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Opened 10 months ago
Closed 10 months ago
#16537 closed defect (duplicate)
Crash in python_instances_of_class
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001dd3b5ec0 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 162 in copy
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 65 in combine_cmd
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56)
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"procLaunch" : "2024-12-26 16:03:05.3281 +0800",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Connector/Corndog_34_portal/fold_corndog_34_portal_1_model_0.cif" format
> mmcif
Chain information for fold_corndog_34_portal_1_model_0.cif #1
---
Chain | Description
A | .
> close
> close #
Expected a models specifier or a keyword
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Adaptor_43_12mer-coot-1.pdb" format pdb
Chain information for Adaptor_43_12mer-coot-1.pdb #1
---
Chain | Description
C | No description available
> rainbow
> lighting soft
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/cryosparc_P2_J176_014_volume_map_sharp Connector.mrc" format mrc
Opened cryosparc_P2_J176_014_volume_map_sharp Connector.mrc as #2, grid size
512,512,512, pixel 1.06, shown at level 0.281, step 2, values float32
> volume #2 step 1
> volume #2 level 0.3
> surface dust #2 size 10.6
> ui mousemode right "map eraser"
Already setting window visible!
> view #1 clip false
> volume erase #2 center 272.63,236.53,233.88 radius 60.29
Opened cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy as #4, grid
size 512,512,512, pixel 1.06, shown at step 1, values float32
> surface dust #4 size 10.6
> close #4
> show #!2 models
> volume erase #2 center 274.5,216.62,232.18 radius 60.027
Opened cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy as #4, grid
size 512,512,512, pixel 1.06, shown at step 1, values float32
> volume erase #4 center 276.41,226.09,232.08 radius 60.027
> volume erase #4 center 276.89,235.64,231.66 radius 60.027
> undo
> close #4
> show #!2 models
> volume erase #2 center 279.36,223.16,232.56 radius 60.027
Opened cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy as #4, grid
size 512,512,512, pixel 1.06, shown at step 1, values float32
> surface dust #4 size 10.6
> hide #3 models
> transparency #4.1 50
> ui mousemode right "translate selected models"
> close #3
> set bgColor white
> set bgColor black
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule Adaptor_43_12mer-coot-1.pdb (#1) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 1567 atoms
average map value = 0.5955, steps = 40
shifted from previous position = 0.0104
rotated from previous position = 0.0247 degrees
atoms outside contour = 647, contour level = 0.3
Position of Adaptor_43_12mer-coot-1.pdb (#1) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates:
Matrix rotation and translation
0.99999992 -0.00033049 -0.00020902 0.15752939
0.00033045 0.99999993 -0.00017957 -0.05875495
0.00020908 0.00017950 0.99999996 -0.12340587
Axis 0.41725084 -0.48583640 0.76802651
Axis point 178.64624203 477.25218445 0.00000000
Rotation angle (degrees) 0.02465345
Shift along axis -0.00050441
> fitmap #1 inMap #2
Fit molecule Adaptor_43_12mer-coot-1.pdb (#1) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 1567 atoms
average map value = 0.5956, steps = 28
shifted from previous position = 0.0187
rotated from previous position = 0.00688 degrees
atoms outside contour = 643, contour level = 0.3
Position of Adaptor_43_12mer-coot-1.pdb (#1) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates:
Matrix rotation and translation
0.99999993 -0.00024857 -0.00029318 0.16521746
0.00024852 0.99999996 -0.00015458 -0.04607092
0.00029322 0.00015450 0.99999995 -0.15299874
Axis 0.37303676 -0.70774694 0.59994820
Axis point 526.89971304 0.00000000 560.28495790
Rotation angle (degrees) 0.02373617
Shift along axis 0.00244742
> fitmap #1 inMap #4
Fit molecule Adaptor_43_12mer-coot-1.pdb (#1) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy (#4) using 1567
atoms
average map value = 0.5955, steps = 40
shifted from previous position = 0.021
rotated from previous position = 0.0198 degrees
atoms outside contour = 647, contour level = 0.3
Position of Adaptor_43_12mer-coot-1.pdb (#1) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy (#4) coordinates:
Matrix rotation and translation
0.99999999 0.00001674 -0.00015462 0.03313623
-0.00001679 0.99999995 -0.00032672 0.08058353
0.00015461 0.00032672 0.99999993 -0.15762887
Axis 0.90292304 -0.42729761 -0.04633287
Axis point 0.00000000 482.11485866 250.21649370
Rotation angle (degrees) 0.02073214
Shift along axis 0.00278971
> fitmap #1 inMap #4
Fit molecule Adaptor_43_12mer-coot-1.pdb (#1) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy (#4) using 1567
atoms
average map value = 0.5955, steps = 28
shifted from previous position = 0.0212
rotated from previous position = 0.0253 degrees
atoms outside contour = 643, contour level = 0.3
Position of Adaptor_43_12mer-coot-1.pdb (#1) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy (#4) coordinates:
Matrix rotation and translation
0.99999985 -0.00028505 -0.00046315 0.21673683
0.00028494 0.99999993 -0.00023018 -0.04011459
0.00046321 0.00023005 0.99999987 -0.22444309
Axis 0.38968716 -0.78435988 0.48262149
Axis point 492.59215065 0.00000000 461.41299305
Rotation angle (degrees) 0.03383415
Shift along axis 0.00760277
> close #1
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Adaptor_2-coot-1.pdb"
Chain information for Adaptor_2-coot-1.pdb #1
---
Chain | Description
C | No description available
> fitmap #1 inMap #2
Fit molecule Adaptor_2-coot-1.pdb (#1) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 1567 atoms
average map value = 0.6217, steps = 40
shifted from previous position = 0.0457
rotated from previous position = 0.075 degrees
atoms outside contour = 614, contour level = 0.3
Position of Adaptor_2-coot-1.pdb (#1) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates:
Matrix rotation and translation
0.99999951 -0.00098248 0.00013979 0.30152291
0.00098260 0.99999915 -0.00085292 -0.07189625
-0.00013895 0.00085306 0.99999963 -0.24322525
Axis 0.65184200 0.10650403 0.75083879
Axis point 74.10947823 302.70658502 0.00000000
Rotation angle (degrees) 0.07497650
Shift along axis 0.00626510
> fitmap #1 inMap #2
Fit molecule Adaptor_2-coot-1.pdb (#1) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 1567 atoms
average map value = 0.6218, steps = 44
shifted from previous position = 0.00793
rotated from previous position = 0.00907 degrees
atoms outside contour = 614, contour level = 0.3
Position of Adaptor_2-coot-1.pdb (#1) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates:
Matrix rotation and translation
0.99999948 -0.00102080 0.00006461 0.33301576
0.00102085 0.99999922 -0.00071901 -0.12180944
-0.00006388 0.00071907 0.99999974 -0.22755992
Axis 0.57509686 0.05138190 0.81647015
Axis point 119.54389250 326.47128569 0.00000000
Rotation angle (degrees) 0.07163647
Shift along axis -0.00053837
> close #1
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Adaptor_2-coot-2.pdb"
Chain information for Adaptor_2-coot-2.pdb #1
---
Chain | Description
C | No description available
> fitmap #1 inMap #2
Fit molecule Adaptor_2-coot-2.pdb (#1) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 1567 atoms
average map value = 0.6578, steps = 40
shifted from previous position = 0.055
rotated from previous position = 0.127 degrees
atoms outside contour = 582, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#1) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates:
Matrix rotation and translation
0.99999761 0.00173928 -0.00132610 -0.18860977
-0.00173975 0.99999842 -0.00035268 0.59975565
0.00132548 0.00035499 0.99999906 -0.54745669
Axis 0.15970351 -0.59839258 -0.78512490
Axis point 358.67246685 112.68204194 0.00000000
Rotation angle (degrees) 0.12694382
Shift along axis 0.04081090
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Adaptor_43_12mer.pdb"
Chain information for Adaptor_43_12mer.pdb #3
---
Chain | Description
A B C D E F G H I J K L | No description available
> hide atoms
> show cartoons
> ui tool show Matchmaker
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Adaptor_2-coot-2.pdb, chain C (#1) with Adaptor_43_12mer.pdb, chain
A (#3), sequence alignment score = 726
RMSD between 72 pruned atom pairs is 1.441 angstroms; (across all 201 pairs:
4.565)
> fitmap #3 inMap #2
Fit molecule Adaptor_43_12mer.pdb (#3) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 18804 atoms
average map value = 0.2915, steps = 92
shifted from previous position = 3.91
rotated from previous position = 5.09 degrees
atoms outside contour = 12050, contour level = 0.3
Position of Adaptor_43_12mer.pdb (#3) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates:
Matrix rotation and translation
0.49992944 -0.86597188 0.01277702 367.74881585
0.86585474 0.50007896 0.01471764 -103.56155269
-0.01913458 0.00370526 0.99981005 4.27642792
Axis -0.00635761 0.01842306 0.99981007
Axis point 273.58159553 266.68175583 0.00000000
Rotation angle (degrees) 60.00600542
Shift along axis 0.02969137
> fitmap #3 inMap #2
Fit molecule Adaptor_43_12mer.pdb (#3) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 18804 atoms
average map value = 0.2915, steps = 28
shifted from previous position = 0.012
rotated from previous position = 0.00736 degrees
atoms outside contour = 12052, contour level = 0.3
Position of Adaptor_43_12mer.pdb (#3) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates:
Matrix rotation and translation
0.50001522 -0.86592204 0.01279857 367.71065865
0.86580648 0.50016484 0.01463780 -103.55550122
-0.01907658 0.00376196 0.99981095 4.25608290
Axis -0.00627915 0.01840307 0.99981093
Axis point 273.56745779 266.68838155 0.00000000
Rotation angle (degrees) 60.00029757
Shift along axis 0.04062990
> fitmap #3 inMap #2
Fit molecule Adaptor_43_12mer.pdb (#3) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 18804 atoms
average map value = 0.2916, steps = 44
shifted from previous position = 0.00871
rotated from previous position = 0.0182 degrees
atoms outside contour = 12041, contour level = 0.3
Position of Adaptor_43_12mer.pdb (#3) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates:
Matrix rotation and translation
0.49979023 -0.86605447 0.01262479 367.85635166
0.86593726 0.49993678 0.01469291 -103.54394916
-0.01903646 0.00358890 0.99981235 4.29548029
Axis -0.00640992 0.01827683 0.99981242
Axis point 273.60362640 266.72390586 0.00000000
Rotation angle (degrees) 60.01523661
Shift along axis 0.04429002
> close #3
> combine #1
> rename #1 id #6
> rename #2 id #1
> rename #4 id #2
> 6
Unknown command: 6
> combine #6
> rename #3 id #15
> rename #6 id #3
> rename #15 id #6
> turn z 30 models #4-14
> undo
> turn z 30 models #4-14
> turn z 30 models #5-14
> turn z 30 models #6-14
> turn z 30 models #7-14
> turn z 30 models #8-14
> turn z 30 models #9-14
> turn z 30 models #10-14
> turn z 30 models #11-14
> turn z 30 models #12-14
> turn z 30 models #13-14
> turn z 30 models #14
> combine #3-14
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #4 to 'D'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #5 to 'E'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #6 to 'F'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #7 to 'G'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #8 to 'H'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #9 to 'I'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #10 to 'J'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #11 to 'K'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #12 to 'L'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #13 to 'M'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #14 to 'N'
> fitmap #15 inMap #1
Fit molecule combination (#15) to map cryosparc_P2_J176_014_volume_map_sharp
Connector.mrc (#1) using 18804 atoms
average map value = 0.2283, steps = 104
shifted from previous position = 0.897
rotated from previous position = 2.27 degrees
atoms outside contour = 13280, contour level = 0.3
Position of combination (#15) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates:
Matrix rotation and translation
0.99942096 -0.02826281 0.01894608 4.24802800
0.02856999 0.99946142 -0.01614373 -4.52134455
-0.01847961 0.01667567 0.99969016 0.24582676
Axis 0.43440789 0.49537815 0.75225679
Axis point 157.45622219 150.29827764 0.00000000
Rotation angle (degrees) 2.16485567
Shift along axis -0.20947355
> close #4-15
> combine #3
> view orient
> turn x 90
> turn y 30 models #4-14
> turn y 30 models #5-14
> turn y 30 models #6-14
> turn y 30 models #7-14
> turn y 30 models #8-14
> turn y 30 models #9-14
> turn y 30 models #10-14
> turn y 30 models #11-14
> turn y 30 models #12-14
> turn y 30 models #13-14
> turn y 30 models #14
> combine #3-14
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #4 to 'D'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #5 to 'E'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #6 to 'F'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #7 to 'G'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #8 to 'H'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #9 to 'I'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #10 to 'J'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #11 to 'K'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #12 to 'L'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #13 to 'M'
Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #14 to 'N'
> fitmap #15 inMap #1
Fit molecule combination (#15) to map cryosparc_P2_J176_014_volume_map_sharp
Connector.mrc (#1) using 18804 atoms
average map value = 0.4918, steps = 80
shifted from previous position = 3.29
rotated from previous position = 4.12 degrees
atoms outside contour = 9084, contour level = 0.3
Position of combination (#15) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates:
Matrix rotation and translation
0.99999628 -0.00000665 -0.00272739 0.63908524
-0.00019030 0.99738981 -0.07220479 18.50702535
0.00272075 0.07220504 0.99738610 -23.02952725
Axis 0.99928829 -0.03770014 -0.00127083
Axis point 0.00000000 327.79605354 244.44764766
Rotation angle (degrees) 4.14359431
Shift along axis -0.02982039
> close #4-14
> select add #15
18804 atoms, 19188 bonds, 2412 residues, 1 model selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Adaptor_43_12mer_1.pdb" models #15 selectedOnly true relModel #1
> select subtract #15
Nothing selected
> hide #15 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Adaptor_43_12mer_1.pdb"
Chain information for Adaptor_43_12mer_1.pdb #4
---
Chain | Description
C D E F G H I J K L M N | No description available
> close #4
> ui tool show "Volume Viewer"
> volume #2 level 0.4
> hide #!2 models
> ui mousemode right "translate selected atoms"
> select #3/C:124
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
58 atoms, 58 bonds, 7 residues, 1 model selected
> select up
1567 atoms, 1599 bonds, 201 residues, 1 model selected
> select down
58 atoms, 58 bonds, 7 residues, 1 model selected
> select #3/C:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #3/C:124
18 atoms, 16 bonds, 2 residues, 1 model selected
> select up
198 atoms, 198 bonds, 25 residues, 1 model selected
> select add #3/C:50
206 atoms, 205 bonds, 26 residues, 1 model selected
> select add #3/C:51
213 atoms, 211 bonds, 27 residues, 1 model selected
> select add #3/C:52
221 atoms, 218 bonds, 28 residues, 1 model selected
> select add #3/C:53
228 atoms, 224 bonds, 29 residues, 1 model selected
> select subtract #3/C:53
221 atoms, 218 bonds, 28 residues, 1 model selected
> select add #3/C:54
229 atoms, 225 bonds, 29 residues, 1 model selected
> select add #3/C:53
236 atoms, 231 bonds, 30 residues, 1 model selected
> show #!2 models
> hide #!2 models
Drag select of 15 residues
> select add #3/C:124
133 atoms, 6 bonds, 16 residues, 1 model selected
> select add #3/C:125
143 atoms, 16 bonds, 17 residues, 1 model selected
> show #!2 models
> undo
> show #!2 models
> select add #3
1567 atoms, 1599 bonds, 201 residues, 1 model selected
> select subtract #3
Nothing selected
> fitmap #3 inMap #1
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 1567 atoms
average map value = 0.6571, steps = 44
shifted from previous position = 0.0337
rotated from previous position = 0.0451 degrees
atoms outside contour = 579, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates:
Matrix rotation and translation
0.99999881 0.00099716 -0.00117907 -0.00451165
-0.00099783 0.99999934 -0.00056808 0.43091602
0.00117850 0.00056926 0.99999914 -0.53651150
Axis 0.34557567 -0.71633837 -0.60616565
Axis point 447.53964939 0.00000000 -8.66775769
Rotation angle (degrees) 0.09428448
Shift along axis 0.01497404
> hide #3 models
> show #15 models
> hide #15 models
> show #3 models
> volume #2 level 0.3
> volume #2 level 0.2
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Adaptor_43_12mer_1.pdb"
Chain information for Adaptor_43_12mer_1.pdb #4
---
Chain | Description
C D E F G H I J K L M N | No description available
> surface dust #2 size 10.6
> hide #!2 models
> show #!1 models
> fitmap #4 inMap #1
Fit molecule Adaptor_43_12mer_1.pdb (#4) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 18804 atoms
average map value = 0.4918, steps = 44
shifted from previous position = 0.00145
rotated from previous position = 0.00179 degrees
atoms outside contour = 9078, contour level = 0.3
Position of Adaptor_43_12mer_1.pdb (#4) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00002927 -0.00000893 0.01078239
0.00002927 1.00000000 -0.00000594 -0.00654465
0.00000893 0.00000594 1.00000000 -0.00279115
Axis 0.19048351 -0.28657387 0.93893102
Axis point 210.78197138 359.84566614 0.00000000
Rotation angle (degrees) 0.00178618
Shift along axis 0.00130870
> fitmap #3 inMap #1
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 1567 atoms
average map value = 0.6571, steps = 40
shifted from previous position = 0.0136
rotated from previous position = 0.0284 degrees
atoms outside contour = 582, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates:
Matrix rotation and translation
0.99999899 0.00120479 -0.00075772 -0.16889046
-0.00120534 0.99999901 -0.00072836 0.53821529
0.00075684 0.00072928 0.99999945 -0.44949892
Axis 0.45579559 -0.47359205 -0.75363184
Axis point 449.11248303 143.16421170 -0.00000000
Rotation angle (degrees) 0.09161645
Shift along axis 0.00688269
> close #4
> show #!2 models
> hide #!1 models
> surface dust #2 size 10.6
> volume #2 level 0.3
> hide #3 models
> show #3 models
> hide #3 models
> ui tool show "Color Zone"
> show #3 models
> volume zone #2 nearAtoms #3 range 6.37
> ui tool show "Volume Viewer"
> fitmap #3 inMap #2
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy (#2) using 1567
atoms
average map value = 0.657, steps = 40
shifted from previous position = 0.00469
rotated from previous position = 0.0147 degrees
atoms outside contour = 580, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy (#2) coordinates:
Matrix rotation and translation
0.99999884 0.00127969 -0.00082816 -0.17761096
-0.00128049 0.99999872 -0.00096330 0.61908370
0.00082692 0.00096436 0.99999919 -0.54443324
Axis 0.53443905 -0.45886642 -0.70980033
Axis point 485.99931216 142.34080285 0.00000000
Rotation angle (degrees) 0.10332988
Shift along axis 0.00743994
> surface dust #2 size 10.6
> volume zone #2 nearAtoms #3 range 6.37
> hide #3 models
> show #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/C
Alignment identifier is 3/C
> select add #3/C:29
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:22
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/C:22-41
158 atoms, 160 bonds, 20 residues, 1 model selected
> hide #3 models
> show #3 models
> select #3/C:20
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:20-22
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #3/C:23
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:23-24
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #3/C:22
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/C:22
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/C:23
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:23-24
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #3/C:24
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/C:24
7 atoms, 6 bonds, 1 residue, 1 model selected
> fitmap #3 inMap #1
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 1567 atoms
average map value = 0.5971, steps = 40
shifted from previous position = 0.0457
rotated from previous position = 0.187 degrees
atoms outside contour = 642, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates:
Matrix rotation and translation
0.99999873 -0.00144948 0.00066657 0.31259248
0.00144945 0.99999895 0.00004585 -0.46826383
-0.00066664 -0.00004489 0.99999978 0.22477488
Axis -0.02842665 0.41765944 0.90815886
Axis point 323.12392904 215.36783362 0.00000000
Rotation angle (degrees) 0.09144699
Shift along axis -0.00032946
> select #3/C:23
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:23
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:24
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/C:24
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/C:25-26
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #3/C:25-26
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #3/C:25
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:25
9 atoms, 8 bonds, 1 residue, 1 model selected
> fitmap #3 inMap #1
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 1567 atoms
average map value = 0.597, steps = 44
shifted from previous position = 0.00485
rotated from previous position = 0.046 degrees
atoms outside contour = 644, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates:
Matrix rotation and translation
0.99999747 -0.00195521 0.00111388 0.36205722
0.00195564 0.99999801 -0.00038824 -0.51847459
-0.00111312 0.00039041 0.99999930 0.22785124
Axis 0.17048196 0.48759232 0.85626493
Axis point 266.30709557 184.48011974 0.00000000
Rotation angle (degrees) 0.13084482
Shift along axis 0.00402102
> fitmap #3 inMap #1
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 1567 atoms
average map value = 0.597, steps = 40
shifted from previous position = 0.0163
rotated from previous position = 0.0273 degrees
atoms outside contour = 644, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates:
Matrix rotation and translation
0.99999741 -0.00174590 0.00145701 0.20811390
0.00174684 0.99999827 -0.00064418 -0.38482860
-0.00145588 0.00064673 0.99999873 0.25808610
Axis 0.27305586 0.61614105 0.73879003
Axis point 224.08093269 117.24487028 0.00000000
Rotation angle (degrees) 0.13543717
Shift along axis 0.01038947
> select #3/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:26-27
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/C:28
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:28
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:27
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:27-28
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #3/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/C:26-27
17 atoms, 16 bonds, 2 residues, 1 model selected
> undo
> redo
> undo
> redo
> undo
> close #3
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Adaptor_2-coot-2.pdb"
Chain information for Adaptor_2-coot-2.pdb #3
---
Chain | Description
C | No description available
> color #3 #e1984eff
> hide #3 models
> show #3 models
> hide #!2 models
> select add #3/C:21
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/C:22
12 atoms, 10 bonds, 2 residues, 1 model selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/123.pdb" models #3 selectedOnly true relModel #1
> select add #3
1567 atoms, 1599 bonds, 201 residues, 1 model selected
> select subtract #3
Nothing selected
> show #!2 models
> hide #3 models
> show #3 models
> hide #!2 models
> rainbow #3
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #!2 models
> show #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/C
Alignment identifier is 3/C
> close #15
> volume #!2 style mesh
> volume #!2 style surface
> volume #!2 style mesh
> color #2 #b2b2b2b3 models
> color #2 #b2b2b2ff models
> volume #!2 style surface
> color #2 #b2b2b280 models
> color #2 #b2b2b24d models
> open /Users/melvinshen/Downloads/00-Portal-12mers-Adaptor-12mers.pdb
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb #4
---
Chain | Description
A B C D E F G H I J K L | No description available
M N O P Q R S T U V W X | No description available
> close #1-2
> hide atoms
> show cartoons
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/P2_J332_011_C12_volume_map_sharp.mrc"
Opened P2_J332_011_C12_volume_map_sharp.mrc as #1, grid size 512,512,512,
pixel 1.06, shown at level 0.285, step 2, values float32
> volume #1 step 1
> volume #1 level 0.3
> surface dust #1 size 10.6
> hide #3 models
> hide #4 models
> close #4
> show #3 models
> color #3 #bcbf184d
> transparency 50
> select add #3
1567 atoms, 1599 bonds, 201 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-18.95,0,1,0,-13.091,0,0,1,70.632
> view matrix models #3,1,0,0,-11.871,0,1,0,-9.273,0,0,1,71.453
> fitmap #3 inMap #1
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms
average map value = 0.2166, steps = 80
shifted from previous position = 1.55
rotated from previous position = 4.52 degrees
atoms outside contour = 1121, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99760716 -0.00575805 -0.06889699 5.97424029
0.00837524 0.99925179 0.03775856 -19.50381451
0.06862803 -0.03824524 0.99690897 62.58862401
Axis -0.48175651 -0.87171393 0.08958507
Axis point -874.75432638 0.00000000 255.05820010
Rotation angle (degrees) 4.52430396
Shift along axis 19.73062421
> view matrix models
> #3,0.99761,-0.0057581,-0.068897,12.266,0.0083752,0.99925,0.037759,-13.4,0.068628,-0.038245,0.99691,59.807
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.87578,0.10978,-0.47006,105.94,-0.23544,0.94726,-0.21742,133.43,0.42139,0.30109,0.85544,-114.74
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.87578,0.10978,-0.47006,112.58,-0.23544,0.94726,-0.21742,136.98,0.42139,0.30109,0.85544,-110.78
> fitmap #3 inMap #1
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms
average map value = 0.242, steps = 104
shifted from previous position = 1.84
rotated from previous position = 4.5 degrees
atoms outside contour = 1103, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.86674560 0.12284752 -0.48338448 115.70681546
-0.21724618 0.96540840 -0.14418985 109.54084581
0.44895008 0.22998935 0.86345164 -98.05323479
Axis 0.35279184 -0.87904411 -0.32065459
Axis point 289.43839471 0.00000000 177.11640020
Rotation angle (degrees) 32.02651011
Shift along axis -24.02959503
> fitmap #3 inMap #1
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms
average map value = 0.2419, steps = 48
shifted from previous position = 0.0173
rotated from previous position = 0.0212 degrees
atoms outside contour = 1102, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.86663964 0.12260116 -0.48363695 115.85755879
-0.21711022 0.96542073 -0.14431201 109.52546092
0.44922031 0.23006903 0.86328984 -98.11157730
Axis 0.35284633 -0.87919853 -0.32017091
Axis point 289.45347606 0.00000000 177.25080832
Rotation angle (degrees) 32.04030564
Shift along axis -24.00223726
> view matrix models
> #3,0.86664,0.1226,-0.48364,118.63,-0.21711,0.96542,-0.14431,109.52,0.44922,0.23007,0.86329,-101.58
> fitmap #3 inMap #1
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms
average map value = 0.2405, steps = 76
shifted from previous position = 2.81
rotated from previous position = 2.25 degrees
atoms outside contour = 1080, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.85444584 0.09816424 -0.51018240 133.79208191
-0.20709205 0.96495486 -0.16116762 112.26995028
0.47648210 0.24336372 0.84483070 -110.15790860
Axis 0.36470413 -0.88952471 -0.27520298
Axis point 305.06812248 0.00000000 190.04606926
Rotation angle (degrees) 33.68331092
Shift along axis -20.75658552
> fitmap #3 inMap #1
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms
average map value = 0.2408, steps = 44
shifted from previous position = 0.0208
rotated from previous position = 0.0174 degrees
atoms outside contour = 1081, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.85452828 0.09825733 -0.51002639 133.70788669
-0.20702362 0.96500590 -0.16094978 112.19049997
0.47636398 0.24312365 0.84496642 -110.09999940
Axis 0.36442404 -0.88960159 -0.27532550
Axis point 304.96722692 0.00000000 190.01192680
Rotation angle (degrees) 33.66940294
Shift along axis -20.76514188
> select subtract #3
Nothing selected
> hide #3 models
> hide #!1 models
> show #!1 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/00-Portal-12mers-Adaptor-12mers.pdb"
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb #2
---
Chain | Description
A B C D E F G H I J K L | No description available
M N O P Q R S T U V W X | No description available
> hide #2 atoms
> show #2 cartoons
> fitmap #2 inMap #1
Fit molecule 00-Portal-12mers-Adaptor-12mers.pdb (#2) to map
P2_J332_011_C12_volume_map_sharp.mrc (#1) using 49956 atoms
average map value = 1.039, steps = 28
shifted from previous position = 0.00906
rotated from previous position = 0.00469 degrees
atoms outside contour = 4456, contour level = 0.3
Position of 00-Portal-12mers-Adaptor-12mers.pdb (#2) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00003549 -0.00006197 0.00701912
-0.00003548 1.00000000 0.00004018 0.00781922
0.00006197 -0.00004018 1.00000000 -0.00498758
Axis -0.49039345 -0.75627130 -0.43309119
Axis point 130.78051680 0.00000000 56.32430662
Rotation angle (degrees) 0.00469460
Shift along axis -0.00719551
> ui tool show Matchmaker
> matchmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 00-Portal-12mers-Adaptor-12mers.pdb, chain M (#2) with
Adaptor_2-coot-2.pdb, chain C (#3), sequence alignment score = 775.9
RMSD between 60 pruned atom pairs is 1.400 angstroms; (across all 200 pairs:
5.942)
> hide #2 models
> show #3 models
> hide #!1 models
> show #2 models
> color #3 #c8c7494d
> color #3 #c8c749ff
> show #!1 models
> hide #3 models
> hide #2 models
> show #3 models
> fitmap #3 inMap #1
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms
average map value = 0.3518, steps = 80
shifted from previous position = 0.612
rotated from previous position = 3.16 degrees
atoms outside contour = 909, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.83332690 0.53356068 0.14449666 324.59128234
0.53760965 0.84309777 -0.01272857 -100.20625812
-0.12861628 0.06707574 -0.98942342 558.74796488
Axis 0.28044566 0.95976444 0.01422876
Axis point 197.74833283 0.00000000 268.05474333
Rotation angle (degrees) 171.82012698
Shift along axis 2.80610688
> fitmap #3 inMap #1
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms
average map value = 0.3518, steps = 60
shifted from previous position = 0.000463
rotated from previous position = 0.00808 degrees
atoms outside contour = 909, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.83335245 0.53350123 0.14456876 324.60043449
0.53754247 0.84313921 -0.01282068 -100.17742127
-0.12873144 0.06702771 -0.98941170 558.79379278
Axis 0.28041137 0.95977500 0.01419201
Axis point 197.76241472 0.00000000 268.06706478
Rotation angle (degrees) 171.81457045
Shift along axis 2.80427569
> fitmap #3 inMap #1
Fit molecule Adaptor_2-coot-2.pdb (#3) to map
P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms
average map value = 0.3519, steps = 80
shifted from previous position = 0.00255
rotated from previous position = 0.00247 degrees
atoms outside contour = 909, contour level = 0.3
Position of Adaptor_2-coot-2.pdb (#3) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.83334836 0.53350474 0.14457944 324.59388486
0.53754133 0.84313930 -0.01286233 -100.16808263
-0.12876272 0.06699862 -0.98940960 558.81313734
Axis 0.28041244 0.95977496 0.01417352
Axis point 197.76178843 0.00000000 268.07404732
Rotation angle (degrees) 171.81330513
Shift along axis 2.80169296
> select add #3
1567 atoms, 1599 bonds, 201 residues, 1 model selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Adaptor_2-coot-3.pdb" models #3 selectedOnly true relModel #1
> select subtract #3
Nothing selected
> hide #3 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Adaptor_2-coot-3.pdb"
Chain information for Adaptor_2-coot-3.pdb #4
---
Chain | Description
C | No description available
> close #4
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Adaptor_2-coot-4.pdb"
Chain information for Adaptor_2-coot-4.pdb #4
---
Chain | Description
C | No description available
> fitmap #4 inMap #1
Fit molecule Adaptor_2-coot-4.pdb (#4) to map
P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms
average map value = 0.8939, steps = 60
shifted from previous position = 0.0283
rotated from previous position = 0.0647 degrees
atoms outside contour = 366, contour level = 0.3
Position of Adaptor_2-coot-4.pdb (#4) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999952 0.00097204 0.00012724 -0.36581334
-0.00097211 0.99999937 0.00056184 0.08623047
-0.00012669 -0.00056196 0.99999983 0.22814539
Axis -0.49728066 0.11236319 -0.86028278
Axis point 88.99826283 378.76771246 0.00000000
Rotation angle (degrees) 0.06474138
Shift along axis -0.00466852
> combine #4
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16U0000PTA/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1 (23B74)
Kernel Version: Darwin 23.1.0
Time since boot: 20 hours, 46 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
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: 2.12.1
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: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
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: 1.8.dev202403220040
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
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-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
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-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
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: 1.37.1
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: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 10 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class |
comment:2 by , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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