
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select #3.2/D:193
24 atoms, 23 bonds, 1 residue, 1 model selected
> select down
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
2119 atoms, 2123 bonds, 129 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> color #!3.1-2 byhetero
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> open 2fol
2fol title:
Crystal structure of human RAB1A in complex with GDP [more info...]
Chain information for 2fol #49
---
Chain | Description | UniProt
A | Ras-related protein Rab-1A | RAB1A_HUMAN
Non-standard residues in 2fol #49
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
UNX — unknown atom or ion
> ui mousemode right zoom
> ui tool show Matchmaker
> matchmaker #!49 to #3.1
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 PI3k_Rab1a_Retry.pdb, chain A (#3.1) with 2fol, chain A (#49),
sequence alignment score = 840
RMSD between 147 pruned atom pairs is 0.427 angstroms; (across all 155 pairs:
1.408)
> hide #!3.2 models
> show #!3.2 models
> hide #!3.1 models
> ui mousemode right translate
> show #!3.1 models
> hide #!49 models
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> open /Users/zekecook/Desktop/LocRef_Rab1a_PI3K.mrc format mrc
Opened LocRef_Rab1a_PI3K.mrc as #50, grid size 360,360,360, pixel 1.11, shown
at level 0.0291, step 2, values float32
> select add #50
2 models selected
> surface dust #50 size 11.1
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #50,0.37492,0.29872,0.87761,-123.83,0.78704,-0.60283,-0.13103,233.05,0.48991,0.73984,-0.46112,35.797
> volume #50 step 1
> view matrix models
> #50,0.99644,0.0030205,0.084303,-12.303,0.044686,-0.86652,-0.49713,518.18,0.071549,0.49913,-0.86357,258.94
> volume #50 level 0.1109
> ui mousemode right "translate selected models"
> view matrix models
> #50,0.99644,0.0030205,0.084303,-3.0184,0.044686,-0.86652,-0.49713,488.2,0.071549,0.49913,-0.86357,253.01
> ui mousemode right "rotate selected models"
> view matrix models
> #50,0.96703,-0.24415,0.072455,61.782,-0.086714,-0.58316,-0.80772,513.82,0.23946,0.7748,-0.5851,98.978
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #50,0.96703,-0.24415,0.072455,56.557,-0.086714,-0.58316,-0.80772,505.89,0.23946,0.7748,-0.5851,109.13
> ui mousemode right "rotate selected models"
> view matrix models
> #50,0.97536,-0.20283,0.086844,42.485,-0.080863,-0.69482,-0.71462,511.06,0.20529,0.68999,-0.6941,157.8
> ui mousemode right "translate selected models"
> ui tool show "Fit in Map"
> fitmap #48 inMap #47
Fit map cryosparc_P34_J148_006_volume_map_sharp (1).mrc in map
cryosparc_P34_J129_006_volume_map_sharp (1).mrc using 163709 points
correlation = 0.9534, correlation about mean = 0.7839, overlap = 3.68e+04
steps = 84, shift = 2.83, angle = 3.54 degrees
Position of cryosparc_P34_J148_006_volume_map_sharp (1).mrc (#48) relative to
cryosparc_P34_J129_006_volume_map_sharp (1).mrc (#47) coordinates:
Matrix rotation and translation
-0.99035857 -0.13619402 0.02531985 441.14529949
0.13574825 -0.99056933 -0.01856941 385.99648527
0.02761011 -0.01495325 0.99950692 -2.46146865
Axis 0.01329589 -0.00842082 0.99987615
Axis point 207.40338113 208.05727415 0.00000000
Rotation angle (degrees) 172.18424605
Shift along axis 0.15384909
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> isolde start
> set selectionWidth 4
Populating font family aliases took 140 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 126 residues in model #3.2 to IUPAC-IUB
standards.
===== Log before crash end =====
Log:
Updating list of available bundles failed: [Errno 8] nodename nor servname
provided, or not known
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
2023-02-13 15:59:08,064 WARNING Retrying (Retry(total=2, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x16a769580>: Failed to establish a new connection: [Errno 8] nodename nor
servname provided, or not known')':
/cxservices/api/v1/chimerax/updates?uuid=0860c083-5a92-5400-9a28-6289d4cbf754&OS=macosx&OSVersion=12.2&ChimeraXVersion=1.5
2023-02-13 15:59:08,086 WARNING Retrying (Retry(total=1, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x16a769640>: Failed to establish a new connection: [Errno 8] nodename nor
servname provided, or not known')':
/cxservices/api/v1/chimerax/updates?uuid=0860c083-5a92-5400-9a28-6289d4cbf754&OS=macosx&OSVersion=12.2&ChimeraXVersion=1.5
2023-02-13 15:59:08,088 WARNING Retrying (Retry(total=0, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x16a7691c0>: Failed to establish a new connection: [Errno 8] nodename nor
servname provided, or not known')':
/cxservices/api/v1/chimerax/updates?uuid=0860c083-5a92-5400-9a28-6289d4cbf754&OS=macosx&OSVersion=12.2&ChimeraXVersion=1.5
> open
> /Users/zekecook/Documents/AY_22_23/PI3k_Rab1_Stuff/run_it025_class002.mrc
> format mrc
Opened run_it025_class002.mrc as #1, grid size 400,400,400, pixel 1.05, shown
at level 0.00189, step 2, values float32
> vop flip #1
Opened run_it025_class002.mrc z flip as #2, grid size 400,400,400, pixel 1.05,
shown at step 1, values float32
> ui tool show Toolbar
> open "/Users/zekecook/Downloads/PI3K and
> Rab1/output_dir%2FPI3KRab1%2Funrelaxed_model_1_multimer_v2_pred_0.pdb"
> format pdb
Chain information for
output_dir%2FPI3KRab1%2Funrelaxed_model_1_multimer_v2_pred_0.pdb #3
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> hide #!2 models
> view
> ui mousemode right zoom
> ui mousemode right translate
> show cartoons
> show atoms
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style stick
Changed 27015 atom styles
> hide atoms
> ui mousemode right select
> select clear
[Repeated 2 time(s)]
> select /B:249
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:245
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:210
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
[Repeated 2 time(s)]
> select /B:251
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
32 atoms, 33 bonds, 3 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select /B:212
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
231 atoms, 231 bonds, 32 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select /B:244
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
27 atoms, 27 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select /B:227
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel magenta
> select /B:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel magenta
> select /B:244
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:243
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel magenta
> open
> /Users/zekecook/Downloads/ATG14_WIPI2d_BECN1_4aec0.result/ATG14_WIPI2d_BECN1_4aec0_unrelaxed_rank_1_model_3.pdb
Chain information for ATG14_WIPI2d_BECN1_4aec0_unrelaxed_rank_1_model_3.pdb #4
---
Chain | Description
B | No description available
C | No description available
D | No description available
> matchmaker #3 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ATG14_WIPI2d_BECN1_4aec0_unrelaxed_rank_1_model_3.pdb, chain B (#4)
with output_dir%2FPI3KRab1%2Funrelaxed_model_1_multimer_v2_pred_0.pdb, chain B
(#3), sequence alignment score = 2432.6
RMSD between 108 pruned atom pairs is 0.404 angstroms; (across all 492 pairs:
88.475)
> select #4/B:232
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
90 atoms, 89 bonds, 12 residues, 1 model selected
> show sel atoms
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right select
> select #4/C:149
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
3462 atoms, 3527 bonds, 454 residues, 1 model selected
> select up
10977 atoms, 11175 bonds, 1396 residues, 1 model selected
> select down
3462 atoms, 3527 bonds, 454 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for ATG14_WIPI2d_BECN1_4aec0_unrelaxed_rank_1_model_3.pdb_C
SES surface #4.1: minimum, -17.54, mean -0.86, maximum 14.40
To also show corresponding color key, enter the above coulombic command and
add key true
> select #4/C:84@OG
1 atom, 1 residue, 1 model selected
> select #4/B:251
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/B:243
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/B:233
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/C:113@CE2
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
56 atoms, 56 bonds, 7 residues, 2 models selected
> hide sel surfaces
> select #4/C:140
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/B:232
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/B:404
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #3/B:390
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/B:384
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:382
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/B:381
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:383
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> open
> /Users/zekecook/Downloads/FIP200_1_640_ATG16L1_e8f76/FIP200_1_640_ATG16L1_e8f76_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
FIP200_1_640_ATG16L1_e8f76_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb
#5
---
Chain | Description
A | No description available
B | No description available
> hide #3 models
> hide #!4 models
> ui mousemode right select
Drag select of 1240 residues
> color bfactor palette alphafold
47850 atoms, 6028 residues, 1 surfaces, atom bfactor range 1 to 98.4
> select clear
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui tool show "AlphaFold Error Plot"
> alphafold pae #5 file
> /Users/zekecook/Downloads/FIP200_1_640_ATG16L1_e8f76/FIP200_1_640_ATG16L1_e8f76_predicted_aligned_error_v1.json
JSON file
"/Users/zekecook/Downloads/FIP200_1_640_ATG16L1_e8f76/FIP200_1_640_ATG16L1_e8f76_predicted_aligned_error_v1.json"
is not AlphaFold predicted aligned error data, expected a top level list
> alphafold pae #5 file
> /Users/zekecook/Downloads/FIP200_1_640_ATG16L1_e8f76/FIP200_1_640_ATG16L1_e8f76_scores_rank_002_alphafold2_multimer_v3_model_1_seed_000.json
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
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: MacBookPro17,1
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 7429.81.3
OS Loader Version: 7429.81.3
Software:
System Software Overview:
System Version: macOS 12.2 (21D49)
Kernel Version: Darwin 21.3.0
Time since boot: 10 days 18:44
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Display Asleep: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Editing |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash clearing aniso_u6 |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #8457