![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Last modified 15 months ago
#15874 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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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"procRole" : "Background",
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"modelCode" : "Mac14,9",
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"captureTime" : "2024-09-04 08:59:23.8882 +1200",
"codeSigningMonitor" : 1,
"incident" : "DC8D44B7-D6ED-4D31-92C9-B5E097D1CE79",
"pid" : 63575,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-04 08:34:04.4198 +1200",
"procStartAbsTime" : 1911866833350,
"procExitAbsTime" : 1948329396030,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"crashReporterKey" : "8D17314D-7B97-9B83-2B60-87B356D0E70E",
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sleepWakeUUID" : "9A5EB1C6-2239-4EE3-B0A5-4A0B195DE409",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000002, 0x0000000139908000","rawCodes":[2,5260738560],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000139908000"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":63575},
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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
> 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 = 84
shifted from previous position = 1.85
rotated from previous position = 0.025 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
0.74393823 -0.66818750 -0.00902424 686.80261191
-0.59323065 -0.65414660 -0.46922241 456.26605189
0.30762540 0.35442592 -0.88303396 240.55166052
Axis 0.93004866 -0.35755499 0.08463991
Axis point 0.00000000 335.22940966 168.55031293
Rotation angle (degrees) 153.71742652
Shift along axis 495.97991433
> select clear
> ui mousemode right zoom
> ui mousemode right clip
> save "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18fitted.cxs" includeMaps true
> ui mousemode right zoom
> surface dust #2 size 17.1
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676109_protein_hypotheticalprotein_aaeab/GeneID_79676109_protein_hypotheticalprotein_aaeab_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
GeneID_79676109_protein_hypotheticalprotein_aaeab_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
#5
---
Chain | Description
A | No description available
> select add #5
1785 atoms, 1805 bonds, 234 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,709.03,0,1,0,285.97,0,0,1,-51.624
> select clear
> ui mousemode right zoom
> select add #5
1785 atoms, 1805 bonds, 234 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,603.94,0,1,0,396.74,0,0,1,267.75
> view matrix models #5,1,0,0,596.1,0,1,0,491.6,0,0,1,335.6
> view matrix models #5,1,0,0,616.06,0,1,0,534.15,0,0,1,230.91
> view matrix models #5,1,0,0,629.58,0,1,0,523.39,0,0,1,239.11
> select clear
> select add #5
1785 atoms, 1805 bonds, 234 residues, 1 model selected
> fitmap sel inMap #2
Fit molecule
GeneID_79676109_protein_hypotheticalprotein_aaeab_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#5) to map bas18_pp_b2_sh3.mrc (#2) using 1785 atoms
average map value = 0.01228, steps = 184
shifted from previous position = 9.06
rotated from previous position = 40.4 degrees
atoms outside contour = 1475, contour level = 0.020062
Position of
GeneID_79676109_protein_hypotheticalprotein_aaeab_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#5) relative to bas18_pp_b2_sh3.mrc (#2) coordinates:
Matrix rotation and translation
0.86942553 0.06442083 0.48984611 630.17394657
-0.28519421 0.87504077 0.39111114 521.06664833
-0.40343961 -0.47974328 0.77915523 249.01440761
Axis -0.67216341 0.68947686 -0.26984813
Axis point 990.21138215 0.00000000 -842.05976502
Rotation angle (degrees) 40.37590848
Shift along axis -131.51254206
> select clear
> ui mousemode right zoom
> select add #5
1785 atoms, 1805 bonds, 234 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.94623,0.28857,0.14623,631.42,-0.28988,0.95698,-0.012785,522.75,-0.14363,-0.030291,0.98917,247.56
> select clear
> ui mousemode right zoom
> select add #5
1785 atoms, 1805 bonds, 234 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.53297,-0.36217,-0.7647,636.15,0.81682,0.45604,0.35331,519.47,0.22077,-0.81293,0.53889,249.06
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.53297,-0.36217,-0.7647,614.08,0.81682,0.45604,0.35331,532.31,0.22077,-0.81293,0.53889,240.55
> fitmap sel inMap #2
Fit molecule
GeneID_79676109_protein_hypotheticalprotein_aaeab_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#5) to map bas18_pp_b2_sh3.mrc (#2) using 1785 atoms
average map value = 0.01133, steps = 92
shifted from previous position = 3.09
rotated from previous position = 10 degrees
atoms outside contour = 1593, contour level = 0.020062
Position of
GeneID_79676109_protein_hypotheticalprotein_aaeab_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#5) relative to bas18_pp_b2_sh3.mrc (#2) coordinates:
Matrix rotation and translation
0.54631391 -0.33404057 -0.76808724 615.69552630
0.75291940 0.59761554 0.27562300 534.46135957
0.36695161 -0.72888446 0.57799132 238.19210654
Axis -0.53856303 -0.60854696 0.58276965
Axis point -576.23139159 0.00000000 778.73292330
Rotation angle (degrees) 68.84081179
Shift along axis -518.02455246
> ui mousemode right zoom
> select clear
> ui mousemode right "translate selected models"
> select add #5
1785 atoms, 1805 bonds, 234 residues, 1 model selected
> view matrix models
> #5,0.54631,-0.33404,-0.76809,611.08,0.75292,0.59762,0.27562,533.76,0.36695,-0.72888,0.57799,228.58
> fitmap sel inMap #2
Fit molecule
GeneID_79676109_protein_hypotheticalprotein_aaeab_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#5) to map bas18_pp_b2_sh3.mrc (#2) using 1785 atoms
average map value = 0.01092, steps = 136
shifted from previous position = 6.41
rotated from previous position = 11.8 degrees
atoms outside contour = 1569, contour level = 0.020062
Position of
GeneID_79676109_protein_hypotheticalprotein_aaeab_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#5) relative to bas18_pp_b2_sh3.mrc (#2) coordinates:
Matrix rotation and translation
0.51425207 -0.50465179 -0.69344890 613.58464479
0.78342667 0.60542024 0.14038868 528.61085910
0.34898060 -0.61546153 0.70669629 227.67322509
Axis -0.41500705 -0.57235626 0.70723225
Axis point 42.41811609 849.22621966 0.00000000
Rotation angle (degrees) 65.59497508
Shift along axis -396.17784061
> select #2
3 models selected
> ui mousemode right zoom
> select clear
> select add #5
1785 atoms, 1805 bonds, 234 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.53666,-0.52456,-0.66093,613.42,0.79054,0.58644,0.17646,528.45,0.29503,-0.6172,0.7294,227.67
> view matrix models
> #5,0.182,-0.41434,-0.89174,614.96,0.98281,0.048045,0.17826,528.27,-0.031018,-0.90885,0.41596,229.63
> fitmap sel inMap #2
Fit molecule
GeneID_79676109_protein_hypotheticalprotein_aaeab_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#5) to map bas18_pp_b2_sh3.mrc (#2) using 1785 atoms
average map value = 0.0114, steps = 104
shifted from previous position = 2.63
rotated from previous position = 24.9 degrees
atoms outside contour = 1534, contour level = 0.020062
Position of
GeneID_79676109_protein_hypotheticalprotein_aaeab_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#5) relative to bas18_pp_b2_sh3.mrc (#2) coordinates:
Matrix rotation and translation
0.34539991 -0.02253347 -0.93818503 614.11369930
0.93822335 0.03053104 0.34468072 529.84490603
0.02087691 -0.99927979 0.03168685 230.36931387
Axis -0.70354943 -0.50205901 0.50294626
Axis point 0.00000000 319.78922544 210.29398453
Rotation angle (degrees) 107.22897475
Shift along axis -582.20936856
> ui mousemode right zoom
> select clear
> select add #5
1785 atoms, 1805 bonds, 234 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
1785 atoms, 1805 bonds, 234 residues, 1 model selected
> hide #5 models
> select subtract #5
Nothing selected
> close #5
> save "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18fitted.cxs" includeMaps true
——— End of log from Thu Apr 18 13:23:07 2024 ———
opened ChimeraX session
> open "/Users/rosheny/Desktop/Ph_D /PHAGE/fitting&segmentation/BAS18_ASU.pdb"
Chain information for BAS18_ASU.pdb
---
Chain | Description
5.1/A 5.2/A 5.3/A 5.4/A 5.5/A 5.6/A 5.7/A 5.8/A 5.9/A 5.10/A 5.11/A 5.12/A 5.13/A | No description available
> hide #!3 models
> close #1
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> hide #3.2 models
> hide #3.3 models
> hide #3.4 models
> hide #3.5 models
> hide #3.6 models
> show #3.1 models
> show #3.2 models
> show #3.3 models
> show #3.4 models
> show #3.5 models
> show #3.6 models
> select add #5
35087 atoms, 35607 bonds, 4758 residues, 14 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,50.993,0,1,0,33.674,0,0,1,106.98
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.90656,0.3849,0.1732,-132.99,-0.24247,0.81082,-0.53272,417.62,-0.34548,0.44094,0.82838,138.86
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.90656,0.3849,0.1732,-136.73,-0.24247,0.81082,-0.53272,408.62,-0.34548,0.44094,0.82838,125.62
> ui tool show "Fit in Map"
> fitmap sel inMap #2
Fit molecules BAS18_ASU.pdb (#5.1), BAS18_ASU.pdb (#5.2), BAS18_ASU.pdb
(#5.3), BAS18_ASU.pdb (#5.4), BAS18_ASU.pdb (#5.5), BAS18_ASU.pdb (#5.6),
BAS18_ASU.pdb (#5.7), BAS18_ASU.pdb (#5.8), BAS18_ASU.pdb (#5.9),
BAS18_ASU.pdb (#5.10), BAS18_ASU.pdb (#5.11), BAS18_ASU.pdb (#5.12),
BAS18_ASU.pdb (#5.13) to map bas18_pp_b2_sh3.mrc (#2) using 35087 atoms
average map value = 0.0116, steps = 152
shifted from previous position = 13.5
rotated from previous position = 17.7 degrees
atoms outside contour = 28987, contour level = 0.020062
Position of BAS18_ASU.pdb (#5.1) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.95748417 -0.07223634 -0.27929550 128.48633720
0.04395420 0.99336874 -0.10623827 -4.33169422
0.28511769 0.08944525 0.95430993 -227.29871869
Axis 0.32154772 -0.92744534 0.19092463
Axis point 851.10781454 0.00000000 328.24944319
Rotation angle (degrees) 17.71508108
Shift along axis 1.93497566
Position of BAS18_ASU.pdb (#5.2) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.95748417 -0.07223634 -0.27929550 128.48633720
0.04395420 0.99336874 -0.10623827 -4.33169422
0.28511769 0.08944525 0.95430993 -227.29871869
Axis 0.32154772 -0.92744534 0.19092463
Axis point 851.10781454 0.00000000 328.24944319
Rotation angle (degrees) 17.71508108
Shift along axis 1.93497566
Position of BAS18_ASU.pdb (#5.3) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.95748417 -0.07223634 -0.27929550 128.48633720
0.04395420 0.99336874 -0.10623827 -4.33169422
0.28511769 0.08944525 0.95430993 -227.29871869
Axis 0.32154772 -0.92744534 0.19092463
Axis point 851.10781454 0.00000000 328.24944319
Rotation angle (degrees) 17.71508108
Shift along axis 1.93497566
Position of BAS18_ASU.pdb (#5.4) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.95748417 -0.07223634 -0.27929550 128.48633720
0.04395420 0.99336874 -0.10623827 -4.33169422
0.28511769 0.08944525 0.95430993 -227.29871869
Axis 0.32154772 -0.92744534 0.19092463
Axis point 851.10781454 0.00000000 328.24944319
Rotation angle (degrees) 17.71508108
Shift along axis 1.93497566
Position of BAS18_ASU.pdb (#5.5) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.95748417 -0.07223634 -0.27929550 128.48633720
0.04395420 0.99336874 -0.10623827 -4.33169422
0.28511769 0.08944525 0.95430993 -227.29871869
Axis 0.32154772 -0.92744534 0.19092463
Axis point 851.10781454 0.00000000 328.24944319
Rotation angle (degrees) 17.71508108
Shift along axis 1.93497566
Position of BAS18_ASU.pdb (#5.6) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.95748417 -0.07223634 -0.27929550 128.48633720
0.04395420 0.99336874 -0.10623827 -4.33169422
0.28511769 0.08944525 0.95430993 -227.29871869
Axis 0.32154772 -0.92744534 0.19092463
Axis point 851.10781454 0.00000000 328.24944319
Rotation angle (degrees) 17.71508108
Shift along axis 1.93497566
Position of BAS18_ASU.pdb (#5.7) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.95748417 -0.07223634 -0.27929550 128.48633720
0.04395420 0.99336874 -0.10623827 -4.33169422
0.28511769 0.08944525 0.95430993 -227.29871869
Axis 0.32154772 -0.92744534 0.19092463
Axis point 851.10781454 0.00000000 328.24944319
Rotation angle (degrees) 17.71508108
Shift along axis 1.93497566
Position of BAS18_ASU.pdb (#5.8) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.95748417 -0.07223634 -0.27929550 128.48633720
0.04395420 0.99336874 -0.10623827 -4.33169422
0.28511769 0.08944525 0.95430993 -227.29871869
Axis 0.32154772 -0.92744534 0.19092463
Axis point 851.10781454 0.00000000 328.24944319
Rotation angle (degrees) 17.71508108
Shift along axis 1.93497566
Position of BAS18_ASU.pdb (#5.9) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.95748417 -0.07223634 -0.27929550 128.48633720
0.04395420 0.99336874 -0.10623827 -4.33169422
0.28511769 0.08944525 0.95430993 -227.29871869
Axis 0.32154772 -0.92744534 0.19092463
Axis point 851.10781454 0.00000000 328.24944319
Rotation angle (degrees) 17.71508108
Shift along axis 1.93497566
Position of BAS18_ASU.pdb (#5.10) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.95748417 -0.07223634 -0.27929550 128.48633720
0.04395420 0.99336874 -0.10623827 -4.33169422
0.28511769 0.08944525 0.95430993 -227.29871869
Axis 0.32154772 -0.92744534 0.19092463
Axis point 851.10781454 0.00000000 328.24944319
Rotation angle (degrees) 17.71508108
Shift along axis 1.93497566
Position of BAS18_ASU.pdb (#5.11) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.95748417 -0.07223634 -0.27929550 128.48633720
0.04395420 0.99336874 -0.10623827 -4.33169422
0.28511769 0.08944525 0.95430993 -227.29871869
Axis 0.32154772 -0.92744534 0.19092463
Axis point 851.10781454 0.00000000 328.24944319
Rotation angle (degrees) 17.71508108
Shift along axis 1.93497566
Position of BAS18_ASU.pdb (#5.12) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.95748417 -0.07223634 -0.27929550 128.48633720
0.04395420 0.99336874 -0.10623827 -4.33169422
0.28511769 0.08944525 0.95430993 -227.29871869
Axis 0.32154772 -0.92744534 0.19092463
Axis point 851.10781454 0.00000000 328.24944319
Rotation angle (degrees) 17.71508108
Shift along axis 1.93497566
Position of BAS18_ASU.pdb (#5.13) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.95748417 -0.07223634 -0.27929550 128.48633720
0.04395420 0.99336874 -0.10623827 -4.33169422
0.28511769 0.08944525 0.95430993 -227.29871869
Axis 0.32154772 -0.92744534 0.19092463
Axis point 851.10781454 0.00000000 328.24944319
Rotation angle (degrees) 17.71508108
Shift along axis 1.93497566
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #5
35087 atoms, 35607 bonds, 4758 residues, 14 models selected
> view matrix models
> #5,0.77494,0.60985,0.16599,-168.15,-0.14265,0.42462,-0.89406,628.8,-0.61573,0.66916,0.41605,273.91
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.77494,0.60985,0.16599,-138.89,-0.14265,0.42462,-0.89406,583.73,-0.61573,0.66916,0.41605,309.2
> fitmap sel inMap #2
Fit molecules BAS18_ASU.pdb (#5.1), BAS18_ASU.pdb (#5.2), BAS18_ASU.pdb
(#5.3), BAS18_ASU.pdb (#5.4), BAS18_ASU.pdb (#5.5), BAS18_ASU.pdb (#5.6),
BAS18_ASU.pdb (#5.7), BAS18_ASU.pdb (#5.8), BAS18_ASU.pdb (#5.9),
BAS18_ASU.pdb (#5.10), BAS18_ASU.pdb (#5.11), BAS18_ASU.pdb (#5.12),
BAS18_ASU.pdb (#5.13) to map bas18_pp_b2_sh3.mrc (#2) using 35087 atoms
average map value = 0.01538, steps = 144
shifted from previous position = 16.8
rotated from previous position = 11.5 degrees
atoms outside contour = 24010, contour level = 0.020062
Position of BAS18_ASU.pdb (#5.1) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88867313 -0.15432532 -0.43179135 257.97408744
0.07412873 0.97762798 -0.19684631 -4.25220376
0.45250967 0.14292388 0.88023165 -353.88605391
Axis 0.34866600 -0.90745362 0.23443539
Axis point 883.21195090 0.00000000 360.98131232
Rotation angle (degrees) 29.15953877
Shift along axis 10.84205321
Position of BAS18_ASU.pdb (#5.2) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88867313 -0.15432532 -0.43179135 257.97408744
0.07412873 0.97762798 -0.19684631 -4.25220376
0.45250967 0.14292388 0.88023165 -353.88605391
Axis 0.34866600 -0.90745362 0.23443539
Axis point 883.21195090 0.00000000 360.98131232
Rotation angle (degrees) 29.15953877
Shift along axis 10.84205321
Position of BAS18_ASU.pdb (#5.3) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88867313 -0.15432532 -0.43179135 257.97408744
0.07412873 0.97762798 -0.19684631 -4.25220376
0.45250967 0.14292388 0.88023165 -353.88605391
Axis 0.34866600 -0.90745362 0.23443539
Axis point 883.21195090 0.00000000 360.98131232
Rotation angle (degrees) 29.15953877
Shift along axis 10.84205321
Position of BAS18_ASU.pdb (#5.4) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88867313 -0.15432532 -0.43179135 257.97408744
0.07412873 0.97762798 -0.19684631 -4.25220376
0.45250967 0.14292388 0.88023165 -353.88605391
Axis 0.34866600 -0.90745362 0.23443539
Axis point 883.21195090 0.00000000 360.98131232
Rotation angle (degrees) 29.15953877
Shift along axis 10.84205321
Position of BAS18_ASU.pdb (#5.5) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88867313 -0.15432532 -0.43179135 257.97408744
0.07412873 0.97762798 -0.19684631 -4.25220376
0.45250967 0.14292388 0.88023165 -353.88605391
Axis 0.34866600 -0.90745362 0.23443539
Axis point 883.21195090 0.00000000 360.98131232
Rotation angle (degrees) 29.15953877
Shift along axis 10.84205321
Position of BAS18_ASU.pdb (#5.6) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88867313 -0.15432532 -0.43179135 257.97408744
0.07412873 0.97762798 -0.19684631 -4.25220376
0.45250967 0.14292388 0.88023165 -353.88605391
Axis 0.34866600 -0.90745362 0.23443539
Axis point 883.21195090 0.00000000 360.98131232
Rotation angle (degrees) 29.15953877
Shift along axis 10.84205321
Position of BAS18_ASU.pdb (#5.7) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88867313 -0.15432532 -0.43179135 257.97408744
0.07412873 0.97762798 -0.19684631 -4.25220376
0.45250967 0.14292388 0.88023165 -353.88605391
Axis 0.34866600 -0.90745362 0.23443539
Axis point 883.21195090 0.00000000 360.98131232
Rotation angle (degrees) 29.15953877
Shift along axis 10.84205321
Position of BAS18_ASU.pdb (#5.8) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88867313 -0.15432532 -0.43179135 257.97408744
0.07412873 0.97762798 -0.19684631 -4.25220376
0.45250967 0.14292388 0.88023165 -353.88605391
Axis 0.34866600 -0.90745362 0.23443539
Axis point 883.21195090 0.00000000 360.98131232
Rotation angle (degrees) 29.15953877
Shift along axis 10.84205321
Position of BAS18_ASU.pdb (#5.9) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88867313 -0.15432532 -0.43179135 257.97408744
0.07412873 0.97762798 -0.19684631 -4.25220376
0.45250967 0.14292388 0.88023165 -353.88605391
Axis 0.34866600 -0.90745362 0.23443539
Axis point 883.21195090 0.00000000 360.98131232
Rotation angle (degrees) 29.15953877
Shift along axis 10.84205321
Position of BAS18_ASU.pdb (#5.10) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88867313 -0.15432532 -0.43179135 257.97408744
0.07412873 0.97762798 -0.19684631 -4.25220376
0.45250967 0.14292388 0.88023165 -353.88605391
Axis 0.34866600 -0.90745362 0.23443539
Axis point 883.21195090 0.00000000 360.98131232
Rotation angle (degrees) 29.15953877
Shift along axis 10.84205321
Position of BAS18_ASU.pdb (#5.11) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88867313 -0.15432532 -0.43179135 257.97408744
0.07412873 0.97762798 -0.19684631 -4.25220376
0.45250967 0.14292388 0.88023165 -353.88605391
Axis 0.34866600 -0.90745362 0.23443539
Axis point 883.21195090 0.00000000 360.98131232
Rotation angle (degrees) 29.15953877
Shift along axis 10.84205321
Position of BAS18_ASU.pdb (#5.12) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88867313 -0.15432532 -0.43179135 257.97408744
0.07412873 0.97762798 -0.19684631 -4.25220376
0.45250967 0.14292388 0.88023165 -353.88605391
Axis 0.34866600 -0.90745362 0.23443539
Axis point 883.21195090 0.00000000 360.98131232
Rotation angle (degrees) 29.15953877
Shift along axis 10.84205321
Position of BAS18_ASU.pdb (#5.13) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88867313 -0.15432532 -0.43179135 257.97408744
0.07412873 0.97762798 -0.19684631 -4.25220376
0.45250967 0.14292388 0.88023165 -353.88605391
Axis 0.34866600 -0.90745362 0.23443539
Axis point 883.21195090 0.00000000 360.98131232
Rotation angle (degrees) 29.15953877
Shift along axis 10.84205321
> select clear
> select add #5
35087 atoms, 35607 bonds, 4758 residues, 14 models selected
> view matrix models
> #5,0.77494,0.60985,0.16599,-137.82,-0.14265,0.42462,-0.89406,582.16,-0.61573,0.66916,0.41605,309.52
> fitmap sel inMap #2
Fit molecules BAS18_ASU.pdb (#5.1), BAS18_ASU.pdb (#5.2), BAS18_ASU.pdb
(#5.3), BAS18_ASU.pdb (#5.4), BAS18_ASU.pdb (#5.5), BAS18_ASU.pdb (#5.6),
BAS18_ASU.pdb (#5.7), BAS18_ASU.pdb (#5.8), BAS18_ASU.pdb (#5.9),
BAS18_ASU.pdb (#5.10), BAS18_ASU.pdb (#5.11), BAS18_ASU.pdb (#5.12),
BAS18_ASU.pdb (#5.13) to map bas18_pp_b2_sh3.mrc (#2) using 35087 atoms
average map value = 0.01538, steps = 52
shifted from previous position = 1.93
rotated from previous position = 0.00871 degrees
atoms outside contour = 24027, contour level = 0.020062
Position of BAS18_ASU.pdb (#5.1) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88868197 -0.15431941 -0.43177526 257.10111798
0.07405759 0.97760691 -0.19697766 -4.34198755
0.45250396 0.14307426 0.88021016 -355.67921552
Axis 0.34893346 -0.90737499 0.23434179
Axis point 886.29694697 0.00000000 358.62661962
Rotation angle (degrees) 29.16152089
Shift along axis 10.30048712
Position of BAS18_ASU.pdb (#5.2) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88868197 -0.15431941 -0.43177526 257.10111798
0.07405759 0.97760691 -0.19697766 -4.34198755
0.45250396 0.14307426 0.88021016 -355.67921552
Axis 0.34893346 -0.90737499 0.23434179
Axis point 886.29694697 0.00000000 358.62661962
Rotation angle (degrees) 29.16152089
Shift along axis 10.30048712
Position of BAS18_ASU.pdb (#5.3) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88868197 -0.15431941 -0.43177526 257.10111798
0.07405759 0.97760691 -0.19697766 -4.34198755
0.45250396 0.14307426 0.88021016 -355.67921552
Axis 0.34893346 -0.90737499 0.23434179
Axis point 886.29694697 0.00000000 358.62661962
Rotation angle (degrees) 29.16152089
Shift along axis 10.30048712
Position of BAS18_ASU.pdb (#5.4) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88868197 -0.15431941 -0.43177526 257.10111798
0.07405759 0.97760691 -0.19697766 -4.34198755
0.45250396 0.14307426 0.88021016 -355.67921552
Axis 0.34893346 -0.90737499 0.23434179
Axis point 886.29694697 0.00000000 358.62661962
Rotation angle (degrees) 29.16152089
Shift along axis 10.30048712
Position of BAS18_ASU.pdb (#5.5) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88868197 -0.15431941 -0.43177526 257.10111798
0.07405759 0.97760691 -0.19697766 -4.34198755
0.45250396 0.14307426 0.88021016 -355.67921552
Axis 0.34893346 -0.90737499 0.23434179
Axis point 886.29694697 0.00000000 358.62661962
Rotation angle (degrees) 29.16152089
Shift along axis 10.30048712
Position of BAS18_ASU.pdb (#5.6) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88868197 -0.15431941 -0.43177526 257.10111798
0.07405759 0.97760691 -0.19697766 -4.34198755
0.45250396 0.14307426 0.88021016 -355.67921552
Axis 0.34893346 -0.90737499 0.23434179
Axis point 886.29694697 0.00000000 358.62661962
Rotation angle (degrees) 29.16152089
Shift along axis 10.30048712
Position of BAS18_ASU.pdb (#5.7) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88868197 -0.15431941 -0.43177526 257.10111798
0.07405759 0.97760691 -0.19697766 -4.34198755
0.45250396 0.14307426 0.88021016 -355.67921552
Axis 0.34893346 -0.90737499 0.23434179
Axis point 886.29694697 0.00000000 358.62661962
Rotation angle (degrees) 29.16152089
Shift along axis 10.30048712
Position of BAS18_ASU.pdb (#5.8) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88868197 -0.15431941 -0.43177526 257.10111798
0.07405759 0.97760691 -0.19697766 -4.34198755
0.45250396 0.14307426 0.88021016 -355.67921552
Axis 0.34893346 -0.90737499 0.23434179
Axis point 886.29694697 0.00000000 358.62661962
Rotation angle (degrees) 29.16152089
Shift along axis 10.30048712
Position of BAS18_ASU.pdb (#5.9) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88868197 -0.15431941 -0.43177526 257.10111798
0.07405759 0.97760691 -0.19697766 -4.34198755
0.45250396 0.14307426 0.88021016 -355.67921552
Axis 0.34893346 -0.90737499 0.23434179
Axis point 886.29694697 0.00000000 358.62661962
Rotation angle (degrees) 29.16152089
Shift along axis 10.30048712
Position of BAS18_ASU.pdb (#5.10) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88868197 -0.15431941 -0.43177526 257.10111798
0.07405759 0.97760691 -0.19697766 -4.34198755
0.45250396 0.14307426 0.88021016 -355.67921552
Axis 0.34893346 -0.90737499 0.23434179
Axis point 886.29694697 0.00000000 358.62661962
Rotation angle (degrees) 29.16152089
Shift along axis 10.30048712
Position of BAS18_ASU.pdb (#5.11) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88868197 -0.15431941 -0.43177526 257.10111798
0.07405759 0.97760691 -0.19697766 -4.34198755
0.45250396 0.14307426 0.88021016 -355.67921552
Axis 0.34893346 -0.90737499 0.23434179
Axis point 886.29694697 0.00000000 358.62661962
Rotation angle (degrees) 29.16152089
Shift along axis 10.30048712
Position of BAS18_ASU.pdb (#5.12) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88868197 -0.15431941 -0.43177526 257.10111798
0.07405759 0.97760691 -0.19697766 -4.34198755
0.45250396 0.14307426 0.88021016 -355.67921552
Axis 0.34893346 -0.90737499 0.23434179
Axis point 886.29694697 0.00000000 358.62661962
Rotation angle (degrees) 29.16152089
Shift along axis 10.30048712
Position of BAS18_ASU.pdb (#5.13) relative to bas18_pp_b2_sh3.mrc (#2)
coordinates:
Matrix rotation and translation
0.88868197 -0.15431941 -0.43177526 257.10111798
0.07405759 0.97760691 -0.19697766 -4.34198755
0.45250396 0.14307426 0.88021016 -355.67921552
Axis 0.34893346 -0.90737499 0.23434179
Axis point 886.29694697 0.00000000 358.62661962
Rotation angle (degrees) 29.16152089
Shift along axis 10.30048712
> select clear
> ui mousemode right clip
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> transparency 50
> transparency 0
> lighting soft
> lighting full
> transparency 50
> transparency 0
> lighting soft
> color bypolymer
> save "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18fitted.cxs" includeMaps true
——— End of log from Fri Apr 19 04:24:23 2024 ———
opened ChimeraX session
> hide #4 models
> show #4 models
> select add #3
16194 atoms, 16434 bonds, 2196 residues, 7 models selected
> select add #4
18893 atoms, 19173 bonds, 2562 residues, 8 models selected
> select add #5
53980 atoms, 54780 bonds, 7320 residues, 22 models selected
> volume zone #2 nearAtoms sel range 2 newMap true
Opened bas18_pp_b2_sh3.mrc zone as #1, grid size 504,504,504, pixel 1.71,
shown at step 1, values float32
> select clear
> hide #!1 models
> show #!2 models
> hide #!5 models
> hide #4 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> volume subtract #1,2
Opened volume difference as #6, grid size 504,504,504, pixel 1.71, shown at
step 1, values float32
> volume #6 level 0.001264
> surface dust #6 size 17.1
> ui mousemode right zoom
> volume #6 level -0.005207
> volume #6 level 0.00373
> volume #6 level -0.0002764
> volume #6 level 0.001264
> volume #6 level 0.000494
> volume #6 level 0.0003399
> close #6
> show #!2 models
> volume subtract #2,1
Opened volume difference as #6, grid size 504,504,504, pixel 1.71, shown at
step 1, values float32
> surface dust #6 size 17.1
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> volume #6 level 0.0176
> save "/Users/rosheny/Desktop/Ph_D
> /PHAGE/fitting&segmentation/BAS18betweenhexamer.cxs"
> 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
#7
---
Chain | Description
A | No description available
> select add #7
2875 atoms, 2926 bonds, 367 residues, 1 model selected
> view sel
> view
> volume #!6 showOutlineBox true
> ui mousemode right clip
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,704.43,0,1,0,658.77,0,0,1,299.05
> view matrix models #7,1,0,0,726.04,0,1,0,536.29,0,0,1,290.65
> volume #!6 showOutlineBox false
> ui mousemode right clip
> ui mousemode right "rotate selected models"
> select clear
> ui mousemode right "translate selected models"
> select add #7
2875 atoms, 2926 bonds, 367 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.07603,-0.18454,0.97988,723.19,0.18642,0.96277,0.19579,535.13,-0.97952,0.19755,-0.038797,296.82
> ui mousemode right "rotate selected models"
> select clear
> ui mousemode right "translate selected models"
> select add #7
2875 atoms, 2926 bonds, 367 residues, 1 model selected
> view matrix models
> #7,-0.07603,-0.18454,0.97988,694.14,0.18642,0.96277,0.19579,554.35,-0.97952,0.19755,-0.038797,334.33
> view matrix models
> #7,-0.07603,-0.18454,0.97988,701.93,0.18642,0.96277,0.19579,512.03,-0.97952,0.19755,-0.038797,345.7
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.19835,0.29817,0.93367,703.52,0.2499,0.9365,-0.24599,513.66,-0.94774,0.18453,-0.26027,346.52
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.19835,0.29817,0.93367,700.52,0.2499,0.9365,-0.24599,516.36,-0.94774,0.18453,-0.26027,347.87
> view matrix models
> #7,-0.19835,0.29817,0.93367,697.47,0.2499,0.9365,-0.24599,517.34,-0.94774,0.18453,-0.26027,346.86
> ui tool show "Fit in Map"
> fitmap sel inMap #2
Fit molecule
GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#7) to map bas18_pp_b2_sh3.mrc (#2) using 2875 atoms
average map value = 0.01199, steps = 212
shifted from previous position = 14.2
rotated from previous position = 27.2 degrees
atoms outside contour = 2408, contour level = 0.020062
Position of
GeneID_79676105_protein_putativeminorcapsidprotein_cde7b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#7) relative to bas18_pp_b2_sh3.mrc (#2) coordinates:
Matrix rotation and translation
0.26923518 0.26120387 0.92697625 697.33610396
0.22474765 0.91890123 -0.32420522 510.18809133
-0.93648327 0.29562318 0.18869558 334.77109525
Axis 0.31556621 0.94872202 -0.01856054
Axis point 485.57799563 0.00000000 -131.90085605
Rotation angle (degrees) 79.13964214
Shift along axis 697.86885260
> select clear
> ui mousemode right zoom
> show #!5 models
> hide #!5 models
> show #4 models
> hide #4 models
> close #7
> ui mousemode right "translate selected models"
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676113_protein_hypotheticalprotein_07d98/GeneID_79676113_protein_hypotheticalprotein_07d98_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
GeneID_79676113_protein_hypotheticalprotein_07d98_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#7
---
Chain | Description
A | No description available
> ui mousemode right zoom
> ui mousemode right clip
> ui mousemode right "translate selected models"
> select add #7
917 atoms, 932 bonds, 119 residues, 1 model selected
> view matrix models #7,1,0,0,467.18,0,1,0,651.74,0,0,1,755.07
> view matrix models #7,1,0,0,632.69,0,1,0,759.54,0,0,1,303.38
> view matrix models #7,1,0,0,763.71,0,1,0,595.02,0,0,1,293.43
> ui mousemode right zoom
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right clip
> ui mousemode right "translate selected models"
> select add #7
917 atoms, 932 bonds, 119 residues, 1 model selected
> view matrix models #7,1,0,0,615.77,0,1,0,545.66,0,0,1,266.24
> select clear
> select add #7
917 atoms, 932 bonds, 119 residues, 1 model selected
> view matrix models #7,1,0,0,638.94,0,1,0,519.17,0,0,1,232.99
> view matrix models #7,1,0,0,635.32,0,1,0,534.55,0,0,1,231.43
> fitmap sel inMap #6
Fit molecule
GeneID_79676113_protein_hypotheticalprotein_07d98_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) to map volume difference (#6) using 917 atoms
average map value = 0.01251, steps = 124
shifted from previous position = 5.3
rotated from previous position = 19.8 degrees
atoms outside contour = 686, contour level = 0.017597
Position of
GeneID_79676113_protein_hypotheticalprotein_07d98_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.94994646 -0.27323031 0.15148237 634.32794664
0.25027700 0.95577490 0.15445312 536.13618015
-0.18698433 -0.10880965 0.97631825 236.25179278
Axis -0.38903741 0.50017026 0.77361463
Axis point -1232.68220827 2838.08187949 0.00000000
Rotation angle (degrees) 19.77646920
Shift along axis 204.14991541
> select clear
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> hide #7 models
> close #7
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676108_protein_hypotheticalprotein_0f5c7/GeneID_79676108_protein_hypotheticalprotein_0f5c7_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
GeneID_79676108_protein_hypotheticalprotein_0f5c7_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
#7
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676109_protein_hypotheticalprotein_aaeab/GeneID_79676109_protein_hypotheticalprotein_aaeab_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
GeneID_79676109_protein_hypotheticalprotein_aaeab_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
#8
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676111_protein_hypotheticalprotein_57cf4/GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#9
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676112_protein_hypotheticalprotein_97f6b/GeneID_79676112_protein_hypotheticalprotein_97f6b_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
Chain information for
GeneID_79676112_protein_hypotheticalprotein_97f6b_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
#10
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676113_protein_hypotheticalprotein_07d98/GeneID_79676113_protein_hypotheticalprotein_07d98_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
GeneID_79676113_protein_hypotheticalprotein_07d98_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#11
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676114_protein_putativetailprotein_16485/GeneID_79676114_protein_putativetailprotein_16485_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
GeneID_79676114_protein_putativetailprotein_16485_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
#12
---
Chain | Description
A | No description available
> close #12
> ui mousemode right zoom
> ui mousemode right clip
> select add #7
2023 atoms, 2061 bonds, 254 residues, 1 model selected
> select add #8
3808 atoms, 3866 bonds, 488 residues, 2 models selected
> select add #9
5075 atoms, 5165 bonds, 654 residues, 3 models selected
> select add #10
5354 atoms, 5451 bonds, 692 residues, 4 models selected
> select add #11
6271 atoms, 6383 bonds, 811 residues, 5 models selected
> ui mousemode right "translate selected models"
> hide #!6 models
> show #!6 models
> view sel
[Repeated 1 time(s)]
> view
> ui mousemode right clip
> select clear
> select add #7
2023 atoms, 2061 bonds, 254 residues, 1 model selected
> select add #8
3808 atoms, 3866 bonds, 488 residues, 2 models selected
> select add #9
5075 atoms, 5165 bonds, 654 residues, 3 models selected
> select add #10
5354 atoms, 5451 bonds, 692 residues, 4 models selected
> select add #11
6271 atoms, 6383 bonds, 811 residues, 5 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,1,0,0,558.81,0,1,0,-24.367,0,0,1,147.05,#8,1,0,0,558.81,0,1,0,-24.367,0,0,1,147.05,#9,1,0,0,558.81,0,1,0,-24.367,0,0,1,147.05,#10,1,0,0,558.81,0,1,0,-24.367,0,0,1,147.05,#11,1,0,0,558.81,0,1,0,-24.367,0,0,1,147.05
> view matrix models
> #7,1,0,0,475.37,0,1,0,565.07,0,0,1,386.31,#8,1,0,0,475.37,0,1,0,565.07,0,0,1,386.31,#9,1,0,0,475.37,0,1,0,565.07,0,0,1,386.31,#10,1,0,0,475.37,0,1,0,565.07,0,0,1,386.31,#11,1,0,0,475.37,0,1,0,565.07,0,0,1,386.31
> view matrix models
> #7,1,0,0,493.68,0,1,0,559.64,0,0,1,343.59,#8,1,0,0,493.68,0,1,0,559.64,0,0,1,343.59,#9,1,0,0,493.68,0,1,0,559.64,0,0,1,343.59,#10,1,0,0,493.68,0,1,0,559.64,0,0,1,343.59,#11,1,0,0,493.68,0,1,0,559.64,0,0,1,343.59
> select clear
> ui mousemode right clip
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> hide #7 models
> hide #8 models
> hide #9 models
> hide #11 models
> show #11 models
> show #9 models
> show #8 models
> show #7 models
> select add #7
2023 atoms, 2061 bonds, 254 residues, 1 model selected
> select add #8
3808 atoms, 3866 bonds, 488 residues, 2 models selected
> select add #9
5075 atoms, 5165 bonds, 654 residues, 3 models selected
> select add #10
5354 atoms, 5451 bonds, 692 residues, 4 models selected
> select add #11
6271 atoms, 6383 bonds, 811 residues, 5 models selected
> view matrix models
> #7,1,0,0,636.82,0,1,0,499.73,0,0,1,297.13,#8,1,0,0,636.82,0,1,0,499.73,0,0,1,297.13,#9,1,0,0,636.82,0,1,0,499.73,0,0,1,297.13,#10,1,0,0,636.82,0,1,0,499.73,0,0,1,297.13,#11,1,0,0,636.82,0,1,0,499.73,0,0,1,297.13
> view matrix models
> #7,1,0,0,594.87,0,1,0,509.29,0,0,1,282.29,#8,1,0,0,594.87,0,1,0,509.29,0,0,1,282.29,#9,1,0,0,594.87,0,1,0,509.29,0,0,1,282.29,#10,1,0,0,594.87,0,1,0,509.29,0,0,1,282.29,#11,1,0,0,594.87,0,1,0,509.29,0,0,1,282.29
> view matrix models
> #7,1,0,0,612.8,0,1,0,545.17,0,0,1,262.76,#8,1,0,0,612.8,0,1,0,545.17,0,0,1,262.76,#9,1,0,0,612.8,0,1,0,545.17,0,0,1,262.76,#10,1,0,0,612.8,0,1,0,545.17,0,0,1,262.76,#11,1,0,0,612.8,0,1,0,545.17,0,0,1,262.76
> view matrix models
> #7,1,0,0,618.67,0,1,0,523.16,0,0,1,251.29,#8,1,0,0,618.67,0,1,0,523.16,0,0,1,251.29,#9,1,0,0,618.67,0,1,0,523.16,0,0,1,251.29,#10,1,0,0,618.67,0,1,0,523.16,0,0,1,251.29,#11,1,0,0,618.67,0,1,0,523.16,0,0,1,251.29
> select clear
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> hide #!6 models
> hide #7 models
> show #7 models
> hide #7 models
> hide #9 models
> hide #8 models
> hide #10 models
> hide #11 models
> show #10 models
> hide #10 models
> show #9 models
> show #!6 models
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #9
1267 atoms, 1299 bonds, 166 residues, 1 model selected
> fitmap sel inMap #6
Fit molecule
GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#9) to map volume difference (#6) using 1267 atoms
average map value = 0.009577, steps = 144
shifted from previous position = 11.4
rotated from previous position = 9.23 degrees
atoms outside contour = 1116, contour level = 0.017597
Position of
GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#9) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.99674849 -0.07168782 -0.03678731 624.44546855
0.06587884 0.98792828 -0.14020590 524.26641880
0.04639428 0.13732651 0.98943873 241.05016253
Axis 0.86531366 -0.25935046 0.42891678
Axis point 0.00000000 189.16154322 4662.22501946
Rotation angle (degrees) 9.22809501
Shift along axis 507.76291928
> select clear
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> select add #9
1267 atoms, 1299 bonds, 166 residues, 1 model selected
> view matrix models
> #9,0.99675,-0.071688,-0.036787,632.81,0.065879,0.98793,-0.14021,539.16,0.046394,0.13733,0.98944,227.63
> fitmap sel inMap #6
Fit molecule
GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#9) to map volume difference (#6) using 1267 atoms
average map value = 0.01232, steps = 96
shifted from previous position = 7.78
rotated from previous position = 31.7 degrees
atoms outside contour = 956, contour level = 0.017597
Position of
GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#9) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.96190067 0.00476756 0.27335758 637.73213388
0.15072653 0.82492895 -0.54476943 535.39631264
-0.22809780 0.56521632 0.79278112 230.05957944
Axis 0.90484398 0.40877901 0.11898359
Axis point 0.00000000 -89.36526445 393.74809350
Rotation angle (degrees) 37.83267320
Shift along axis 823.28017228
> select clear
> hide #!6 models
> show #!6 models
> ui mousemode right zoom
> transparency #6.1 50
> lighting full
> lighting soft
> lighting simple
> select add #9
1267 atoms, 1299 bonds, 166 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.9619,0.0047676,0.27336,642.46,0.15073,0.82493,-0.54477,535.86,-0.2281,0.56522,0.79278,238.38
> fitmap sel inMap #6
Fit molecule
GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#9) to map volume difference (#6) using 1267 atoms
average map value = 0.01232, steps = 92
shifted from previous position = 9.58
rotated from previous position = 0.014 degrees
atoms outside contour = 956, contour level = 0.017597
Position of
GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#9) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.96188456 0.00455077 0.27341797 637.73277468
0.15095344 0.82487814 -0.54478355 535.39973142
-0.22801569 0.56529226 0.79275059 230.06063278
Axis 0.90482483 0.40871950 0.11933309
Axis point 0.00000000 -88.85309671 393.64895921
Rotation angle (degrees) 37.83722464
Shift along axis 823.31861063
> select clear
> ui mousemode right "rotate selected models"
> select add #9
1267 atoms, 1299 bonds, 166 residues, 1 model selected
> view matrix models
> #9,0.95066,0.039124,0.30775,637.51,0.15947,0.78928,-0.59296,535.64,-0.2661,0.61278,0.7441,229.84
> view matrix models
> #9,0.94076,0.092562,0.32619,637.18,0.13855,0.77311,-0.61896,535.78,-0.30947,0.62748,0.71449,229.82
> view matrix models
> #9,0.93833,0.11476,0.32614,637.05,0.12243,0.77191,-0.62383,535.8,-0.32334,0.62529,0.71026,229.85
> view matrix models
> #9,0.98281,0.13008,0.13099,637.05,0.0057117,0.68782,-0.72586,536.5,-0.18451,0.71414,0.67525,229.19
> view matrix models
> #9,0.85365,-0.001513,-0.52085,638.42,-0.48557,0.35947,-0.79687,539.02,0.18844,0.93315,0.30613,227.75
> fitmap sel inMap #6
Fit molecule
GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#9) to map volume difference (#6) using 1267 atoms
average map value = 0.01224, steps = 132
shifted from previous position = 6.15
rotated from previous position = 20.7 degrees
atoms outside contour = 940, contour level = 0.017597
Position of
GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#9) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.81999210 -0.31156746 -0.48014444 634.66487363
-0.29409822 0.49031193 -0.82042699 534.28961212
0.49103890 0.81395327 0.31042047 227.18573383
Axis 0.85964059 -0.51081663 0.00918836
Axis point 0.00000000 275.58858234 651.08877222
Rotation angle (degrees) 71.91893733
Shift along axis 274.74713266
> select clear
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> select add #9
1267 atoms, 1299 bonds, 166 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.36336,-0.93113,-0.031268,639.28,-0.15244,0.092531,-0.98397,536.68,0.91909,-0.35276,-0.17556,234.19
> fitmap sel inMap #6
Fit molecule
GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#9) to map volume difference (#6) using 1267 atoms
average map value = 0.01227, steps = 148
shifted from previous position = 4.02
rotated from previous position = 40.8 degrees
atoms outside contour = 938, contour level = 0.017597
Position of
GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#9) relative to volume difference (#6) coordinates:
Matrix rotation and translation
-0.23754122 -0.97080991 -0.03320077 636.03923522
-0.73844842 0.20268057 -0.64312869 536.14427656
0.63108486 -0.12825252 -0.76503803 232.61382243
Axis 0.59046181 -0.76180510 0.26647297
Axis point 491.93087169 0.00000000 303.28429933
Rotation angle (degrees) 154.15140923
Shift along axis 29.10473318
> select clear
> ui mousemode right "translate selected models"
> select add #9
1267 atoms, 1299 bonds, 166 residues, 1 model selected
> view matrix models
> #9,-0.23754,-0.97081,-0.033201,642.71,-0.73845,0.20268,-0.64313,524.33,0.63108,-0.12825,-0.76504,226.37
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.53492,-0.078876,0.84121,635.94,-0.25998,-0.96269,0.075051,530.45,0.80391,-0.25884,-0.53547,226.84
> fitmap sel inMap #6
Fit molecule
GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#9) to map volume difference (#6) using 1267 atoms
average map value = 0.01136, steps = 96
shifted from previous position = 4.17
rotated from previous position = 16.5 degrees
atoms outside contour = 983, contour level = 0.017597
Position of
GeneID_79676111_protein_hypotheticalprotein_57cf4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#9) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.59375367 -0.24878731 0.76521987 638.06020796
-0.18112240 -0.96791846 -0.17415091 532.40595032
0.78399698 -0.03519572 -0.61976609 230.01851871
Axis 0.89250668 -0.12060498 0.43461048
Axis point 0.00000000 310.03483963 -27.12302650
Rotation angle (degrees) 175.53526630
Shift along axis 605.23064451
> select clear
> ui mousemode right zoom
> show #8 models
> close #8
> show #7 models
> close #7
> show #10 models
> select add #10
279 atoms, 286 bonds, 38 residues, 1 model selected
> show #11 models
> close #10
> select add #11
917 atoms, 932 bonds, 119 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,614.68,0,1,0,531.47,0,0,1,251.57
> view matrix models #11,1,0,0,618.52,0,1,0,501.55,0,0,1,280.35
> fitmap sel inMap #6
Fit molecule
GeneID_79676113_protein_hypotheticalprotein_07d98_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#11) to map volume difference (#6) using 917 atoms
average map value = 0.008023, steps = 176
shifted from previous position = 20.9
rotated from previous position = 19.9 degrees
atoms outside contour = 912, contour level = 0.017597
Position of
GeneID_79676113_protein_hypotheticalprotein_07d98_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#11) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.94042542 -0.25815890 0.22125553 638.30206975
0.25667067 0.96582947 0.03596678 496.19428477
-0.22298026 0.02296573 0.97455240 277.90541755
Axis -0.01911580 0.65317215 0.75696812
Axis point -261.78656655 2571.59987031 0.00000000
Rotation angle (degrees) 19.88054615
Shift along axis 522.26417491
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.48238,-0.87371,0.06273,636,0.76191,0.45383,0.46209,486.94,-0.4322,-0.17511,0.88461,277.68
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.48238,-0.87371,0.06273,624.79,0.76191,0.45383,0.46209,511.89,-0.4322,-0.17511,0.88461,276.34
> fitmap sel inMap #6
Fit molecule
GeneID_79676113_protein_hypotheticalprotein_07d98_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#11) to map volume difference (#6) using 917 atoms
average map value = 0.01029, steps = 268
shifted from previous position = 17.2
rotated from previous position = 44.8 degrees
atoms outside contour = 874, contour level = 0.017597
Position of
GeneID_79676113_protein_hypotheticalprotein_07d98_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#11) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.30435800 -0.69662132 -0.64968066 627.46134848
0.91422865 0.02209933 0.40459561 521.24325154
-0.26749241 -0.71709858 0.64359727 261.52617411
Axis -0.56090997 -0.19111554 0.80551527
Axis point 114.20150674 592.70754341 0.00000000
Rotation angle (degrees) 90.85790443
Shift along axis -240.90368428
> close #11
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676114_protein_putativetailprotein_16485/GeneID_79676114_protein_putativetailprotein_16485_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
GeneID_79676114_protein_putativetailprotein_16485_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
#7
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676115_protein_putativetailprotein_7918e/GeneID_79676115_protein_putativetailprotein_7918e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
GeneID_79676115_protein_putativetailprotein_7918e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#8
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676116_protein_majortailprotein_80e33/GeneID_79676116_protein_majortailprotein_80e33_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
GeneID_79676116_protein_majortailprotein_80e33_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#10
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676117_protein_hypotheticalprotein_67b12/GeneID_79676117_protein_hypotheticalprotein_67b12_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
Chain information for
GeneID_79676117_protein_hypotheticalprotein_67b12_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
#11
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676118_protein_hypotheticalprotein_8bf64/GeneID_79676118_protein_hypotheticalprotein_8bf64_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
GeneID_79676118_protein_hypotheticalprotein_8bf64_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
#12
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676119_protein_hypotheticalprotein_7be82/GeneID_79676119_protein_hypotheticalprotein_7be82_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
Chain information for
GeneID_79676119_protein_hypotheticalprotein_7be82_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
#13
---
Chain | Description
A | No description available
> ui mousemode right zoom
> select add #7
1320 atoms, 1348 bonds, 167 residues, 1 model selected
> select add #8
2391 atoms, 2441 bonds, 307 residues, 2 models selected
> select add #10
4197 atoms, 4278 bonds, 548 residues, 3 models selected
> select add #11
5179 atoms, 5287 bonds, 668 residues, 4 models selected
> select add #12
5407 atoms, 5518 bonds, 699 residues, 5 models selected
> select add #13
5809 atoms, 5927 bonds, 753 residues, 6 models selected
> ui mousemode right clip
> ui mousemode right zoom
> ui mousemode right clip
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #7,1,0,0,586.06,0,1,0,695.73,0,0,1,391.68,#8,1,0,0,586.06,0,1,0,695.73,0,0,1,391.68,#10,1,0,0,586.06,0,1,0,695.73,0,0,1,391.68,#11,1,0,0,586.06,0,1,0,695.73,0,0,1,391.68,#12,1,0,0,586.06,0,1,0,695.73,0,0,1,391.68,#13,1,0,0,586.06,0,1,0,695.73,0,0,1,391.68
> view matrix models
> #7,1,0,0,688.83,0,1,0,480.8,0,0,1,285.15,#8,1,0,0,688.83,0,1,0,480.8,0,0,1,285.15,#10,1,0,0,688.83,0,1,0,480.8,0,0,1,285.15,#11,1,0,0,688.83,0,1,0,480.8,0,0,1,285.15,#12,1,0,0,688.83,0,1,0,480.8,0,0,1,285.15,#13,1,0,0,688.83,0,1,0,480.8,0,0,1,285.15
> ui mousemode right zoom
> select clear
> ui mousemode right clip
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> hide #13 models
> hide #12 models
> hide #11 models
> hide #10 models
> hide #9 models
> hide #8 models
> hide #7 models
> show #7 models
> close #7
> show #8 models
> select add #8
1071 atoms, 1093 bonds, 140 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,644.03,0,1,0,513.7,0,0,1,292.83
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.99981,-0.018675,0.0051593,644.04,0.018731,0.99976,-0.01113,513.76,-0.0049502,0.011225,0.99992,292.8
> view matrix models
> #8,-0.63474,0.15162,-0.7577,640.17,-0.7688,-0.025181,0.63899,511.81,0.077804,0.98812,0.13255,293.08
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.63474,0.15162,-0.7577,660.88,-0.7688,-0.025181,0.63899,507.53,0.077804,0.98812,0.13255,306.55
> fitmap sel inMap #6
Fit molecule
GeneID_79676115_protein_putativetailprotein_7918e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#8) to map volume difference (#6) using 1071 atoms
average map value = 0.009735, steps = 156
shifted from previous position = 3.17
rotated from previous position = 33.9 degrees
atoms outside contour = 1062, contour level = 0.017597
Position of
GeneID_79676115_protein_putativetailprotein_7918e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#8) relative to volume difference (#6) coordinates:
Matrix rotation and translation
-0.70374734 -0.14929571 -0.69458656 659.29570951
-0.55338528 -0.49792542 0.66770878 509.69575381
-0.44553836 0.85427225 0.26779564 305.19901657
Axis 0.36579714 -0.48831167 -0.79230307
Axis point 431.83374733 99.38807112 0.00000000
Rotation angle (degrees) 165.22585419
Shift along axis -249.53202267
> select clear
> ui mousemode right zoom
> close #8
> show #9 models
> show #10 models
> close #10
> show #11 models
> close #11
> show #12 models
> show #13 models
> hide #12 models
> close #12-13
> ui mousemode right clip
> select clear
> ui mousemode right "translate selected models"
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676120_protein_tailtapemeasureprotein_7487b/GeneID_79676120_protein_tailtapemeasureprotein_7487b_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
GeneID_79676120_protein_tailtapemeasureprotein_7487b_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
#7
---
Chain | Description
A | No description available
> close #7
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676126_protein_hypotheticalprotein_e23ff/GeneID_79676126_protein_hypotheticalprotein_e23ff_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
GeneID_79676126_protein_hypotheticalprotein_e23ff_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#7
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676127_protein_hypotheticalprotein_ebb57/GeneID_79676127_protein_hypotheticalprotein_ebb57_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
GeneID_79676127_protein_hypotheticalprotein_ebb57_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#8
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676129_protein_hypotheticalprotein_0b491/GeneID_79676129_protein_hypotheticalprotein_0b491_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
GeneID_79676129_protein_hypotheticalprotein_0b491_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
#10
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676130_protein_hypotheticalprotein_bc422/GeneID_79676130_protein_hypotheticalprotein_bc422_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
GeneID_79676130_protein_hypotheticalprotein_bc422_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
#11
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676132_protein_hypotheticalprotein_2f54a/GeneID_79676132_protein_hypotheticalprotein_2f54a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
GeneID_79676132_protein_hypotheticalprotein_2f54a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
#12
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676134_protein_hypotheticalprotein_1f7fd/GeneID_79676134_protein_hypotheticalprotein_1f7fd_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
Chain information for
GeneID_79676134_protein_hypotheticalprotein_1f7fd_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
#13
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676135_protein_hypotheticalprotein_eea42/GeneID_79676135_protein_hypotheticalprotein_eea42_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
Chain information for
GeneID_79676135_protein_hypotheticalprotein_eea42_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
#14
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676139_protein_hypotheticalprotein_a7d56/GeneID_79676139_protein_hypotheticalprotein_a7d56_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
GeneID_79676139_protein_hypotheticalprotein_a7d56_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#15
---
Chain | Description
A | No description available
> select add #7
2421 atoms, 2465 bonds, 321 residues, 1 model selected
> select add #8
2962 atoms, 3012 bonds, 394 residues, 2 models selected
> select add #9
4229 atoms, 4311 bonds, 560 residues, 3 models selected
> select add #10
5733 atoms, 5845 bonds, 751 residues, 4 models selected
> select add #11
7075 atoms, 7208 bonds, 924 residues, 5 models selected
> select add #12
7666 atoms, 7809 bonds, 998 residues, 6 models selected
> select add #13
8901 atoms, 9062 bonds, 1150 residues, 7 models selected
> select subtract #9
7634 atoms, 7763 bonds, 984 residues, 6 models selected
> select add #14
8311 atoms, 8459 bonds, 1064 residues, 7 models selected
> select add #15
8919 atoms, 9085 bonds, 1138 residues, 8 models selected
> view matrix models
> #7,1,0,0,215.24,0,1,0,126.7,0,0,1,165.06,#8,1,0,0,215.24,0,1,0,126.7,0,0,1,165.06,#10,1,0,0,215.24,0,1,0,126.7,0,0,1,165.06,#11,1,0,0,215.24,0,1,0,126.7,0,0,1,165.06,#12,1,0,0,215.24,0,1,0,126.7,0,0,1,165.06,#13,1,0,0,215.24,0,1,0,126.7,0,0,1,165.06,#14,1,0,0,215.24,0,1,0,126.7,0,0,1,165.06,#15,1,0,0,215.24,0,1,0,126.7,0,0,1,165.06
> ui mousemode right zoom
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models
> #7,1,0,0,591.97,0,1,0,434.26,0,0,1,457.03,#8,1,0,0,591.97,0,1,0,434.26,0,0,1,457.03,#10,1,0,0,591.97,0,1,0,434.26,0,0,1,457.03,#11,1,0,0,591.97,0,1,0,434.26,0,0,1,457.03,#12,1,0,0,591.97,0,1,0,434.26,0,0,1,457.03,#13,1,0,0,591.97,0,1,0,434.26,0,0,1,457.03,#14,1,0,0,591.97,0,1,0,434.26,0,0,1,457.03,#15,1,0,0,591.97,0,1,0,434.26,0,0,1,457.03
> view matrix models
> #7,1,0,0,664.31,0,1,0,484.83,0,0,1,472.48,#8,1,0,0,664.31,0,1,0,484.83,0,0,1,472.48,#10,1,0,0,664.31,0,1,0,484.83,0,0,1,472.48,#11,1,0,0,664.31,0,1,0,484.83,0,0,1,472.48,#12,1,0,0,664.31,0,1,0,484.83,0,0,1,472.48,#13,1,0,0,664.31,0,1,0,484.83,0,0,1,472.48,#14,1,0,0,664.31,0,1,0,484.83,0,0,1,472.48,#15,1,0,0,664.31,0,1,0,484.83,0,0,1,472.48
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #7,1,0,0,642.9,0,1,0,511.2,0,0,1,440.67,#8,1,0,0,642.9,0,1,0,511.2,0,0,1,440.67,#10,1,0,0,642.9,0,1,0,511.2,0,0,1,440.67,#11,1,0,0,642.9,0,1,0,511.2,0,0,1,440.67,#12,1,0,0,642.9,0,1,0,511.2,0,0,1,440.67,#13,1,0,0,642.9,0,1,0,511.2,0,0,1,440.67,#14,1,0,0,642.9,0,1,0,511.2,0,0,1,440.67,#15,1,0,0,642.9,0,1,0,511.2,0,0,1,440.67
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #7,1,0,0,632.41,0,1,0,629.86,0,0,1,397.78,#8,1,0,0,632.41,0,1,0,629.86,0,0,1,397.78,#10,1,0,0,632.41,0,1,0,629.86,0,0,1,397.78,#11,1,0,0,632.41,0,1,0,629.86,0,0,1,397.78,#12,1,0,0,632.41,0,1,0,629.86,0,0,1,397.78,#13,1,0,0,632.41,0,1,0,629.86,0,0,1,397.78,#14,1,0,0,632.41,0,1,0,629.86,0,0,1,397.78,#15,1,0,0,632.41,0,1,0,629.86,0,0,1,397.78
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #7,1,0,0,626.79,0,1,0,577.05,0,0,1,377.39,#8,1,0,0,626.79,0,1,0,577.05,0,0,1,377.39,#10,1,0,0,626.79,0,1,0,577.05,0,0,1,377.39,#11,1,0,0,626.79,0,1,0,577.05,0,0,1,377.39,#12,1,0,0,626.79,0,1,0,577.05,0,0,1,377.39,#13,1,0,0,626.79,0,1,0,577.05,0,0,1,377.39,#14,1,0,0,626.79,0,1,0,577.05,0,0,1,377.39,#15,1,0,0,626.79,0,1,0,577.05,0,0,1,377.39
> view matrix models
> #7,1,0,0,658.9,0,1,0,578,0,0,1,387.19,#8,1,0,0,658.9,0,1,0,578,0,0,1,387.19,#10,1,0,0,658.9,0,1,0,578,0,0,1,387.19,#11,1,0,0,658.9,0,1,0,578,0,0,1,387.19,#12,1,0,0,658.9,0,1,0,578,0,0,1,387.19,#13,1,0,0,658.9,0,1,0,578,0,0,1,387.19,#14,1,0,0,658.9,0,1,0,578,0,0,1,387.19,#15,1,0,0,658.9,0,1,0,578,0,0,1,387.19
> view matrix models
> #7,1,0,0,671.9,0,1,0,612.14,0,0,1,359.27,#8,1,0,0,671.9,0,1,0,612.14,0,0,1,359.27,#10,1,0,0,671.9,0,1,0,612.14,0,0,1,359.27,#11,1,0,0,671.9,0,1,0,612.14,0,0,1,359.27,#12,1,0,0,671.9,0,1,0,612.14,0,0,1,359.27,#13,1,0,0,671.9,0,1,0,612.14,0,0,1,359.27,#14,1,0,0,671.9,0,1,0,612.14,0,0,1,359.27,#15,1,0,0,671.9,0,1,0,612.14,0,0,1,359.27
> select clear
> ui mousemode right clip
> ui mousemode right zoom
> ui mousemode right clip
> ui mousemode right zoom
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> select add #7
2421 atoms, 2465 bonds, 321 residues, 1 model selected
> select add #8
2962 atoms, 3012 bonds, 394 residues, 2 models selected
> select add #10
4466 atoms, 4546 bonds, 585 residues, 3 models selected
> select add #11
5808 atoms, 5909 bonds, 758 residues, 4 models selected
> select add #12
6399 atoms, 6510 bonds, 832 residues, 5 models selected
> select add #13
7634 atoms, 7763 bonds, 984 residues, 6 models selected
> select add #14
8311 atoms, 8459 bonds, 1064 residues, 7 models selected
> select add #15
8919 atoms, 9085 bonds, 1138 residues, 8 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,1,0,0,688.34,0,1,0,549.6,0,0,1,360.37,#8,1,0,0,688.34,0,1,0,549.6,0,0,1,360.37,#10,1,0,0,688.34,0,1,0,549.6,0,0,1,360.37,#11,1,0,0,688.34,0,1,0,549.6,0,0,1,360.37,#12,1,0,0,688.34,0,1,0,549.6,0,0,1,360.37,#13,1,0,0,688.34,0,1,0,549.6,0,0,1,360.37,#14,1,0,0,688.34,0,1,0,549.6,0,0,1,360.37,#15,1,0,0,688.34,0,1,0,549.6,0,0,1,360.37
> select clear
> ui mousemode right zoom
> hide #14 models
> hide #13 models
> hide #12 models
> hide #11 models
> hide #10 models
> hide #9 models
> hide #8 models
> hide #15 models
> select add #7
2421 atoms, 2465 bonds, 321 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,705.62,0,1,0,526.9,0,0,1,358.62
> fitmap sel inMap #6
Fit molecule
GeneID_79676126_protein_hypotheticalprotein_e23ff_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) to map volume difference (#6) using 2421 atoms
average map value = 0.01044, steps = 132
shifted from previous position = 8.28
rotated from previous position = 29.5 degrees
atoms outside contour = 2046, contour level = 0.017597
Position of
GeneID_79676126_protein_hypotheticalprotein_e23ff_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#7) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.87148309 -0.24597786 -0.42427834 702.54283380
0.22564148 0.96922440 -0.09843775 519.47917804
0.43543442 -0.00994796 0.90016548 358.36279874
Axis 0.08987737 -0.87319359 0.47901463
Axis point -629.69569458 0.00000000 1892.94306601
Rotation angle (degrees) 29.49059818
Shift along axis -218.80216305
> select clear
> ui mousemode right zoom
> close #7
> show #8 models
> close #8
> show #9 models
> hide #9 models
> show #10 models
> select add #10
1504 atoms, 1534 bonds, 191 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,704.4,0,1,0,532.78,0,0,1,361.47
> fitmap sel inMap #6
Fit molecule
GeneID_79676129_protein_hypotheticalprotein_0b491_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#10) to map volume difference (#6) using 1504 atoms
average map value = 0.01161, steps = 120
shifted from previous position = 14.1
rotated from previous position = 10.8 degrees
atoms outside contour = 1181, contour level = 0.017597
Position of
GeneID_79676129_protein_hypotheticalprotein_0b491_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#10) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.99556445 0.01100959 0.09343565 709.18154256
-0.02601079 0.98662924 0.16089181 524.19442991
-0.09041499 -0.16260850 0.98253937 350.92436839
Axis -0.86513487 0.49167061 -0.09900338
Axis point 0.00000000 2377.09625346 -4253.99217490
Rotation angle (degrees) 10.77573238
Shift along axis -390.54938405
> select #6
3 models selected
> ui mousemode right "rotate selected models"
> select add #10
1504 atoms, 1534 bonds, 191 residues, 4 models selected
> select subtract #6
1504 atoms, 1534 bonds, 191 residues, 1 model selected
> view matrix models
> #10,0.99792,0.064453,0.0027708,709.13,-0.011426,0.21885,-0.97569,520.24,-0.063492,0.97363,0.21913,352.13
> fitmap sel inMap #6
Fit molecule
GeneID_79676129_protein_hypotheticalprotein_0b491_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#10) to map volume difference (#6) using 1504 atoms
average map value = 0.01164, steps = 64
shifted from previous position = 0.864
rotated from previous position = 12 degrees
atoms outside contour = 1179, contour level = 0.017597
Position of
GeneID_79676129_protein_hypotheticalprotein_0b491_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#10) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.96634516 0.20815020 0.15116390 709.02991442
0.10513850 0.21673070 -0.97055330 520.62564513
-0.23478272 0.95378263 0.18755207 352.60572338
Axis 0.97912706 0.19637464 -0.05241369
Axis point -0.00000000 -53.09714681 421.86055850
Rotation angle (degrees) 79.32056219
Shift along axis 777.98668483
> select clear
> select add #10
1504 atoms, 1534 bonds, 191 residues, 1 model selected
> view matrix models
> #10,0.955,0.2281,0.1896,709.11,0.1588,0.14669,-0.97635,520.64,-0.25051,0.96253,0.10387,352.4
> view matrix models
> #10,0.8756,-0.0087844,-0.48296,706.96,-0.46172,-0.30895,-0.83148,517.67,-0.14191,0.95104,-0.27458,352.02
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.8756,-0.0087844,-0.48296,705.21,-0.46172,-0.30895,-0.83148,519.51,-0.14191,0.95104,-0.27458,350.68
> fitmap sel inMap #6
Fit molecule
GeneID_79676129_protein_hypotheticalprotein_0b491_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#10) to map volume difference (#6) using 1504 atoms
average map value = 0.0107, steps = 56
shifted from previous position = 2.02
rotated from previous position = 10.1 degrees
atoms outside contour = 1203, contour level = 0.017597
Position of
GeneID_79676129_protein_hypotheticalprotein_0b491_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#10) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.92954309 0.02823106 -0.36763113 705.52435166
-0.32350715 -0.41591578 -0.84991599 520.98765465
-0.17689762 0.90896483 -0.37747869 351.81023041
Axis 0.97508753 -0.10573876 -0.19499646
Axis point 0.00000000 149.58522948 433.98580009
Rotation angle (degrees) 115.58983150
Shift along axis 564.25766187
> select clear
> close #10
> show #11 models
> select add #11
1342 atoms, 1363 bonds, 173 residues, 1 model selected
> view matrix models #11,1,0,0,672.32,0,1,0,524.02,0,0,1,318.65
> view matrix models #11,1,0,0,666.94,0,1,0,516.02,0,0,1,305.18
> fitmap sel inMap #6
Fit molecule
GeneID_79676130_protein_hypotheticalprotein_bc422_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#11) to map volume difference (#6) using 1342 atoms
average map value = 0.008428, steps = 164
shifted from previous position = 3.92
rotated from previous position = 10.3 degrees
atoms outside contour = 1284, contour level = 0.017597
Position of
GeneID_79676130_protein_hypotheticalprotein_bc422_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
(#11) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.99898034 0.04446570 -0.00781519 664.04273521
-0.04514726 0.98396658 -0.17254417 513.07361534
0.00001759 0.17272107 0.98497078 305.62453307
Axis 0.96769565 -0.02195342 -0.25116363
Axis point 0.00000000 -2292.47465097 3257.16275399
Rotation angle (degrees) 10.27632016
Shift along axis 554.56577996
> select clear
> close #11
> show #12 models
> select add #12
591 atoms, 601 bonds, 74 residues, 1 model selected
> view matrix models #12,1,0,0,665.76,0,1,0,518.2,0,0,1,312.61
> fitmap sel inMap #6
Fit molecule
GeneID_79676132_protein_hypotheticalprotein_2f54a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
(#12) to map volume difference (#6) using 591 atoms
average map value = 0.009988, steps = 132
shifted from previous position = 9.31
rotated from previous position = 34.6 degrees
atoms outside contour = 559, contour level = 0.017597
Position of
GeneID_79676132_protein_hypotheticalprotein_2f54a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
(#12) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.96306363 -0.20297952 -0.17693997 658.24704924
0.08302725 0.84892527 -0.52195054 522.12776725
0.25615408 0.48798075 0.83442188 308.82872564
Axis 0.88942540 -0.38141688 0.25188019
Axis point 0.00000000 55.71534801 1323.35640346
Rotation angle (degrees) 34.59303491
Shift along axis 464.10113648
> view matrix models
> #12,0.96306,-0.20298,-0.17694,653.81,0.083027,0.84893,-0.52195,525.53,0.25615,0.48798,0.83442,300.03
> view matrix models
> #12,0.96306,-0.20298,-0.17694,655.56,0.083027,0.84893,-0.52195,528.3,0.25615,0.48798,0.83442,293.69
> fitmap sel inMap #6
Fit molecule
GeneID_79676132_protein_hypotheticalprotein_2f54a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
(#12) to map volume difference (#6) using 591 atoms
average map value = 0.009708, steps = 88
shifted from previous position = 8.5
rotated from previous position = 13.9 degrees
atoms outside contour = 565, contour level = 0.017597
Position of
GeneID_79676132_protein_hypotheticalprotein_2f54a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
(#12) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.97283616 -0.22744314 -0.04312112 654.47828763
0.19825855 0.91474838 -0.35203543 521.82279225
0.11951302 0.33392366 0.93499285 298.88665988
Axis 0.83294358 -0.19748271 0.51691931
Axis point 0.00000000 364.97666976 1728.58936937
Rotation angle (degrees) 24.31594875
Shift along axis 596.59279816
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.76209,0.64722,0.01779,655.34,-0.57521,0.6894,-0.44031,520.81,-0.29724,0.32532,0.89767,298.48
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.76209,0.64722,0.01779,656.34,-0.57521,0.6894,-0.44031,526.99,-0.29724,0.32532,0.89767,292.72
> fitmap sel inMap #6
Fit molecule
GeneID_79676132_protein_hypotheticalprotein_2f54a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
(#12) to map volume difference (#6) using 591 atoms
average map value = 0.009607, steps = 140
shifted from previous position = 8.2
rotated from previous position = 36.2 degrees
atoms outside contour = 562, contour level = 0.017597
Position of
GeneID_79676132_protein_hypotheticalprotein_2f54a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
(#12) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.99367238 0.10299966 0.04479149 657.34676462
-0.08964463 0.96755614 -0.23621804 523.22562654
-0.06766866 0.23070802 0.97066717 299.93478050
Axis 0.90231840 0.21732532 -0.37227841
Axis point 0.00000000 -2013.31746779 1943.95067544
Rotation angle (degrees) 14.99512503
Shift along axis 595.18701586
> close #12
> show #13 models
> ui mousemode right zoom
> close #13
> show #14 models
> close #14
> show #15 models
> ui mousemode right "translate selected models"
> select add #15
608 atoms, 626 bonds, 74 residues, 1 model selected
> view matrix models #15,1,0,0,669.06,0,1,0,532.71,0,0,1,295.9
> fitmap sel inMap #6
Fit molecule
GeneID_79676139_protein_hypotheticalprotein_a7d56_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#15) to map volume difference (#6) using 608 atoms
average map value = 0.009504, steps = 60
shifted from previous position = 3.51
rotated from previous position = 7.21 degrees
atoms outside contour = 518, contour level = 0.017597
Position of
GeneID_79676139_protein_hypotheticalprotein_a7d56_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#15) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.99220548 0.09677753 -0.07850096 670.50171427
-0.09555849 0.99523963 0.01914838 533.10405089
0.07998040 -0.01149769 0.99673012 292.44925184
Axis -0.12204973 -0.63116112 -0.76598923
Axis point 1634.53462986 -5986.57654586 0.00000000
Rotation angle (degrees) 7.21237255
Shift along axis -642.32208047
> select clear
> ui mousemode right zoom
> hide #15 models
> show #15 models
> select add #15
608 atoms, 626 bonds, 74 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.99221,0.096778,-0.078501,669.38,-0.095558,0.99524,0.019148,531.78,0.07998,-0.011498,0.99673,290.02
> fitmap sel inMap #6
Fit molecule
GeneID_79676139_protein_hypotheticalprotein_a7d56_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#15) to map volume difference (#6) using 608 atoms
average map value = 0.01049, steps = 152
shifted from previous position = 3.33
rotated from previous position = 7.23 degrees
atoms outside contour = 503, contour level = 0.017597
Position of
GeneID_79676139_protein_hypotheticalprotein_a7d56_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#15) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.98153167 0.04303974 -0.18639519 672.49092479
-0.03493989 0.99830584 0.04652594 529.74737859
0.18808187 -0.03915405 0.98137260 289.55976896
Axis -0.21857784 -0.95532675 -0.19893347
Axis point -508.09251238 0.00000000 2824.83898903
Rotation angle (degrees) 11.30280944
Shift along axis -710.67658387
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.35115,-0.93535,0.042551,674.91,-0.10399,0.084124,0.99101,524.85,-0.93053,0.34357,-0.12681,298.6
> fitmap sel inMap #6
Fit molecule
GeneID_79676139_protein_hypotheticalprotein_a7d56_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#15) to map volume difference (#6) using 608 atoms
average map value = 0.01022, steps = 76
shifted from previous position = 2.07
rotated from previous position = 15.2 degrees
atoms outside contour = 487, contour level = 0.017597
Position of
GeneID_79676139_protein_hypotheticalprotein_a7d56_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#15) relative to volume difference (#6) coordinates:
Matrix rotation and translation
-0.31002435 -0.91496685 0.25830325 676.09234552
0.10713132 0.23633885 0.96574677 525.21766121
-0.94467337 0.32707738 0.02475081 297.83434642
Axis -0.37505665 0.70644435 0.60022403
Axis point 524.91429580 0.00000000 -385.38196142
Rotation angle (degrees) 121.63239237
Shift along axis 296.23145062
> select clear
> select add #15
608 atoms, 626 bonds, 74 residues, 1 model selected
> view matrix models
> #15,-0.48095,-0.67053,0.56486,674.44,0.70873,0.081927,0.7007,525.56,-0.51612,0.73734,0.43582,294.03
> fitmap sel inMap #6
Fit molecule
GeneID_79676139_protein_hypotheticalprotein_a7d56_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#15) to map volume difference (#6) using 608 atoms
average map value = 0.01039, steps = 84
shifted from previous position = 4.78
rotated from previous position = 17.7 degrees
atoms outside contour = 502, contour level = 0.017597
Position of
GeneID_79676139_protein_hypotheticalprotein_a7d56_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#15) relative to volume difference (#6) coordinates:
Matrix rotation and translation
-0.69587264 -0.60887248 0.38083536 670.96897840
0.48948389 -0.01407284 0.87189877 526.84812363
-0.52551574 0.79314327 0.30782618 294.08958230
Axis -0.05522031 0.63549835 0.77012503
Axis point 293.31109682 332.58150821 0.00000000
Rotation angle (degrees) 134.51208180
Shift along axis 524.24574478
> select clear
> close #15
> ui mousemode right zoom
> ui mousemode right clip
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676140_protein_hypotheticalprotein_bf6f1/GeneID_79676140_protein_hypotheticalprotein_bf6f1_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
GeneID_79676140_protein_hypotheticalprotein_bf6f1_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
#7
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676141_protein_hypotheticalprotein_42742/GeneID_79676141_protein_hypotheticalprotein_42742_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
GeneID_79676141_protein_hypotheticalprotein_42742_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#8
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676143_protein_hypotheticalprotein_09f3c/GeneID_79676143_protein_hypotheticalprotein_09f3c_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
GeneID_79676143_protein_hypotheticalprotein_09f3c_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#10
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676145_protein_hypotheticalprotein_31b79/GeneID_79676145_protein_hypotheticalprotein_31b79_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
GeneID_79676145_protein_hypotheticalprotein_31b79_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#11
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676147_protein_hypotheticalprotein_677ae/GeneID_79676147_protein_hypotheticalprotein_677ae_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
Chain information for
GeneID_79676147_protein_hypotheticalprotein_677ae_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
#12
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676148_protein_hypotheticalprotein_306cc/GeneID_79676148_protein_hypotheticalprotein_306cc_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
GeneID_79676148_protein_hypotheticalprotein_306cc_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#13
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676149_protein_hypotheticalprotein_2addd/GeneID_79676149_protein_hypotheticalprotein_2addd_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
GeneID_79676149_protein_hypotheticalprotein_2addd_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#14
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676150_protein_hypotheticalprotein_59807/GeneID_79676150_protein_hypotheticalprotein_59807_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
GeneID_79676150_protein_hypotheticalprotein_59807_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
#15
---
Chain | Description
A | No description available
> select add #10
434 atoms, 438 bonds, 56 residues, 1 model selected
> select add #11
1084 atoms, 1106 bonds, 136 residues, 2 models selected
> select add #12
1587 atoms, 1618 bonds, 198 residues, 3 models selected
> select add #13
2295 atoms, 2344 bonds, 281 residues, 4 models selected
> select add #14
4165 atoms, 4238 bonds, 518 residues, 5 models selected
> select add #15
4453 atoms, 4531 bonds, 554 residues, 6 models selected
> select add #8
5172 atoms, 5261 bonds, 646 residues, 7 models selected
> select add #7
5645 atoms, 5740 bonds, 703 residues, 8 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,1,0,0,481.87,0,1,0,480.93,0,0,1,509.28,#8,1,0,0,481.87,0,1,0,480.93,0,0,1,509.28,#10,1,0,0,481.87,0,1,0,480.93,0,0,1,509.28,#11,1,0,0,481.87,0,1,0,480.93,0,0,1,509.28,#12,1,0,0,481.87,0,1,0,480.93,0,0,1,509.28,#13,1,0,0,481.87,0,1,0,480.93,0,0,1,509.28,#14,1,0,0,481.87,0,1,0,480.93,0,0,1,509.28,#15,1,0,0,481.87,0,1,0,480.93,0,0,1,509.28
> view matrix models
> #7,1,0,0,544.79,0,1,0,427.53,0,0,1,319.41,#8,1,0,0,544.79,0,1,0,427.53,0,0,1,319.41,#10,1,0,0,544.79,0,1,0,427.53,0,0,1,319.41,#11,1,0,0,544.79,0,1,0,427.53,0,0,1,319.41,#12,1,0,0,544.79,0,1,0,427.53,0,0,1,319.41,#13,1,0,0,544.79,0,1,0,427.53,0,0,1,319.41,#14,1,0,0,544.79,0,1,0,427.53,0,0,1,319.41,#15,1,0,0,544.79,0,1,0,427.53,0,0,1,319.41
> view matrix models
> #7,1,0,0,677.42,0,1,0,457.77,0,0,1,336.61,#8,1,0,0,677.42,0,1,0,457.77,0,0,1,336.61,#10,1,0,0,677.42,0,1,0,457.77,0,0,1,336.61,#11,1,0,0,677.42,0,1,0,457.77,0,0,1,336.61,#12,1,0,0,677.42,0,1,0,457.77,0,0,1,336.61,#13,1,0,0,677.42,0,1,0,457.77,0,0,1,336.61,#14,1,0,0,677.42,0,1,0,457.77,0,0,1,336.61,#15,1,0,0,677.42,0,1,0,457.77,0,0,1,336.61
> view matrix models
> #7,1,0,0,606.66,0,1,0,568.3,0,0,1,347.66,#8,1,0,0,606.66,0,1,0,568.3,0,0,1,347.66,#10,1,0,0,606.66,0,1,0,568.3,0,0,1,347.66,#11,1,0,0,606.66,0,1,0,568.3,0,0,1,347.66,#12,1,0,0,606.66,0,1,0,568.3,0,0,1,347.66,#13,1,0,0,606.66,0,1,0,568.3,0,0,1,347.66,#14,1,0,0,606.66,0,1,0,568.3,0,0,1,347.66,#15,1,0,0,606.66,0,1,0,568.3,0,0,1,347.66
> view matrix models
> #7,1,0,0,633.64,0,1,0,584.76,0,0,1,363.04,#8,1,0,0,633.64,0,1,0,584.76,0,0,1,363.04,#10,1,0,0,633.64,0,1,0,584.76,0,0,1,363.04,#11,1,0,0,633.64,0,1,0,584.76,0,0,1,363.04,#12,1,0,0,633.64,0,1,0,584.76,0,0,1,363.04,#13,1,0,0,633.64,0,1,0,584.76,0,0,1,363.04,#14,1,0,0,633.64,0,1,0,584.76,0,0,1,363.04,#15,1,0,0,633.64,0,1,0,584.76,0,0,1,363.04
> view matrix models
> #7,1,0,0,638.8,0,1,0,600.15,0,0,1,364.43,#8,1,0,0,638.8,0,1,0,600.15,0,0,1,364.43,#10,1,0,0,638.8,0,1,0,600.15,0,0,1,364.43,#11,1,0,0,638.8,0,1,0,600.15,0,0,1,364.43,#12,1,0,0,638.8,0,1,0,600.15,0,0,1,364.43,#13,1,0,0,638.8,0,1,0,600.15,0,0,1,364.43,#14,1,0,0,638.8,0,1,0,600.15,0,0,1,364.43,#15,1,0,0,638.8,0,1,0,600.15,0,0,1,364.43
> select clear
> ui mousemode right clip
> select clear
> select add #7
473 atoms, 479 bonds, 57 residues, 1 model selected
> select add #8
1192 atoms, 1209 bonds, 149 residues, 2 models selected
> select add #10
1626 atoms, 1647 bonds, 205 residues, 3 models selected
> select add #11
2276 atoms, 2315 bonds, 285 residues, 4 models selected
> select add #12
2779 atoms, 2827 bonds, 347 residues, 5 models selected
> select add #13
3487 atoms, 3553 bonds, 430 residues, 6 models selected
> select add #14
5357 atoms, 5447 bonds, 667 residues, 7 models selected
> select add #15
5645 atoms, 5740 bonds, 703 residues, 8 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,1,0,0,721.36,0,1,0,418.75,0,0,1,341.21,#8,1,0,0,721.36,0,1,0,418.75,0,0,1,341.21,#10,1,0,0,721.36,0,1,0,418.75,0,0,1,341.21,#11,1,0,0,721.36,0,1,0,418.75,0,0,1,341.21,#12,1,0,0,721.36,0,1,0,418.75,0,0,1,341.21,#13,1,0,0,721.36,0,1,0,418.75,0,0,1,341.21,#14,1,0,0,721.36,0,1,0,418.75,0,0,1,341.21,#15,1,0,0,721.36,0,1,0,418.75,0,0,1,341.21
> select clear
> ui mousemode right zoom
> select add #7
473 atoms, 479 bonds, 57 residues, 1 model selected
> select add #8
1192 atoms, 1209 bonds, 149 residues, 2 models selected
> select add #10
1626 atoms, 1647 bonds, 205 residues, 3 models selected
> select add #11
2276 atoms, 2315 bonds, 285 residues, 4 models selected
> select add #12
2779 atoms, 2827 bonds, 347 residues, 5 models selected
> select add #13
3487 atoms, 3553 bonds, 430 residues, 6 models selected
> select add #14
5357 atoms, 5447 bonds, 667 residues, 7 models selected
> select add #15
5645 atoms, 5740 bonds, 703 residues, 8 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,1,0,0,732.62,0,1,0,473.41,0,0,1,364.99,#8,1,0,0,732.62,0,1,0,473.41,0,0,1,364.99,#10,1,0,0,732.62,0,1,0,473.41,0,0,1,364.99,#11,1,0,0,732.62,0,1,0,473.41,0,0,1,364.99,#12,1,0,0,732.62,0,1,0,473.41,0,0,1,364.99,#13,1,0,0,732.62,0,1,0,473.41,0,0,1,364.99,#14,1,0,0,732.62,0,1,0,473.41,0,0,1,364.99,#15,1,0,0,732.62,0,1,0,473.41,0,0,1,364.99
> select clear
> select add #7
473 atoms, 479 bonds, 57 residues, 1 model selected
> select subtract #7
Nothing selected
> hide #7 models
> hide #8 models
> hide #15 models
> hide #14 models
> hide #13 models
> hide #12 models
> hide #11 models
> ui mousemode right zoom
> select add #10
434 atoms, 438 bonds, 56 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,727.26,0,1,0,496.31,0,0,1,330.72
> view matrix models #10,1,0,0,722.25,0,1,0,530.53,0,0,1,292.64
> select clear
> ui mousemode right zoom
> select add #10
434 atoms, 438 bonds, 56 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,701.16,0,1,0,553.19,0,0,1,281.17
> view matrix models #10,1,0,0,671.09,0,1,0,547.95,0,0,1,280
> view matrix models #10,1,0,0,679.06,0,1,0,533.86,0,0,1,294.49
> view matrix models #10,1,0,0,675.82,0,1,0,532.31,0,0,1,297.39
> fitmap sel inMap #6
Fit molecule
GeneID_79676143_protein_hypotheticalprotein_09f3c_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#10) to map volume difference (#6) using 434 atoms
average map value = 0.01095, steps = 76
shifted from previous position = 1.2
rotated from previous position = 19 degrees
atoms outside contour = 340, contour level = 0.017597
Position of
GeneID_79676143_protein_hypotheticalprotein_09f3c_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#10) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.96105302 -0.19579714 -0.19503992 674.72257209
0.15831436 0.96850628 -0.19217740 531.29927899
0.22652517 0.15381505 0.96178338 297.54424220
Axis 0.53209282 -0.64831402 0.54457889
Axis point -374.00564051 0.00000000 3052.29820183
Rotation angle (degrees) 18.97309702
Shift along axis 176.60258189
> select clear
> hide #10 models
> show #11 models
> close #10-11
> show #8 models
> select add #8
719 atoms, 730 bonds, 92 residues, 1 model selected
> view matrix models #8,1,0,0,645.54,0,1,0,518.27,0,0,1,316.61
> fitmap sel inMap #6
Fit molecule
GeneID_79676141_protein_hypotheticalprotein_42742_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#8) to map volume difference (#6) using 719 atoms
average map value = 0.01054, steps = 208
shifted from previous position = 18.2
rotated from previous position = 88 degrees
atoms outside contour = 708, contour level = 0.017597
Position of
GeneID_79676141_protein_hypotheticalprotein_42742_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#8) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.28295821 -0.66940168 0.68690323 659.06655805
0.95321053 0.11680477 -0.27883030 506.93669486
0.10641589 0.73366071 0.67113159 305.00489361
Axis 0.50656386 0.29042619 0.81181629
Axis point 45.92903526 383.92943385 0.00000000
Rotation angle (degrees) 87.96859465
Shift along axis 728.69492960
> view matrix models
> #8,0.28296,-0.6694,0.6869,718.05,0.95321,0.1168,-0.27883,523.19,0.10642,0.73366,0.67113,337.15
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.15791,-0.34407,0.92557,717.87,0.92027,0.28856,0.26428,523.73,-0.35801,0.89351,0.27107,336.27
> fitmap sel inMap #6
Fit molecule
GeneID_79676141_protein_hypotheticalprotein_42742_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#8) to map volume difference (#6) using 719 atoms
average map value = 0.01328, steps = 104
shifted from previous position = 13.4
rotated from previous position = 26.8 degrees
atoms outside contour = 515, contour level = 0.017597
Position of
GeneID_79676141_protein_hypotheticalprotein_42742_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#8) relative to volume difference (#6) coordinates:
Matrix rotation and translation
-0.15995084 -0.28448940 0.94524151 715.40138567
0.66964966 0.67226216 0.31564683 524.42425372
-0.72524827 0.68346863 0.08297934 350.31550180
Axis 0.18779597 0.85288921 0.48714749
Axis point 292.25032104 0.00000000 -248.75136835
Rotation angle (degrees) 101.67468768
Shift along axis 752.28059770
> select clear
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> select add #8
719 atoms, 730 bonds, 92 residues, 1 model selected
> view matrix models
> #8,-0.013063,0.12455,-0.99213,708.91,0.061919,0.99041,0.12352,523.55,0.998,-0.059818,-0.02065,350.61
> fitmap sel inMap #6
Fit molecule
GeneID_79676141_protein_hypotheticalprotein_42742_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#8) to map volume difference (#6) using 719 atoms
average map value = 0.01382, steps = 92
shifted from previous position = 4.93
rotated from previous position = 11.3 degrees
atoms outside contour = 494, contour level = 0.017597
Position of
GeneID_79676141_protein_hypotheticalprotein_42742_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#8) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.09976812 0.12210491 -0.98749012 707.39068100
0.22064427 0.96501832 0.14161838 520.99032967
0.97023835 -0.23201303 0.06933632 346.80791541
Axis -0.18723720 -0.98107276 0.04938084
Axis point 98.09102335 0.00000000 508.14746819
Rotation angle (degrees) 86.15477995
Shift along axis -626.45360537
> select clear
> select add #8
719 atoms, 730 bonds, 92 residues, 1 model selected
> view matrix models
> #8,-0.77372,-0.60337,0.19312,714.68,0.04222,0.25504,0.96601,526.29,-0.63212,0.75557,-0.17186,344.46
> fitmap sel inMap #6
Fit molecule
GeneID_79676141_protein_hypotheticalprotein_42742_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#8) to map volume difference (#6) using 719 atoms
average map value = 0.01393, steps = 84
shifted from previous position = 3.68
rotated from previous position = 24.2 degrees
atoms outside contour = 503, contour level = 0.017597
Position of
GeneID_79676141_protein_hypotheticalprotein_42742_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
(#8) relative to volume difference (#6) coordinates:
Matrix rotation and translation
-0.88671048 -0.43385266 0.15973864 714.08380376
0.21032377 -0.07085685 0.97506064 525.15759438
-0.41171406 0.89819331 0.15407904 347.48133034
Axis -0.08891121 0.66099019 0.74510856
Axis point 352.37144509 224.72899412 0.00000000
Rotation angle (degrees) 154.38828198
Shift along axis 542.54527507
> select clear
> close #8
> show #7 models
> ui mousemode right zoom
> close #7
> show #12 models
> select add #12
503 atoms, 512 bonds, 62 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,729.17,0,1,0,531.34,0,0,1,362.95
> view matrix models #12,1,0,0,721.38,0,1,0,521.19,0,0,1,352.64
> fitmap sel inMap #6
Fit molecule
GeneID_79676147_protein_hypotheticalprotein_677ae_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
(#12) to map volume difference (#6) using 503 atoms
average map value = 0.01417, steps = 136
shifted from previous position = 7.51
rotated from previous position = 28.1 degrees
atoms outside contour = 340, contour level = 0.017597
Position of
GeneID_79676147_protein_hypotheticalprotein_677ae_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
(#12) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.93952264 -0.27272393 -0.20716869 715.18078701
0.32690897 0.89447380 0.30503629 526.83229533
0.10211627 -0.35431381 0.92953429 353.93129647
Axis -0.69892567 -0.32784890 0.63562411
Axis point 0.00000000 1917.78062857 -582.57655205
Rotation angle (degrees) 28.14394282
Shift along axis -447.61232791
> select clear
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> select add #12
503 atoms, 512 bonds, 62 residues, 1 model selected
> view matrix models
> #12,0.93952,-0.27272,-0.20717,710.4,0.32691,0.89447,0.30504,532.96,0.10212,-0.35431,0.92953,349.9
> fitmap sel inMap #6
Fit molecule
GeneID_79676147_protein_hypotheticalprotein_677ae_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
(#12) to map volume difference (#6) using 503 atoms
average map value = 0.01346, steps = 156
shifted from previous position = 5.32
rotated from previous position = 19.3 degrees
atoms outside contour = 360, contour level = 0.017597
Position of
GeneID_79676147_protein_hypotheticalprotein_677ae_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
(#12) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.78666227 -0.55668612 -0.26695137 713.07518880
0.61645733 0.73193449 0.29026242 530.83476208
0.03380585 -0.39290262 0.91895848 353.01752335
Axis -0.49131594 -0.21629739 0.84369668
Axis point -265.37855732 1234.95384019 -0.00000000
Rotation angle (degrees) 44.04634932
Shift along axis -167.32366675
> view matrix models
> #12,0.78666,-0.55669,-0.26695,711.89,0.61646,0.73193,0.29026,532.81,0.033806,-0.3929,0.91896,351.79
> view matrix models
> #12,0.78666,-0.55669,-0.26695,710.28,0.61646,0.73193,0.29026,531.56,0.033806,-0.3929,0.91896,352.6
> fitmap sel inMap #6
Fit molecule
GeneID_79676147_protein_hypotheticalprotein_677ae_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
(#12) to map volume difference (#6) using 503 atoms
average map value = 0.01346, steps = 72
shifted from previous position = 2.93
rotated from previous position = 0.0872 degrees
atoms outside contour = 360, contour level = 0.017597
Position of
GeneID_79676147_protein_hypotheticalprotein_677ae_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
(#12) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.78672247 -0.55726234 -0.26556813 713.09278537
0.61645247 0.73184255 0.29050443 530.84790541
0.03246687 -0.39225649 0.91928273 352.99101293
Axis -0.49113215 -0.21438627 0.84429126
Axis point -266.09963667 1235.17569422 0.00000000
Rotation angle (degrees) 44.03429469
Shift along axis -166.00207177
> select clear
> ui mousemode right zoom
> close #12
> show #13 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #13 models
> show #13 models
> ui mousemode right "translate selected models"
> select add #13
708 atoms, 726 bonds, 83 residues, 1 model selected
> view matrix models #13,1,0,0,714.62,0,1,0,482.12,0,0,1,299.67
> fitmap sel inMap #6
Fit molecule
GeneID_79676148_protein_hypotheticalprotein_306cc_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#13) to map volume difference (#6) using 708 atoms
average map value = 0.009929, steps = 112
shifted from previous position = 9.87
rotated from previous position = 34.6 degrees
atoms outside contour = 603, contour level = 0.017597
Position of
GeneID_79676148_protein_hypotheticalprotein_306cc_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
(#13) relative to volume difference (#6) coordinates:
Matrix rotation and translation
0.99899872 0.02288778 -0.03844088 706.68655676
0.00290344 0.82425200 0.56621569 476.18272680
0.04464439 -0.56576036 0.82336025 300.84821245
Axis -0.99716262 -0.07319017 -0.01760429
Axis point 0.00000000 675.62097239 -535.00724565
Rotation angle (degrees) 34.58293217
Shift along axis -744.82953211
> select clear
> ui mousemode right zoom
> close #13
> show #14 models
> close #14
> show #15 models
> close #15
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676151_protein_hypotheticalprotein_9d7cf/GeneID_79676151_protein_hypotheticalprotein_9d7cf_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
GeneID_79676151_protein_hypotheticalprotein_9d7cf_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#7
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676153_protein_hypotheticalprotein_f276c/GeneID_79676153_protein_hypotheticalprotein_f276c_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
GeneID_79676153_protein_hypotheticalprotein_f276c_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
#8
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676154_protein_hypotheticalprotein_16e8e/GeneID_79676154_protein_hypotheticalprotein_16e8e_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
GeneID_79676154_protein_hypotheticalprotein_16e8e_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#10
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676155_protein_hypotheticalprotein_8d028/GeneID_79676155_protein_hypotheticalprotein_8d028_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
GeneID_79676155_protein_hypotheticalprotein_8d028_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
#11
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676157_protein_hypotheticalprotein_9e6cc/GeneID_79676157_protein_hypotheticalprotein_9e6cc_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
GeneID_79676157_protein_hypotheticalprotein_9e6cc_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
#12
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676158_protein_hypotheticalprotein_2332e/GeneID_79676158_protein_hypotheticalprotein_2332e_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
GeneID_79676158_protein_hypotheticalprotein_2332e_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#13
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676159_protein_hypotheticalprotein_41355/GeneID_79676159_protein_hypotheticalprotein_41355_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
Chain information for
GeneID_79676159_protein_hypotheticalprotein_41355_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
#14
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676160_protein_hypotheticalprotein_ef41f/GeneID_79676160_protein_hypotheticalprotein_ef41f_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
GeneID_79676160_protein_hypotheticalprotein_ef41f_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#15
---
Chain | Description
A | No description available
> open "/Users/rosheny/Desktop/Ph_D
> /PHAGE/alphafold/GeneID_79676161_protein_hypotheticalprotein_86754/GeneID_79676161_protein_hypotheticalprotein_86754_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
GeneID_79676161_protein_hypotheticalprotein_86754_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#16
---
Chain | Description
A | No description available
> 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
#17
---
Chain | Description
A | No description available
> 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
#18
---
Chain | Description
A | No description available
> ui mousemode right clip
> ui mousemode right zoom
> select add #8
448 atoms, 458 bonds, 61 residues, 1 model selected
> select add #10
1239 atoms, 1260 bonds, 162 residues, 2 models selected
> select add #11
1998 atoms, 2040 bonds, 251 residues, 3 models selected
> select add #12
2382 atoms, 2428 bonds, 301 residues, 4 models selected
> select add #13
3892 atoms, 3967 bonds, 485 residues, 5 models selected
> select add #15
4139 atoms, 4218 bonds, 518 residues, 6 models selected
> select add #14
4532 atoms, 4620 bonds, 566 residues, 7 models selected
> select add #16
5359 atoms, 5475 bonds, 665 residues, 8 models selected
> select add #17
5751 atoms, 5877 bonds, 720 residues, 9 models selected
> select add #18
8757 atoms, 8947 bonds, 1100 residues, 10 models selected
> select add #7
9631 atoms, 9831 bonds, 1209 residues, 11 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,1,0,0,699.68,0,1,0,397.4,0,0,1,275.18,#8,1,0,0,699.68,0,1,0,397.4,0,0,1,275.18,#10,1,0,0,699.68,0,1,0,397.4,0,0,1,275.18,#11,1,0,0,699.68,0,1,0,397.4,0,0,1,275.18,#12,1,0,0,699.68,0,1,0,397.4,0,0,1,275.18,#13,1,0,0,699.68,0,1,0,397.4,0,0,1,275.18,#14,1,0,0,699.68,0,1,0,397.4,0,0,1,275.18,#15,1,0,0,699.68,0,1,0,397.4,0,0,1,275.18,#16,1,0,0,699.68,0,1,0,397.4,0,0,1,275.18,#17,1,0,0,699.68,0,1,0,397.4,0,0,1,275.18,#18,1,0,0,699.68,0,1,0,397.4,0,0,1,275.18
> view matrix models
> #7,1,0,0,699.99,0,1,0,397.82,0,0,1,277.72,#8,1,0,0,699.99,0,1,0,397.82,0,0,1,277.72,#10,1,0,0,699.99,0,1,0,397.82,0,0,1,277.72,#11,1,0,0,699.99,0,1,0,397.82,0,0,1,277.72,#12,1,0,0,699.99,0,1,0,397.82,0,0,1,277.72,#13,1,0,0,699.99,0,1,0,397.82,0,0,1,277.72,#14,1,0,0,699.99,0,1,0,397.82,0,0,1,277.72,#15,1,0,0,699.99,0,1,0,397.82,0,0,1,277.72,#16,1,0,0,699.99,0,1,0,397.82,0,0,1,277.72,#17,1,0,0,699.99,0,1,0,397.82,0,0,1,277.72,#18,1,0,0,699.99,0,1,0,397.82,0,0,1,277.72
> ui mousemode right zoom
> 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
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