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Opened 20 months ago
Last modified 18 months ago
#14599 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild5_Current.cxs"
> format session
Opened postprocess_masked.mrc as #2, grid size 384,384,384, pixel 0.94, shown
at level 0.0177, step 2, values float32
Opened Rhom_22-Ring_v5.pdb map 2 as #3, grid size 203,203,379, pixel 0.667,
shown at level 0.15, step 1, values float32
Opened postprocess_masked.mrc masked as #1.1.1.1, grid size 136,136,260, pixel
0.94, shown at level 0.0302, step 1, values float32
Opened postprocess_masked.mrc masked gaussian as #1.1.1.2, grid size
136,136,260, pixel 0.94, shown at level 0.00208, step 1, values float32
Restoring stepper: Rhom_22-Ring_v5.pdb
Log from Fri Feb 16 17:32:49 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild5_Current.cxs"
Opened postprocess_masked.mrc as #2, grid size 384,384,384, pixel 0.94, shown
at level 0.0177, step 2, values float32
Opened Rhom_22-Ring_v5.pdb map 2 as #3, grid size 203,203,379, pixel 0.667,
shown at level 0.15, step 1, values float32
Opened postprocess_masked.mrc masked as #1.1.1.1, grid size 136,136,260, pixel
0.94, shown at level 0.0216, step 1, values float32
Opened postprocess_masked.mrc masked gaussian as #1.1.1.2, grid size
136,136,260, pixel 0.94, shown at level 0.00321, step 1, values float32
Restoring stepper: Rhom_22-Ring_v5.pdb
Log from Tue Feb 13 14:02:34 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
> format session
Opened PP234_Masked10A_2Ring.mrc as #1.1.1.1, grid size 138,139,259, pixel
0.94,0.94,0.94, shown at level 0.012, step 1, values float32
Opened PP234_Masked10A_2Ring.mrc gaussian as #1.1.1.2, grid size 138,139,259,
pixel 0.94,0.94,0.94, shown at level -0.000618, step 1, values float32
Restoring stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
Log from Mon Feb 12 16:01:42 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
> format session
Opened PP234_Masked10A_2Ring.mrc as #1.1.1.1, grid size 138,139,259, pixel
0.94,0.94,0.94, shown at level 0.012, step 1, values float32
Opened PP234_Masked10A_2Ring.mrc gaussian as #1.1.1.2, grid size 138,139,259,
pixel 0.94,0.94,0.94, shown at level -0.000618, step 1, values float32
Restoring stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
Log from Thu Feb 8 16:08:43 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
> format session
Opened PP234_Masked10A_2Ring.mrc as #1.1.1.1, grid size 138,139,259, pixel
0.94,0.94,0.94, shown at level 0.00872, step 1, values float32
Opened PP234_Masked10A_2Ring.mrc gaussian as #1.1.1.2, grid size 138,139,259,
pixel 0.94,0.94,0.94, shown at level -0.00154, step 1, values float32
Restoring stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
Log from Tue Feb 6 15:50:30 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
> format session
Opened PP234_Masked10A_2Ring.mrc as #1.1.1.1, grid size 138,139,259, pixel
0.94,0.94,0.94, shown at level 0.0257, step 1, values float32
Opened PP234_Masked10A_2Ring.mrc gaussian as #1.1.1.2, grid size 138,139,259,
pixel 0.94,0.94,0.94, shown at level 0.000339, step 1, values float32
Restoring stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
Log from Wed Jan 31 17:03:39 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
> format session
Opened PP234_Masked10A_2Ring.mrc as #1.1.1.1, grid size 138,139,259, pixel
0.94,0.94,0.94, shown at level 0.0257, step 1, values float32
Opened PP234_Masked10A_2Ring.mrc gaussian as #1.1.1.2, grid size 138,139,259,
pixel 0.94,0.94,0.94, shown at level 0.00427, step 1, values float32
Restoring stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
Log from Thu Jan 25 14:40:09 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Successfully installed
'ChimeraX_Clipper-0.22.3-cp311-cp311-macosx_10_13_universal2.whl'
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing
/Users/mbell/Library/Caches/ChimeraX/1.7/installers/ChimeraX_Clipper-0.22.3-cp311-cp311-macosx_10_13_universal2.whl
Requirement already satisfied: ChimeraX-Core~=1.7 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Clipper==0.22.3) (1.7)
Requirement already satisfied: ChimeraX-Atomic~=1.36 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Clipper==0.22.3) (1.49.1)
Requirement already satisfied: ChimeraX-AtomicLibrary~=12.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Clipper==0.22.3) (12.1.3)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Clipper==0.22.3) (1.1)
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.3) (2.0.1)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.3) (1.3)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.3) (1.1.1)
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.3) (2.12.1)
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.3) (2.0.3)
Requirement already satisfied: ChimeraX-PDB~=2.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.3) (2.7.3)
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.3) (1.0.3)
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.22.3) (1.2.3)
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.22.3) (1.13.1)
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.22.3) (1.5.1)
Requirement already satisfied: ChimeraX-Surface~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.22.3) (1.0.1)
Requirement already satisfied: ChimeraX-UI~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.22.3) (1.33.2)
Requirement already satisfied: ChimeraX-IO~=1.0.1 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.22.3) (1.0.1)
Requirement already satisfied: ChimeraX-Map~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.22.3) (1.1.4)
Requirement already satisfied: ChimeraX-MapData~=2.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.22.3) (2.0)
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.22.3) (1.12.3)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.22.3) (1.2)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.22.3) (1.0)
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.3) (2.0.1)
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.3) (2.1.1)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.3) (1.0.1)
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.3) (1.4)
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.3) (2.0)
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.3) (2.0)
ChimeraX-Clipper is already installed with the same version as the provided
wheel. Use --force-reinstall to force an installation of the wheel.
[notice] A new release of pip is available: 23.0 -> 23.3.2
[notice] To update, run:
/Applications/ChimeraX-1.7.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip
> toolshed show
Downloading bundle MolecularDynamicsViewer-1.4-py3-none-any.whl
Installed MolecularDynamicsViewer (1.4)
Downloading bundle ChimeraX_PDBImages-1.2-py3-none-any.whl
Installed ChimeraX-PDBImages (1.2)
Downloading bundle ChimeraX_QScore-1.1-cp311-cp311-macosx_10_13_universal2.whl
Installed ChimeraX-QScore (1.1)
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/job234/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #1, grid size 384,384,384, pixel 0.94, shown
at level 0.0177, step 2, values float32
> color #1 #b2b2b280 models
> color #1 #b2b2b257 models
> set bgColor white
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #1 level 9.457e-07,0 level 0.02185,0.8 level 0.07555,1
> volume #1 level 9.457e-07,0 level 0.01763,0.9077 level 0.07555,1
> volume #1 level -0.000665,0 level 0.01763,0.9077 level 0.07555,1
> volume #1 level 0.0002229,0 level 0.01763,0.9077 level 0.07555,1
> volume #1 level 0.0002229,0 level 0.01763,0.9077 level 0.06046,0.7077
> volume #1 level 0.0002229,0 level 0.01763,0.9077 level 0.07444,1
> volume #1 region 0,0,0,383,383,383 step 2
> volume #1 region 0,0,0,383,383,383 step 1 colorMode opaque8 showOutlineBox
> true orthoplanes xyz positionPlanes 191,191,191 imageMode orthoplanes
> volume #1 imageMode "box faces"
> volume #1 region 0,0,0,383,383,383 step 2 colorMode auto8 imageMode "tilted
> slab" tiltedSlabAxis -0.05781,-0.9976,0.03756 tiltedSlabOffset -200.6
> tiltedSlabSpacing 0.94 tiltedSlabPlaneCount 38
> volume #1 level 0.0002229,0 level 0.02337,0.8769 level 0.07444,1
> volume #1 level 0.0002229,0 level 0.02337,0.8769 level 0.03242,1
> volume #1 level 0.0002229,0 level 0.01398,0.9385 level 0.03242,1
> volume #1 level 0.0104,0 level 0.01398,0.9385 level 0.03242,1
> volume #1 level 0.0104,0 level 0.0299,0.7385 level 0.03242,1
> volume #1 level 0.0104,0 level 0.0299,0.7385 level 0.07548,1
> volume #1 level 0.0104,0 level 0.0299,0.7385 level 0.0687,0.9385
> volume #1 level 0.001006,0 level 0.0299,0.7385 level 0.0687,0.9385
> volume #1 level 0.001006,0 level 0.01267,0.9692 level 0.0687,0.9385
> volume #1 style mesh
> volume #1 style surface
> volume #1 style image imageMode "full region"
> volume #1 level 0.001006,0 level 0.01032,1 level 0.0687,0.9385
> volume #1 level 0.001006,0 level 0.01032,1 level 0.02094,0.9692
> volume #1 level 0.001006,0 level 0.01032,1 level 0.01911,1
> volume #1 maximumIntensityProjection true
> volume #1 maximumIntensityProjection false imageMode "tilted slab"
> tiltedSlabAxis 0.5112,0.4584,-0.727 tiltedSlabOffset 25.69
> volume #1 imageMode "full region"
> volume #1 style surface
> volume #1 color #b2b2b280
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/6-Flagellin_Rebuild4_RelToModel.pdb"
Chain information for 6-Flagellin_Rebuild4_RelToModel.pdb #2
---
Chain | Description
A B C D E F | No description available
> show cartoons
> hide atoms
> mmaker #2 #1
> matchmaker #2 #1
Missing required "to" argument
> mmaker #2 to #1
No 'to' model specified
> mmaker #1 to #2
No molecules/chains to match specified
Must specify one map, got 0
> fitmap #2 inMap #1
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#2) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.0134, steps = 44
shifted from previous position = 0.849
rotated from previous position = 0.327 degrees
atoms outside contour = 19208, contour level = 0.017739
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#2) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
0.99998369 -0.00569271 -0.00047028 1.15015997
0.00569271 0.99998380 -0.00000253 -0.99032832
0.00047029 -0.00000014 0.99999989 0.72458362
Axis 0.00020904 -0.08233133 0.99660499
Axis point 162.91138798 201.54428700 0.00000000
Rotation angle (degrees) 0.32728141
Shift along axis 0.80389913
> volume #1 color #b2b2b274
> volume #1 color #b2b2b275
> volume #1 level 0.01539
Drag select of 1 postprocess_masked.mrc , 4 residues
> select #1
3 models selected
> volume #1 tiltedSlabAxis -0.597,-0.09826,0.7962 tiltedSlabOffset 0.2744
> select #1
3 models selected
Drag select of 1 postprocess_masked.mrc
[Repeated 1 time(s)]
> volume #1 tiltedSlabAxis -0.6007,-0.09668,0.7936 tiltedSlabOffset -0.5827
> select clear
> volume #1 tiltedSlabAxis -0.9124,0.196,0.3593 tiltedSlabOffset -81.71
> combine #2 #3
> select add #3
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> volume #1 tiltedSlabAxis -0.785,-0.3811,0.4884 tiltedSlabOffset -169.1
Drag select of 1 postprocess_masked.mrc , 86 residues
> select add #3
25482 atoms, 24906 bonds, 1681 residues, 4 models selected
> select add #1
25482 atoms, 24906 bonds, 1681 residues, 5 models selected
> select add #1
25482 atoms, 24906 bonds, 1681 residues, 5 models selected
> select add #1
25482 atoms, 24906 bonds, 1681 residues, 5 models selected
> select add #1
25482 atoms, 24906 bonds, 1681 residues, 5 models selected
> select add #2
49668 atoms, 49812 bonds, 3276 residues, 5 models selected
> select #1
3 models selected
> select clear
> select add #3
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> volume #1 tiltedSlabAxis 0.8568,-0.3828,0.3456 tiltedSlabOffset 187.8
> volume #1 tiltedSlabAxis 0.1595,0.9748,0.156 tiltedSlabOffset 206.9
> volume #1 tiltedSlabAxis 0.1595,0.9748,0.156 tiltedSlabOffset 114.9
> volume #1 tiltedSlabAxis -0.9317,-0.2385,0.2741 tiltedSlabOffset -210.5
Drag select of 1 postprocess_masked.mrc , 6 residues
> volume #1 tiltedSlabAxis -0.9317,-0.2385,0.2741 tiltedSlabOffset -208.9
> select clear
> select add #3
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99998,-0.0056927,-0.00047028,-32.801,0.0056927,0.99998,-2.5327e-06,-16.642,0.00047029,-1.4457e-07,1,4.0895
> view matrix models
> #3,0.99998,-0.0056927,-0.00047028,-37.624,0.0056927,0.99998,-2.5327e-06,19.581,0.00047029,-1.4457e-07,1,-1.6923
> view matrix models
> #3,0.99998,-0.0056927,-0.00047028,-42.421,0.0056927,0.99998,-2.5327e-06,24.955,0.00047029,-1.4457e-07,1,-3.4175
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.37592,-0.92258,-0.086766,293.33,0.9263,0.37155,0.062594,-52.365,-0.02551,-0.1039,0.99426,24.429
> view matrix models
> #3,0.2828,-0.94893,-0.13981,328.57,0.95911,0.27803,0.052976,-38.276,-0.0114,-0.14907,0.98876,31.765
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.2828,-0.94893,-0.13981,321.31,0.95911,0.27803,0.052976,-39.951,-0.0114,-0.14907,0.98876,32.169
> select up
49668 atoms, 49812 bonds, 3276 residues, 4 models selected
> select up
49668 atoms, 49812 bonds, 3276 residues, 5 models selected
> select down
49668 atoms, 49812 bonds, 3276 residues, 4 models selected
> select down
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> fitmap #3 inMap #1
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.002269, steps = 80
shifted from previous position = 3.42
rotated from previous position = 2.62 degrees
atoms outside contour = 22126, contour level = 0.01539
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
0.27065280 -0.95465221 -0.12404119 323.57838159
0.96109654 0.26057565 0.09161754 -46.99451913
-0.05514078 -0.14401210 0.98803847 39.44691470
Axis -0.12199849 -0.03567355 0.99188899
Axis point 195.08356436 190.07619930 0.00000000
Rotation angle (degrees) 74.95168621
Shift along axis 1.32734831
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.27065,-0.95465,-0.12404,310.98,0.9611,0.26058,0.091618,-52.091,-0.055141,-0.14401,0.98804,37.241
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.077337,-0.97201,-0.22184,374.13,0.99665,0.081312,-0.0088272,-3.4904,0.026619,-0.22042,0.97504,38.173
> view matrix models
> #3,0.15031,-0.9782,-0.14326,344.85,0.97996,0.16657,-0.10923,1.9602,0.13072,-0.12397,0.98364,-5.1501
> view matrix models
> #3,0.076208,-0.97874,-0.19043,369.67,0.99139,0.094769,-0.090331,10.6,0.10646,-0.18191,0.97754,12.996
> view matrix models
> #3,0.18783,-0.97155,-0.14424,335.78,0.97914,0.1968,-0.050557,-15.383,0.077504,-0.13173,0.98825,6.7542
> view matrix models
> #3,0.089564,-0.9748,-0.20433,368.74,0.98705,0.11428,-0.11256,11.811,0.13307,-0.1916,0.97241,10.366
> view matrix models
> #3,0.059047,-0.97851,-0.19757,374.62,0.97663,0.097596,-0.19148,32.66,0.20665,-0.18165,0.96141,-5.0401
> view matrix models
> #3,0.11216,-0.98024,-0.16294,357.1,0.96121,0.14861,-0.23237,33.362,0.25199,-0.13055,0.95888,-24.56
> view matrix models
> #3,0.16853,-0.97734,-0.12809,337.91,0.94052,0.19834,-0.27585,35.936,0.295,-0.07398,0.95263,-43.989
> view matrix models
> #3,0.14218,-0.98204,-0.12401,343.63,0.981,0.12309,0.14999,-39.411,-0.13203,-0.14298,0.98088,54.604
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.14218,-0.98204,-0.12401,340.63,0.981,0.12309,0.14999,-39.941,-0.13203,-0.14298,0.98088,53.431
> view matrix models
> #3,0.14218,-0.98204,-0.12401,337.72,0.981,0.12309,0.14999,-47.67,-0.13203,-0.14298,0.98088,53.353
> fitmap #3 inMap #1
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.002065, steps = 204
shifted from previous position = 3.3
rotated from previous position = 6.9 degrees
atoms outside contour = 22230, contour level = 0.01539
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
0.02347642 -0.99151233 -0.12787555 364.57048245
0.99287465 0.00817636 0.11888262 -17.93772375
-0.11682803 -0.12975533 0.98463941 46.44771746
Axis -0.12432310 -0.00552394 0.99222641
Axis point 194.30577109 176.43087003 0.00000000
Rotation angle (degrees) 89.53325801
Shift along axis 0.86120500
> view matrix models
> #3,0.023476,-0.99151,-0.12788,364.38,0.99287,0.0081764,0.11888,-22.715,-0.11683,-0.12976,0.98464,42.346
> fitmap #3 inMap #1
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.001863, steps = 80
shifted from previous position = 2.35
rotated from previous position = 3.2 degrees
atoms outside contour = 22342, contour level = 0.01539
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
-0.01927539 -0.99321299 -0.11470141 370.27419502
0.99630196 -0.02868848 0.08098995 -6.77992684
-0.08373088 -0.11271613 0.99009303 30.53482642
Axis -0.09689361 -0.01549176 0.99517417
Axis point 189.97352374 177.32059140 0.00000000
Rotation angle (degrees) 91.65810865
Shift along axis -5.38470011
> view matrix models
> #3,-0.019275,-0.99321,-0.1147,378.7,0.9963,-0.028688,0.08099,-9.3416,-0.083731,-0.11272,0.99009,29.341
> fitmap #3 inMap #1
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.004772, steps = 172
shifted from previous position = 4.01
rotated from previous position = 9.87 degrees
atoms outside contour = 20578, contour level = 0.01539
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
-0.12572969 -0.99206341 -0.00149187 382.61047458
0.99206331 -0.12573176 0.00138377 23.55757873
-0.00156036 -0.00130605 0.99999793 -11.97441994
Axis -0.00135567 0.00003452 0.99999908
Axis point 180.91672521 180.36166577 0.00000000
Rotation angle (degrees) 97.22301593
Shift along axis -12.49228874
> view matrix models
> #3,-0.12573,-0.99206,-0.0014919,384.81,0.99206,-0.12573,0.0013838,23.553,-0.0015604,-0.0013061,1,-7.3999
> fitmap #3 inMap #1
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.003798, steps = 68
shifted from previous position = 2.09
rotated from previous position = 0.385 degrees
atoms outside contour = 21130, contour level = 0.01539
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
-0.12238088 -0.99247521 0.00398440 381.13025571
0.99247917 -0.12236794 0.00334469 22.49829575
-0.00283196 0.00436376 0.99998647 -7.82442052
Axis 0.00051339 0.00343399 0.99999397
Axis point 180.60837555 179.77551755 0.00000000
Rotation angle (degrees) 97.02954713
Shift along axis -7.55144499
Drag select of 1 postprocess_masked.mrc
> select #1
3 models selected
> select #1
3 models selected
> select clear
> select add #3
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> view matrix models
> #3,-0.12238,-0.99248,0.0039844,378.18,0.99248,-0.12237,0.0033447,17.826,-0.002832,0.0043638,0.99999,-10.292
> view matrix models
> #3,-0.12238,-0.99248,0.0039844,379.24,0.99248,-0.12237,0.0033447,19.203,-0.002832,0.0043638,0.99999,-10.615
> fitmap #3 inMap #1
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.004772, steps = 72
shifted from previous position = 4.28
rotated from previous position = 0.386 degrees
atoms outside contour = 20574, contour level = 0.01539
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
-0.12574589 -0.99206136 -0.00149260 382.61592382
0.99206126 -0.12574795 0.00137859 23.56220792
-0.00155534 -0.00130740 0.99999794 -11.96850659
Axis -0.00135374 0.00003162 0.99999908
Axis point 180.91761254 180.36360420 0.00000000
Rotation angle (degrees) 97.22395120
Shift along axis -12.48571277
> combine #2 #4
> select subtract #3
Nothing selected
> select add #4
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> view matrix models
> #4,0.99998,-0.0056927,-0.00047028,4.9247,0.0056927,0.99998,-2.5327e-06,-44.31,0.00047029,-1.4457e-07,1,8.3529
> view matrix models
> #4,0.99998,-0.0056927,-0.00047028,-0.70767,0.0056927,0.99998,-2.5327e-06,-55.868,0.00047029,-1.4457e-07,1,8.1624
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.77611,0.62425,-0.08921,-65.369,-0.62165,0.73365,-0.27443,183.74,-0.10587,0.26845,0.95746,-16.177
> view matrix models
> #4,0.52818,0.8264,-0.19518,-34.073,-0.8257,0.44622,-0.34513,299.19,-0.19812,0.34344,0.91804,-4.4887
> view matrix models
> #4,0.67778,0.61445,-0.40381,18.09,-0.72254,0.65835,-0.21098,208.15,0.13621,0.43476,0.89018,-88.207
> view matrix models
> #4,0.30566,0.85076,-0.42754,52.667,-0.93931,0.19597,-0.28157,362.07,-0.15576,0.48766,0.85903,-31.532
> view matrix models
> #4,0.14707,0.95118,-0.27132,35.343,-0.97543,0.18496,0.11969,294.45,0.16403,0.24706,0.95502,-68.162
> view matrix models
> #4,0.22505,0.97212,-0.065803,-25.047,-0.97334,0.22738,0.030286,302.59,0.044404,0.057232,0.99737,-12.297
> view matrix models
> #4,0.29018,0.95524,-0.057521,-36.907,-0.95479,0.29305,0.049871,281.46,0.064496,0.040449,0.9971,-13.039
> ui mousemode right "move picked models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.29018,0.95524,-0.057521,-39.953,-0.95479,0.29305,0.049871,276.43,0.064496,0.040449,0.9971,-21.941
> view matrix models
> #4,0.29018,0.95524,-0.057521,-45.569,-0.95479,0.29305,0.049871,272.94,0.064496,0.040449,0.9971,-20.75
> view matrix models
> #4,0.29018,0.95524,-0.057521,-47.628,-0.95479,0.29305,0.049871,272.39,0.064496,0.040449,0.9971,-22.435
> view matrix models
> #4,0.29018,0.95524,-0.057521,-51.083,-0.95479,0.29305,0.049871,276.21,0.064496,0.040449,0.9971,-23.235
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.041854,0.99307,-0.10982,3.5665,-0.99634,0.033278,-0.078792,362.97,-0.074591,0.11272,0.99082,-7.5255
> view matrix models
> #4,-0.0022067,0.99686,0.079118,-24.413,-0.99778,0.0030699,-0.06651,367.09,-0.066544,-0.079089,0.99464,29.301
> view matrix models
> #4,-0.39054,0.92025,-0.024971,93.143,-0.91468,-0.39096,-0.10254,437.2,-0.10413,-0.017207,0.99442,24.594
> view matrix models
> #4,-0.31946,0.94757,-0.0080495,69.316,-0.94559,-0.31932,-0.062437,421.3,-0.061733,-0.012335,0.99802,13.973
> view matrix models
> #4,-0.3347,0.93983,0.068503,59.327,-0.94179,-0.33117,-0.058032,422.07,-0.031855,-0.083938,0.99596,22.734
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.3347,0.93983,0.068503,48.708,-0.94179,-0.33117,-0.058032,419.83,-0.031855,-0.083938,0.99596,12.753
> fitmap #4 inMap #1
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.00506, steps = 248
shifted from previous position = 3.6
rotated from previous position = 20.7 degrees
atoms outside contour = 20538, contour level = 0.01539
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
-0.63573853 0.77189924 0.00284379 155.05584510
-0.77185256 -0.63573419 0.00925525 431.91002042
0.00895201 0.00368893 0.99995313 -16.44042435
Axis -0.00360565 -0.00395668 -0.99998567
Axis point 179.47771409 179.39085907 0.00000000
Rotation angle (degrees) 129.47636001
Shift along axis 14.17217952
> view matrix models
> #4,-0.63574,0.7719,0.0028438,160.79,-0.77185,-0.63573,0.0092552,437.9,0.008952,0.0036889,0.99995,-16.121
> fitmap #4 inMap #1
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.00506, steps = 156
shifted from previous position = 8.3
rotated from previous position = 0.00659 degrees
atoms outside contour = 20541, contour level = 0.01539
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
-0.63581490 0.77183612 0.00290076 155.07518084
-0.77178935 -0.63581112 0.00924226 431.91323525
0.00897784 0.00363759 0.99995308 -16.43989206
Axis -0.00363080 -0.00393683 -0.99998566
Axis point 179.47516905 179.39236216 0.00000000
Rotation angle (degrees) 129.48205141
Shift along axis 14.17624006
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.43274,0.9006,0.040728,78.653,-0.90101,-0.43054,-0.053016,429.13,-0.030211,-0.059639,0.99776,5.1871
> view matrix models
> #4,-0.35508,0.93364,0.047216,54.283,-0.93407,-0.3523,-0.058252,421.09,-0.037752,-0.064788,0.99718,7.9407
> ui mousemode right "move picked models"
> view matrix models #1,1,0,0,0.98441,0,1,0,0.78079,0,0,1,0.79767
> undo
> view matrix models #1,1,0,0,0.4962,0,1,0,0.40244,0,0,1,0.27256
> undo
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.35508,0.93364,0.047216,59.104,-0.93407,-0.3523,-0.058252,425.1,-0.037752,-0.064788,0.99718,9.1742
> select up
74502 atoms, 74718 bonds, 4914 residues, 5 models selected
> fitmap #4 inMap #1
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.005061, steps = 236
shifted from previous position = 5.34
rotated from previous position = 19.3 degrees
atoms outside contour = 20535, contour level = 0.01539
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
-0.63580310 0.77184584 0.00290081 155.06713677
-0.77179915 -0.63579934 0.00923406 431.91809193
0.00897160 0.00363220 0.99995316 -16.42958387
Axis -0.00362893 -0.00393271 -0.99998568
Axis point 179.47425807 179.39592170 0.00000000
Rotation angle (degrees) 129.48117350
Shift along axis 14.16801296
> select subtract #2
49668 atoms, 49812 bonds, 3276 residues, 4 models selected
> select clear
> select add #4
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #1
24834 atoms, 24906 bonds, 1638 residues, 4 models selected
> select add #1
24834 atoms, 24906 bonds, 1638 residues, 4 models selected
> select subtract #4
3 models selected
> hide #!1 models
> select add #1
3 models selected
> select clear
> select add #4
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.28748,0.95519,0.070407,31.154,-0.95657,-0.29004,0.029109,396.22,0.048225,-0.058981,0.99709,-11.328
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.28748,0.95519,0.070407,38.943,-0.95657,-0.29004,0.029109,399.03,0.048225,-0.058981,0.99709,-26.025
> view matrix models
> #4,-0.28748,0.95519,0.070407,40.444,-0.95657,-0.29004,0.029109,400.04,0.048225,-0.058981,0.99709,-25.571
> fitmap #4 inMap #1
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.002525, steps = 124
shifted from previous position = 8.67
rotated from previous position = 5.54 degrees
atoms outside contour = 21838, contour level = 0.01539
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
-0.35499428 0.93485088 0.00573463 79.01494062
-0.93475506 -0.35504008 0.01339806 409.45261193
0.01456121 -0.00060424 0.99989380 -29.37897482
Axis -0.00748915 -0.00472091 -0.99996081
Axis point 180.90389763 177.46969345 0.00000000
Rotation angle (degrees) 110.79775201
Shift along axis 26.85308157
> view matrix models
> #4,-0.35499,0.93485,0.0057346,81.177,-0.93476,-0.35504,0.013398,414.02,0.014561,-0.00060424,0.99989,-28.926
> fitmap #4 inMap #1
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.004753, steps = 116
shifted from previous position = 0.725
rotated from previous position = 11.8 degrees
atoms outside contour = 20644, contour level = 0.01539
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
-0.15652788 0.98767308 0.00095219 30.13378142
-0.98767232 -0.15652610 -0.00172325 387.54390204
-0.00155296 -0.00121019 0.99999806 -26.09640976
Axis 0.00025973 0.00126821 -0.99999916
Axis point 180.53025771 180.89123491 0.00000000
Rotation angle (degrees) 99.00542381
Shift along axis 26.59570171
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.19497,0.98032,0.030824,-48.149,-0.97973,0.19319,0.052998,303.73,0.046001,-0.040532,0.99812,-27.699
> ui mousemode right "translate selected models"
> fitmap #4 inMap #1
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.004753, steps = 172
shifted from previous position = 1.77
rotated from previous position = 20.5 degrees
atoms outside contour = 20648, contour level = 0.01539
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
-0.15656772 0.98766680 0.00091404 30.15275510
-0.98766603 -0.15656603 -0.00169953 387.54724879
-0.00153547 -0.00116885 0.99999814 -26.11370803
Axis 0.00026865 0.00124004 -0.99999920
Axis point 180.53460699 180.88579160 0.00000000
Rotation angle (degrees) 99.00773532
Shift along axis 26.60236339
> show #!1 models
Drag select of 1 postprocess_masked.mrc , 74 residues
> select clear
> combine #2 #5
> select add #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.99998,-0.0056927,-0.00047028,-50.692,0.0056927,0.99998,-2.5327e-06,-46.502,0.00047029,-1.4457e-07,1,-2.6315
Drag select of 1 postprocess_masked.mrc , 98 residues
> select clear
> select add #4
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> view matrix models
> #5,0.99998,-0.0056927,-0.00047028,-53.13,0.0056927,0.99998,-2.5327e-06,-46.736,0.00047029,-1.4457e-07,1,-22.062
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.65217,0.73915,-0.16831,174.73,-0.7572,-0.64579,0.097942,431.87,-0.036299,0.19132,0.98086,-49.782
> view matrix models
> #5,-0.67851,0.73196,0.06213,137.26,-0.73429,-0.67337,-0.085921,468.19,-0.021054,-0.10392,0.99436,4.8298
> view matrix models
> #5,-0.99169,0.063111,0.11209,330.46,-0.061122,-0.99791,0.021094,372.19,0.11318,0.014068,0.99347,-47.416
> view matrix models
> #5,-0.99541,0.066575,0.06871,338.91,-0.062759,-0.99644,0.056281,365.44,0.072212,0.051711,0.99605,-46.991
> view matrix models
> #5,-0.96569,0.25874,-0.022535,310.94,-0.25467,-0.96037,-0.11333,431.22,-0.050965,-0.1037,0.9933,11.289
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.96569,0.25874,-0.022535,308.84,-0.25467,-0.96037,-0.11333,431.14,-0.050965,-0.1037,0.9933,0.20792
> select up
99336 atoms, 99624 bonds, 6552 residues, 6 models selected
> select up
99336 atoms, 99624 bonds, 6552 residues, 7 models selected
> fitmap #5 inMap #1
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#1) using 24834 atoms
average map value = 0.004728, steps = 124
shifted from previous position = 11.1
rotated from previous position = 6.58 degrees
atoms outside contour = 20685, contour level = 0.01539
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
-0.96386049 0.26640682 -0.00059237 306.66758935
-0.26640597 -0.96386013 -0.00122923 402.91931130
-0.00089844 -0.00102700 0.99999907 -30.95500847
Axis 0.00037956 0.00057444 -0.99999976
Axis point 180.65560612 180.65115377 0.00000000
Rotation angle (degrees) 164.54945844
Shift along axis 31.30285276
> select add #1
99336 atoms, 99624 bonds, 6552 residues, 7 models selected
> select add #1
99336 atoms, 99624 bonds, 6552 residues, 7 models selected
> hide #!1 models
> select clear
> select add #2
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 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 #!5 models
> show #!5 models
> select #5/C
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> hide #!5 models
> show #!5 models
> select #5/D
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> delete #5/D
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> delete #5/E
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!1 models
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/job234/postprocess.mrc"
Opened postprocess.mrc as #6, grid size 384,384,384, pixel 0.94, shown at
level 0.0181, step 2, values float32
> hide #!1 models
> volume mask #6 nearAtoms #2-5
Expected a keyword
> volume mask #6 near #2-5
Expected a keyword
> volume mask #6 near #2-5
Expected a keyword
> volume mask #6 #2-5
Missing required "surfaces" argument
> volume mask #6 surfaces #2-5
No surfaces specified
> molmap #2-5 5
Opened map 5 as #7, grid size 92,92,171, pixel 1.67, shown at level 0.125,
step 1, values float32
> volume mask #6 near #7
Expected a keyword
> volume mask #6 surfaces #7
Opened postprocess.mrc masked as #8, grid size 137,136,276, pixel 0.94, shown
at step 1, values float32
> hide #!7 models
> show #!6 models
> hide #!6 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> color #8 #ffffb27b models
> color #8 #ffffb245 models
> fitmap #2 #8
Missing required "in_map" argument
> fitmap #2 inMap #8
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#2) to map postprocess.mrc
masked (#8) using 24834 atoms
average map value = 0.01341, steps = 28
shifted from previous position = 0.0194
rotated from previous position = 0.0111 degrees
atoms outside contour = 16043, contour level = 0.018088
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#2) relative to
postprocess.mrc masked (#8) coordinates:
Matrix rotation and translation
0.99998385 -0.00567124 -0.00035687 1.13438200
0.00567129 0.99998391 0.00015325 -0.99857102
0.00035600 -0.00015527 0.99999992 0.78254699
Axis -0.02713635 -0.06270237 0.99766329
Axis point 167.66841805 203.43442403 0.00000000
Rotation angle (degrees) 0.32570226
Shift along axis 0.81254819
> fitmap #3 inMap #8
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) to map
postprocess.mrc masked (#8) using 24834 atoms
average map value = 0.004774, steps = 44
shifted from previous position = 0.0231
rotated from previous position = 0.00754 degrees
atoms outside contour = 19772, contour level = 0.018088
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#3) relative to
postprocess.mrc masked (#8) coordinates:
Matrix rotation and translation
-0.12585655 -0.99204723 -0.00155735 382.64916066
0.99204718 -0.12585874 0.00140496 23.56781933
-0.00158979 -0.00136814 0.99999780 -11.96693066
Axis -0.00139766 0.00001635 0.99999902
Axis point 180.93274891 180.36174405 0.00000000
Rotation angle (degrees) 97.23034988
Shift along axis -12.50134792
> fitmap #4 inMap #8
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) to map
postprocess.mrc masked (#8) using 24834 atoms
average map value = 0.004758, steps = 48
shifted from previous position = 0.0315
rotated from previous position = 0.0273 degrees
atoms outside contour = 19775, contour level = 0.018088
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#4) relative to
postprocess.mrc masked (#8) coordinates:
Matrix rotation and translation
-0.15609663 0.98774135 0.00092995 30.02585385
-0.98774059 -0.15609490 -0.00170771 387.48273091
-0.00154161 -0.00118511 0.99999811 -26.13564511
Axis 0.00026454 0.00125112 -0.99999918
Axis point 180.52342897 180.90132394 0.00000000
Rotation angle (degrees) 98.98040740
Shift along axis 26.62835287
> fitmap #5 inMap #8
Fit molecule copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess.mrc masked (#8) using 16556 atoms
average map value = 0.004729, steps = 52
shifted from previous position = 0.207
rotated from previous position = 0.408 degrees
atoms outside contour = 13272, contour level = 0.018088
Position of copy of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess.mrc masked (#8) coordinates:
Matrix rotation and translation
-0.96572892 0.25955070 -0.00104485 308.63543660
-0.25954944 -0.96572907 -0.00120040 401.66374847
-0.00132061 -0.00088807 0.99999873 -30.89931594
Axis 0.00060167 0.00053122 -0.99999968
Axis point 180.82468532 180.44916785 0.00000000
Rotation angle (degrees) 164.95662838
Shift along axis 31.29837601
> fitmap #6 inMap #8
Fit map postprocess.mrc in map postprocess.mrc masked using 70747 points
correlation = 0.6211, correlation about mean = 0.3968, overlap = 24.4
steps = 28, shift = 0.0178, angle = 0.0289 degrees
Position of postprocess.mrc (#6) relative to postprocess.mrc masked (#8)
coordinates:
Matrix rotation and translation
0.99999988 0.00049210 -0.00006550 -0.07885211
-0.00049210 0.99999987 0.00009229 0.09019055
0.00006555 -0.00009226 0.99999999 0.00447757
Axis -0.18273817 -0.12977076 -0.97455955
Axis point 182.79996672 160.89686681 0.00000000
Rotation angle (degrees) 0.02893123
Shift along axis -0.00165846
> volume #8 level 0.01191
> isolde start
> set selectionWidth 4
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> Combine #2-#5 #9 RoughRebuild
Unknown command: Combine #2-#5 #9 RoughRebuild
> combine #2-#5 #9 name RoughRebuild
Expected a keyword
> combine #2-5 #9 name RoughRebuild
Remapping chain ID 'A' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #3 to
'G'
Remapping chain ID 'B' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #3 to
'H'
Remapping chain ID 'C' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #3 to
'I'
Remapping chain ID 'D' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #3 to
'J'
Remapping chain ID 'E' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #3 to
'K'
Remapping chain ID 'F' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #3 to
'L'
Remapping chain ID 'A' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #4 to
'M'
Remapping chain ID 'B' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #4 to
'N'
Remapping chain ID 'C' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #4 to
'O'
Remapping chain ID 'D' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #4 to
'P'
Remapping chain ID 'E' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #4 to
'Q'
Remapping chain ID 'F' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #4 to
'R'
Remapping chain ID 'A' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #5 to
'S'
Remapping chain ID 'B' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #5 to
'T'
Remapping chain ID 'C' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #5 to
'U'
Remapping chain ID 'F' in copy of 6-Flagellin_Rebuild4_RelToModel.pdb #5 to
'V'
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!8 models
> hide #!9 models
> show #!9 models
> show #!8 models
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/Chimera_Analysis/Rough_Full-build.cxs"
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time
> clipper associate #8 toModel #9
Opened postprocess.mrc masked as #9.1.1.1, grid size 137,136,276, pixel 0.94,
shown at step 1, values float32
> volume #9.1.1.1 region 0,0,0,136,135,275 step 1
[Repeated 1 time(s)]
> volume #7 level 0.5692
> volume #6 level 0.01648
> volume #9.1.1.1 level 0.006384
> volume gaussian #9 bfactor 150
Opened postprocess.mrc masked gaussian as #8, grid size 137,136,276, pixel
0.94, shown at step 1, values float32
> clipper associate #8 toModel #9
Opened postprocess.mrc masked gaussian as #9.1.1.2, grid size 137,136,276,
pixel 0.94, shown at step 1, values float32
> volume #9.1.1.2 region 0,0,0,136,135,275 step 1
[Repeated 1 time(s)]
> volume #9.1.1.1 style surface
> volume #9.1.1.1 color #00ffff3f
> volume #9.1.1.2
> volume #9.1.1.1 color #00ffff40
> volume #9.1.1.2 level 0.006482
> volume #9.1.1.1 level 0.01432
> volume #9.1.1.2 level 0.00311
> volume #9.1.1.1 level 0.01724
> ui tool show "Change Chain IDs"
[Repeated 1 time(s)]
> view #9/A:1
> view #9/B:1
[Repeated 2 time(s)]
> view #9/B:2
> view #9/B:3
> view #9/B:4
> view #9/C:1
> view #9/D:1
> view #9/E:1
> view #9/F:1
> view #9/G:1
[Repeated 1 time(s)]
> view #9/H:1
[Repeated 1 time(s)]
> view #9/I:1
> view #9/J:1
> view #9/J:1-6
> view #9/K:1-6
> view #9/L:1-6
> view #9/M:1-6
> view #9/M:
Expected an objects specifier or a view name or a keyword
> view #9/M:1
> view #9/N:1
> view #9/O:1
> view #9/P:1
[Repeated 1 time(s)]
> view #9/Q:1
> view #9/R:1
> view #9/S:1
> view #9/T:1
> view #9/U:1
> view #9/V:1
> view #9/W:1
No objects specified.
> view #9/V:1
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/Chimera_Analysis/Isolde-ReFitting-Needed.cxs"
> view matrix models #9.2,1,0,0,-0.0061897,0,1,0,0.17444,0,0,1,0.32061
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/Rhom_2Ring_Trimmed.pdb"
Chain information for Rhom_2Ring_Trimmed.pdb #8
---
Chain | Description
A B C D E F G H I J K L M N O P Q R S T U V W X Y | No description available
> close session
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/Rhom_2Ring_Trimmed.pdb" format pdb
Chain information for Rhom_2Ring_Trimmed.pdb #1
---
Chain | Description
A B C D E F G H I J K L M N O P Q R S T U V W X Y | No description available
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/job234/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #2, grid size 384,384,384, pixel 0.94, shown
at level 0.0177, step 2, values float32
> hide cartoons
> show cartoons
> hide atoms
> volume #2 color #fefefe
> volume #2 color #35f8fe80
> volume #2 level 0.01617
> volume #2 level 0.01983
> molmap #1 10
Opened Rhom_2Ring_Trimmed.pdb map 10 as #3, grid size 56,56,90, pixel 3.33,
shown at level 0.088, step 1, values float32
> volume mask #2 surfaces #3
Opened postprocess_masked.mrc masked as #4, grid size 138,139,259, pixel 0.94,
shown at step 1, values float32
> hide #!3 models
> mmaker #1 #2
> matchmaker #1 #2
Missing required "to" argument
> mmaker #1 to #2
No 'to' model specified
> fitmap #1 inMap #2
Fit molecule Rhom_2Ring_Trimmed.pdb (#1) to map postprocess_masked.mrc (#2)
using 52150 atoms
average map value = 0.0175, steps = 68
shifted from previous position = 1.56
rotated from previous position = 0.0291 degrees
atoms outside contour = 37704, contour level = 0.019827
Position of Rhom_2Ring_Trimmed.pdb (#1) relative to postprocess_masked.mrc
(#2) coordinates:
Matrix rotation and translation
0.99999987 0.00048309 0.00015503 -0.10510376
-0.00048309 0.99999988 0.00002194 0.09643120
-0.00015502 -0.00002202 0.99999999 -1.52443033
Axis -0.04328098 0.30527462 -0.95128028
Axis point -738.27097804 84.40182646 0.00000000
Rotation angle (degrees) 0.02909649
Shift along axis 1.48414750
> fitmap #1 inMap #2
Fit molecule Rhom_2Ring_Trimmed.pdb (#1) to map postprocess_masked.mrc (#2)
using 52150 atoms
average map value = 0.0175, steps = 40
shifted from previous position = 0.0163
rotated from previous position = 0.00657 degrees
atoms outside contour = 37685, contour level = 0.019827
Position of Rhom_2Ring_Trimmed.pdb (#1) relative to postprocess_masked.mrc
(#2) coordinates:
Matrix rotation and translation
0.99999987 0.00048065 0.00014742 -0.11898328
-0.00048064 0.99999988 -0.00009252 0.11025397
-0.00014747 0.00009245 0.99999998 -1.54483470
Axis 0.18092801 0.28843449 -0.94025029
Axis point -648.65184068 798.01207139 0.00000000
Rotation angle (degrees) 0.02928876
Shift along axis 1.46280490
> fitmap #1 inMap #2
Fit molecule Rhom_2Ring_Trimmed.pdb (#1) to map postprocess_masked.mrc (#2)
using 52150 atoms
average map value = 0.01749, steps = 28
shifted from previous position = 0.00391
rotated from previous position = 0.0041 degrees
atoms outside contour = 37679, contour level = 0.019827
Position of Rhom_2Ring_Trimmed.pdb (#1) relative to postprocess_masked.mrc
(#2) coordinates:
Matrix rotation and translation
0.99999987 0.00049087 0.00015473 -0.12395839
-0.00049087 0.99999988 -0.00002210 0.09717875
-0.00015474 0.00002203 0.99999999 -1.53045664
Axis 0.04283209 0.30035932 -0.95286394
Axis point -709.06835344 381.66848867 0.00000000
Rotation angle (degrees) 0.02951601
Shift along axis 1.48219609
> fitmap #1 inMap #2
Fit molecule Rhom_2Ring_Trimmed.pdb (#1) to map postprocess_masked.mrc (#2)
using 52150 atoms
average map value = 0.01749, steps = 28
shifted from previous position = 0.00422
rotated from previous position = 0.000796 degrees
atoms outside contour = 37688, contour level = 0.019827
Position of Rhom_2Ring_Trimmed.pdb (#1) relative to postprocess_masked.mrc
(#2) coordinates:
Matrix rotation and translation
0.99999987 0.00048618 0.00015516 -0.12455318
-0.00048617 0.99999988 -0.00003516 0.09453007
-0.00015518 0.00003509 0.99999999 -1.53207948
Axis 0.06866925 0.30333163 -0.95040752
Axis point -726.71808325 464.50071967 0.00000000
Rotation angle (degrees) 0.02930925
Shift along axis 1.47622085
> fitmap #1 inMap #2
Fit molecule Rhom_2Ring_Trimmed.pdb (#1) to map postprocess_masked.mrc (#2)
using 52150 atoms
average map value = 0.01749, steps = 28
shifted from previous position = 0.00231
rotated from previous position = 0.000463 degrees
atoms outside contour = 37695, contour level = 0.019827
Position of Rhom_2Ring_Trimmed.pdb (#1) relative to postprocess_masked.mrc
(#2) coordinates:
Matrix rotation and translation
0.99999987 0.00049085 0.00015580 -0.12597523
-0.00049084 0.99999988 -0.00004174 0.09420012
-0.00015582 0.00004166 0.99999999 -1.53324278
Axis 0.08070635 0.30157521 -0.95002046
Axis point -714.36444091 498.95401240 0.00000000
Rotation angle (degrees) 0.02960287
Shift along axis 1.47485343
> hide #!4 models
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/6-Flagellin_Rebuild4_RelToModel.pdb"
Chain information for 6-Flagellin_Rebuild4_RelToModel.pdb #5
---
Chain | Description
A B C D E F | No description available
> hide cartoons
> show cartoons
> hide atoms
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.0134, steps = 44
shifted from previous position = 0.849
rotated from previous position = 0.327 degrees
atoms outside contour = 20275, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.99998369 -0.00569271 -0.00047028 1.15015997
0.00569271 0.99998380 -0.00000253 -0.99032832
0.00047029 -0.00000014 0.99999989 0.72458362
Axis 0.00020904 -0.08233133 0.99660499
Axis point 162.91138798 201.54428700 0.00000000
Rotation angle (degrees) 0.32728141
Shift along axis 0.80389913
> show #!4 models
> hide #!5 models
> show #!5 models
> select add #4
2 models selected
> select subtract #4
Nothing selected
> select add #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> view matrix models
> #5,0.99998,-0.0056927,-0.00047028,1.604,0.0056927,0.99998,-2.5327e-06,-4.2769,0.00047029,-1.4457e-07,1,-18.339
> view matrix models
> #5,0.99998,-0.0056927,-0.00047028,-3.4203,0.0056927,0.99998,-2.5327e-06,6.5873,0.00047029,-1.4457e-07,1,-20.783
> view matrix models
> #5,0.99998,-0.0056927,-0.00047028,-9.2672,0.0056927,0.99998,-2.5327e-06,-2.2906,0.00047029,-1.4457e-07,1,-22.996
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.0008029, steps = 72
shifted from previous position = 1.58
rotated from previous position = 1.27 degrees
atoms outside contour = 23427, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.99977411 -0.00506656 0.02064100 -13.19896983
0.00520941 0.99996281 -0.00687295 0.41775835
-0.02060541 0.00697892 0.99976333 -19.09968663
Axis 0.30983517 0.92258932 0.22985021
Axis point -842.47990399 0.00000000 508.73552966
Rotation angle (degrees) 1.28087466
Shift along axis -8.09415268
> view matrix models
> #5,0.99977,-0.0050666,0.020641,-1.8645,0.0052094,0.99996,-0.0068729,5.713,-0.020605,0.0069789,0.99976,-21.754
> view matrix models
> #5,0.99977,-0.0050666,0.020641,-5.1013,0.0052094,0.99996,-0.0068729,7.7737,-0.020605,0.0069789,0.99976,-18.672
> view matrix models
> #5,0.99977,-0.0050666,0.020641,-4.5819,0.0052094,0.99996,-0.0068729,4.0884,-0.020605,0.0069789,0.99976,-18.915
> view matrix models
> #5,0.99977,-0.0050666,0.020641,-14.335,0.0052094,0.99996,-0.0068729,8.9826,-0.020605,0.0069789,0.99976,-23.662
> view matrix models
> #5,0.99977,-0.0050666,0.020641,-13.208,0.0052094,0.99996,-0.0068729,6.4581,-0.020605,0.0069789,0.99976,-21.905
> view matrix models
> #5,0.99977,-0.0050666,0.020641,0.95187,0.0052094,0.99996,-0.0068729,-11.298,-0.020605,0.0069789,0.99976,-29.122
> view matrix models
> #5,0.99977,-0.0050666,0.020641,1.3865,0.0052094,0.99996,-0.0068729,4.5195,-0.020605,0.0069789,0.99976,-35.568
> view matrix models
> #5,0.99977,-0.0050666,0.020641,1.5112,0.0052094,0.99996,-0.0068729,5.1884,-0.020605,0.0069789,0.99976,-43.503
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.004682, steps = 84
shifted from previous position = 7.01
rotated from previous position = 1.73 degrees
atoms outside contour = 22357, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.99987285 0.01592517 0.00081722 -3.24483378
-0.01592675 0.99987124 0.00196124 2.44073389
-0.00078588 -0.00197400 0.99999774 -44.90287364
Axis -0.12246304 0.04988801 -0.99121844
Axis point 13.35661060 -142.39696360 0.00000000
Rotation angle (degrees) 0.92061400
Shift along axis 45.02769180
> view matrix models
> #5,0.99987,0.015925,0.00081722,-2.082,-0.015927,0.99987,0.0019612,2.8316,-0.00078588,-0.001974,1,-50.184
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.01281, steps = 52
shifted from previous position = 1.53
rotated from previous position = 1.53 degrees
atoms outside contour = 20614, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.99994333 -0.01064358 -0.00020879 1.99976342
0.01064363 0.99994333 0.00022728 -1.91141734
0.00020636 -0.00022949 0.99999995 -50.84225760
Axis -0.02144888 -0.01949447 0.99957987
Axis point 273.12239039 84.00502688 0.00000000
Rotation angle (degrees) 0.61010166
Shift along axis -50.82652773
> view matrix models
> #5,0.99994,-0.010644,-0.00020879,-5.2043,0.010644,0.99994,0.00022728,3.4082,0.00020636,-0.00022949,1,-22.96
> view matrix models
> #5,0.99994,-0.010644,-0.00020879,-9.6619,0.010644,0.99994,0.00022728,2.604,0.00020636,-0.00022949,1,-22.21
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.002311, steps = 140
shifted from previous position = 5.28
rotated from previous position = 15.2 degrees
atoms outside contour = 23075, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.96227159 -0.26620691 -0.05627843 64.06555888
0.26715068 0.96360461 0.00983169 -41.78527684
0.05161289 -0.02449558 0.99836670 -27.45233423
Axis -0.06295782 -0.19787775 0.97820280
Axis point 201.33507376 206.77699646 0.00000000
Rotation angle (degrees) 15.82030175
Shift along axis -22.61900134
> view matrix models
> #5,0.96227,-0.26621,-0.056278,64.795,0.26715,0.9636,0.0098317,-42.479,0.051613,-0.024496,0.99837,-28.115
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.002311, steps = 72
shifted from previous position = 1.21
rotated from previous position = 0.00778 degrees
atoms outside contour = 23067, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.96227630 -0.26621683 -0.05615081 64.03132972
0.26715515 0.96360384 0.00978643 -41.77085516
0.05150183 -0.02441823 0.99837433 -27.45906013
Axis -0.06273766 -0.19745476 0.97830241
Axis point 201.23845109 206.67347327 0.00000000
Rotation angle (degrees) 15.81908656
Shift along axis -22.63258616
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.93557,-0.35111,-0.037823,83.492,0.35079,0.93633,-0.014992,-49.016,0.040678,0.00075813,0.99917,-30.487
> view matrix models
> #5,0.89894,-0.43596,0.042909,92.983,0.43741,0.89863,-0.033745,-55.919,-0.023848,0.049104,0.99851,-26.667
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.002052, steps = 88
shifted from previous position = 2
rotated from previous position = 4.18 degrees
atoms outside contour = 23183, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.92406760 -0.37866760 0.05205690 73.89695462
0.38169123 0.92139174 -0.07313723 -40.57922884
-0.02027010 0.08745341 0.99596236 -32.99758859
Axis 0.20575592 0.09266859 0.97420585
Axis point 138.09250324 178.70777332 0.00000000
Rotation angle (degrees) 22.96977419
Shift along axis -20.70212771
> view matrix models
> #5,0.90369,-0.41191,0.11696,72.462,0.42201,0.90303,-0.08027,-43.934,-0.072554,0.1219,0.98989,-27.864
> view matrix models
> #5,0.90022,-0.41912,0.1181,74.449,0.42492,0.9048,-0.027908,-55.02,-0.095159,0.075306,0.99261,-14.094
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.001909, steps = 404
shifted from previous position = 3.17
rotated from previous position = 6.17 degrees
atoms outside contour = 23221, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.93656786 -0.32121576 0.14021796 44.62472122
0.32805506 0.94424041 -0.02810572 -41.12297379
-0.12337146 0.07232213 0.98972167 -4.88221826
Axis 0.14186795 0.37235577 0.91718301
Axis point 130.32589263 119.13280959 0.00000000
Rotation angle (degrees) 20.72900456
Shift along axis -13.45944659
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.93657,-0.32122,0.14022,32.763,0.32806,0.94424,-0.028106,-29.6,-0.12337,0.072322,0.98972,-5.3666
> view matrix models
> #5,0.93657,-0.32122,0.14022,28.22,0.32806,0.94424,-0.028106,-38.75,-0.12337,0.072322,0.98972,-7.9647
> view matrix models
> #5,0.93657,-0.32122,0.14022,25.245,0.32806,0.94424,-0.028106,-41.161,-0.12337,0.072322,0.98972,-6.5536
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.001401, steps = 60
shifted from previous position = 1.26
rotated from previous position = 1.17 degrees
atoms outside contour = 23384, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.93219333 -0.32865938 0.15165293 26.52063693
0.33817841 0.94017952 -0.04120487 -39.39528113
-0.12903861 0.08969665 0.98757458 -8.92742124
Axis 0.17803624 0.38176233 0.90695128
Axis point 107.80856997 68.42642644 0.00000000
Rotation angle (degrees) 21.56928248
Shift along axis -18.41473587
> view matrix models
> #5,0.93219,-0.32866,0.15165,25.256,0.33818,0.94018,-0.041205,-35.516,-0.12904,0.089697,0.98757,-12.737
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.001878, steps = 140
shifted from previous position = 6.24
rotated from previous position = 6.15 degrees
atoms outside contour = 23188, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.89615602 -0.42170549 0.13809005 57.15450912
0.42449067 0.90537618 0.01008206 -59.37195822
-0.12927510 0.04958284 0.99036836 -9.43010926
Axis 0.04446741 0.30098223 0.95259243
Axis point 145.42872810 102.28389026 0.00000000
Rotation angle (degrees) 26.36924769
Shift along axis -24.31144247
> view matrix models
> #5,0.89616,-0.42171,0.13809,53.866,0.42449,0.90538,0.010082,-61.878,-0.12928,0.049583,0.99037,-4.2952
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.001688, steps = 100
shifted from previous position = 2.56
rotated from previous position = 1.51 degrees
atoms outside contour = 23237, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.88597015 -0.43676391 0.15586592 58.11946311
0.44136459 0.89731023 0.00562578 -62.21068705
-0.14231722 0.06380943 0.98776220 -4.28648020
Axis 0.06261709 0.32090390 0.94503957
Axis point 148.74128880 97.15627990 0.00000000
Rotation angle (degrees) 27.68426024
Shift along axis -20.37527351
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.85599,-0.51139,0.075936,95.141,0.51232,0.85875,0.0080607,-69.732,-0.069332,0.032004,0.99708,-14.945
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.01333, steps = 116
shifted from previous position = 7.91
rotated from previous position = 4.99 degrees
atoms outside contour = 20284, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.83683614 -0.54745338 -0.00027652 128.32384038
0.54745337 0.83683618 -0.00009279 -69.29117619
0.00028220 -0.00007373 0.99999996 -22.70827733
Axis 0.00001741 -0.00051029 0.99999987
Axis point 180.42570459 180.62776583 0.00000000
Rotation angle (degrees) 33.19248364
Shift along axis -22.67068115
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.01333, steps = 40
shifted from previous position = 0.0155
rotated from previous position = 0.0065 degrees
atoms outside contour = 20283, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.83683861 -0.54744959 -0.00029675 128.32330644
0.54744955 0.83683866 -0.00020432 -69.25506361
0.00036019 0.00000853 0.99999994 -22.73829665
Axis 0.00019441 -0.00060000 0.99999980
Axis point 180.37124399 180.65241600 0.00000000
Rotation angle (degrees) 33.19222565
Shift along axis -22.67179200
> combine #5 #6 name 6-Fla_2
> select add #6
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> view matrix models
> #6,-0.0033124,-0.99463,0.10341,376.75,0.99996,-0.0042073,-0.0084366,9.1925,0.0088264,0.10338,0.9946,-44.637
> view matrix models
> #6,-0.022273,-0.99906,-0.037086,408.78,0.99533,-0.018675,-0.094678,29.78,0.093897,-0.039022,0.99482,-33.446
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.022273,-0.99906,-0.037086,373.69,0.99533,-0.018675,-0.094678,8.7357,0.093897,-0.039022,0.99482,-27.404
> view matrix models
> #6,-0.022273,-0.99906,-0.037086,368.08,0.99533,-0.018675,-0.094678,16.252,0.093897,-0.039022,0.99482,-27.184
> view matrix models
> #6,-0.022273,-0.99906,-0.037086,362.97,0.99533,-0.018675,-0.094678,2.1247,0.093897,-0.039022,0.99482,-29.071
> select add #5
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.34295,-0.9393,-0.010251,413.08,0.92819,-0.33717,-0.15738,93.561,0.14437,-0.063487,0.98748,-33.277
> mmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Rhom_2Ring_Trimmed.pdb, chain A (#1) with 6-Fla_2, chain A (#6),
sequence alignment score = 2158.5
RMSD between 254 pruned atom pairs is 0.784 angstroms; (across all 273 pairs:
1.043)
> select add #5
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #5
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> view matrix models
> #5,0.93477,-0.35494,0.015253,70.104,0.35399,0.93419,0.044597,-62.86,-0.030078,-0.036288,0.99889,-10.023,#6,-0.87971,-0.47526,0.015731,419.23,0.47546,-0.87859,0.045013,242.64,-0.007572,0.047078,0.99886,-19.709
> undo
> select subtract #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> view matrix models
> #6,-0.9036,-0.42669,0.037878,415.1,0.42761,-0.90373,0.020478,256.42,0.025493,0.034701,0.99907,-25.535
> view matrix models
> #6,-0.8445,-0.49104,-0.21379,464.42,0.4721,-0.87103,0.13575,218.1,-0.25287,0.013705,0.9674,43.497
> view matrix models
> #6,-0.81535,-0.57726,0.044421,426.07,0.57884,-0.81118,0.083177,193.53,-0.011982,0.093531,0.99554,-29.004
> view matrix models
> #6,-0.9227,-0.38529,0.013304,415.39,0.38547,-0.92147,0.048129,263.59,-0.0062843,0.049537,0.99875,-21.818
> view matrix models
> #6,-0.76232,-0.6043,0.23169,384.28,0.62063,-0.78409,-0.0030567,195.83,0.18351,0.14146,0.97279,-75.588
> view matrix models
> #6,-0.75172,-0.65903,-0.024572,442.73,0.65527,-0.7506,0.084961,164.69,-0.074435,0.047766,0.99608,-6.5883
> view matrix models
> #6,-0.73011,-0.67966,-0.070675,451.31,0.68297,-0.72918,-0.043123,179.2,-0.022226,-0.079753,0.99657,8.4246
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.73011,-0.67966,-0.070675,455.64,0.68297,-0.72918,-0.043123,194.39,-0.022226,-0.079753,0.99657,3.2864
> select up
101818 atoms, 102262 bonds, 10101 residues, 9 models selected
> select up
101818 atoms, 102262 bonds, 10101 residues, 9 models selected
> select down
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> mmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Rhom_2Ring_Trimmed.pdb, chain A (#1) with 6-Fla_2, chain A (#6),
sequence alignment score = 2158.5
RMSD between 254 pruned atom pairs is 0.784 angstroms; (across all 273 pairs:
1.043)
> select subtract #6
Nothing selected
> select add #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #6
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> fitmap #6 #2
Missing required "in_map" argument
> fitmap #6 inMap #2
Fit molecule 6-Fla_2 (#6) to map postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.01338, steps = 28
shifted from previous position = 0.0537
rotated from previous position = 0.0411 degrees
atoms outside contour = 20261, contour level = 0.019827
Position of 6-Fla_2 (#6) relative to postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
-0.96147984 -0.27487507 0.00045540 403.48472611
0.27487505 -0.96147995 -0.00011577 304.41101302
0.00046968 0.00001386 0.99999989 -13.36530660
Axis 0.00023581 -0.00002598 0.99999997
Axis point 180.41440512 180.47703552 0.00000000
Rotation angle (degrees) 164.04543077
Shift along axis -13.27806788
> select clear
> fitmap #6 inMap #2
Fit molecule 6-Fla_2 (#6) to map postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.01338, steps = 36
shifted from previous position = 0.0251
rotated from previous position = 0.00535 degrees
atoms outside contour = 20280, contour level = 0.019827
Position of 6-Fla_2 (#6) relative to postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
-0.96148667 -0.27485133 0.00036776 403.47973857
0.27485130 -0.96148674 -0.00013663 304.40474128
0.00039115 -0.00003029 0.99999992 -13.33423168
Axis 0.00019345 -0.00004255 0.99999998
Axis point 180.41399663 180.47086028 0.00000000
Rotation angle (degrees) 164.04684576
Shift along axis -13.26912867
> fitmap #5 inMap #2
Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.01333, steps = 28
shifted from previous position = 0.018
rotated from previous position = 0.00757 degrees
atoms outside contour = 20281, contour level = 0.019827
Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
0.83684417 -0.54744105 -0.00036124 128.33217468
0.54744106 0.83684424 -0.00008955 -69.29329170
0.00035132 -0.00012281 0.99999993 -22.71472391
Axis -0.00003038 -0.00065081 0.99999979
Axis point 180.44135023 180.64306030 0.00000000
Rotation angle (degrees) 33.19164325
Shift along axis -22.67352109
> combine #6 #7 6-Fla_3
Expected a keyword
> combine #6 #7 name 6-Fla_3
> select add #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.99053,-0.0060293,0.13718,328.15,0.0041013,-0.99989,-0.014333,372.02,0.13725,-0.013635,0.99044,-37.525
> view matrix models
> #7,-0.97138,0.14652,-0.18697,355.49,-0.15486,-0.98746,0.030725,394.25,-0.18012,0.058799,0.98189,16.135
> view matrix models
> #7,-0.99651,0.022749,0.080302,334.51,-0.02303,-0.99973,-0.0025785,375.43,0.080222,-0.0044189,0.99677,-28.623
> view matrix models
> #7,-0.85586,0.42143,0.29984,180.89,-0.40834,-0.90637,0.10838,416.04,0.31744,-0.029683,0.94781,-63.953
> view matrix models
> #7,-0.70631,0.60075,0.37447,98.288,-0.63673,-0.7703,0.034806,450.49,0.30936,-0.21385,0.92659,-20.457
> view matrix models
> #7,-0.65592,0.7548,0.0074148,127.02,-0.74849,-0.65165,0.12294,432.72,0.097629,0.075091,0.99239,-47.717
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.65592,0.7548,0.0074148,177.11,-0.74849,-0.65165,0.12294,425.83,0.097629,0.075091,0.99239,-46.232
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.18744,0.96449,-0.18607,72.901,-0.93028,-0.11349,0.34886,310.34,0.31535,0.23849,0.91852,-111.26
> view matrix models
> #7,0.33326,0.93334,0.13345,-92.072,-0.92753,0.29915,0.22407,249.4,0.16921,-0.19846,0.96539,-0.10432
> view matrix models
> #7,0.46698,0.83035,0.30406,-132.09,-0.8842,0.43399,0.17276,222.58,0.011492,-0.34952,0.93686,69.54
> view matrix models
> #7,0.61056,0.76184,0.21635,-131.37,-0.78416,0.54327,0.29992,154.59,0.11095,-0.35277,0.92911,50.757
> view matrix models
> #7,0.49978,0.8021,0.3269,-137.63,-0.86609,0.46746,0.17711,211.08,-0.010752,-0.37164,0.92831,80.401
> view matrix models
> #7,0.31329,0.93666,0.15658,-93.011,-0.93889,0.28074,0.19915,260.37,0.14257,-0.2094,0.96738,7.3615
> view matrix models
> #7,0.26776,0.90309,0.33576,-111.15,-0.96301,0.26176,0.063941,295.44,-0.030143,-0.34046,0.93977,75.889
> view matrix models
> #7,0.39729,0.91661,0.044669,-84.987,-0.86432,0.35738,0.35387,199.11,0.3084,-0.1792,0.93423,-27.338
> view matrix models
> #7,0.42412,0.89838,-0.11415,-56.241,-0.89161,0.43631,0.12112,233.64,0.15861,0.050406,0.98605,-52.799
> select add #6
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #6
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> view matrix models
> #7,0.40471,0.91379,0.034637,-84.036,-0.90929,0.39813,0.12116,245.17,0.096924,-0.08053,0.99203,-14.162
> select add #6
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #5
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #5
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> mmaker #7 #1
> matchmaker #7 #1
Missing required "to" argument
> mmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Rhom_2Ring_Trimmed.pdb, chain A (#1) with 6-Fla_3, chain A (#7),
sequence alignment score = 2158.5
RMSD between 254 pruned atom pairs is 0.784 angstroms; (across all 273 pairs:
1.043)
> undo
> select subtract #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #6
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select add #7
74502 atoms, 74718 bonds, 4914 residues, 3 models selected
> select subtract #7
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #7
Nothing selected
> undo
[Repeated 5 time(s)]
> select subtract #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #6
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #7
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #6
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #5
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> view matrix models
> #7,-0.96136,-0.27523,-0.0063932,404.81,0.27522,-0.96138,0.0019673,303.89,-0.0066878,0.00013167,0.99998,-11.857
> view matrix models
> #7,-0.3805,0.92477,-0.0048112,36.57,-0.92454,-0.38028,0.024655,433.22,0.020971,0.01383,0.99968,-20.429
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.3805,0.92477,-0.0048112,90.625,-0.92454,-0.38028,0.024655,414.72,0.020971,0.01383,0.99968,-19.177
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.18901,0.98195,-0.0071606,39.049,-0.98165,-0.18875,0.027125,387.06,0.025284,0.012156,0.99961,-19.728
> select add #6
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select add #5
74502 atoms, 74718 bonds, 4914 residues, 3 models selected
> select add #4
74502 atoms, 74718 bonds, 4914 residues, 6 models selected
> select subtract #4
74502 atoms, 74718 bonds, 4914 residues, 3 models selected
> select subtract #5
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> view matrix models
> #7,-0.18666,0.98228,-0.016851,40.358,-0.98227,-0.1863,0.020866,387.9,0.017357,0.020448,0.99964,-19.762
> fitmap #7 inMap #2
Fit molecule 6-Fla_3 (#7) to map postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.002948, steps = 80
shifted from previous position = 1.64
rotated from previous position = 1.99 degrees
atoms outside contour = 22938, contour level = 0.019827
Position of 6-Fla_3 (#7) relative to postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
-0.17039812 0.98536777 0.00385086 32.94944410
-0.98537471 -0.17039244 -0.00175857 388.91585111
-0.00107668 -0.00409420 0.99999104 -9.62680299
Axis -0.00118515 0.00250034 -0.99999617
Axis point 180.18663414 180.57028280 0.00000000
Rotation angle (degrees) 99.81106279
Shift along axis 10.56013679
> mmaker #7 #1
> matchmaker #7 #1
Missing required "to" argument
> mmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Rhom_2Ring_Trimmed.pdb, chain A (#1) with 6-Fla_3, chain A (#7),
sequence alignment score = 2158.5
RMSD between 254 pruned atom pairs is 0.784 angstroms; (across all 273 pairs:
1.043)
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.18901,0.98195,-0.0071606,42.068,-0.98165,-0.18875,0.027125,385.13,0.025284,0.012156,0.99961,-36.918
> view matrix models
> #7,-0.18901,0.98195,-0.0071606,40.657,-0.98165,-0.18875,0.027125,387.3,0.025284,0.012156,0.99961,-40.674
> fitmap #7 inMap #2
Fit molecule 6-Fla_3 (#7) to map postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.01322, steps = 84
shifted from previous position = 1.01
rotated from previous position = 3.61 degrees
atoms outside contour = 20292, contour level = 0.019827
Position of 6-Fla_3 (#7) relative to postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
-0.13312076 0.99109981 0.00014608 25.62829726
-0.99109973 -0.13312081 0.00041842 383.23840063
0.00043415 -0.00008908 0.99999990 -32.12944258
Axis -0.00025603 -0.00014533 -0.99999996
Axis point 180.42269068 180.40987157 0.00000000
Rotation angle (degrees) 97.64997121
Shift along axis 32.06718481
> select clear
> fitmap #7 inMap #2
Fit molecule 6-Fla_3 (#7) to map postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.01322, steps = 28
shifted from previous position = 0.00789
rotated from previous position = 0.0046 degrees
atoms outside contour = 20288, contour level = 0.019827
Position of 6-Fla_3 (#7) relative to postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
-0.13311082 0.99110115 0.00006736 25.63719568
-0.99110107 -0.13311084 0.00040580 383.24602689
0.00041115 -0.00001275 0.99999991 -32.14108844
Axis -0.00021115 -0.00017344 -0.99999996
Axis point 180.43184899 180.41076127 0.00000000
Rotation angle (degrees) 97.64939516
Shift along axis 32.06920413
> mmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Rhom_2Ring_Trimmed.pdb, chain A (#1) with 6-Fla_3, chain A (#7),
sequence alignment score = 2158.5
RMSD between 254 pruned atom pairs is 0.784 angstroms; (across all 273 pairs:
1.043)
> select add #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #6
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #7
Nothing selected
> undo
[Repeated 3 time(s)]
> select add #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> undo
[Repeated 3 time(s)]
> select subtract #7
Nothing selected
> select add #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select up
126652 atoms, 127168 bonds, 11739 residues, 10 models selected
> select up
126652 atoms, 127168 bonds, 11739 residues, 10 models selected
> select down
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> fitmap #7 inMap #2
Fit molecule 6-Fla_3 (#7) to map postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.004753, steps = 76
shifted from previous position = 4.26
rotated from previous position = 2.55 degrees
atoms outside contour = 22292, contour level = 0.019827
Position of 6-Fla_3 (#7) relative to postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
-0.15645985 0.98768383 0.00098440 30.11038902
-0.98768324 -0.15645813 -0.00163356 387.51635627
-0.00145942 -0.00122786 0.99999818 -26.10685507
Axis 0.00020538 0.00123715 -0.99999921
Axis point 180.51939745 180.88633563 0.00000000
Rotation angle (degrees) 99.00147566
Shift along axis 26.59243395
> select clear
> select add #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> view matrix models
> #7,-0.15646,0.98768,0.0009844,30.102,-0.98768,-0.15646,-0.0016336,386.29,-0.0014594,-0.0012279,1,-28.373
> view matrix models
> #7,-0.15646,0.98768,0.0009844,31.432,-0.98768,-0.15646,-0.0016336,385.41,-0.0014594,-0.0012279,1,-31.436
> fitmap #7 inMap #2
Fit molecule 6-Fla_3 (#7) to map postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.01322, steps = 60
shifted from previous position = 2.23
rotated from previous position = 1.36 degrees
atoms outside contour = 20305, contour level = 0.019827
Position of 6-Fla_3 (#7) relative to postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
-0.13310064 0.99110252 0.00004395 25.64193442
-0.99110246 -0.13310065 0.00035545 383.24194175
0.00035813 0.00000375 0.99999993 -32.13108482
Axis -0.00017743 -0.00015850 -0.99999997
Axis point 180.43341724 180.40676231 0.00000000
Rotation angle (degrees) 97.64880580
Shift along axis 32.06579051
> fitmap #7 inMap #2
Fit molecule 6-Fla_3 (#7) to map postprocess_masked.mrc (#2) using 24834 atoms
average map value = 0.01322, steps = 24
shifted from previous position = 0.0081
rotated from previous position = 0.00345 degrees
atoms outside contour = 20302, contour level = 0.019827
Position of 6-Fla_3 (#7) relative to postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
-0.13311188 0.99110101 0.00008566 25.64479424
-0.99110093 -0.13311190 0.00039740 383.23592512
0.00040526 -0.00003200 0.99999991 -32.13263726
Axis -0.00021663 -0.00016124 -0.99999996
Axis point 180.43096548 180.40212616 0.00000000
Rotation angle (degrees) 97.64945630
Shift along axis 32.06528877
> select add #6
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #6
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select add #5
74502 atoms, 74718 bonds, 4914 residues, 3 models selected
> select subtract #5
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select add #5
74502 atoms, 74718 bonds, 4914 residues, 3 models selected
> combine #7/A #8 name 6_Fla_Monomer1
> select subtract #5
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select add #5
74502 atoms, 74718 bonds, 4914 residues, 3 models selected
> select add #8
99336 atoms, 99624 bonds, 6552 residues, 4 models selected
> select subtract #8
74502 atoms, 74718 bonds, 4914 residues, 3 models selected
> select subtract #7
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #7
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #8
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #7
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #8
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #8
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #7
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #7
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> delete #8/B-F
> select add #7
28973 atoms, 29057 bonds, 1911 residues, 2 models selected
> select subtract #7
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> view matrix models
> #8,-0.13311,0.9911,8.5659e-05,44.795,-0.9911,-0.13311,0.0003974,427.64,0.00040526,-3.1999e-05,1,-33.511
> view matrix models
> #8,-0.13311,0.9911,8.5659e-05,41.571,-0.9911,-0.13311,0.0003974,423.63,0.00040526,-3.1999e-05,1,-33.376
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.67167,0.73957,0.043424,-84.466,-0.73824,0.67307,-0.044412,216.17,-0.062073,-0.0022272,0.99807,-19.472
> view matrix models
> #8,0.67292,0.7391,0.03027,-81.935,-0.73832,0.6736,-0.033979,213.94,-0.045504,0.00051658,0.99896,-23.677
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.67292,0.7391,0.03027,-82.426,-0.73832,0.6736,-0.033979,210.59,-0.045504,0.00051658,0.99896,-23.56
> select add #7
28973 atoms, 29057 bonds, 1911 residues, 2 models selected
> select subtract #7
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> select add #6
28973 atoms, 29057 bonds, 1911 residues, 2 models selected
> select subtract #6
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> select up
130791 atoms, 131319 bonds, 12012 residues, 11 models selected
> select down
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> fitmap #8 inMap #2
Fit molecule 6_Fla_Monomer1 (#8) to map postprocess_masked.mrc (#2) using 4139
atoms
average map value = 0.005275, steps = 252
shifted from previous position = 4.08
rotated from previous position = 19.9 degrees
atoms outside contour = 3692, contour level = 0.019827
Position of 6_Fla_Monomer1 (#8) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.88039194 0.47320616 -0.03140001 -56.14567410
-0.47304862 0.88094421 0.01273975 102.14463011
0.03369018 0.00363775 0.99942570 -40.30507882
Axis -0.00959585 -0.06862185 -0.99759659
Axis point 179.70163110 163.38691856 0.00000000
Rotation angle (degrees) 28.31165131
Shift along axis 33.73762183
> view matrix models
> #8,0.88039,0.47321,-0.0314,-56.666,-0.47305,0.88094,0.01274,101.26,0.03369,0.0036378,0.99943,-35.255
> fitmap #8 inMap #2
Fit molecule 6_Fla_Monomer1 (#8) to map postprocess_masked.mrc (#2) using 4139
atoms
average map value = 0.01362, steps = 72
shifted from previous position = 0.757
rotated from previous position = 4.49 degrees
atoms outside contour = 3391, contour level = 0.019827
Position of 6_Fla_Monomer1 (#8) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.84534656 0.53421830 -0.00000202 -68.46907860
-0.53421830 0.84534656 -0.00002583 124.36855897
-0.00001209 0.00002292 1.00000000 -27.37540725
Axis 0.00004563 0.00000942 -1.00000000
Axis point 180.56711272 180.44243762 0.00000000
Rotation angle (degrees) 32.29091433
Shift along axis 27.37345516
> fitmap #8 inMap #2
Fit molecule 6_Fla_Monomer1 (#8) to map postprocess_masked.mrc (#2) using 4139
atoms
average map value = 0.01361, steps = 40
shifted from previous position = 0.00296
rotated from previous position = 0.0911 degrees
atoms outside contour = 3392, contour level = 0.019827
Position of 6_Fla_Monomer1 (#8) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.84453848 0.53549483 0.00017731 -68.59387229
-0.53549471 0.84453844 -0.00049030 124.89151405
-0.00041230 0.00031913 0.99999986 -27.35105929
Axis 0.00075578 0.00055052 -0.99999956
Axis point 180.76429705 180.61135552 0.00000000
Rotation angle (degrees) 32.37748776
Shift along axis 27.36796099
> fitmap #8 inMap #2
Fit molecule 6_Fla_Monomer1 (#8) to map postprocess_masked.mrc (#2) using 4139
atoms
average map value = 0.01361, steps = 40
shifted from previous position = 0.000859
rotated from previous position = 0.00142 degrees
atoms outside contour = 3392, contour level = 0.019827
Position of 6_Fla_Monomer1 (#8) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.84454327 0.53548729 0.00015643 -68.58842105
-0.53548718 0.84454322 -0.00048031 124.88709384
-0.00038931 0.00032188 0.99999987 -27.35631170
Axis 0.00074903 0.00050957 -0.99999959
Axis point 180.76501432 180.60196756 0.00000000
Rotation angle (degrees) 32.37697559
Shift along axis 27.36856450
> fitmap #8 inMap #2
Fit molecule 6_Fla_Monomer1 (#8) to map postprocess_masked.mrc (#2) using 4139
atoms
average map value = 0.01361, steps = 40
shifted from previous position = 0.000154
rotated from previous position = 0.000457 degrees
atoms outside contour = 3392, contour level = 0.019827
Position of 6_Fla_Monomer1 (#8) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.84454160 0.53548991 0.00016297 -68.58994058
-0.53548979 0.84454156 -0.00048364 124.88878117
-0.00039663 0.00032119 0.99999987 -27.35464582
Axis 0.00075149 0.00052251 -0.99999958
Axis point 180.76527318 180.60468360 0.00000000
Rotation angle (degrees) 32.37715340
Shift along axis 27.36834565
> fitmap #8 inMap #2
Fit molecule 6_Fla_Monomer1 (#8) to map postprocess_masked.mrc (#2) using 4139
atoms
average map value = 0.01361, steps = 40
shifted from previous position = 0.000216
rotated from previous position = 0.00017 degrees
atoms outside contour = 3392, contour level = 0.019827
Position of 6_Fla_Monomer1 (#8) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.84454029 0.53549199 0.00016433 -68.59055554
-0.53549187 0.84454024 -0.00048461 124.88961280
-0.00039829 0.00032128 0.99999987 -27.35433597
Axis 0.00075248 0.00052534 -0.99999958
Axis point 180.76526451 180.60562425 0.00000000
Rotation angle (degrees) 32.37729427
Shift along axis 27.36832082
> select add #7
28973 atoms, 29057 bonds, 1911 residues, 2 models selected
> select subtract #7
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> select add #6
28973 atoms, 29057 bonds, 1911 residues, 2 models selected
> select add #7
53807 atoms, 53963 bonds, 3549 residues, 3 models selected
> select add #5
78641 atoms, 78869 bonds, 5187 residues, 4 models selected
> select add #4
78641 atoms, 78869 bonds, 5187 residues, 8 models selected
> select subtract #4
78641 atoms, 78869 bonds, 5187 residues, 4 models selected
> combine #8 #9 name 6_Fla_Monomer2
> select subtract #8
74502 atoms, 74718 bonds, 4914 residues, 3 models selected
> select subtract #7
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #9
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> select add #8
8278 atoms, 8302 bonds, 546 residues, 2 models selected
> select subtract #8
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> view matrix models
> #9,0.84454,0.53549,0.00016433,-147.63,-0.53549,0.84454,-0.00048461,150.22,-0.00039829,0.00032128,1,-30.937
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.071953,-0.99709,0.025378,320.07,0.9899,0.074504,0.12061,-37.067,-0.12215,0.016444,0.99238,-7.1972
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.071953,-0.99709,0.025378,336.17,0.9899,0.074504,0.12061,-39.657,-0.12215,0.016444,0.99238,-6.6416
> select up
134930 atoms, 135470 bonds, 12285 residues, 12 models selected
> select down
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> fitmap #9 inMap #2
Fit molecule 6_Fla_Monomer2 (#9) to map postprocess_masked.mrc (#2) using 4139
atoms
average map value = 0.003164, steps = 80
shifted from previous position = 2.13
rotated from previous position = 2.79 degrees
atoms outside contour = 3796, contour level = 0.019827
Position of 6_Fla_Monomer2 (#9) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.06608397 -0.99773206 0.01279239 340.82449864
0.99499722 0.06685465 0.07423609 -31.20329529
-0.07492295 0.00782258 0.99715864 -17.44096315
Axis -0.03327723 0.04395076 0.99847932
Axis point 186.09105146 166.40592038 0.00000000
Rotation angle (degrees) 86.27035458
Shift along axis -30.12754573
> select add #8
8278 atoms, 8302 bonds, 546 residues, 2 models selected
> select add #7
33112 atoms, 33208 bonds, 2184 residues, 3 models selected
> select add #6
57946 atoms, 58114 bonds, 3822 residues, 4 models selected
> select add #5
82780 atoms, 83020 bonds, 5460 residues, 5 models selected
> select subtract #5
57946 atoms, 58114 bonds, 3822 residues, 4 models selected
> select subtract #6
33112 atoms, 33208 bonds, 2184 residues, 3 models selected
> select subtract #7
8278 atoms, 8302 bonds, 546 residues, 2 models selected
> select subtract #8
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> view matrix models
> #9,0.066084,-0.99773,0.012792,341.43,0.995,0.066855,0.074236,-33.495,-0.074923,0.0078226,0.99716,-4.1931
> fitmap #9 inMap #2
Fit molecule 6_Fla_Monomer2 (#9) to map postprocess_masked.mrc (#2) using 4139
atoms
average map value = 0.01364, steps = 100
shifted from previous position = 3.33
rotated from previous position = 12.9 degrees
atoms outside contour = 3342, contour level = 0.019827
Position of 6_Fla_Monomer2 (#9) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
-0.14498463 -0.98943378 0.00051181 384.96719737
0.98943293 -0.14498374 0.00147862 27.68621852
-0.00138880 0.00072078 0.99999878 -17.81806743
Axis -0.00038297 0.00096045 0.99999947
Axis point 180.51027029 180.18269389 0.00000000
Rotation angle (degrees) 98.33639859
Shift along axis -17.93889795
> fitmap #9 inMap #2
Fit molecule 6_Fla_Monomer2 (#9) to map postprocess_masked.mrc (#2) using 4139
atoms
average map value = 0.01364, steps = 40
shifted from previous position = 0.00127
rotated from previous position = 0.109 degrees
atoms outside contour = 3345, contour level = 0.019827
Position of 6_Fla_Monomer2 (#9) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
-0.14676224 -0.98917172 0.00039066 385.31476749
0.98917148 -0.14676187 0.00085590 28.22606872
-0.00078929 0.00051204 0.99999956 -17.90327289
Axis -0.00017381 0.00059643 0.99999981
Axis point 180.47761578 180.29906026 0.00000000
Rotation angle (degrees) 98.43934213
Shift along axis -17.95340589
> fitmap #9 inMap #2
Fit molecule 6_Fla_Monomer2 (#9) to map postprocess_masked.mrc (#2) using 4139
atoms
average map value = 0.01365, steps = 28
shifted from previous position = 0.0164
rotated from previous position = 0.0109 degrees
atoms outside contour = 3351, contour level = 0.019827
Position of 6_Fla_Monomer2 (#9) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
-0.14675343 -0.98917308 0.00022654 385.35781735
0.98917269 -0.14675316 0.00095140 28.19548176
-0.00090785 0.00036371 0.99999952 -17.85199234
Axis -0.00029706 0.00057341 0.99999979
Axis point 180.51130704 180.30264652 0.00000000
Rotation angle (degrees) 98.43883572
Shift along axis -17.95029652
> fitmap #9 inMap #2
Fit molecule 6_Fla_Monomer2 (#9) to map postprocess_masked.mrc (#2) using 4139
atoms
average map value = 0.01365, steps = 28
shifted from previous position = 0.0115
rotated from previous position = 0.0103 degrees
atoms outside contour = 3346, contour level = 0.019827
Position of 6_Fla_Monomer2 (#9) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
-0.14681231 -0.98916430 0.00035831 385.33422856
0.98916406 -0.14681197 0.00084478 28.23755612
-0.00078302 0.00047845 0.99999958 -17.89901299
Axis -0.00018517 0.00057692 0.99999982
Axis point 180.48306518 180.30442734 0.00000000
Rotation angle (degrees) 98.44224246
Shift along axis -17.95407060
> fitmap #9 inMap #2
Fit molecule 6_Fla_Monomer2 (#9) to map postprocess_masked.mrc (#2) using 4139
atoms
average map value = 0.01365, steps = 36
shifted from previous position = 0.00316
rotated from previous position = 0.00893 degrees
atoms outside contour = 3347, contour level = 0.019827
Position of 6_Fla_Monomer2 (#9) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
-0.14676431 -0.98917146 0.00026204 385.34321950
0.98917107 -0.14676400 0.00095726 28.20713253
-0.00090844 0.00039970 0.99999951 -17.85590075
Axis -0.00028184 0.00059165 0.99999979
Axis point 180.49911304 180.30061414 0.00000000
Rotation angle (degrees) 98.43946491
Shift along axis -17.94781150
> select add #8
8278 atoms, 8302 bonds, 546 residues, 2 models selected
> select add #7
33112 atoms, 33208 bonds, 2184 residues, 3 models selected
> select add #6
57946 atoms, 58114 bonds, 3822 residues, 4 models selected
> select add #5
82780 atoms, 83020 bonds, 5460 residues, 5 models selected
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select subtract #5
57946 atoms, 58114 bonds, 3822 residues, 4 models selected
> select add #5
82780 atoms, 83020 bonds, 5460 residues, 5 models selected
> select subtract #8
78641 atoms, 78869 bonds, 5187 residues, 4 models selected
> select add #8
82780 atoms, 83020 bonds, 5460 residues, 5 models selected
> select subtract #7
57946 atoms, 58114 bonds, 3822 residues, 4 models selected
> select subtract #6
33112 atoms, 33208 bonds, 2184 residues, 3 models selected
> select subtract #5
8278 atoms, 8302 bonds, 546 residues, 2 models selected
> select subtract #8
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> select add #8
8278 atoms, 8302 bonds, 546 residues, 2 models selected
> combine #9 #10 name 6_Fla_Monomer3
> combine #9 #11 name 6_Fla_Monomer4
> select subtract #8
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> select subtract #9
Nothing selected
> select add #4
4 models selected
> select subtract #4
Nothing selected
> select add #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select add #7
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select add #6
74502 atoms, 74718 bonds, 4914 residues, 3 models selected
> select add #8
78641 atoms, 78869 bonds, 5187 residues, 4 models selected
> select add #10
82780 atoms, 83020 bonds, 5460 residues, 5 models selected
> select add #9
86919 atoms, 87171 bonds, 5733 residues, 6 models selected
> select subtract #10
82780 atoms, 83020 bonds, 5460 residues, 5 models selected
> select subtract #9
78641 atoms, 78869 bonds, 5187 residues, 4 models selected
> select subtract #8
74502 atoms, 74718 bonds, 4914 residues, 3 models selected
> select subtract #7
49668 atoms, 49812 bonds, 3276 residues, 2 models selected
> select subtract #6
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #10
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> view matrix models
> #10,-0.14676,-0.98917,0.00026204,377.36,0.98917,-0.14676,0.00095726,41.468,-0.00090844,0.0003997,1,-25.047
> view matrix models
> #10,-0.14676,-0.98917,0.00026204,391.76,0.98917,-0.14676,0.00095726,25.981,-0.00090844,0.0003997,1,-63.238
> view matrix models
> #10,-0.14676,-0.98917,0.00026204,384.23,0.98917,-0.14676,0.00095726,30.554,-0.00090844,0.0003997,1,-70.058
> view matrix models
> #10,-0.14676,-0.98917,0.00026204,382.35,0.98917,-0.14676,0.00095726,31.703,-0.00090844,0.0003997,1,-69.935
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.16966,-0.98153,-0.088369,403.74,0.98269,-0.17526,0.060025,26.747,-0.074404,-0.076656,0.99428,-37.743
> view matrix models
> #10,-0.17265,-0.97427,-0.14486,414.46,0.97684,-0.18823,0.10174,22.061,-0.12639,-0.12394,0.98421,-15.207
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.17265,-0.97427,-0.14486,408.91,0.97684,-0.18823,0.10174,22.165,-0.12639,-0.12394,0.98421,-14.388
> select add #9
8278 atoms, 8302 bonds, 546 residues, 2 models selected
> select subtract #9
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> view matrix models
> #10,-0.17265,-0.97427,-0.14486,408.04,0.97684,-0.18823,0.10174,22.453,-0.12639,-0.12394,0.98421,-12.738
> fitmap #10 inMap #2
Fit molecule 6_Fla_Monomer3 (#10) to map postprocess_masked.mrc (#2) using
4139 atoms
average map value = 0.003256, steps = 324
shifted from previous position = 2.15
rotated from previous position = 8.13 degrees
atoms outside contour = 3868, contour level = 0.019827
Position of 6_Fla_Monomer3 (#10) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
-0.30727066 -0.94030200 -0.14634510 430.33688794
0.94669191 -0.31767640 0.05344291 66.76667909
-0.09674286 -0.12212228 0.98778893 -20.36766932
Axis -0.09260781 -0.02616438 0.99535884
Axis point 190.69511849 186.44740585 0.00000000
Rotation angle (degrees) 108.57701430
Shift along axis -61.87260426
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.38441,-0.91262,-0.13909,439.36,0.92314,-0.37906,-0.064162,108.25,0.0058315,-0.15307,0.9882,-35.611
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.38441,-0.91262,-0.13909,440.02,0.92314,-0.37906,-0.064162,101.51,0.0058315,-0.15307,0.9882,-35.909
> view matrix models
> #10,-0.38441,-0.91262,-0.13909,440.38,0.92314,-0.37906,-0.064162,102.09,0.0058315,-0.15307,0.9882,-36.575
> fitmap #10 inMap #2
Fit molecule 6_Fla_Monomer3 (#10) to map postprocess_masked.mrc (#2) using
4139 atoms
average map value = 0.01282, steps = 188
shifted from previous position = 6.87
rotated from previous position = 16.4 degrees
atoms outside contour = 3431, contour level = 0.019827
Position of 6_Fla_Monomer3 (#10) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
-0.15210785 -0.98836389 0.00013844 386.19706766
0.98836390 -0.15210783 0.00011519 29.47743686
-0.00009279 0.00015435 0.99999998 -69.64503544
Axis 0.00001981 0.00011698 0.99999999
Axis point 180.45175955 180.39768622 0.00000000
Rotation angle (degrees) 98.74909916
Shift along axis -69.63393480
> select clear
> fitmap #10 inMap #2
Fit molecule 6_Fla_Monomer3 (#10) to map postprocess_masked.mrc (#2) using
4139 atoms
average map value = 0.01282, steps = 28
shifted from previous position = 0.0101
rotated from previous position = 0.121 degrees
atoms outside contour = 3429, contour level = 0.019827
Position of 6_Fla_Monomer3 (#10) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
-0.15009935 -0.98867089 0.00022026 385.82172304
0.98867071 -0.15009917 0.00068194 28.90158341
-0.00064115 0.00032012 0.99999974 -69.56249875
Axis -0.00018298 0.00043564 0.99999989
Axis point 180.46898771 180.29429093 0.00000000
Rotation angle (degrees) 98.63268654
Shift along axis -69.62049814
> select add #9
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> select add #10
8278 atoms, 8302 bonds, 546 residues, 2 models selected
> select add #4
8278 atoms, 8302 bonds, 546 residues, 6 models selected
> select subtract #4
8278 atoms, 8302 bonds, 546 residues, 2 models selected
> select add #5
33112 atoms, 33208 bonds, 2184 residues, 3 models selected
> select add #6
57946 atoms, 58114 bonds, 3822 residues, 4 models selected
> select add #7
82780 atoms, 83020 bonds, 5460 residues, 5 models selected
> select add #8
86919 atoms, 87171 bonds, 5733 residues, 6 models selected
> select add #11
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> view matrix models
> #11,-0.14676,-0.98917,0.00026204,456.86,0.98917,-0.14676,0.00095726,-0.099371,-0.00090844,0.0003997,1,-25.193
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.71651,0.6735,0.18169,-98.564,-0.69095,0.72103,0.052022,164.41,-0.095966,-0.16281,0.98198,31.528
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.71651,0.6735,0.18169,-100.07,-0.69095,0.72103,0.052022,170.7,-0.095966,-0.16281,0.98198,31.71
> view matrix models
> #11,0.71651,0.6735,0.18169,-107.74,-0.69095,0.72103,0.052022,173.76,-0.095966,-0.16281,0.98198,-20.719
> view matrix models
> #11,0.71651,0.6735,0.18169,-100.24,-0.69095,0.72103,0.052022,177.8,-0.095966,-0.16281,0.98198,-22.944
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.94859,0.30979,0.064806,-50.932,-0.3152,0.94324,0.10467,43.316,-0.028702,-0.11972,0.99239,-47.895
> view matrix models
> #11,0.94451,0.3281,-0.015844,-37.277,-0.32821,0.94459,-0.004972,68.222,0.013335,0.0098964,0.99986,-84.544
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.94451,0.3281,-0.015844,-40.657,-0.32821,0.94459,-0.004972,60.612,0.013335,0.0098964,0.99986,-81.548
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.95708,0.28603,0.046744,-47.559,-0.28881,0.9547,0.071633,34.63,-0.024137,-0.082059,0.99634,-54.31
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.95708,0.28603,0.046744,-45.233,-0.28881,0.9547,0.071633,37.519,-0.024137,-0.082059,0.99634,-55.228
> fitmap #11 inMap #2
Fit molecule 6_Fla_Monomer4 (#11) to map postprocess_masked.mrc (#2) using
4139 atoms
average map value = 0.003344, steps = 84
shifted from previous position = 0.623
rotated from previous position = 1.4 degrees
atoms outside contour = 3835, contour level = 0.019827
Position of 6_Fla_Monomer4 (#11) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.96307272 0.26729387 0.03232519 -39.23847922
-0.26896467 0.96056575 0.07050845 32.41090759
-0.01220400 -0.07659910 0.99698728 -58.95744077
Axis -0.26370445 0.07982286 -0.96129510
Axis point 86.63481695 90.09261132 0.00000000
Rotation angle (degrees) 16.19605786
Shift along axis 69.60999184
> view matrix models
> #11,0.96307,0.26729,0.032325,-41.575,-0.26896,0.96057,0.070508,33.398,-0.012204,-0.076599,0.99699,-60.307
> fitmap #11 inMap #2
Fit molecule 6_Fla_Monomer4 (#11) to map postprocess_masked.mrc (#2) using
4139 atoms
average map value = 0.003226, steps = 88
shifted from previous position = 2.42
rotated from previous position = 1.57 degrees
atoms outside contour = 3856, contour level = 0.019827
Position of 6_Fla_Monomer4 (#11) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.96039732 0.27799392 0.01887770 -38.57917168
-0.27853682 0.95606531 0.09141314 32.15060089
0.00736398 -0.09305107 0.99563411 -59.44005072
Axis -0.31456096 0.01963398 -0.94903420
Axis point 98.78772311 74.57330397 0.00000000
Rotation angle (degrees) 17.05017251
Shift along axis 69.17738637
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.90415,0.42479,-0.045421,-43.471,-0.42017,0.90343,0.085232,73.721,0.077241,-0.057977,0.99533,-81.111
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.90415,0.42479,-0.045421,-48.569,-0.42017,0.90343,0.085232,76.107,0.077241,-0.057977,0.99533,-83.543
> fitmap #11 inMap #2
Fit molecule 6_Fla_Monomer4 (#11) to map postprocess_masked.mrc (#2) using
4139 atoms
average map value = 0.01254, steps = 116
shifted from previous position = 4.46
rotated from previous position = 9.04 degrees
atoms outside contour = 3470, contour level = 0.019827
Position of 6_Fla_Monomer4 (#11) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.84647631 0.53242613 0.00052982 -68.47324164
-0.53242584 0.84647644 -0.00059386 124.07981372
-0.00076467 0.00022059 0.99999968 -78.91212291
Axis 0.00076485 0.00121566 -0.99999897
Axis point 180.72371449 180.83080451 0.00000000
Rotation angle (degrees) 32.16955305
Shift along axis 79.01050812
> select clear
> fitmap #11 inMap #2
Fit molecule 6_Fla_Monomer4 (#11) to map postprocess_masked.mrc (#2) using
4139 atoms
average map value = 0.01254, steps = 28
shifted from previous position = 0.0215
rotated from previous position = 0.101 degrees
atoms outside contour = 3469, contour level = 0.019827
Position of 6_Fla_Monomer4 (#11) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.84558674 0.53383723 0.00093164 -68.64814399
-0.53383639 0.84558718 -0.00101661 124.62125189
-0.00133049 0.00036229 0.99999905 -78.81907728
Axis 0.00129149 0.00211874 -0.99999692
Axis point 180.75669809 181.06903942 0.00000000
Rotation angle (degrees) 32.26517239
Shift along axis 78.99421609
> select add #5
24834 atoms, 24906 bonds, 1638 residues, 1 model selected
> select subtract #5
Nothing selected
> combine #5-11 name 22-Flagellin_double-ring
Remapping chain ID 'A' in 6-Fla_2 #6 to 'G'
Remapping chain ID 'B' in 6-Fla_2 #6 to 'H'
Remapping chain ID 'C' in 6-Fla_2 #6 to 'I'
Remapping chain ID 'D' in 6-Fla_2 #6 to 'J'
Remapping chain ID 'E' in 6-Fla_2 #6 to 'K'
Remapping chain ID 'F' in 6-Fla_2 #6 to 'L'
Remapping chain ID 'A' in 6-Fla_3 #7 to 'M'
Remapping chain ID 'B' in 6-Fla_3 #7 to 'N'
Remapping chain ID 'C' in 6-Fla_3 #7 to 'O'
Remapping chain ID 'D' in 6-Fla_3 #7 to 'P'
Remapping chain ID 'E' in 6-Fla_3 #7 to 'Q'
Remapping chain ID 'F' in 6-Fla_3 #7 to 'R'
Remapping chain ID 'A' in 6_Fla_Monomer1 #8 to 'S'
Remapping chain ID 'A' in 6_Fla_Monomer2 #9 to 'T'
Remapping chain ID 'A' in 6_Fla_Monomer3 #10 to 'U'
Remapping chain ID 'A' in 6_Fla_Monomer4 #11 to 'V'
> select add #11
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> select subtract #11
Nothing selected
> select add #12
91058 atoms, 91322 bonds, 6006 residues, 1 model selected
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> select clear
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb"
> models #12 relModel #4
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/Rhom_2Ring_Rebuild4_Building.cxs"
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/PP234_Masked10A_2Ring.mrc" models #4
> close session
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb"
Chain information for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb #1
---
Chain | Description
A B C D E F G H I J K L M N O P Q R S T U V | No description available
> hide atoms
> show cartoons
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/PP234_Masked10A_2Ring.mrc"
Opened PP234_Masked10A_2Ring.mrc as #2, grid size 138,139,259, pixel
0.94,0.94,0.94, shown at level 0.0371, step 1, values float32
> volume #2 level 0.0118
> isolde start
> clipper associate #2 #1
The toModel argument must be provided!
> clipper associate #2 toModel #1
Opened PP234_Masked10A_2Ring.mrc as #1.1.1.1, grid size 138,139,259, pixel
0.94,0.94,0.94, shown at level 0.0212, step 1, values float32
Chain information for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
---
Chain | Description
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H 1.2/I 1.2/J 1.2/K 1.2/L 1.2/M
1.2/N 1.2/O 1.2/P 1.2/Q 1.2/R 1.2/S 1.2/T 1.2/U 1.2/V | No description
available
> volume #1.1.1.1 style surface
> volume #1.1.1.1
> volume #1.1.1.1 level 0.01248
> volume #1.1.1.1 level 0.005977
> volume #1.1.1.1 level 0.009264
> volume #1.1.1.1 color #00ffff3f
> volume #1.1.1.1 color #00ffff40
> volume gaussian #1 bfactor 150
Opened PP234_Masked10A_2Ring.mrc gaussian as #2, grid size 138,139,259, pixel
0.94,0.94,0.94, shown at step 1, values float32
> clipper associate #2 #1
The toModel argument must be provided!
> clipper associate #2 toModel #1
Opened PP234_Masked10A_2Ring.mrc gaussian as #1.1.1.2, grid size 138,139,259,
pixel 0.94,0.94,0.94, shown at step 1, values float32
> volume #1.1.1.2 level -5.071e-35
> volume #1.1.1.2 level -5.656e-36
> volume #1.1.1.2 region 0,0,0,137,138,258 step 1
[Repeated 1 time(s)]
> volume #1.1.1.1 level 0.01795
> volume #1.1.1.1 level 0.02103
> volume #1.1.1.1 level 0.02162
> volume #1.1.1.2 level 0.002942
> volume #1.1.1.1 level 0.01044
> volume #1.1.1.2 level 0.004965
> view #1/A:1
> view #1/A:1-5
> hide atoms
> view #1/B:1-5
No displayed objects specified.
> view #1/C:1-5
No displayed objects specified.
> view #1/D:1-5
No displayed objects specified.
> view #1/E:1-5
No displayed objects specified.
> view #1/F:1-5
No displayed objects specified.
> view #1/G:1-5
No displayed objects specified.
> select /B
4139 atoms, 4151 bonds, 273 residues, 1 model selected
> view #1/G:1-5
No displayed objects specified.
> view #1
> view #1:F
No objects specified.
> view #1:A
No objects specified.
> view #1:C
No objects specified.
> view #1:B
No objects specified.
> view #1/A:1
No displayed objects specified.
> view #1/A
No displayed objects specified.
> select add #1.2
91058 atoms, 91322 bonds, 6006 residues, 1 model selected
> select subtract #1.2
Nothing selected
> view #1/A
No displayed objects specified.
> view #1
> view all
> show all
> hide cartoons
> show cartoons
> hide atoms
> select #1/A:1-5
97 atoms, 97 bonds, 5 residues, 1 model selected
> view #1/A:1-5
No displayed objects specified.
> select #1/A:1-5
97 atoms, 97 bonds, 5 residues, 1 model selected
> select #1/A:1-5
97 atoms, 97 bonds, 5 residues, 1 model selected
> view sel
No displayed objects specified.
> select #1/A:1-5
97 atoms, 97 bonds, 5 residues, 1 model selected
> view sel
No displayed objects specified.
> select #1/A:1-5
97 atoms, 97 bonds, 5 residues, 1 model selected
> view sel
No displayed objects specified.
> select #1/A:1-5
97 atoms, 97 bonds, 5 residues, 1 model selected
> view sel
No displayed objects specified.
> show sel cartoons
> show sel atoms
> select #1/A:1-5
97 atoms, 97 bonds, 5 residues, 1 model selected
> view sel
> select #1/B:1-5
97 atoms, 97 bonds, 5 residues, 1 model selected
> view sel
No displayed objects specified.
> select #1/B:1-5
97 atoms, 97 bonds, 5 residues, 1 model selected
> show all
> select up
111 atoms, 111 bonds, 6 residues, 1 model selected
> select up
2162 atoms, 2166 bonds, 143 residues, 1 model selected
> select #1/B:1-5
97 atoms, 97 bonds, 5 residues, 1 model selected
> select #1/B:1-5
97 atoms, 97 bonds, 5 residues, 1 model selected
> view sel
> hide all
> select #1/B:1-5
97 atoms, 97 bonds, 5 residues, 1 model selected
> show sel
> view sel
> select #1/B:1-5
97 atoms, 97 bonds, 5 residues, 1 model selected
> show sel
> view sel
> hide sel
> volume #1.1.1.2 level 0.004271
> volume #1.1.1.1 level 0.02312
> select #1/B:1-10
159 atoms, 159 bonds, 10 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/B:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/C:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/D:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/E:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/F:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/G:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/H:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/I:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/J:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/K:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/L:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/M:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/N:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/O:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/P:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/Q:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/R:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/S:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/T:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/U:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/V:1-8
138 atoms, 138 bonds, 8 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/W:1-8
Nothing selected
> show sel
> view sel
No objects specified.
> select #1/A:500
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel
> view sel
> hide sel
> select #1/A:500-505
107 atoms, 106 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/A:500-506
125 atoms, 124 bonds, 7 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/A:500-507
125 atoms, 124 bonds, 7 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/A:507
Nothing selected
> show sel
> view sel
No objects specified.
> select #1/A:502-506
92 atoms, 91 bonds, 5 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/A:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/B:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/C:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/D:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> volume #1.1.1.1 level 0.02568
> select #1/E:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/F:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/G:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/H:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/I:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/J:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/K:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/L:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/M:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> view matrix models #1.2,1,0,0,0.86557,0,1,0,-0.55253,0,0,1,6.461
> undo
> ui mousemode right translate
> select up
578 atoms, 580 bonds, 37 residues, 1 model selected
> select #1/N:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/O:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/P:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/Q:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/R:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/S:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/S:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/T:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/U:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/V:501-506
108 atoms, 107 bonds, 6 residues, 1 model selected
> show sel
> view sel
> hide sel
> select #1/W:501-506
Nothing selected
> show sel
> view sel
No objects specified.
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_PreSim.cxs"
> view all
> show all
> view all
> select all
91058 atoms, 91322 bonds, 6006 residues, 9 models selected
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> sell all
Unknown command: sell all
> select all
91058 atoms, 91322 bonds, 6006 residues, 19 models selected
> isolde sim start /A-V
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> select all
91058 atoms, 91322 bonds, 6006 residues, 24 models selected
> isolde sim start /A-V
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 70 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_All-
> Sim.cxs"
Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> isolde sim start /F:107
ISOLDE: started sim
> isolde pepflip /F:107
> select clear
> isolde pepflip /F:108
> ui mousemode right translate
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /E:107
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /K:107
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /L:107
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /Q:107
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /R:107
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /K:4
ISOLDE: started sim
> isolde pepflip /K:4
> isolde pepflip /K:5
> isolde pepflip /K:6
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /M:501
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:133
ISOLDE: started sim
> isolde pepflip /A:133
> isolde pepflip /A:134
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:133
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /K:383
ISOLDE: started sim
> isolde pepflip #!1.2/K:383
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /D:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /F:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /L:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /N:410
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /J:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /G:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /F:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /H:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /I:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /M:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /T:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /O:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /R:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /F:383
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /O:133
ISOLDE: started sim
> isolde pepflip /O:133
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /N:133
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /D:133
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /C:133
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /R:133
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /G:133
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /P:133
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /Q:133
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:133
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:133
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /J:133
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /E:133
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /F:133
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /T:438
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /Q:438
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
> addh
Summary of feedback from adding hydrogens to
22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb #1.2
---
notes | Termini for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb (#1.2) chain
A determined from SEQRES records
Termini for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb (#1.2) chain B
determined from SEQRES records
Termini for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb (#1.2) chain C
determined from SEQRES records
Termini for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb (#1.2) chain D
determined from SEQRES records
Termini for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb (#1.2) chain E
determined from SEQRES records
17 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET
1, /D MET 1, /E MET 1, /F MET 1, /G MET 1, /H MET 1, /I MET 1, /J MET 1, /K
MET 1, /L MET 1, /M MET 1, /N MET 1, /O MET 1, /P MET 1, /Q MET 1, /R MET 1,
/S MET 1, /T MET 1, /U MET 1, /V MET 1
Chain-initial residues that are not actual N termini: /A GLY 377, /B GLY 377,
/C GLY 377, /D GLY 377, /E GLY 377, /F GLY 377, /G GLY 377, /H GLY 377, /I GLY
377, /J GLY 377, /K GLY 377, /L GLY 377, /M GLY 377, /N GLY 377, /O GLY 377,
/P GLY 377, /Q GLY 377, /R GLY 377, /S GLY 377, /T GLY 377, /U GLY 377, /V GLY
377
Chain-final residues that are actual C termini: /A GLN 506, /B GLN 506, /C GLN
506, /D GLN 506, /E GLN 506, /F GLN 506, /G GLN 506, /H GLN 506, /I GLN 506,
/J GLN 506, /K GLN 506, /L GLN 506, /M GLN 506, /N GLN 506, /O GLN 506, /P GLN
506, /Q GLN 506, /R GLN 506, /S GLN 506, /T GLN 506, /U GLN 506, /V GLN 506
Chain-final residues that are not actual C termini: /A THR 143, /B THR 143, /C
THR 143, /D THR 143, /E THR 143, /F THR 143, /G THR 143, /H THR 143, /I THR
143, /J THR 143, /K THR 143, /L THR 143, /M THR 143, /N THR 143, /O THR 143,
/P THR 143, /Q THR 143, /R THR 143, /S THR 143, /T THR 143, /U THR 143, /V THR
143
6583 hydrogen bonds
/A THR 143 is not terminus, removing H atom from 'C'
/B THR 143 is not terminus, removing H atom from 'C'
/C THR 143 is not terminus, removing H atom from 'C'
/D THR 143 is not terminus, removing H atom from 'C'
/E THR 143 is not terminus, removing H atom from 'C'
17 messages similar to the above omitted
13 hydrogens added
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
——— End of log from Thu Jan 25 14:40:09 2024 ———
opened ChimeraX session
> view all
> isolde start
> set selectionWidth 4
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> ui tool show "Ramachandran Plot"
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> select clear
> isolde sim start /V:497
ISOLDE: started sim
> isolde pepflip /V:497
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /V:497
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /D:498
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /H:499
ISOLDE: started sim
> isolde pepflip /H:499
> isolde cisflip /H:499
> isolde cisflip /H:500
> isolde pepflip /H:500
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /G:441
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /M:106
ISOLDE: started sim
> select clear
> ui tool show "Show Volume Menu"
> ui tool show "Volume Viewer"
> volume #1.1.1.2 level 0.002141
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /O:50
ISOLDE: started sim
> volume #1.1.1.2 level 0.007621
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #!1.2/H:50
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /U:50
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /G:429
ISOLDE: started sim
> volume #1.1.1.2 level 0.003035
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /J:40
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /C:40
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /C:17
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /R:479
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /C:142
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /C:50
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:429
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /R:445
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /R:142
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:458
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /P:106
ISOLDE: started sim
> isolde pepflip /P:106
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /F:142
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /I:17
ISOLDE: started sim
> volume #1.1.1.2 level 0.003035
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /C:445
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /T:445
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:84
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /N:50
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /G:407
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /G:407
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /C:388
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /M:17
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /J:394
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /N:3
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /I:50
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /J:429
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /P:445
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /H:429
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:50
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start /Q:445
ISOLDE: started sim
> volume #1.1.1.2 level 0.00159
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:50
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /V:50
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /P:50
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /D:17
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /U:3
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:106
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /I:40
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /I:3
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /I:3
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /I:2
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /O:394
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /N:504
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /P:3
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:445
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /V:1
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /V:3
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /D:3
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /D:501
ISOLDE: started sim
> isolde pepflip /D:501
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /U:502
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /J:50
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /P:84
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:100
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /O:3
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /F:429
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /D:500
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /V:3
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /S:100
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /N:141
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /E:84
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /E:119
ISOLDE: started sim
> volume #1.1.1.2 level 0.0003392
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /E:84
ISOLDE: started sim
> select clear
> isolde pepflip /E:84
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
——— End of log from Wed Jan 31 17:03:39 2024 ———
opened ChimeraX session
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x600001d095a0, name="DELL U2415") screenTo: QScreen(0x0) wdgScreen:
QScreen(0x600001d095a0, name="DELL U2415") orgWdgScreen
QScreen(0x600001d09670, name="Built-in Retina Display")
[Repeated 39 time(s)]
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> isolde sim start /V:3
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /E:84
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:142
ISOLDE: started sim
> isolde pepflip /A:142
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:2
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /V:3
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /O:143
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /T:84
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /V:432
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:388
ISOLDE: started sim
> isolde pepflip /D:389
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /F:1
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /F:1
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /K:100
ISOLDE: started sim
> isolde pepflip /K:100
> select clear
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start /M:1
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /R:20
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /T:84
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /M:3
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /K:1
ISOLDE: started sim
> isolde pepflip /K:2
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /M:142
ISOLDE: started sim
> ui tool show "Volume Viewer"
> volume #1.1.1.1 level 0.005023
> volume #1.1.1.2 level 0.0007055
> volume #1.1.1.1 level 0.01489
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /V:445
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:40
ISOLDE: started sim
> volume #1.1.1.1 level 0.00336
> volume #1.1.1.1 level 0.01945
> select clear
[Repeated 2 time(s)]
> volume #1.1.1.1 level 0.01248
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:445
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /D:472
ISOLDE: started sim
> volume #1.1.1.1 level 0.0001158
> volume #1.1.1.1 level 0.008715
> volume #1.1.1.2 level -0.001536
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /I:441
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:100
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
——— End of log from Tue Feb 6 15:50:30 2024 ———
opened ChimeraX session
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> select clear
> isolde sim start /S:441
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /V:40
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /F:3
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Show Volume Menu"
> ui tool show "Volume Viewer"
> volume #1.1.1.1 level 0.007575
> volume #1.1.1.1 level 0.001855
> volume #1.1.1.1 level 0.008033
> isolde sim start /C:40
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /C:50
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /K:100
ISOLDE: started sim
> isolde pepflip /K:100
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:100
ISOLDE: started sim
> isolde pepflip /A:101
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start /D:498
ISOLDE: started sim
> isolde pepflip /D:498
> volume #1.1.1.1 level 0.01525
> isolde pepflip /D:501
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view all
> select #1/A
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> view #1/A
> isolde sim start /A
ISOLDE: started sim
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
> select #1/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> view #1/A:1
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/A:1-200
2162 atoms, 2166 bonds, 143 residues, 1 model selected
> isolde sim start /A:1-143
ISOLDE: started sim
> select #1/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> volume #1.1.1.1 level 0.006304
> isolde pepflip /A:2
> select #1/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> volume #1.1.1.1 level 0.01796
> st
> isolde pepflip /A:3
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/A:1-200
2162 atoms, 2166 bonds, 143 residues, 1 model selected
> isolde sim start /A:1-143
ISOLDE: started sim
> select #1/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> st
> st -1
Unrecognised residue argument! If specified, must be either a residue,
"first", "last", "next" or "prev"
> st prev
[Repeated 1 time(s)]
> volume #1.1.1.1 level 0.006033
> st
[Repeated 10 time(s)]
> volume #1.1.1.1 level 0.012
> st
[Repeated 11 time(s)]
> select clear
[Repeated 1 time(s)]
> st
[Repeated 24 time(s)]
> st prev
[Repeated 16 time(s)]
> st
[Repeated 18 time(s)]
> st prev
> st
[Repeated 33 time(s)]
> st prev
> st
[Repeated 6 time(s)]
> volume #1.1.1.2 level -0.0006175
> st
[Repeated 13 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/A:100-300
676 atoms, 676 bonds, 44 residues, 1 model selected
> select #1/A:100-200
676 atoms, 676 bonds, 44 residues, 1 model selected
> isolde sim start /A:100-143
ISOLDE: started sim
> st
[Repeated 40 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/A:300-400
362 atoms, 363 bonds, 24 residues, 1 model selected
> isolde sim start /A:377-400
ISOLDE: started sim
> st prev
> st
[Repeated 28 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/A:350-500
1870 atoms, 1878 bonds, 124 residues, 1 model selected
> isolde sim start /A:377-500
ISOLDE: started sim
> st
[Repeated 91 time(s)]
> isolde pepflip /A:499
> select clear
> st
[Repeated 7 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
——— End of log from Thu Feb 8 16:08:43 2024 ———
opened ChimeraX session
> view all
> combine #1/A #2
> hide #2 models
> show #2 models
> ui mousemode right "translate selected models"
> select add #2
91090 atoms, 91353 bonds, 6007 residues, 2 models selected
> select subtract #2
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #1.2
91071 atoms, 91335 bonds, 6006 residues, 25 models selected
> select add #1.2
91071 atoms, 91335 bonds, 6006 residues, 25 models selected
> select add #1
91071 atoms, 91335 bonds, 6006 residues, 35 models selected
> select add #1
91071 atoms, 91335 bonds, 6006 residues, 35 models selected
> select add #1
91071 atoms, 91335 bonds, 6006 residues, 35 models selected
> hide #!1 models
> show #!1 models
> select clear
> select add #2
91071 atoms, 91335 bonds, 6006 residues, 1 model selected
> view matrix models #2,1,0,0,42.021,0,1,0,149.92,0,0,1,36.759
> view matrix models #2,1,0,0,53.235,0,1,0,239.35,0,0,1,110.74
> hide sel atoms
> delete #2/B-L
> delete #2/L-Q
> delete #2/R-U
> delete #2/V
> select #2/A
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> view matrix models #2,1,0,0,-4.4005,0,1,0,91.276,0,0,1,62.808
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_Monomer-v5.pdb" models #2
> close #2
> select clear
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb
——— End of log from Mon Feb 12 16:01:42 2024 ———
opened ChimeraX session
> close session
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb"
> format pdb
Chain information for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb #1
---
Chain | Description
A B C D E F G H I J K L M N O P Q R S T U V | No description available
> hide atoms
> show cartoons
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_Monomer-v5.pdb" format pdb
Chain information for Rhom_Monomer-v5.pdb #2
---
Chain | Description
A | No description available
> combine #2 #3 name Rhom_Monomer-V5_B
> combine #2 #4 name Rhom_Monomer-V5_C
> combine #2 #5 name Rhom_Monomer-V5_C
> combine #2 #6 name Rhom_Monomer-V5_D
> combine #2 #7 name Rhom_Monomer-V5_E
> combine #2 #8 name Rhom_Monomer-V5_F
> combine #2 #9 name Rhom_Monomer-V5_G
> combine #2 #10 name Rhom_Monomer-V5_H
> combine #2 #11 name Rhom_Monomer-V5_I
> combine #2 #12 name Rhom_Monomer-V5_J
> combine #2 #13 name Rhom_Monomer-V5_K
> combine #2 #14 name Rhom_Monomer-V5_L
> combine #2 #15 name Rhom_Monomer-V5_M
> combine #2 #16 name Rhom_Monomer-V5_N
> combine #2 #17 name Rhom_Monomer-V5_O
> combine #2 #18 name Rhom_Monomer-V5_P
> combine #2 #19 name Rhom_Monomer-V5_Q
> combine #2 #20 name Rhom_Monomer-V5_R
> combine #2 #21 name Rhom_Monomer-V5_S
> combine #2 #22 name Rhom_Monomer-V5_T
> mmaker #2 #1/A
> matchmaker #2 #1/A
Missing required "to" argument
> mmaker #2 to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain A (#1) with
Rhom_Monomer-v5.pdb, chain A (#2), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #3 to #1/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain B (#1) with
Rhom_Monomer-V5_B, chain A (#3), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #4 to #1/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain C (#1) with
Rhom_Monomer-V5_C, chain A (#4), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #5 to #1/D
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain D (#1) with
Rhom_Monomer-V5_C, chain A (#5), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #6 to #1/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain E (#1) with
Rhom_Monomer-V5_D, chain A (#6), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #7 to #1/F
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain F (#1) with
Rhom_Monomer-V5_E, chain A (#7), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #8 to #1/G
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain G (#1) with
Rhom_Monomer-V5_F, chain A (#8), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #9 to #1/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain H (#1) with
Rhom_Monomer-V5_G, chain A (#9), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #10 to #1/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain I (#1) with
Rhom_Monomer-V5_H, chain A (#10), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #11 to #1/J
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain J (#1) with
Rhom_Monomer-V5_I, chain A (#11), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #12 to #1/K
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain K (#1) with
Rhom_Monomer-V5_J, chain A (#12), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #13 to #1/L
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain L (#1) with
Rhom_Monomer-V5_K, chain A (#13), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #14 to #1/M
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain M (#1) with
Rhom_Monomer-V5_L, chain A (#14), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #15 to #1/N
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain N (#1) with
Rhom_Monomer-V5_M, chain A (#15), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #16 to #1/O
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain O (#1) with
Rhom_Monomer-V5_N, chain A (#16), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #17 to #1/P
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain P (#1) with
Rhom_Monomer-V5_O, chain A (#17), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #18 to #1/Q
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain Q (#1) with
Rhom_Monomer-V5_P, chain A (#18), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #19 to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain R (#1) with
Rhom_Monomer-V5_Q, chain A (#19), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #20 to #1/S
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain S (#1) with
Rhom_Monomer-V5_R, chain A (#20), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #21 to #1/T
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain T (#1) with
Rhom_Monomer-V5_S, chain A (#21), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #22 to #1U
> matchmaker #22 to #1U
Invalid "to" argument: only initial part "#1" of atom specifier valid
> mmaker #22 to #1/U
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain U (#1) with
Rhom_Monomer-V5_T, chain A (#22), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> combine #2 #23 name Rhom_Monomer-V5_U
> combine #2 #24 name Rhom_Monomer-V5_V
> mmaker #23 to #1/V
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain V (#1) with
Rhom_Monomer-V5_U, chain A (#23), sequence alignment score = 2177.7
RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
0.277)
> mmaker #24 to #1/W
No 'to' model specified
> ui mousemode right "translate selected models"
> select add #24
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> view matrix models
> #24,1,-0.001903,-0.0019137,-43.385,0.0019027,1,-0.00018112,-57.254,0.001914,0.00017748,1,0.29519
> 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
> color #3 #38ef78ff
> color #3 #34ee63ff
> color #3 #2dd157ff
> color #4 #a7ef36ff
> color #5 #ef4123ff
> color #6 #ef4ce8ff
> color #7 #8e3eefff
> color #8 #0c23efff
> color #9 #c6ebefff
> color #10 #10ef0cff
> color #10 #11ff0dff
> color #11 #ef9b00ff
> color #12 #ef0679ff
> color #13 #efb8b7ff
> color #14 #efeeaeff
> color #15 #a5b0efff
> color #16 #ef64c7ff
> color #17 #efa767ff
> color #18 #83b0efff
> color #19 #6c9cadff
> color #19 #ad2b3dff
> color #19 #943fadff
> color #20 #6d9dafff
> color #20 #2f69afff
> color #21 #70a1b2ff
> color #21 #58b244ff
> color #21 #51b244ff
> color #22 #af9c2eff
> color #23 #93c06cff
> select clear
[Repeated 2 time(s)]Drag select of 227 residues
> select add #24
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> select subtract #24
Nothing selected
> select add #24
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> view matrix models
> #24,1,-0.001903,-0.0019137,-38.583,0.0019027,1,-0.00018112,80.577,0.001914,0.00017748,1,-2.4242
> combine #2-23 name 22-Flagellin_Rebuild5
Remapping chain ID 'A' in Rhom_Monomer-V5_B #3 to 'B'
Remapping chain ID 'A' in Rhom_Monomer-V5_C #4 to 'C'
Remapping chain ID 'A' in Rhom_Monomer-V5_C #5 to 'D'
Remapping chain ID 'A' in Rhom_Monomer-V5_D #6 to 'E'
Remapping chain ID 'A' in Rhom_Monomer-V5_E #7 to 'F'
Remapping chain ID 'A' in Rhom_Monomer-V5_F #8 to 'G'
Remapping chain ID 'A' in Rhom_Monomer-V5_G #9 to 'H'
Remapping chain ID 'A' in Rhom_Monomer-V5_H #10 to 'I'
Remapping chain ID 'A' in Rhom_Monomer-V5_I #11 to 'J'
Remapping chain ID 'A' in Rhom_Monomer-V5_J #12 to 'K'
Remapping chain ID 'A' in Rhom_Monomer-V5_K #13 to 'L'
Remapping chain ID 'A' in Rhom_Monomer-V5_L #14 to 'M'
Remapping chain ID 'A' in Rhom_Monomer-V5_M #15 to 'N'
Remapping chain ID 'A' in Rhom_Monomer-V5_N #16 to 'O'
Remapping chain ID 'A' in Rhom_Monomer-V5_O #17 to 'P'
Remapping chain ID 'A' in Rhom_Monomer-V5_P #18 to 'Q'
Remapping chain ID 'A' in Rhom_Monomer-V5_Q #19 to 'R'
Remapping chain ID 'A' in Rhom_Monomer-V5_R #20 to 'S'
Remapping chain ID 'A' in Rhom_Monomer-V5_S #21 to 'T'
Remapping chain ID 'A' in Rhom_Monomer-V5_T #22 to 'U'
Remapping chain ID 'A' in Rhom_Monomer-V5_U #23 to 'V'
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild5.cxs"
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-Ring_v5.pdb" models #25
> close session
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-Ring_v5.pdb"
Chain information for Rhom_22-Ring_v5.pdb #1
---
Chain | Description
A B C D E F G H I J K L M N O P Q R S T U V | No description available
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/job234/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #2, grid size 384,384,384, pixel 0.94, shown
at level 0.0177, step 2, values float32
> fitmap #1 inMap #2
Fit molecule Rhom_22-Ring_v5.pdb (#1) to map postprocess_masked.mrc (#2) using
91080 atoms
average map value = 0.01352, steps = 44
shifted from previous position = 0.0209
rotated from previous position = 0.031 degrees
atoms outside contour = 70404, contour level = 0.017739
Position of Rhom_22-Ring_v5.pdb (#1) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.99999986 0.00053437 0.00002071 -0.09756272
-0.00053437 0.99999985 -0.00008341 0.12510606
-0.00002076 0.00008340 1.00000000 0.00294575
Axis 0.15410529 0.03830679 -0.98731158
Axis point 235.01181344 178.84439944 0.00000000
Rotation angle (degrees) 0.03101077
Shift along axis -0.01315089
> volume #2 color #b2b2b27e
> volume #2 color #b2b2b280
> hide atoms
> show cartoons
> volume #2 color #b2b2b24e
> volume #2 color #b2b2b24d
> volume #2 color #b2b2b2a6
> fitmap #1 inMap #2
Fit molecule Rhom_22-Ring_v5.pdb (#1) to map postprocess_masked.mrc (#2) using
91080 atoms
average map value = 0.01352, steps = 40
shifted from previous position = 0.0181
rotated from previous position = 0.00761 degrees
atoms outside contour = 70402, contour level = 0.017739
Position of Rhom_22-Ring_v5.pdb (#1) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.99999984 0.00055578 0.00007217 -0.10933460
-0.00055578 0.99999984 0.00003718 0.09136404
-0.00007215 -0.00003722 1.00000000 0.03367751
Axis -0.06623089 0.12847923 -0.98949813
Axis point 167.64958758 198.48073340 0.00000000
Rotation angle (degrees) 0.03218170
Shift along axis -0.01434412
> select #1/A
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> select #1/B
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> select #1/A
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x600003dac380, name="DELL U2415") screenTo: QScreen(0x0) wdgScreen:
QScreen(0x600003dac380, name="DELL U2415") orgWdgScreen
QScreen(0x600003da75a0, name="Built-in Retina Display")
[Repeated 11 time(s)]
> clipper associate #1 #2
The toModel argument must be provided!
> clipper associate #2 toModel #1
Opened postprocess_masked.mrc as #1.1.1.1, grid size 384,384,384, pixel 0.94,
shown at level 0.0216, step 1, values float32
Chain information for Rhom_22-Ring_v5.pdb
---
Chain | Description
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H 1.2/I 1.2/J 1.2/K 1.2/L 1.2/M
1.2/N 1.2/O 1.2/P 1.2/Q 1.2/R 1.2/S 1.2/T 1.2/U 1.2/V | No description
available
> undo
> close session
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-Ring_v5.pdb" format pdb
Chain information for Rhom_22-Ring_v5.pdb #1
---
Chain | Description
A B C D E F G H I J K L M N O P Q R S T U V | No description available
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/job234/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #2, grid size 384,384,384, pixel 0.94, shown
at level 0.0177, step 2, values float32
> fitmap #1 inMap #2
Fit molecule Rhom_22-Ring_v5.pdb (#1) to map postprocess_masked.mrc (#2) using
91080 atoms
average map value = 0.01352, steps = 44
shifted from previous position = 0.0209
rotated from previous position = 0.031 degrees
atoms outside contour = 70404, contour level = 0.017739
Position of Rhom_22-Ring_v5.pdb (#1) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.99999986 0.00053437 0.00002071 -0.09756272
-0.00053437 0.99999985 -0.00008341 0.12510606
-0.00002076 0.00008340 1.00000000 0.00294575
Axis 0.15410529 0.03830679 -0.98731158
Axis point 235.01181344 178.84439944 0.00000000
Rotation angle (degrees) 0.03101077
Shift along axis -0.01315089
> hide atoms
> show cartoons
> lighting simple
> volume #2 color #b2b2b27e
> volume #2 color #b2b2b27d
> molmap #1
Missing or invalid "resolution" argument: Expected a number
> molmap #1 resolution 3
Missing or invalid "resolution" argument: Expected a number
> molmap #1 3
Opened Rhom_22-Ring_v5.pdb map 3 as #3, grid size 141,142,259, pixel 1, shown
at level 0.119, step 1, values float32
> molmap #1 2
Opened Rhom_22-Ring_v5.pdb map 2 as #3, grid size 203,203,379, pixel 0.667,
shown at level 0.15, step 1, values float32
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild5_PreSim.cxs"
> volume mask #3 #2
Missing required "surfaces" argument
> volume mask #2 surfaces #3
Opened postprocess_masked.mrc masked as #4, grid size 136,136,260, pixel 0.94,
shown at step 1, values float32
> hide #!3 models
> show #!3 models
> hide #!3 models
> isolde start
> clipper associate #1 #4
The toModel argument must be provided!
> clipper associate #4 toModel #1
Opened postprocess_masked.mrc masked as #1.1.1.1, grid size 136,136,260, pixel
0.94, shown at level 0.0187, step 1, values float32
Chain information for Rhom_22-Ring_v5.pdb
---
Chain | Description
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H 1.2/I 1.2/J 1.2/K 1.2/L 1.2/M
1.2/N 1.2/O 1.2/P 1.2/Q 1.2/R 1.2/S 1.2/T 1.2/U 1.2/V | No description
available
> select all
91080 atoms, 91344 bonds, 6006 residues, 11 models selected
> select all
91080 atoms, 91344 bonds, 6006 residues, 11 models selected
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde sim start /A-V
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 76 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/A:1
> volume gaussian #1 bfactor 150
Opened postprocess_masked.mrc masked gaussian as #4, grid size 136,136,260,
pixel 0.94, shown at step 1, values float32
> clipper associate #4 toModel #1
Opened postprocess_masked.mrc masked gaussian as #1.1.1.2, grid size
136,136,260, pixel 0.94, shown at step 1, values float32
> volume #1.1.1.1 style surface
> volume #1.1.1.1 color #00ffff34
> volume #1.1.1.1 color #00ffff33
> volume #1.1.1.2 region 0,0,0,135,135,259 step 1
[Repeated 1 time(s)]
> volume #1.1.1.1 level 0.02312
> volume #1.1.1.2 level 0.004236
> view #1/A:1
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
> st
[Repeated 1 time(s)]
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> isolde sim start /A:2
ISOLDE: started sim
> isolde pepflip /A:2
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start /A:3
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 9 time(s)]
> isolde sim start /A:13
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> volume #1.1.1.2 level 0.003616
> st
[Repeated 9 time(s)]
> volume #1.1.1.2 level 0.002229
> st
[Repeated 7 time(s)]
> volume #1.1.1.1 level 0.001899
> volume #1.1.1.1 level 0.02252
> isolde sim start /A:35
ISOLDE: started sim
> volume #1.1.1.2 level 0.001528
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 41 time(s)]
> isolde sim start /A:77
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> volume #1.1.1.2 level 9.276e-05
> volume #1.1.1.2 level 0.002873
> volume #1.1.1.1 level 0.001436
> volume #1.1.1.2 level 0.0007206
> volume #1.1.1.1 level 0.01483
> volume #1.1.1.1 level 0.02559
> st
[Repeated 1 time(s)]
> isolde sim start /A:84
ISOLDE: started sim
> volume #1.1.1.2 level 0.003232
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> volume #1.1.1.1 level 0.02405
> volume #1.1.1.1 level 0.02691
> volume #1.1.1.2 level 0.0004515
> isolde sim start /A:85
ISOLDE: started sim
> volume #1.1.1.2 level 0.001262
> volume #1.1.1.1 level 0.005169
> volume #1.1.1.1 level 0.02296
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 5 time(s)]
> volume #1.1.1.1 level 0.001779
> isolde sim start /A:91
ISOLDE: started sim
> volume #1.1.1.1 level 2.26e-05
> volume #1.1.1.1 level 0.0143
> volume #1.1.1.2 level 0.002428
> volume #1.1.1.1 level 0.02001
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> st prev
> st
[Repeated 10 time(s)]
> isolde sim start /A:105
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> volume #1.1.1.1 level 0.0182
> volume #1.1.1.2 level 0.0004029
> isolde sim start /A:106
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> volume #1.1.1.2 level 0.001857
> volume #1.1.1.1 level 0.0297
> st
[Repeated 31 time(s)]
> volume #1.1.1.2 level 0.00294
> st
[Repeated 7 time(s)]
> isolde sim start /A:381
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 9 time(s)]
> isolde sim start /A:391
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> st prev
[Repeated 85 time(s)]
> st
[Repeated 35 time(s)]
> select clear
> isolde sim start /A:391
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 35 time(s)]
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1.2/A
> select /A:7-32,43-98,105-128,415-466,470-505
2941 atoms, 2944 bonds, 194 residues, 1 model selected
> select clear
> st
[Repeated 3 time(s)]
> st prev
[Repeated 16 time(s)]
> st
[Repeated 18 time(s)]
> isolde sim start /A:433
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start /A:436
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> st prev
> st
[Repeated 5 time(s)]
> st prev
[Repeated 5 time(s)]
> st
[Repeated 7 time(s)]
> isolde sim start /A:448
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start /A:449
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> st prev
> st
[Repeated 2 time(s)]
> isolde sim start /A:453
ISOLDE: started sim
> volume #1.1.1.2 level 0.001327
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start /A:456
ISOLDE: started sim
> volume #1.1.1.1 level 0.000749
> volume #1.1.1.1 level 0.02158
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> isolde sim start /A:463
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> volume #1.1.1.2 level 0.006082
> st
[Repeated 4 time(s)]
> volume #1.1.1.2 level 0.003741
> isolde sim start /A:472
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 5 time(s)]
> isolde sim start /A:478
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start /A:479
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> volume #1.1.1.2 level 0.002231
> isolde sim start /A:484
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> volume #1.1.1.2 level 0.003208
> st
[Repeated 7 time(s)]
> isolde sim start /A:496
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> st prev
> isolde sim start /A:496
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st prev
> st
[Repeated 11 time(s)]
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild5_Current.cxs"
Taking snapshot of stepper: Rhom_22-Ring_v5.pdb
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild5_Current.cxs"
Taking snapshot of stepper: Rhom_22-Ring_v5.pdb
——— End of log from Tue Feb 13 14:02:34 2024 ———
opened ChimeraX session
> select #1/M
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> select #1/A]
Nothing selected
> select #1/A
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> select ~sel & ##selected
86940 atoms, 87192 bonds, 5733 residues, 1 model selected
> select ~sel & ##selected
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> select #1/B
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> select ~sel & ##selected
86940 atoms, 87192 bonds, 5733 residues, 1 model selected
> select down
86940 atoms, 87192 bonds, 5733 residues, 2 models selected
> select up
91080 atoms, 91344 bonds, 6006 residues, 2 models selected
> select down
86940 atoms, 87192 bonds, 5733 residues, 2 models selected
> select #1/C
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> select #1/D
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> select #1/D:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/D:90
17 atoms, 16 bonds, 1 residue, 1 model selected
> view #1/D:90
> st
> view #1/D:90
[Repeated 1 time(s)]
> select #1/D:90
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /D:90
17 atoms, 16 bonds, 1 residue, 1 model selected
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> isolde stepto /D:90
> st
> volume #1.1.1.2 level -0.0001976
> volume #1.1.1.2 level 0.0005322
> view #1/A:91
> view #1/B:91
> volume #1.1.1.2 level 0.005833
> volume #1.1.1.2 level 0.001767
> view #1/C:91
> view #1/D:91
> view #1/E:91
> volume #1.1.1.1 level 0.0006354
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> isolde sim start /E:91
ISOLDE: started sim
> volume #1.1.1.1 level 0.0002176
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/F:91
> volume #1.1.1.1 level 0.01124
> volume #1.1.1.2 level 0.00583
> volume #1.1.1.1 level 0.00634
> view #1/G:91
> view #1/H:91
> volume #1.1.1.1 level 0.01485
> volume #1.1.1.2 level 0.001053
> view #1/I:91
> view #1/J:91
> view #1/K:91
> view #1/L:91
> volume #1.1.1.2 level 0.003594
> volume #1.1.1.1 level 0.008011
> volume #1.1.1.1 level 0.01094
> view #1/M:91
> view #1/N:91
> view #1/O:91
> view #1/P:91
> view #1/Q:91
> view #1/R:91
> view #1/S:91
> volume #1.1.1.2 level 0.002077
> view #1/T:91
> view #1/U:91
> view #1/V:91
> volume #1.1.1.2 level 0.001709
> view #1/W:91
No objects specified.
> view #1/J:91
> view #1/C:91
> view #1/B:91
> view #1/D:91
> view #1/E:91
> view #1/F:91
> volume #1.1.1.2 level 0.002124
> volume #1.1.1.1 level 0.0005339
> view #1/G:91
> isolde sim start /G:91
ISOLDE: started sim
> volume #1.1.1.2 level 0.004674
> volume #1.1.1.1 level -0.0006614
> volume #1.1.1.1 level 0.0005339
> volume #1.1.1.1 level 0.03424
> volume #1.1.1.2 level 0.003229
> volume #1.1.1.1 level 0.000773
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/G:1
> volume #1.1.1.2 level 0.003522
> volume #1.1.1.1 level 0.02145
> isolde stepto /G:1
> st
[Repeated 83 time(s)]
> volume #1.1.1.1 level 0.02026
> volume #1.1.1.2 level 0.0007171
> st
[Repeated 1 time(s)]
> volume #1.1.1.2 level 0.002077
> volume #1.1.1.1 level 0.0302
> st
[Repeated 2 time(s)]
> isolde stepto prev
> st
[Repeated 46 time(s)]
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild5_Current.cxs"
Taking snapshot of stepper: Rhom_22-Ring_v5.pdb
——— End of log from Fri Feb 16 17:32:49 2024 ———
opened ChimeraX session
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_Monomer-v6.pdb" format pdb
Chain information for Rhom_Monomer-v6.pdb #4
---
Chain | Description
A | No description available
> hide #4 models
> show #4 models
> select clear
> select add #4
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,48.108,0,1,0,-140.89,0,0,1,101.47
> view matrix models #4,1,0,0,184.09,0,1,0,-196.58,0,0,1,127.52
> view matrix models #4,1,0,0,211.05,0,1,0,-218,0,0,1,123.33
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/job234/postprocess_masked.mrc" format mrc
Opened postprocess_masked.mrc as #5, grid size 384,384,384, pixel 0.94, shown
at level 0.0177, step 2, values float32
> select subtract #4
Nothing selected
> select add #5
2 models selected
> view matrix models #5,1,0,0,268.01,0,1,0,-72.522,0,0,1,36.956
> fitmap #4 inMap #5
Fit molecule Rhom_Monomer-v6.pdb (#4) to map postprocess_masked.mrc (#5) using
4140 atoms
average map value = 0.002182, steps = 132
shifted from previous position = 2.54
rotated from previous position = 5.85 degrees
atoms outside contour = 3900, contour level = 0.017739
Position of Rhom_Monomer-v6.pdb (#4) relative to postprocess_masked.mrc (#5)
coordinates:
Matrix rotation and translation
0.99596468 -0.00645146 -0.08951383 -37.50635942
0.01076559 0.99879909 0.04779632 -153.56752897
0.08909798 -0.04856712 0.99483807 81.48274188
Axis -0.47311777 -0.87693449 0.08453092
Axis point -736.96396648 0.00000000 456.19593597
Rotation angle (degrees) 5.84506312
Shift along axis 159.30139847
> select clear
> select add #4
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> view matrix models
> #4,0.99596,-0.0064515,-0.089514,270.58,0.010766,0.9988,0.047796,-145.6,0.089098,-0.048567,0.99484,83.535
> fitmap #4 inMap #5
Fit molecule Rhom_Monomer-v6.pdb (#4) to map postprocess_masked.mrc (#5) using
4140 atoms
average map value = 0.0009212, steps = 88
shifted from previous position = 2.47
rotated from previous position = 4.07 degrees
atoms outside contour = 3812, contour level = 0.017739
Position of Rhom_Monomer-v6.pdb (#4) relative to postprocess_masked.mrc (#5)
coordinates:
Matrix rotation and translation
0.98871089 0.03425987 -0.14586648 5.43922050
-0.02495788 0.99756462 0.06513018 -67.83410272
0.14774259 -0.06075440 0.98715806 39.48270353
Axis -0.38745649 -0.90369082 -0.18226458
Axis point -314.02794466 0.00000000 199.71006694
Rotation angle (degrees) 9.34912949
Shift along axis 51.99729633
> view matrix models
> #4,0.98871,0.03426,-0.14587,280.46,-0.024958,0.99756,0.06513,-132.11,0.14774,-0.060754,0.98716,76.182
> fitmap #4 inMap #5
Fit molecule Rhom_Monomer-v6.pdb (#4) to map postprocess_masked.mrc (#5) using
4140 atoms
average map value = 0.003546, steps = 256
shifted from previous position = 3.55
rotated from previous position = 9.76 degrees
atoms outside contour = 3660, contour level = 0.017739
Position of Rhom_Monomer-v6.pdb (#4) relative to postprocess_masked.mrc (#5)
coordinates:
Matrix rotation and translation
0.97572573 0.19574979 -0.09819025 -38.58360905
-0.19001409 0.97964051 0.06480055 -19.83173175
0.10887584 -0.04457004 0.99305567 39.26988893
Axis -0.24235732 -0.45884349 -0.85482488
Axis point -161.85150968 195.75391709 0.00000000
Rotation angle (degrees) 13.04046385
Shift along axis -15.11819695
> select clear
> combine #1 #6
> hide #6 models
> show #6 models
> select add #6
91080 atoms, 91344 bonds, 6006 residues, 1 model selected
> view matrix models #6,1,0,0,389.06,0,1,0,-157.76,0,0,1,24.644
> view matrix models #6,1,0,0,424.75,0,1,0,-194.38,0,0,1,28.303
> hide sel atoms
> show sel cartoons
> select add #4
95220 atoms, 95496 bonds, 6279 residues, 2 models selected
> select subtract #6
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> close #4
> select add #6
91080 atoms, 91344 bonds, 6006 residues, 1 model selected
> view matrix models #6,1,0,0,271.48,0,1,0,-86.434,0,0,1,32.855
> fitmap #6 inMap #5
Fit molecule copy of Rhom_22-Ring_v5.pdb (#6) to map postprocess_masked.mrc
(#5) using 91080 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 91080, contour level = 0.017739
Position of copy of Rhom_22-Ring_v5.pdb (#6) relative to
postprocess_masked.mrc (#5) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 156.73646357
0.00000000 1.00000000 0.00000000 -121.85380860
0.00000000 0.00000000 1.00000000 -8.65322630
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -8.65322630
> select clear
> select add #6
91080 atoms, 91344 bonds, 6006 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
91080 atoms, 91344 bonds, 6006 residues, 1 model selected
> view matrix models #6,1,0,0,262.69,0,1,0,-74.562,0,0,1,32.195
> fitmap #6 inMap #5
Fit molecule copy of Rhom_22-Ring_v5.pdb (#6) to map postprocess_masked.mrc
(#5) using 91080 atoms
average map value = 0.004625, steps = 92
shifted from previous position = 5.74
rotated from previous position = 0.72 degrees
atoms outside contour = 79187, contour level = 0.017739
Position of copy of Rhom_22-Ring_v5.pdb (#6) relative to
postprocess_masked.mrc (#5) coordinates:
Matrix rotation and translation
0.99992100 -0.01251931 -0.00112287 2.47259250
0.01251967 0.99992158 0.00031296 -2.33239216
0.00111887 -0.00032700 0.99999932 -5.48893742
Axis -0.02544851 -0.08914440 0.99569355
Axis point 225.34109297 185.26549467 0.00000000
Rotation angle (degrees) 0.72043550
Shift along axis -5.32030370
> color #5 #ffffb23b models
> select clear
> molmap #6 5
Opened copy of Rhom_22-Ring_v5.pdb map 5 as #4, grid size 93,93,163, pixel
1.67, shown at level 0.127, step 1, values float32
> molmap #6 10
Opened copy of Rhom_22-Ring_v5.pdb map 10 as #4, grid size 56,56,91, pixel
3.33, shown at level 0.0916, step 1, values float32
> mask #5 surfaces #4
Unknown command: mask #5 surfaces #4
> volume mask #5 surfaces #4
Opened postprocess_masked.mrc masked as #7, grid size 138,138,262, pixel 0.94,
shown at step 1, values float32
> hide #!4 models
> select clear
> fitmap #6 inMap #5
Fit molecule copy of Rhom_22-Ring_v5.pdb (#6) to map postprocess_masked.mrc
(#5) using 91080 atoms
average map value = 0.004625, steps = 40
shifted from previous position = 0.0121
rotated from previous position = 0.00351 degrees
atoms outside contour = 79164, contour level = 0.017739
Position of copy of Rhom_22-Ring_v5.pdb (#6) relative to
postprocess_masked.mrc (#5) coordinates:
Matrix rotation and translation
0.99992122 -0.01250524 -0.00108129 2.46420631
0.01250563 0.99992174 0.00035564 -2.33498896
0.00107676 -0.00036913 0.99999935 -5.48568372
Axis -0.02885872 -0.08592926 0.99588319
Axis point 224.51055862 183.33110897 0.00000000
Rotation angle (degrees) 0.71948959
Shift along axis -5.33357017
> select clear
[Repeated 1 time(s)]
> select add #6
91080 atoms, 91344 bonds, 6006 residues, 1 model selected
> view matrix models
> #6,0.99992,-0.012505,-0.0010813,270.21,0.012506,0.99992,0.00035564,-73.308,0.0010768,-0.00036913,1,35.457
> fitmap #6 inMap #5
Fit molecule copy of Rhom_22-Ring_v5.pdb (#6) to map postprocess_masked.mrc
(#5) using 91080 atoms
average map value = 0.01351, steps = 48
shifted from previous position = 2.07
rotated from previous position = 0.737 degrees
atoms outside contour = 70454, contour level = 0.017739
Position of copy of Rhom_22-Ring_v5.pdb (#6) relative to
postprocess_masked.mrc (#5) coordinates:
Matrix rotation and translation
0.99999995 0.00031474 -0.00009895 -0.04164618
-0.00031474 0.99999995 -0.00006619 0.07517500
0.00009893 0.00006622 0.99999999 -0.00015932
Axis 0.19673893 -0.29402579 -0.93533022
Axis point 210.66390146 113.51227009 0.00000000
Rotation angle (degrees) 0.01928007
Shift along axis -0.03014780
> select clear
> select #6/C
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> select #6/D
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> delete #6/A-C
> delete #6/E-W
> molmap #6
Missing or invalid "resolution" argument: Expected a number
> molmap #6
Missing or invalid "resolution" argument: Expected a number
> molmap #6 3
Opened copy of Rhom_22-Ring_v5.pdb map 3 as #4, grid size 63,70,161, pixel 1,
shown at level 0.115, step 1, values float32
> molmap #6 2
Opened copy of Rhom_22-Ring_v5.pdb map 2 as #4, grid size 85,95,233, pixel
0.667, shown at level 0.15, step 1, values float32
> volume mask #5 near #4
Expected a keyword
> hide #!4 models
> show #!4 models
> volume mask #5 surfaces #4
Opened postprocess_masked.mrc masked as #8, grid size 51,59,156, pixel 0.94,
shown at step 1, values float32
> hide #!7 models
> show #!7 models
> show #!5 models
> hide #!5 models
> hide #!7 models
> hide #!8 models
> hide #!4 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!8 models
> view sel
No displayed objects specified.
> view sel
No displayed objects specified.
> view #6
No displayed objects specified.
> view sel
No displayed objects specified.
> view sel
No displayed objects specified.
> select #6
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> view sel
No displayed objects specified.
> view sel
No displayed objects specified.
> hide #6 models
> show #6 models
> hide #!8 models
> show #!8 models
> clipper associate #6 #8
The toModel argument must be provided!
> clipper associate #8 toModel #6
Opened postprocess_masked.mrc masked as #6.1.1.1, grid size 51,59,156, pixel
0.94, shown at level 0, step 1, values float32
> hide #!6 models
> show #!6 models
> show #!7 models
> hide #!7 models
> show #!4 models
> close #4
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!7 models
> close #7
> volume #6.1.1.1 region 0,0,0,50,58,155 step 1
> volume #6.1.1.1 style surface region 0,0,0,50,58,155 step 1
> volume #6.1.1.1 level 0.005231
> volume #6.1.1.1 level 1.165e+308
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
/Users/mbell/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py:2052: RuntimeWarning: divide by zero
encountered in scalar divide
self.global_k = scaling_constant/ref_g
> view matrix models #6.2,1,0,0,0.68808,0,1,0,1.1117,0,0,1,-2.2927
> volume #6.1.1.1 region 0,0,0,50,58,155 step 1
> volume #6.1.1.1 style mesh region 0,0,0,50,58,155 step 1
> volume #6.1.1.1 style surface
> volume #6.1.1.1
> view matrix models #6.2,1,0,0,1.1976,0,1,0,-3.7182,0,0,1,0.51965
> volume #6.1.1.1 style mesh
> view matrix models #6.2,1,0,0,0.63717,0,1,0,-4.348,0,0,1,5.2647
> view matrix models #6.2,1,0,0,-3.2129,0,1,0,-7.7954,0,0,1,6.9054
> hide #6.3 models
> show #6.3 models
Window position QRect(3490,765 104x152) outside any known screen, using
primary screen
> volume #6.1.1.1 region 0,0,0,50,58,155 step 1
> volume #6.1.1.1 style surface region 0,0,0,50,58,155 step 1
> volume #6.1.1.1 color #00ffff47
> volume #6.1.1.1 style mesh
> show #!5 models
> hide #!5 models
> volume gaussian #6 bfactor 150
Opened postprocess_masked.mrc masked gaussian as #4, grid size 51,59,156,
pixel 0.94, shown at step 1, values float32
> volume #4 level 0.007942
> hide #6.3 models
> show #6.3 models
> hide #6.3 models
> show #6.3 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1 models
> select add #4
4140 atoms, 4152 bonds, 273 residues, 4 models selected
> view matrix models
> #6.2,1,0,0,44.585,0,1,0,-22.452,0,0,1,-1.5583,#4,1,0,0,47.798,0,1,0,-14.656,0,0,1,-8.4636
> view matrix models
> #6.2,1,0,0,56.016,0,1,0,-5.4433,0,0,1,-24.552,#4,1,0,0,59.229,0,1,0,2.3522,0,0,1,-31.458
> view matrix models
> #6.2,1,0,0,105.6,0,1,0,-28.597,0,0,1,-24.057,#4,1,0,0,108.81,0,1,0,-20.801,0,0,1,-30.963
> view matrix models
> #6.2,1,0,0,73.997,0,1,0,-20.444,0,0,1,-10.575,#4,1,0,0,77.21,0,1,0,-12.649,0,0,1,-17.48
> select add #4
2 models selected
> select add #4
2 models selected
> select subtract #4
Nothing selected
> select add #4
2 models selected
> view matrix models #4,1,0,0,199.99,0,1,0,-47.157,0,0,1,-22.734
> view matrix models #4,1,0,0,337.3,0,1,0,-100.94,0,0,1,-21.986
> view matrix models #4,1,0,0,355.13,0,1,0,-99.106,0,0,1,2.7347
> select add #4
2 models selected
> view matrix models #4,1,0,0,338.22,0,1,0,-94.024,0,0,1,9.3623
> view matrix models #4,1,0,0,342.68,0,1,0,-94.791,0,0,1,16.599
> view matrix models #4,1,0,0,338.63,0,1,0,-93.237,0,0,1,23.86
> view matrix models #4,1,0,0,340.22,0,1,0,-94.649,0,0,1,26.432
> fitmap #6 inMap #4
Fit molecule copy of Rhom_22-Ring_v5.pdb (#6.2) to map postprocess_masked.mrc
masked gaussian (#4) using 4140 atoms
average map value = 0.009699, steps = 68
shifted from previous position = 2.48
rotated from previous position = 0.123 degrees
atoms outside contour = 1889, contour level = 0.0079416
Position of copy of Rhom_22-Ring_v5.pdb (#6.2) relative to
postprocess_masked.mrc masked gaussian (#4) coordinates:
Matrix rotation and translation
0.99999769 0.00214757 -0.00012798 -268.33529849
-0.00214758 0.99999769 -0.00006607 73.47466536
0.00012784 0.00006635 0.99999999 -37.00038776
Axis 0.03076206 -0.05942744 -0.99775853
Axis point 34750.39263357 125333.72683245 0.00000000
Rotation angle (degrees) 0.12332354
Shift along axis 24.29649492
> select clear
> clipper associate #4 toModel #6
Opened postprocess_masked.mrc masked gaussian as #6.1.1.2, grid size
51,59,156, pixel 0.94, shown at step 1, values float32
/Users/mbell/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py:2052: RuntimeWarning: divide by zero
encountered in scalar divide
self.global_k = scaling_constant/ref_g
> volume #6.1.1.2 region 0,0,0,50,58,155 step 1
[Repeated 1 time(s)]
> volume #6.1.1.2 level 0.0128
> show #!1 models
> hide #!1 models
> view all
> show #!1 models
> hide #!6 models
> show #!6 models
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_Monomer_v6.2.pdb" models #6
> close session
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_Monomer_v6.2.pdb" format
> pdb
Chain information for Rhom_Monomer_v6.2.pdb #1
---
Chain | Description
D | No description available
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/job234/postprocess_masked.mrc" format mrc
Opened postprocess_masked.mrc as #2, grid size 384,384,384, pixel 0.94, shown
at level 0.0177, step 2, values float32
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> fitmap #1 inMap #2
Fit molecule Rhom_Monomer_v6.2.pdb (#1) to map postprocess_masked.mrc (#2)
using 4140 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 4140, contour level = 0.017739
Position of Rhom_Monomer_v6.2.pdb (#1) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
> view matrix models #1,1,0,0,-343.54,0,1,0,49.434,0,0,1,-19.553
> fitmap #1 inMap #2
Fit molecule Rhom_Monomer_v6.2.pdb (#1) to map postprocess_masked.mrc (#2)
using 4140 atoms
average map value = 0.002803, steps = 504
shifted from previous position = 5.16
rotated from previous position = 17.7 degrees
atoms outside contour = 3731, contour level = 0.017739
Position of Rhom_Monomer_v6.2.pdb (#1) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.95824253 0.27703679 -0.07086508 -346.96098505
-0.26780039 0.95630483 0.11732015 167.87435178
0.10027062 -0.09344346 0.99056253 -55.22911778
Axis -0.34623306 -0.28113410 -0.89503424
Axis point 562.10520864 1184.19606137 0.00000000
Rotation angle (degrees) 17.72006541
Shift along axis 122.36611086
> view matrix models
> #1,0.95824,0.27704,-0.070865,-331.11,-0.2678,0.9563,0.11732,191.9,0.10027,-0.093443,0.99056,-55.438
> view matrix models
> #1,0.95824,0.27704,-0.070865,-322.59,-0.2678,0.9563,0.11732,208.87,0.10027,-0.093443,0.99056,-55.48
> fitmap #1 inMap #2
Fit molecule Rhom_Monomer_v6.2.pdb (#1) to map postprocess_masked.mrc (#2)
using 4140 atoms
average map value = 0.002383, steps = 216
shifted from previous position = 5.12
rotated from previous position = 6.01 degrees
atoms outside contour = 3719, contour level = 0.017739
Position of Rhom_Monomer_v6.2.pdb (#1) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.94868287 0.31281621 -0.04633394 -326.65725590
-0.31195800 0.94976936 0.02490702 253.41093231
0.05179788 -0.00917462 0.99861544 -44.21389912
Axis -0.05381156 -0.15494051 -0.98645717
Axis point 638.80733285 1145.26980011 0.00000000
Rotation angle (degrees) 18.46200953
Shift along axis 21.92943506
> view matrix models
> #1,0.94868,0.31282,-0.046334,-325.42,-0.31196,0.94977,0.024907,259.52,0.051798,-0.0091746,0.99862,-49.499
> fitmap #1 inMap #2
Fit molecule Rhom_Monomer_v6.2.pdb (#1) to map postprocess_masked.mrc (#2)
using 4140 atoms
average map value = 0.003652, steps = 128
shifted from previous position = 2.62
rotated from previous position = 5.22 degrees
atoms outside contour = 3708, contour level = 0.017739
Position of Rhom_Monomer_v6.2.pdb (#1) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.93953470 0.33707208 -0.06047283 -319.22803550
-0.34049333 0.93834388 -0.05979173 289.47921635
0.03659019 0.07676700 0.99637743 -50.62539141
Axis 0.19565083 -0.13906442 -0.97076354
Axis point 641.59442611 1031.06010332 0.00000000
Rotation angle (degrees) 20.42529561
Shift along axis -53.56820397
> view matrix models
> #1,0.93953,0.33707,-0.060473,-318,-0.34049,0.93834,-0.059792,279.98,0.03659,0.076767,0.99638,-40.495
> fitmap #1 inMap #2
Fit molecule Rhom_Monomer_v6.2.pdb (#1) to map postprocess_masked.mrc (#2)
using 4140 atoms
average map value = 0.005173, steps = 376
shifted from previous position = 8.61
rotated from previous position = 9.78 degrees
atoms outside contour = 3570, contour level = 0.017739
Position of Rhom_Monomer_v6.2.pdb (#1) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.87176791 0.48884967 -0.03235286 -307.75036276
-0.48967768 0.87150919 -0.02622032 365.87182246
0.01537802 0.03870051 0.99913252 -20.64399548
Axis 0.06612163 -0.04861372 -0.99662663
Axis point 543.45182125 769.71957744 0.00000000
Rotation angle (degrees) 29.40105068
Shift along axis -17.56099220
> close #1
> open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/22-ring_Sims/Rhom_22-Ring_v5.pdb"
Chain information for Rhom_22-Ring_v5.pdb #1
---
Chain | Description
A B C D E F G H I J K L M N O P Q R S T U V | No description available
> fitmap #1 inMap #2
Fit molecule Rhom_22-Ring_v5.pdb (#1) to map postprocess_masked.mrc (#2) using
91080 atoms
average map value = 0.01352, steps = 44
shifted from previous position = 0.0209
rotated from previous position = 0.031 degrees
atoms outside contour = 70404, contour level = 0.017739
Position of Rhom_22-Ring_v5.pdb (#1) relative to postprocess_masked.mrc (#2)
coordinates:
Matrix rotation and translation
0.99999986 0.00053437 0.00002071 -0.09756272
-0.00053437 0.99999985 -0.00008341 0.12510606
-0.00002076 0.00008340 1.00000000 0.00294575
Axis 0.15410529 0.03830679 -0.98731158
Axis point 235.01181344 178.84439944 0.00000000
Rotation angle (degrees) 0.03101077
Shift along axis -0.01315089
> molmap #1 3
Opened Rhom_22-Ring_v5.pdb map 3 as #3, grid size 141,142,259, pixel 1, shown
at level 0.119, step 1, values float32
> molmap #1 20
Opened Rhom_22-Ring_v5.pdb map 20 as #3, grid size 37,37,55, pixel 6.67, shown
at level 0.0615, step 1, values float32
> volume mask #2 surfaces #3
Opened postprocess_masked.mrc masked as #4, grid size 139,140,263, pixel 0.94,
shown at step 1, values float32
> hide #!3 models
> hide atoms
> show cartoons
> color #4 #b2b2b24d models
> fitmap #1 inMap #4
Fit molecule Rhom_22-Ring_v5.pdb (#1) to map postprocess_masked.mrc masked
(#4) using 91080 atoms
average map value = 0.01351, steps = 28
shifted from previous position = 0.00875
rotated from previous position = 0.00529 degrees
atoms outside contour = 58256, contour level = 0.017739
Position of Rhom_22-Ring_v5.pdb (#1) relative to postprocess_masked.mrc masked
(#4) coordinates:
Matrix rotation and translation
0.99999985 0.00053812 0.00007733 -0.11198298
-0.00053811 0.99999986 -0.00001053 0.12142316
-0.00007734 0.00001049 1.00000000 0.02573056
Axis 0.01933404 0.14222718 -0.98964520
Axis point 228.32780476 207.79275223 0.00000000
Rotation angle (degrees) 0.03115430
Shift along axis -0.01035954
> color #4 #b2b2b27a models
> molmap #1 2
Opened Rhom_22-Ring_v5.pdb map 2 as #3, grid size 203,203,379, pixel 0.667,
shown at level 0.15, step 1, values float32
> molmap #1 3
Opened Rhom_22-Ring_v5.pdb map 3 as #3, grid size 141,142,259, pixel 1, shown
at level 0.119, step 1, values float32
> molmap #1 1
Opened Rhom_22-Ring_v5.pdb map 1 as #3, grid size 387,388,740, pixel 0.333,
shown at level 0.535, step 1, values float32
> molmap #1 1
Opened Rhom_22-Ring_v5.pdb map 1 as #3, grid size 387,388,740, pixel 0.333,
shown at level 0.535, step 1, values float32
> molmap #1 2
Opened Rhom_22-Ring_v5.pdb map 2 as #3, grid size 203,203,379, pixel 0.667,
shown at level 0.15, step 1, values float32
> volume mask #2 surfaces #3
Opened postprocess_masked.mrc masked as #5, grid size 136,136,260, pixel 0.94,
shown at step 1, values float32
> hide #!4 models
> close #4
> hide #!5 models
> show #!5 models
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> isolde start
> show #!5 models
> fitmap #1 inMap #5
Fit molecule Rhom_22-Ring_v5.pdb (#1) to map postprocess_masked.mrc masked
(#5) using 91080 atoms
average map value = 0.01385, steps = 28
shifted from previous position = 0.00653
rotated from previous position = 0.00731 degrees
atoms outside contour = 58615, contour level = 0.017739
Position of Rhom_22-Ring_v5.pdb (#1) relative to postprocess_masked.mrc masked
(#5) coordinates:
Matrix rotation and translation
0.99999990 0.00043703 0.00011524 -0.09335343
-0.00043702 0.99999990 -0.00007850 0.11376340
-0.00011528 0.00007845 0.99999999 0.02013549
Axis 0.17107239 0.25125948 -0.95268196
Axis point 264.04250190 211.09742048 0.00000000
Rotation angle (degrees) 0.02628361
Shift along axis -0.00656878
> select clear
> select #1/D
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> view matrix models
> #1,1,0.00043703,0.00011524,-0.44789,-0.00043702,1,-7.8502e-05,-40.518,-0.00011528,7.8452e-05,1,49.715
> undo
> select up
91080 atoms, 91344 bonds, 6006 residues, 1 model selected
> select #1/C
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> select #1/E
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> select ~sel & ##selected
86940 atoms, 87192 bonds, 5733 residues, 1 model selected
> select #1/F
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> select #1/D
4140 atoms, 4152 bonds, 273 residues, 1 model selected
> delete #1/A-C
> delete #1/E-M
> delete #1/E-W
> molmap #1 2
Opened Rhom_22-Ring_v5.pdb map 2 as #3, grid size 85,96,231, pixel 0.667,
shown at level 0.15, step 1, values float32
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> close #5
> volume mask #2 surfaces #3
Opened postprocess_masked.mrc masked as #4, grid size 51,59,155, pixel 0.94,
shown at step 1, values float32
> hide #!3 models
> isolde start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for Rhom_22-Ring_v5.pdb
---
Chain | Description
1.2/D | No description available
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> clipper associate #4 #1
The toModel argument must be provided!
> clipper associate #4 toModel #1
Opened postprocess_masked.mrc masked as #1.1.1.1, grid size 51,59,155, pixel
0.94, shown at step 1, values float32
> volume #1.1.1.1 style surface
> volume #1.1.1.1 color #00ffff33
> volume gaussian #1 bfactor 150
Opened postprocess_masked.mrc masked gaussian as #4, grid size 51,59,155,
pixel 0.94, shown at step 1, values float32
> clipper associate #4 toModel #1
Opened postprocess_masked.mrc masked gaussian as #1.1.1.2, grid size
51,59,155, pixel 0.94, shown at step 1, values float32
> volume #1.1.1.2 region 0,0,0,50,58,154 step 1
[Repeated 1 time(s)]
> volume #1.1.1.2 level 0.01257
> volume #1.1.1.2 level 0.006541
> volume #1.1.1.1 level 0.02293
> view #1:1
> volume #1.1.1.2 level 0.005947
> volume #1.1.1.2 level 0.002012
> volume #1.1.1.1 level 0.01373
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/v6_MonomerSims/Monomer_Presim.cxs"
Taking snapshot of stepper: Rhom_22-Ring_v5.pdb
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, in take_snapshot
'positions': self.positions.array(),
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 2'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x2ebb9f9d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x3cb6a4690>
'Rhom_22-Ring_v5.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 2' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x2ebb9f9d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x3cb6a4690>
'Rhom_22-Ring_v5.pdb': Error while saving session data for 'isolde residue
stepper 2' -> <chimerax.isolde.navigate.ResidueStepper object at 0x2ebb9f9d0>
-> <chimerax.atomic.structure.AtomicStructure object at 0x3cb6a4690>
'Rhom_22-Ring_v5.pdb'
Window position QRect(2378,432 600x300) outside any known screen, using
primary screen
ValueError: error processing: 'isolde residue stepper 2' -> ->
'Rhom_22-Ring_v5.pdb': Error while saving session data for 'isolde residue
stepper 2' -> -> 'Rhom_22-Ring_v5.pdb'
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, in take_snapshot
'positions': self.positions.array(),
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 2'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x2ebb9f9d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x3cb6a4690>
'Rhom_22-Ring_v5.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 2' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x2ebb9f9d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x3cb6a4690>
'Rhom_22-Ring_v5.pdb': Error while saving session data for 'isolde residue
stepper 2' -> <chimerax.isolde.navigate.ResidueStepper object at 0x2ebb9f9d0>
-> <chimerax.atomic.structure.AtomicStructure object at 0x3cb6a4690>
'Rhom_22-Ring_v5.pdb'
ValueError: error processing: 'isolde residue stepper 2' -> ->
'Rhom_22-Ring_v5.pdb': Error while saving session data for 'isolde residue
stepper 2' -> -> 'Rhom_22-Ring_v5.pdb'
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/v6_MonomerSims/test.pdb"
> save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
> determination/Reference_models/v6_MonomerSims/test.cxs"
Taking snapshot of stepper: Rhom_22-Ring_v5.pdb
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, in take_snapshot
'positions': self.positions.array(),
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 2'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x2ebb9f9d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x3cb6a4690>
'Rhom_22-Ring_v5.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 2' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x2ebb9f9d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x3cb6a4690>
'Rhom_22-Ring_v5.pdb': Error while saving session data for 'isolde residue
stepper 2' -> <chimerax.isolde.navigate.ResidueStepper object at 0x2ebb9f9d0>
-> <chimerax.atomic.structure.AtomicStructure object at 0x3cb6a4690>
'Rhom_22-Ring_v5.pdb'
ValueError: error processing: 'isolde residue stepper 2' -> ->
'Rhom_22-Ring_v5.pdb': Error while saving session data for 'isolde residue
stepper 2' -> -> 'Rhom_22-Ring_v5.pdb'
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, in take_snapshot
'positions': self.positions.array(),
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 2'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x2ebb9f9d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x3cb6a4690>
'Rhom_22-Ring_v5.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 2' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x2ebb9f9d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x3cb6a4690>
'Rhom_22-Ring_v5.pdb': Error while saving session data for 'isolde residue
stepper 2' -> <chimerax.isolde.navigate.ResidueStepper object at 0x2ebb9f9d0>
-> <chimerax.atomic.structure.AtomicStructure object at 0x3cb6a4690>
'Rhom_22-Ring_v5.pdb'
ValueError: error processing: 'isolde residue stepper 2' -> ->
'Rhom_22-Ring_v5.pdb': Error while saving session data for 'isolde residue
stepper 2' -> -> 'Rhom_22-Ring_v5.pdb'
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,11
Model Number: Z1AH000BGD/A
Chip: Apple M3 Max
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 36 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 29 days, 5 hours, 5 minutes
Graphics/Displays:
Apple M3 Max:
Chipset Model: Apple M3 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBImages: 1.2
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
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: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.4
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
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