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Opened 20 months ago
Closed 18 months ago
#14599 closed defect (fixed)
ISOLDE session save: ResidueStepper referenced closed AtomicStructure
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: 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
[deleted to fit within ticket limits]
> 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
Change History (2)
comment:1 by , 20 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE session save: ResidueStepper referenced closed AtomicStructure |
comment:2 by , 18 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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