The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000002022d0c00 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2744 in update_buffer_data
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1912 in update_buffers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1924 in activate_bindings
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 814 in _draw_geometry
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 787 in draw_self
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1554 in draw_opaque
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1579 in draw_depth
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 255 in _draw_scene
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume_viewer.py", line 2245 in moved_marker_cb
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/histogram.py", line 416 in move_marker_cb
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume_viewer.py", line 2171 in _drag
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume_viewer.py", line 2174 in mouseReleaseEvent
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, 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.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 53)
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/kuros488/Library/CloudStorage/OneDrive-
> UniversityofOtago/Desktop/j2008/cryosparc_P22_J2008_010_volume_map_sharp.mrc
Opened cryosparc_P22_J2008_010_volume_map_sharp.mrc as #1, grid size
1100,1100,1100, pixel 0.855, shown at step 1, values float32
> open /Users/kuros488/Library/CloudStorage/OneDrive-
> UniversityofOtago/Desktop/j2008/cryosparc_P22_J2008_010_volume_map_sharp.mrc
Opened cryosparc_P22_J2008_010_volume_map_sharp.mrc as #2, grid size
1100,1100,1100, pixel 0.855, shown at step 1, values float32
> close #2
> open "/Users/kuros488/Library/CloudStorage/OneDrive-UniversityofOtago/Ph_D
> copy/PHAGE/bas18_j63_pp_ewald.mrc"
Opened bas18_j63_pp_ewald.mrc as #2, grid size 1280,1280,1280, pixel 0.855,
shown at step 1, values float32
> volume #1 region 0,0,0,1099,1099,1099 step 8
> volume #2 level -0.001387,0 level 0.006443,0.8 level 0.02233,1
> volume #2 region 0,0,0,1279,1279,1279 step 8
> volume #1 step 1
> volume #2 step 1
> lighting soft
> select add #2
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,24.07,0,1,0,-101.18,0,0,1,-85.125
> view matrix models #2,1,0,0,-98.235,0,1,0,16.713,0,0,1,-69.492
> view matrix models #2,1,0,0,-69.64,0,1,0,-33.554,0,0,1,-107.18
> fitmap #2 inMap #1
Fit map bas18_j63_pp_ewald.mrc in map
cryosparc_P22_J2008_010_volume_map_sharp.mrc using 21065208 points
correlation = 0.4942, correlation about mean = 0.03872, overlap = 1.608e+04
steps = 324, shift = 53.3, angle = 0.939 degrees
Position of bas18_j63_pp_ewald.mrc (#2) relative to
cryosparc_P22_J2008_010_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99993432 0.01142401 -0.00091886 -83.02059852
-0.01143398 0.99986621 -0.01169690 -63.81166925
0.00078512 0.01170664 0.99993117 -83.33731127
Axis 0.71442733 -0.05201648 -0.69777351
Axis point 0.00000000 6957.71454456 -5525.42025810
Rotation angle (degrees) 0.93850253
Shift along axis 2.15764248
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.90528,0.32804,-0.26993,-57.275,-0.3725,0.91843,-0.13314,244.78,0.20423,0.22108,0.95363,-283.9
> view matrix models
> #2,0.48132,0.53212,-0.69655,296.48,-0.77748,0.62614,-0.058917,585.71,0.40478,0.56991,0.71509,-453.99
> select clear
> select subtract #2
Nothing selected
> select add #2
3 models selected
> view matrix models
> #2,0.59844,0.38951,-0.70011,312.39,-0.66777,0.72534,-0.16725,530.68,0.44267,0.5676,0.69417,-462.01
> select clear
> select subtract #2
Nothing selected
> select add #2
3 models selected
> view matrix models
> #2,0.55426,0.30022,-0.77632,427.12,-0.80315,0.43776,-0.40412,891.74,0.21851,0.84749,0.48375,-377.36
> select clear
> fitmap #1 inMap #2
Fit map cryosparc_P22_J2008_010_volume_map_sharp.mrc in map
bas18_j63_pp_ewald.mrc using 13445725 points
correlation = 0.9903, correlation about mean = 0.9084, overlap = 6.028e+04
steps = 244, shift = 0.685, angle = 6.66 degrees
Position of cryosparc_P22_J2008_010_volume_map_sharp.mrc (#1) relative to
bas18_j63_pp_ewald.mrc (#2) coordinates:
Matrix rotation and translation
0.50001403 -0.80901315 0.30900434 547.19954452
0.30900978 0.49999327 0.80902391 -213.67620028
-0.80901108 -0.30903794 0.49999663 837.85088406
Axis -0.57736496 0.57734098 0.57734487
Axis point 0.00000000 1074.79503380 960.08635002
Rotation angle (degrees) 75.52237176
Shift along axis 44.43103663
> lighting soft
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #2 level -0.003225
> view
> open "/Users/kuros488/Library/CloudStorage/OneDrive-UniversityofOtago/Ph_D
> copy/PHAGE/CAPSID_fitting&segmentation/BAS18_refinedHEXAMER.pdb"
Summary of feedback from opening
/Users/kuros488/Library/CloudStorage/OneDrive-UniversityofOtago/Ph_D
copy/PHAGE/CAPSID_fitting&segmentation/BAS18_refinedHEXAMER.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 2 ALA A 17 1 16
Start residue of secondary structure not found: HELIX 2 2 PRO A 22 HIS A 34 1
13
Start residue of secondary structure not found: HELIX 1 1 LEU A 2 ALA A 17 1
16
Start residue of secondary structure not found: HELIX 2 2 PRO A 22 HIS A 34 1
13
Start residue of secondary structure not found: HELIX 1 1 LEU A 2 ALA A 17 1
16
9 messages similar to the above omitted
Chain information for BAS18_refinedHEXAMER.pdb
---
Chain | Description
3.1/A 3.2/A | No description available
3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A | No description available
> volume #2 level 0.00254
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/kuros488/Library/CloudStorage/OneDrive-UniversityofOtago/Ph_D
> copy/PHAGE/CAPSID_fitting&segmentation/fittings.cxs"
Opened bas18_pp_b2_sh3.mrc as #2, grid size 504,504,504, pixel 1.71, shown at
level 0.0201, step 1, values float32
Opened bas18_pp_b2_sh3.mrc zone as #8, grid size 504,504,504, pixel 1.71,
shown at level 0.0201, step 1, values float32
Opened bas18_pp_b2_sh3.mrc zone as #9, grid size 504,504,504, pixel 1.71,
shown at level 0.0201, step 1, values float32
Opened cryosparc_P22_J363_013_volume_map_sharp.mrc as #10, grid size
200,200,200, pixel 1.71, shown at level 0.644, step 1, values float32
Log from Wed May 8 08:36:36 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/roshenykumaran/Desktop/Ph_D
> /PHAGE/fitting&segmentation/fittings.cxs"
Opened bas18_pp_b2_sh3.mrc as #2, grid size 504,504,504, pixel 1.71, shown at
level 0.0201, step 1, values float32
Opened bas18_pp_b2_sh3.mrc zone as #8, grid size 504,504,504, pixel 1.71,
shown at level 0.0201, step 1, values float32
Opened bas18_pp_b2_sh3.mrc zone as #9, grid size 504,504,504, pixel 1.71,
shown at level 0.0201, step 1, values float32
Log from Tue May 7 20:32:44 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/roshenykumaran/Desktop/Ph_D
> /PHAGE/fitting&segmentation/fittings.cxs"
Opened bas18_pp_b2_sh3.mrc as #2, grid size 504,504,504, pixel 1.71, shown at
level 0.0201, step 1, values float32
Opened bas18_pp_b2_sh3.mrc zone as #8, grid size 504,504,504, pixel 1.71,
shown at level 0.0201, step 1, values float32
Opened bas18_pp_b2_sh3.mrc zone as #9, grid size 504,504,504, pixel 1.71,
shown at level 0.0201, step 1, values float32
Log from Tue May 7 20:31:44 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/roshenykumaran/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18hexamer_dimer.cxs"
Opened bas18_pp_b2_sh3.mrc as #2, grid size 504,504,504, pixel 1.71, shown at
level 0.0201, step 1, values float32
Opened bas18_pp_b2_sh3.mrc zone as #1, grid size 504,504,504, pixel 1.71,
shown at level 0.0201, step 1, values float32
Opened volume difference as #6, grid size 504,504,504, pixel 1.71, shown at
level 0.0176, step 1, values float32
Opened bas18_pp_b2_sh3.mrc zone as #3, grid size 504,504,504, pixel 1.71,
shown at level 0.0201, step 1, values float32
Log from Fri Apr 19 09:45:44 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18withinhexamer2.cxs"
Opened bas18_pp_b2_sh3.mrc as #2, grid size 504,504,504, pixel 1.71, shown at
level 0.0201, step 1, values float32
Opened bas18_pp_b2_sh3.mrc zone as #1, grid size 504,504,504, pixel 1.71,
shown at level 0.0201, step 1, values float32
Opened volume difference as #6, grid size 504,504,504, pixel 1.71, shown at
level 0.0176, step 1, values float32
Log from Fri Apr 19 06:37:24 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18fitted.cxs"
Opened bas18_pp_b2_sh3.mrc as #2, grid size 504,504,504, pixel 1.71, shown at
level 0.0201, step 1, values float32
Log from Fri Apr 19 04:24:23 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18fitted.cxs"
Opened bas18_pp_b2_sh3.mrc as #2, grid size 504,504,504, pixel 1.71, shown at
level 0.0201, step 1, values float32
Log from Thu Apr 18 13:23:07 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18pentamer.pdb"
Chain information for BAS18pentamer.pdb
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A | No description available
> open "/Users/rosheny/Desktop/Ph_D /PHAGE/bas18_pp_b2_sh3.mrc"
Opened bas18_pp_b2_sh3.mrc as #2, grid size 504,504,504, pixel 1.71, shown at
level 0.0209, step 2, values float32
> select add #2
2 models selected
> volume #2 step 1
> select clear
> lighting soft
> ui tool show "Surface Color"
> color radial #2.1 palette #ff0000:#ffffff:#0000ff center
> 430.92,430.92,430.92
> select add #1
16194 atoms, 16434 bonds, 2196 residues, 7 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-242.6,0,1,0,2.7592,0,0,1,-118.15
> view matrix models #1,1,0,0,-426.49,0,1,0,227.06,0,0,1,-141.89
> select clear
> select add #1
16194 atoms, 16434 bonds, 2196 residues, 7 models selected
> view matrix models #1,1,0,0,-343.86,0,1,0,55.676,0,0,1,-181.44
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.26555,-0.71737,0.6441,344.27,0.89963,-0.055818,-0.43306,-124.78,0.34662,0.69446,0.63054,-628.78
> select clear
> select add #1
16194 atoms, 16434 bonds, 2196 residues, 7 models selected
> ui tool show "Fit in Map"
> fitmap sel inMap #2
Fit molecules BAS18pentamer.pdb (#1.1), BAS18pentamer.pdb (#1.2),
BAS18pentamer.pdb (#1.3), BAS18pentamer.pdb (#1.4), BAS18pentamer.pdb (#1.5),
BAS18pentamer.pdb (#1.6) to map bas18_pp_b2_sh3.mrc (#2) using 16194 atoms
average map value = 0.01131, steps = 312
shifted from previous position = 70.4
rotated from previous position = 38.2 degrees
atoms outside contour = 13798, contour level = 0.020908
Position of BAS18pentamer.pdb (#1.1) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.84556140 0.44322078 0.29762604 -155.57342720
-0.51967853 0.81102542 0.26864847 368.53801208
-0.12231170 -0.38182864 0.91610411 309.79577553
Axis -0.52645741 0.33987258 -0.77931331
Axis point 522.88309209 573.90821412 0.00000000
Rotation angle (degrees) 38.15471130
Shift along axis -34.26922294
Position of BAS18pentamer.pdb (#1.2) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.84556140 0.44322078 0.29762604 -155.57342720
-0.51967853 0.81102542 0.26864847 368.53801208
-0.12231170 -0.38182864 0.91610411 309.79577553
Axis -0.52645741 0.33987258 -0.77931331
Axis point 522.88309209 573.90821412 0.00000000
Rotation angle (degrees) 38.15471130
Shift along axis -34.26922294
Position of BAS18pentamer.pdb (#1.3) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.84556140 0.44322078 0.29762604 -155.57342720
-0.51967853 0.81102542 0.26864847 368.53801208
-0.12231170 -0.38182864 0.91610411 309.79577553
Axis -0.52645741 0.33987258 -0.77931331
Axis point 522.88309209 573.90821412 0.00000000
Rotation angle (degrees) 38.15471130
Shift along axis -34.26922294
Position of BAS18pentamer.pdb (#1.4) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.84556140 0.44322078 0.29762604 -155.57342720
-0.51967853 0.81102542 0.26864847 368.53801208
-0.12231170 -0.38182864 0.91610411 309.79577553
Axis -0.52645741 0.33987258 -0.77931331
Axis point 522.88309209 573.90821412 0.00000000
Rotation angle (degrees) 38.15471130
Shift along axis -34.26922294
Position of BAS18pentamer.pdb (#1.5) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.84556140 0.44322078 0.29762604 -155.57342720
-0.51967853 0.81102542 0.26864847 368.53801208
-0.12231170 -0.38182864 0.91610411 309.79577553
Axis -0.52645741 0.33987258 -0.77931331
Axis point 522.88309209 573.90821412 0.00000000
Rotation angle (degrees) 38.15471130
Shift along axis -34.26922294
Position of BAS18pentamer.pdb (#1.6) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.84556140 0.44322078 0.29762604 -155.57342720
-0.51967853 0.81102542 0.26864847 368.53801208
-0.12231170 -0.38182864 0.91610411 309.79577553
Axis -0.52645741 0.33987258 -0.77931331
Axis point 522.88309209 573.90821412 0.00000000
Rotation angle (degrees) 38.15471130
Shift along axis -34.26922294
> select clear
> hide #!2 models
> show #!2 models
> select add #1
16194 atoms, 16434 bonds, 2196 residues, 7 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.26555,-0.71737,0.6441,352.66,0.89963,-0.055818,-0.43306,-110.41,0.34662,0.69446,0.63054,-599.34
> fitmap sel inMap #2
Fit molecules BAS18pentamer.pdb (#1.1), BAS18pentamer.pdb (#1.2),
BAS18pentamer.pdb (#1.3), BAS18pentamer.pdb (#1.4), BAS18pentamer.pdb (#1.5),
BAS18pentamer.pdb (#1.6) to map bas18_pp_b2_sh3.mrc (#2) using 16194 atoms
average map value = 0.01146, steps = 100
shifted from previous position = 13.8
rotated from previous position = 8.52 degrees
atoms outside contour = 13760, contour level = 0.020908
Position of BAS18pentamer.pdb (#1.1) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.89629452 0.40292049 0.18523289 -135.55881707
-0.44338460 0.82188852 0.35764417 241.40281393
-0.00813862 -0.40268392 0.91530291 215.67193680
Axis -0.65886128 0.16756581 -0.73336452
Axis point 363.76951034 476.51068949 0.00000000
Rotation angle (degrees) 35.23993035
Shift along axis -28.40083259
Position of BAS18pentamer.pdb (#1.2) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.89629452 0.40292049 0.18523289 -135.55881707
-0.44338460 0.82188852 0.35764417 241.40281393
-0.00813862 -0.40268392 0.91530291 215.67193680
Axis -0.65886128 0.16756581 -0.73336452
Axis point 363.76951034 476.51068949 0.00000000
Rotation angle (degrees) 35.23993035
Shift along axis -28.40083259
Position of BAS18pentamer.pdb (#1.3) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.89629452 0.40292049 0.18523289 -135.55881707
-0.44338460 0.82188852 0.35764417 241.40281393
-0.00813862 -0.40268392 0.91530291 215.67193680
Axis -0.65886128 0.16756581 -0.73336452
Axis point 363.76951034 476.51068949 0.00000000
Rotation angle (degrees) 35.23993035
Shift along axis -28.40083259
Position of BAS18pentamer.pdb (#1.4) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.89629452 0.40292049 0.18523289 -135.55881707
-0.44338460 0.82188852 0.35764417 241.40281393
-0.00813862 -0.40268392 0.91530291 215.67193680
Axis -0.65886128 0.16756581 -0.73336452
Axis point 363.76951034 476.51068949 0.00000000
Rotation angle (degrees) 35.23993035
Shift along axis -28.40083259
Position of BAS18pentamer.pdb (#1.5) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.89629452 0.40292049 0.18523289 -135.55881707
-0.44338460 0.82188852 0.35764417 241.40281393
-0.00813862 -0.40268392 0.91530291 215.67193680
Axis -0.65886128 0.16756581 -0.73336452
Axis point 363.76951034 476.51068949 0.00000000
Rotation angle (degrees) 35.23993035
Shift along axis -28.40083259
Position of BAS18pentamer.pdb (#1.6) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.89629452 0.40292049 0.18523289 -135.55881707
-0.44338460 0.82188852 0.35764417 241.40281393
-0.00813862 -0.40268392 0.91530291 215.67193680
Axis -0.65886128 0.16756581 -0.73336452
Axis point 363.76951034 476.51068949 0.00000000
Rotation angle (degrees) 35.23993035
Shift along axis -28.40083259
> select clear
> color #1.1 #941751ff
> color #1.2 #fffb00ff
> color #1.3 #008f00ff
> color #1.4 #ff8ad8ff
> color #1.4 #ff2f92ff
> color #1.5 #0433ffff
> color #1.6 #ffd479ff
> select add #1.1
2699 atoms, 2739 bonds, 366 residues, 1 model selected
> select subtract #1.1
Nothing selected
> select add #1.1
2699 atoms, 2739 bonds, 366 residues, 1 model selected
> view matrix models
> #1.1,0.89629,0.40292,0.18523,-136.5,-0.44338,0.82189,0.35764,242.35,-0.0081386,-0.40268,0.9153,210.95
> fitmap sel inMap #2
Fit molecule BAS18pentamer.pdb (#1.1) to map bas18_pp_b2_sh3.mrc (#2) using
2699 atoms
average map value = 0.01592, steps = 116
shifted from previous position = 1.89
rotated from previous position = 17.9 degrees
atoms outside contour = 1839, contour level = 0.020908
Position of BAS18pentamer.pdb (#1.1) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.84184440 0.53242738 -0.08842563 -12.42053792
-0.48379972 0.81704697 0.31364324 303.10191416
0.23924014 -0.22125851 0.94541463 -112.22290185
Axis -0.44790247 -0.27437245 -0.85094250
Axis point 569.54570403 177.45498529 0.00000000
Rotation angle (degrees) 36.66380642
Shift along axis 17.89561005
> select #2
2 models selected
> select #2
2 models selected
> select #2
2 models selected
> select #2
2 models selected
> select clear
> select add #1.2
2699 atoms, 2739 bonds, 366 residues, 1 model selected
> view matrix models
> #1.2,0.89629,0.40292,0.18523,-127.29,-0.44338,0.82189,0.35764,247.09,-0.0081386,-0.40268,0.9153,214.9
> fitmap sel inMap #2
Fit molecule BAS18pentamer.pdb (#1.2) to map bas18_pp_b2_sh3.mrc (#2) using
2699 atoms
average map value = 0.01646, steps = 116
shifted from previous position = 0.968
rotated from previous position = 18.8 degrees
atoms outside contour = 1767, contour level = 0.020908
Position of BAS18pentamer.pdb (#1.2) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.87480067 0.46679702 -0.12970859 2.52566719
-0.41073866 0.85655610 0.31241861 221.43289905
0.25693877 -0.22002768 0.94104744 -128.57381974
Axis -0.48543537 -0.35250937 -0.80005603
Axis point 521.00200984 109.80231056 0.00000000
Rotation angle (degrees) 33.25878159
Shift along axis 23.58303971
> select #2
2 models selected
> select clear
> select add #1.3
2699 atoms, 2739 bonds, 366 residues, 1 model selected
> view matrix models
> #1.3,0.89629,0.40292,0.18523,-136.07,-0.44338,0.82189,0.35764,232.59,-0.0081386,-0.40268,0.9153,229.82
> undo
> select #2
2 models selected
> ui mousemode right zoom
> select clear
> select add #1.3
2699 atoms, 2739 bonds, 366 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1.3,0.77032,0.63296,-0.07722,-21.43,-0.61149,0.76761,0.19196,484.46,0.18078,-0.10065,0.97836,-118.01
> ui mousemode right "translate selected models"
> view matrix models
> #1.3,0.77032,0.63296,-0.07722,-11.466,-0.61149,0.76761,0.19196,493.67,0.18078,-0.10065,0.97836,-125.65
> ui mousemode right "rotate selected models"
> view matrix models
> #1.3,0.53877,0.74184,-0.39925,277.18,-0.78962,0.60986,0.067607,776.39,0.29364,0.27883,0.91435,-375
> ui mousemode right "translate selected models"
> view matrix models
> #1.3,0.53877,0.74184,-0.39925,292.47,-0.78962,0.60986,0.067607,783.33,0.29364,0.27883,0.91435,-373.8
> fitmap sel inMap #2
Fit molecule BAS18pentamer.pdb (#1.3) to map bas18_pp_b2_sh3.mrc (#2) using
2699 atoms
average map value = 0.01194, steps = 120
shifted from previous position = 5.34
rotated from previous position = 17.2 degrees
atoms outside contour = 2241, contour level = 0.020908
Position of BAS18pentamer.pdb (#1.3) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.42135404 0.76045046 -0.49414155 427.68002946
-0.71936832 0.61204664 0.32849374 613.65220788
0.55224089 0.21705761 0.80493229 -532.21802177
Axis -0.06136963 -0.57625929 -0.81495951
Axis point 852.14890712 81.67094824 0.00000000
Rotation angle (degrees) 65.21802469
Shift along axis 53.86678974
> select #2
2 models selected
> ui mousemode right zoom
> select clear
> select add #1.3
2699 atoms, 2739 bonds, 366 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #1.3,0.42135,0.76045,-0.49414,420.84,-0.71937,0.61205,0.32849,606,0.55224,0.21706,0.80493,-523.2
> ui mousemode right "rotate selected models"
> view matrix models
> #1.3,0.52965,0.49144,-0.69135,527.54,-0.77005,0.62034,-0.14898,841.96,0.35566,0.61128,0.707,-488.11
> fitmap sel inMap #2
Fit molecule BAS18pentamer.pdb (#1.3) to map bas18_pp_b2_sh3.mrc (#2) using
2699 atoms
average map value = 0.01243, steps = 136
shifted from previous position = 6.65
rotated from previous position = 26.8 degrees
atoms outside contour = 2216, contour level = 0.020908
Position of BAS18pentamer.pdb (#1.3) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.24363438 0.71215543 -0.65838965 675.22052950
-0.77520465 0.55093925 0.30906907 689.53752829
0.58283791 0.43508687 0.68629395 -600.85766721
Axis 0.06491309 -0.63936934 -0.76615478
Axis point 920.97827976 35.78646103 0.00000000
Rotation angle (degrees) 76.08785574
Shift along axis 63.31147482
> select clear
> ui mousemode right "translate selected models"
> select add #1.3
2699 atoms, 2739 bonds, 366 residues, 1 model selected
> view matrix models
> #1.3,0.24363,0.71216,-0.65839,660.08,-0.7752,0.55094,0.30907,703.3,0.58284,0.43509,0.68629,-616.79
> fitmap sel inMap #2
Fit molecule BAS18pentamer.pdb (#1.3) to map bas18_pp_b2_sh3.mrc (#2) using
2699 atoms
average map value = 0.01163, steps = 140
shifted from previous position = 10.4
rotated from previous position = 17.1 degrees
atoms outside contour = 2270, contour level = 0.020908
Position of BAS18pentamer.pdb (#1.3) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.03354568 0.85950212 -0.51003020 731.03591191
-0.80257668 0.32728521 0.49875351 746.02002120
0.59560504 0.39260731 0.70079536 -611.27733923
Axis -0.05309831 -0.55308024 -0.83143419
Axis point 867.20231537 121.06885088 0.00000000
Rotation angle (degrees) 88.23425844
Shift along axis 56.81117462
> select #2
2 models selected
> ui mousemode right zoom
> select clear
> select add #1.4
2699 atoms, 2739 bonds, 366 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1.4,0.90087,0.23524,0.36484,-140.68,-0.38115,0.83089,0.4054,163.73,-0.20777,-0.50427,0.83818,465.08
> ui mousemode right "translate selected models"
> view matrix models
> #1.4,0.90087,0.23524,0.36484,-144.36,-0.38115,0.83089,0.4054,159.36,-0.20777,-0.50427,0.83818,477.63
> fitmap sel inMap #2
Fit molecule BAS18pentamer.pdb (#1.4) to map bas18_pp_b2_sh3.mrc (#2) using
2699 atoms
average map value = 0.01381, steps = 112
shifted from previous position = 4.3
rotated from previous position = 17.3 degrees
atoms outside contour = 2105, contour level = 0.020908
Position of BAS18pentamer.pdb (#1.4) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.84690290 0.01789768 0.53144628 -74.51965551
-0.24688661 0.89841468 0.36317772 28.54325758
-0.47095910 -0.43878324 0.76528870 715.87211610
Axis -0.61183310 0.76475642 -0.20200958
Axis point 1200.41004141 0.00000000 574.89692437
Rotation angle (degrees) 40.94813518
Shift along axis -77.19079273
> ui mousemode right zoom
> select clear
> select add #1.6
2699 atoms, 2739 bonds, 366 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #1.6,0.89629,0.40292,0.18523,-134.11,-0.44338,0.82189,0.35764,235.33,-0.0081386,-0.40268,0.9153,204.18
> fitmap sel inMap #2
Fit molecule BAS18pentamer.pdb (#1.6) to map bas18_pp_b2_sh3.mrc (#2) using
2699 atoms
average map value = 0.01647, steps = 120
shifted from previous position = 7.7
rotated from previous position = 16.6 degrees
atoms outside contour = 1782, contour level = 0.020908
Position of BAS18pentamer.pdb (#1.6) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.81361042 0.57906642 0.05215526 -71.27586429
-0.57796750 0.79578388 0.18078050 456.65103655
0.06317960 -0.17722895 0.98213962 14.16921811
Axis -0.29558099 -0.00910195 -0.95527432
Axis point 670.95990879 337.33255494 0.00000000
Rotation angle (degrees) 37.27224289
Shift along axis 3.37588359
> select clear
> select add #1.5
2699 atoms, 2739 bonds, 366 residues, 1 model selected
> view matrix models
> #1.5,0.89629,0.40292,0.18523,-140.02,-0.44338,0.82189,0.35764,240.7,-0.0081386,-0.40268,0.9153,210.45
> view matrix models
> #1.5,0.89629,0.40292,0.18523,-125.18,-0.44338,0.82189,0.35764,239.5,-0.0081386,-0.40268,0.9153,167.62
> ui mousemode right "rotate selected models"
> view matrix models
> #1.5,0.61244,0.50218,-0.61051,434.29,-0.42903,0.85981,0.27687,247.16,0.66396,0.092362,0.74204,-545.76
> ui mousemode right "translate selected models"
> view matrix models
> #1.5,0.61244,0.50218,-0.61051,442.29,-0.42903,0.85981,0.27687,250.14,0.66396,0.092362,0.74204,-560.57
> fitmap sel inMap #2
Fit molecule BAS18pentamer.pdb (#1.5) to map bas18_pp_b2_sh3.mrc (#2) using
2699 atoms
average map value = 0.01284, steps = 160
shifted from previous position = 22.5
rotated from previous position = 15.4 degrees
atoms outside contour = 2159, contour level = 0.020908
Position of BAS18pentamer.pdb (#1.5) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.53583071 0.47649439 -0.69702120 557.52267963
-0.58469753 0.80496428 0.10080334 508.92628332
0.60910939 0.35353305 0.70992967 -596.47461426
Axis 0.14851102 -0.76751875 -0.62358595
Axis point 977.87959500 0.00000000 134.99640350
Rotation angle (degrees) 58.30736205
Shift along axis 64.14098843
> select #2
2 models selected
> ui mousemode right zoom
> select clear
> select add #1.3
2699 atoms, 2739 bonds, 366 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #1.3,0.033546,0.8595,-0.51003,749.67,-0.80258,0.32729,0.49875,748.32,0.59561,0.39261,0.7008,-607.21
> ui mousemode right "rotate selected models"
> view matrix models
> #1.3,0.34406,0.90794,-0.23931,338.89,-0.74475,0.41911,0.51932,645.96,0.57181,-0.00044819,0.82039,-454.09
> ui mousemode right "translate selected models"
> view matrix models
> #1.3,0.34406,0.90794,-0.23931,326.54,-0.74475,0.41911,0.51932,647.57,0.57181,-0.00044819,0.82039,-471.52
> fitmap sel inMap #2
Fit molecule BAS18pentamer.pdb (#1.3) to map bas18_pp_b2_sh3.mrc (#2) using
2699 atoms
average map value = 0.01179, steps = 84
shifted from previous position = 3.58
rotated from previous position = 7.94 degrees
atoms outside contour = 2282, contour level = 0.020908
Position of BAS18pentamer.pdb (#1.3) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.42268100 0.84352961 -0.33135868 321.00627051
-0.68211612 0.53683950 0.49650876 549.22631120
0.59670627 0.01616028 0.80229700 -492.71286362
Axis -0.25975661 -0.50186690 -0.82501886
Axis point 756.75580876 122.75940254 0.00000000
Rotation angle (degrees) 67.61001620
Shift along axis 47.47540000
> view matrix models
> #1.3,0.42268,0.84353,-0.33136,323.21,-0.68212,0.53684,0.49651,549.2,0.59671,0.01616,0.8023,-490.81
> fitmap sel inMap #2
Fit molecule BAS18pentamer.pdb (#1.3) to map bas18_pp_b2_sh3.mrc (#2) using
2699 atoms
average map value = 0.01205, steps = 108
shifted from previous position = 3.73
rotated from previous position = 7.37 degrees
atoms outside contour = 2251, contour level = 0.020908
Position of BAS18pentamer.pdb (#1.3) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.47816450 0.83738342 -0.26485416 249.48911364
-0.62247948 0.53586379 0.57041151 468.70150361
0.61957890 -0.10788425 0.77748503 -446.41157301
Axis -0.36929916 -0.48153092 -0.79482457
Axis point 693.60123291 117.98276676 0.00000000
Rotation angle (degrees) 66.68682663
Shift along axis 36.98850099
> select #2
2 models selected
> ui mousemode right zoom
> select clear
> save "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18fitted.cxs" includeMaps true
> transparency 50
> select add #1.3
2699 atoms, 2739 bonds, 366 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #1.3,0.47816,0.83738,-0.26485,244.08,-0.62248,0.53586,0.57041,455.91,0.61958,-0.10788,0.77749,-437.79
> ui mousemode right "rotate selected models"
> view matrix models
> #1.3,-0.8462,-0.42644,0.31952,1773.7,-0.44161,0.22568,-0.86836,1021.8,0.29819,-0.87591,-0.37929,673.75
> fitmap sel inMap #2
Fit molecule BAS18pentamer.pdb (#1.3) to map bas18_pp_b2_sh3.mrc (#2) using
2699 atoms
average map value = 0.01641, steps = 148
shifted from previous position = 15.2
rotated from previous position = 14.7 degrees
atoms outside contour = 1784, contour level = 0.020908
Position of BAS18pentamer.pdb (#1.3) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
-0.88905571 -0.39593890 0.22980932 1849.48857926
-0.41012921 0.46581613 -0.78409780 845.45808973
0.20340593 -0.79135814 -0.57652260 798.40762325
Axis -0.23540604 0.85609125 -0.46009974
Axis point 1044.41747570 0.00000000 618.15073935
Rotation angle (degrees) 179.11641252
Shift along axis -78.93865588
> select clear
> save "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18fitted.cxs" includeMaps true
> ui mousemode right zoom
> hide #!2 models
> show #!2 models
> save "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18pentamer.pdb"
> transparency 0
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676105_protein_putativeminorcapsidprotein_cde7b/GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#3
---
Chain | Description
A | No description available
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> select add #3
2875 atoms, 2926 bonds, 367 residues, 1 model selected
> show #3 target m
[Repeated 1 time(s)]
> hide #!1 models
> hide #!2 models
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,291.4,0,1,0,69.45,0,0,1,597.99
> show #!2 models
> hide #!2 models
> show #!2 models
> transparency 50
> show #!1 models
> view matrix models #3,1,0,0,340.79,0,1,0,666.06,0,0,1,321.09
> view matrix models #3,1,0,0,535.07,0,1,0,480.25,0,0,1,347.58
> view matrix models #3,1,0,0,540.12,0,1,0,468.82,0,0,1,344.68
> ui mousemode right zoom
> hide #3 models
> select subtract #3
Nothing selected
> transparency 0
> show #3 models
> select add #3
2875 atoms, 2926 bonds, 367 residues, 1 model selected
> fitmap sel inMap #2
Fit molecule
GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#3) to map bas18_pp_b2_sh3.mrc (#2) using 2875 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 2875, contour level = 0.020908
Position of
GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#3) relative to bas18_pp_b2_sh3.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 540.12440163
0.00000000 1.00000000 0.00000000 468.82120218
0.00000000 0.00000000 1.00000000 344.68285382
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 344.68285382
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,527.09,0,1,0,449.97,0,0,1,307.5
> fitmap sel inMap #2
Fit molecule
GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#3) to map bas18_pp_b2_sh3.mrc (#2) using 2875 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 2875, contour level = 0.020908
Position of
GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#3) relative to bas18_pp_b2_sh3.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 527.09112553
0.00000000 1.00000000 0.00000000 449.97244242
0.00000000 0.00000000 1.00000000 307.50399434
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 307.50399434
> fitmap sel inMap #2
Fit molecule
GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#3) to map bas18_pp_b2_sh3.mrc (#2) using 2875 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 2875, contour level = 0.020908
Position of
GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#3) relative to bas18_pp_b2_sh3.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 527.09112553
0.00000000 1.00000000 0.00000000 449.97244242
0.00000000 0.00000000 1.00000000 307.50399434
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 307.50399434
> select #1.5/A:174
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #1.5,0.53583,0.47649,-0.69702,504.05,-0.5847,0.80496,0.1008,488.36,0.60911,0.35353,0.70993,-665.14
> undo
> ui mousemode right translate
Drag select of 8 residues, 2 bas18_pp_b2_sh3.mrc
> ui mousemode right zoom
> select clear
> hide #3 models
> show #3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #3 models
> hide #!2 models
> show #3 models
> ui mousemode right "translate selected models"
> select add #3
2875 atoms, 2926 bonds, 367 residues, 1 model selected
> view matrix models #3,1,0,0,651.05,0,1,0,482.71,0,0,1,262.31
> view matrix models #3,1,0,0,623.99,0,1,0,538.19,0,0,1,235.69
> show #!2 models
> fitmap sel inMap #2
Fit molecule
GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#3) to map bas18_pp_b2_sh3.mrc (#2) using 2875 atoms
average map value = 0.01239, steps = 76
shifted from previous position = 5.09
rotated from previous position = 4.88 degrees
atoms outside contour = 2406, contour level = 0.020908
Position of
GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#3) relative to bas18_pp_b2_sh3.mrc (#2) coordinates:
Matrix rotation and translation
0.99888566 0.02377300 -0.04077101 627.68836761
-0.02660091 0.99717238 -0.07028248 541.09508706
0.03898490 0.07128871 0.99669358 233.76827355
Axis 0.83218250 -0.46882047 -0.29610750
Axis point 0.00000000 -3681.98090239 9177.45839439
Rotation angle (degrees) 4.87948572
Shift along axis 199.45428365
> select #2
2 models selected
> view matrix models #2,1,0,0,-2.1445,0,1,0,33.399,0,0,1,28.318
> undo
> ui mousemode right zoom
> select clear
> ui mousemode right clip
> ui mousemode right zoom
> hide #3 models
> show #3 models
> hide #!2 models
> hide #!1 models
> hide #3 models
> show #!2 models
> show #!1 models
> show #3 models
> hide #!2 models
> hide #!1 models
> hide #3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #3 models
> hide #3 models
> show #!2 models
> show #!1 models
> show #3 models
> select add #3
2875 atoms, 2926 bonds, 367 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99889,0.023773,-0.040771,619.74,-0.026601,0.99717,-0.070282,539.35,0.038985,0.071289,0.99669,231.89
> fitmap sel inMap #2
Fit molecule
GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#3) to map bas18_pp_b2_sh3.mrc (#2) using 2875 atoms
average map value = 0.01224, steps = 216
shifted from previous position = 6.54
rotated from previous position = 7.67 degrees
atoms outside contour = 2425, contour level = 0.020908
Position of
GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#3) relative to bas18_pp_b2_sh3.mrc (#2) coordinates:
Matrix rotation and translation
0.99924756 -0.01977724 0.03336418 623.93878322
0.02523729 0.98475279 -0.17211919 543.70313928
-0.02945142 0.17283170 0.98451095 234.38748243
Axis 0.97581201 0.17769549 0.12733904
Axis point 0.00000000 -594.61608674 2452.42034349
Rotation angle (degrees) 10.18055344
Shift along axis 735.30723065
> select clear
> hide #3 models
> close #3
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18hexamerpdb.pdb"
Chain information for BAS18hexamerpdb.pdb
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A | No description available
> ui mousemode right zoom
> lighting soft
[Repeated 1 time(s)]
> ui mousemode right clip
> ui mousemode right zoom
> transparency 50
> lighting simple
> ui mousemode right "translate selected models"
> transparency 0
> transparency 50
> color single #2.1
> transparency 0
> transparency 50
> hide #!1 models
> show #!1 models
> ui mousemode right zoom
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676110_protein_majorcapsidprotein_01eb3/GeneID_79676110_protein_majorcapsidprotein_01eb3_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
GeneID_79676110_protein_majorcapsidprotein_01eb3_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#4
---
Chain | Description
A | No description available
> select add #4
2699 atoms, 2739 bonds, 366 residues, 1 model selected
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show target m
> ui mousemode right clip
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,466.74,0,1,0,837.56,0,0,1,471.26
> view matrix models #4,1,0,0,586.81,0,1,0,420.27,0,0,1,464.73
> view matrix models #4,1,0,0,778.23,0,1,0,605.54,0,0,1,256.42
> view matrix models #4,1,0,0,698.39,0,1,0,524.49,0,0,1,197.26
> ui mousemode right zoom
> transparency 0
> volume #2 level 0.02006
> lighting soft
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.63145,0.76603,-0.12028,698.62,-0.15761,0.27867,0.94736,536.75,0.75923,-0.57926,0.29671,185.2
> view matrix models
> #4,-0.001711,0.11934,0.99285,713.9,0.84646,-0.52847,0.06498,521.41,0.53244,0.84052,-0.10011,182.67
> view matrix models
> #4,-0.56809,-0.65353,0.50017,705.8,0.62536,-0.73789,-0.25385,516.62,0.53497,0.16858,0.82788,194.6
> view matrix models
> #4,-0.31327,-0.37691,0.87167,711.44,0.68254,-0.72755,-0.069288,519.24,0.6603,0.57324,0.48518,190.39
> view matrix models
> #4,-0.51799,-0.69853,0.4937,705.56,0.71618,-0.66976,-0.19623,517.5,0.46774,0.25194,0.8472,195.11
> view matrix models
> #4,-0.9152,0.28538,0.28456,704.99,-0.37596,-0.35029,-0.85787,509.76,-0.14514,-0.89211,0.42788,187.35
> view matrix models
> #4,0.4491,-0.63059,0.63298,706.73,-0.3164,-0.77478,-0.54737,513.28,0.83558,0.045553,-0.54747,174.3
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.4491,-0.63059,0.63298,678.02,-0.3164,-0.77478,-0.54737,449.15,0.83558,0.045553,-0.54747,205.86
> view matrix models
> #4,0.4491,-0.63059,0.63298,706.47,-0.3164,-0.77478,-0.54737,467.47,0.83558,0.045553,-0.54747,224.58
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.13108,-0.63391,0.76222,708.64,-0.43361,-0.72807,-0.53094,467.92,0.89152,-0.26091,-0.3703,226.43
> fitmap sel inMap #2
Fit molecule
GeneID_79676110_protein_majorcapsidprotein_01eb3_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#4) to map bas18_pp_b2_sh3.mrc (#2) using 2699 atoms
average map value = 0.01292, steps = 284
shifted from previous position = 27.9
rotated from previous position = 42.9 degrees
atoms outside contour = 2182, contour level = 0.020062
Position of
GeneID_79676110_protein_majorcapsidprotein_01eb3_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#4) relative to bas18_pp_b2_sh3.mrc (#2) coordinates:
Matrix rotation and translation
0.66582607 -0.47567736 0.57481018 692.71923879
0.00450536 -0.76783517 -0.64063165 451.51528083
0.74609344 0.42913895 -0.50910159 243.38277045
Axis 0.90272865 -0.14453782 0.40520341
Axis point 0.00000000 285.48964971 65.59640225
Rotation angle (degrees) 143.66392021
Shift along axis 658.69599603
> view matrix models
> #4,0.75449,-0.38384,0.53236,692.21,0.025279,-0.79355,-0.60798,451.91,0.65582,0.47218,-0.58902,242.42
> view matrix models
> #4,0.6012,-0.56738,0.56271,692.42,0.019986,-0.69328,-0.72039,450.51,0.79885,0.44434,-0.40546,244.85
> view matrix models
> #4,0.58846,-0.80852,-0.0022275,683.83,-0.53721,-0.38893,-0.74843,451.3,0.60425,0.44162,-0.66321,241.34
> fitmap sel inMap #2
Fit molecule
GeneID_79676110_protein_majorcapsidprotein_01eb3_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#4) to map bas18_pp_b2_sh3.mrc (#2) using 2699 atoms
average map value = 0.01457, steps = 116
shifted from previous position = 4.93
rotated from previous position = 23.8 degrees
atoms outside contour = 2019, contour level = 0.020062
Position of
GeneID_79676110_protein_majorcapsidprotein_01eb3_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#4) relative to bas18_pp_b2_sh3.mrc (#2) coordinates:
Matrix rotation and translation
0.74418212 -0.66791482 -0.00910078 686.79440575
-0.59294825 -0.65425915 -0.46942239 456.25600512
0.30757993 0.35473202 -0.88292688 240.55141416
Axis 0.93011323 -0.35739531 0.08460477
Axis point 0.00000000 335.14022257 168.60201317
Rotation angle (degrees) 153.70200529
Shift along axis 496.08460832
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.74418,-0.66791,-0.0091008,685.55,-0.59295,-0.65426,-0.46942,455.45,0.30758,0.35473,-0.88293,239.46
[deleted to fit within ticket limits]
> select clear
> ui mousemode right clip
> ui mousemode right zoom
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #8 models
> select add #7
874 atoms, 884 bonds, 109 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,704.46,0,1,0,483.24,0,0,1,305.38
> close #7
> show #8 models
> ui mousemode right zoom
> show #!3 models
> show #!5 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> hide #!1 models
> hide #!5 models
> close #8
> show #9 models
> hide #9 models
> show #10 models
> ui mousemode right "translate selected models"
> select add #10
791 atoms, 802 bonds, 101 residues, 1 model selected
> view matrix models #10,1,0,0,729.12,0,1,0,460.69,0,0,1,276.64
> view matrix models #10,1,0,0,691.87,0,1,0,525.45,0,0,1,339.78
> view matrix models #10,1,0,0,705.92,0,1,0,518.51,0,0,1,356.01
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.99398,0.063948,-0.089009,705.65,-0.093647,0.91747,-0.38662,517.53,0.05694,0.39263,0.91793,355.6
> fitmap sel inMap #6
Fit molecule
GeneID_79676154_protein_hypotheticalprotein_16e8e_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#10) to map volume difference (#6) using 791 atoms
average map value = 0.01363, steps = 84
shifted from previous position = 6.99
rotated from previous position = 22.9 degrees
atoms outside contour = 553, contour level = 0.017597
Position of
GeneID_79676154_protein_hypotheticalprotein_16e8e_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#10) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.95087194 -0.29914102 -0.07973207 711.23974587
0.20773877 0.80748747 -0.55209473 520.50409624
0.22953682 0.50840794 0.82996037 353.03747684
Axis 0.87254171 -0.25445481 0.41704163
Axis point 0.00000000 214.97869987 1160.65533479
Rotation angle (degrees) 37.42402320
Shift along axis 635.37289553
> select clear
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> close #10
> show #11 models
> ui mousemode right zoom
> select add #11
759 atoms, 780 bonds, 89 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,697.9,0,1,0,500.39,0,0,1,320.99
> view matrix models #11,1,0,0,699.83,0,1,0,501.63,0,0,1,325.68
> select clear
> ui mousemode right zoom
> select add #11
759 atoms, 780 bonds, 89 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,703.42,0,1,0,515.82,0,0,1,348.4
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.65253,-0.60395,-0.45766,701.03,0.72693,0.32836,0.60312,525.98,-0.21398,-0.72624,0.65329,347.86
> view matrix models
> #11,0.36727,-0.66915,-0.64603,698.41,0.83208,-0.074014,0.5497,527.88,-0.41565,-0.73943,0.5296,345.94
> fitmap sel inMap #6
Fit molecule
GeneID_79676155_protein_hypotheticalprotein_8d028_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
(#11) to map volume difference (#6) using 759 atoms
average map value = 0.01274, steps = 124
shifted from previous position = 12.6
rotated from previous position = 25.7 degrees
atoms outside contour = 560, contour level = 0.017597
Position of
GeneID_79676155_protein_hypotheticalprotein_8d028_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
(#11) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.57098307 -0.29459099 -0.76628616 708.90322041
0.78567396 -0.07463499 0.61412217 525.30204894
-0.23810662 -0.95270445 0.18883715 351.54239595
Axis -0.79330282 -0.26742354 0.54695090
Axis point 0.00000000 482.39176462 211.08703630
Rotation angle (degrees) 99.05644364
Shift along axis -510.57662542
> select clear
> ui mousemode right "translate selected models"
> select add #11
759 atoms, 780 bonds, 89 residues, 1 model selected
> view matrix models
> #11,0.57098,-0.29459,-0.76629,715.63,0.78567,-0.074635,0.61412,524.81,-0.23811,-0.9527,0.18884,347.51
> fitmap sel inMap #6
Fit molecule
GeneID_79676155_protein_hypotheticalprotein_8d028_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
(#11) to map volume difference (#6) using 759 atoms
average map value = 0.01274, steps = 84
shifted from previous position = 7.84
rotated from previous position = 0.0382 degrees
atoms outside contour = 559, contour level = 0.017597
Position of
GeneID_79676155_protein_hypotheticalprotein_8d028_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
(#11) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.57047358 -0.29461595 -0.76665594 708.92213859
0.78597929 -0.07502590 0.61368369 525.29497370
-0.23832005 -0.95266603 0.18876174 351.54422258
Axis -0.79312391 -0.26752380 0.54716129
Axis point 0.00000000 482.23879671 211.31282918
Rotation angle (degrees) 99.08475218
Shift along axis -510.44061900
> select clear
> close #11
> show #12 models
> ui mousemode right zoom
> hide #12 models
> show #12 models
> select add #12
384 atoms, 388 bonds, 50 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,704.28,0,1,0,469.91,0,0,1,308.06
> select clear
> ui mousemode right zoom
> close #12
> show #13 models
> select add #13
1510 atoms, 1539 bonds, 184 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #13,1,0,0,683.99,0,1,0,447.8,0,0,1,295.34
> close #13
> show #14 models
> select add #14
393 atoms, 402 bonds, 48 residues, 1 model selected
> view matrix models #14,1,0,0,698.2,0,1,0,466.19,0,0,1,300.04
> view matrix models #14,1,0,0,698.2,0,1,0,460.38,0,0,1,281.82
> ui mousemode right zoom
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models #14,1,0,0,692.8,0,1,0,448.84,0,0,1,268.35
> select clear
> ui mousemode right zoom
> close #14
> show #15 models
> select add #15
247 atoms, 251 bonds, 33 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #15,1,0,0,720.83,0,1,0,511.62,0,0,1,313.02
> close #15
> show #9 models
> hide #9 models
> show #16 models
> close #16
> show #17 models
> select add #17
392 atoms, 402 bonds, 55 residues, 1 model selected
> view matrix models #17,1,0,0,739.09,0,1,0,484.05,0,0,1,325.46
> select clear
> ui mousemode right zoom
> select add #17
392 atoms, 402 bonds, 55 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #17,1,0,0,741.92,0,1,0,502.64,0,0,1,365.63
> view matrix models #17,1,0,0,721.14,0,1,0,522.07,0,0,1,352.65
> view matrix models #17,1,0,0,718.55,0,1,0,523.52,0,0,1,357.88
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) to map volume difference (#6) using 392 atoms
average map value = 0.01222, steps = 140
shifted from previous position = 1.18
rotated from previous position = 19.2 degrees
atoms outside contour = 290, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.97601098 -0.21300450 0.04507385 717.28054263
0.19489575 0.94703945 0.25520959 523.77331799
-0.09704750 -0.24030266 0.96583457 357.09312061
Axis -0.75379888 0.21620235 0.62051897
Axis point 0.00000000 2267.29027640 -1756.21941064
Rotation angle (degrees) 19.18847617
Shift along axis -205.86119744
> select clear
> select add #17
392 atoms, 402 bonds, 55 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.92513,-0.37961,0.0058087,717.29,0.36074,0.8837,0.29822,525.41,-0.11834,-0.27379,0.95448,357
> view matrix models
> #17,0.8,-0.59877,-0.038384,716.62,0.5747,0.74631,0.33577,527.73,-0.1724,-0.29067,0.94116,356.53
> view matrix models
> #17,0.73855,-0.60743,-0.29254,717.61,0.63878,0.76923,0.015439,530.44,0.21565,-0.19827,0.95613,360.46
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.73855,-0.60743,-0.29254,713.33,0.63878,0.76923,0.015439,523.4,0.21565,-0.19827,0.95613,356.24
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) to map volume difference (#6) using 392 atoms
average map value = 0.01292, steps = 80
shifted from previous position = 3.65
rotated from previous position = 9.09 degrees
atoms outside contour = 298, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.78184859 -0.59720246 -0.17905868 714.35198574
0.59430632 0.80068873 -0.07548207 520.38387607
0.18844834 -0.04740015 0.98093855 354.18952232
Axis 0.02251572 -0.29466232 0.95533615
Axis point -513.77799949 1376.25872850 0.00000000
Rotation angle (degrees) 38.58002406
Shift along axis 201.11668025
> select clear
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> select add #17
392 atoms, 402 bonds, 55 residues, 1 model selected
> view matrix models
> #17,0.80913,-0.54132,-0.22866,714.86,0.50606,0.83968,-0.19709,520.14,0.29869,0.043756,0.95335,355.39
> view matrix models
> #17,0.3037,-0.60741,-0.73405,712.77,0.91367,0.40411,0.043627,523.8,0.27013,-0.68393,0.6777,358.2
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.3037,-0.60741,-0.73405,715.49,0.91367,0.40411,0.043627,517.17,0.27013,-0.68393,0.6777,358.22
> view matrix models
> #17,0.3037,-0.60741,-0.73405,710.93,0.91367,0.40411,0.043627,516.74,0.27013,-0.68393,0.6777,350.17
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.23194,-0.10848,-0.96666,710.73,0.5212,0.85293,0.029339,511.76,0.82131,-0.51063,0.25437,358.54
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.23194,-0.10848,-0.96666,711,0.5212,0.85293,0.029339,517,0.82131,-0.51063,0.25437,349.86
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) to map volume difference (#6) using 392 atoms
average map value = 0.01511, steps = 196
shifted from previous position = 4.83
rotated from previous position = 44.9 degrees
atoms outside contour = 244, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.66266377 -0.28313191 -0.69333473 713.33614777
0.09631265 0.95031354 -0.29602035 520.31549567
0.74269819 0.12938506 0.65700754 350.06662852
Axis 0.27533676 -0.92944905 0.24558935
Axis point -21.09734978 0.00000000 1119.02383738
Rotation angle (degrees) 50.58057706
Shift along axis -201.22644326
> select clear
> show #17 atoms
> hide #17 atoms
> select add #17
392 atoms, 402 bonds, 55 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.48958,0.64582,-0.58585,709.06,0.87059,-0.39966,0.28696,527.42,-0.048815,-0.65053,-0.75791,352.06
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) to map volume difference (#6) using 392 atoms
average map value = 0.01371, steps = 136
shifted from previous position = 2.82
rotated from previous position = 17.2 degrees
atoms outside contour = 269, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.27027077 0.82676249 -0.49337360 707.27859371
0.96209763 -0.21257005 0.17082780 526.16179180
0.03635756 -0.52084333 -0.85287770 354.54680902
Axis -0.78450233 -0.60082793 0.15349887
Axis point 0.00000000 63.29298751 241.20530791
Rotation angle (degrees) 153.84287264
Shift along axis -816.57186816
> select clear
> ui mousemode right "translate selected models"
> select add #17
392 atoms, 402 bonds, 55 residues, 1 model selected
> view matrix models
> #17,0.27027,0.82676,-0.49337,711.3,0.9621,-0.21257,0.17083,517.36,0.036358,-0.52084,-0.85288,347.66
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.27154,0.81228,-0.51621,711.49,0.96225,-0.21887,0.16177,517.43,0.018417,-0.54065,-0.84105,347.42
> view matrix models
> #17,0.28209,0.95503,-0.09133,708.6,0.78052,-0.28381,-0.55699,520.22,-0.55787,0.085836,-0.82548,339.94
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.28209,0.95503,-0.09133,714.9,0.78052,-0.28381,-0.55699,513.09,-0.55787,0.085836,-0.82548,352.59
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) to map volume difference (#6) using 392 atoms
average map value = 0.01402, steps = 96
shifted from previous position = 3.58
rotated from previous position = 24.2 degrees
atoms outside contour = 259, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.52807231 0.76720707 -0.36405078 716.26967492
0.56794637 -0.63778790 -0.52025333 515.15433953
-0.63132921 0.06797006 -0.77253060 350.31091504
Axis 0.86998796 0.39530732 -0.29470845
Axis point 0.00000000 38.43993276 319.40784855
Rotation angle (degrees) 160.24102785
Shift along axis 723.55068957
> select clear
> select add #17
392 atoms, 402 bonds, 55 residues, 1 model selected
> view matrix models
> #17,0.52807,0.76721,-0.36405,718.52,0.56795,-0.63779,-0.52025,516.76,-0.63133,0.06797,-0.77253,351.56
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) to map volume difference (#6) using 392 atoms
average map value = 0.01401, steps = 56
shifted from previous position = 3.06
rotated from previous position = 0.0935 degrees
atoms outside contour = 258, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.52887236 0.76730275 -0.36268518 716.27769022
0.56786839 -0.63751763 -0.52066956 515.13288338
-0.63072937 0.06941029 -0.77289242 350.29238087
Axis 0.87019935 0.39528868 -0.29410876
Axis point 0.00000000 38.34864186 319.17414338
Rotation angle (degrees) 160.18107624
Shift along axis 723.90651644
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.7723,0.36453,-0.52026,720.67,-0.31505,0.93095,0.18461,498.16,0.55163,0.021338,0.83381,352.82
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.7723,0.36453,-0.52026,728.47,-0.31505,0.93095,0.18461,515.2,0.55163,0.021338,0.83381,345.47
> view matrix models
> #17,0.7723,0.36453,-0.52026,712.8,-0.31505,0.93095,0.18461,523.07,0.55163,0.021338,0.83381,354.27
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) to map volume difference (#6) using 392 atoms
average map value = 0.01484, steps = 76
shifted from previous position = 3.73
rotated from previous position = 14.6 degrees
atoms outside contour = 246, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.90158090 0.27608135 -0.33306300 709.38199325
-0.21361337 0.95359140 0.21220928 523.28510128
0.37619304 -0.12017712 0.91871446 353.13894849
Axis -0.35982043 -0.76779559 -0.53011243
Axis point 483.21507727 0.00000000 1075.03199460
Rotation angle (degrees) 27.50836897
Shift along axis -844.22947513
> view matrix models
> #17,0.90158,0.27608,-0.33306,712.05,-0.21361,0.95359,0.21221,525.54,0.37619,-0.12018,0.91871,351.45
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) to map volume difference (#6) using 392 atoms
average map value = 0.01484, steps = 72
shifted from previous position = 3.89
rotated from previous position = 0.0595 degrees
atoms outside contour = 248, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.90154140 0.27681193 -0.33256315 709.37849442
-0.21414155 0.95330201 0.21297577 523.28146070
0.37598735 -0.12079088 0.91871817 353.14420199
Axis -0.36107063 -0.76651390 -0.53111623
Axis point 485.85873431 0.00000000 1072.00531621
Rotation angle (degrees) 27.52853109
Shift along axis -844.79886783
> select clear
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> select add #17
392 atoms, 402 bonds, 55 residues, 1 model selected
> view matrix models
> #17,0.90154,0.27681,-0.33256,711.23,-0.21414,0.9533,0.21298,524.66,0.37599,-0.12079,0.91872,351.96
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) to map volume difference (#6) using 392 atoms
average map value = 0.01484, steps = 56
shifted from previous position = 2.6
rotated from previous position = 0.0119 degrees
atoms outside contour = 247, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.90158556 0.27663391 -0.33259156 709.37094855
-0.21400930 0.95336441 0.21282933 523.26936324
0.37595677 -0.12070616 0.91874182 353.14398376
Axis -0.36091813 -0.76671880 -0.53092409
Axis point 485.40626737 0.00000000 1072.56465534
Rotation angle (degrees) 27.52045885
Shift along axis -844.71793905
> select clear
> ui mousemode right zoom
> select add #17
392 atoms, 402 bonds, 55 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.90159,0.27663,-0.33259,707.15,-0.21401,0.95336,0.21283,534.78,0.37596,-0.12071,0.91874,351.03
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) to map volume difference (#6) using 392 atoms
average map value = 0.01385, steps = 136
shifted from previous position = 5.48
rotated from previous position = 19.2 degrees
atoms outside contour = 265, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.96301493 -0.03330271 -0.26738209 709.13047685
0.09002453 0.97507535 0.20278965 532.32280035
0.25396424 -0.21936040 0.94201018 354.08807026
Axis -0.61892296 -0.76435669 0.18081264
Axis point -1704.59985316 0.00000000 1078.33412494
Rotation angle (degrees) 19.94000647
Shift along axis -781.75803223
> select clear
> show #18 models
> ui mousemode right zoom
> close #18
> show #9 models
> hide #9 models
> hide #17 models
> show #17 models
> show #9 models
> save "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18withinhexamer2.cxs"
> select clear
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676166_protein_hypotheticalprotein_bafdb/GeneID_79676166_protein_hypotheticalprotein_bafdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
GeneID_79676166_protein_hypotheticalprotein_bafdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#7
---
Chain | Description
A | No description available
> hide #17 models
> show #17 models
> close #7
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676165_protein_hypotheticalprotein_f1234/GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#7
---
Chain | Description
A | No description available
> hide #7 models
> show #7 models
> ui tool show Matchmaker
> matchmaker #7/A to #17/A pairing ss showAlignment true
Parameters
---
Chain pairing | ss
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
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#17) with
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#7), sequence alignment score = 280.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#7/A,
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#17/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 55 pruned atom pairs is 0.000 angstroms; (across all 55 pairs:
0.000)
> matchmaker #7/A to #17/A pairing ss showAlignment true
Parameters
---
Chain pairing | ss
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
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#17) with
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#7), sequence alignment score = 280.8
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2:
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#7/A,
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#17/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 55 pruned atom pairs is 0.000 angstroms; (across all 55 pairs:
0.000)
> hide #7 models
> show #7 models
> ui mousemode right clip
> ui mousemode right "translate selected models"
> select add #7
392 atoms, 402 bonds, 55 residues, 1 model selected
> select #6
3 models selected
> select clear
> ui mousemode right zoom
> hide #7 models
> hide #17 models
> show #17 models
> show #7 models
> hide #7 models
> show #7 models
> select add #7
392 atoms, 402 bonds, 55 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #17
392 atoms, 402 bonds, 55 residues, 1 model selected
> select subtract #17
Nothing selected
> select add #7
392 atoms, 402 bonds, 55 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.96301,-0.033303,-0.26738,714.19,0.090025,0.97508,0.20279,520.98,0.25396,-0.21936,0.94201,356.56
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) to map volume difference (#6) using 392 atoms
average map value = 0.01495, steps = 140
shifted from previous position = 8.86
rotated from previous position = 24.8 degrees
atoms outside contour = 235, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.85115811 -0.02997286 -0.52405295 708.68145104
-0.02682838 0.99457947 -0.10045852 518.81487517
0.52422334 0.09956557 0.84574026 351.05167026
Axis 0.18742995 -0.98227355 0.00294650
Axis point -216.22023410 0.00000000 1548.11060998
Rotation angle (degrees) 32.24880826
Shift along axis -375.75562659
> select #6
3 models selected
> select clear
> select add #7
392 atoms, 402 bonds, 55 residues, 1 model selected
> view matrix models
> #7,0.85116,-0.029973,-0.52405,711.66,-0.026828,0.99458,-0.10046,520.94,0.52422,0.099566,0.84574,351.9
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) to map volume difference (#6) using 392 atoms
average map value = 0.01487, steps = 72
shifted from previous position = 2
rotated from previous position = 7.81 degrees
atoms outside contour = 259, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.79369421 -0.11819050 -0.59672482 710.08742477
0.06658482 0.99192909 -0.10790336 520.04506502
0.60466186 0.04590946 0.79515807 351.68471136
Axis 0.12554035 -0.98055876 0.15081161
Axis point -218.42324653 0.00000000 1342.85870246
Rotation angle (degrees) 37.77796355
Shift along axis -367.75197950
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.24133,0.89246,-0.38114,700.87,-0.64675,-0.14491,-0.74881,518.55,-0.72351,0.42721,0.54224,338.25
> view matrix models
> #7,0.34463,0.75411,-0.55905,703.38,-0.59941,-0.28155,-0.74929,519.32,-0.72245,0.59333,0.35499,339.16
> view matrix models
> #7,0.41985,0.90538,0.063383,699.91,0.36915,-0.10655,-0.92324,530.59,-0.82913,0.41102,-0.37896,343.07
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.41985,0.90538,0.063383,705.55,0.36915,-0.10655,-0.92324,513.84,-0.82913,0.41102,-0.37896,336.69
> view matrix models
> #7,0.41985,0.90538,0.063383,702.2,0.36915,-0.10655,-0.92324,508.9,-0.82913,0.41102,-0.37896,351.66
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.0015172,0.93222,-0.3619,700.33,0.32136,-0.34225,-0.88294,508.55,-0.94696,-0.11764,-0.29906,350.84
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) to map volume difference (#6) using 392 atoms
average map value = 0.01338, steps = 192
shifted from previous position = 11.7
rotated from previous position = 38.3 degrees
atoms outside contour = 269, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.40689710 0.91162029 0.05816516 707.86279986
0.10297741 0.01749169 -0.99452987 516.04766641
-0.90765102 0.41066103 -0.08675898 356.29906569
Axis 0.74461734 0.51179058 -0.42850370
Axis point 0.00000000 -285.05110554 471.90571601
Rotation angle (degrees) 109.34072177
Shift along axis 638.51977893
> select #6
3 models selected
> select clear
> ui mousemode right "translate selected models"
> select add #7
392 atoms, 402 bonds, 55 residues, 1 model selected
> view matrix models
> #7,0.4069,0.91162,0.058165,714.72,0.10298,0.017492,-0.99453,509.33,-0.90765,0.41066,-0.086759,350.89
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) to map volume difference (#6) using 392 atoms
average map value = 0.01307, steps = 92
shifted from previous position = 8.19
rotated from previous position = 14.6 degrees
atoms outside contour = 277, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.36436132 0.91150555 -0.19078380 715.73864231
-0.01228128 -0.20014578 -0.97968914 516.94237568
-0.93117667 0.35930390 -0.06173092 351.23112580
Axis 0.74916793 0.41425054 -0.51685965
Axis point 0.00000000 -205.04219104 538.32484854
Rotation angle (degrees) 116.66400694
Shift along axis 568.81490342
> view matrix models
> #7,0.36436,0.91151,-0.19078,718.52,-0.012281,-0.20015,-0.97969,513.24,-0.93118,0.3593,-0.061731,358.04
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.21138,0.95558,-0.20539,716.88,-0.057005,-0.19773,-0.9786,512.75,-0.97574,0.21857,0.012675,357.33
> view matrix models
> #7,0.20315,0.95573,-0.21287,716.84,-0.029846,-0.21126,-0.97697,513.06,-0.97869,0.20482,-0.014393,357.5
> view matrix models
> #7,0.20153,0.95573,-0.21439,716.83,-0.024412,-0.21391,-0.97655,513.12,-0.97918,0.20204,-0.019778,357.54
> view matrix models
> #7,0.11779,0.93937,-0.32203,716.65,0.31563,-0.34288,-0.88476,516.44,-0.94154,0.0025757,-0.33689,360.35
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.11779,0.93937,-0.32203,716.81,0.31563,-0.34288,-0.88476,511.65,-0.94154,0.0025757,-0.33689,355.88
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) to map volume difference (#6) using 392 atoms
average map value = 0.0114, steps = 80
shifted from previous position = 4.95
rotated from previous position = 11.6 degrees
atoms outside contour = 296, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.14031692 0.85282216 -0.50299653 712.27359032
0.29904821 -0.52080055 -0.79958547 510.44438424
-0.94386509 -0.03822484 -0.32811207 356.34537304
Axis 0.73238207 0.42408842 -0.53269646
Axis point 0.00000000 -75.08984589 490.39261845
Rotation angle (degrees) 148.68225133
Shift along axis 548.30604254
> view matrix models
> #7,0.14032,0.85282,-0.503,715.34,0.29905,-0.5208,-0.79959,514.65,-0.94387,-0.038225,-0.32811,353.96
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) to map volume difference (#6) using 392 atoms
average map value = 0.01441, steps = 288
shifted from previous position = 9.43
rotated from previous position = 41.1 degrees
atoms outside contour = 255, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.53902714 0.67077714 -0.50941903 711.86915594
0.62376353 -0.72432093 -0.29373155 513.36098651
-0.56601128 -0.15942774 -0.80883496 348.33294835
Axis 0.87702609 0.36955674 -0.30700662
Axis point 0.00000000 94.33967411 304.27208446
Rotation angle (degrees) 175.60869364
Shift along axis 707.10331192
> view matrix models
> #7,0.53903,0.67078,-0.50942,714.15,0.62376,-0.72432,-0.29373,519.01,-0.56601,-0.15943,-0.80883,348.41
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) to map volume difference (#6) using 392 atoms
average map value = 0.01441, steps = 72
shifted from previous position = 6.08
rotated from previous position = 0.0404 degrees
atoms outside contour = 257, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.53942595 0.67029193 -0.50963552 711.85706495
0.62354016 -0.72472810 -0.29320102 513.38454878
-0.56587746 -0.15961798 -0.80889108 348.32429746
Axis 0.87714205 0.36929966 -0.30698467
Axis point 0.00000000 94.54872215 304.21395314
Rotation angle (degrees) 175.63288514
Shift along axis 707.06228637
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.99567,0.05613,-0.074084,715.12,-0.089925,0.78331,-0.61509,504.97,0.023506,0.61909,0.78497,343
> view matrix models
> #7,0.9037,-0.25721,-0.34229,716.43,-0.044586,0.73857,-0.67271,505.91,0.42584,0.62319,0.65597,348.17
> view matrix models
> #7,0.90267,-0.13338,-0.40915,716.62,-0.16533,0.77031,-0.61587,504.18,0.39732,0.62357,0.67328,347.75
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.90267,-0.13338,-0.40915,712.77,-0.16533,0.77031,-0.61587,516.65,0.39732,0.62357,0.67328,352.74
> fitmap sel inMap #6
Fit molecule
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) to map volume difference (#6) using 392 atoms
average map value = 0.01511, steps = 108
shifted from previous position = 5.14
rotated from previous position = 35.1 degrees
atoms outside contour = 245, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.66242098 -0.28413211 -0.69315752 713.34938560
0.09648753 0.94993427 -0.29717843 520.30297087
0.74289202 0.12997618 0.65667160 350.05669044
Axis 0.27632817 -0.92898667 0.24622450
Axis point -20.44069994 0.00000000 1118.83279433
Rotation angle (degrees) 50.61609334
Shift along axis -200.04346576
> select add #17
784 atoms, 804 bonds, 110 residues, 2 models selected
> view matrix models
> #17,0.96301,-0.033303,-0.26738,708.67,0.090025,0.97508,0.20279,531.74,0.25396,-0.21936,0.94201,354.74,#7,0.66242,-0.28413,-0.69316,712.89,0.096488,0.94993,-0.29718,519.72,0.74289,0.12998,0.65667,350.71
> fitmap sel inMap #6
Fit molecules
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17),
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) to map volume difference (#6) using 784 atoms
average map value = 0.01448, steps = 68
shifted from previous position = 0.977
rotated from previous position = 0.0187 degrees
atoms outside contour = 511, contour level = 0.017597
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#17) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.96309999 -0.03332194 -0.26707313 709.12872813
0.08998881 0.97506502 0.20285518 532.30301943
0.25365414 -0.21940341 0.94208371 354.08260640
Axis -0.61945339 -0.76390694 0.18089688
Axis point -1707.45354435 -0.00000000 1077.66108221
Rotation angle (degrees) 19.92754814
Shift along axis -781.84972844
Position of
GeneID_79676165_protein_hypotheticalprotein_f1234_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.66266132 -0.28404193 -0.69296473 713.34573947
0.09649416 0.94995606 -0.29710661 520.28275093
0.74267679 0.13001401 0.65690753 350.05055037
Axis 0.27637931 -0.92896852 0.24623560
Axis point -20.60514667 -0.00000000 1119.20017349
Rotation angle (degrees) 50.59763036
Shift along axis -199.97738859
> select clear
> save "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18withinhexamer2.cxs" includeMaps true
——— End of log from Fri Apr 19 06:37:24 2024 ———
opened ChimeraX session
> ui mousemode right zoom
> close #9
> show #!5 models
> show #!3 models
> show #4 models
> open "/Users/rosheny/Desktop/Ph_D /PHAGE/fitting&segmentation/BAS18_ASU.pdb"
Chain information for BAS18_ASU.pdb
---
Chain | Description
8.1/A 8.2/A 8.3/A 8.4/A 8.5/A 8.6/A 8.7/A 8.8/A 8.9/A 8.10/A 8.11/A 8.12/A 8.13/A | No description available
> close #4
> close #3
> save "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18withinhexamer2.cxs" includeMaps true
> show #!1 models
> hide #!6 models
> surface dust #1 size 17.1
> show #!6 models
> select add #7
392 atoms, 402 bonds, 55 residues, 1 model selected
> select add #17
784 atoms, 804 bonds, 110 residues, 2 models selected
> volume zone #2 nearAtoms #4 range 2 newMap true
no atoms specified for zone
> volume zone #2 nearAtoms sel range 2 newMap true
Opened bas18_pp_b2_sh3.mrc zone as #3, grid size 504,504,504, pixel 1.71,
shown at step 1, values float32
> select clear
> hide #!3 models
> hide #!6 models
> hide #!1 models
> show #!3 models
> show #!6 models
> volume subtract #6,3
Opened volume difference as #4, grid size 504,504,504, pixel 1.71, shown at
step 1, values float32
> hide #!5 models
> hide #!4 models
> show #!3 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!5 models
> show #!6 models
> hide #!3 models
> show #!4 models
> close #4
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> hide #!5 models
> show #!2 models
> hide #!1 models
> transparency #2.1 50
> show #!5 models
> show #!6 models
> hide #!5 models
> hide #!2 models
> show #!2 models
> show #!5 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #!5 models
> ui mousemode right clip
> ui mousemode right zoom
> ui mousemode right clip
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right zoom
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> show #!2 models
> save "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18withinhexamer2.cxs" includeMaps true
——— End of log from Fri Apr 19 09:45:44 2024 ———
opened ChimeraX session
> hide #!2 models
> show #!2 models
> close #7,17#3,5-6,8
> close #1
> open "/Users/roshenykumaran/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18_refinedHEXAMER.pdb"
Chain information for BAS18_refinedHEXAMER.pdb
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A | No description available
> open "/Users/roshenykumaran/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18_refinedHEXAMER.pdb"
Chain information for BAS18_refinedHEXAMER.pdb
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A | No description available
> select add #1
38045 atoms, 38325 bonds, 2562 residues, 8 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,59.202,0,1,0,-9.5925,0,0,1,109.15
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.92878,0.35222,0.11538,-105.33,-0.21952,0.7736,-0.59443,393.13,-0.29863,0.52676,0.79583,78.122
> view matrix models
> #1,0.85642,0.42729,-0.28977,3.0676,-0.51558,0.67883,-0.52285,610.54,-0.026703,0.59718,0.80166,-130.8
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.85642,0.42729,-0.28977,-4.3475,-0.51558,0.67883,-0.52285,605.29,-0.026703,0.59718,0.80166,-149.14
> select clear
> select add #1
38045 atoms, 38325 bonds, 2562 residues, 8 models selected
> ui tool show "Fit in Map"
> fitmap sel inMap #2
Fit molecules BAS18_refinedHEXAMER.pdb (#1.1), BAS18_refinedHEXAMER.pdb
(#1.2), BAS18_refinedHEXAMER.pdb (#1.3), BAS18_refinedHEXAMER.pdb (#1.4),
BAS18_refinedHEXAMER.pdb (#1.5), BAS18_refinedHEXAMER.pdb (#1.6),
BAS18_refinedHEXAMER.pdb (#1.7) to map bas18_pp_b2_sh3.mrc (#2) using 38045
atoms
average map value = 0.0123, steps = 100
shifted from previous position = 10.2
rotated from previous position = 6.25 degrees
atoms outside contour = 30889, contour level = 0.020062
Position of BAS18_refinedHEXAMER.pdb (#1.1) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99904887 -0.01742702 0.03997059 1.79521867
0.02133034 0.99481828 -0.09940624 13.25122905
-0.03803111 0.10016428 0.99424381 -36.30543642
Axis 0.91651477 0.35821780 0.17799069
Axis point 0.00000000 368.90480583 114.32575845
Rotation angle (degrees) 6.25045021
Shift along axis -0.06985920
Position of BAS18_refinedHEXAMER.pdb (#1.2) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99904887 -0.01742702 0.03997059 1.79521867
0.02133034 0.99481828 -0.09940624 13.25122905
-0.03803111 0.10016428 0.99424381 -36.30543642
Axis 0.91651477 0.35821780 0.17799069
Axis point 0.00000000 368.90480583 114.32575845
Rotation angle (degrees) 6.25045021
Shift along axis -0.06985920
Position of BAS18_refinedHEXAMER.pdb (#1.3) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99904887 -0.01742702 0.03997059 1.79521867
0.02133034 0.99481828 -0.09940624 13.25122905
-0.03803111 0.10016428 0.99424381 -36.30543642
Axis 0.91651477 0.35821780 0.17799069
Axis point 0.00000000 368.90480583 114.32575845
Rotation angle (degrees) 6.25045021
Shift along axis -0.06985920
Position of BAS18_refinedHEXAMER.pdb (#1.4) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99904887 -0.01742702 0.03997059 1.79521867
0.02133034 0.99481828 -0.09940624 13.25122905
-0.03803111 0.10016428 0.99424381 -36.30543642
Axis 0.91651477 0.35821780 0.17799069
Axis point 0.00000000 368.90480583 114.32575845
Rotation angle (degrees) 6.25045021
Shift along axis -0.06985920
Position of BAS18_refinedHEXAMER.pdb (#1.5) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99904887 -0.01742702 0.03997059 1.79521867
0.02133034 0.99481828 -0.09940624 13.25122905
-0.03803111 0.10016428 0.99424381 -36.30543642
Axis 0.91651477 0.35821780 0.17799069
Axis point 0.00000000 368.90480583 114.32575845
Rotation angle (degrees) 6.25045021
Shift along axis -0.06985920
Position of BAS18_refinedHEXAMER.pdb (#1.6) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99904887 -0.01742702 0.03997059 1.79521867
0.02133034 0.99481828 -0.09940624 13.25122905
-0.03803111 0.10016428 0.99424381 -36.30543642
Axis 0.91651477 0.35821780 0.17799069
Axis point 0.00000000 368.90480583 114.32575845
Rotation angle (degrees) 6.25045021
Shift along axis -0.06985920
Position of BAS18_refinedHEXAMER.pdb (#1.7) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99904887 -0.01742702 0.03997059 1.79521867
0.02133034 0.99481828 -0.09940624 13.25122905
-0.03803111 0.10016428 0.99424381 -36.30543642
Axis 0.91651477 0.35821780 0.17799069
Axis point 0.00000000 368.90480583 114.32575845
Rotation angle (degrees) 6.25045021
Shift along axis -0.06985920
> select clear
> select add #1
38045 atoms, 38325 bonds, 2562 residues, 8 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.73454,0.60374,-0.30976,-13.064,-0.56186,0.28517,-0.77653,897.54,-0.38048,0.74443,0.54868,59.691
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.73454,0.60374,-0.30976,-6.1731,-0.56186,0.28517,-0.77653,895.49,-0.38048,0.74443,0.54868,76
> fitmap sel inMap #2
Fit molecules BAS18_refinedHEXAMER.pdb (#1.1), BAS18_refinedHEXAMER.pdb
(#1.2), BAS18_refinedHEXAMER.pdb (#1.3), BAS18_refinedHEXAMER.pdb (#1.4),
BAS18_refinedHEXAMER.pdb (#1.5), BAS18_refinedHEXAMER.pdb (#1.6),
BAS18_refinedHEXAMER.pdb (#1.7) to map bas18_pp_b2_sh3.mrc (#2) using 38045
atoms
average map value = 0.01821, steps = 80
shifted from previous position = 6.33
rotated from previous position = 6.28 degrees
atoms outside contour = 22623, contour level = 0.020062
Position of BAS18_refinedHEXAMER.pdb (#1.1) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99275527 -0.11407376 0.03773803 52.19083086
0.11571853 0.99227482 -0.04472033 -62.47413058
-0.03234509 0.04876333 0.99828650 -17.06516697
Axis 0.36263588 0.27186199 0.89139569
Axis point 539.77544805 465.42200078 0.00000000
Rotation angle (degrees) 7.40572377
Shift along axis -13.26989023
Position of BAS18_refinedHEXAMER.pdb (#1.2) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99275527 -0.11407376 0.03773803 52.19083086
0.11571853 0.99227482 -0.04472033 -62.47413058
-0.03234509 0.04876333 0.99828650 -17.06516697
Axis 0.36263588 0.27186199 0.89139569
Axis point 539.77544805 465.42200078 0.00000000
Rotation angle (degrees) 7.40572377
Shift along axis -13.26989023
Position of BAS18_refinedHEXAMER.pdb (#1.3) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99275527 -0.11407376 0.03773803 52.19083086
0.11571853 0.99227482 -0.04472033 -62.47413058
-0.03234509 0.04876333 0.99828650 -17.06516697
Axis 0.36263588 0.27186199 0.89139569
Axis point 539.77544805 465.42200078 0.00000000
Rotation angle (degrees) 7.40572377
Shift along axis -13.26989023
Position of BAS18_refinedHEXAMER.pdb (#1.4) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99275527 -0.11407376 0.03773803 52.19083086
0.11571853 0.99227482 -0.04472033 -62.47413058
-0.03234509 0.04876333 0.99828650 -17.06516697
Axis 0.36263588 0.27186199 0.89139569
Axis point 539.77544805 465.42200078 0.00000000
Rotation angle (degrees) 7.40572377
Shift along axis -13.26989023
Position of BAS18_refinedHEXAMER.pdb (#1.5) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99275527 -0.11407376 0.03773803 52.19083086
0.11571853 0.99227482 -0.04472033 -62.47413058
-0.03234509 0.04876333 0.99828650 -17.06516697
Axis 0.36263588 0.27186199 0.89139569
Axis point 539.77544805 465.42200078 0.00000000
Rotation angle (degrees) 7.40572377
Shift along axis -13.26989023
Position of BAS18_refinedHEXAMER.pdb (#1.6) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99275527 -0.11407376 0.03773803 52.19083086
0.11571853 0.99227482 -0.04472033 -62.47413058
-0.03234509 0.04876333 0.99828650 -17.06516697
Axis 0.36263588 0.27186199 0.89139569
Axis point 539.77544805 465.42200078 0.00000000
Rotation angle (degrees) 7.40572377
Shift along axis -13.26989023
Position of BAS18_refinedHEXAMER.pdb (#1.7) relative to bas18_pp_b2_sh3.mrc
(#2) coordinates:
Matrix rotation and translation
0.99275527 -0.11407376 0.03773803 52.19083086
0.11571853 0.99227482 -0.04472033 -62.47413058
-0.03234509 0.04876333 0.99828650 -17.06516697
Axis 0.36263588 0.27186199 0.89139569
Axis point 539.77544805 465.42200078 0.00000000
Rotation angle (degrees) 7.40572377
Shift along axis -13.26989023
> select clear
> save /Users/roshenykumaran/Desktop/fittings.cxs includeMaps true
> open "/Users/roshenykumaran/Desktop/Ph_D
> /PHAGE/fitting&segmentation/Dimer/112/112refined.pdb"
Chain information for 112refined.pdb #4
---
Chain | Description
A | No description available
> open "/Users/roshenykumaran/Desktop/Ph_D
> /PHAGE/fitting&segmentation/Dimer/112/112refined.pdb"
Chain information for 112refined.pdb #5
---
Chain | Description
A | No description available
> select add #5
551 atoms, 558 bonds, 38 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.99909,0.029209,0.030951,-22.197,-0.03158,0.99637,0.079092,4.0586,-0.028529,-0.079998,0.99639,62.064
> view matrix models
> #5,-0.53392,0.81828,-0.21296,601.38,0.0035946,-0.24966,-0.96833,890.17,-0.84553,-0.51777,0.13036,1023.8
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.53392,0.81828,-0.21296,589.18,0.0035946,-0.24966,-0.96833,891.34,-0.84553,-0.51777,0.13036,1017.9
> fitmap sel inMap #2
Fit molecule 112refined.pdb (#5) to map bas18_pp_b2_sh3.mrc (#2) using 551
atoms
average map value = 0.01772, steps = 64
shifted from previous position = 3.54
rotated from previous position = 39.9 degrees
atoms outside contour = 349, contour level = 0.020062
Position of 112refined.pdb (#5) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
-0.34905936 0.54666307 -0.76112880 740.80733894
0.51253667 -0.56859475 -0.64343311 661.73790755
-0.78451496 -0.61470277 -0.08171155 1077.61790948
Axis 0.57040635 0.46430404 -0.67753845
Axis point 830.16792563 693.21761568 0.00000000
Rotation angle (degrees) 178.55690467
Shift along axis -0.31876937
> select clear
> save /Users/roshenykumaran/Desktop/fittings.cxs includeMaps true
> open "/Users/roshenykumaran/Desktop/Ph_D
> /PHAGE/fitting&segmentation/Dimer/165/dimer1_real_space_refined_002.pdb"
Chain information for dimer1_real_space_refined_002.pdb #6
---
Chain | Description
A | No description available
> close #6
> open "/Users/roshenykumaran/Desktop/Ph_D
> /PHAGE/fitting&segmentation/Dimer/165/165refined.pdb"
Chain information for 165refined.pdb #6
---
Chain | Description
A | No description available
> open "/Users/roshenykumaran/Desktop/Ph_D
> /PHAGE/fitting&segmentation/Dimer/165/165refined.pdb"
Chain information for 165refined.pdb #7
---
Chain | Description
A | No description available
> select add #7
786 atoms, 796 bonds, 55 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.81336,0.54506,-0.20334,927.38,0.098062,-0.21608,-0.97144,812,-0.57343,-0.81007,0.1223,1007.1
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.81336,0.54506,-0.20334,911.46,0.098062,-0.21608,-0.97144,813.11,-0.57343,-0.81007,0.1223,1002.2
> fitmap sel inMap #2
Fit molecule 165refined.pdb (#7) to map bas18_pp_b2_sh3.mrc (#2) using 786
atoms
average map value = 0.01497, steps = 116
shifted from previous position = 3.84
rotated from previous position = 13 degrees
atoms outside contour = 579, contour level = 0.020062
Position of 165refined.pdb (#7) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
-0.73972394 0.55683297 -0.37781679 894.41980849
0.31072072 -0.21537389 -0.92577898 662.34937261
-0.59687613 -0.80221639 -0.01370232 1044.45580836
Axis 0.35114071 0.62252378 -0.69940284
Axis point 751.54359601 739.21436963 -0.00000000
Rotation angle (degrees) 169.86636979
Shift along axis -4.09991805
> select clear
> select add #7
786 atoms, 796 bonds, 55 residues, 1 model selected
> view matrix models
> #7,-0.73972,0.55683,-0.37782,897.59,0.31072,-0.21537,-0.92578,661.48,-0.59688,-0.80222,-0.013702,1045.9
> fitmap sel inMap #2
Fit molecule 165refined.pdb (#7) to map bas18_pp_b2_sh3.mrc (#2) using 786
atoms
average map value = 0.01497, steps = 112
shifted from previous position = 3.57
rotated from previous position = 0.0235 degrees
atoms outside contour = 580, contour level = 0.020062
Position of 165refined.pdb (#7) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
-0.73951001 0.55715638 -0.37775881 894.09617152
0.31074942 -0.21524720 -0.92579881 662.26450894
-0.59712624 -0.80202582 -0.01395857 1044.58149082
Axis 0.35126766 0.62256460 -0.69930276
Axis point 751.60410725 739.25971550 0.00000000
Rotation angle (degrees) 169.85263937
Shift along axis -4.10920620
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.71093,0.45815,-0.53356,964.43,0.49442,-0.21394,-0.84248,523.63,-0.50013,-0.86275,-0.074417,1028.3
> view matrix models
> #7,-0.70939,0.4571,-0.53649,964.66,0.50054,-0.20917,-0.84007,516.56,-0.49621,-0.86447,-0.080411,1028
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.70939,0.4571,-0.53649,968.69,0.50054,-0.20917,-0.84007,519.29,-0.49621,-0.86447,-0.080411,1027
> fitmap sel inMap #2
Fit molecule 165refined.pdb (#7) to map bas18_pp_b2_sh3.mrc (#2) using 786
atoms
average map value = 0.01528, steps = 80
shifted from previous position = 2.44
rotated from previous position = 31.1 degrees
atoms outside contour = 578, contour level = 0.020062
Position of 165refined.pdb (#7) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
-0.27813552 0.73649981 -0.61661062 558.93706770
0.71128756 -0.27349380 -0.64751150 374.89600311
-0.64553128 -0.61868341 -0.44779482 1076.20988368
Axis 0.60069977 0.60262876 -0.52535546
Axis point 103.31576026 -0.00000000 695.93008661
Rotation angle (degrees) 178.62503174
Shift along axis -3.71625328
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.49924,0.41677,-0.75965,906.51,0.6343,-0.42147,-0.64809,504.35,-0.59028,-0.8054,-0.053936,1050.6
> fitmap sel inMap #2
Fit molecule 165refined.pdb (#7) to map bas18_pp_b2_sh3.mrc (#2) using 786
atoms
average map value = 0.01619, steps = 68
shifted from previous position = 2.6
rotated from previous position = 17.6 degrees
atoms outside contour = 551, contour level = 0.020062
Position of 165refined.pdb (#7) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
-0.31460586 0.58092102 -0.75070229 697.95550452
0.51593112 -0.55918975 -0.64893906 656.04808019
-0.79676737 -0.59147070 -0.12379085 1082.62808140
Axis 0.58506429 0.46897169 -0.66163837
Axis point 839.82769374 698.74626244 0.00000000
Rotation angle (degrees) 177.18490806
Shift along axis -0.29145886
> select clear
> select add #4
551 atoms, 558 bonds, 38 residues, 1 model selected
> select add #5
1102 atoms, 1116 bonds, 76 residues, 2 models selected
> select add #6
1888 atoms, 1912 bonds, 131 residues, 3 models selected
> select add #7
2674 atoms, 2708 bonds, 186 residues, 4 models selected
> save /Users/roshenykumaran/Desktop/fittings.cxs includeMaps true
> select clear
[Repeated 1 time(s)]
> select add #1
38045 atoms, 38325 bonds, 2562 residues, 8 models selected
> select add #3
76090 atoms, 76650 bonds, 5124 residues, 16 models selected
> volume zone #2 neaAtoms sel newMap Hexamer
Expected a keyword
> volume zone #2 neaAtoms sel newMap true Hexamer
Expected a keyword
> volume zone #2 neaAtoms sel newMap
Expected a keyword
> volume zone #2 nearAtoms sel newMap Hexamer
Invalid "newMap" argument: Expected true or false (or 1 or 0)
> volume zone #2 nearAtoms sel newMap true Hexamer
Expected a keyword
> volume zone #2 nearAtoms sel newMap true map name
Expected a keyword
> volume zone #2 nearAtoms sel newMap true mapname
Expected a keyword
> volume zone #2 nearAtoms sel newMap true
Opened bas18_pp_b2_sh3.mrc zone as #8, grid size 504,504,504, pixel 1.71,
shown at step 1, values float32
> select clear
> select add #4
551 atoms, 558 bonds, 38 residues, 1 model selected
> select add #5
1102 atoms, 1116 bonds, 76 residues, 2 models selected
> select add #6
1888 atoms, 1912 bonds, 131 residues, 3 models selected
> select add #7
2674 atoms, 2708 bonds, 186 residues, 4 models selected
> volume zone #2 nearAtoms sel newMap true
Opened bas18_pp_b2_sh3.mrc zone as #9, grid size 504,504,504, pixel 1.71,
shown at step 1, values float32
> select clear
> hide #!9 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> lighting soft
> transparency #8.1 50
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> hide #!8 models
> hide #!3 models
> hide #!1 models
> show #!9 models
> show #!8 models
> ui mousemode right "translate selected models"
> show #7 models
> show #6 models
> hide #!8 models
> transparency #9.1 50
> hide #7 models
> hide #6 models
> show #5 models
> show #4 models
> save /Users/roshenykumaran/Desktop/fittings.cxs includeMaps true
——— End of log from Tue May 7 20:31:44 2024 ———
opened ChimeraX session
> show #!1 models
> show #!2 models
> show #!3 models
> show #6 models
> show #7 models
> show #!8 models
> save "/Users/roshenykumaran/Desktop/Ph_D
> /PHAGE/fitting&segmentation/fittings.cxs" includeMaps true
——— End of log from Tue May 7 20:32:44 2024 ———
opened ChimeraX session
> open
> /Users/roshenykumaran/Desktop/cryosparc_P22_J363_013_volume_map_sharp.mrc
Opened cryosparc_P22_J363_013_volume_map_sharp.mrc as #10, grid size
200,200,200, pixel 1.71, shown at level 0.644, step 1, values float32
> select add #10
2 models selected
> view sel
> select subtract #10
Nothing selected
> select add #1
38045 atoms, 38325 bonds, 2562 residues, 8 models selected
> view sel
> select clear
> ui mousemode right "rotate selected models"
> ui mousemode right zoom
> hide #!2 models
> ui mousemode right "translate selected models"
> save "/Users/roshenykumaran/Desktop/Ph_D
> /PHAGE/fitting&segmentation/fittings.cxs" includeMaps true
> hide #!10 models
> show #!10 models
> select add #10
2 models selected
> select clear
> select add #10
4 models selected
> view matrix models #10,1,0,0,452.64,0,1,0,80.553,0,0,1,-290.61
> view matrix models #10,1,0,0,207.46,0,1,0,522.68,0,0,1,-263.98
> view matrix models #10,1,0,0,-11.267,0,1,0,955.59,0,0,1,-208.49
> view matrix models #10,1,0,0,-166.19,0,1,0,1228.1,0,0,1,-197.29
> show #!2 models
> ui mousemode right clip
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,558.75,0,1,0,238.18,0,0,1,284.11
> view matrix models #10,1,0,0,740.55,0,1,0,125.57,0,0,1,161.22
> view matrix models #10,1,0,0,641.88,0,1,0,188.23,0,0,1,-112.44
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.65835,0.15155,-0.7373,1025.6,-0.14676,0.93488,0.32321,169.21,0.73827,0.32099,-0.59323,-21.179
> select clear
> ui mousemode right clip
> ui mousemode right "translate selected models"
> select add #10
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.65835,0.15155,-0.7373,1041,-0.14676,0.93488,0.32321,140.11,0.73827,0.32099,-0.59323,-59.322
> select clear
> save "/Users/roshenykumaran/Desktop/Ph_D
> /PHAGE/fitting&segmentation/fittings.cxs" includeMaps true
——— End of log from Wed May 8 08:36:36 2024 ———
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: MPHH3X/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 5 days, 37 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2422H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
DELL P2422H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
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: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
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: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.0.15
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: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
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: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
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: 2.0.1
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: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Crashed on OpenGL glBufferData(). User was showing large maps 1280 x 1280 x 1280 at step 1 surface and image style and crashed after surface threshold changed. Machine only has 16 GB of memory. Might have run out of memory.