![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9455 closed defect (fixed)
Segger drawing is None
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Tried to fit a model into a segment and received that error.
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\Jack Botting\Documents\Chimera\Saved
> Sessions\Bb_modeling.cxs" format session
Opened Bb058-stator-msk-4.2A.mrc as #2, grid size 140,140,140, pixel 4.2,
shown at level 1.07, step 1, values float32
Opened Bb326-nostat-msk-4.2A.mrc as #3, grid size 140,140,140, pixel 4.2,
shown at level 4.04, step 1, values float32
Opened Bb326-stator-msk-4.2A.mrc as #4, grid size 140,140,140, pixel 4.2,
shown at level 0.492, step 1, values float32
Opened Bb624-nostat-msk-4.2A.mrc as #5, grid size 140,140,140, pixel 4.2,
shown at level 0.0602, step 1, values float32
Opened Bb624-stator-msk-4.2A.mrc as #6, grid size 140,140,140, pixel 4.2,
shown at level 1.33, step 1, values float32
Opened MotB-nostat-msk-4.2A.mrc as #7, grid size 140,140,140, pixel 4.2, shown
at level 0.479, step 1, values float32
Opened WTCC-stator-msk-4.2A.mrc as #8, grid size 140,140,140, pixel 4.2, shown
at level 0.0321, step 1, values float32
Log from Mon Jul 24 16:28:43 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved
> Sessions/Bb_modeling.cxs"
Opened Bb058-stator-msk-4.2A.mrc as #2, grid size 140,140,140, pixel 4.2,
shown at level 1.07, step 1, values float32
Opened Bb326-nostat-msk-4.2A.mrc as #3, grid size 140,140,140, pixel 4.2,
shown at level 4.04, step 1, values float32
Opened Bb326-stator-msk-4.2A.mrc as #4, grid size 140,140,140, pixel 4.2,
shown at level 0.492, step 1, values float32
Opened Bb624-nostat-msk-4.2A.mrc as #5, grid size 140,140,140, pixel 4.2,
shown at level 0.0602, step 1, values float32
Opened Bb624-stator-msk-4.2A.mrc as #6, grid size 140,140,140, pixel 4.2,
shown at level 1.33, step 1, values float32
Opened MotB-nostat-msk-4.2A.mrc as #7, grid size 140,140,140, pixel 4.2, shown
at level 0.479, step 1, values float32
Opened WTCC-stator-msk-4.2A.mrc as #8, grid size 140,140,140, pixel 4.2, shown
at level 0.0321, step 1, values float32
Log from Mon Jul 24 11:23:42 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\Jack Botting\Documents\Chimera\Saved
> Sessions\Bb_modeling.cxs" format session
Error opening map "C:\Users\Jack Botting\Documents\Chimera\Saved
Sessions\Bb_modeling.cxs": File Bb_modeling.cxs, format mrc
MRC header value nsymbt (875113504) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened Bb058-stator-msk-4.2A.mrc as #2, grid size 140,140,140, pixel 4.2,
shown at level 2.58, step 1, values float32
Opened Bb326-nostat-msk-4.2A.mrc as #3, grid size 140,140,140, pixel 4.2,
shown at level 4.04, step 1, values float32
Opened Bb326-stator-msk-4.2A.mrc as #4, grid size 140,140,140, pixel 4.2,
shown at level 1.4, step 1, values float32
Opened Bb624-nostat-msk-4.2A.mrc as #5, grid size 140,140,140, pixel 4.2,
shown at level 2.55, step 1, values float32
Opened Bb624-stator-msk-4.2A.mrc as #6, grid size 140,140,140, pixel 4.2,
shown at level 1.33, step 1, values float32
Opened MotB-nostat-msk-4.2A.mrc as #7, grid size 140,140,140, pixel 4.2, shown
at level 4.13, step 1, values float32
Opened WTCC-stator-msk-4.2A.mrc as #8, grid size 140,140,140, pixel 4.2, shown
at level 0.125, step 1, values float32
Log from Fri Jul 21 16:08:54 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\Jack Botting\Documents\Chimera\Saved
> Sessions\Bb_modeling.cxs" format session
Opened WTCW-stator-msk-4.2A.mrc as #1, grid size 140,140,140, pixel 4.2, shown
at level 0.0647, step 1, values float32
Opened Bb058-stator-msk-4.2A.mrc as #2, grid size 140,140,140, pixel 4.2,
shown at level 2.58, step 1, values float32
Opened Bb326-nostat-msk-4.2A.mrc as #3, grid size 140,140,140, pixel 4.2,
shown at level 4.04, step 1, values float32
Opened Bb326-stator-msk-4.2A.mrc as #4, grid size 140,140,140, pixel 4.2,
shown at level 1.4, step 1, values float32
Opened Bb624-nostat-msk-4.2A.mrc as #5, grid size 140,140,140, pixel 4.2,
shown at level 2.55, step 1, values float32
Opened Bb624-stator-msk-4.2A.mrc as #6, grid size 140,140,140, pixel 4.2,
shown at level 1.33, step 1, values float32
Opened MotB-nostat-msk-4.2A.mrc as #7, grid size 140,140,140, pixel 4.2, shown
at level 4.13, step 1, values float32
Opened WTCC-stator-msk-4.2A.mrc as #8, grid size 140,140,140, pixel 4.2, shown
at level 0.125, step 1, values float32
Log from Fri Jul 21 11:50:13 2023 Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
> alphafold predict
> MFISRELKYILLTSVSALFISAVLGLFCGLSFFTILVRSLLQFVFFFVIGLLIEYIFKKYLSNLFSTELSGNMENKPQDDKKSDKDFKENLDFQNKNSLYENSQNISSSGDFIEEVKKYKFETEDVSRGSDKNKKMSFIEDNDPKVVADAIKTLMSKKE
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/Borrelia
> mapping 071923.py"
ChimeraX cannot open a regular Chimera session. An exporter from Chimera
to ChimeraX is being worked on but only handles molecules and molecular
surfaces
(not volumes) at this time. If that is sufficient, use the latest Chimera
daily build and its File->Export Scene menu item, and change the resulting
dialog's "File Type" to ChimeraX.
> open "C:/Users/Jack Botting/Documents/borrelia maps/BbWT-FlbB-256-2.7A.mrc"
Opened BbWT-FlbB-256-2.7A.mrc as #1, grid size 256,256,256, pixel 2.7, shown
at level 3.99, step 1, values float32
> volume #1 level 0.9046
> open "C:/Users/Jack Botting/Documents/alphafold
> results/Bb_0058_50988/Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2
---
Chain | Description
A | No description available
> select add #2
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> hide #!1 models
> show #!1 models
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> set bgColor black
> fitmap #2 #1 search 500
Missing required "in_map" argument
> fitmap #2 inMap #1 search 500
Found 268 unique fits from 500 random placements having fraction of points
inside contour >= 0.100 (271 of 500).
Average map values and times found:
2.886 (1), 2.85 (1), 2.849 (1), 2.789 (1), 2.759 (1), 2.713 (1), 2.682 (1),
2.681 (1), 2.574 (1), 2.547 (1), 2.529 (1), 2.517 (1), 2.453 (1), 2.424 (1),
2.42 (1), 2.379 (1), 2.378 (1), 2.319 (1), 2.312 (1), 2.224 (1), 2.203 (1),
2.192 (1), 2.191 (1), 2.179 (1), 2.161 (1), 2.144 (1), 2.052 (1), 2.052 (1),
2.003 (1), 1.997 (1), 1.996 (1), 1.994 (1), 1.99 (1), 1.926 (1), 1.911 (1),
1.905 (1), 1.849 (1), 1.813 (1), 1.793 (1), 1.773 (1), 1.76 (1), 1.743 (1),
1.735 (1), 1.712 (1), 1.667 (1), 1.657 (1), 1.619 (1), 1.617 (1), 1.615 (1),
1.599 (1), 1.591 (1), 1.586 (1), 1.586 (2), 1.582 (1), 1.58 (1), 1.569 (1),
1.548 (1), 1.537 (1), 1.531 (1), 1.508 (1), 1.493 (1), 1.474 (1), 1.47 (1),
1.467 (1), 1.462 (1), 1.461 (1), 1.449 (1), 1.442 (1), 1.438 (1), 1.434 (1),
1.433 (1), 1.431 (1), 1.426 (1), 1.42 (1), 1.403 (1), 1.399 (1), 1.397 (1),
1.391 (1), 1.389 (1), 1.389 (1), 1.381 (1), 1.381 (1), 1.369 (1), 1.355 (1),
1.347 (1), 1.341 (1), 1.34 (1), 1.339 (1), 1.338 (1), 1.336 (1), 1.33 (1),
1.325 (1), 1.323 (1), 1.323 (1), 1.322 (1), 1.312 (1), 1.312 (1), 1.294 (1),
1.287 (1), 1.281 (1), 1.279 (1), 1.273 (1), 1.225 (1), 1.224 (1), 1.182 (1),
1.156 (1), 1.144 (1), 1.129 (1), 1.124 (1), 1.123 (1), 1.121 (1), 1.121 (1),
1.119 (1), 1.118 (1), 1.117 (1), 1.117 (1), 1.113 (1), 1.11 (1), 1.1 (1),
1.094 (1), 1.091 (1), 1.086 (1), 1.086 (1), 1.086 (1), 1.084 (1), 1.082 (1),
1.082 (1), 1.08 (1), 1.072 (1), 1.072 (1), 1.069 (1), 1.067 (1), 1.062 (1),
1.061 (1), 1.052 (1), 1.043 (2), 1.024 (1), 1.013 (1), 1.013 (1), 1.013 (1),
1.008 (1), 1.007 (1), 1.006 (1), 1.006 (1), 1.006 (1), 1.003 (1), 0.9874 (1),
0.9473 (1), 0.941 (1), 0.9345 (1), 0.9295 (1), 0.9236 (1), 0.8902 (1), 0.8896
(1), 0.8896 (1), 0.8896 (1), 0.8893 (1), 0.8892 (1), 0.8888 (1), 0.8888 (1),
0.8873 (1), 0.8865 (1), 0.8772 (1), 0.8761 (1), 0.8749 (1), 0.8693 (1), 0.8574
(1), 0.8556 (1), 0.8504 (1), 0.8316 (1), 0.8303 (1), 0.8254 (1), 0.823 (1),
0.8179 (1), 0.8096 (1), 0.8054 (1), 0.8053 (1), 0.8051 (1), 0.8046 (1), 0.8043
(1), 0.8008 (1), 0.7923 (1), 0.7871 (1), 0.7801 (1), 0.7707 (1), 0.7653 (1),
0.7546 (1), 0.7512 (1), 0.7413 (1), 0.7364 (1), 0.7335 (1), 0.7306 (1), 0.7287
(1), 0.7255 (1), 0.7165 (1), 0.7163 (1), 0.7134 (1), 0.6715 (1), 0.6577 (1),
0.6543 (1), 0.6525 (1), 0.651 (1), 0.651 (1), 0.648 (1), 0.635 (1), 0.6265
(1), 0.6091 (1), 0.6078 (1), 0.6065 (1), 0.6021 (1), 0.5896 (1), 0.5857 (1),
0.5574 (1), 0.551 (1), 0.5492 (1), 0.5456 (1), 0.5437 (1), 0.5416 (1), 0.541
(1), 0.5401 (1), 0.5397 (1), 0.5374 (1), 0.5369 (1), 0.5361 (1), 0.5355 (1),
0.5316 (1), 0.5309 (1), 0.5271 (1), 0.5225 (1), 0.5174 (1), 0.5172 (1), 0.5166
(1), 0.5082 (1), 0.4948 (1), 0.4933 (1), 0.4907 (1), 0.4854 (1), 0.4784 (1),
0.4774 (1), 0.4606 (1), 0.4572 (1), 0.4461 (1), 0.44 (1), 0.4382 (1), 0.4355
(2), 0.4312 (1), 0.4304 (1), 0.4242 (1), 0.4185 (1), 0.4154 (1), 0.4106 (1),
0.41 (1), 0.4096 (1), 0.4016 (1), 0.4007 (1), 0.3995 (1), 0.396 (1), 0.3936
(1), 0.359 (1), 0.3493 (1), 0.3371 (1), 0.3172 (1), 0.2938 (1), 0.2738 (1),
0.2655 (1), 0.2619 (1), 0.2271 (1), 0.2161 (1)
Best fit found:
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#2) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.886, steps = 172
shifted from previous position = 21.4
rotated from previous position = 60.5 degrees
atoms outside contour = 1958, contour level = 0.90463
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#2) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.56948425 0.64824464 0.50543703 -198.83637025
0.77982332 -0.23162418 -0.58157192 -80.90375878
-0.25992941 0.72534764 -0.63742263 57.81577092
Axis 0.85967831 0.50345020 0.08655110
Axis point 0.00000000 -2.51621404 45.11815878
Rotation angle (degrees) 130.52511130
Shift along axis -206.66230995
Found 268 fits.
> volume #1 style image
> volume #1 style surface
> volume #1 change image level -0.745,0 level 3.993,0.8 level 8.429,1
> ui tool show "Map Eraser"
> transparency 0
> close #3
> transparency 50
> measure symmetry #1
Symmetry BbWT-FlbB-256-2.7A.mrc: C8, center 128 128 120
> fitmap #2 inMap #1 search 500
Found 255 unique fits from 500 random placements having fraction of points
inside contour >= 0.100 (279 of 500).
Average map values and times found:
2.886 (1), 2.789 (1), 2.761 (1), 2.661 (1), 2.542 (1), 2.529 (1), 2.464 (1),
2.451 (1), 2.38 (1), 2.378 (1), 2.346 (1), 2.334 (1), 2.313 (1), 2.278 (1),
2.274 (1), 2.267 (1), 2.267 (1), 2.267 (1), 2.265 (1), 2.25 (1), 2.242 (1),
2.222 (1), 2.201 (1), 2.191 (1), 2.179 (1), 2.112 (1), 2.108 (1), 2.104 (1),
2.083 (1), 2.079 (2), 2.072 (1), 2.037 (1), 2.029 (1), 1.994 (2), 1.962 (1),
1.95 (1), 1.948 (1), 1.899 (1), 1.893 (1), 1.893 (1), 1.885 (2), 1.883 (1),
1.874 (1), 1.873 (1), 1.871 (1), 1.826 (1), 1.823 (1), 1.801 (1), 1.789 (2),
1.786 (1), 1.774 (1), 1.768 (1), 1.76 (1), 1.735 (1), 1.734 (1), 1.718 (1),
1.693 (1), 1.684 (1), 1.679 (1), 1.673 (1), 1.641 (1), 1.627 (1), 1.618 (1),
1.605 (1), 1.6 (1), 1.599 (1), 1.586 (1), 1.573 (1), 1.569 (1), 1.558 (1),
1.527 (1), 1.525 (1), 1.521 (1), 1.519 (1), 1.503 (1), 1.493 (1), 1.485 (1),
1.485 (2), 1.478 (1), 1.474 (1), 1.469 (2), 1.465 (1), 1.439 (1), 1.438 (1),
1.431 (1), 1.427 (2), 1.42 (1), 1.407 (1), 1.391 (1), 1.391 (1), 1.391 (1),
1.378 (1), 1.369 (1), 1.369 (1), 1.356 (1), 1.351 (1), 1.342 (1), 1.341 (1),
1.34 (2), 1.34 (1), 1.321 (1), 1.318 (1), 1.311 (1), 1.279 (1), 1.279 (1),
1.274 (1), 1.263 (1), 1.253 (1), 1.217 (1), 1.208 (1), 1.198 (1), 1.191 (1),
1.178 (1), 1.164 (1), 1.158 (1), 1.155 (1), 1.153 (1), 1.146 (1), 1.144 (1),
1.135 (1), 1.135 (1), 1.128 (2), 1.128 (1), 1.126 (1), 1.125 (1), 1.123 (1),
1.121 (2), 1.12 (2), 1.119 (1), 1.117 (1), 1.116 (1), 1.116 (1), 1.114 (2),
1.113 (1), 1.11 (1), 1.106 (1), 1.096 (1), 1.092 (2), 1.091 (1), 1.091 (1),
1.087 (1), 1.087 (1), 1.085 (1), 1.082 (1), 1.08 (2), 1.077 (1), 1.074 (1),
1.074 (2), 1.073 (1), 1.07 (1), 1.069 (1), 1.06 (1), 1.053 (1), 1.047 (1),
1.04 (1), 1.038 (1), 1.034 (1), 1.032 (1), 1.024 (1), 1.022 (1), 1.021 (1),
1.019 (2), 1.004 (1), 0.9808 (1), 0.9779 (1), 0.9637 (1), 0.9586 (1), 0.9583
(1), 0.9552 (1), 0.9433 (1), 0.941 (1), 0.937 (1), 0.9335 (1), 0.9316 (1),
0.9174 (1), 0.9102 (1), 0.9063 (1), 0.8986 (1), 0.8902 (1), 0.8888 (3), 0.8873
(1), 0.8867 (2), 0.8825 (1), 0.8795 (1), 0.8791 (1), 0.879 (1), 0.8734 (1),
0.8615 (1), 0.8558 (1), 0.8427 (1), 0.8411 (1), 0.8407 (1), 0.8322 (1), 0.8308
(1), 0.8256 (2), 0.8201 (1), 0.8166 (1), 0.8164 (2), 0.8116 (1), 0.8082 (1),
0.8044 (1), 0.8028 (2), 0.7888 (1), 0.7852 (1), 0.779 (1), 0.7658 (1), 0.764
(1), 0.763 (1), 0.7486 (1), 0.7419 (1), 0.7411 (1), 0.741 (1), 0.7321 (1),
0.7281 (1), 0.7255 (1), 0.7052 (1), 0.7003 (1), 0.6306 (1), 0.6009 (1), 0.5968
(1), 0.5544 (1), 0.554 (1), 0.5526 (1), 0.5508 (1), 0.5376 (1), 0.536 (1),
0.5323 (1), 0.5321 (1), 0.5265 (1), 0.5168 (1), 0.5165 (1), 0.5034 (1), 0.4949
(2), 0.4914 (2), 0.4822 (1), 0.4801 (1), 0.4796 (1), 0.4749 (1), 0.45 (1),
0.4336 (1), 0.4022 (1), 0.4002 (1), 0.3927 (1), 0.3923 (1), 0.3825 (1), 0.359
(1), 0.3563 (1), 0.3502 (1), 0.335 (1), 0.3003 (1), 0.2953 (1), 0.2819 (1),
0.2791 (1), 0.2697 (1), 0.219 (1)
Best fit found:
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#2) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.886, steps = 40
shifted from previous position = 0.0776
rotated from previous position = 0.0701 degrees
atoms outside contour = 1956, contour level = 0.90463
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#2) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
-0.82467234 -0.51021505 -0.24412331 214.64658051
-0.50207751 0.46159858 0.73133102 -1.31656487
-0.26044911 0.72567720 -0.63683510 57.81914676
Axis -0.29604915 0.85486315 0.42610315
Axis point 107.30442002 0.00000000 28.67137755
Rotation angle (degrees) 179.45288662
Shift along axis -40.03449924
Found 255 fits.
> center #1
Unknown command: center #1
> center
Unknown command: center
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right translate
> ui mousemode right "clip rotate"
> ui mousemode right translate
> ui mousemode right clip
> ui tool show "Side View"
[Repeated 1 time(s)]
> fitmap #2 inMap #1 search 500 asymmetricUnit true
Found 250 unique fits from 500 random placements having fraction of points
inside contour >= 0.100 (280 of 500).
Average map values and times found:
2.711 (1), 2.682 (1), 2.563 (2), 2.547 (1), 2.545 (1), 2.535 (1), 2.529 (1),
2.524 (1), 2.451 (1), 2.45 (1), 2.4 (1), 2.378 (1), 2.346 (1), 2.337 (1),
2.312 (1), 2.311 (1), 2.274 (1), 2.267 (1), 2.265 (1), 2.257 (1), 2.251 (1),
2.25 (1), 2.242 (1), 2.224 (2), 2.205 (1), 2.203 (1), 2.143 (1), 2.079 (1),
2.053 (1), 2.029 (1), 2.025 (1), 2.003 (1), 1.987 (1), 1.974 (1), 1.948 (1),
1.92 (1), 1.919 (1), 1.914 (3), 1.901 (1), 1.899 (1), 1.892 (1), 1.885 (1),
1.87 (1), 1.848 (1), 1.842 (1), 1.826 (1), 1.824 (1), 1.821 (1), 1.8 (1),
1.798 (1), 1.782 (1), 1.778 (1), 1.753 (1), 1.752 (1), 1.735 (1), 1.732 (1),
1.719 (1), 1.704 (1), 1.703 (1), 1.655 (1), 1.641 (2), 1.611 (1), 1.61 (1),
1.605 (1), 1.599 (1), 1.598 (1), 1.597 (1), 1.585 (1), 1.546 (1), 1.531 (1),
1.526 (1), 1.515 (1), 1.504 (1), 1.502 (1), 1.485 (1), 1.478 (1), 1.469 (2),
1.456 (1), 1.443 (1), 1.44 (1), 1.436 (1), 1.435 (1), 1.394 (1), 1.385 (1),
1.384 (1), 1.381 (2), 1.361 (1), 1.359 (1), 1.342 (2), 1.336 (1), 1.322 (1),
1.321 (1), 1.318 (1), 1.312 (1), 1.311 (1), 1.293 (1), 1.279 (2), 1.275 (1),
1.274 (1), 1.262 (1), 1.245 (2), 1.245 (1), 1.225 (1), 1.217 (1), 1.2 (1),
1.189 (1), 1.168 (1), 1.167 (1), 1.164 (1), 1.159 (1), 1.155 (3), 1.153 (1),
1.145 (2), 1.144 (1), 1.143 (1), 1.141 (1), 1.138 (1), 1.129 (1), 1.128 (1),
1.122 (1), 1.12 (1), 1.117 (1), 1.111 (1), 1.106 (1), 1.102 (1), 1.101 (2),
1.096 (2), 1.092 (1), 1.092 (1), 1.091 (2), 1.09 (1), 1.087 (1), 1.087 (1),
1.086 (2), 1.082 (1), 1.076 (1), 1.074 (1), 1.073 (1), 1.071 (1), 1.07 (2),
1.069 (1), 1.059 (1), 1.052 (1), 1.048 (1), 1.045 (2), 1.044 (1), 1.037 (1),
1.036 (1), 1.032 (1), 1.03 (1), 1.024 (1), 1.021 (1), 1.019 (1), 1.001 (1),
0.9995 (1), 0.9936 (1), 0.9779 (1), 0.9496 (1), 0.9279 (1), 0.9173 (1), 0.9172
(1), 0.8902 (3), 0.8888 (2), 0.8873 (2), 0.8867 (2), 0.8808 (1), 0.8795 (1),
0.8791 (1), 0.879 (1), 0.8749 (1), 0.8645 (1), 0.8633 (1), 0.8466 (1), 0.8419
(1), 0.8415 (1), 0.8409 (1), 0.8394 (1), 0.8331 (1), 0.8247 (1), 0.8236 (1),
0.8179 (1), 0.8159 (1), 0.8132 (1), 0.8082 (1), 0.7973 (1), 0.7972 (1), 0.7889
(1), 0.7866 (1), 0.7813 (1), 0.7486 (1), 0.7445 (1), 0.7363 (1), 0.7344 (1),
0.7339 (1), 0.732 (1), 0.7163 (1), 0.7134 (1), 0.6941 (1), 0.6801 (1), 0.6706
(1), 0.6657 (1), 0.635 (1), 0.6305 (1), 0.6229 (1), 0.6166 (2), 0.6148 (1),
0.6094 (1), 0.6087 (1), 0.5913 (2), 0.574 (1), 0.5492 (1), 0.539 (1), 0.5376
(1), 0.5361 (1), 0.5239 (1), 0.5155 (1), 0.515 (2), 0.5141 (2), 0.5035 (1),
0.4948 (1), 0.4861 (1), 0.48 (2), 0.4707 (1), 0.4646 (2), 0.4627 (1), 0.4583
(1), 0.4567 (1), 0.4537 (1), 0.4532 (1), 0.4528 (1), 0.4487 (1), 0.4404 (1),
0.4364 (1), 0.4346 (1), 0.3959 (1), 0.3931 (1), 0.3798 (1), 0.3778 (1), 0.3678
(1), 0.3678 (1), 0.3667 (1), 0.3631 (1), 0.3371 (1), 0.3265 (1), 0.295 (1),
0.28 (1), 0.2694 (1), 0.2254 (1), 0.196 (1), 0.07582 (1)
Best fit found:
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#2) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.711, steps = 44
shifted from previous position = 0.0582
rotated from previous position = 0.0561 degrees
atoms outside contour = 1805, contour level = 0.90463
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#2) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.47655618 0.82696777 0.29835977 198.20835333
-0.12064821 0.39768253 -0.90955635 106.33290007
-0.87082620 0.39745807 0.28929028 39.66514180
Axis 0.65570269 0.58655695 -0.47539977
Axis point 0.00000000 -136.57502008 95.47398165
Rotation angle (degrees) 85.31000420
Shift along axis 173.47925161
Found 250 fits.
> select down
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right zone
> view orient
> ui mousemode right translate
> select #1
4 models selected
> select clear
> ui tool show "Side View"
[Repeated 1 time(s)]
> select /A:102
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
241 atoms, 241 bonds, 14 residues, 1 model selected
> select up
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> select down
241 atoms, 241 bonds, 14 residues, 1 model selected
> select down
22 atoms, 21 bonds, 1 residue, 1 model selected
> select down
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1
5 models selected
> select #1
5 models selected
> select clear
> color #3 red
> ui mousemode right "translate selected models"
> select add #3
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> view matrix models
> #3,0.93881,0.3415,0.044932,141.53,0.25269,-0.59417,-0.76361,50.344,-0.23408,0.72824,-0.64411,7.833
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.1731,-0.31128,0.93442,145.76,0.48768,-0.79718,-0.35591,52.274,0.85569,0.5173,0.013818,10.937
> view matrix models
> #3,0.63887,0.42415,0.64183,146.59,0.76902,-0.32905,-0.54803,52.771,-0.021253,0.8437,-0.5364,9.0025
> fitmap #3 inMap #1
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#3) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.447, steps = 100
shifted from previous position = 28.3
rotated from previous position = 17.8 degrees
atoms outside contour = 2902, contour level = 0.90463
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#3) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.41987160 0.64023399 0.64327935 139.63319741
0.89439213 -0.17147830 -0.41310773 25.91332531
-0.15417713 0.74879612 -0.64461920 8.18930403
Axis 0.81139927 0.55689256 0.17748777
Axis point 0.00000000 -31.13146986 -23.13616055
Rotation angle (degrees) 134.27579744
Shift along axis 129.18271321
> fitmap #3 inMap #1
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#3) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.447, steps = 40
shifted from previous position = 0.0346
rotated from previous position = 0.155 degrees
atoms outside contour = 2893, contour level = 0.90463
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#3) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.42042268 0.63846747 0.64467364 139.60757853
0.89451187 -0.17266156 -0.41235491 25.91126411
-0.15196481 0.75003151 -0.64370766 8.16909418
Axis 0.81158192 0.55621552 0.17877102
Axis point 0.00000000 -31.00651753 -23.22775114
Rotation angle (degrees) 134.26462108
Shift along axis 129.17563161
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.42042,0.63847,0.64467,141.52,0.89451,-0.17266,-0.41235,53.084,-0.15196,0.75003,-0.64371,18.781
> view matrix models
> #3,0.42042,0.63847,0.64467,140.24,0.89451,-0.17266,-0.41235,51.724,-0.15196,0.75003,-0.64371,17.671
> view matrix models
> #3,0.42042,0.63847,0.64467,144.79,0.89451,-0.17266,-0.41235,52.918,-0.15196,0.75003,-0.64371,20.317
> view matrix models
> #3,-0.067385,0.99251,0.10192,142.74,0.83277,0.11221,-0.54212,53.303,-0.5495,0.048343,-0.8341,15.984
> view matrix models
> #3,-0.026728,0.99576,0.087996,142.62,0.90441,0.061585,-0.42219,53.911,-0.42582,0.0683,-0.90223,15.473
> view matrix models
> #3,-0.026728,0.99576,0.087996,143.61,0.90441,0.061585,-0.42219,54.565,-0.42582,0.0683,-0.90223,16.189
> view matrix models
> #3,-0.026728,0.99576,0.087996,145.27,0.90441,0.061585,-0.42219,54.589,-0.42582,0.0683,-0.90223,17.008
> view matrix models
> #3,-0.026728,0.99576,0.087996,143.62,0.90441,0.061585,-0.42219,55.849,-0.42582,0.0683,-0.90223,16.649
> view matrix models
> #3,-0.002108,0.99852,-0.054386,142.55,0.66455,-0.039241,-0.74622,53.154,-0.74724,-0.037715,-0.66348,18.19
> view matrix models
> #3,-0.002108,0.99852,-0.054386,143.16,0.66455,-0.039241,-0.74622,63.076,-0.74724,-0.037715,-0.66348,22.024
> fitmap #3 inMap #1
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#3) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.682, steps = 160
shifted from previous position = 37.8
rotated from previous position = 27 degrees
atoms outside contour = 2807, contour level = 0.90463
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#3) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.03545278 0.89442339 -0.44581382 122.92833350
0.81569068 -0.28363515 -0.50418241 37.69484423
-0.57740093 -0.34577143 -0.73962853 1.17165477
Axis 0.71850730 0.59684187 -0.35710929
Axis point 0.00000000 -33.77090457 30.04956318
Rotation angle (degrees) 173.67107083
Shift along axis 110.40435760
> close #3
> ui mousemode right translate
> volume #1 level 0.2443
> volume #1 level 1.196
> volume #1 level 1.177
> volume hide
> volume show
> volume #1 orthoplanes xyz positionPlanes 128,128,128 style image region all
> mousemode rightMode "move planes"
> volume #1 orthoplanes xyz positionPlanes 128,128,128 style image region all
> mousemode rightMode "move planes"
> volume #1 orthoplanes xyz positionPlanes 128,128,128 style image region all
> mousemode rightMode "move planes"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume style surface
> volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 0 tiltedSlabSpacing 2.7 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1 orthoplanes xyz positionPlanes 128,128,128 style image region all
> mousemode rightMode "move planes"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume zone #1 nearAtoms #2 range 16.2
[Repeated 1 time(s)]
> volume show
[Repeated 1 time(s)]
> volume style surface
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume style surface
> transparency 0
> transparency 50
> volume showOutlineBox false
> open "C:/Users/Jack Botting/Documents/borrelia maps/Bb58-int-lp-8.6A.mrc"
Opened Bb58-int-lp-8.6A.mrc as #3, grid size 120,120,120, pixel 8.6, shown at
level 0.179, step 1, values float32
> volume #1 region 0,0,0,255,255,255
[Repeated 1 time(s)]
> ui mousemode right translate
> select #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-481.68,0,1,0,-529.4,0,0,1,22.566
> select clear
> select #3
2 models selected
> view matrix models #3,1,0,0,-512.73,0,1,0,-474.52,0,0,1,-580.41
> volume #3 level 0.09486
> view matrix models #3,1,0,0,-516.67,0,1,0,-476.79,0,0,1,-549.02
> fitmap #3 inMap #1
Fit map Bb58-int-lp-8.6A.mrc in map BbWT-FlbB-256-2.7A.mrc using 41514 points
correlation = 0.09856, correlation about mean = 0.01057, overlap = 1505
steps = 92, shift = 18, angle = 4.14 degrees
Position of Bb58-int-lp-8.6A.mrc (#3) relative to BbWT-FlbB-256-2.7A.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999685 0.00153941 -0.00198226 -518.18213488
-0.00139252 0.99739785 0.07208049 -500.67949002
0.00208807 -0.07207751 0.99739685 -522.47912436
Axis -0.99939511 -0.02821813 -0.02032598
Axis point 0.00000000 -7329.47034017 6469.09352419
Rotation angle (degrees) 4.13591293
Shift along axis 542.61683286
> fitmap #3 inMap #1
Fit map Bb58-int-lp-8.6A.mrc in map BbWT-FlbB-256-2.7A.mrc using 41514 points
correlation = 0.09856, correlation about mean = 0.01059, overlap = 1505
steps = 40, shift = 0.0317, angle = 0.00454 degrees
Position of Bb58-int-lp-8.6A.mrc (#3) relative to BbWT-FlbB-256-2.7A.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999698 0.00150924 -0.00194189 -518.16670464
-0.00136547 0.99740230 0.07201939 -500.67929371
0.00204554 -0.07201652 0.99740134 -522.47710943
Axis -0.99941815 -0.02766742 -0.01994665
Axis point 0.00000000 -7338.59465684 6479.03594590
Rotation angle (degrees) 4.13230863
Shift along axis 542.13938666
> view matrix models
> #3,1,0.0015092,-0.0019419,-518.38,-0.0013655,0.9974,0.072019,-503.19,0.0020455,-0.072017,0.9974,-492.8
> fitmap #3 inMap #1
Fit map Bb58-int-lp-8.6A.mrc in map BbWT-FlbB-256-2.7A.mrc using 41514 points
correlation = 0.09898, correlation about mean = 0.01322, overlap = 1515
steps = 224, shift = 31.8, angle = 1.02 degrees
Position of Bb58-int-lp-8.6A.mrc (#3) relative to BbWT-FlbB-256-2.7A.mrc (#1)
coordinates:
Matrix rotation and translation
0.99981817 -0.00093033 -0.01904615 -519.70946489
0.00221638 0.99770914 0.06761327 -502.20604120
0.01893961 -0.06764319 0.99752979 -533.24912777
Axis -0.96251173 -0.27031416 0.02239261
Axis point 0.00000000 -8259.76141828 4652.89620093
Rotation angle (degrees) 4.02904951
Shift along axis 624.03901715
> select clear
> transparency 0
> transparency 50
> fitmap #3 inMap #1
Fit map Bb58-int-lp-8.6A.mrc in map BbWT-FlbB-256-2.7A.mrc using 41514 points
correlation = 0.09899, correlation about mean = 0.01321, overlap = 1515
steps = 28, shift = 0.0582, angle = 0.00564 degrees
Position of Bb58-int-lp-8.6A.mrc (#3) relative to BbWT-FlbB-256-2.7A.mrc (#1)
coordinates:
Matrix rotation and translation
0.99981836 -0.00091220 -0.01903724 -519.74435455
0.00219587 0.99771567 0.06751760 -502.12855421
0.01893216 -0.06754714 0.99753644 -533.35026027
Axis -0.96244742 -0.27056320 0.02214758
Axis point 0.00000000 -8270.45519215 4655.54384324
Rotation angle (degrees) 4.02359817
Shift along axis 624.27170424
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit map Bb58-int-lp-8.6A.mrc in map BbWT-FlbB-256-2.7A.mrc using 41514 points
correlation = 0.09898, correlation about mean = 0.01322, overlap = 1515
steps = 40, shift = 0.0448, angle = 0.00573 degrees
Position of Bb58-int-lp-8.6A.mrc (#3) relative to BbWT-FlbB-256-2.7A.mrc (#1)
coordinates:
Matrix rotation and translation
0.99981806 -0.00093480 -0.01905211 -519.71063176
0.00222124 0.99770914 0.06761312 -502.20626397
0.01894526 -0.06764314 0.99752969 -533.26377153
Axis -0.96248869 -0.27039073 0.02245852
Axis point 0.00000000 -8260.57150775 4652.20675133
Rotation angle (degrees) 4.02914018
Shift along axis 624.03120227
> select #3
2 models selected
> view matrix models
> #3,0.99982,-0.0009348,-0.019052,-510.76,0.0022212,0.99771,0.067613,-558.62,0.018945,-0.067643,0.99753,-540.86
> fitmap #3 inMap #1
Fit map Bb58-int-lp-8.6A.mrc in map BbWT-FlbB-256-2.7A.mrc using 41514 points
correlation = 0.7894, correlation about mean = 0.5441, overlap = 1.551e+04
steps = 88, shift = 11.1, angle = 4.07 degrees
Position of Bb58-int-lp-8.6A.mrc (#3) relative to BbWT-FlbB-256-2.7A.mrc (#1)
coordinates:
Matrix rotation and translation
0.99996436 0.00844221 0.00008398 -520.42571889
-0.00844221 0.99996436 -0.00003942 -511.58905065
-0.00008431 0.00003871 1.00000000 -559.50108005
Axis 0.00462659 0.00996614 -0.99993963
Axis point -61510.95029628 61688.46675513 0.00000000
Rotation angle (degrees) 0.48373804
Shift along axis 551.96093603
> view matrix models
> #3,0.99996,0.0084422,8.3976e-05,-521.18,-0.0084422,0.99996,-3.9416e-05,-511.66,-8.4306e-05,3.8706e-05,1,-559.54
> fitmap #3 inMap #1
Fit map Bb58-int-lp-8.6A.mrc in map BbWT-FlbB-256-2.7A.mrc using 41514 points
correlation = 0.7894, correlation about mean = 0.5441, overlap = 1.551e+04
steps = 60, shift = 0.776, angle = 0.00614 degrees
Position of Bb58-int-lp-8.6A.mrc (#3) relative to BbWT-FlbB-256-2.7A.mrc (#1)
coordinates:
Matrix rotation and translation
0.99996355 0.00853778 0.00004599 -520.43359034
-0.00853778 0.99996355 -0.00000956 -511.57336036
-0.00004607 0.00000917 1.00000000 -559.49947916
Axis 0.00109688 0.00539144 -0.99998486
Axis point -60529.40332980 60769.58450036 0.00000000
Rotation angle (degrees) 0.48919217
Shift along axis 556.16204005
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> vop subtract #1 #3 minrms True
Opened volume difference as #4, grid size 256,256,256, pixel 2.7, shown at
step 1, values float32
Minimum RMS scale factor for "Bb58-int-lp-8.6A.mrc #3" above level 0.094864 is
10.23
> close #4
> show #!1 models
> show #!3 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> volume #3 level 0.0934
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #3 level 0.1139
> vop subtract #1 #3 minrms True
Opened volume difference as #4, grid size 256,256,256, pixel 2.7, shown at
step 1, values float32
Minimum RMS scale factor for "Bb58-int-lp-8.6A.mrc #3" above level 0.11395 is
10.352
> transparency #4.1 50
> close #4
> show #!3 models
> show #!1 models
> hide #!3 models
> view orient
> sym #2 C16 center #1
Made 16 graphical clones for
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb symmetry
C16
> open "C:/Users/Jack Botting/Documents/alphafold results/Borrelia 0286
> dimer/0286dimer_9e9c4_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb"
Chain information for
0286dimer_9e9c4_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#4
---
Chain | Description
A B | No description available
> close #4
> open "C:/Users/Jack Botting/Documents/Chimera/PDB/Bb_0286 ring.pdb"
Chain information for Bb_0286 ring.pdb
---
Chain | Description
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A
4.13/A 4.14/A 4.15/A 4.16/A 4.1/B 4.2/B 4.3/B 4.4/B 4.5/B 4.6/B 4.7/B 4.8/B
4.9/B 4.10/B 4.11/B 4.12/B 4.13/B 4.14/B 4.15/B 4.16/B | No description
available
> select add #4
111872 atoms, 112832 bonds, 6560 residues, 17 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-379.35,0,1,0,-536.39,0,0,1,0
> view matrix models #4,1,0,0,-526.01,0,1,0,-529.08,0,0,1,0
> view matrix models #4,1,0,0,-513.04,0,1,0,-514.19,0,0,1,-340.28
> view matrix models #4,1,0,0,-510.69,0,1,0,-526.28,0,0,1,-568.19
> view orient
> view matrix models #4,1,0,0,-513.83,0,1,0,-521.07,0,0,1,-568.19
> show #!3 models
> hide #!1 models
> view matrix models #4,1,0,0,-514.89,0,1,0,-520.02,0,0,1,-568.19
> view matrix models
> #4,0.99718,-0.075027,0,-474.45,0.075027,0.99718,0,-557.13,0,0,1,-568.19
> show #!1 models
> hide #!3 models
> select clear
> hide #!1 models
> show #!3 models
> hide #2 models
> select add #4
111872 atoms, 112832 bonds, 6560 residues, 17 models selected
> view matrix models
> #4,0.99718,-0.075027,0,-473.87,0.075027,0.99718,0,-557.14,0,0,1,-557.82
> view matrix models
> #4,0.99718,-0.075027,0,-473.22,0.075027,0.99718,0,-557.19,0,0,1,-557.55
> view matrix models
> #4,0.99707,-0.075072,-0.014688,-465.44,0.075097,0.99718,0.0011832,-557.84,0.014558,-0.0022827,0.99989,-563.78
> select clear
> show #2 models
> hide #!3 models
> show #!1 models
> select add #2
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> ui tool show Clashes
> hide #!1 models
> clashes intraModel false ignoreHiddenModels true
4626 clashes
> select clear
> clashes intraModel false ignoreHiddenModels true
4626 clashes
> clashes intraModel false ignoreHiddenModels true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
4626 clashes
atom1 atom2 overlap distance
Bb_0286 ring.pdb #4.5/B MET 164 CG Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2/A ASN 555 C 3.193 0.207
Bb_0286 ring.pdb #4.6/B LEU 112 CD2 Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2/A ILE 514 C 3.176 0.224
[deleted]
Bb_0286 ring.pdb #4.6/A ASP 121 HB3 Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2/A PHE 591 HE1 0.600 1.400
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2/A PHE 487 CG Bb_0286 ring.pdb #4.6/A LYS 115 N 0.600 2.725
4626 clashes
> select #2/A:276
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
241 atoms, 240 bonds, 14 residues, 1 model selected
> select up
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> select down
241 atoms, 240 bonds, 14 residues, 1 model selected
> select up
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> select down
241 atoms, 240 bonds, 14 residues, 1 model selected
> select down
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #4.14/B:127
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
1414 atoms, 1417 bonds, 83 residues, 1 model selected
> select up
3496 atoms, 3526 bonds, 205 residues, 1 model selected
> select add #4.14/A:183
3520 atoms, 3551 bonds, 206 residues, 1 model selected
> select up
3620 atoms, 3653 bonds, 212 residues, 1 model selected
> select up
6992 atoms, 7052 bonds, 410 residues, 1 model selected
> clashes sel restrict cross intraModel false ignoreHiddenModels true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> view matrix models
> #4.14,1,1.8717e-16,9.8879e-17,2.1477,4.2412e-16,1,5.6379e-18,0.32377,2.2551e-17,6.9389e-18,1,0.0019147
> undo
> ui mousemode right translate
> clashes sel intraModel false ignoreHiddenModels true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> select #2/A:255
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:255
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
249 atoms, 253 bonds, 14 residues, 1 model selected
> select up
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> clashes sel intraModel false ignoreHiddenModels true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
4626 clashes
atom1 atom2 overlap distance
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2/A ASN 555 C Bb_0286 ring.pdb #4.5/B MET 164 CG 3.193 0.207
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2/A ILE 514 C Bb_0286 ring.pdb #4.6/B LEU 112 CD2 3.176 0.224
[deleted] Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2/A LEU 623 N Bb_0286 ring.pdb #4.5/B LEU 155 HA 0.601 2.024
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2/A PHE 591 HE1 Bb_0286 ring.pdb #4.6/A ASP 121 HB3 0.600 1.400
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2/A PHE 487 CG Bb_0286 ring.pdb #4.6/A LYS 115 N 0.600 2.725
4626 clashes
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> select add #5
10479 atoms, 10585 bonds, 4626 pseudobonds, 637 residues, 2 models selected
> select clear
> select add #5
4626 pseudobonds, 1 model selected
> select clear
> show #!1 models
> ~sym #2
Unknown command: ~sym #2
> ~sym
Unknown command: ~sym
> ~sym
Unknown command: ~sym
> sym clear
> close #5
> select add #1
4 models selected
> select add #1
4 models selected
> select add #2
10479 atoms, 10585 bonds, 637 residues, 5 models selected
> select add #1
10479 atoms, 10585 bonds, 637 residues, 5 models selected
> select #1
4 models selected
> select add #1
4 models selected
> select clear
> select #2
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.93881,0.3415,0.044932,147.66,0.25269,-0.59417,-0.76361,55.206,-0.23408,0.72824,-0.64411,12.062
> view matrix models
> #2,0.92581,-0.36897,0.082147,144.69,-0.14946,-0.55693,-0.817,55.287,0.3472,0.74411,-0.57075,12.236
> view matrix models
> #2,0.92581,-0.36897,0.082147,148.64,-0.14946,-0.55693,-0.817,49.748,0.3472,0.74411,-0.57075,9.1338
> view matrix models
> #2,0.93935,-0.3366,0.065786,148.65,-0.16483,-0.61128,-0.77406,49.831,0.30076,0.71626,-0.62969,8.6022
> view matrix models
> #2,0.89006,-0.20976,0.40473,151.8,0.12554,-0.74072,-0.65998,49.866,0.43822,0.63823,-0.63295,8.1146
> view matrix models
> #2,0.89006,-0.20976,0.40473,145.43,0.12554,-0.74072,-0.65998,51.886,0.43822,0.63823,-0.63295,10.034
> fitmap #2 inMap #1
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#2) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.659, steps = 204
shifted from previous position = 9.54
rotated from previous position = 43.1 degrees
atoms outside contour = 2703, contour level = 1.1765
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#2) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.62185037 -0.59892883 0.50456548 148.01931203
0.40539486 -0.30505928 -0.86173885 43.27830419
0.67004258 0.74042094 0.05310151 10.85281328
Axis 0.84406486 -0.08717820 0.52910724
Axis point 0.00000000 53.34995986 -17.73507827
Rotation angle (degrees) 108.36405535
Shift along axis 126.90727813
> select clear
> fitmap #2 inMap #1
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#2) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.659, steps = 28
shifted from previous position = 0.065
rotated from previous position = 0.0331 degrees
atoms outside contour = 2706, contour level = 1.1765
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#2) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.62188983 -0.59881130 0.50465634 148.06529610
0.40508293 -0.30553016 -0.86171872 43.26378383
0.67019458 0.74032184 0.05256220 10.89601879
Axis 0.84414548 -0.08722523 0.52897086
Axis point 0.00000000 53.32347794 -17.72722513
Rotation angle (degrees) 108.39335925
Shift along axis 126.97863281
> fitmap #2 inMap #1
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#2) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.659, steps = 28
shifted from previous position = 0.0582
rotated from previous position = 0.0578 degrees
atoms outside contour = 2705, contour level = 1.1765
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#2) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.62203625 -0.59922283 0.50398696 148.03074713
0.40502127 -0.30461853 -0.86207037 43.28462168
0.67009597 0.74036453 0.05321429 10.85335757
Axis 0.84410072 -0.08749980 0.52899694
Axis point 0.00000000 53.38412627 -17.69805864
Rotation angle (degrees) 108.34173773
Shift along axis 126.90685713
> fitmap #2 inMap #1
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#2) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.659, steps = 44
shifted from previous position = 0.00749
rotated from previous position = 0.033 degrees
atoms outside contour = 2701, contour level = 1.1765
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#2) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.62198883 -0.59889332 0.50443695 148.02561070
0.40524370 -0.30502560 -0.86182187 43.28086822
0.67000549 0.74046354 0.05297530 10.85475234
Axis 0.84412426 -0.08722568 0.52900464
Axis point 0.00000000 53.35037316 -17.72075575
Rotation angle (degrees) 108.36266900
Shift along axis 126.91902068
> fitmap #2 inMap #1
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#2) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.659, steps = 44
shifted from previous position = 0.00676
rotated from previous position = 0.00981 degrees
atoms outside contour = 2700, contour level = 1.1765
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#2) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.62194731 -0.59902123 0.50433626 148.03036514
0.40519831 -0.30493561 -0.86187506 43.28007237
0.67007149 0.74039714 0.05306857 10.85047720
Axis 0.84409638 -0.08731132 0.52903500
Axis point 0.00000000 53.36286138 -17.72188657
Rotation angle (degrees) 108.35839053
Shift along axis 126.91333710
> fitmap #2 inMap #1
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#2) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.659, steps = 48
shifted from previous position = 0.0121
rotated from previous position = 0.0264 degrees
atoms outside contour = 2700, contour level = 1.1765
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#2) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.62178803 -0.59890143 0.50467482 148.02357875
0.40560406 -0.30499251 -0.86166404 43.28181729
0.66997382 0.74047061 0.05327622 10.84151769
Axis 0.84402518 -0.08708164 0.52918644
Axis point 0.00000000 53.35568572 -17.75165533
Rotation angle (degrees) 108.35864803
Shift along axis 126.90376005
> fitmap #2 inMap #1
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#2) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.659, steps = 36
shifted from previous position = 0.0467
rotated from previous position = 0.0405 degrees
atoms outside contour = 2705, contour level = 1.1765
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#2) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.62180264 -0.59890224 0.50465585 148.04443737
0.40511655 -0.30550219 -0.86171283 43.26916148
0.67025516 0.74025982 0.05266321 10.88024251
Axis 0.84410351 -0.08725677 0.52903262
Axis point 0.00000000 53.33254630 -17.73184055
Rotation angle (degrees) 108.39209760
Shift along axis 126.94530569
> fitmap #2 inMap #1
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#2) to map
BbWT-FlbB-256-2.7A.mrc (#1) using 10479 atoms
average map value = 2.659, steps = 48
shifted from previous position = 0.0516
rotated from previous position = 0.0422 degrees
atoms outside contour = 2700, contour level = 1.1765
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#2) relative to BbWT-FlbB-256-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.62185866 -0.59902404 0.50444223 148.01113363
0.40542796 -0.30484442 -0.86179931 43.28136664
0.67001485 0.74043241 0.05329102 10.84333931
Axis 0.84404187 -0.08722223 0.52913666
Axis point 0.00000000 53.36306924 -17.73208234
Rotation angle (degrees) 108.35159987
Shift along axis 126.89010479
> view orient
> sym #2 C16 center #1
Made 16 graphical clones for
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb symmetry
C16
> view orient
> volume #1 level 0.4914
> open "C:/Users/Jack Botting/Documents/alphafold
> results/Bb_0624_23c4c/Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #5
---
Chain | Description
A | No description available
> select add #5
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> view matrix models #5,1,0,0,-155.43,0,1,0,45.74,0,0,1,0
> view matrix models #5,1,0,0,-157.97,0,1,0,31.764,0,0,1,0
> help help:user
> hide #!4 models
> hide #2 models
> view matrix models #5,1,0,0,-188.84,0,1,0,33.161,0,0,1,32.353
> view matrix models
> #5,0.70111,0.35375,0.61912,-187.93,-0.6658,0.63561,0.39079,31.772,-0.25527,-0.6862,0.68115,30.201
> view matrix models
> #5,0.70111,0.35375,0.61912,-188.75,-0.6658,0.63561,0.39079,31.824,-0.25527,-0.6862,0.68115,38.694
> view matrix models
> #5,0.79527,0.2466,0.55383,-188.87,-0.52051,0.74611,0.4152,32.322,-0.31083,-0.61847,0.72172,38.774
> view matrix models
> #5,0.84822,0.39967,0.34755,-188.74,-0.52238,0.73963,0.42435,32.318,-0.087459,-0.54149,0.83615,39.46
> view matrix models
> #5,0.84822,0.39967,0.34755,-186.19,-0.52238,0.73963,0.42435,32.212,-0.087459,-0.54149,0.83615,42
> view matrix models
> #5,0.84822,0.39967,0.34755,-193.76,-0.52238,0.73963,0.42435,32.579,-0.087459,-0.54149,0.83615,62.399
> view matrix models
> #5,0.92606,0.2651,0.26859,-193.98,-0.36853,0.78852,0.49237,33.031,-0.081261,-0.55494,0.82791,62.374
> view matrix models
> #5,0.57196,-0.023178,0.81995,-194.47,-0.56922,0.70854,0.41709,32.427,-0.59064,-0.70529,0.39206,60.638
> view matrix models
> #5,0.57196,-0.023178,0.81995,7.0186,-0.56922,0.70854,0.41709,23.722,-0.59064,-0.70529,0.39206,68.121
> view orient
> view matrix models
> #5,0.57196,-0.023178,0.81995,66.794,-0.56922,0.70854,0.41709,115.38,-0.59064,-0.70529,0.39206,68.121
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.57196,-0.023178,0.81995,107.04,-0.56922,0.70854,0.41709,177.87,-0.59064,-0.70529,0.39206,46.916
> view matrix models
> #5,0.57196,-0.023178,0.81995,7.5037,-0.56922,0.70854,0.41709,180.63,-0.59064,-0.70529,0.39206,74.356
> view matrix models
> #5,0.57196,-0.023178,0.81995,0.83183,-0.56922,0.70854,0.41709,180.56,-0.59064,-0.70529,0.39206,71.078
> view matrix models
> #5,0.29299,-0.81091,0.50654,-1.5485,0.49319,0.58205,0.64652,182.5,-0.8191,0.060392,0.57046,72.344
> view matrix models
> #5,0.29299,-0.81091,0.50654,-223.29,0.49319,0.58205,0.64652,190.84,-0.8191,0.060392,0.57046,177.41
> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/Bb_modeling
> FlbB Bb_0058.cxs"
> rename #2 Bb_0058
> rename #3 "D58 map"
> rename #1 "WT map"
> rename #5 Bb_0624
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #4.1 models
> hide #4.2-16 target m
> show #4.1 models
> hide #!1 models
> color bfactor palate alphafold
> color byattribute bfactor palate alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color 4.1 bfactor palate alphafold
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color bfactor palate alphafold 4.1
> color byattribute bfactor palate alphafold 4.1
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor palate alphafold #4.1
> color byattribute bfactor palate alphafold #4.1
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor palate alphafold ribbons
> color byattribute bfactor palate alphafold ribbons
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> select clear
> select #4.1/B:99
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
1414 atoms, 1417 bonds, 83 residues, 1 model selected
> select up
3496 atoms, 3526 bonds, 205 residues, 1 model selected
> select add #4.1/A:107
3513 atoms, 3542 bonds, 206 residues, 1 model selected
> select up
4910 atoms, 4943 bonds, 288 residues, 1 model selected
> select up
6992 atoms, 7052 bonds, 410 residues, 1 model selected
> color bfactor palate alphafold
> color byattribute bfactor palate alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor palate alphafold #4.1
> color byattribute bfactor palate alphafold #4.1
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor #4.1 palate alphafold
> color byattribute bfactor #4.1 palate alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor #4 palate alphafold
> color byattribute bfactor #4 palate alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color r:bfactor palate alphafold
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color bfactor palate alphafold
> color byattribute bfactor palate alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor palate alphafold #4
> color byattribute bfactor palate alphafold #4
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor palate alphafold #4.1
> color byattribute bfactor palate alphafold #4.1
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor #4
111872 atoms, 6560 residues, atom bfactor range 24.7 to 94.4
> color bfactor #4 palate alphafold
> color byattribute bfactor #4 palate alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> view matrix models
> #4.1,1,2.0348e-16,1.0929e-16,-30.953,4.2521e-16,1,5.6379e-18,22.177,2.2551e-17,6.9389e-18,1,95.894
> view matrix models
> #4.1,1,3.914e-16,1.648e-16,8.8099,4.3687e-16,1,6.0715e-18,69.216,2.2551e-17,1.301e-17,1,87.499
> select clear
> undo
[Repeated 1 time(s)]
> select #4
111872 atoms, 112832 bonds, 6560 residues, 17 models selected
> select
> #4.1/B#4.2/B#4.3/B#4.4/B#4.5/B#4.6/B#4.7/B#4.8/B#4.9/B#4.10/B#4.11/B#4.12/B#4.13/B#4.14/B#4.15/B#4.16/B
55936 atoms, 56416 bonds, 3280 residues, 16 models selected
> color (#4.1 & sel) red
> select
> #2/A#4.1/A#4.2/A#4.3/A#4.4/A#4.5/A#4.6/A#4.7/A#4.8/A#4.9/A#4.10/A#4.11/A#4.12/A#4.13/A#4.14/A#4.15/A#4.16/A#5/A
71359 atoms, 72000 bonds, 4216 residues, 18 models selected
> color (#5#4.1 & sel) orange
> select #2
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> color #5#4.1#!4 cyan
> undo
> select #2
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> color #5#4.1#!4 cyan
> show #2 models
> view matrix models
> #2,0.62186,-0.59902,0.50444,147.03,0.40543,-0.30484,-0.8618,44.375,0.67001,0.74043,0.053291,20.163
> undo
> hide #2 models
> show #2 models
> undo
[Repeated 5 time(s)]
> redo
> show #2 models
> select add #4
127295 atoms, 128416 bonds, 7496 residues, 19 models selected
> select subtract #4
15423 atoms, 15584 bonds, 936 residues, 2 models selected
> select subtract #5
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> view matrix models
> #2,0.62186,-0.59902,0.50444,125.18,0.40543,-0.30484,-0.8618,7.6226,0.67001,0.74043,0.053291,27.895
> show #!1 models
> close session
> open "C:/Users/Jack Botting/Desktop/Jack-collar-data-2023-07-21/WTCW-stator-
> msk-4.2A.mrc"
Opened WTCW-stator-msk-4.2A.mrc as #1, grid size 140,140,140, pixel 4.2, shown
at level 0.141, step 1, values float32
> open "C:/Users/Jack Botting/Desktop/Jack-collar-
> data-2023-07-21/Bb058-stator-msk-4.2A.mrc"
Opened Bb058-stator-msk-4.2A.mrc as #2, grid size 140,140,140, pixel 4.2,
shown at level 4.24, step 1, values float32
> open "C:/Users/Jack Botting/Desktop/Jack-collar-
> data-2023-07-21/Bb326-nostat-msk-4.2A.mrc"
Opened Bb326-nostat-msk-4.2A.mrc as #3, grid size 140,140,140, pixel 4.2,
shown at level 4.04, step 1, values float32
> open "C:/Users/Jack Botting/Desktop/Jack-collar-
> data-2023-07-21/Bb326-stator-msk-4.2A.mrc"
Opened Bb326-stator-msk-4.2A.mrc as #4, grid size 140,140,140, pixel 4.2,
shown at level 4.01, step 1, values float32
> open "C:/Users/Jack Botting/Desktop/Jack-collar-
> data-2023-07-21/Bb624-nostat-msk-4.2A.mrc"
Opened Bb624-nostat-msk-4.2A.mrc as #5, grid size 140,140,140, pixel 4.2,
shown at level 4.1, step 1, values float32
> open "C:/Users/Jack Botting/Desktop/Jack-collar-
> data-2023-07-21/Bb624-stator-msk-4.2A.mrc"
Opened Bb624-stator-msk-4.2A.mrc as #6, grid size 140,140,140, pixel 4.2,
shown at level 4.21, step 1, values float32
> open "C:/Users/Jack Botting/Desktop/Jack-collar-data-2023-07-21/MotB-nostat-
> msk-4.2A.mrc"
Opened MotB-nostat-msk-4.2A.mrc as #7, grid size 140,140,140, pixel 4.2, shown
at level 4.13, step 1, values float32
> open "C:/Users/Jack Botting/Desktop/Jack-collar-data-2023-07-21/WTCC-stator-
> msk-4.2A.mrc"
Opened WTCC-stator-msk-4.2A.mrc as #8, grid size 140,140,140, pixel 4.2, shown
at level 0.125, step 1, values float32
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> select add #8
2 models selected
> select add #1
4 models selected
> view matrix models
> #1,1,0,0,-259.79,0,1,0,-267.05,0,0,1,0,#8,1,0,0,-259.79,0,1,0,-267.05,0,0,1,0
> select clear
> select add #8
2 models selected
> select add #1
4 models selected
> view matrix models
> #1,1,0,0,-230.35,0,1,0,-288.71,0,0,1,-288.51,#8,1,0,0,-230.35,0,1,0,-288.71,0,0,1,-288.51
> select clear
> select add #1
2 models selected
> select add #8
4 models selected
> view matrix models
> #1,1,0,0,-294.85,0,1,0,-292.47,0,0,1,-286.2,#8,1,0,0,-294.85,0,1,0,-292.47,0,0,1,-286.2
> select clear
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit map Bb058-stator-msk-4.2A.mrc in map WTCW-stator-msk-4.2A.mrc using 27420
points
correlation = 0.9776, correlation about mean = 0.6036, overlap = 2.536e+04
steps = 68, shift = 7.26, angle = 0.291 degrees
Position of Bb058-stator-msk-4.2A.mrc (#2) relative to WTCW-stator-
msk-4.2A.mrc (#1) coordinates:
Matrix rotation and translation
0.99998827 0.00374519 -0.00307079 293.99735193
-0.00374982 0.99999184 -0.00150490 293.36153952
0.00306513 0.00151640 0.99999415 293.45035799
Axis 0.29776547 -0.60472879 -0.73867368
Axis point 29008.07034320 -102787.90531389 0.00000000
Rotation angle (degrees) 0.29067912
Shift along axis -306.62596538
> fitmap #3 inMap #1
Fit map Bb326-nostat-msk-4.2A.mrc in map WTCW-stator-msk-4.2A.mrc using 27424
points
correlation = 0.9671, correlation about mean = 0.531, overlap = 2.383e+04
steps = 56, shift = 7.87, angle = 0.327 degrees
Position of Bb326-nostat-msk-4.2A.mrc (#3) relative to WTCW-stator-
msk-4.2A.mrc (#1) coordinates:
Matrix rotation and translation
0.99998385 -0.00085166 0.00561935 292.57791727
0.00084907 0.99999953 0.00046296 293.28131882
-0.00561975 -0.00045818 0.99998410 293.28711535
Axis -0.08077158 0.98551314 0.14913017
Axis point 44144.61011761 0.00000000 -56382.73207576
Rotation angle (degrees) 0.32671125
Shift along axis 309.13857001
> fitmap #4 inMap #1
Fit map Bb326-stator-msk-4.2A.mrc in map WTCW-stator-msk-4.2A.mrc using 27437
points
correlation = 0.9695, correlation about mean = 0.5492, overlap = 2.34e+04
steps = 56, shift = 7.71, angle = 0.603 degrees
Position of Bb326-stator-msk-4.2A.mrc (#4) relative to WTCW-stator-
msk-4.2A.mrc (#1) coordinates:
Matrix rotation and translation
0.99994491 -0.00086145 0.01046101 292.09141575
0.00085239 0.99999926 0.00087047 293.24573028
-0.01046175 -0.00086151 0.99994490 292.61217080
Axis -0.08222385 0.99328710 0.08136327
Axis point 25864.38747591 0.00000000 -30073.50725679
Rotation angle (degrees) 0.60345511
Shift along axis 291.06820451
> fitmap #5 inMap #1
Fit map Bb624-nostat-msk-4.2A.mrc in map WTCW-stator-msk-4.2A.mrc using 27429
points
correlation = 0.9655, correlation about mean = 0.6391, overlap = 2.149e+04
steps = 52, shift = 6.42, angle = 2.48 degrees
Position of Bb624-nostat-msk-4.2A.mrc (#5) relative to WTCW-stator-
msk-4.2A.mrc (#1) coordinates:
Matrix rotation and translation
0.99906503 -0.00469436 -0.04297701 293.74808303
0.00460069 0.99998682 -0.00227819 295.02631907
0.04298714 0.00207833 0.99907346 296.71907241
Axis 0.05032081 -0.99294549 0.10736421
Axis point -7360.69225372 0.00000000 7283.53171507
Rotation angle (degrees) 2.48096328
Shift along axis -246.30640267
> fitmap #6 inMap #1
Fit map Bb624-stator-msk-4.2A.mrc in map WTCW-stator-msk-4.2A.mrc using 27426
points
correlation = 0.9713, correlation about mean = 0.6145, overlap = 2.436e+04
steps = 56, shift = 8.14, angle = 1.73 degrees
Position of Bb624-stator-msk-4.2A.mrc (#6) relative to WTCW-stator-
msk-4.2A.mrc (#1) coordinates:
Matrix rotation and translation
0.99954391 -0.00226625 -0.03011372 293.75296160
0.00226763 0.99999743 0.00001160 294.15268208
0.03011361 -0.00007988 0.99954648 295.60055175
Axis -0.00151468 -0.99717734 0.07506703
Axis point -10344.09972655 0.00000000 9897.79702668
Rotation angle (degrees) 1.73053293
Shift along axis -271.57747402
> fitmap #7 inMap #1
Fit map MotB-nostat-msk-4.2A.mrc in map WTCW-stator-msk-4.2A.mrc using 27418
points
correlation = 0.9661, correlation about mean = 0.5574, overlap = 2.586e+04
steps = 60, shift = 12.3, angle = 0.841 degrees
Position of MotB-nostat-msk-4.2A.mrc (#7) relative to WTCW-stator-msk-4.2A.mrc
(#1) coordinates:
Matrix rotation and translation
0.99989287 -0.00108163 0.01459720 292.21986848
0.00106662 0.99999889 0.00103622 292.87106308
-0.01459831 -0.00102054 0.99989292 297.49793440
Axis -0.07008530 0.99485146 0.07320257
Axis point 19067.52366133 0.00000000 -21284.10293567
Rotation angle (degrees) 0.84074840
Shift along axis 292.66050022
> fitmap #8 inMap #1
Fit map WTCC-stator-msk-4.2A.mrc in map WTCW-stator-msk-4.2A.mrc using 27430
points
correlation = 0.9958, correlation about mean = 0.8667, overlap = 742.3
steps = 52, shift = 0.714, angle = 0.475 degrees
Position of WTCC-stator-msk-4.2A.mrc (#8) relative to WTCW-stator-msk-4.2A.mrc
(#1) coordinates:
Matrix rotation and translation
0.99996571 0.00091191 -0.00823062 2.15008656
-0.00090788 0.99999947 0.00049282 0.05414541
0.00823107 -0.00048533 0.99996601 -1.32232675
Axis -0.05895727 -0.99221618 -0.10968637
Axis point 162.19802618 0.00000000 260.30045538
Rotation angle (degrees) 0.47529784
Shift along axis -0.03544596
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> show #!2 models
> hide #!1 models
> volume #1 level 0.1259
> volume #2 level 3.287
> hide #!1 models
> volume #2 level 1.975
> volume #2 level 1.552
> volume #2 level 1.752
> show #!1 models
> volume #1 level 0.1133
> hide #!2 models
> show #!2 models
> volume #1 level 0.06527
> show #!6 models
> hide #!1 models
> hide #!2 models
> volume #6 level 1.985
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!3 models
> show #!4 models
> hide #!3 models
> volume #4 level 1.4
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!2 models
> hide #!1 models
> open "C:/Users/Jack Botting/Documents/Chimera/PDB/Bb_0286 ring.pdb"
Chain information for Bb_0286 ring.pdb
---
Chain | Description
9.1/A 9.2/A 9.3/A 9.4/A 9.5/A 9.6/A 9.7/A 9.8/A 9.9/A 9.10/A 9.11/A 9.12/A
9.13/A 9.14/A 9.15/A 9.16/A 9.1/B 9.2/B 9.3/B 9.4/B 9.5/B 9.6/B 9.7/B 9.8/B
9.9/B 9.10/B 9.11/B 9.12/B 9.13/B 9.14/B 9.15/B 9.16/B | No description
available
> select add #9
111872 atoms, 112832 bonds, 6560 residues, 17 models selected
> view matrix models #9,1,0,0,-752.51,0,1,0,-492,0,0,1,-103.67
> select clear
> select add #9
111872 atoms, 112832 bonds, 6560 residues, 17 models selected
> view matrix models #9,1,0,0,-749.03,0,1,0,-528.58,0,0,1,-505.04
> select clear
> select add #9
111872 atoms, 112832 bonds, 6560 residues, 17 models selected
> select subtract #9
Nothing selected
> select add #9
111872 atoms, 112832 bonds, 6560 residues, 17 models selected
> view matrix models #9,1,0,0,-773.16,0,1,0,-522.28,0,0,1,-506.54
> view matrix models
> #9,0.99777,-0.066748,-0.00048141,-737.07,0.06675,0.99776,0.0042187,-557.67,0.00019874,-0.0042414,0.99999,-504.43
> select clear
> select add #9
111872 atoms, 112832 bonds, 6560 residues, 17 models selected
> view matrix models
> #9,0.99646,-0.084003,-0.0021508,-726.55,0.084014,0.99645,0.0057452,-566.67,0.0016606,-0.0059056,0.99998,-504.31
> select clear
> hide #!3 models
> transparency #2.1 50
> show #!1 models
> transparency #1.1#2.1 0
> transparency #1.1#2.1 50
> show #!3 models
> show #!4-8 target m
> transparency 0
> transparency 50
> hide #!1 target m
> hide #!3-8 target m
> volume #2 level 1.663
> open "C:/Users/Jack Botting/Documents/alphafold
> results/Bb_0058_50988/Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #10
---
Chain | Description
A | No description available
> select add #10
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> show #!1 models
> hide #!2 models
> view matrix models #10,1,0,0,-102.17,0,1,0,17.859,0,0,1,6.8265
> select clear
> select add #10
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> view matrix models #10,1,0,0,-128.95,0,1,0,15.272,0,0,1,121.6
> view matrix models
> #10,0.65002,-0.26362,-0.71272,-135.21,-0.39561,0.68338,-0.61358,9.5474,0.64881,0.68081,0.33992,119.3
> view matrix models
> #10,0.65002,-0.26362,-0.71272,-116.93,-0.39561,0.68338,-0.61358,11.021,0.64881,0.68081,0.33992,65.795
> select clear
> select add #10
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> view matrix models
> #10,0.65002,-0.26362,-0.71272,-108.01,-0.39561,0.68338,-0.61358,-12.977,0.64881,0.68081,0.33992,69.207
> view matrix models
> #10,0.77287,-0.58817,-0.23818,-106.05,0.23655,0.61533,-0.75194,-14.806,0.58883,0.52481,0.6147,70.588
> view matrix models
> #10,0.77287,-0.58817,-0.23818,-101.24,0.23655,0.61533,-0.75194,-24.605,0.58883,0.52481,0.6147,72.063
> view matrix models
> #10,0.62797,-0.75995,-0.16775,-101.39,-0.12694,0.11264,-0.98549,-28.373,0.76782,0.64015,-0.025736,67.678
> view matrix models
> #10,0.62797,-0.75995,-0.16775,-96.785,-0.12694,0.11264,-0.98549,-23.337,0.76782,0.64015,-0.025736,67.42
> fitmap #10 inMap #1 search 500
Found 283 unique fits from 500 random placements having fraction of points
inside contour >= 0.100 (345 of 500).
Average map values and times found:
0.137 (2), 0.1343 (1), 0.1328 (1), 0.1297 (1), 0.126 (1), 0.1253 (1), 0.1234
(1), 0.1229 (1), 0.1216 (1), 0.1215 (1), 0.1126 (1), 0.1123 (1), 0.1101 (1),
0.11 (1), 0.1099 (1), 0.1097 (1), 0.1084 (1), 0.1083 (1), 0.1083 (1), 0.1079
(1), 0.1077 (1), 0.1063 (1), 0.106 (1), 0.1049 (1), 0.104 (1), 0.1035 (1),
0.1021 (1), 0.1018 (1), 0.1016 (1), 0.1011 (1), 0.1004 (2), 0.1001 (1),
0.09789 (1), 0.09758 (1), 0.09757 (1), 0.09747 (1), 0.09731 (1), 0.09701 (1),
0.09693 (1), 0.0963 (1), 0.096 (1), 0.09591 (1), 0.0956 (1), 0.09545 (1),
0.09435 (1), 0.0936 (1), 0.09348 (1), 0.0934 (1), 0.09312 (1), 0.09288 (1),
0.09221 (1), 0.09211 (1), 0.09079 (1), 0.09068 (2), 0.08955 (1), 0.08877 (1),
0.0887 (1), 0.0885 (1), 0.0883 (2), 0.08773 (1), 0.08738 (1), 0.08723 (1),
0.08684 (1), 0.08669 (1), 0.08601 (1), 0.08588 (1), 0.08567 (1), 0.08558 (1),
0.08531 (1), 0.0852 (1), 0.08291 (2), 0.08237 (1), 0.08221 (1), 0.08219 (1),
0.08209 (2), 0.08114 (1), 0.08073 (1), 0.07991 (1), 0.07918 (1), 0.07912 (1),
0.07864 (1), 0.07841 (1), 0.07814 (1), 0.07798 (1), 0.07792 (1), 0.07791 (3),
0.07771 (1), 0.07727 (1), 0.07665 (1), 0.07583 (1), 0.07559 (1), 0.07501 (1),
0.0745 (1), 0.07435 (3), 0.07434 (1), 0.07418 (1), 0.07416 (1), 0.07415 (1),
0.07382 (1), 0.07377 (1), 0.07336 (1), 0.0733 (1), 0.07313 (1), 0.07269 (1),
0.07199 (1), 0.07198 (1), 0.07169 (1), 0.07096 (1), 0.0707 (1), 0.06958 (1),
0.06935 (1), 0.06908 (2), 0.06884 (1), 0.06849 (1), 0.06802 (1), 0.06669 (1),
0.06655 (3), 0.06608 (2), 0.06605 (1), 0.06601 (1), 0.06549 (1), 0.06476 (1),
0.06469 (1), 0.06469 (2), 0.06463 (1), 0.06458 (2), 0.06455 (2), 0.06432 (1),
0.06424 (1), 0.06398 (2), 0.06381 (1), 0.06366 (1), 0.06361 (4), 0.06358 (4),
0.06358 (3), 0.06352 (1), 0.06342 (1), 0.06316 (1), 0.06311 (1), 0.06305 (1),
0.06259 (1), 0.06243 (1), 0.06189 (1), 0.06149 (3), 0.06147 (1), 0.0609 (2),
0.06083 (1), 0.06068 (1), 0.06065 (1), 0.06051 (1), 0.06046 (1), 0.06035 (1),
0.06006 (1), 0.05967 (1), 0.0596 (1), 0.0595 (3), 0.05939 (1), 0.05888 (4),
0.05845 (2), 0.05785 (1), 0.0576 (1), 0.05759 (1), 0.0572 (1), 0.05715 (1),
0.05687 (1), 0.05675 (1), 0.05651 (1), 0.05646 (1), 0.05631 (1), 0.05629 (2),
0.05565 (1), 0.05519 (1), 0.05499 (1), 0.05488 (1), 0.05459 (1), 0.05455 (1),
0.05448 (1), 0.05439 (1), 0.05434 (1), 0.05411 (1), 0.05396 (1), 0.05371 (1),
0.05365 (1), 0.05324 (1), 0.05249 (2), 0.05237 (1), 0.05222 (1), 0.05186 (2),
0.05144 (3), 0.05138 (1), 0.0513 (1), 0.05122 (1), 0.05105 (1), 0.05097 (1),
0.05077 (1), 0.05075 (1), 0.05062 (1), 0.0505 (2), 0.05016 (3), 0.05015 (3),
0.05007 (1), 0.04982 (1), 0.04964 (1), 0.04913 (3), 0.04871 (1), 0.04854 (1),
0.0484 (1), 0.04834 (1), 0.04828 (1), 0.04822 (1), 0.04822 (2), 0.04821 (3),
0.04808 (1), 0.0479 (1), 0.04781 (1), 0.04777 (3), 0.04777 (1), 0.04759 (1),
0.04753 (1), 0.04745 (1), 0.04721 (1), 0.04703 (1), 0.04688 (3), 0.04685 (1),
0.04683 (2), 0.04667 (1), 0.04663 (3), 0.04546 (2), 0.04534 (1), 0.04526 (1),
0.04525 (1), 0.04508 (1), 0.04465 (1), 0.04416 (2), 0.04403 (1), 0.04395 (1),
0.04393 (1), 0.04349 (1), 0.04346 (1), 0.0433 (1), 0.0433 (1), 0.04265 (1),
0.04251 (1), 0.04208 (1), 0.04157 (1), 0.04156 (1), 0.0415 (1), 0.04101 (1),
0.04092 (1), 0.04092 (1), 0.04087 (1), 0.04083 (1), 0.04067 (1), 0.04014 (1),
0.04 (1), 0.03999 (1), 0.03973 (1), 0.03948 (1), 0.03899 (1), 0.03891 (1),
0.0389 (1), 0.03878 (3), 0.03867 (1), 0.03853 (2), 0.03848 (1), 0.03788 (1),
0.03755 (1), 0.03736 (1), 0.03715 (1), 0.03645 (1), 0.03621 (1), 0.03614 (1),
0.03558 (1), 0.03528 (1), 0.03246 (1), 0.03227 (1), 0.03117 (1), 0.03054 (1),
0.03053 (1), 0.02851 (1), 0.02732 (1), 0.02723 (1), 0.0241 (1)
Best fit found:
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#10) to
map WTCW-stator-msk-4.2A.mrc (#1) using 10479 atoms
average map value = 0.137, steps = 212
shifted from previous position = 50.6
rotated from previous position = 65.8 degrees
atoms outside contour = 1942, contour level = 0.065265
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#10) relative to WTCW-stator-msk-4.2A.mrc (#1) coordinates:
Matrix rotation and translation
0.29952760 0.95337615 0.03683830 257.02798990
0.31726540 -0.06311467 -0.94623420 311.87463057
-0.89979213 0.29511078 -0.32137784 403.39413523
Axis 0.73883682 0.55747360 -0.37860712
Axis point 0.00000000 -119.15581445 339.13810828
Rotation angle (degrees) 122.85279236
Shift along axis 211.03572414
Found 283 fits.
> select down
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> select down
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> select down
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> view matrix models
> #10,0.364,0.59892,-0.7133,-182.82,0.83819,-0.54458,-0.029516,135.34,-0.40613,-0.58714,-0.70023,57.85
> undo
> select clear
> select add #10
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> view matrix models
> #10,0.15749,0.26658,0.95086,-172.05,0.90073,-0.4335,-0.027652,132.66,0.40483,0.86082,-0.30839,65.999
> view matrix models
> #10,0.63361,-0.036927,0.77277,-175.13,0.68339,-0.44149,-0.58143,128.66,0.36264,0.89651,-0.2545,66.597
> view matrix models
> #10,0.63361,-0.036927,0.77277,-174.27,0.68339,-0.44149,-0.58143,140.34,0.36264,0.89651,-0.2545,61.291
> select clear
> select add #10
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> view matrix models
> #10,0.51622,-0.013955,0.85634,-173.45,0.78962,-0.37947,-0.48218,141.28,0.33169,0.9251,-0.18487,61.966
> view matrix models
> #10,0.51622,-0.013955,0.85634,-176.92,0.78962,-0.37947,-0.48218,144.78,0.33169,0.9251,-0.18487,61.15
> select clear
> view orient
> sym #10 C16 center #9
Made 16 graphical clones for
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb symmetry
C16
> select clear
> undo
> sym clear
> select add #10
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> select clear
> select #10/A:44
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
221 atoms, 225 bonds, 13 residues, 1 model selected
> select up
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> view matrix models
> #10,0.54799,0.086329,0.83202,-176.67,0.72693,-0.54126,-0.42262,144.53,0.41386,0.83641,-0.35936,59.379
> view matrix models
> #10,0.89887,-0.38715,0.20529,-183.78,-0.040805,-0.5404,-0.84042,142.01,0.43631,0.74705,-0.50154,57.891
> view matrix models
> #10,0.89887,-0.38715,0.20529,-107.57,-0.040805,-0.5404,-0.84042,-12.912,0.43631,0.74705,-0.50154,63.443
> view matrix models
> #10,0.87611,-0.26615,0.40199,-105.53,0.18566,-0.58324,-0.79079,-12.912,0.44493,0.76746,-0.46157,63.828
> view matrix models
> #10,0.87611,-0.26615,0.40199,-98.798,0.18566,-0.58324,-0.79079,-17.324,0.44493,0.76746,-0.46157,64.847
> view matrix models
> #10,0.87611,-0.26615,0.40199,-97.844,0.18566,-0.58324,-0.79079,-17.423,0.44493,0.76746,-0.46157,65.022
> view matrix models
> #10,0.79921,-0.44552,0.40345,-98.597,0.24773,-0.36742,-0.89646,-17.269,0.54763,0.8164,-0.18328,67.243
> fitmap #10 inMap map #1
Invalid "inMap" argument: invalid density map specifier
> fitmap #10 inMap #1
Fit molecule
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#10) to
map WTCW-stator-msk-4.2A.mrc (#1) using 10479 atoms
average map value = 0.1055, steps = 80
shifted from previous position = 8
rotated from previous position = 23.7 degrees
atoms outside contour = 2826, contour level = 0.065265
Position of Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#10) relative to WTCW-stator-msk-4.2A.mrc (#1) coordinates:
Matrix rotation and translation
0.73255405 -0.66513792 0.14476215 194.64959360
0.16578487 -0.03192982 -0.98564487 276.39427784
0.66021209 0.74603751 0.08687948 345.85962904
Axis 0.87077007 -0.25919209 0.41782645
Axis point 0.00000000 40.92789079 301.30393983
Rotation angle (degrees) 96.09908242
Shift along axis 242.36512913
> select clear
> view orient
> sym #10 C16 center #9
Made 16 graphical clones for
Bb_0058_50988_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb symmetry
C16
> select clear
> show #!6 models
> hide #!1 models
> open "C:/Users/Jack Botting/Documents/alphafold
> results/Bb_0624_23c4c/Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #11
---
Chain | Description
A | No description available
> select add #11
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> view matrix models #11,1,0,0,6.0195,0,1,0,-1.633,0,0,1,128.78
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #11/A:169
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
225 atoms, 226 bonds, 13 residues, 1 model selected
> select up
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> view matrix models #11,1,0,0,91.067,0,1,0,166.95,0,0,1,145.83
> view matrix models
> #11,0.90924,0.39106,-0.14264,91.467,-0.41495,0.87869,-0.23604,165.69,0.033033,0.27381,0.96122,146.36
> view matrix models
> #11,0.99552,-0.092936,0.017422,90.904,0.091757,0.99401,0.059347,167.18,-0.022833,-0.057482,0.99809,145.68
> view matrix models
> #11,0.87622,-0.48118,0.026577,89.968,0.4486,0.83455,0.31982,167.84,-0.17607,-0.26831,0.9471,144.95
> view matrix models
> #11,-0.076111,0.5842,-0.80803,89.246,-0.86747,-0.43837,-0.23522,162.39,-0.49163,0.68304,0.54014,145.68
> view matrix models
> #11,0.55607,0.70812,-0.43515,91.073,-0.82497,0.40663,-0.39252,163.87,-0.101,0.57725,0.81029,146.51
> view matrix models
> #11,0.75951,0.5871,-0.28009,91.4,-0.65041,0.67856,-0.34136,164.76,-0.010361,0.44144,0.89723,146.52
> view matrix models
> #11,0.98922,0.14154,-0.037672,91.268,-0.14438,0.98558,-0.088188,166.56,0.024647,0.092676,0.99539,146.05
> view matrix models
> #11,0.060276,0.1999,0.97796,90.991,0.33197,0.91996,-0.2085,167.13,-0.94136,0.33722,-0.010908,143.53
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #6 level 1.07
> hide #!6 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select add #11
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> view matrix models
> #11,0.060276,0.1999,0.97796,0.97242,0.33197,0.91996,-0.2085,97.182,-0.94136,0.33722,-0.010908,33.787
> select clear
> view orient
> select add #11
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> view matrix models
> #11,0.060276,0.1999,0.97796,-76.398,0.33197,0.91996,-0.2085,88.146,-0.94136,0.33722,-0.010908,33.787
> select clear
> select add #11
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> view matrix models
> #11,0.060276,0.1999,0.97796,-71.082,0.33197,0.91996,-0.2085,45.914,-0.94136,0.33722,-0.010908,123.05
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select add #11
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> view matrix models
> #11,0.060276,0.1999,0.97796,-96.856,0.33197,0.91996,-0.2085,-54.615,-0.94136,0.33722,-0.010908,116.75
> view matrix models
> #11,-0.48834,0.42651,-0.76133,-99.576,0.054036,-0.85597,-0.51419,-58.855,-0.87098,-0.29224,0.39496,116.19
> view matrix models
> #11,-0.48834,0.42651,-0.76133,-101.11,0.054036,-0.85597,-0.51419,-59.665,-0.87098,-0.29224,0.39496,113.44
> view matrix models
> #11,-0.48834,0.42651,-0.76133,-75.65,0.054036,-0.85597,-0.51419,-67.067,-0.87098,-0.29224,0.39496,115.96
> view matrix models
> #11,-0.48834,0.42651,-0.76133,-72.665,0.054036,-0.85597,-0.51419,-60.835,-0.87098,-0.29224,0.39496,109.5
> view matrix models
> #11,-0.057098,-0.24057,-0.96895,-73.419,0.28385,-0.93439,0.21526,-59.663,-0.95717,-0.26275,0.12164,109.06
> view matrix models
> #11,-0.057098,-0.24057,-0.96895,-70.247,0.28385,-0.93439,0.21526,-53.578,-0.95717,-0.26275,0.12164,109.65
> view matrix models
> #11,-0.74638,-0.51237,-0.42473,-71.311,0.60037,-0.79376,-0.097477,-53.138,-0.28719,-0.32775,0.90006,111.7
> view matrix models
> #11,-0.74638,-0.51237,-0.42473,-70.612,0.60037,-0.79376,-0.097477,-51.859,-0.28719,-0.32775,0.90006,112.29
> view matrix models
> #11,-0.74638,-0.51237,-0.42473,-66.875,0.60037,-0.79376,-0.097477,-44.374,-0.28719,-0.32775,0.90006,111.72
> select #11 :1-135
2212 atoms, 2234 bonds, 135 residues, 1 model selected
> ui tool show "Fit in Map"
> fitmap sel inMap #1
Fit molecule
Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb (#11) to
map WTCW-stator-msk-4.2A.mrc (#1) using 2212 atoms
average map value = 0.131, steps = 116
shifted from previous position = 15.9
rotated from previous position = 70.7 degrees
atoms outside contour = 441, contour level = 0.065265
Position of Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#11) relative to WTCW-stator-msk-4.2A.mrc (#1) coordinates:
Matrix rotation and translation
0.30785311 -0.91787200 -0.25047446 235.42284171
0.94797990 0.27350353 0.16288016 250.92299522
-0.08099749 -0.28758792 0.95432311 391.57566999
Axis -0.23377539 -0.08795195 0.96830446
Axis point -23.57328059 351.19605835 0.00000000
Rotation angle (degrees) 74.46423309
Shift along axis 302.05923529
> fitmap sel inMap #1 moveWholeMolecules false
Fit molecule
Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb (#11) to
map WTCW-stator-msk-4.2A.mrc (#1) using 2212 atoms
average map value = 0.1309, steps = 48
shifted from previous position = 0.119
rotated from previous position = 0.324 degrees
atoms outside contour = 445, contour level = 0.065265
> select #11 :168-299
2237 atoms, 2267 bonds, 132 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules false
Fit molecule
Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb (#11) to
map WTCW-stator-msk-4.2A.mrc (#1) using 2237 atoms
average map value = 0.1774, steps = 92
shifted from previous position = 28.2
rotated from previous position = 52.1 degrees
atoms outside contour = 76, contour level = 0.065265
> view matrix models
> #11,0.30785,-0.91787,-0.25047,-60.161,0.94798,0.2735,0.16288,-42.726,-0.080997,-0.28759,0.95432,104.96
> view matrix models
> #11,0.30785,-0.91787,-0.25047,-60.066,0.94798,0.2735,0.16288,-43.498,-0.080997,-0.28759,0.95432,106.68
> select clear
> undo
[Repeated 9 time(s)]
> view matrix models
> #11,-0.057098,-0.24057,-0.96895,-6.8155,0.28385,-0.93439,0.21526,25.012,-0.95717,-0.26275,0.12164,184.87
> close #11
> open "C:/Users/Jack Botting/Documents/alphafold
> results/Bb_0624_23c4c/Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #11
---
Chain | Description
A | No description available
> select add #11
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> view matrix models #11,1,0,0,22.249,0,1,0,-18.03,0,0,1,76.726
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> view matrix models #11,1,0,0,23.336,0,1,0,-19.63,0,0,1,81.273
> help help:user
> view matrix models #11,1,0,0,-46.021,0,1,0,-6.6058,0,0,1,79.666
> view matrix models #11,1,0,0,-42.452,0,1,0,-1.0487,0,0,1,83.795
> view matrix models #11,1,0,0,-40.711,0,1,0,8.4167,0,0,1,86.242
> view matrix models
> #11,0.58267,-0.69453,0.42205,-42.243,-0.71008,-0.18245,0.68007,5.761,-0.39533,-0.69594,-0.59948,82.222
> view matrix models
> #11,0.50327,-0.060559,0.86201,-40.635,-0.72706,-0.56879,0.38453,4.6301,0.46701,-0.82025,-0.33028,83.86
> view matrix models
> #11,0.20862,0.85581,0.47336,-39.91,-0.81146,-0.1187,0.57223,5.5664,0.5459,-0.50349,0.66969,85.849
> view matrix models
> #11,0.20862,0.85581,0.47336,-48.534,-0.81146,-0.1187,0.57223,8.6059,0.5459,-0.50349,0.66969,76.925
> view matrix models
> #11,0.20862,0.85581,0.47336,-48.91,-0.81146,-0.1187,0.57223,8.4354,0.5459,-0.50349,0.66969,76.517
> view matrix models
> #11,0.20862,0.85581,0.47336,-66.25,-0.81146,-0.1187,0.57223,0.76308,0.5459,-0.50349,0.66969,84.688
> view matrix models
> #11,0.20862,0.85581,0.47336,-63.722,-0.81146,-0.1187,0.57223,2.5171,0.5459,-0.50349,0.66969,87.9
> select clear
> select add #11
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> view matrix models
> #11,0.20862,0.85581,0.47336,-61.029,-0.81146,-0.1187,0.57223,-4.4112,0.5459,-0.50349,0.66969,87.983
> view matrix models
> #11,0.20862,0.85581,0.47336,-59.873,-0.81146,-0.1187,0.57223,-4.3191,0.5459,-0.50349,0.66969,89.305
> view matrix models
> #11,0.37149,0.87038,0.32317,-59.743,-0.83621,0.16242,0.52381,-3.8913,0.40342,-0.46483,0.78815,89.272
> view matrix models
> #11,0.37149,0.87038,0.32317,-59.124,-0.83621,0.16242,0.52381,-1.417,0.40342,-0.46483,0.78815,89.494
> view matrix models
> #11,0.07964,0.86515,0.49514,-59.439,-0.76677,-0.26423,0.58502,-2.0248,0.63696,-0.42625,0.64233,89.801
> select #11 :168-299
2237 atoms, 2267 bonds, 132 residues, 1 model selected
> select #11 :1-135
2212 atoms, 2234 bonds, 135 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules false shift false
Fit molecule
Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb (#11) to
map WTCW-stator-msk-4.2A.mrc (#1) using 2212 atoms
average map value = 0.1385, steps = 100
shifted from previous position = 7.25e-14
rotated from previous position = 131 degrees
atoms outside contour = 439, contour level = 0.065265
> fitmap sel inMap #1 moveWholeMolecules false
Fit molecule
Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb (#11) to
map WTCW-stator-msk-4.2A.mrc (#1) using 2212 atoms
average map value = 0.1817, steps = 76
shifted from previous position = 16.2
rotated from previous position = 60 degrees
atoms outside contour = 52, contour level = 0.065265
> fitmap sel inMap #1 moveWholeMolecules false
Fit molecule
Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb (#11) to
map WTCW-stator-msk-4.2A.mrc (#1) using 2212 atoms
average map value = 0.1817, steps = 40
shifted from previous position = 0.0314
rotated from previous position = 0.156 degrees
atoms outside contour = 53, contour level = 0.065265
> select #6
3 models selected
> select clear
> hide #!1 models
> select #11 :1-135
2212 atoms, 2234 bonds, 135 residues, 1 model selected
> view matrix models
> #11,0.07964,0.86515,0.49514,-58.288,-0.76677,-0.26423,0.58502,-1.8378,0.63696,-0.42625,0.64233,91.097
> undo
> show #!1 models
> ui mousemode right "translate selected atoms"
> select clear
> select #11 :1-135
2212 atoms, 2234 bonds, 135 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules false shift false
Fit molecule
Bb_0624_23c4c_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb (#11) to
map WTCW-stator-msk-4.2A.mrc (#1) using 2212 atoms
average map value = 0.156, steps = 64
shifted from previous position = 1.43e-14
rotated from previous position = 73.8 degrees
atoms outside contour = 321, contour level = 0.065265
> select clear
> select #11 :1-135
2212 atoms, 2234 bonds, 135 residues, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.07964,0.86515,0.49514,-59.038,-0.76677,-0.26423,0.58502,-9.1874,0.63696,-0.42625,0.64233,91.778
> show #!1 models
> view matrix models
> #11,0.07964,0.86515,0.49514,-59.393,-0.76677,-0.26423,0.58502,-8.0544,0.63696,-0.42625,0.64233,91.163
> ui mousemode right "translate selected atoms"
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ui tool show "Map Eraser"
Can only have one displayed volume when erasing
[Repeated 1 time(s)]
> close #12
> close #11
> open "C:/Users/Jack Botting/Downloads/Bb_0624.pdb"
Chain information for Bb_0624.pdb #11
---
Chain | Description
A | No description available
> select add #11
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> close #12
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,-127.51,0,1,0,69.233,0,0,1,-101.62
> view matrix models #11,1,0,0,-135.95,0,1,0,79.196,0,0,1,44.596
> view matrix models #11,1,0,0,-223.65,0,1,0,73.365,0,0,1,6.595
> view matrix models #11,1,0,0,-217.63,0,1,0,68.603,0,0,1,33.38
> view matrix models #11,1,0,0,-237.77,0,1,0,68.931,0,0,1,29.378
> view matrix models #11,1,0,0,-237.56,0,1,0,69.116,0,0,1,36.698
> view matrix models #11,1,0,0,-241.43,0,1,0,69.209,0,0,1,35.638
> fitmap #11 inMap #1 shift false
Fit molecule Bb_0624.pdb (#11) to map WTCW-stator-msk-4.2A.mrc (#1) using 4944
atoms
average map value = 0.1161, steps = 52
shifted from previous position = 3.34e-14
rotated from previous position = 16.5 degrees
atoms outside contour = 1327, contour level = 0.065265
Position of Bb_0624.pdb (#11) relative to WTCW-stator-msk-4.2A.mrc (#1)
coordinates:
Matrix rotation and translation
0.95893012 -0.04508084 0.28003704 38.98984686
0.03937584 0.99888698 0.02596795 352.54852710
-0.28089601 -0.01387475 0.95963791 375.70088202
Axis -0.07006505 0.98642411 0.14852059
Axis point 1136.05053105 0.00000000 -72.90661505
Rotation angle (degrees) 16.51859492
Shift along axis 400.82985746
> fitmap #11 inMap #1
Fit molecule Bb_0624.pdb (#11) to map WTCW-stator-msk-4.2A.mrc (#1) using 4944
atoms
average map value = 0.145, steps = 144
shifted from previous position = 20.7
rotated from previous position = 81.8 degrees
atoms outside contour = 761, contour level = 0.065265
Position of Bb_0624.pdb (#11) relative to WTCW-stator-msk-4.2A.mrc (#1)
coordinates:
Matrix rotation and translation
0.25737492 -0.82622928 -0.50110211 187.72943640
0.93446053 0.34485476 -0.08864940 145.48223513
0.24605217 -0.44544401 0.86083562 273.85984300
Axis -0.18338027 -0.38401184 0.90493457
Axis point -22.45958074 282.36330367 0.00000000
Rotation angle (degrees) 76.61267816
Shift along axis 157.53246358
> select clear
> view orient
> sym #11 C16 center #9
Made 16 graphical clones for Bb_0624.pdb symmetry C16
> hide #!5 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> open "C:/Users/Jack Botting/Documents/Chimera/PDB/FliL_MotA_MotB.pdb"
Summary of feedback from opening C:/Users/Jack
Botting/Documents/Chimera/PDB/FliL_MotA_MotB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER A 85
VAL A 87 1 3
Start residue of secondary structure not found: HELIX 2 2 ARG A 88 LYS A 107 1
20
Start residue of secondary structure not found: HELIX 3 3 ALA A 128 ALA A 130
1 3
Start residue of secondary structure not found: HELIX 4 4 LEU A 141 ALA A 152
1 12
Start residue of secondary structure not found: HELIX 5 5 PHE A 154 PHE A 157
1 4
247 messages similar to the above omitted
Chain information for FliL_MotA_MotB.pdb
---
Chain | Description
12.3/? | No description available
12.14/? 12.15/? 12.16/? 12.17/? 12.18/? 12.19/? 12.20/? 12.21/? 12.22/?
12.23/? | No description available
12.1/A 12.2/A | No description available
12.4/B 12.5/B 12.6/B 12.7/B 12.8/B 12.9/B 12.10/B 12.11/B 12.12/B 12.13/B | No
description available
> hide #12.1 models
> show #12.1 models
> hide #12.2 models
> show #12.2 models
> rename #12.1 MotB.pdb
> rename #12.2 MotB.pdb
> hide #12.3 models
> show #12.3 models
> rename #12.3 MotA.pdb
> hide #12.4 models
> show #12.4 models
> hide #12.5 models
> show #12.5 models
> hide #12.7 models
> show #12.7 models
> hide #12.6 models
> show #12.6 models
> hide #12.10 models
> show #12.10 models
> hide #12.11 models
> show #12.11 models
> hide #12.12 models
> show #12.12 models
> hide #12.13 models
> show #12.13 models
> hide #12.14 models
> show #12.14 models
> rename #12.13 FliLc.pdb
> rename #12.12 FliLc.pdb
> rename #12.11 FliLc.pdb
> rename #12.10 FliLc.pdb
> rename #12.9 FliLc.pdb
> rename #12.8 FliLc.pdb
> rename #12.7 FliLc.pdb
> rename #12.6 FliLc.pdb
> rename #12.5 FliLc.pdb
> rename #12.4 FliL.c.pdb
> rename #12.14 FliLTM.pdb
> rename #12.15 FliLTM.pdb
> rename #12.16 FliLTM.pdb
> rename #12.17 FliLTM.pdb
> rename #12.18 FliLTM.pdb
> rename #12.19 FliLTM.pdb
> rename #12.20 FliLTM.pdb
> rename #12.21 FliLTM.pdb
> rename #12.22 FliLTM.pdb
> rename #12.23 FliLTM.pdb
> select add #12.4
799 atoms, 807 bonds, 98 residues, 1 model selected
> select add #12.5
1598 atoms, 1614 bonds, 196 residues, 2 models selected
> select add #12.6
2397 atoms, 2421 bonds, 294 residues, 3 models selected
> select add #12.7
3196 atoms, 3228 bonds, 392 residues, 4 models selected
> select add #12.8
3995 atoms, 4035 bonds, 490 residues, 5 models selected
> select add #12.9
4794 atoms, 4842 bonds, 588 residues, 6 models selected
> select add #12.10
5593 atoms, 5649 bonds, 686 residues, 7 models selected
> select add #12.11
6392 atoms, 6456 bonds, 784 residues, 8 models selected
> select add #12.12
7191 atoms, 7263 bonds, 882 residues, 9 models selected
> select add #12.13
7990 atoms, 8070 bonds, 980 residues, 10 models selected
> view matrix models
> #12.4,1,0,0,4.5885,0,1,0,4.3422,0,0,1,-0.75398,#12.5,1,0,0,4.5885,0,1,0,4.3422,0,0,1,-0.75398,#12.6,1,0,0,4.5885,0,1,0,4.3422,0,0,1,-0.75398,#12.7,1,0,0,4.5885,0,1,0,4.3422,0,0,1,-0.75398,#12.8,1,0,0,4.5885,0,1,0,4.3422,0,0,1,-0.75398,#12.9,1,0,0,4.5885,0,1,0,4.3422,0,0,1,-0.75398,#12.10,1,0,0,4.5885,0,1,0,4.3422,0,0,1,-0.75398,#12.11,1,0,0,4.5885,0,1,0,4.3422,0,0,1,-0.75398,#12.12,1,0,0,4.5885,0,1,0,4.3422,0,0,1,-0.75398,#12.13,1,0,0,4.5885,0,1,0,4.3422,0,0,1,-0.75398
> undo
> select add #12.14
8176 atoms, 8258 bonds, 1004 residues, 11 models selected
> select add #12.15
8362 atoms, 8446 bonds, 1028 residues, 12 models selected
> select add #12.16
8548 atoms, 8634 bonds, 1052 residues, 13 models selected
> select add #12.17
8734 atoms, 8822 bonds, 1076 residues, 14 models selected
> select add #12.18
8920 atoms, 9010 bonds, 1100 residues, 15 models selected
> select add #12.19
9106 atoms, 9198 bonds, 1124 residues, 16 models selected
> select add #12.20
9292 atoms, 9386 bonds, 1148 residues, 17 models selected
> select add #12.21
9478 atoms, 9574 bonds, 1172 residues, 18 models selected
> select add #12.22
9664 atoms, 9762 bonds, 1196 residues, 19 models selected
> select add #12.23
9850 atoms, 9950 bonds, 1220 residues, 20 models selected
> view matrix models
> #12.4,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.5,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.6,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.7,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.8,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.9,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.10,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.11,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.12,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.13,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.14,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.15,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.16,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.17,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.18,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.19,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.20,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.21,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.22,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83,#12.23,1,0,0,-385.38,0,1,0,-163.53,0,0,1,54.83
> view matrix models
> #12.4,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.5,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.6,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.7,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.8,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.9,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.10,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.11,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.12,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.13,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.14,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.15,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.16,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.17,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.18,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.19,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.20,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.21,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.22,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989,#12.23,1,0,0,-324.88,0,1,0,9.7311,0,0,1,39.989
> log metadata #12.4
The model has no metadata
> log chains #12.4
Chain information for FliL.c.pdb #12.4
---
Chain | Description
B | No description available
> log metadata #12.5
The model has no metadata
> log chains #12.5
Chain information for FliLc.pdb #12.5
---
Chain | Description
B | No description available
> log metadata #12.6
The model has no metadata
> log chains #12.6
Chain information for FliLc.pdb #12.6
---
Chain | Description
B | No description available
> log metadata #12.7
The model has no metadata
> log chains #12.7
Chain information for FliLc.pdb #12.7
---
Chain | Description
B | No description available
> log metadata #12.8
The model has no metadata
> log chains #12.8
Chain information for FliLc.pdb #12.8
---
Chain | Description
B | No description available
> log metadata #12.9
The model has no metadata
> log chains #12.9
Chain information for FliLc.pdb #12.9
---
Chain | Description
B | No description available
> log metadata #12.10
The model has no metadata
> log chains #12.10
Chain information for FliLc.pdb #12.10
---
Chain | Description
B | No description available
> log metadata #12.11
The model has no metadata
> log chains #12.11
Chain information for FliLc.pdb #12.11
---
Chain | Description
B | No description available
> log metadata #12.12
The model has no metadata
> log chains #12.12
Chain information for FliLc.pdb #12.12
---
Chain | Description
B | No description available
> log metadata #12.13
The model has no metadata
> log chains #12.13
Chain information for FliLc.pdb #12.13
---
Chain | Description
B | No description available
> log metadata #12.14
The model has no metadata
> log chains #12.14
Chain information for FliLTM.pdb #12.14
---
Chain | Description
? | No description available
> log metadata #12.15
The model has no metadata
> log chains #12.15
Chain information for FliLTM.pdb #12.15
---
Chain | Description
? | No description available
> log metadata #12.16
The model has no metadata
> log chains #12.16
Chain information for FliLTM.pdb #12.16
---
Chain | Description
? | No description available
> log metadata #12.17
The model has no metadata
> log chains #12.17
Chain information for FliLTM.pdb #12.17
---
Chain | Description
? | No description available
> log metadata #12.18
The model has no metadata
> log chains #12.18
Chain information for FliLTM.pdb #12.18
---
Chain | Description
? | No description available
> log metadata #12.19
The model has no metadata
> log chains #12.19
Chain information for FliLTM.pdb #12.19
---
Chain | Description
? | No description available
> log metadata #12.20
The model has no metadata
> log chains #12.20
Chain information for FliLTM.pdb #12.20
---
Chain | Description
? | No description available
> log metadata #12.21
The model has no metadata
> log chains #12.21
Chain information for FliLTM.pdb #12.21
---
Chain | Description
? | No description available
> log metadata #12.22
The model has no metadata
> log chains #12.22
Chain information for FliLTM.pdb #12.22
---
Chain | Description
? | No description available
> log metadata #12.23
The model has no metadata
> log chains #12.23
Chain information for FliLTM.pdb #12.23
---
Chain | Description
? | No description available
> combine
> #12.4,12.5,12.6,12.7,12.8,12.9,12.10,12.11,12.12,12.13,12.14,12.15,12.16,12.17,12.18,12.19,12.20,12.21,12.22,12.23
No structures specified
> combine #12.4-12.23
No structures specified
> combine #12.4-end
Remapping chain ID 'B' in FliLc.pdb #12.5 to 'C'
Remapping chain ID 'B' in FliLc.pdb #12.6 to 'D'
Remapping chain ID 'B' in FliLc.pdb #12.7 to 'E'
Remapping chain ID 'B' in FliLc.pdb #12.8 to 'F'
Remapping chain ID 'B' in FliLc.pdb #12.9 to 'G'
Remapping chain ID 'B' in FliLc.pdb #12.10 to 'H'
Remapping chain ID 'B' in FliLc.pdb #12.11 to 'I'
Remapping chain ID 'B' in FliLc.pdb #12.12 to 'J'
Remapping chain ID 'B' in FliLc.pdb #12.13 to 'K'
Remapping chain ID ' ' in FliLTM.pdb #12.15 to 'A'
Remapping chain ID ' ' in FliLTM.pdb #12.16 to 'L'
Remapping chain ID ' ' in FliLTM.pdb #12.17 to 'M'
Remapping chain ID ' ' in FliLTM.pdb #12.18 to 'N'
Remapping chain ID ' ' in FliLTM.pdb #12.19 to 'O'
Remapping chain ID ' ' in FliLTM.pdb #12.20 to 'P'
Remapping chain ID ' ' in FliLTM.pdb #12.21 to 'Q'
Remapping chain ID ' ' in FliLTM.pdb #12.22 to 'R'
Remapping chain ID ' ' in FliLTM.pdb #12.23 to 'S'
> view matrix models
> #12.4,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.5,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.6,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.7,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.8,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.9,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.10,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.11,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.12,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.13,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.14,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.15,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.16,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.17,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.18,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.19,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.20,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.21,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.22,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635,#12.23,1,0,0,-466.9,0,1,0,104.79,0,0,1,53.635
> select add #13
19700 atoms, 19900 bonds, 2440 residues, 21 models selected
> view matrix models
> #12.4,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.5,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.6,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.7,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.8,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.9,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.10,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.11,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.12,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.13,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.14,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.15,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.16,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.17,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.18,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.19,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.20,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.21,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.22,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#12.23,1,0,0,-435.23,0,1,0,64.711,0,0,1,49.772,#13,1,0,0,-293.21,0,1,0,-30.348,0,0,1,36.126
> select clear
> close #12.4-23
> select add #13
9850 atoms, 9950 bonds, 1220 residues, 1 model selected
> view matrix models #13,1,0,0,-349.52,0,1,0,-28.537,0,0,1,45
> view matrix models #13,1,0,0,-423.33,0,1,0,-116.99,0,0,1,-287.45
> view matrix models #13,1,0,0,-421.87,0,1,0,-114.7,0,0,1,-282.65
> view matrix models #13,1,0,0,-444.48,0,1,0,-150.69,0,0,1,-280.69
> view matrix models #13,1,0,0,-485.95,0,1,0,-177.49,0,0,1,-368.9
> view matrix models #13,1,0,0,-453.47,0,1,0,-207.84,0,0,1,-595.78
> view matrix models #13,1,0,0,-509.45,0,1,0,-142.73,0,0,1,-596.39
> fitmap #13 inMap #1
Fit molecule combination (#13) to map WTCW-stator-msk-4.2A.mrc (#1) using 9850
atoms
average map value = 0.05845, steps = 76
shifted from previous position = 24
rotated from previous position = 7.98 degrees
atoms outside contour = 5762, contour level = 0.065265
Position of combination (#13) relative to WTCW-stator-msk-4.2A.mrc (#1)
coordinates:
Matrix rotation and translation
0.99684942 0.00941085 0.07875701 -266.03329074
-0.01834844 0.99336376 0.11354199 93.06209931
-0.07716584 -0.11462933 0.99040676 -210.58884981
Axis -0.82150102 0.56137985 -0.09994371
Axis point 0.00000000 -1626.88498890 528.19944949
Rotation angle (degrees) 7.98273182
Shift along axis 291.83683635
> select clear
> select add #13
9850 atoms, 9950 bonds, 1220 residues, 1 model selected
> color sel white
> select clear
> select add #12.3
9605 atoms, 9765 bonds, 1250 residues, 1 model selected
> view matrix models #12.3,1,0,0,-572.19,0,1,0,-155.33,0,0,1,-25.206
> view matrix models #12.3,1,0,0,-581.38,0,1,0,-204.33,0,0,1,-546.48
> view matrix models #12.3,1,0,0,-625.63,0,1,0,-168.39,0,0,1,-541.13
> view matrix models #12.3,1,0,0,-631.01,0,1,0,-168.13,0,0,1,-542.16
> fitmap #12.3 inMap #1
Fit molecule MotA.pdb (#12.3) to map WTCW-stator-msk-4.2A.mrc (#1) using 9605
atoms
average map value = 0.04311, steps = 100
shifted from previous position = 30.1
rotated from previous position = 17.5 degrees
atoms outside contour = 8176, contour level = 0.065265
Position of MotA.pdb (#12.3) relative to WTCW-stator-msk-4.2A.mrc (#1)
coordinates:
Matrix rotation and translation
0.95856624 0.25607779 0.12479954 -459.57486159
-0.26707236 0.96027045 0.08095066 265.22761027
-0.09911165 -0.11092708 0.98887414 -181.85222432
Axis -0.31951263 0.37285436 -0.87114367
Axis point 231.33815983 1327.83410676 0.00000000
Rotation angle (degrees) 17.47359761
Shift along axis 404.15066050
> select clear
> select add #12.3
9605 atoms, 9765 bonds, 1250 residues, 1 model selected
> view matrix models
> #12.3,0.95857,0.25608,0.1248,-757.1,-0.26707,0.96027,0.080951,-32.462,-0.099112,-0.11093,0.98887,-474.94
> view matrix models
> #12.3,0.94968,0.28286,0.13456,-763.95,-0.28803,0.95741,0.020209,14.825,-0.12311,-0.057948,0.9907,-474.88
> view matrix models
> #12.3,0.94968,0.28286,0.13456,-763.22,-0.28803,0.95741,0.020209,13.181,-0.12311,-0.057948,0.9907,-473.9
> fitmap #12.3 inMap #1
Fit molecule MotA.pdb (#12.3) to map WTCW-stator-msk-4.2A.mrc (#1) using 9605
atoms
average map value = 0.04311, steps = 72
shifted from previous position = 9.08
rotated from previous position = 3.76 degrees
atoms outside contour = 8169, contour level = 0.065265
Position of MotA.pdb (#12.3) relative to WTCW-stator-msk-4.2A.mrc (#1)
coordinates:
Matrix rotation and translation
0.95748490 0.25914735 0.12674904 -460.69548780
-0.27057999 0.95910910 0.08304336 266.78018222
-0.10004570 -0.11380851 0.98845257 -180.24736957
Axis -0.32327425 0.37244705 -0.86992928
Axis point 230.35306817 1310.18976726 0.00000000
Rotation angle (degrees) 17.72602490
Shift along axis 405.09494436
> view matrix models
> #12.3,0.95748,0.25915,0.12675,-754.81,-0.27058,0.95911,0.083043,-29.077,-0.10005,-0.11381,0.98845,-465.95
> select clear
> select add #12.3
9605 atoms, 9765 bonds, 1250 residues, 1 model selected
> view matrix models
> #12.3,0.95748,0.25915,0.12675,-760.32,-0.27058,0.95911,0.083043,-26.227,-0.10005,-0.11381,0.98845,-463.55
> view matrix models
> #12.3,0.95183,0.19071,0.24008,-799,-0.20756,0.97711,0.046703,-52.689,-0.22568,-0.094284,0.96963,-376.77
> view matrix models
> #12.3,0.95183,0.19071,0.24008,-793.58,-0.20756,0.97711,0.046703,-53.37,-0.22568,-0.094284,0.96963,-379.09
> select add #12
14819 atoms, 15021 bonds, 1582 residues, 4 models selected
> select subtract #12
Nothing selected
> hide #!1 models
> show #!6 models
> volume #6 level 0.7305
> volume #6 level 1.332
> fitmap #12.3 inMap #6
Fit molecule MotA.pdb (#12.3) to map Bb624-stator-msk-4.2A.mrc (#6) using 9605
atoms
average map value = 1.195, steps = 80
shifted from previous position = 3.81
rotated from previous position = 11.3 degrees
atoms outside contour = 4873, contour level = 1.3317
Position of MotA.pdb (#12.3) relative to Bb624-stator-msk-4.2A.mrc (#6)
coordinates:
Matrix rotation and translation
0.98557506 0.03706281 0.16513072 -731.23337094
-0.04282106 0.99858772 0.03144721 -163.61332845
-0.16373198 -0.03806466 0.98577022 -454.06339303
Axis -0.20119737 0.95187062 -0.23121838
Axis point -2989.07170119 0.00000000 4049.67978117
Rotation angle (degrees) 9.94748584
Shift along axis 96.37131301
> fitmap #13 inMap #6
Fit molecule combination (#13) to map Bb624-stator-msk-4.2A.mrc (#6) using
9850 atoms
average map value = 1.356, steps = 56
shifted from previous position = 2.61
rotated from previous position = 2.56 degrees
atoms outside contour = 5633, contour level = 1.3317
Position of combination (#13) relative to Bb624-stator-msk-4.2A.mrc (#6)
coordinates:
Matrix rotation and translation
0.99366880 0.03950316 0.10517516 -580.55593312
-0.04790521 0.99575479 0.07859698 -163.85190663
-0.10162384 -0.08313781 0.99134288 -499.79922744
Axis -0.58450818 0.74736988 -0.31589310
Axis point -4025.35161946 0.00000000 3194.83717264
Rotation angle (degrees) 7.95244718
Shift along axis 374.76483529
> view orient
> sym #12.3 C16 center #9
Made 16 graphical clones for MotA.pdb symmetry C16
> sym #13 C16 center #9
Made 16 graphical clones for combination symmetry C16
> open "C:/Users/Jack Botting/Documents/alphafold
> results/Bb_0236_50bac/Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #14
---
Chain | Description
A | No description available
> select add #14
10622 atoms, 10736 bonds, 668 residues, 1 model selected
> view matrix models #14,1,0,0,-28.222,0,1,0,36.627,0,0,1,16.151
> view matrix models #14,1,0,0,-32.62,0,1,0,32.634,0,0,1,17.708
> view matrix models
> #14,0.35227,0.20089,-0.91408,-40.116,0.5273,0.76431,0.37119,38.959,0.77321,-0.61276,0.16331,27.805
> view matrix models
> #14,0.29715,-0.69271,0.65716,-46.635,0.95424,0.19115,-0.22998,43.789,0.033691,0.69542,0.71781,21.36
> view matrix models
> #14,-0.76957,-0.63071,0.099823,-61.347,0.20479,-0.095704,0.97412,29.957,-0.60483,0.7701,0.20281,12.951
> view matrix models
> #14,-0.76957,-0.63071,0.099823,-40.515,0.20479,-0.095704,0.97412,32.829,-0.60483,0.7701,0.20281,3.9891
> view matrix models
> #14,-0.5791,-0.81339,0.055133,-38.375,0.17065,-0.054811,0.98381,32.476,-0.7972,0.57913,0.17055,0.43734
> view matrix models
> #14,-0.5791,-0.81339,0.055133,-51.348,0.17065,-0.054811,0.98381,31.149,-0.7972,0.57913,0.17055,6.064
> select clear
> select add #14
10622 atoms, 10736 bonds, 668 residues, 1 model selected
> view matrix models
> #14,-0.5791,-0.81339,0.055133,-49.69,0.17065,-0.054811,0.98381,27.428,-0.7972,0.57913,0.17055,38.446
> select clear
> hide #!9 models
> hide #10 models
> hide #11 models
> hide #!12 models
> hide #12.1 models
> hide #12.2 models
> hide #12.3 models
> hide #13 models
> select #14 :1-18
308 atoms, 313 bonds, 18 residues, 1 model selected
> cartoon hide sel
> select add #14
10622 atoms, 10736 bonds, 668 residues, 1 model selected
> select subtract #14
Nothing selected
> select add #14
10622 atoms, 10736 bonds, 668 residues, 1 model selected
> view matrix models
> #14,-0.5791,-0.81339,0.055133,-37.608,0.17065,-0.054811,0.98381,42.383,-0.7972,0.57913,0.17055,44.331
> view matrix models
> #14,-0.5791,-0.81339,0.055133,-36.27,0.17065,-0.054811,0.98381,22.319,-0.7972,0.57913,0.17055,45.81
> show #!12 models
> hide #!12 models
> show #12.3 models
> hide #12.3 models
> show #13 models
> view matrix models
> #14,-0.66692,-0.73992,0.087904,-37.35,0.16156,-0.028431,0.98645,19.509,-0.7274,0.67209,0.1385,45.141
> view matrix models
> #14,-0.66692,-0.73992,0.087904,-14.704,0.16156,-0.028431,0.98645,29.833,-0.7274,0.67209,0.1385,70.89
> fitmap #14 inMap #6
Fit molecule
Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#14) to
map Bb624-stator-msk-4.2A.mrc (#6) using 10622 atoms
average map value = 4.725, steps = 148
shifted from previous position = 8.43
rotated from previous position = 76.8 degrees
atoms outside contour = 1819, contour level = 1.3317
Position of Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#14) relative to Bb624-stator-msk-4.2A.mrc (#6) coordinates:
Matrix rotation and translation
-0.48053490 0.01755266 -0.87679993 -9.18932021
-0.65310835 -0.67439708 0.34443877 23.92159963
-0.58526549 0.73816020 0.33553512 70.04592157
Axis 0.47405530 -0.35101835 -0.80750089
Axis point 15.91096872 -6.45063988 0.00000000
Rotation angle (degrees) 155.46370989
Shift along axis -69.31531044
> select clear
> view orient
> sym #14 C16 center #9
Made 16 graphical clones for
Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb symmetry
C16
> show #10 models
> show #11 models
> show #12.3 models
> hide #!6 models
> show #!9 models
> view orient
> open "C:/Users/Jack Botting/Documents/Chimera/PDB/Huaxin Bb RBM3-c46.pdb"
Chain information for Huaxin Bb RBM3-c46.pdb
---
Chain | Description
15.1/C 15.2/C 15.3/C 15.4/C 15.5/C 15.6/C 15.7/C 15.8/C 15.9/C 15.10/C 15.11/C
15.12/C 15.13/C 15.14/C 15.15/C 15.16/C 15.17/C 15.18/C 15.19/C 15.20/C
15.21/C 15.22/C 15.23/C 15.24/C 15.25/C 15.26/C 15.27/C 15.28/C 15.29/C
15.30/C 15.31/C 15.32/C 15.33/C 15.34/C 15.35/C 15.36/C 15.37/C 15.38/C
15.39/C 15.40/C 15.41/C 15.42/C 15.43/C 15.44/C 15.45/C 15.46/C | No
description available
> select add #15
54510 atoms, 55016 bonds, 46 pseudobonds, 6900 residues, 93 models selected
> view matrix models #15,1,0,0,-268.25,0,1,0,-7.2971,0,0,1,-10.149
> view matrix models #15,1,0,0,-269.66,0,1,0,-8.8032,0,0,1,-40.638
> combine 15
Expected a keyword
> combine #15
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.2 to 'D'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.3 to 'E'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.4 to 'F'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.5 to 'G'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.6 to 'H'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.7 to 'I'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.8 to 'J'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.9 to 'K'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.10 to 'L'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.11 to 'M'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.12 to 'N'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.13 to 'O'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.14 to 'P'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.15 to 'Q'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.16 to 'R'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.17 to 'S'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.18 to 'T'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.19 to 'U'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.20 to 'V'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.21 to 'W'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.22 to 'X'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.23 to 'Y'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.24 to 'Z'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.25 to 'a'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.26 to 'b'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.27 to 'c'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.28 to 'd'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.29 to 'e'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.30 to 'f'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.31 to 'g'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.32 to 'h'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.33 to 'i'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.34 to 'j'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.35 to 'k'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.36 to 'l'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.37 to 'm'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.38 to 'n'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.39 to 'o'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.40 to 'p'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.41 to 'q'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.42 to 'r'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.43 to 's'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.44 to 't'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.45 to 'u'
Remapping chain ID 'C' in Huaxin Bb RBM3-c46.pdb #15.46 to 'v'
> close #15
> show #!6 models
> show #!5 models
> hide #!6 models
> volume #5 level 0.9099
> hide #!9 models
> hide #10 models
> hide #11 models
> hide #12.3 models
> hide #13 models
> hide #14 models
> select add #16
54510 atoms, 55016 bonds, 46 pseudobonds, 6900 residues, 2 models selected
> view matrix models #16,1,0,0,-272.45,0,1,0,-2.3423,0,0,1,-77.198
> fitmap #16 inMap #6
Fit molecule combination (#16) to map Bb624-stator-msk-4.2A.mrc (#6) using
54510 atoms
average map value = 1.773, steps = 144
shifted from previous position = 12.9
rotated from previous position = 7.46 degrees
atoms outside contour = 36237, contour level = 1.3317
Position of combination (#16) relative to Bb624-stator-msk-4.2A.mrc (#6)
coordinates:
Matrix rotation and translation
0.99500087 -0.01228511 -0.09910777 -251.23012302
0.01216724 0.99992437 -0.00179365 0.50587313
0.09912231 0.00057881 0.99507509 -75.08884768
Axis 0.01187736 -0.99240770 0.12241681
Axis point 614.46733278 0.00000000 -2564.39370868
Rotation angle (degrees) 5.73187505
Shift along axis -12.67811973
> view matrix models
> #16,0.99794,-0.014147,-0.062637,-256.69,0.014291,0.9999,0.0018622,1.2201,0.062604,-0.0027536,0.99803,-73.946
> view matrix models
> #16,0.99794,-0.014147,-0.062637,-256.19,0.014291,0.9999,0.0018622,1.2723,0.062604,-0.0027536,0.99803,-70.864
> select clear
> show #!9 models
> hide #!5 models
> show #10 models
> show #11 models
> show #12.3 models
> show #13 models
> show #14 models
> rename #16 "MS ring RBM3"
> rename #13 FliL
> rename #10 Bb_0058.pdb
> select add #10
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> color sel cyan
> select subtract #10
Nothing selected
> select add #11
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> color sel purple
> select add #12.3
14549 atoms, 14764 bonds, 1549 residues, 2 models selected
> select subtract #11
9605 atoms, 9765 bonds, 1250 residues, 1 model selected
> color sel white
> select subtract #12.3
Nothing selected
> rename #14 Bb_0236.pdb
> select add #14
10622 atoms, 10736 bonds, 668 residues, 1 model selected
> color sel hot pink
> select subtract #14
Nothing selected
> select add #16
54510 atoms, 55016 bonds, 46 pseudobonds, 6900 residues, 2 models selected
> color (#!16 & sel) forest green
> select #9/A
55936 atoms, 56416 bonds, 3280 residues, 16 models selected
> color sel red
> select #9/B
55936 atoms, 56416 bonds, 3280 residues, 16 models selected
> color sel orange
> select clear
> save "C:/Users/Jack Botting/Documents/Chimera/Saved
> Sessions/Bb_modeling.cxs"
> show #!1 models
> hide #!1 models
> show #!5 models
> hide #12.3 models
> hide #13 models
> show #13 models
> hide #!9 models
> hide #!16 models
> volume #5 color #00000080
> volume #5 color #ffffff80
> volume #5 color #ffaa0080
> hide #!5 models
> show #!2 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> view orient
> hide #!2 models
> show #!9 models
> show #!6 models
> show #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> hide #!6 models
> show #!6 models
> ui tool show "Segment Map"
Select a density map in the Segment map field
Segmenting Bb624-stator-msk-4.2A.mrc, density threshold 1.331708
Only showing 60 of 112 regions.
Showing 60 of 112 region surfaces
770 watershed regions, grouped to 112 regions
Showing Bb624-stator-msk-4.2A.seg - 112 regions, 60 surfaces
> hide #!6 models
> hide #!15 models
> show #!1 models
> transparency #1.1 0
> hide #!1 models
> show #!1 models
> sym clear #10
> transparency #1.1 50
> view orient
> sym #10 C16 center #9
Made 16 graphical clones for Bb_0058.pdb symmetry C16
> hide #!1 models
> show #!5 models
> hide #!9 models
> save "C:/Users/Jack Botting/Documents/Chimera/Saved
> Sessions/Bb_modeling.cxs"
> select #10/A:240
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
224 atoms, 224 bonds, 14 residues, 1 model selected
> select up
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> select down
224 atoms, 224 bonds, 14 residues, 1 model selected
> sym clear #10
> select #10/A:240
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #10/A:240
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
224 atoms, 224 bonds, 14 residues, 1 model selected
> select up
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> view matrix models
> #10,0.74765,-0.65,0.13609,-100.21,0.18422,0.0061183,-0.98287,-15.899,0.63803,0.75991,0.12432,60.022
> undo
> view matrix models
> #10,0.73255,-0.66514,0.14476,-98.943,0.16578,-0.03193,-0.98564,-21.243,0.66021,0.74604,0.086879,60.392
> view matrix models
> #10,0.73255,-0.66514,0.14476,-98.376,0.16578,-0.03193,-0.98564,-21.285,0.66021,0.74604,0.086879,60.503
> view matrix models
> #10,0.73255,-0.66514,0.14476,-99.756,0.16578,-0.03193,-0.98564,-20.749,0.66021,0.74604,0.086879,60.191
> view matrix models
> #10,0.70891,-0.64494,0.28548,-98.596,0.28719,-0.10574,-0.95202,-20.93,0.64418,0.75689,0.11025,60.427
> view matrix models
> #10,0.70891,-0.64494,0.28548,-97.821,0.28719,-0.10574,-0.95202,-21.856,0.64418,0.75689,0.11025,60.662
> view matrix models
> #10,0.70891,-0.64494,0.28548,-96.653,0.28719,-0.10574,-0.95202,-19.083,0.64418,0.75689,0.11025,59.801
> view matrix models
> #10,0.70891,-0.64494,0.28548,-96.262,0.28719,-0.10574,-0.95202,-19.236,0.64418,0.75689,0.11025,59.986
> fitmap #10 inMap #5
Fit molecule Bb_0058.pdb (#10) to map Bb624-nostat-msk-4.2A.mrc (#5) using
10479 atoms
average map value = 4.264, steps = 56
shifted from previous position = 5.17
rotated from previous position = 9.23 degrees
atoms outside contour = 1637, contour level = 0.90987
Position of Bb_0058.pdb (#10) relative to Bb624-nostat-msk-4.2A.mrc (#5)
coordinates:
Matrix rotation and translation
0.71700253 -0.68184706 0.14488593 -97.49305466
0.16626486 -0.03456669 -0.98547506 -20.82954560
0.67695158 0.73067754 0.08858280 56.58980653
Axis 0.86375609 -0.26779375 0.42686288
Axis point 0.00000000 -66.72598613 34.11001792
Rotation angle (degrees) 96.57424911
Shift along axis -54.47611015
> view orient
> select up
90405 atoms, 91286 bonds, 9724 residues, 24 models selected
> select up
90405 atoms, 91286 bonds, 9724 residues, 24 models selected
> select up
90405 atoms, 91286 bonds, 9724 residues, 24 models selected
> sym #10 C16 center #9
Made 16 graphical clones for Bb_0058.pdb symmetry C16
> select clear
> volume #5 level 2.554
> sym clear #10
> fitmap #10 inMap #5
Fit molecule Bb_0058.pdb (#10) to map Bb624-nostat-msk-4.2A.mrc (#5) using
10479 atoms
average map value = 4.264, steps = 40
shifted from previous position = 0.0591
rotated from previous position = 0.0295 degrees
atoms outside contour = 2881, contour level = 2.5542
Position of Bb_0058.pdb (#10) relative to Bb624-nostat-msk-4.2A.mrc (#5)
coordinates:
Matrix rotation and translation
0.71723816 -0.68156888 0.14502845 -97.50026873
0.16657150 -0.03439694 -0.98542922 -20.80957252
0.67662650 0.73094504 0.08885914 56.53550935
Axis 0.86383355 -0.26754784 0.42686035
Axis point 0.00000000 -66.69480591 34.08832892
Rotation angle (degrees) 96.55459052
Shift along axis -54.52367972
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 level 2.62
> hide #!5 models
> volume #2 level 7.115
> show #!5 models
> hide #!5 models
> volume #1 level 0.06466
> volume #2 level 2.575
> hide #!2 models
> hide #!1 models
> select #14/A:131
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
65 atoms, 65 bonds, 4 residues, 1 model selected
> select up
10622 atoms, 10736 bonds, 668 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross ignoreHiddenModels true select true
4 contacts
> contacts sel restrict cross ignoreHiddenModels true select true
2 contacts
> contacts sel restrict cross ignoreHiddenModels true select true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
3 contacts
atom1 atom2 overlap distance
Bb_0236.pdb #14/A ARG 99 NH2 Bb_0624.pdb #11/A ASN 218 ND2 -0.114 3.364
Bb_0236.pdb #14/A ARG 99 NH2 Bb_0624.pdb #11/A ASN 218 HD21 -0.196 2.821
Bb_0236.pdb #14/A VAL 95 CG1 Bb_0236.pdb #14/A ARG 99 HH22 -0.353 3.053
3 contacts
> contacts sel restrict cross ignoreHiddenModels true select true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
3 contacts
atom1 atom2 overlap distance
Bb_0624.pdb #11/A ASN 218 HD21 Bb_0236.pdb #14/A ARG 99 HH21 -0.086 2.086
Bb_0624.pdb #11/A ASN 218 ND2 Bb_0236.pdb #14/A ARG 99 HH21 -0.136 2.761
Bb_0236.pdb #14/A ARG 99 NH2 Bb_0236.pdb #14/A VAL 95 HG11 -0.242 2.867
3 contacts
> contacts sel restrict cross ignoreHiddenModels true select true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
1 contacts
atom1 atom2 overlap distance
Bb_0236.pdb #14/A ARG 99 NH2 Bb_0236.pdb #14/A VAL 95 CG1 -0.141 3.466
1 contacts
> contacts sel restrict cross ignoreHiddenModels true select true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
4 contacts
atom1 atom2 overlap distance
Bb_0236.pdb #14/A ARG 99 NH2 Bb_0624.pdb #11/A ASN 218 ND2 -0.114 3.364
Bb_0236.pdb #14/A ARG 99 NH2 Bb_0624.pdb #11/A ASN 218 HD21 -0.196 2.821
Bb_0236.pdb #14/A ARG 99 NH2 Bb_0236.pdb #14/A VAL 95 HG11 -0.242 2.867
Bb_0236.pdb #14/A VAL 95 CG1 Bb_0236.pdb #14/A ARG 99 HH22 -0.353 3.053
4 contacts
> contacts sel restrict cross ignoreHiddenModels true select true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
2 contacts
atom1 atom2 overlap distance
Bb_0624.pdb #11/A ASN 218 HD21 Bb_0236.pdb #14/A ARG 99 HH21 -0.086 2.086
Bb_0624.pdb #11/A ASN 218 ND2 Bb_0236.pdb #14/A ARG 99 HH21 -0.136 2.761
2 contacts
> contacts sel restrict cross ignoreHiddenModels true select true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
2 contacts
atom1 atom2 overlap distance
Bb_0624.pdb #11/A ASN 218 ND2 Bb_0236.pdb #14/A ARG 99 NH2 -0.114 3.364
Bb_0624.pdb #11/A ASN 218 HD21 Bb_0236.pdb #14/A ARG 99 NH2 -0.196 2.821
2 contacts
> select clear
[Repeated 2 time(s)]
> view orient
> sym #10 C16 center #9
Made 16 graphical clones for Bb_0058.pdb symmetry C16
> sym clear #11
> view orient
> sym #11 C16 center #9
Made 16 graphical clones for Bb_0624.pdb symmetry C16
> select clear
[Repeated 1 time(s)]
> select add #11
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross ignoreHiddenModels true select true
> makePseudobonds false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
10 contacts
atom1 atom2 overlap distance
Bb_0624.pdb #11/A ASN 218 HD21 Bb_0236.pdb #14/A ARG 99 HH21 -0.086 2.086
Bb_0624.pdb #11/A THR 58 CG2 Bb_0058.pdb #10/A GLN 138 OE1 -0.090 3.270
Bb_0624.pdb #11/A ASN 218 ND2 Bb_0236.pdb #14/A ARG 99 NH2 -0.114 3.364
Bb_0624.pdb #11/A ASN 218 ND2 Bb_0236.pdb #14/A ARG 99 HH21 -0.136 2.761
Bb_0624.pdb #11/A THR 58 CG2 Bb_0058.pdb #10/A GLN 138 HB3 -0.187 2.887
Bb_0624.pdb #11/A LYS 105 NZ Bb_0058.pdb #10/A VAL 169 CG1 -0.192 3.517
Bb_0624.pdb #11/A ASN 218 HD21 Bb_0236.pdb #14/A ARG 99 NH2 -0.196 2.821
Bb_0624.pdb #11/A THR 58 HG22 Bb_0058.pdb #10/A GLN 138 CD -0.250 2.950
Bb_0624.pdb #11/A THR 58 CG2 Bb_0058.pdb #10/A GLN 138 CD -0.264 3.664
Bb_0624.pdb #11/A THR 58 HG22 Bb_0058.pdb #10/A GLN 138 HB3 -0.354 2.354
10 contacts
> select clear
> select add #11
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> hide sel atoms
> select clear
> show #!16 models
> hide #!16 models
> show #12.3 models
> show #!9 models
> show #!16 models
> show #!15 models
> select #15.5
1 model selected
> select add #15.3
2 models selected
> select add #15.7
3 models selected
> ui tool show "Segment Map"
> select #15.2
1 model selected
> select add #15.60
2 models selected
> select add #15.1
3 models selected
> select add #15.56
4 models selected
> select add #15.33
5 models selected
> select #15.15
1 model selected
> select add #15.4
2 models selected
> select add #15.16
3 models selected
> select #15.59
1 model selected
> select add #15.12
2 models selected
> select add #15.32
3 models selected
> select clear
> select #15.50
1 model selected
> select add #15.45
2 models selected
> select add #15.41
3 models selected
> select add #15.44
4 models selected
> select add #15.46
5 models selected
> select add #15.49
6 models selected
> select add #15.54
7 models selected
> select #15.53
1 model selected
> select add #15.58
2 models selected
> select add #15.9
3 models selected
> select add #15.14
4 models selected
> select add #15.57
5 models selected
> select add #15.23
6 models selected
Ungrouped to 12 regions
> select #15.72
1 model selected
> select add #15.68
2 models selected
> select add #15.70
3 models selected
> select add #15.64
4 models selected
> select add #15.61
5 models selected
> select add #15.66
6 models selected
Ungrouped to 13 regions, but did not show all surfaces, see Options
> select #15.14
1 model selected
> select #15.9
1 model selected
> select add #15.67
2 models selected
> select #15.71
1 model selected
> select add #15.67
2 models selected
> select add #15.9
3 models selected
> select add #15.58
4 models selected
> close #15
> view orient
> select add #14
10622 atoms, 10736 bonds, 668 residues, 1 model selected
> color sel blue
> select clear
> save "C:/Users/Jack Botting/Documents/Chimera/Saved
> Sessions/Bb_modeling.cxs"
——— End of log from Fri Jul 21 11:50:13 2023 ———
opened ChimeraX session
> hide #12.3 models
> hide #13 models
> select add #16
54510 atoms, 55016 bonds, 46 pseudobonds, 6900 residues, 2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.99955,-0.0085215,0.028701,-265.47,0.0086928,0.99995,-0.005851,2.0499,-0.028649,0.0060979,0.99957,-71.121
> select clear
> hide #10 models
> hide #11 models
> hide #!12 models
> hide #14 models
> hide #!16 models
> color #9 bfactor palate alphafold
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color bfactor palate alphafold
> color byattribute bfactor palate alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor #9 palate alphafold
> color byattribute bfactor #9 palate alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> ui tool show AlphaFold
> alphafold predict #9.1
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
[Repeated 1 time(s)]
> color bfactor #9 palate alphafold
> color byattribute bfactor #9 palate alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
Running AlphaFold prediction
AlphaFold prediction finished
Results in C:\Users\Jack Botting/Downloads/ChimeraX/AlphaFold/prediction_1
> open C:\Users\Jack
> Botting/Downloads/ChimeraX/AlphaFold/prediction_1\best_model.pdb
Chain information for best_model.pdb #15
---
Chain | Description
A B | No description available
> hide #!9 models
> ui mousemode right translate
> show #!9 models
> ui mousemode right "translate selected models"
> select add #15
3432 atoms, 3492 bonds, 410 residues, 1 model selected
> view matrix models
> #15,-0.12232,-0.71198,0.69146,-263.58,-0.0311,-0.6936,-0.71969,-131.22,0.992,-0.10954,0.062698,53.767
> close #15
> show #10 models
> show #11 models
> show #!12 models
> show #12.1 models
> show #12.2 models
> show #12.3 models
> show #13 models
> show #14 models
> show #!16 models
> ui tool show "Side View"
> select add #12.1
2607 atoms, 2628 bonds, 166 residues, 1 model selected
> select add #12.2
5214 atoms, 5256 bonds, 332 residues, 2 models selected
> view matrix models
> #12.1,1,0,0,-174.27,0,1,0,-294.14,0,0,1,3.7275,#12.2,1,0,0,-174.27,0,1,0,-294.14,0,0,1,3.7275
> view matrix models
> #12.1,1,0,0,-250.78,0,1,0,-418.09,0,0,1,5.1596,#12.2,1,0,0,-250.78,0,1,0,-418.09,0,0,1,5.1596
> show #!1 models
> view matrix models
> #12.1,1,0,0,-251.52,0,1,0,-528.48,0,0,1,-435.96,#12.2,1,0,0,-251.52,0,1,0,-528.48,0,0,1,-435.96
> hide #!1 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> view matrix models
> #12.1,1,0,0,41.486,0,1,0,-301.04,0,0,1,-444.26,#12.2,1,0,0,41.486,0,1,0,-301.04,0,0,1,-444.26
> hide #!12 models
> hide #12.1 models
> hide #12.2 models
> select subtract #12.2
2607 atoms, 2628 bonds, 166 residues, 1 model selected
> select subtract #12.1
Nothing selected
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select #9/B
55936 atoms, 56416 bonds, 3280 residues, 16 models selected
> color sel orange
> color sel orange red
> select clear
> save "C:\Users\Jack Botting\Desktop\image1.png" supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode "C:\Users\Jack Botting\Desktop\movie1.mp4"
Movie saved to \C:Users\\...\Desktop\movie1.mp4
> save "C:\Users\Jack Botting\Desktop\image2.png" supersample 3
> save "C:/Users/Jack Botting/Documents/Chimera/Images/group shot 624
> asymmetric map.jpg" width 2863 height 1180 supersample 3
> hide #!6 models
> hide #12.3 models
> show #12.3 models
> save "C:/Users/Jack Botting/Documents/Chimera/Images/group shot 624
> asymmetric map.jpg" width 2863 height 1180 supersample 3
> show #!6 models
> show #!1 models
> hide #!9 models
> hide #10 models
> hide #11 models
> show #11 models
> hide #!12 models
> hide #12.3 models
> hide #13 models
> hide #14 models
> hide #!16 models
> hide #!1 models
> save "C:/Users/Jack Botting/Documents/Chimera/Images/624 in D624 map.jpg"
> width 2863 height 1180 supersample 3
> show #!1 models
> hide #!6 models
> save "C:/Users/Jack Botting/Documents/Chimera/Images/624 in WT map.jpg"
> width 2863 height 1180 supersample 3
> save "C:/Users/Jack Botting/Documents/Chimera/Images/624 in WT map_top.jpg"
> width 2863 height 1180 supersample 3
> hide #!1 models
> show #!6 models
> save "C:/Users/Jack Botting/Documents/Chimera/Images/624 in D624
> map_top.jpg" width 2863 height 1180 supersample 3
> hide #11 models
> show #10 models
> show #!1 models
> hide #!6 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> select add #10
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> hide sel atoms
> select clear
> save "C:/Users/Jack Botting/Documents/Chimera/Images/58 in D58 map.jpg"
> width 2863 height 1180 supersample 3
> show #!1 models
> hide #!2 models
> save "C:/Users/Jack Botting/Documents/Chimera/Images/58 in WT map.jpg" width
> 2863 height 1180 supersample 3
> save "C:/Users/Jack Botting/Documents/Chimera/Images/58 in WT map_top.jpg"
> width 2863 height 1180 supersample 3
> hide #!1 models
> show #!2 models
> save "C:/Users/Jack Botting/Documents/Chimera/Images/58 in D58 map_top.jpg"
> width 2863 height 1180 supersample 3
> save "C:/Users/Jack Botting/Documents/Chimera/Saved
> Sessions/Bb_modeling.cxs"
——— End of log from Fri Jul 21 16:08:54 2023 ———
opened ChimeraX session
> hide #10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> show #!7 models
> hide #!2 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> volume #7 level 2.731
> volume #8 level 0.07035
> volume #7 level 1.719
> ui tool show "Side View"
> hide #!8 models
> show #!8 models
> hide #!7 models
> volume #8 level 0.03606
> show #!7 models
> volume #7 level 0.6387
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #12.1 models
> show #12.2 models
> select add #12.1
2607 atoms, 2628 bonds, 166 residues, 1 model selected
> select add #12.2
5214 atoms, 5256 bonds, 332 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #12.1,1,0,0,-96.602,0,1,0,-561.6,0,0,1,-401.08,#12.2,1,0,0,-96.602,0,1,0,-561.6,0,0,1,-401.08
> view matrix models
> #12.1,1,0,0,-95.044,0,1,0,-552.01,0,0,1,-530.19,#12.2,1,0,0,-95.044,0,1,0,-552.01,0,0,1,-530.19
> view matrix models
> #12.1,1,0,0,-126.82,0,1,0,-558.24,0,0,1,-503.58,#12.2,1,0,0,-126.82,0,1,0,-558.24,0,0,1,-503.58
> view matrix models
> #12.1,-0.60265,0.74611,-0.28308,32.97,-0.78128,-0.62389,0.018912,493.94,-0.1625,0.23256,0.95891,-564.14,#12.2,-0.60265,0.74611,-0.28308,32.97,-0.78128,-0.62389,0.018912,493.94,-0.1625,0.23256,0.95891,-564.14
> volume #7 level 0.4786
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> view matrix models
> #12.1,-0.60265,0.74611,-0.28308,-42.467,-0.78128,-0.62389,0.018912,527.43,-0.1625,0.23256,0.95891,-588.9,#12.2,-0.60265,0.74611,-0.28308,-42.467,-0.78128,-0.62389,0.018912,527.43,-0.1625,0.23256,0.95891,-588.9
> view matrix models
> #12.1,-0.60265,0.74611,-0.28308,-38.391,-0.78128,-0.62389,0.018912,525.58,-0.1625,0.23256,0.95891,-596.79,#12.2,-0.60265,0.74611,-0.28308,-38.391,-0.78128,-0.62389,0.018912,525.58,-0.1625,0.23256,0.95891,-596.79
> ui tool show "Fit in Map"
> fitmap #12.1 inMap #8
Fit molecule MotB.pdb (#12.1) to map WTCC-stator-msk-4.2A.mrc (#8) using 2607
atoms
average map value = 0.06178, steps = 76
shifted from previous position = 16.7
rotated from previous position = 55.4 degrees
atoms outside contour = 621, contour level = 0.036057
Position of MotB.pdb (#12.1) relative to WTCC-stator-msk-4.2A.mrc (#8)
coordinates:
Matrix rotation and translation
-0.79883076 0.04228201 -0.60006804 910.54373696
0.00856504 -0.99662620 -0.08162637 906.34092275
-0.60149486 -0.07034526 0.79577351 62.13947497
Axis 0.31703854 0.04009850 -0.94756460
Axis point 469.87184139 450.60693636 0.00000000
Rotation angle (degrees) 178.98057511
Shift along axis 266.13920719
> fitmap #12.2 inMap #8
Fit molecule MotB.pdb (#12.2) to map WTCC-stator-msk-4.2A.mrc (#8) using 2607
atoms
average map value = 0.06884, steps = 80
shifted from previous position = 15.8
rotated from previous position = 50.6 degrees
atoms outside contour = 406, contour level = 0.036057
Position of MotB.pdb (#12.2) relative to WTCC-stator-msk-4.2A.mrc (#8)
coordinates:
Matrix rotation and translation
-0.12143838 0.58901030 -0.79894905 575.39358186
-0.99124198 -0.02988935 0.12863109 458.19012669
0.05188497 0.80757260 0.58748145 -426.91475870
Axis 0.35382287 -0.44340276 -0.82353104
Axis point 475.11445372 139.15619111 0.00000000
Rotation angle (degrees) 106.37501723
Shift along axis 352.00219616
> view matrix models
> #12.1,-0.60265,0.74611,-0.28308,-97.343,-0.78128,-0.62389,0.018912,824.73,-0.1625,0.23256,0.95891,-501.48,#12.2,-0.60265,0.74611,-0.28308,-97.343,-0.78128,-0.62389,0.018912,824.73,-0.1625,0.23256,0.95891,-501.48
> view matrix models
> #12.1,-0.89724,0.43335,-0.08465,9.1396,-0.39916,-0.7141,0.57509,412.21,0.18877,0.54978,0.8137,-659.28,#12.2,-0.89724,0.43335,-0.08465,9.1396,-0.39916,-0.7141,0.57509,412.21,0.18877,0.54978,0.8137,-659.28
> view matrix models
> #12.1,-0.94929,0.20001,0.24258,-71.272,0.097164,-0.54716,0.83137,33.566,0.29901,0.81278,0.49998,-617.65,#12.2,-0.94929,0.20001,0.24258,-71.272,0.097164,-0.54716,0.83137,33.566,0.29901,0.81278,0.49998,-617.65
> view matrix models
> #12.1,-0.70841,0.65891,-0.25299,-45.047,-0.70448,-0.68203,0.19633,719.75,-0.043183,0.3173,0.94734,-568.01,#12.2,-0.70841,0.65891,-0.25299,-45.047,-0.70448,-0.68203,0.19633,719.75,-0.043183,0.3173,0.94734,-568.01
> view matrix models
> #12.1,-0.55761,0.70574,-0.43704,18.478,-0.79789,-0.60091,0.047664,797.09,-0.22898,0.37529,0.89818,-523.17,#12.2,-0.55761,0.70574,-0.43704,18.478,-0.79789,-0.60091,0.047664,797.09,-0.22898,0.37529,0.89818,-523.17
> view matrix models
> #12.1,-0.55761,0.70574,-0.43704,77.399,-0.79789,-0.60091,0.047664,497.42,-0.22898,0.37529,0.89818,-618.51,#12.2,-0.55761,0.70574,-0.43704,77.399,-0.79789,-0.60091,0.047664,497.42,-0.22898,0.37529,0.89818,-618.51
> view matrix models
> #12.1,-0.46932,0.84026,-0.2715,-127.02,-0.76513,-0.54044,-0.34999,723.38,-0.44082,0.043476,0.89654,-387.22,#12.2,-0.46932,0.84026,-0.2715,-127.02,-0.76513,-0.54044,-0.34999,723.38,-0.44082,0.043476,0.89654,-387.22
> combine #12.1,12.2
No structures specified
> combine #12.1,2
Remapping chain ID 'A' in MotB.pdb #12.2 to 'B'
> view matrix models
> #12.1,-0.46932,0.84026,-0.2715,-167.31,-0.76513,-0.54044,-0.34999,1217.4,-0.44082,0.043476,0.89654,-375.56,#12.2,-0.46932,0.84026,-0.2715,-167.31,-0.76513,-0.54044,-0.34999,1217.4,-0.44082,0.043476,0.89654,-375.56
> close #12.1-2
> rename #1 MotB
> select add #1
5214 atoms, 5256 bonds, 332 residues, 1 model selected
> view matrix models
> #1,-0.43208,0.85512,-0.28648,-133.88,-0.79016,-0.51208,-0.33677,705.06,-0.43469,0.080853,0.89695,-409.23
> view matrix models
> #1,-0.44468,0.87297,-0.20045,-198.07,-0.80791,-0.48755,-0.33103,692.1,-0.38671,0.014741,0.92208,-401.46
> view matrix models
> #1,-0.53442,0.81683,-0.21722,-135.19,-0.79851,-0.57218,-0.18706,639.64,-0.27708,0.073483,0.95803,-483.27
> volume #8 level 0.01692
> fitmap #1 inMap #8
Fit molecule MotB (#1) to map WTCC-stator-msk-4.2A.mrc (#8) using 5214 atoms
average map value = 0.09059, steps = 124
shifted from previous position = 51.7
rotated from previous position = 33.9 degrees
atoms outside contour = 291, contour level = 0.016919
Position of MotB (#1) relative to WTCC-stator-msk-4.2A.mrc (#8) coordinates:
Matrix rotation and translation
-0.79030189 0.56724704 0.23163274 76.25786219
-0.61251230 -0.72162030 -0.32263420 1043.23444099
-0.01586241 -0.39685632 0.91774368 -21.16197120
Axis -0.06145625 0.20492708 -0.97684596
Axis point 210.12540182 503.85294067 0.00000000
Rotation angle (degrees) 142.85303898
Shift along axis 229.77245151
> fitmap #1 inMap #8 shift false
Fit molecule MotB (#1) to map WTCC-stator-msk-4.2A.mrc (#8) using 5214 atoms
average map value = 0.03921, steps = 88
shifted from previous position = 1.31e-13
rotated from previous position = 94 degrees
atoms outside contour = 1910, contour level = 0.016919
Position of MotB (#1) relative to WTCC-stator-msk-4.2A.mrc (#8) coordinates:
Matrix rotation and translation
-0.47349005 0.50564702 -0.72119919 654.34784273
-0.58262729 0.43427098 0.68698920 -253.41449228
0.66056992 0.74547288 0.08898076 -200.12159245
Axis 0.03323233 -0.78516615 -0.61839286
Axis point 316.91183109 0.00000000 243.94622082
Rotation angle (degrees) 118.36710838
Shift along axis 344.47174659
> hide #!8 models
> show #!8 models
> color sel white
> select clear
> sym #1 C16 center #9
Made 16 graphical clones for MotB symmetry C16
> sym clear #1
> view orient
> sym #1 C16 center #9
Made 16 graphical clones for MotB symmetry C16
> select clear
> volume #8 level 0.03207
> show #12.3 models
> show #13 models
> sym clear #1
> hide #!7 models
> hide #!8 models
> show #!8 models
> show #!7 models
> select add #1
5214 atoms, 5256 bonds, 332 residues, 1 model selected
> view matrix models
> #1,-0.53442,0.81683,-0.21722,-21.125,-0.79851,-0.57218,-0.18706,928.68,-0.27708,0.073483,0.95803,-488.63
> select subtract #1
Nothing selected
> hide #1 models
> hide #!7 models
> show #!9 models
> show #10 models
> show #11 models
> hide #12.3 models
> hide #!12 models
> show #12.3 models
> hide #!12 models
> show #14 models
> hide #!9 models
> hide #10 models
> hide #11 models
> hide #13 models
> hide #!8 models
> show #!5 models
> volume #5 level 0.06019
> hide #!5 models
> show #!6 models
> show #10 models
> show #!2 models
> volume #2 level 1.069
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #11 models
> hide #!2 models
> show #13 models
> show #!12 models
> show #!16 models
> show #!9 models
> select clear
> select #10/A:196
22 atoms, 21 bonds, 1 residue, 1 model selected
> select add #14/A:363
33 atoms, 31 bonds, 2 residues, 2 models selected
> select add #9.4/A:82
50 atoms, 47 bonds, 3 residues, 3 models selected
> select add #10/A:476
70 atoms, 67 bonds, 4 residues, 3 models selected
> select up
1939 atoms, 1944 bonds, 117 residues, 3 models selected
> select up
24597 atoms, 24847 bonds, 1510 residues, 3 models selected
> select add #9.4/B:91
24616 atoms, 24865 bonds, 1511 residues, 3 models selected
> select up
26011 atoms, 26264 bonds, 1593 residues, 3 models selected
> select up
28093 atoms, 28373 bonds, 1715 residues, 3 models selected
> select up
132973 atoms, 134153 bonds, 7865 residues, 18 models selected
> select up
132973 atoms, 134153 bonds, 7865 residues, 19 models selected
> select down
132973 atoms, 134153 bonds, 7865 residues, 18 models selected
> select down
28093 atoms, 28373 bonds, 1715 residues, 3 models selected
> select up
132973 atoms, 134153 bonds, 7865 residues, 18 models selected
> select down
28093 atoms, 28373 bonds, 1715 residues, 3 models selected
> select add #11
33037 atoms, 33372 bonds, 2014 residues, 4 models selected
> select add #13
42887 atoms, 43322 bonds, 3234 residues, 5 models selected
> select ~sel
174209 atoms, 175817 bonds, 46 pseudobonds, 14632 residues, 35 models selected
> cartoon hide (#9.1-3,5-16#12.3#!16 & sel)
> select #10/A:199
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select #10/A:199
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
281 atoms, 282 bonds, 18 residues, 1 model selected
> select up
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> select down
281 atoms, 282 bonds, 18 residues, 1 model selected
> select down
19 atoms, 18 bonds, 1 residue, 1 model selected
> select
217096 atoms, 219139 bonds, 46 pseudobonds, 17866 residues, 40 models selected
> cartoon (#10-11,13-14#9.1-16#12.3#!16 & sel)
> select clear
Drag select of 8466 residues, 19 atoms, 18 bonds, 8 pseudobonds
> select clear
Drag select of 964 residues, 2 pseudobonds
> select clear
> select #14/A:535
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select #14:1-18
308 atoms, 313 bonds, 18 residues, 1 model selected
> split #14:1-18
Did not split Bb_0236.pdb, has only one piece
> split #14 atoms:1-18
Expected a keyword
> split #14 atoms :1-18
Split Bb_0236.pdb (#14) into 2 models
Chain information for Bb_0236.pdb 1 #14.1
---
Chain | Description
A | No description available
Chain information for Bb_0236.pdb 2 #14.2
---
Chain | Description
A | No description available
> hide #14.2 models
> show #14.2 models
> hide #14.1 models
> show #14.1 models
> close #14.1
> sym #14 C16 center #9
Made 16 graphical clones for Bb_0236.pdb 2 symmetry C16
> select #14.2/A:619
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
170 atoms, 170 bonds, 10 residues, 1 model selected
> select up
10314 atoms, 10422 bonds, 650 residues, 1 model selected
> select clear
> sym clear
> sym #14 C16 center #9 copies true
Made 16 copies for Bb_0236.pdb 2 symmetry C16
> sym #10 C16 center #9 copies true
Made 16 copies for Bb_0058.pdb symmetry C16
> sym #12 C16 center #9 copies true
Made 16 copies for MotA.pdb symmetry C16
> sym clear #12
> close #18
> show #12.3 models
> sym #12 C16 center #9
Made 16 graphical clones for MotA.pdb symmetry C16
> sym #13 C16 center #9
Made 16 graphical clones for FliL symmetry C16
> sym #11 C16 center #9 copies true
Made 16 copies for Bb_0624.pdb symmetry C16
> show #14.2 models
> hide #14.2 models
> show #14.2 models
> hide #14.2 models
> select subtract #14.2
Nothing selected
> show #14.2 models
> hide #14.2 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #14.2 models
> hide #14.2 models
> close #14
> show #!15 models
> close #10-11
> undo
[Repeated 1 time(s)]
> show #!15 models
> view orient
[Repeated 1 time(s)]
> graphics silhouettes true
> graphics silhouettes false
> select #18.4/A:131
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
110 atoms, 110 bonds, 6 residues, 1 model selected
> select up
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> select down
110 atoms, 110 bonds, 6 residues, 1 model selected
> select down
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
110 atoms, 110 bonds, 6 residues, 1 model selected
> select up
4944 atoms, 4999 bonds, 299 residues, 1 model selected
> view matrix models
> #18.4,0.33059,-0.9401,0.083174,-321.53,0.901,0.34061,0.26866,0.84566,-0.2809,-0.013875,0.95964,76.706
> undo
> ui mousemode right rotate
> ui mousemode right "translate selected models"
> select add #17.4/A:118
4959 atoms, 5013 bonds, 300 residues, 2 models selected
> select add #18.3/A:113
4966 atoms, 5019 bonds, 301 residues, 3 models selected
> select add #9.8/A:82
4983 atoms, 5035 bonds, 302 residues, 4 models selected
> select add #9.9/B:87
5002 atoms, 5053 bonds, 303 residues, 5 models selected
> select add #9.8/B:85
5017 atoms, 5067 bonds, 304 residues, 5 models selected
> select add #9.9/A:89
5032 atoms, 5081 bonds, 305 residues, 5 models selected
> select add #15.4/A:85
5056 atoms, 5106 bonds, 306 residues, 6 models selected
> select add #15.3/A:576
5070 atoms, 5119 bonds, 307 residues, 7 models selected
> select add #18.3/A:26
5089 atoms, 5137 bonds, 308 residues, 7 models selected
> select up
11463 atoms, 11534 bonds, 684 residues, 7 models selected
> select up
54979 atoms, 55531 bonds, 3355 residues, 7 models selected
> select add #17.3/A:169
54995 atoms, 55546 bonds, 3356 residues, 8 models selected
> select up
55053 atoms, 55605 bonds, 3359 residues, 8 models selected
> select up
65458 atoms, 66116 bonds, 3992 residues, 8 models selected
> select add #17.5/A:165
65472 atoms, 66129 bonds, 3993 residues, 9 models selected
> select up
65659 atoms, 66318 bonds, 4003 residues, 9 models selected
> select up
75937 atoms, 76701 bonds, 4629 residues, 9 models selected
> select up
173825 atoms, 175429 bonds, 10369 residues, 23 models selected
> select up
318221 atoms, 321337 bonds, 19469 residues, 37 models selected
> select down
173825 atoms, 175429 bonds, 10369 residues, 23 models selected
> select down
75937 atoms, 76701 bonds, 4629 residues, 9 models selected
> hide #12.3 models
> select ~sel
526906 atoms, 532214 bonds, 46 pseudobonds, 37009 residues, 79 models selected
> select subtract #13
517056 atoms, 522264 bonds, 46 pseudobonds, 35789 residues, 78 models selected
> cartoon hide (#9.1-7,10-16#15.1-2,5-16#17.1-2,6-16#18.1-2,5-16#!16 & sel)
> hide (#9.1-7,10-16#15.1-2,5-16#17.1-2,6-16#18.1-2,5-16#!16 & sel) target a
> select clear
Drag select of 747 residues
> select clear
> select #15.3/A:581
20 atoms, 20 bonds, 1 residue, 1 model selected
> select add #18.3/A:26
39 atoms, 38 bonds, 2 residues, 2 models selected
> select add #17.3/A:115
50 atoms, 48 bonds, 3 residues, 3 models selected
> select add #9.8/B:84
69 atoms, 66 bonds, 4 residues, 4 models selected
> select add #9.8/A:89
84 atoms, 80 bonds, 5 residues, 4 models selected
> select up
3293 atoms, 3300 bonds, 194 residues, 4 models selected
> select up
32729 atoms, 33058 bonds, 1996 residues, 4 models selected
> cartoon hide sel
> hide sel target a
> select clear
Drag select of 4609 residues, 19 atoms, 18 bonds
> hide sel target ab
> select clear
> sym clear #13
> sym #13 C16 center #9 copies true
Made 16 copies for FliL symmetry C16
> select #10.3/D:131
11 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 4852 residues
> select up
61749 atoms, 29315 bonds, 4928 residues, 7 models selected
> select up
62536 atoms, 30109 bonds, 5025 residues, 7 models selected
> select ~sel
697907 atoms, 704948 bonds, 46 pseudobonds, 56133 residues, 99 models selected
> cartoon hide
> (#9.1-8,10-16#10.1-3,5-16#15.1-3,5-16#17.1-3,6-16#18.1-3,5-16#!16 & sel)
> select add #18.4
702851 atoms, 709947 bonds, 46 pseudobonds, 56432 residues, 100 models
selected
> select clear
> select add #15
165024 atoms, 166752 bonds, 10400 residues, 17 models selected
> select add #18
244128 atoms, 246736 bonds, 15184 residues, 34 models selected
> select subtract #18
165024 atoms, 166752 bonds, 10400 residues, 17 models selected
> select add #18.3
169968 atoms, 171751 bonds, 10699 residues, 18 models selected
> select add #18.5
174912 atoms, 176750 bonds, 10998 residues, 19 models selected
> select add #9.8
181904 atoms, 183802 bonds, 11408 residues, 20 models selected
> select add #9.10
188896 atoms, 190854 bonds, 11818 residues, 21 models selected
> select subtract #15
23872 atoms, 24102 bonds, 1418 residues, 4 models selected
> select add #15.3
34186 atoms, 34524 bonds, 2068 residues, 5 models selected
> select add #15.5
44500 atoms, 44946 bonds, 2718 residues, 6 models selected
> cartoon sel
> select clear
> select #15.3/A:88
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #18.3/A:110
39 atoms, 38 bonds, 2 residues, 2 models selected
> select add #9.8/B:80
61 atoms, 59 bonds, 3 residues, 3 models selected
> select add #9.8/A:85
76 atoms, 73 bonds, 4 residues, 3 models selected
> select subtract #9.8/A:85
61 atoms, 59 bonds, 3 residues, 3 models selected
> select subtract #9.8/B:80
39 atoms, 38 bonds, 2 residues, 2 models selected
> select add #9.8/B:80
61 atoms, 59 bonds, 3 residues, 3 models selected
> select add #9.8/A:85
76 atoms, 73 bonds, 4 residues, 3 models selected
> select up
3198 atoms, 3207 bonds, 188 residues, 3 models selected
> select up
22250 atoms, 22473 bonds, 1359 residues, 3 models selected
> cartoon hide sel
> select add #17.6
32729 atoms, 33058 bonds, 1996 residues, 4 models selected
> cartoon sel
> cartoon hide sel
> select clear
> select add #17.6
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> cartoon sel
> select clear
> select #17.4/A:394
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
275 atoms, 277 bonds, 16 residues, 1 model selected
> select up
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> cartoon hide sel
> select clear
> show #!6 models
> hide #!6 models
> show #!8 models
> show #!6 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!6 models
> select #10.3/F:174
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select add #10.3/F:102
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #15.4/A:301
23 atoms, 21 bonds, 2 residues, 2 models selected
> select add #18.4/A:205
44 atoms, 42 bonds, 3 residues, 3 models selected
> select add #17.5/A:617
60 atoms, 57 bonds, 4 residues, 4 models selected
> select add #9.9/B:73
75 atoms, 71 bonds, 5 residues, 5 models selected
> select add #9.9/A:74
99 atoms, 94 bonds, 6 residues, 5 models selected
> select up
3176 atoms, 3182 bonds, 193 residues, 5 models selected
> select up
33528 atoms, 33865 bonds, 2094 residues, 5 models selected
> cartoon hide sel
> select clear
> select #10.3/D:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
100 atoms, 100 bonds, 11 residues, 1 model selected
> select up
799 atoms, 807 bonds, 98 residues, 1 model selected
> select up
9850 atoms, 9950 bonds, 1220 residues, 1 model selected
> cartoon hide sel
> save "C:/Users/Jack Botting/Documents/Chimera/Images/motor rep unit1.jpg"
> width 2863 height 1180 supersample 3
> save "C:/Users/Jack Botting/Documents/Chimera/Images/motor rep unit2.jpg"
> width 2863 height 1180 supersample 3
> show #!8 models
> show #!6 models
> hide #!8 models
> select
760443 atoms, 768115 bonds, 46 pseudobonds, 61158 residues, 105 models
selected
> cartoon (#9.1-16#10.1-16#15.1-16#17.1-16#18.1-16#!16 & sel)
> select clear
> hide #!6 models
> select #10.16/E:174
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #15.1/A:310
29 atoms, 28 bonds, 2 residues, 2 models selected
> select add #18.1/A:293
43 atoms, 41 bonds, 3 residues, 3 models selected
> select add #9.6/A:71
59 atoms, 56 bonds, 4 residues, 4 models selected
> select add #9.6/B:69
83 atoms, 79 bonds, 5 residues, 4 models selected
> select add #17.2/A:488
102 atoms, 97 bonds, 6 residues, 5 models selected
> select up
3343 atoms, 3352 bonds, 201 residues, 5 models selected
> select up
33528 atoms, 33865 bonds, 2094 residues, 5 models selected
> select up
42579 atoms, 43008 bonds, 3216 residues, 5 models selected
> select add #17.1/A:165
42593 atoms, 43021 bonds, 3217 residues, 6 models selected
> select up
42780 atoms, 43210 bonds, 3227 residues, 6 models selected
> select up
53058 atoms, 53593 bonds, 3853 residues, 6 models selected
> select ~sel
707385 atoms, 714522 bonds, 46 pseudobonds, 57305 residues, 99 models selected
> cartoon hide (#9.1-5,7-16#10.1-15#15.2-16#17.3-16#18.2-16#!16 & sel)
> show #!6 models
> select clear
> select #17.1/A:158
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
201 atoms, 202 bonds, 11 residues, 1 model selected
> select up
10479 atoms, 10585 bonds, 637 residues, 1 model selected
> cartoon hide sel
> hide #!18 models
> hide #!9 models
> hide #!10 models
> save "C:/Users/Jack Botting/Documents/Chimera/Images/unassigned
> density_58-236.jpg" width 2863 height 1180 supersample 3
> hide #!6 models
> show #!9 models
> select
760443 atoms, 768115 bonds, 46 pseudobonds, 61158 residues, 105 models
selected
> cartoon (#9.1-16#15.1-16#17.1-16#!16 & sel)
> select clear
> hide #!17 models
> hide #!15 models
Drag select of 13460 residues, 46 pseudobonds
> select add #9
166382 atoms, 112832 bonds, 46 pseudobonds, 13460 residues, 19 models selected
> select subtract #9
54510 atoms, 46 pseudobonds, 6900 residues, 2 models selected
> select add #9
166382 atoms, 112832 bonds, 46 pseudobonds, 13460 residues, 19 models selected
> select add #16
166382 atoms, 167848 bonds, 46 pseudobonds, 13460 residues, 19 models selected
> surface (#9.1-16#!16 & sel)
> select clear
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> view orient
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select add #16
54510 atoms, 55016 bonds, 46 pseudobonds, 6900 residues, 2 models selected
> view matrix models
> #16,0.99955,-0.0085215,0.028701,-261,0.0086928,0.99995,-0.005851,-0.18467,-0.028649,0.0060979,0.99957,-71.121
> select clear
> show #!8 models
> hide #!8 models
> ui tool show "Surface Color"
> save "C:/Users/Jack Botting/Documents/Chimera/Images/FlbB-RBM3 surface
> top.jpg" width 2863 height 1180 supersample 3
> save "C:/Users/Jack Botting/Documents/Chimera/Images/FlbB-RBM3 surface
> tilt.jpg" width 2863 height 1180 supersample 3
> select add #9
111872 atoms, 112832 bonds, 6560 residues, 49 models selected
> preset apply int 3
No preset name matches 'apply int 3'
> ui tool show "Render By Attribute"
> mlp #9
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.58, mean
0.01426, maximum 27.41
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -26.83, mean
-0.179, maximum 24.12
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.29, mean
-0.06388, maximum 25.99
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -26.71, mean
-0.1625, maximum 24.16
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.04, mean
-0.06077, maximum 25.62
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -26.84, mean
-0.1249, maximum 24.55
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.76, mean
-0.02788, maximum 24.38
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.96, mean
-0.148, maximum 23.87
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.97, mean
-0.05591, maximum 23.63
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.65, mean
-0.1789, maximum 23.56
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.06, mean
-0.01454, maximum 26.73
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.57, mean
-0.1655, maximum 24.09
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.03, mean
-0.06536, maximum 24.78
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.14, mean
-0.1513, maximum 23.68
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.44, mean
-0.0357, maximum 23.74
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.85, mean
-0.1753, maximum 23.95
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.99, mean
0.002005, maximum 24.15
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -28.25, mean
-0.1699, maximum 23.78
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.7, mean
-0.04827, maximum 23.29
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.63, mean
-0.1771, maximum 23.47
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.38, mean
-0.02141, maximum 23.71
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -27.48, mean
-0.1804, maximum 23.79
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.21, mean
-0.05091, maximum 23.44
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -26.79, mean
-0.1449, maximum 24.02
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.96, mean
-0.02683, maximum 26.68
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -26.79, mean
-0.1565, maximum 23.77
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.59, mean
-0.04363, maximum 23.28
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.78, mean
-0.1388, maximum 24
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.17, mean
-0.02852, maximum 24.1
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.54, mean
-0.1729, maximum 24.59
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.13, mean
-0.01706, maximum 25.49
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -28.09, mean
-0.1651, maximum 23.9
> select clear
> save "C:/Users/Jack Botting/Documents/Chimera/Images/FlbB-RBM3 surface tilt
> hydrophobicity.jpg" width 2863 height 1180 supersample 3
> select
760443 atoms, 768115 bonds, 46 pseudobonds, 61158 residues, 183 models
selected
> surface hidePatches (#!16#!9.1-16 & sel)
> select clear
> hide #!16 models
> hide #!9 models
> set bgColor black
> show #!8 models
> show #!4 models
> show #13 models
> show #12.3 models
> hide #!8 models
> volume #4 level 0.4923
> hide #13 models
> show #!10 models
> select add #10
157600 atoms, 159200 bonds, 19520 residues, 17 models selected
> cartoon sel
> select clear
> ui tool show "Side View"
> view orient
> show #!8 models
> open "C:/Users/Jack Botting/Documents/alphafold
> results/Bb_0326_eacff/Bb_0326_eacff_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
Bb_0326_eacff_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #11
---
Chain | Description
A | No description available
> select add #11
15081 atoms, 15218 bonds, 931 residues, 1 model selected
> view matrix models #11,1,0,0,229.86,0,1,0,76.13,0,0,1,-9.4734
> view matrix models #11,1,0,0,389.64,0,1,0,122.03,0,0,1,-54.446
> hide #12.3 models
> hide #!12 models
> hide #!10 models
> hide #!4 models
> hide #!8 models
> select clear
> select #11 :1-320
5044 atoms, 5084 bonds, 320 residues, 1 model selected
> cartoon hide sel
> show #!8 models
> select clear
> select #11/A:480
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
215 atoms, 217 bonds, 13 residues, 1 model selected
> select up
15081 atoms, 15218 bonds, 931 residues, 1 model selected
> view matrix models #11,1,0,0,176.65,0,1,0,279.64,0,0,1,57.33
> show #!4 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!10 models
> view orient
> set bgColor gray
> set bgColor black
> show #!8 models
> hide #!8 models
> show #!8 models
> view matrix models #11,1,0,0,190.39,0,1,0,122.06,0,0,1,57.33
Drag select of 36 residues
> view matrix models
> #11,0.90612,-0.42302,0,190.36,0.42302,0.90612,0,125.44,0,0,1,57.33
> select up
1530 atoms, 1541 bonds, 92 residues, 1 model selected
> select up
15081 atoms, 15218 bonds, 931 residues, 1 model selected
> view matrix models
> #11,0.90612,-0.42302,0,181.55,0.42302,0.90612,0,85.434,0,0,1,57.33
> view matrix models
> #11,0.42079,-0.90716,0,178.64,0.90716,0.42079,0,89.917,0,0,1,57.33
> view matrix models
> #11,0.98987,-0.14201,0,181.74,0.14201,0.98987,0,83.153,0,0,1,57.33
> view matrix models
> #11,-0.0584,-0.33187,0.94152,169.23,-0.80867,0.56874,0.15031,75.811,-0.58536,-0.75259,-0.30158,60.738
> view matrix models
> #11,-0.0584,-0.33187,0.94152,97.007,-0.80867,0.56874,0.15031,57.073,-0.58536,-0.75259,-0.30158,60.738
> view matrix models
> #11,-0.56233,0.23489,0.79285,93,-0.68992,0.39528,-0.60643,62.13,-0.45585,-0.88802,-0.060219,60.713
> view matrix models
> #11,0.12301,-0.12986,0.98387,97.847,-0.88152,0.44109,0.16843,56.631,-0.45585,-0.88802,-0.060219,60.713
> lighting soft
> hide #!8 models
> hide #!4 models
> surface sel
> select add #10
172681 atoms, 174418 bonds, 20451 residues, 19 models selected
> surface (#10.1-16#!11 & sel)
> lighting soft
> set bgColor white
> color (#!11#!10.1-16 & sel) cornflower blue
> select subtract #10
15081 atoms, 15218 bonds, 931 residues, 322 models selected
> hide #!10 models
> hide #!11 models
> show #!8 models
> show #!18 models
> hide #!8 models
> show #!6 models
> set bgColor black
> show #!8 models
> show #!15 models
> hide #!6 models
> hide #!8 models
> show #!6 models
> show #!17 models
> show #!8 models
> hide #!6 models
> select subtract #11
1 model selected
> show #13 models
> hide #13 models
> show #!10 models
> lighting simple
> select add #10
157600 atoms, 159200 bonds, 19520 residues, 17 models selected
> surface hidePatches (#!10.1-16 & sel)
> ui tool show "Segment Map"
> select clear
> select add #11
15081 atoms, 15218 bonds, 931 residues, 1 model selected
> select subtract #11
1 model selected
> select add #10
157600 atoms, 159200 bonds, 19520 residues, 17 models selected
> color (#!10.1-16 & sel) white
> select clear
Segmenting WTCC-stator-msk-4.2A.mrc, density threshold 0.032070
Only showing 60 of 107 regions.
Showing 60 of 107 region surfaces
2613 watershed regions, grouped to 107 regions
Showing WTCC-stator-msk-4.2A.seg - 107 regions, 60 surfaces
> close #14
> save "C:/Users/Jack Botting/Documents/Chimera/Saved
> Sessions/Bb_modeling.cxs"
——— End of log from Mon Jul 24 11:23:42 2023 ———
opened ChimeraX session
> hide #!8 models
> select add #10
157600 atoms, 159200 bonds, 19520 residues, 17 models selected
> color (#!10.1-16 & sel) purple
> select subtract #10
320 models selected
> select add #18
79104 atoms, 79984 bonds, 4784 residues, 17 models selected
> color sel cyan
> select add #17
246768 atoms, 249344 bonds, 14976 residues, 34 models selected
> select subtract #18
167664 atoms, 169360 bonds, 10192 residues, 17 models selected
> color sel lime
> select add #16
222174 atoms, 224376 bonds, 46 pseudobonds, 17092 residues, 19 models selected
> select subtract #17
54510 atoms, 55016 bonds, 46 pseudobonds, 6900 residues, 48 models selected
> show #!16 models
> color (#!16 & sel) red
> select subtract #16
46 models selected
> select add #9
111872 atoms, 112832 bonds, 6560 residues, 17 models selected
> show #!9 models
> select clear
> select add #9.3/B:80
22 atoms, 21 bonds, 1 residue, 1 model selected
> select add #9.2/B:82
39 atoms, 37 bonds, 2 residues, 3 models selected
> select add #9.1/B:87
58 atoms, 55 bonds, 3 residues, 5 models selected
> select add #9.16/B:86
80 atoms, 76 bonds, 4 residues, 7 models selected
> select add #9.15/B:84
99 atoms, 94 bonds, 5 residues, 9 models selected
> select add #9.14/B:84
118 atoms, 112 bonds, 6 residues, 10 models selected
> select add #9.13/B:87
137 atoms, 130 bonds, 7 residues, 13 models selected
> select add #9.12/B:87
156 atoms, 148 bonds, 8 residues, 14 models selected
> select add #9.11/B:89
171 atoms, 162 bonds, 9 residues, 17 models selected
> select add #9.10/B:94
193 atoms, 183 bonds, 10 residues, 18 models selected
> select add #9.9/B:119
212 atoms, 201 bonds, 11 residues, 21 models selected
> select add #9.8/B:119
231 atoms, 219 bonds, 12 residues, 23 models selected
> select add #9.5/B:86
253 atoms, 240 bonds, 13 residues, 25 models selected
> select add #9.4/B:83
270 atoms, 256 bonds, 14 residues, 27 models selected
> select up
19796 atoms, 19838 bonds, 1162 residues, 28 models selected
> select up
48944 atoms, 49364 bonds, 2870 residues, 28 models selected
> color (#!9.1-5,8-16 & sel) orange
> select clear
> select #9.4/A:78
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #9.3/A:82
29 atoms, 27 bonds, 2 residues, 3 models selected
> select add #9.2/A:85
44 atoms, 41 bonds, 3 residues, 5 models selected
> select add #9.1/A:89
59 atoms, 55 bonds, 4 residues, 6 models selected
> select add #9.16/A:89
74 atoms, 69 bonds, 5 residues, 9 models selected
> select add #9.15/A:93
93 atoms, 87 bonds, 6 residues, 10 models selected
> select add #9.14/A:93
112 atoms, 105 bonds, 7 residues, 13 models selected
> select add #9.13/A:96
124 atoms, 116 bonds, 8 residues, 14 models selected
> select add #9.12/A:97
135 atoms, 126 bonds, 9 residues, 15 models selected
> select add #9.11/A:97
146 atoms, 136 bonds, 10 residues, 19 models selected
> select add #9.9/A:126
167 atoms, 157 bonds, 11 residues, 20 models selected
> select add #9.8/A:129
182 atoms, 171 bonds, 12 residues, 23 models selected
> select add #9.7/A:132
196 atoms, 184 bonds, 13 residues, 24 models selected
> select add #16/q:435
202 atoms, 189 bonds, 14 residues, 25 models selected
> select add #9.5/A:128
214 atoms, 200 bonds, 15 residues, 29 models selected
> select add #9.4/A:129
229 atoms, 214 bonds, 16 residues, 29 models selected
> select up
19826 atoms, 19869 bonds, 1166 residues, 30 models selected
> select up
49231 atoms, 49654 bonds, 2907 residues, 30 models selected
> color (#!16#!9.1-5,7-9,11-16 & sel) yellow
> select clear
> select add #17
167664 atoms, 169360 bonds, 10192 residues, 17 models selected
> color sel forest green
> select clear
> select #9.6/B:83
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #9.6/A:85
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
1414 atoms, 1417 bonds, 83 residues, 2 models selected
> select up
3496 atoms, 3526 bonds, 205 residues, 2 models selected
> select up
6992 atoms, 7052 bonds, 410 residues, 2 models selected
> select down
3496 atoms, 3526 bonds, 205 residues, 3 models selected
> color (#!9.6 & sel) yellow
> select #9.6/B:83
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
1414 atoms, 1417 bonds, 83 residues, 2 models selected
> select up
3496 atoms, 3526 bonds, 205 residues, 2 models selected
> color (#!9.6 & sel) orange
> select add #18
82600 atoms, 83510 bonds, 4989 residues, 19 models selected
> cartoon (#18.1-16#!9.6 & sel)
> select clear
> view orient
> set bgColor white
> lighting soft
> save "C:/Users/Jack Botting/Documents/Chimera/Saved
> Sessions/Bb_modeling.cxs"
> hide #!10 models
> hide #!15 models
> hide #!18 models
> hide #!17 models
> select #9.10/A:118
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
1414 atoms, 1417 bonds, 83 residues, 2 models selected
> select up
3496 atoms, 3526 bonds, 205 residues, 2 models selected
> color (#!9.10 & sel) yellow
> select clear
> select #9.7/B:116
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
1414 atoms, 1417 bonds, 83 residues, 2 models selected
> select up
3496 atoms, 3526 bonds, 205 residues, 2 models selected
> color (#!9.7 & sel) orange
> select #9/B
55936 atoms, 56416 bonds, 3280 residues, 16 models selected
> color (#!9.1-16 & sel) #ffaa00ff
> color (#!9.1-16 & sel) #fea900ff
> color (#!9.1-16 & sel) #e59900ff
> color (#!9.1-16 & sel) #dd9300ff
> select clear
> view orient
> surface #9,16
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> save "C:/Users/Jack Botting/Documents/Chimera/Images/FlbB-RBM3 surface
> top.jpg" width 2809 height 1156 supersample 3
> save "C:/Users/Jack Botting/Documents/Chimera/Images/FlbB-RBM3 surface
> tilt.jpg" width 2809 height 1156 supersample 3
> toolshed show
> mlp #!16#!9.1-16
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.06, mean
-0.01454, maximum 26.73
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.57, mean
-0.1655, maximum 24.09
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.58, mean
0.01426, maximum 27.41
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -26.83, mean
-0.179, maximum 24.12
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.99, mean
0.002005, maximum 24.15
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -28.25, mean
-0.1699, maximum 23.78
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.7, mean
-0.04827, maximum 23.29
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.63, mean
-0.1771, maximum 23.47
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.04, mean
-0.06077, maximum 25.62
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -26.84, mean
-0.1249, maximum 24.55
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.21, mean
-0.05091, maximum 23.44
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -26.79, mean
-0.1449, maximum 24.02
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.97, mean
-0.05591, maximum 23.63
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.65, mean
-0.1789, maximum 23.56
Map values for surface "MS ring RBM3_C SES surface": minimum -27.96, mean
-6.184, maximum 23.63
Map values for surface "MS ring RBM3_D SES surface": minimum -28.14, mean
-6.247, maximum 24.2
Map values for surface "MS ring RBM3_E SES surface": minimum -28.74, mean
-6.19, maximum 23.8
Map values for surface "MS ring RBM3_F SES surface": minimum -29.05, mean
-6.1, maximum 23.41
Map values for surface "MS ring RBM3_G SES surface": minimum -28.51, mean
-6.177, maximum 23.36
Map values for surface "MS ring RBM3_H SES surface": minimum -28.22, mean
-6.073, maximum 24.57
Map values for surface "MS ring RBM3_I SES surface": minimum -29.18, mean
-6.139, maximum 24.28
Map values for surface "MS ring RBM3_J SES surface": minimum -28.9, mean
-6.141, maximum 24.45
Map values for surface "MS ring RBM3_K SES surface": minimum -28.94, mean
-6.126, maximum 23.95
Map values for surface "MS ring RBM3_L SES surface": minimum -28.37, mean
-6.148, maximum 24.05
Map values for surface "MS ring RBM3_M SES surface": minimum -28.26, mean
-6.219, maximum 24.19
Map values for surface "MS ring RBM3_N SES surface": minimum -29.43, mean
-6.191, maximum 23.61
Map values for surface "MS ring RBM3_O SES surface": minimum -28.7, mean
-6.196, maximum 23.56
Map values for surface "MS ring RBM3_P SES surface": minimum -28.15, mean
-6.185, maximum 23.12
Map values for surface "MS ring RBM3_Q SES surface": minimum -28.18, mean
-6.198, maximum 23.97
Map values for surface "MS ring RBM3_R SES surface": minimum -28.39, mean
-6.176, maximum 23.48
Map values for surface "MS ring RBM3_S SES surface": minimum -29.86, mean
-6.197, maximum 24.03
Map values for surface "MS ring RBM3_T SES surface": minimum -29.44, mean
-6.129, maximum 24.48
Map values for surface "MS ring RBM3_U SES surface": minimum -27.93, mean
-6.211, maximum 23.82
Map values for surface "MS ring RBM3_V SES surface": minimum -28.01, mean
-6.106, maximum 24.68
Map values for surface "MS ring RBM3_W SES surface": minimum -28.3, mean
-6.239, maximum 22.88
Map values for surface "MS ring RBM3_X SES surface": minimum -28.14, mean
-6.223, maximum 23.74
Map values for surface "MS ring RBM3_Y SES surface": minimum -28.67, mean
-6.131, maximum 24.81
Map values for surface "MS ring RBM3_Z SES surface": minimum -28.06, mean
-6.086, maximum 23.3
Map values for surface "MS ring RBM3_a SES surface": minimum -29.53, mean
-6.199, maximum 22.89
Map values for surface "MS ring RBM3_b SES surface": minimum -28.13, mean
-6.163, maximum 23.61
Map values for surface "MS ring RBM3_c SES surface": minimum -28.49, mean
-6.154, maximum 22.66
Map values for surface "MS ring RBM3_d SES surface": minimum -29.16, mean
-6.111, maximum 24.27
Map values for surface "MS ring RBM3_e SES surface": minimum -28.42, mean
-6.187, maximum 23.8
Map values for surface "MS ring RBM3_f SES surface": minimum -29.64, mean
-6.184, maximum 23.58
Map values for surface "MS ring RBM3_g SES surface": minimum -29.06, mean
-6.179, maximum 23.48
Map values for surface "MS ring RBM3_h SES surface": minimum -29.02, mean
-6.246, maximum 24.06
Map values for surface "MS ring RBM3_i SES surface": minimum -28.13, mean
-6.22, maximum 23.75
Map values for surface "MS ring RBM3_j SES surface": minimum -27.97, mean
-6.199, maximum 23.54
Map values for surface "MS ring RBM3_k SES surface": minimum -28.38, mean
-6.125, maximum 23.93
Map values for surface "MS ring RBM3_l SES surface": minimum -27.84, mean
-6.088, maximum 24.41
Map values for surface "MS ring RBM3_m SES surface": minimum -28.39, mean
-6.185, maximum 23.14
Map values for surface "MS ring RBM3_n SES surface": minimum -28.79, mean
-6.092, maximum 23.52
Map values for surface "MS ring RBM3_o SES surface": minimum -28.9, mean
-6.211, maximum 23.76
Map values for surface "MS ring RBM3_p SES surface": minimum -28.08, mean
-6.092, maximum 24.08
Map values for surface "MS ring RBM3_q SES surface": minimum -28.74, mean
-6.075, maximum 24.43
Map values for surface "MS ring RBM3_r SES surface": minimum -28.08, mean
-6.269, maximum 23.91
Map values for surface "MS ring RBM3_s SES surface": minimum -29.2, mean
-6.171, maximum 24.52
Map values for surface "MS ring RBM3_t SES surface": minimum -29.63, mean
-6.229, maximum 23.61
Map values for surface "MS ring RBM3_u SES surface": minimum -28.24, mean
-6.246, maximum 23.81
Map values for surface "MS ring RBM3_v SES surface": minimum -27.91, mean
-6.19, maximum 23.22
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.59, mean
-0.04363, maximum 23.28
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.78, mean
-0.1388, maximum 24
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.29, mean
-0.06388, maximum 25.99
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -26.71, mean
-0.1625, maximum 24.16
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.03, mean
-0.06536, maximum 24.78
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.14, mean
-0.1513, maximum 23.68
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.44, mean
-0.0357, maximum 23.74
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.85, mean
-0.1753, maximum 23.95
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.76, mean
-0.02788, maximum 24.38
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.96, mean
-0.148, maximum 23.87
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.96, mean
-0.02683, maximum 26.68
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -26.79, mean
-0.1565, maximum 23.77
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.38, mean
-0.02141, maximum 23.71
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -27.48, mean
-0.1804, maximum 23.79
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -26.13, mean
-0.01706, maximum 25.49
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -28.09, mean
-0.1651, maximum 23.9
Map values for surface "Bb_0286 ring.pdb_A SES surface": minimum -27.17, mean
-0.02852, maximum 24.1
Map values for surface "Bb_0286 ring.pdb_B SES surface": minimum -25.54, mean
-0.1729, maximum 24.59
To also show corresponding color key, enter the above mlp command and add key
true
> select #16/V:304@CG1
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
40 atoms, 39 bonds, 5 residues, 2 models selected
> select add #16
54510 atoms, 55016 bonds, 46 pseudobonds, 6900 residues, 3 models selected
> select clear
> select add #16
54510 atoms, 55016 bonds, 46 pseudobonds, 6900 residues, 2 models selected
> color (#!16 & sel) red
> select clear
> save "C:/Users/Jack Botting/Documents/Chimera/Images/FlbB-RBM3 surface side
> hydrophobicity.jpg" width 2809 height 1156 supersample 3
> hide #!16 models
> show #!16 models
> hide #9.1.1 models
> select add #9
111872 atoms, 112832 bonds, 6560 residues, 17 models selected
> surface hidePatches (#!9.1-16 & sel)
> hide #9.1#!9#!9.2-16 target m
> select subtract #9
32 models selected
> hide #!16 models
> show #!9.1 models
> save "C:/Users/Jack Botting/Documents/Chimera/Saved
> Sessions/Bb_modeling.cxs"
——— End of log from Mon Jul 24 16:28:43 2023 ———
opened ChimeraX session
> open "C:/Users/Jack Botting/Documents/alphafold
> results/FlbBNtermdimer_8df73/FlbBNtermdimer_8df73_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"
Chain information for
FlbBNtermdimer_8df73_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#14
---
Chain | Description
A B | No description available
> select add #14
2676 atoms, 2714 bonds, 154 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #14,1,0,0,-120.57,0,1,0,-181.38,0,0,1,-2.6158
> view matrix models
> #14,0.91451,-0.0043031,-0.40454,-122.47,0.3807,0.34749,0.85693,-182.22,0.13688,-0.93768,0.31942,-12.637
> view matrix models
> #14,0.89768,-0.24516,-0.36615,-124.31,0.37448,-0.013488,0.92714,-184.89,-0.23224,-0.96939,0.079702,-14.817
> view matrix models
> #14,0.90133,-0.23041,-0.36675,-124.18,0.37883,0.0089108,0.92542,-184.7,-0.20996,-0.97305,0.095319,-14.726
> view matrix models
> #14,0.7948,0.016559,-0.60665,-123.42,0.60437,-0.11228,0.78875,-185.66,-0.055055,-0.99354,-0.09925,-15.283
> surface sel
> mlp sel
Map values for surface
"FlbBNtermdimer_8df73_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A
SES surface": minimum -23.5, mean 2.25, maximum 25.6
Map values for surface
"FlbBNtermdimer_8df73_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B
SES surface": minimum -24.13, mean 2.246, maximum 24.96
To also show corresponding color key, enter the above mlp command and add key
true
> view matrix models
> #14,0.7948,0.016559,-0.60665,-134.91,0.60437,-0.11228,0.78875,-203.07,-0.055055,-0.99354,-0.09925,-12.991
> view matrix models
> #14,0.72276,-0.21305,-0.65744,-137.06,0.51684,-0.46491,0.71884,-206.29,-0.4588,-0.85934,-0.22591,-13.491
> view matrix models
> #14,0.44057,-0.19426,0.87645,-129.12,-0.89766,-0.084244,0.43256,-207.29,-0.01019,-0.97733,-0.21149,-13.441
> view matrix models
> #14,0.99796,-0.018032,-0.061212,-131.09,0.048848,-0.40135,0.91462,-205.85,-0.04106,-0.91575,-0.39965,-14.133
> surface hidePatches (#!14 & sel)
> view matrix models
> #14,0.99796,-0.018032,-0.061212,-172.29,0.048848,-0.40135,0.91462,-268.34,-0.04106,-0.91575,-0.39965,-5.1328
> view matrix models
> #14,0.97698,-0.18801,0.1008,-173.07,-0.14923,-0.26469,0.95272,-267.58,-0.15244,-0.94583,-0.28665,-5.2053
> hide #!14 models
> select subtract #14
2 models selected
> select #9.1:77,84,91,105,112
190 atoms, 180 bonds, 10 residues, 1 model selected
> show (#!9.1 & sel) target ab
> lighting soft
> select #9.1:1-56
1982 atoms, 2016 bonds, 112 residues, 1 model selected
> cartoon hide (#!9.1 & sel)
> save "C:/Users/Jack Botting/Documents/Chimera/Images/coiled coil
> residues.jpg" width 2160 height 905 supersample 3
> cartoon (#!9.1 & sel)
> hide (#!9.1 & sel) target a
> select #9.1/A:75
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #9.1/B:74
39 atoms, 37 bonds, 2 residues, 2 models selected
> select up
2828 atoms, 2834 bonds, 166 residues, 3 models selected
> hide (#!9.1 & sel) target a
> save "C:/Users/Jack Botting/Documents/Chimera/Images/FlbB dimer side.jpg"
> width 2160 height 905 supersample 3
> view matrix models
> #9.1,1,2.607e-16,7.5894e-18,3.8356,1.7673e-16,1,2.5153e-17,12.434,3.6863e-18,-2.4286e-17,1,1.2261
> select #9:197,168
1248 atoms, 1184 bonds, 64 residues, 16 models selected
> select clear
> select #9.1/A:197
24 atoms, 23 bonds, 1 residue, 1 model selected
> select add #9.1/B:169
39 atoms, 37 bonds, 2 residues, 2 models selected
> select #9.1/B:169
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #9.1/B:168
30 atoms, 28 bonds, 2 residues, 2 models selected
> select clear
> select #9.1/B:168
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #9.1/A:197
39 atoms, 37 bonds, 2 residues, 2 models selected
> show (#!9.1 & sel) target ab
> select clear
> save "C:/Users/Jack Botting/Documents/Chimera/Images/FlbB heads
> residues.jpg" width 2160 height 905 supersample 3
> select #9.1/A:197
24 atoms, 23 bonds, 1 residue, 1 model selected
> select add #9.1/B:168
39 atoms, 37 bonds, 2 residues, 2 models selected
> select up
426 atoms, 426 bonds, 25 residues, 3 models selected
> hide (#!9.1 & sel) target a
> select clear
> show #!15 models
> show #!16 models
> show #!17 models
> show #!18 models
> show #!9.2 models
> show #!9.3-16 target m
> select #9.1/A:192
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add #9.1/B:200
21 atoms, 19 bonds, 2 residues, 2 models selected
> select up
248 atoms, 246 bonds, 15 residues, 3 models selected
> select up
6992 atoms, 7052 bonds, 410 residues, 3 models selected
> view orient
> view matrix models
> #9.1,1,2.7868e-16,8.2399e-18,-5.1922,1.8886e-16,1,2.6888e-17,-0.42304,3.6863e-18,-2.4286e-17,1,1.1651
> view matrix models
> #9.1,1,2.9667e-16,8.6736e-18,0.35351,2.0099e-16,1,2.8623e-17,4.7835,3.6863e-18,-2.4286e-17,1,1.1867
> view matrix models
> #9.1,1,3.2366e-16,9.1073e-18,-2.5652,2.1916e-16,1,3.1225e-17,-2.9141,4.5536e-18,-2.4286e-17,1,1.1461
> hide #!17 models
> hide #!15 models
> view matrix models
> #9.1,1,3.6866e-16,1.0192e-17,-1.1679,2.494e-16,1,3.5562e-17,0.94818,5.421e-18,-2.4286e-17,1,1.1665
> view matrix models
> #9.1,1,3.9567e-16,1.1493e-17,-0.72475,2.6752e-16,1,3.8164e-17,0.75774,5.421e-18,-2.4286e-17,1,1.1647
> select clear
> close session
> open "C:\Users\Jack Botting\Documents\Chimera\Saved Sessions\Bb624-stator-
> msk-4.2A.seg" format segger
Summary of feedback from opening C:\Users\Jack Botting\Documents\Chimera\Saved
Sessions\Bb624-stator-msk-4.2A.seg
---
notes | Opened BbWT-FlbB-256-2.7A.mrc as #1, grid size 256,256,256, pixel 2.7,
shown at level 3.99, step 1, values float32
Only showing 60 of 1606 regions.
Showing 60 of 1606 region surfaces
Opened Bb624-stator-msk-4.2A.seg
Showing Bb624-stator-msk-4.2A.seg - 1606 regions, 60 surfaces
> hide #!1 models
> open "C:/Users/Jack Botting/Documents/alphafold
> results/Bb_0236_50bac/Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3
---
Chain | Description
A | No description available
> split #3 atoms :1-18
Split Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb (#3)
into 2 models
Chain information for
Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb 1 #3.1
---
Chain | Description
A | No description available
Chain information for
Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb 2 #3.2
---
Chain | Description
A | No description available
> hide #3.1 models
> show #3.1 models
> close #3.1
> select #2.47
1 model selected
Simulating map res 4.000, grid 2.000
> molmap #3.2 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false
Opened Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb 2
map 4 as #4, grid size 40,46,64, pixel 2, shown at level 0.115, step 1, values
float32
Making groups around 1 regions - target vol 72064.000, b-Rad 57.905
Making groups around 1 regions
Fitting Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb 2
map 4 to 12/12 groups...
Fitting to group 1/12, dVolume 0.0587, 1 regions
Fitting to group 2/12, dVolume 0.3864, 2 regions
Fitting to group 3/12, dVolume 0.3894, 2 regions
Fitting to group 4/12, dVolume 0.4547, 2 regions
Fitting to group 5/12, dVolume 0.4703, 2 regions
Fitting to group 6/12, dVolume 0.4787, 2 regions
Fitting to group 7/12, dVolume 0.4815, 2 regions
Fitting to group 8/12, dVolume 0.6552, 3 regions
Fitting to group 9/12, dVolume 0.6819, 3 regions
Fitting to group 10/12, dVolume 0.7240, 2 regions
Fitting to group 11/12, dVolume 0.7360, 3 regions
Fitting to group 12/12, dVolume 0.7379, 2 regions
Best cross-correlation: 0.6604
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit
self.Fit()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit
func()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2571, in
FitMapToRegionsAroundSel
self.FitMapToGroupsAround ( fmap, smod, regs, dmap )
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2541, in FitMapToGroupsAround
self.cfits.sort()
TypeError: '<' not supported between instances of 'Place' and 'Place'
TypeError: '
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2541, in FitMapToGroupsAround
self.cfits.sort()
See log for complete Python traceback.
Making groups around 1 regions - target vol 72064.000, b-Rad 57.905
Making groups around 1 regions
Fitting Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb 2
map 4 to 12/12 groups...
Fitting to group 1/12, dVolume 0.0587, 1 regions
Fitting to group 2/12, dVolume 0.3864, 2 regions
Fitting to group 3/12, dVolume 0.3894, 2 regions
Fitting to group 4/12, dVolume 0.4547, 2 regions
Fitting to group 5/12, dVolume 0.4703, 2 regions
Fitting to group 6/12, dVolume 0.4787, 2 regions
Fitting to group 7/12, dVolume 0.4815, 2 regions
Fitting to group 8/12, dVolume 0.6552, 3 regions
Fitting to group 9/12, dVolume 0.6819, 3 regions
Fitting to group 10/12, dVolume 0.7240, 2 regions
Fitting to group 11/12, dVolume 0.7360, 3 regions
Fitting to group 12/12, dVolume 0.7379, 2 regions
Best cross-correlation: 0.6603
Top score: 0.66034, z-score: 1.66942 (avg: 0.6107, stdev: 0.0297)
Found 2 regions overlapping
Opened BbWT-FlbB-256-2.7A_masked as #5, grid size 256,256,256, pixel 2.7,
shown at step 1, values float32
Cross-correlation of fit: 0.633797
Top score: 0.63380, z-score: 1.16442 (avg: 0.5742, stdev: 0.0512)
> select /A:290
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
92 atoms, 92 bonds, 6 residues, 1 model selected
> select up
10314 atoms, 10422 bonds, 650 residues, 1 model selected
Overlapping 10314 atoms with 1606 regions
Selected 2 regions
Ungrouped to 5 regions, but did not show all surfaces, see Options
Grouped 3 regions
Ungrouped to 3 regions
Overlapping 10314 atoms with 1609 regions
Selected 4 regions
Ungrouped to 2 regions
Ungrouped to 0 regions
Overlapping 10314 atoms with 1610 regions
Selected 5 regions
Grouped 5 regions
> select #2.25
1 model selected
> select add #2.19
2 models selected
> select add #2.54
3 models selected
> select add #2.24
4 models selected
> select add #2.59
5 models selected
> select add #2.31
6 models selected
> select add #2.35
7 models selected
> select add #2.27
8 models selected
> select add #2.18
9 models selected
> select add #2.53
10 models selected
> select add #2.22
11 models selected
> select add #2.57
12 models selected
> select add #2.30
13 models selected
> select add #2.34
14 models selected
> select add #2.26
15 models selected
> select add #2.17
16 models selected
> select add #2.55
17 models selected
> select add #2.21
18 models selected
> select add #2.56
19 models selected
> select add #2.29
20 models selected
> select add #2.33
21 models selected
> select add #2.28
22 models selected
> select add #2.20
23 models selected
> select add #2.52
24 models selected
> select add #2.23
25 models selected
> select add #2.58
26 models selected
> select add #2.32
27 models selected
> select add #2.36
28 models selected
> select #2.47
1 model selected
Opened BbWT-FlbB-256-2.7A_masked as #5, grid size 256,256,256, pixel 2.7,
shown at step 1, values float32
Cross-correlation of fit: 0.660362
Top score: 0.66036, z-score: 1.73708 (avg: 0.6603, stdev: 0.0000)
> open "C:/Users/Jack Botting/Documents/borrelia maps/Bb624-stator-
> msk-4.2A.mrc"
Opened Bb624-stator-msk-4.2A.mrc as #5, grid size 140,140,140, pixel 4.2,
shown at level 4.21, step 1, values float32
> ui tool show "Fit in Map"
> fitmap #5 inMap #1
Fit map Bb624-stator-msk-4.2A.mrc in map BbWT-FlbB-256-2.7A.mrc using 27426
points
correlation = 0.1851, correlation about mean = -0.00347, overlap = 5.359e+04
steps = 140, shift = 33.1, angle = 7.23 degrees
Position of Bb624-stator-msk-4.2A.mrc (#5) relative to BbWT-FlbB-256-2.7A.mrc
(#1) coordinates:
Matrix rotation and translation
0.99523604 0.00624983 -0.09729426 18.99804591
0.00153766 0.99681286 0.07976058 14.07808971
0.09748266 -0.07953020 0.99205447 29.27957999
Axis -0.63295500 -0.77396212 -0.01872421
Axis point -291.21577965 0.00000000 56.84335984
Rotation angle (degrees) 7.22875020
Shift along axis -23.46905341
> show #!1 models
> select add #5
3 models selected
> select add #2
63 models selected
> select subtract #2
2 models selected
> view matrix models
> #5,0.99524,0.0062498,-0.097294,202.8,0.0015377,0.99681,0.079761,24.072,0.097483,-0.07953,0.99205,97.104
> view matrix models
> #5,0.99524,0.0062498,-0.097294,204.64,0.0015377,0.99681,0.079761,22.696,0.097483,-0.07953,0.99205,-28.112
> view matrix models
> #5,0.99524,0.0062498,-0.097294,206.92,0.0015377,0.99681,0.079761,15.521,0.097483,-0.07953,0.99205,-26.897
> view matrix models
> #5,0.99524,0.0062498,-0.097294,250.87,0.0015377,0.99681,0.079761,0.89661,0.097483,-0.07953,0.99205,-15.3
> fitmap #5 inMap #1
Fit map Bb624-stator-msk-4.2A.mrc in map BbWT-FlbB-256-2.7A.mrc using 27426
points
correlation = 0.8949, correlation about mean = 0.3731, overlap = 5.466e+05
steps = 80, shift = 18.5, angle = 5.41 degrees
Position of Bb624-stator-msk-4.2A.mrc (#5) relative to BbWT-FlbB-256-2.7A.mrc
(#1) coordinates:
Matrix rotation and translation
0.99882865 0.00409670 -0.04821345 252.02576789
-0.00412211 0.99999141 -0.00042760 0.15048473
0.04821129 0.00062584 0.99883696 -36.22309521
Axis 0.01088495 -0.99632810 -0.08492255
Axis point 866.91674654 0.00000000 5204.94986276
Rotation angle (degrees) 2.77362891
Shift along axis 5.66951374
> volume #5 level 0.6418
> ui tool show "Side View"
> show #!4 models
> select add #4
4 models selected
> close #4
> select add #3
10314 atoms, 10422 bonds, 650 residues, 4 models selected
> view matrix models
> #3,1,0,0,74.358,0,1,0,-38.955,0,0,1,-1.5267,#5,0.99883,0.0040967,-0.048213,326.38,-0.0041221,0.99999,-0.0004276,-38.804,0.048211,0.00062584,0.99884,-37.75
> undo
> select add #5
10314 atoms, 10422 bonds, 650 residues, 5 models selected
> select subtract #5
10314 atoms, 10422 bonds, 650 residues, 2 models selected
> view matrix models #3,1,0,0,266.25,0,1,0,-198.74,0,0,1,12.477
> hide #!2 models
> volume #1 level 3.314
> volume #1 level 1.415
> hide #!1 models
> view matrix models #3,1,0,0,258.92,0,1,0,-203.72,0,0,1,13.208
> ui tool show "Fit in Map"
> fitmap #3.2 inMap #5
Fit molecule
Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb 2 (#3.2) to
map Bb624-stator-msk-4.2A.mrc (#5) using 10314 atoms
average map value = 4.756, steps = 76
shifted from previous position = 15.1
rotated from previous position = 48 degrees
atoms outside contour = 1196, contour level = 0.64185
Position of Bb_0236_50bac_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
2 (#3.2) relative to Bb624-stator-msk-4.2A.mrc (#5) coordinates:
Matrix rotation and translation
0.96182482 -0.27072534 -0.04001027 -275.13825099
0.27214502 0.96159421 0.03568862 232.42859175
0.02881183 -0.04521481 0.99856171 64.38863716
Axis -0.14625585 -0.12441543 0.98139188
Axis point -1005.85226284 -834.20944184 0.00000000
Rotation angle (degrees) 16.05630415
Shift along axis 74.51336026
Segmenting Bb624-stator-msk-4.2A.mrc, density threshold 0.641846
Showing 118 region surfaces
872 watershed regions, grouped to 118 regions
Showing Bb624-stator-msk-4.2A.seg - 118 regions, 118 surfaces
> select add #2
10314 atoms, 10422 bonds, 650 residues, 121 models selected
> view matrix models
> #3,1,0,0,292.38,0,1,0,-195.35,0,0,1,9.1772,#2,1,0,0,33.463,0,1,0,8.3692,0,0,1,-4.0309
> undo
> select subtract #3
119 models selected
> view matrix models #2,1,0,0,246.51,0,1,0,13.138,0,0,1,-8.3841
> view matrix models #2,1,0,0,239.97,0,1,0,6.7586,0,0,1,-49.519
> ui tool show "Side View"
> view matrix models #2,1,0,0,247.46,0,1,0,0.12356,0,0,1,-49.709
> view matrix models #2,1,0,0,248.43,0,1,0,-1.2621,0,0,1,-36.598
> view matrix models #2,1,0,0,245.71,0,1,0,-0.90776,0,0,1,-43.236
> view matrix models #2,1,0,0,246.35,0,1,0,1.312,0,0,1,-44.503
> select clear
> hide #!5 models
> select add #3
10314 atoms, 10422 bonds, 650 residues, 2 models selected
Overlapping 10314 atoms with 118 regions
Selected 1 regions
Ungrouped to 2 regions
Ungrouped to 3 regions
Ungrouped to 4 regions
Ungrouped to 0 regions
Overlapping 10314 atoms with 123 regions
Selected 6 regions
Grouped 6 regions
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit
self.Fit()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit
func()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1827, in FitToEachRegion
fmap.display = False
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 727, in _set_display
if display == self.display:
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit
self.Fit()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit
func()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1827, in FitToEachRegion
fmap.display = False
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 727, in _set_display
if display == self.display:
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit
self.Fit()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit
func()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1827, in FitToEachRegion
fmap.display = False
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 727, in _set_display
if display == self.display:
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit
self.Fit()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit
func()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1827, in FitToEachRegion
fmap.display = False
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 727, in _set_display
if display == self.display:
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit
self.Fit()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit
func()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1827, in FitToEachRegion
fmap.display = False
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 727, in _set_display
if display == self.display:
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit
self.Fit()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit
func()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1827, in FitToEachRegion
fmap.display = False
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 727, in _set_display
if display == self.display:
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
See log for complete Python traceback.
> select add #2
10314 atoms, 10422 bonds, 650 residues, 121 models selected
> select subtract #2
10314 atoms, 10422 bonds, 650 residues, 2 models selected
> view matrix models #3,1,0,0,255.23,0,1,0,-199.89,0,0,1,28.024
> select add #2
10314 atoms, 10422 bonds, 650 residues, 121 models selected
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit
self.Fit()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit
func()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1827, in FitToEachRegion
fmap.display = False
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 727, in _set_display
if display == self.display:
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
See log for complete Python traceback.
> select subtract #2
10314 atoms, 10422 bonds, 650 residues, 2 models selected
> view matrix models #3,1,0,0,259.69,0,1,0,-204.86,0,0,1,9.7637
> select #2.46
1 model selected
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit
self.Fit()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit
func()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1827, in FitToEachRegion
fmap.display = False
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 727, in _set_display
if display == self.display:
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
See log for complete Python traceback.
> select #2.70
1 model selected
> select /A:20
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
83 atoms, 82 bonds, 6 residues, 1 model selected
> select up
10314 atoms, 10422 bonds, 650 residues, 1 model selected
> select #2.46
1 model selected
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit
self.Fit()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit
func()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1827, in FitToEachRegion
fmap.display = False
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 727, in _set_display
if display == self.display:
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit
self.Fit()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit
func()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1827, in FitToEachRegion
fmap.display = False
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 727, in _set_display
if display == self.display:
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display
return self._any_displayed_positions and len(self._positions) > 0
See log for complete Python traceback.
OpenGL version: 3.3.0 Core Profile Context 22.20.26.08.221227
OpenGL renderer: AMD Radeon (TM) Graphics
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: HP
Model: HP ProBook 455 15.6 inch G9 Notebook PC
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 16,442,773,504
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5825U with Radeon Graphics
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-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: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
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-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
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: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Segger drawing is None |
comment:2 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
Fixed.
The user deleted the simulated map for an atomic model after fitting and then tried to fit again. The Segger code tried to used the deleted map. Made it create a new simulated map.