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Opened 9 months ago
Closed 9 months ago
#16785 closed defect (duplicate)
Crash in python_instances_of_class
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001dd3b5ec0 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 162 in copy
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 65 in combine_cmd
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 56)
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"exception" : {"codes":"0x0000000000000001, 0x0000000000000102","rawCodes":[1,258],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000102"},
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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Corndog-Head-
> Cap-C5-2_96A/cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc" format mrc
Opened cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc as #1, grid size
512,512,512, pixel 1.06, shown at level 0.327, step 2, values float32
> volume #1 step 1
> surface dust #1 size 10.6
> transparency 50
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/RealSpaceRefine_50/6mer-coot-3_real_space_refined_050.pdb"
Chain information for 6mer-coot-3_real_space_refined_050.pdb #2
---
Chain | Description
A B D | No description available
C E F | No description available
> hide atoms
> show cartoons
Already setting window visible!
> rename #2 6mer
> select add #2
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> color sel lime
> color sel blue
> set bgColor white
> lighting full
> combine #2
> select subtract #2
Nothing selected
> select add #3
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> turn z 35 models #3
> turn z 45 models #3
> turn z 50 models #3
> turn z 72 models #3
> turn z 72 models #4
> turn z 72 models #5
> turn z 72 models #6
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule 6mer (#2) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc
(#1) using 12123 atoms
average map value = 0.5971, steps = 48
shifted from previous position = 0.0157
rotated from previous position = 0.0136 degrees
atoms outside contour = 1805, contour level = 0.32686
Position of 6mer (#2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999997 0.00012777 -0.00019933 0.01431921
-0.00012777 0.99999999 0.00001581 0.02840818
0.00019933 -0.00001579 0.99999998 -0.06334560
Axis -0.06657835 -0.84001942 -0.53845585
Axis point 292.69790683 0.00000000 74.89958351
Rotation angle (degrees) 0.01359583
Shift along axis 0.00929204
> fitmap #2 inMap #1
Fit molecule 6mer (#2) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc
(#1) using 12123 atoms
average map value = 0.5972, steps = 28
shifted from previous position = 0.00326
rotated from previous position = 0.0216 degrees
atoms outside contour = 1801, contour level = 0.32686
Position of 6mer (#2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 -0.00017114 0.00003000 0.02560880
0.00017114 0.99999999 -0.00000506 -0.04438449
-0.00003000 0.00000506 1.00000000 -0.00932575
Axis 0.02911192 0.17259329 0.98456287
Axis point 243.12539268 152.35316711 0.00000000
Rotation angle (degrees) 0.00995935
Shift along axis -0.01609673
> fitmap #3 inMap #1
Fit molecule copy of 6mer (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5945, steps = 48
shifted from previous position = 1.33
rotated from previous position = 0.774 degrees
atoms outside contour = 1839, contour level = 0.32686
Position of copy of 6mer (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30915180 0.95101277 -0.00001993 -70.66638157
-0.95101276 0.30915180 0.00003992 445.95418284
0.00004414 0.00000663 1.00000014 -0.02330355
Axis -0.00001750 -0.00003369 -1.00000000
Axis point 271.61420743 271.61630794 0.00000000
Rotation angle (degrees) 71.99187589
Shift along axis 0.00951846
> fitmap #3 inMap #1
Fit molecule copy of 6mer (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5946, steps = 40
shifted from previous position = 0.0165
rotated from previous position = 0.000609 degrees
atoms outside contour = 1843, contour level = 0.32686
Position of copy of 6mer (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30915693 0.95101110 -0.00002676 -70.67838872
-0.95101110 0.30915693 0.00003380 445.96138297
0.00004043 0.00001500 1.00000014 -0.01538748
Axis -0.00000988 -0.00003532 -1.00000000
Axis point 271.61489923 271.62844819 0.00000000
Rotation angle (degrees) 71.99156702
Shift along axis 0.00033293
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1845, steps = 68
shifted from previous position = 1.9
rotated from previous position = 4.08 degrees
atoms outside contour = 9219, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.83904555 0.53416467 0.10329921 320.27049241
-0.53829659 -0.84262068 -0.01507429 651.77175810
0.07898989 -0.06825362 0.99453616 0.41877452
Axis -0.04951272 0.02263323 -0.99851701
Axis point 255.20082799 279.18525498 0.00000000
Rotation angle (degrees) 147.51851553
Shift along axis -1.52391618
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1845, steps = 36
shifted from previous position = 0.00241
rotated from previous position = 0.00284 degrees
atoms outside contour = 9218, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.83905269 0.53414683 0.10333348 320.26959548
-0.53827880 -0.84263255 -0.01504611 651.76431077
0.07903532 -0.06824670 0.99453303 0.40410607
Axis -0.04953411 0.02262358 -0.99851617
Axis point 255.19607661 279.18324210 0.00000000
Rotation angle (degrees) 147.51969661
Shift along axis -1.52253500
> fitmap #6 inMap #1
Fit molecule copy of 6mer (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5942, steps = 124
shifted from previous position = 11.3
rotated from previous position = 4.91 degrees
atoms outside contour = 1847, contour level = 0.32686
Position of copy of 6mer (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30905036 -0.95104573 -0.00008262 446.00565706
0.95104573 0.30905037 -0.00013614 -70.61627379
0.00015502 -0.00003651 1.00000012 -0.05068862
Axis 0.00005238 -0.00012494 0.99999999
Axis point 271.60210790 271.64026021 0.00000000
Rotation angle (degrees) 71.99798764
Shift along axis -0.01850394
> fitmap #6 inMap #1
Fit molecule copy of 6mer (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5942, steps = 40
shifted from previous position = 0.0037
rotated from previous position = 0.0107 degrees
atoms outside contour = 1843, contour level = 0.32686
Position of copy of 6mer (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30890998 -0.95109134 -0.00003218 446.04041003
0.95109134 0.30890998 -0.00003344 -70.62404507
0.00004176 -0.00002028 1.00000013 -0.02465661
Axis 0.00000692 -0.00003887 1.00000000
Axis point 271.61728767 271.61265679 0.00000000
Rotation angle (degrees) 72.00644421
Shift along axis -0.01882609
> fitmap #5 inMap #1
Fit molecule copy of 6mer (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1845, steps = 80
shifted from previous position = 3.15
rotated from previous position = 2.7 degrees
atoms outside contour = 9257, contour level = 0.32686
Position of copy of 6mer (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.77566576 -0.62453881 0.09107134 627.14504485
0.61874492 -0.78093067 -0.08545236 342.34719171
0.12448872 -0.00993255 0.99217141 -27.07841160
Axis 0.06060867 -0.02681922 0.99780124
Axis point 254.41705383 280.64821400 0.00000000
Rotation angle (degrees) 141.46359900
Shift along axis 1.81006754
> fitmap #5 inMap #1
Fit molecule copy of 6mer (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1845, steps = 80
shifted from previous position = 0.00327
rotated from previous position = 0.00558 degrees
atoms outside contour = 9258, contour level = 0.32686
Position of copy of 6mer (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.77570814 -0.62449206 0.09103103 627.15651176
0.61870670 -0.78096831 -0.08538505 342.35029741
0.12441463 -0.00991237 0.99218090 -27.06477737
Axis 0.06057514 -0.02679401 0.99780396
Axis point 254.42698435 280.64201567 0.00000000
Rotation angle (degrees) 141.46684213
Shift along axis 1.81181186
> fitmap #3 inMap #1
Fit molecule copy of 6mer (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5945, steps = 40
shifted from previous position = 0.00536
rotated from previous position = 0.0102 degrees
atoms outside contour = 1851, contour level = 0.32686
Position of copy of 6mer (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30902322 0.95105455 -0.00004428 -70.64693142
-0.95105454 0.30902322 0.00014085 445.97327384
0.00014765 -0.00000141 1.00000013 -0.03885636
Axis -0.00007479 -0.00010090 -0.99999999
Axis point 271.59343957 271.60555565 0.00000000
Rotation angle (degrees) 71.99962256
Shift along axis -0.00085939
> fitmap #3 inMap #1
Fit molecule copy of 6mer (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5946, steps = 28
shifted from previous position = 0.00181
rotated from previous position = 0.0153 degrees
atoms outside contour = 1843, contour level = 0.32686
Position of copy of 6mer (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30921944 0.95099077 -0.00001701 -70.69079030
-0.95099077 0.30921944 -0.00002737 445.94865542
-0.00002076 0.00002465 1.00000014 -0.00067896
Axis 0.00002735 0.00000197 -1.00000000
Axis point 271.62115609 271.63398356 0.00000000
Rotation angle (degrees) 71.98780055
Shift along axis -0.00037598
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1845, steps = 44
shifted from previous position = 0.0184
rotated from previous position = 0.0141 degrees
atoms outside contour = 9220, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.83908755 0.53405297 0.10353536 320.27267497
-0.53819131 -0.84269003 -0.01495632 651.73574366
0.07926074 -0.06827149 0.99451338 0.36888032
Axis -0.04964893 0.02260536 -0.99851088
Axis point 255.17638962 279.17705680 0.00000000
Rotation angle (degrees) 147.52567092
Shift along axis -1.53680522
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1845, steps = 48
shifted from previous position = 0.0217
rotated from previous position = 0.0202 degrees
atoms outside contour = 9217, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.83902341 0.53420860 0.10325185 320.26166007
-0.53833679 -0.84259514 -0.01506608 651.77738938
0.07895108 -0.06822507 0.99454120 0.41900852
Axis -0.04948995 0.02262354 -0.99851836
Axis point 255.20578702 279.18513958 0.00000000
Rotation angle (degrees) 147.51570335
Shift along axis -1.52261190
> select subtract #3
Nothing selected
> select add #4
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.8249,-0.30485,0.47604,398.66,0.25362,-0.9522,-0.17029,491.26,0.50519,-0.019743,0.86278,-96.406
> view matrix models
> #4,-0.8249,-0.30485,0.47604,400.82,0.25362,-0.9522,-0.17029,492.1,0.50519,-0.019743,0.86278,-96.23
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1857, steps = 140
shifted from previous position = 3.48
rotated from previous position = 13.7 degrees
atoms outside contour = 9253, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.78811263 -0.13509126 0.60052387 344.90310377
0.17499086 -0.98453613 0.00817667 489.28560070
0.59013282 0.11153032 0.79956510 -133.17191991
Axis 0.31604865 0.03177516 0.94821073
Axis point 173.40702932 261.86722582 0.00000000
Rotation angle (degrees) 170.58936521
Shift along axis -1.72175537
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1857, steps = 56
shifted from previous position = 0.00719
rotated from previous position = 0.00619 degrees
atoms outside contour = 9250, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.78810454 -0.13519819 0.60051042 344.92444175
0.17507491 -0.98452172 0.00811273 489.27598686
0.59011869 0.11152798 0.79957586 -133.16484124
Axis 0.31604317 0.03175775 0.94821314
Axis point 173.40334944 261.87124873 0.00000000
Rotation angle (degrees) 170.58354077
Shift along axis -1.71933199
> view matrix models
> #4,-0.84916,-0.17455,0.49845,383.64,0.29292,-0.94099,0.16949,425.73,0.43945,0.28993,0.85019,-132.62
> view matrix models
> #4,-0.84916,-0.17455,0.49845,391.62,0.29292,-0.94099,0.16949,421.55,0.43945,0.28993,0.85019,-138.3
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.433, steps = 100
shifted from previous position = 0.896
rotated from previous position = 10.2 degrees
atoms outside contour = 4783, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.79668015 -0.17839237 0.57747466 366.68391139
0.23889037 -0.97059110 0.02973840 461.64732773
0.55518663 0.16164511 0.81586688 -140.59358662
Axis 0.30101803 0.05086246 0.95226107
Axis point 178.68220678 255.93029488 0.00000000
Rotation angle (degrees) 167.34376304
Shift along axis -0.02281124
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.433, steps = 48
shifted from previous position = 0.0117
rotated from previous position = 0.00209 degrees
atoms outside contour = 4783, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.79666382 -0.17841445 0.57749036 366.67809608
0.23892108 -0.97058354 0.02973843 461.64720220
0.55519684 0.16166613 0.81585577 -140.59111012
Axis 0.30102687 0.05086838 0.95225796
Axis point 178.67599751 255.93306391 0.00000000
Rotation angle (degrees) 167.34209321
Shift along axis -0.01579567
> view matrix models
> #4,-0.76272,-0.1433,0.63065,343.49,0.20992,-0.9772,0.031836,469.9,0.61171,0.15667,0.77541,-147.82
> view matrix models
> #4,-0.87648,0.44435,0.18532,344.83,-0.43327,-0.89583,0.098814,611.02,0.20992,0.0063149,0.9777,-51.376
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1923, steps = 64
shifted from previous position = 2.73
rotated from previous position = 2.36 degrees
atoms outside contour = 9139, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.88857723 0.42352489 0.17623063 350.34868470
-0.41918584 -0.90570863 0.06304896 615.17705598
0.18631640 -0.01784951 0.98232771 -41.06315246
Axis -0.09555183 -0.01191263 -0.99535317
Axis point 245.78049761 268.74526194 0.00000000
Rotation angle (degrees) 154.95547250
Shift along axis 0.06750275
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1924, steps = 48
shifted from previous position = 0.0185
rotated from previous position = 0.0137 degrees
atoms outside contour = 9150, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.88861110 0.42352189 0.17606697 350.37631805
-0.41921172 -0.90570838 0.06288026 615.22602339
0.18609649 -0.01793325 0.98236787 -41.00530375
Axis -0.09544989 -0.01184599 -0.99536375
Axis point 245.79542345 268.76447049 0.00000000
Rotation angle (degrees) 154.95503024
Shift along axis 0.08384849
> view matrix models
> #4,-0.90982,0.39659,0.12221,369.01,-0.38828,-0.91746,0.086647,605.44,0.14649,0.031381,0.98871,-40.155
> view matrix models
> #4,-0.67295,0.72049,-0.16742,299.7,-0.72102,-0.68947,-0.069004,677.52,-0.16515,0.074278,0.98347,33.672
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2126, steps = 116
shifted from previous position = 2.62
rotated from previous position = 7.3 degrees
atoms outside contour = 8723, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.72738438 0.68373450 -0.05847352 303.18671904
-0.68065906 -0.72969086 -0.06522693 675.71577700
-0.08726549 -0.00764452 0.99615582 26.54152276
Axis 0.04215676 0.02107894 -0.99888863
Axis point 285.64110543 278.24670028 0.00000000
Rotation angle (degrees) 136.92494637
Shift along axis 0.51271658
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2126, steps = 44
shifted from previous position = 0.00398
rotated from previous position = 0.00222 degrees
atoms outside contour = 8722, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.72739948 0.68371585 -0.05850377 303.20023892
-0.68064057 -0.72970857 -0.06522176 675.71163137
-0.08728384 -0.00762224 0.99615439 26.54591763
Axis 0.04217042 0.02107080 -0.99888822
Axis point 285.64249711 278.24402704 0.00000000
Rotation angle (degrees) 136.92638292
Shift along axis 0.50746101
> view matrix models
> #4,-0.65916,0.74763,0.080926,252.5,-0.74478,-0.66392,0.067182,659.9,0.10396,-0.015988,0.99445,-21.004
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5948, steps = 148
shifted from previous position = 4.37
rotated from previous position = 13.8 degrees
atoms outside contour = 1848, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80892382 0.58791353 0.00000798 331.66439831
-0.58791353 -0.80892382 0.00001366 651.03354735
0.00001449 0.00000635 1.00000006 -0.01781274
Axis -0.00000621 -0.00000554 -1.00000000
Axis point 271.62754373 271.62008986 0.00000000
Rotation angle (degrees) 143.99091484
Shift along axis 0.01214789
> fitmap #4 inMap #1
Fit molecule copy of 6mer (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5948, steps = 40
shifted from previous position = 0.0173
rotated from previous position = 0.013 degrees
atoms outside contour = 1846, contour level = 0.32686
Position of copy of 6mer (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80903107 0.58776592 0.00012683 331.68351738
-0.58776591 -0.80903107 0.00007981 650.99887055
0.00014952 -0.00000998 1.00000005 -0.04134824
Axis -0.00007638 -0.00001930 -1.00000000
Axis point 271.59863814 271.61637251 0.00000000
Rotation angle (degrees) 144.00136929
Shift along axis 0.00344610
> select subtract #4
Nothing selected
> select add #5
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> fitmap #5 inMap #1
Fit molecule copy of 6mer (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1845, steps = 64
shifted from previous position = 0.0209
rotated from previous position = 0.00309 degrees
atoms outside contour = 9263, contour level = 0.32686
Position of copy of 6mer (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.77570628 -0.62448702 0.09108137 627.14519666
0.61869888 -0.78097255 -0.08540294 342.36963930
0.12446507 -0.00989566 0.99217474 -27.09508079
Axis 0.06060343 -0.02679433 0.99780223
Axis point 254.41986507 280.64841144 0.00000000
Rotation angle (degrees) 141.46723492
Shift along axis 1.79805337
> fitmap #5 inMap #1
Fit molecule copy of 6mer (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1845, steps = 64
shifted from previous position = 0.0188
rotated from previous position = 0.0124 degrees
atoms outside contour = 9265, contour level = 0.32686
Position of copy of 6mer (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.77583641 -0.62432215 0.09110332 627.13874725
0.61854069 -0.78110484 -0.08533892 342.40574618
0.12444021 -0.00985794 0.99217824 -27.09383564
Axis 0.06059814 -0.02676375 0.99780337
Axis point 254.43026255 280.62892825 0.00000000
Rotation angle (degrees) 141.47914352
Shift along axis 1.80506129
> view matrix models
> #5,-0.77584,-0.62432,0.091103,634.38,0.61854,-0.7811,-0.085339,333.02,0.12444,-0.0098579,0.99218,-29.129
> fitmap #5 inMap #1
Fit molecule copy of 6mer (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5943, steps = 100
shifted from previous position = 0.473
rotated from previous position = 7.62 degrees
atoms outside contour = 1841, contour level = 0.32686
Position of copy of 6mer (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80900402 -0.58780317 0.00011232 650.98886699
0.58780316 -0.80900403 -0.00010266 331.71297478
0.00015122 -0.00001704 1.00000009 -0.05292041
Axis 0.00007284 -0.00003309 1.00000000
Axis point 271.60236591 271.62002325 0.00000000
Rotation angle (degrees) 143.99873144
Shift along axis -0.01648193
> lighting simple
> fitmap #5 inMap #1
Fit molecule copy of 6mer (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5943, steps = 40
shifted from previous position = 0.000409
rotated from previous position = 0.00957 degrees
atoms outside contour = 1844, contour level = 0.32686
Position of copy of 6mer (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80908134 -0.58769676 0.00003791 651.00279961
0.58769676 -0.80908134 -0.00003146 331.74214537
0.00004917 -0.00000318 1.00000010 -0.02933098
Axis 0.00002406 -0.00000958 1.00000000
Axis point 271.61665088 271.61320741 0.00000000
Rotation angle (degrees) 144.00626717
Shift along axis -0.01684514
> fitmap #5 inMap #1
Fit molecule copy of 6mer (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5943, steps = 44
shifted from previous position = 0.00454
rotated from previous position = 0.00491 degrees
atoms outside contour = 1845, contour level = 0.32686
Position of copy of 6mer (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80912142 -0.58764157 0.00000591 651.00466277
0.58764157 -0.80912142 0.00000922 331.75523118
-0.00000063 0.00001093 1.00000010 -0.02011609
Axis 0.00000145 0.00000556 1.00000000
Axis point 271.62171079 271.60778038 0.00000000
Rotation angle (degrees) 144.01017531
Shift along axis -0.01732522
> fitmap #6 inMap #1
Fit molecule copy of 6mer (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5942, steps = 28
shifted from previous position = 0.0029
rotated from previous position = 0.0176 degrees
atoms outside contour = 1860, contour level = 0.32686
Position of copy of 6mer (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30913319 -0.95101881 -0.00013085 445.98423656
0.95101879 0.30913321 -0.00020546 -70.61758789
0.00023586 -0.00006093 1.00000010 -0.06834976
Axis 0.00007599 -0.00019280 0.99999998
Axis point 271.59675596 271.65297151 0.00000000
Rotation angle (degrees) 71.99299757
Shift along axis -0.02084419
> fitmap #6 inMap #1
Fit molecule copy of 6mer (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5943, steps = 40
shifted from previous position = 0.0226
rotated from previous position = 0.018 degrees
atoms outside contour = 1835, contour level = 0.32686
Position of copy of 6mer (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30890813 -0.95109194 -0.00002058 446.05338226
0.95109194 0.30890813 -0.00003073 -70.62591827
0.00003559 -0.00001009 1.00000013 -0.01007392
Axis 0.00001085 -0.00002953 1.00000000
Axis point 271.62496293 271.62001930 0.00000000
Rotation angle (degrees) 72.00655559
Shift along axis -0.00314870
> select subtract #5
Nothing selected
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/RealSpaceRefine_49/5mer-coot-4_real_space_refined_049.pdb"
Chain information for 5mer-coot-4_real_space_refined_049.pdb #7
---
Chain | Description
A B C D E | No description available
> hide atoms
> show cartoons
> select add #7
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> fitmap #7 inMap #1
Fit molecule 5mer-coot-4_real_space_refined_049.pdb (#7) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.5737, steps = 40
shifted from previous position = 0.0157
rotated from previous position = 0.00811 degrees
atoms outside contour = 1914, contour level = 0.32686
Position of 5mer-coot-4_real_space_refined_049.pdb (#7) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 -0.00014057 0.00001192 0.03484136
0.00014057 0.99999999 -0.00001249 -0.02981246
-0.00001192 0.00001250 1.00000000 -0.01411241
Axis 0.08822514 0.08414332 0.99254029
Axis point 204.05244399 256.27698605 0.00000000
Rotation angle (degrees) 0.00811469
Shift along axis -0.01344177
> fitmap #7 inMap #1
Fit molecule 5mer-coot-4_real_space_refined_049.pdb (#7) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.5737, steps = 40
shifted from previous position = 0.00163
rotated from previous position = 0.00972 degrees
atoms outside contour = 1911, contour level = 0.32686
Position of 5mer-coot-4_real_space_refined_049.pdb (#7) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00002897 0.00000840 -0.01226715
-0.00002897 1.00000000 -0.00000990 0.01656830
-0.00000840 0.00000990 1.00000000 -0.01401616
Axis 0.31198897 0.26463587 -0.91248602
Axis point 450.04157829 567.26206652 0.00000000
Rotation angle (degrees) 0.00181881
Shift along axis 0.01334690
> rename #7 5mer
> fitmap #7 inMap #1
Fit molecule 5mer (#7) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc
(#1) using 10090 atoms
average map value = 0.5736, steps = 40
shifted from previous position = 0.00354
rotated from previous position = 0.0161 degrees
atoms outside contour = 1912, contour level = 0.32686
Position of 5mer (#7) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999997 -0.00025171 -0.00001032 0.06308315
0.00025171 0.99999997 -0.00001101 -0.06137321
0.00001032 0.00001100 1.00000000 -0.01953280
Axis 0.04364599 -0.04092885 0.99820832
Axis point 246.17096996 253.05485448 0.00000000
Rotation angle (degrees) 0.01444783
Shift along axis -0.01423254
> fitmap #7 inMap #1
Fit molecule 5mer (#7) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc
(#1) using 10090 atoms
average map value = 0.5736, steps = 40
shifted from previous position = 0.00657
rotated from previous position = 0.0211 degrees
atoms outside contour = 1913, contour level = 0.32686
Position of 5mer (#7) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00011655 -0.00001430 -0.04248213
-0.00011655 0.99999999 -0.00001980 0.03756204
0.00001430 0.00001980 1.00000000 -0.02128675
Axis 0.16623805 -0.12009134 -0.97874562
Axis point 331.79083177 377.71365223 0.00000000
Rotation angle (degrees) 0.00682307
Shift along axis 0.00926129
> combine #2
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Fitting/5mer_side-
> coot-1.pdb"
Chain information for 5mer_side-coot-1.pdb #9
---
Chain | Description
A B C D E | No description available
> select add #8
22213 atoms, 22620 bonds, 3083 residues, 2 models selected
> select subtract #7
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> turn y 30 models #8
> turn z 30 models #8
> turn x 30 models #8
> undo
> turn x 72 models #8
> turn x 60 models #8
> turn x 53 models #8
> undo
> turn x 50 models #8
> turn x 45 models #8
> turn x 46 models #8
> view matrix models
> #8,0.99124,-0.0434,0.12475,-16.13,-0.058359,0.70339,0.70841,-89.924,-0.11849,-0.70948,0.69469,308.2
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1413, steps = 88
shifted from previous position = 7.54
rotated from previous position = 3.62 degrees
atoms outside contour = 12106, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99628424 -0.02408367 0.08269029 -11.92743982
-0.03869592 0.73257412 0.67958648 -88.17900799
-0.07694370 -0.68026107 0.72892011 288.21478910
Axis -0.99312352 0.11658386 -0.01067161
Axis point 0.00000000 321.62175670 256.05701271
Rotation angle (degrees) 43.20664438
Shift along axis -1.51054500
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1413, steps = 48
shifted from previous position = 0.0281
rotated from previous position = 0.0178 degrees
atoms outside contour = 12106, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99630369 -0.02416481 0.08243188 -11.89387485
-0.03844945 0.73267056 0.67949649 -88.26414027
-0.07681532 -0.68015432 0.72903327 288.13414509
Axis -0.99315673 0.11632209 -0.01043421
Axis point 0.00000000 321.55860927 256.15477384
Rotation angle (degrees) 43.19705913
Shift along axis -1.46103980
> view matrix models
> #8,0.9963,-0.024165,0.082432,-12.685,-0.038449,0.73267,0.6795,-88.955,-0.076815,-0.68015,0.72903,290.76
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1415, steps = 88
shifted from previous position = 3.08
rotated from previous position = 1.03 degrees
atoms outside contour = 12113, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99486450 -0.02523321 0.09801991 -17.32544397
-0.04903507 0.72703491 0.68484728 -85.12039677
-0.08854479 -0.68613666 0.72206391 294.86958058
Axis -0.99072106 0.13481820 -0.01720006
Axis point 0.00000000 326.63605012 254.60250799
Rotation angle (degrees) 43.78166644
Shift along axis 0.61713042
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1415, steps = 80
shifted from previous position = 0.02
rotated from previous position = 0.00571 degrees
atoms outside contour = 12113, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99486011 -0.02526214 0.09805698 -17.31953801
-0.04903184 0.72709518 0.68478352 -85.13789330
-0.08859586 -0.68607172 0.72211935 294.85344929
Axis -0.99071122 0.13489321 -0.01717827
Axis point 0.00000000 326.65332772 254.62837948
Rotation angle (degrees) 43.77705687
Shift along axis 0.60906627
> view matrix models
> #8,0.48699,-0.70629,0.5138,161.89,0.25059,0.67653,0.69246,-154.97,-0.83668,-0.20847,0.50646,441.31
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1433, steps = 128
shifted from previous position = 5.17
rotated from previous position = 8.22 degrees
atoms outside contour = 12116, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.41706861 -0.65850158 0.62644189 158.86369557
0.18522726 0.73636741 0.65073335 -141.97683141
-0.88980033 -0.15536634 0.42908818 456.38877639
Axis -0.42131675 0.79248046 0.44098404
Axis point 422.16872563 0.00000000 124.57811182
Rotation angle (degrees) 73.06646854
Shift along axis 21.81436619
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1433, steps = 60
shifted from previous position = 0.0187
rotated from previous position = 0.0148 degrees
atoms outside contour = 12117, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.41709078 -0.65832673 0.62661088 158.80681696
0.18505243 0.73651445 0.65061668 -141.92057924
-0.88982632 -0.15541035 0.42901835 456.41647581
Axis -0.42128544 0.79259490 0.44080824
Axis point 422.16009409 0.00000000 124.62063779
Rotation angle (degrees) 73.06349280
Shift along axis 21.80361850
> view matrix models
> #8,-0.09845,-0.73973,0.66567,299.03,0.27735,0.62201,0.73224,-159.41,-0.95571,0.25671,0.14393,449.42
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1418, steps = 80
shifted from previous position = 1.12
rotated from previous position = 3.39 degrees
atoms outside contour = 12116, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.08110395 -0.70725926 0.70228661 283.29345387
0.25462467 0.66652515 0.70065005 -156.25774208
-0.96363293 0.23564498 0.12602784 458.93373670
Axis -0.23496080 0.84176670 0.48602700
Axis point 349.34586246 0.00000000 126.04740788
Rotation angle (degrees) 98.29532626
Shift along axis 24.95876511
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1418, steps = 40
shifted from previous position = 0.00246
rotated from previous position = 0.00239 degrees
atoms outside contour = 12116, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.08114042 -0.70726761 0.70227399 283.30584395
0.25460966 0.66651159 0.70066840 -156.25688763
-0.96363382 0.23565827 0.12599614 458.93625046
Axis -0.23496477 0.84176585 0.48602656
Axis point 349.34427868 0.00000000 126.04831658
Rotation angle (degrees) 98.29769224
Shift along axis 24.95660067
> view matrix models
> #8,-0.70614,-0.49745,0.5039,440.54,0.25009,0.49057,0.83474,-146.85,-0.66244,0.71547,-0.222,356.07
> view matrix models
> #8,-0.70614,-0.49745,0.5039,436.31,0.25009,0.49057,0.83474,-146.57,-0.66244,0.71547,-0.222,357.11
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1412, steps = 80
shifted from previous position = 6.73
rotated from previous position = 4.78 degrees
atoms outside contour = 12114, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.68164733 -0.46139520 0.56786563 420.41480788
0.28285027 0.54960684 0.78608399 -157.62890934
-0.67479822 0.69645300 -0.24413228 365.44937963
Axis -0.06176091 0.85626693 0.51282797
Axis point 292.84400987 0.00000000 123.99133478
Rotation angle (degrees) 133.47882015
Shift along axis 26.47504006
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1412, steps = 36
shifted from previous position = 0.0031
rotated from previous position = 0.0066 degrees
atoms outside contour = 12114, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.68160212 -0.46148970 0.56784311 420.42515028
0.28284004 0.54955116 0.78612660 -157.62171340
-0.67484817 0.69643433 -0.24404748 365.45205721
Axis -0.06180014 0.85624424 0.51286113
Axis point 292.85392094 0.00000000 123.98158492
Rotation angle (degrees) 133.47588557
Shift along axis 26.48113838
> view matrix models
> #8,-0.6816,-0.46149,0.56784,416.95,0.28284,0.54955,0.78613,-181.71,-0.67485,0.69643,-0.24405,356.8
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3977, steps = 128
shifted from previous position = 6.85
rotated from previous position = 9.18 degrees
atoms outside contour = 5040, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.55795149 -0.52566136 0.64216062 377.64021561
0.29883693 0.59462769 0.74640096 -188.37423268
-0.77420063 0.60835684 -0.17468638 385.65818247
Axis -0.08393434 0.86118369 0.50131594
Axis point 297.08427814 0.00000000 132.75774782
Rotation angle (degrees) 124.68087700
Shift along axis -0.58520412
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3977, steps = 44
shifted from previous position = 0.00334
rotated from previous position = 0.00285 degrees
atoms outside contour = 5040, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.55794811 -0.52567126 0.64215545 377.64295482
0.29886944 0.59459372 0.74641501 -188.38018966
-0.77419052 0.60838148 -0.17464537 385.64790260
Axis -0.08392753 0.86117062 0.50133953
Axis point 297.08497470 0.00000000 132.75419739
Rotation angle (degrees) 124.68051384
Shift along axis -0.58158643
> view matrix models
> #8,-0.55711,-0.51936,0.64799,375.43,0.31316,0.5913,0.74317,-190.98,-0.76913,0.61695,-0.16678,381.64
> view matrix models
> #8,-0.94709,-0.15176,0.28281,472.22,0.18742,0.45381,0.87116,-155.89,-0.26055,0.87808,-0.40136,244.16
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.179, steps = 140
shifted from previous position = 1.46
rotated from previous position = 9.47 degrees
atoms outside contour = 9279, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.95902765 0.01294196 0.28301673 448.93388240
0.25749816 0.45643132 0.85168371 -171.39532497
-0.11815525 0.88966452 -0.44106278 211.91852574
Axis 0.08057544 0.85107745 0.51882056
Axis point 247.45222145 0.00000000 126.67805008
Rotation angle (degrees) 166.36800909
Shift along axis 0.25003567
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.179, steps = 28
shifted from previous position = 0.0204
rotated from previous position = 0.0116 degrees
atoms outside contour = 9274, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.95906264 0.01280677 0.28290427 448.97550809
0.25732751 0.45651600 0.85168990 -171.34887768
-0.11824293 0.88962302 -0.44112298 211.96322782
Axis 0.08048167 0.85110311 0.51879301
Axis point 247.46193594 0.00000000 126.68298174
Rotation angle (degrees) 166.36928635
Shift along axis 0.26377869
> view matrix models
> #8,-0.88424,0.43607,-0.16722,430.3,0.046174,0.43792,0.89783,-121.23,0.46474,0.78618,-0.40736,73.937
> view matrix models
> #8,0.1448,0.7594,-0.63431,185.56,-0.25576,0.64801,0.71741,-50.092,0.95583,0.058356,0.28805,-40.927
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.175, steps = 124
shifted from previous position = 6.86
rotated from previous position = 11.1 degrees
atoms outside contour = 9358, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.21307645 0.81987823 -0.53141143 144.60464188
-0.14222739 0.56413655 0.81333961 -80.08230914
0.96662805 -0.09772225 0.23681336 -15.50112032
Axis -0.45554214 -0.74903816 -0.48106464
Axis point 106.56716269 0.00000000 115.65206791
Rotation angle (degrees) 89.59817110
Shift along axis 1.56823941
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.175, steps = 48
shifted from previous position = 0.00205
rotated from previous position = 0.00572 degrees
atoms outside contour = 9360, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.21301396 0.81991603 -0.53137817 144.60887405
-0.14229694 0.56409539 0.81335599 -80.05902779
0.96663159 -0.09764269 0.23683174 -15.52006190
Axis -0.45551041 -0.74902308 -0.48111818
Axis point 106.57540195 0.00000000 115.63726336
Rotation angle (degrees) 89.60061395
Shift along axis 1.56219577
> view matrix models
> #8,0.44663,0.72683,-0.52176,98.648,-0.14344,0.63378,0.7601,-83.007,0.88315,-0.26464,0.38732,10.081
> view matrix models
> #8,0.44663,0.72683,-0.52176,91.499,-0.14344,0.63378,0.7601,-85.118,0.88315,-0.26464,0.38732,18.845
> view matrix models
> #8,0.62038,0.61738,-0.4837,59.158,-0.12795,0.68813,0.71421,-90.939,0.77379,-0.3812,0.5059,47.697
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4932, steps = 92
shifted from previous position = 1.69
rotated from previous position = 8.19 degrees
atoms outside contour = 3218, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.58313780 0.70036211 -0.41163481 44.46613060
-0.12997575 0.58061399 0.80373733 -85.28362687
0.80190810 -0.41518708 0.42960806 58.86867206
Axis -0.63819571 -0.63537810 -0.43474235
Axis point 0.00000000 -2.05265127 104.86657613
Rotation angle (degrees) 72.74169964
Shift along axis 0.21655043
> fitmap #8 inMap #1
Fit molecule copy of 6mer (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4932, steps = 48
shifted from previous position = 0.00974
rotated from previous position = 0.00133 degrees
atoms outside contour = 3220, contour level = 0.32686
Position of copy of 6mer (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.58312615 0.70037850 -0.41162343 44.47407786
-0.12998883 0.58060054 0.80374493 -85.28130468
0.80191446 -0.41517824 0.42960473 58.86622060
Axis -0.63819211 -0.63537254 -0.43475576
Axis point 0.00000000 -2.06165175 104.86317194
Rotation angle (degrees) 72.74255249
Shift along axis 0.20996461
> color sel orange
> select subtract #8
Nothing selected
> select add #7
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> select add #9
20180 atoms, 20550 bonds, 2800 residues, 2 models selected
> select subtract #9
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> color sel orange red
> select subtract #7
Nothing selected
> hide cartoons
> show atoms
> hide atoms
> show cartoons
> hide atoms
> show atoms
> hide #!1 models
> select add #9
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> color sel lime
> select subtract #9
Nothing selected
> view
> view orient
> turn x 90
> turn y 180
> turn y 30
> turn y 15
> show #!1 models
> combine #8
> turn z 72 models #10
> undo
> turn y 72 models #10
> show #!1 models
> turn x 72 models #10
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> turn x 72 models #10
> turn z 72 models #10
> turn z 72 models #11
> turn z 72 models #12
> turn z 72 models #13
> select add #10
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view matrix models
> #10,0.070433,0.76153,0.64429,-109.65,-0.62463,-0.46992,0.62371,347.04,0.77774,-0.44637,0.44258,68.227
> view matrix models
> #10,0.017505,0.78537,0.61878,-94.205,-0.57769,-0.49718,0.64737,336.67,0.81607,-0.3688,0.445,44.965
> view matrix models
> #10,0.017505,0.78537,0.61878,-108.77,-0.57769,-0.49718,0.64737,343.37,0.81607,-0.3688,0.445,44.008
> fitmap #10 inMap #1
Fit molecule copy of copy of 6mer (#10) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1758, steps = 168
shifted from previous position = 11.2
rotated from previous position = 10.3 degrees
atoms outside contour = 9388, contour level = 0.32686
Position of copy of copy of 6mer (#10) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.13880590 0.83030559 0.53974584 -145.44278086
-0.48542925 -0.41800891 0.76787175 283.42757148
0.86318692 -0.36859366 0.34503262 48.56360908
Axis -0.64264280 -0.18289785 -0.74401519
Axis point 21.50971771 193.22277106 0.00000000
Rotation angle (degrees) 117.84525517
Shift along axis 5.49739918
> fitmap #10 inMap #1
Fit molecule copy of copy of 6mer (#10) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1758, steps = 64
shifted from previous position = 0.0071
rotated from previous position = 0.0038 degrees
atoms outside contour = 9390, contour level = 0.32686
Position of copy of copy of 6mer (#10) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.13879628 0.83033939 0.53969631 -145.43708082
-0.48544558 -0.41795970 0.76788822 283.41596005
0.86317928 -0.36857332 0.34507344 48.55069519
Axis -0.64262518 -0.18291715 -0.74402567
Axis point 21.51862224 193.21800669 0.00000000
Rotation angle (degrees) 117.84264988
Shift along axis 5.49692808
> select subtract #10
Nothing selected
> hide #7-13 atoms
> show #7-13 cartoons
> select add #10
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view matrix models
> #10,0.1388,0.83034,0.5397,-152.78,-0.48545,-0.41796,0.76789,310.19,0.86318,-0.36857,0.34507,48.647
> view matrix models
> #10,0.1388,0.83034,0.5397,-155.35,-0.48545,-0.41796,0.76789,319.04,0.86318,-0.36857,0.34507,49.641
> fitmap #10 inMap #1
Fit molecule copy of copy of 6mer (#10) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4943, steps = 104
shifted from previous position = 2.16
rotated from previous position = 10.4 degrees
atoms outside contour = 3189, contour level = 0.32686
Position of copy of copy of 6mer (#10) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.05660718 0.76861752 0.63719916 -138.01612681
-0.59477318 -0.48665003 0.63985673 377.35922485
0.80189824 -0.41520955 0.42960528 58.89230061
Axis -0.60923167 -0.09510293 -0.78726883
Axis point 46.59818554 235.30629068 0.00000000
Rotation angle (degrees) 120.01447493
Shift along axis 1.83175439
> fitmap #10 inMap #1
Fit molecule copy of copy of 6mer (#10) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4943, steps = 48
shifted from previous position = 0.0183
rotated from previous position = 0.0194 degrees
atoms outside contour = 3200, contour level = 0.32686
Position of copy of copy of 6mer (#10) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.05671196 0.76863385 0.63717013 -138.03593608
-0.59502560 -0.48644838 0.63977537 377.40186089
0.80170355 -0.41541556 0.42976946 58.93355276
Axis -0.60920804 -0.09499236 -0.78730046
Axis point 46.62797145 235.34769806 0.00000000
Rotation angle (degrees) 119.99890633
Shift along axis 1.84389454
> select subtract #10
Nothing selected
> select add #11
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view matrix models
> #11,-0.55884,-0.21896,0.79985,256.57,-0.28978,-0.85215,-0.43574,695.47,0.777,-0.47529,0.41277,66.146
> view matrix models
> #11,-0.55884,-0.21896,0.79985,253.59,-0.28978,-0.85215,-0.43574,695.96,0.777,-0.47529,0.41277,80.14
> fitmap #11 inMap #1
Fit molecule copy of copy of 6mer (#11) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4947, steps = 116
shifted from previous position = 12.2
rotated from previous position = 3.85 degrees
atoms outside contour = 3195, contour level = 0.32686
Position of copy of copy of 6mer (#11) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.54811411 -0.22522001 0.80551031 245.56497526
-0.23767249 -0.88142397 -0.40817101 693.86863146
0.80192441 -0.41517195 0.42959233 58.86948033
Axis -0.47532473 0.24346307 -0.84545380
Axis point 107.74363243 354.87327745 0.00000000
Rotation angle (degrees) 179.57804850
Shift along axis 2.43685909
> fitmap #11 inMap #1
Fit molecule copy of copy of 6mer (#11) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4947, steps = 44
shifted from previous position = 0.0187
rotated from previous position = 0.0151 degrees
atoms outside contour = 3189, contour level = 0.32686
Position of copy of copy of 6mer (#11) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.54828959 -0.22508253 0.80542932 245.58633244
-0.23779109 -0.88138617 -0.40818356 693.89140459
0.80176928 -0.41532673 0.42973226 58.92609651
Axis -0.47523194 0.24350084 -0.84549509
Axis point 107.77338878 354.88268105 -0.00000000
Rotation angle (degrees) 179.56939211
Shift along axis 2.43094312
> select subtract #11
Nothing selected
> select add #12
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view matrix models
> #12,-0.43506,-0.88609,-0.15992,681.5,0.41181,-0.037866,-0.91048,421.68,0.80071,-0.46197,0.38137,81.99
> fitmap #12 inMap #1
Fit molecule copy of copy of 6mer (#12) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1734, steps = 88
shifted from previous position = 6.4
rotated from previous position = 3.88 degrees
atoms outside contour = 9453, contour level = 0.32686
Position of copy of copy of 6mer (#12) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.39924658 -0.89228197 -0.21079623 685.61016206
0.45815877 0.00498638 -0.88885639 403.95078872
0.79416169 -0.45145104 0.40681604 78.28540810
Axis 0.25149230 -0.57781457 0.77645473
Axis point 178.72923799 488.15696844 0.00000000
Rotation angle (degrees) 119.58551787
Shift along axis -0.19789645
> fitmap #12 inMap #1
Fit molecule copy of copy of 6mer (#12) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1734, steps = 48
shifted from previous position = 0.0269
rotated from previous position = 0.0192 degrees
atoms outside contour = 9450, contour level = 0.32686
Position of copy of copy of 6mer (#12) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.39947603 -0.89223570 -0.21055727 685.60980733
0.45801205 0.00471464 -0.88893348 404.02584694
0.79413093 -0.45154541 0.40677134 78.30565805
Axis 0.25152721 -0.57776248 0.77648218
Axis point 178.75213410 488.09455536 0.00000000
Rotation angle (degrees) 119.60350291
Shift along axis -0.17850772
> view matrix models
> #12,-0.39948,-0.89224,-0.21056,675.91,0.45801,0.0047146,-0.88893,414.02,0.79413,-0.45155,0.40677,70.157
> fitmap #12 inMap #1
Fit molecule copy of copy of 6mer (#12) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4967, steps = 84
shifted from previous position = 1.49
rotated from previous position = 4.31 degrees
atoms outside contour = 3155, contour level = 0.32686
Position of copy of copy of 6mer (#12) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.39543017 -0.90786006 -0.13937395 665.16617788
0.44797613 -0.05815935 -0.89215183 426.82769165
0.80184315 -0.41521997 0.42969762 58.88190866
Axis 0.27760305 -0.54784502 0.78917829
Axis point 169.11909545 473.55973623 0.00000000
Rotation angle (degrees) 120.79353561
Shift along axis -2.71494052
> fitmap #12 inMap #1
Fit molecule copy of copy of 6mer (#12) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4967, steps = 44
shifted from previous position = 0.00765
rotated from previous position = 0.0125 degrees
atoms outside contour = 3146, contour level = 0.32686
Position of copy of copy of 6mer (#12) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.39557692 -0.90779185 -0.13940179 665.19196834
0.44807448 -0.05826023 -0.89209585 426.81373577
0.80171581 -0.41535494 0.42980479 58.91525322
Axis 0.27750543 -0.54781380 0.78923430
Axis point 169.16234970 473.53179900 0.00000000
Rotation angle (degrees) 120.79821987
Shift along axis -2.72213019
> select subtract #12
Nothing selected
> select add #13
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view matrix models
> #13,0.27072,-0.31791,-0.90865,535.97,0.51056,0.84762,-0.14444,-64.166,0.81611,-0.42482,0.39178,45.598
> view matrix models
> #13,0.27072,-0.31791,-0.90865,538.64,0.51056,0.84762,-0.14444,-61.656,0.81611,-0.42482,0.39178,58.984
> view matrix models
> #13,0.27072,-0.31791,-0.90865,545.1,0.51056,0.84762,-0.14444,-52.844,0.81611,-0.42482,0.39178,63.119
> view matrix models
> #13,0.27072,-0.31791,-0.90865,546.03,0.51056,0.84762,-0.14444,-51.585,0.81611,-0.42482,0.39178,63.722
> fitmap #13 inMap #1
Fit molecule copy of copy of 6mer (#13) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4947, steps = 80
shifted from previous position = 3.86
rotated from previous position = 2.39 degrees
atoms outside contour = 3158, contour level = 0.32686
Position of copy of copy of 6mer (#13) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30397219 -0.33581311 -0.89153265 540.80701902
0.51456722 0.84544038 -0.14300748 -54.74836826
0.80176155 -0.41528322 0.42978881 58.90718049
Axis -0.14223290 -0.88455230 0.44422633
Axis point 229.15542691 0.00000000 427.32908121
Rotation angle (degrees) 73.16594928
Shift along axis -2.32463275
> fitmap #13 inMap #1
Fit molecule copy of copy of 6mer (#13) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4947, steps = 44
shifted from previous position = 0.0141
rotated from previous position = 0.00196 degrees
atoms outside contour = 3165, contour level = 0.32686
Position of copy of copy of 6mer (#13) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30397712 -0.33581739 -0.89152935 540.80653457
0.51459443 0.84542601 -0.14299453 -54.74741845
0.80174221 -0.41530901 0.42979996 58.90279714
Axis -0.14225317 -0.88454071 0.44424291
Axis point 229.15394829 0.00000000 427.33036101
Rotation angle (degrees) 73.16589793
Shift along axis -2.33797306
> show #6 models
> combine #13
> select subtract #13
Nothing selected
> select add #14
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> turn y 32 models #14
> view matrix models
> #14,0.54496,0.1551,-0.82399,304.14,0.28488,0.89003,0.35594,-165.23,0.78858,-0.42872,0.44085,36.105
> undo
> turn x 30 models #14
> view matrix models
> #14,0.35279,0.29709,-0.88728,341.48,0.63561,0.61981,0.46026,-202.11,0.68669,-0.72634,0.029832,265.59
> undo
> turn x 20 models #14
> view matrix models
> #14,0.41397,0.24147,-0.87768,339.3,0.52469,0.7246,0.44683,-196.69,0.74386,-0.64549,0.17326,211.7
> undo
> turn y 35 models #14
> turn x 20 models #14
> turn x 22 models #14
> turn x 23 models #14
> view matrix models
> #14,0.41573,0.29865,-0.85906,322.91,0.53525,0.68331,0.49658,-199.57,0.73531,-0.66625,0.12422,231.72
> turn y 37 models #14
> turn x 22 models #14
> undo
> turn x 23 models #14
> view matrix models
> #14,0.42457,0.32829,-0.84378,313.63,0.51763,0.6766,0.52371,-198.3,0.74283,-0.65912,0.11732,228.47
> undo
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2822, steps = 204
shifted from previous position = 14.2
rotated from previous position = 16.4 degrees
atoms outside contour = 7032, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.50290290 0.24148910 -0.82992271 312.54167989
0.32806076 0.83499992 0.44175931 -175.55267708
0.79966550 -0.49442714 0.34070082 150.44906858
Axis -0.49761281 -0.86617784 0.04601559
Axis point 83.17962619 0.00000000 328.84282297
Rotation angle (degrees) 70.16565819
Shift along axis 3.45809818
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2822, steps = 64
shifted from previous position = 0.0101
rotated from previous position = 0.00598 degrees
atoms outside contour = 7036, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.50283781 0.24152577 -0.82995148 312.54908754
0.32811603 0.83496765 0.44177926 -175.57110208
0.79968376 -0.49446372 0.34060486 150.46441475
Axis -0.49762441 -0.86617074 0.04602376
Axis point 83.19045634 0.00000000 328.83298366
Rotation angle (degrees) 70.17154567
Shift along axis 3.46743390
> view matrix models
> #14,0.80581,-0.55299,-0.21183,269.76,0.51001,0.4663,0.72281,-205.13,-0.30093,-0.69048,0.65778,416.14
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3112, steps = 172
shifted from previous position = 2.06
rotated from previous position = 16.2 degrees
atoms outside contour = 6693, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.84386705 -0.36310195 -0.39502590 258.62589916
0.52089636 0.37785611 0.76543570 -198.73970111
-0.12866817 -0.85169348 0.50799879 422.34817846
Axis -0.86843254 -0.14303973 0.47472577
Axis point 0.00000000 234.05975249 449.07687053
Rotation angle (degrees) 68.60097401
Shift along axis 4.32809200
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3112, steps = 96
shifted from previous position = 0.0143
rotated from previous position = 0.00861 degrees
atoms outside contour = 6698, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.84391093 -0.36305091 -0.39497907 258.60559340
0.52081435 0.37777724 0.76553043 -198.71328677
-0.12871234 -0.85175022 0.50789245 422.37542847
Axis -0.86848806 -0.14298661 0.47464021
Axis point 0.00000000 234.06934827 449.02540829
Rotation angle (degrees) 68.60532219
Shift along axis 4.29382883
> view matrix models
> #14,0.75453,-0.60483,-0.2547,299.99,0.48941,0.26001,0.83239,-181.44,-0.43723,-0.75271,0.49219,487.59
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1637, steps = 76
shifted from previous position = 1.91
rotated from previous position = 4.41 degrees
atoms outside contour = 9631, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.75717830 -0.61740562 -0.21328723 296.78142335
0.49305501 0.32603105 0.80659815 -189.80602917
-0.42845991 -0.71590091 0.55127853 469.79535201
Axis -0.80271454 0.11344654 0.58547353
Axis point 0.00000000 324.78431625 508.84704162
Rotation angle (degrees) 71.50366927
Shift along axis 15.28914045
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1637, steps = 44
shifted from previous position = 0.0267
rotated from previous position = 0.0127 degrees
atoms outside contour = 9642, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.75707472 -0.61747649 -0.21344968 296.83962900
0.49317403 0.32584360 0.80660114 -189.78658289
-0.42850596 -0.71592512 0.55121129 469.80380832
Axis -0.80267818 0.11337800 0.58553665
Axis point 0.00000000 324.72452944 508.84721197
Rotation angle (degrees) 71.51449159
Shift along axis 15.30303503
> view matrix models
> #14,0.18241,-0.97889,0.092165,456.9,0.23999,0.13523,0.96131,-117.18,-0.95349,-0.15323,0.25959,556.61
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2815, steps = 112
shifted from previous position = 2.3
rotated from previous position = 7.31 degrees
atoms outside contour = 7059, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.28432038 -0.95365483 0.09851126 423.76133922
0.29852160 0.18570470 0.93616167 -136.46252861
-0.91106909 -0.23676205 0.33748614 546.07585000
Axis -0.58919705 0.50714446 0.62900822
Axis point 575.13375741 27.93952587 0.00000000
Rotation angle (degrees) 95.52294608
Shift along axis 24.60105030
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2815, steps = 48
shifted from previous position = 0.00526
rotated from previous position = 0.0201 degrees
atoms outside contour = 7057, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.28405138 -0.95372661 0.09859243 423.82795400
0.29834812 0.18564154 0.93622950 -136.42021222
-0.91120981 -0.23652236 0.33727422 546.10039638
Axis -0.58912631 0.50726934 0.62897377
Axis point 575.10690304 27.85831007 0.00000000
Rotation angle (degrees) 95.53860585
Shift along axis 24.59283813
> view matrix models
> #14,-0.57904,-0.8061,0.12216,617.32,-0.11327,0.22792,0.96707,-42.526,-0.80739,0.54613,-0.22328,476.94
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3118, steps = 164
shifted from previous position = 1.26
rotated from previous position = 11.5 degrees
atoms outside contour = 6662, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.52719951 -0.84129578 0.11950778 609.61820528
-0.27988490 0.30471346 0.91039231 -3.96722261
-0.80232489 0.44650999 -0.39611080 518.68348197
Axis -0.39486219 0.78467501 0.47787966
Axis point 410.71272815 0.00000000 134.10667855
Rotation angle (degrees) 144.02744011
Shift along axis 4.04012679
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3118, steps = 84
shifted from previous position = 0.0212
rotated from previous position = 0.0314 degrees
atoms outside contour = 6665, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.52751254 -0.84108432 0.11961482 609.66073955
-0.28006039 0.30509434 0.91021077 -3.94381419
-0.80205786 0.44664825 -0.39649552 518.64650110
Axis -0.39473670 0.78483057 0.47772787
Axis point 410.66447553 0.00000000 134.15641530
Rotation angle (degrees) 144.04289709
Shift along axis 4.02119573
> view matrix models
> #14,-0.87877,-0.34678,-0.32788,688.26,-0.47175,0.52718,0.70678,40.473,-0.072242,0.77577,-0.62686,312.05
> view matrix models
> #14,-0.87877,-0.34678,-0.32788,686.41,-0.47175,0.52718,0.70678,39.558,-0.072242,0.77577,-0.62686,313.11
> view matrix models
> #14,-0.87877,-0.34678,-0.32788,686.54,-0.47175,0.52718,0.70678,39.076,-0.072242,0.77577,-0.62686,313.02
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2814, steps = 256
shifted from previous position = 0.922
rotated from previous position = 13 degrees
atoms outside contour = 7044, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.91223240 -0.13232002 -0.38771586 668.63652794
-0.39048521 0.56708848 0.72521168 9.16001601
0.12390910 0.81295886 -0.56898548 246.64048828
Axis 0.15135374 -0.88249387 -0.44530509
Axis point 315.03037979 0.00000000 177.33314031
Rotation angle (degrees) 163.14955717
Shift along axis -16.71328142
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2813, steps = 48
shifted from previous position = 0.0263
rotated from previous position = 0.0252 degrees
atoms outside contour = 7057, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.91232673 -0.13255267 -0.38741432 668.67471463
-0.39039688 0.56694424 0.72537200 9.15041563
0.12349225 0.81302156 -0.56898651 246.73660348
Axis 0.15139210 -0.88245978 -0.44535959
Axis point 315.06936338 0.00000000 177.30852125
Rotation angle (degrees) 163.17325318
Shift along axis -16.72931669
> view matrix models
> #14,-0.87117,-0.042966,-0.48909,659.23,-0.39032,0.66492,0.63682,6.7626,0.29784,0.74568,-0.59603,217.56
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2813, steps = 176
shifted from previous position = 0.286
rotated from previous position = 11 degrees
atoms outside contour = 7057, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.91233697 -0.13252241 -0.38740054 668.66896354
-0.39037047 0.56693511 0.72539334 9.14160922
0.12350003 0.81303286 -0.56896868 246.73049026
Axis 0.15137608 -0.88245719 -0.44537018
Axis point 315.06644174 0.00000000 177.30681514
Rotation angle (degrees) 163.17340581
Shift along axis -16.73299339
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2814, steps = 44
shifted from previous position = 0.00767
rotated from previous position = 0.0251 degrees
atoms outside contour = 7060, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.91217120 -0.13250054 -0.38779818 668.67868323
-0.39067151 0.56695453 0.72521608 9.24083234
0.12377234 0.81302289 -0.56892376 246.65779708
Axis 0.15146611 -0.88245544 -0.44534304
Axis point 315.05829907 0.00000000 177.32363608
Rotation angle (degrees) 163.15064794
Shift along axis -16.71979890
> view matrix models
> #14,-0.65154,0.12185,-0.74877,616.42,-0.27607,0.88126,0.38363,-18.649,0.7066,0.45666,-0.54053,152.26
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1565, steps = 124
shifted from previous position = 1.69
rotated from previous position = 7.87 degrees
atoms outside contour = 9744, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.65186418 0.25466524 -0.71429605 588.32110678
-0.18903137 0.85762474 0.47827500 -53.50926658
0.73439794 0.44679466 -0.51091508 142.48381299
Axis -0.02077301 -0.95595319 -0.29278315
Axis point 260.76736169 0.00000000 220.51220779
Rotation angle (degrees) 130.73619742
Shift along axis -2.78570657
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1565, steps = 80
shifted from previous position = 0.0168
rotated from previous position = 0.0138 degrees
atoms outside contour = 9748, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.65202372 0.25460628 -0.71417145 588.36412183
-0.18909028 0.85756336 0.47836177 -53.49221410
0.73424114 0.44694605 -0.51100802 142.50234954
Axis -0.02073406 -0.95593805 -0.29283536
Axis point 260.79250118 0.00000000 220.49442802
Rotation angle (degrees) 130.74806474
Shift along axis -2.79366426
> view matrix models
> #14,-0.27073,0.25509,-0.92824,524.4,0.11673,0.96584,0.23138,-110.96,0.95555,-0.045714,-0.29126,133.55
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3112, steps = 216
shifted from previous position = 1.27
rotated from previous position = 17.4 degrees
atoms outside contour = 6710, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.43854818 0.38050748 -0.81418037 528.07525760
-0.00619389 0.90464446 0.42612212 -98.97405793
0.89868640 0.19191798 -0.39437330 125.23417607
Axis -0.13220479 -0.96688809 -0.21828723
Axis point 231.72454815 0.00000000 238.93488354
Rotation angle (degrees) 117.65448085
Shift along axis -1.45426508
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3112, steps = 60
shifted from previous position = 0.0137
rotated from previous position = 0.00758 degrees
atoms outside contour = 6702, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.43850479 0.38045576 -0.81422791 528.07953738
-0.00631639 0.90465021 0.42610812 -98.94422127
0.89870672 0.19199338 -0.39429028 125.21658070
Axis -0.13214916 -0.96688860 -0.21831866
Axis point 231.72405202 0.00000000 238.93950202
Rotation angle (degrees) 117.65020679
Shift along axis -1.45434250
> view matrix models
> #14,0.011291,0.2236,-0.97461,464.46,0.40853,0.88859,0.2086,-168.2,0.91268,-0.40051,-0.081315,171.58
> view matrix models
> #14,0.011291,0.2236,-0.97461,463.66,0.40853,0.88859,0.2086,-169.21,0.91268,-0.40051,-0.081315,172.82
> view matrix models
> #14,0.11308,0.13823,-0.98392,453.35,0.51717,0.83737,0.17708,-183.46,0.84838,-0.52888,0.023198,194.16
> view matrix models
> #14,0.11308,0.13823,-0.98392,453.81,0.51717,0.83737,0.17708,-183.01,0.84838,-0.52888,0.023198,194.05
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2822, steps = 260
shifted from previous position = 0.513
rotated from previous position = 25.7 degrees
atoms outside contour = 7038, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.50279769 0.24164906 -0.82993989 312.55088468
0.32797448 0.83500273 0.44181806 -175.53774202
0.79976705 -0.49434423 0.34058276 150.42672909
Axis -0.49757893 -0.86620435 0.04588276
Axis point 83.21122911 0.00000000 328.80352538
Rotation angle (degrees) 70.17237190
Shift along axis 3.43481319
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2822, steps = 76
shifted from previous position = 0.0149
rotated from previous position = 0.00164 degrees
atoms outside contour = 7039, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.50278280 0.24166844 -0.82994327 312.54211291
0.32798124 0.83499313 0.44183118 -175.54627154
0.79977364 -0.49435097 0.34055750 150.42102150
Axis -0.49758475 -0.86620139 0.04587561
Axis point 83.21807756 0.00000000 328.79089034
Rotation angle (degrees) 70.17388686
Shift along axis 3.44289190
> view matrix models
> #14,0.72279,-0.2495,-0.64445,309.17,0.67457,0.45727,0.57953,-223.02,0.1501,-0.85361,0.49882,353.03
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1573, steps = 96
shifted from previous position = 4.36
rotated from previous position = 6.86 degrees
atoms outside contour = 9734, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.79375444 -0.23453320 -0.56120239 279.58899936
0.59004989 0.52086473 0.61688014 -217.27422471
0.14763173 -0.82078874 0.55182498 339.17190107
Axis -0.79756419 -0.39323429 0.45744743
Axis point -0.00000000 152.53341118 459.46743960
Rotation angle (degrees) 64.32778550
Shift along axis 17.60281876
> view matrix models
> #14,0.79375,-0.23453,-0.5612,276.94,0.59005,0.52086,0.61688,-219.87,0.14763,-0.82079,0.55182,339.79
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3112, steps = 272
shifted from previous position = 2.89
rotated from previous position = 16.9 degrees
atoms outside contour = 6697, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.84391665 -0.36297475 -0.39503685 258.59168695
0.52085135 0.37794803 0.76542094 -198.74484093
-0.12852501 -0.85170691 0.50801251 422.29724961
Axis -0.86846021 -0.14312717 0.47464880
Axis point 0.00000000 234.03183345 449.04394253
Rotation angle (degrees) 68.59619739
Shift along axis 4.31207799
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3112, steps = 100
shifted from previous position = 0.014
rotated from previous position = 0.00239 degrees
atoms outside contour = 6690, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.84389584 -0.36299179 -0.39506563 258.61122057
0.52088627 0.37794533 0.76539851 -198.74659171
-0.12852009 -0.85170085 0.50802392 422.30495176
Axis -0.86844269 -0.14314490 0.47467549
Axis point 0.00000000 234.03484977 449.06139322
Rotation angle (degrees) 68.59656942
Shift along axis 4.31834707
> view matrix models
> #14,0.8439,-0.36299,-0.39507,259.75,0.52089,0.37795,0.7654,-197.82,-0.12852,-0.8517,0.50802,421.28
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3112, steps = 72
shifted from previous position = 1.79
rotated from previous position = 0.0144 degrees
atoms outside contour = 6693, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.84397402 -0.36288956 -0.39499253 258.56114111
0.52074606 0.37782203 0.76555478 -198.70728194
-0.12857489 -0.85179911 0.50784528 422.36394318
Axis -0.86853848 -0.14306947 0.47452295
Axis point 0.00000000 234.05299493 448.97840959
Rotation angle (degrees) 68.60345434
Shift along axis 4.28002953
> fitmap #14 inMap #1
Fit molecule copy of copy of copy of 6mer (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3112, steps = 76
shifted from previous position = 0.0139
rotated from previous position = 0.00902 degrees
atoms outside contour = 6697, contour level = 0.32686
Position of copy of copy of copy of 6mer (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.84392467 -0.36295375 -0.39503900 258.59020671
0.52083454 0.37789894 0.76545662 -198.73358494
-0.12854046 -0.85173764 0.50795707 422.31480639
Axis -0.86847823 -0.14311712 0.47461885
Axis point 0.00000000 234.03186989 449.02551493
Rotation angle (degrees) 68.59916655
Shift along axis 4.30078163
> color sel forest green
> rename #14 6mer_side_2
> rename #14 6mer_side_straight
> rename #3 6mer
> rename #4 6mer
> rename #5 6mer
> rename #6 6mer
> select add #8
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select subtract #8
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> rename #8 6mer_side_tilt
> rename #2 6mer_top
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/6mer_side_straight.pdb" models #14 selectedOnly
> true relModel #1
> select subtract #14
Nothing selected
> select add #13
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select subtract #13
Nothing selected
> select add #8
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> fitmap #8 inMap #1
Fit molecule 6mer_side_tilt (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4932, steps = 40
shifted from previous position = 0.0139
rotated from previous position = 0.0177 degrees
atoms outside contour = 3213, contour level = 0.32686
Position of 6mer_side_tilt (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.58336927 0.70019355 -0.41159359 44.42508377
-0.12994578 0.58069351 0.80368472 -85.29749046
0.80174458 -0.41536013 0.42974595 58.92255225
Axis -0.63830539 -0.63531731 -0.43467015
Axis point 0.00000000 -1.96859960 104.93019580
Rotation angle (degrees) 72.72823303
Shift along axis 0.22232726
> fitmap #8 inMap #1
Fit molecule 6mer_side_tilt (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4932, steps = 48
shifted from previous position = 0.0128
rotated from previous position = 0.00279 degrees
atoms outside contour = 3208, contour level = 0.32686
Position of 6mer_side_tilt (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.58339020 0.70019969 -0.41155348 44.42246489
-0.12997849 0.58067730 0.80369115 -85.28719142
0.80172406 -0.41537244 0.42977234 58.91793759
Axis -0.63831844 -0.63528878 -0.43469269
Axis point 0.00000000 -1.96915140 104.92191901
Rotation angle (degrees) 72.72730002
Shift along axis 0.21512065
> select subtract #8
Nothing selected
> fitmap #2 inMap #1
Fit molecule 6mer_top (#2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5971, steps = 40
shifted from previous position = 0.00386
rotated from previous position = 0.0184 degrees
atoms outside contour = 1808, contour level = 0.32686
Position of 6mer_top (#2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 0.00008083 -0.00016755 0.01527051
-0.00008083 1.00000000 0.00002546 0.01862840
0.00016755 -0.00002544 0.99999999 -0.05668812
Axis -0.13554277 -0.89236290 -0.43048415
Axis point 323.67095592 0.00000000 95.72672132
Rotation angle (degrees) 0.01075784
Shift along axis 0.00571024
> select add #8
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/6mer_side_tilt.pdb" models #8 selectedOnly true
> relModel #1
> select subtract #8
Nothing selected
> select add #2
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #6
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select subtract #6
Nothing selected
> combine #6
> hide #!1 models
> turn x 46 models #15
> close #15
> show #6-14 atoms
> show #!1 models
> hide #!1 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> select add #14
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> color sel purple
> select subtract #14
Nothing selected
> hide #11 models
> hide #10 models
> hide #12 models
> undo
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Tail/RealSpaceRefine_53/6mer_side_tilt_real_space_refined_053.pdb"
Chain information for 6mer_side_tilt_real_space_refined_053.pdb #15
---
Chain | Description
A B D | No description available
C E F | No description available
> hide #2-9,12-15 atoms
> show #2-9,12-15 cartoons
> hide #14 models
> hide #13 models
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> show #!1 models
> fitmap #15 inMap #1
Fit molecule 6mer_side_tilt_real_space_refined_053.pdb (#15) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5291, steps = 28
shifted from previous position = 0.021
rotated from previous position = 0.00955 degrees
atoms outside contour = 2529, contour level = 0.32686
Position of 6mer_side_tilt_real_space_refined_053.pdb (#15) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 -0.00011628 0.00010712 -0.01772208
0.00011629 0.99999999 -0.00005287 -0.03031564
-0.00010711 0.00005288 0.99999999 0.03491034
Axis 0.31719168 0.64252999 0.69752752
Axis point 256.55054473 -150.39309088 0.00000000
Rotation angle (degrees) 0.00955160
Shift along axis -0.00074908
> fitmap #15 inMap #1
Fit molecule 6mer_side_tilt_real_space_refined_053.pdb (#15) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5291, steps = 48
shifted from previous position = 0.0292
rotated from previous position = 0.00224 degrees
atoms outside contour = 2524, contour level = 0.32686
Position of 6mer_side_tilt_real_space_refined_053.pdb (#15) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 -0.00013003 0.00014220 -0.02254617
0.00013004 0.99999999 -0.00004254 -0.03109672
-0.00014219 0.00004255 0.99999999 0.01614807
Axis 0.21560343 0.72060208 0.65897481
Axis point 190.61336459 -0.00000000 133.36565652
Rotation angle (degrees) 0.01130625
Shift along axis -0.01662822
> show #7 models
> view #7 clip false
> ui tool show "Show Sequence Viewer"
> sequence chain #2/C #2/E #2/F #3/C #3/E #3/F #4/C #4/E #4/F #5/C #5/E #5/F
> #6/C #6/E #6/F #8/C #8/E #8/F #10/C #10/E #10/F #11/C #11/E #11/F #12/C
> #12/E #12/F #13/C #13/E #13/F #14/C #14/E #14/F #15/C #15/E #15/F
Alignment identifier is 1
> select #2/C,E-F:317 #3/C,E-F:317 #4/C,E-F:317 #5/C,E-F:317 #6/C,E-F:317
> #8/C,E-F:317 #10/C,E-F:317 #11/C,E-F:317 #12/C,E-F:317 #13/C,E-F:317
> #14/C,E-F:317 #15/C,E-F:317
180 atoms, 144 bonds, 36 residues, 12 models selected
> select #2/C,E-F:317-333 #3/C,E-F:317-333 #4/C,E-F:317-333 #5/C,E-F:317-333
> #6/C,E-F:317-333 #8/C,E-F:317-333 #10/C,E-F:317-333 #11/C,E-F:317-333
> #12/C,E-F:317-333 #13/C,E-F:317-333 #14/C,E-F:317-333 #15/C,E-F:317-333
4356 atoms, 4464 bonds, 612 residues, 12 models selected
1 [ID: 1] region 36 chains [188-204] RMSD: 223.913
> select #2/C,E-F:334 #3/C,E-F:334 #4/C,E-F:334 #5/C,E-F:334 #6/C,E-F:334
> #8/C,E-F:334 #10/C,E-F:334 #11/C,E-F:334 #12/C,E-F:334 #13/C,E-F:334
> #14/C,E-F:334 #15/C,E-F:334
396 atoms, 396 bonds, 36 residues, 12 models selected
> select #2/C,E-F:334-342 #3/C,E-F:334-342 #4/C,E-F:334-342 #5/C,E-F:334-342
> #6/C,E-F:334-342 #8/C,E-F:334-342 #10/C,E-F:334-342 #11/C,E-F:334-342
> #12/C,E-F:334-342 #13/C,E-F:334-342 #14/C,E-F:334-342 #15/C,E-F:334-342
2196 atoms, 2196 bonds, 324 residues, 12 models selected
1 [ID: 1] region 36 chains [205-213] RMSD: 216.632
> select #2/C,E-F:350 #3/C,E-F:350 #4/C,E-F:350 #5/C,E-F:350 #6/C,E-F:350
> #8/C,E-F:350 #10/C,E-F:350 #11/C,E-F:350 #12/C,E-F:350 #13/C,E-F:350
> #14/C,E-F:350 #15/C,E-F:350
216 atoms, 180 bonds, 36 residues, 12 models selected
> select #2/C,E-F:350-355 #3/C,E-F:350-355 #4/C,E-F:350-355 #5/C,E-F:350-355
> #6/C,E-F:350-355 #8/C,E-F:350-355 #10/C,E-F:350-355 #11/C,E-F:350-355
> #12/C,E-F:350-355 #13/C,E-F:350-355 #14/C,E-F:350-355 #15/C,E-F:350-355
1224 atoms, 1188 bonds, 216 residues, 12 models selected
1 [ID: 1] region 36 chains [221-226] RMSD: 223.881
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:315-316
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #7/A:315-334
151 atoms, 156 bonds, 20 residues, 1 model selected
> select #7/A:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:320-323
30 atoms, 30 bonds, 4 residues, 1 model selected
> select #7/A:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:320-330
82 atoms, 84 bonds, 11 residues, 1 model selected
> select #7/A:321
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:321-329
65 atoms, 67 bonds, 9 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 5mer_A SES surface #7.1: minimum, -26.16, mean -2.94,
maximum 10.22
To also show corresponding color key, enter the above coulombic command and
add key true
> select #7/A:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:320-330
82 atoms, 84 bonds, 11 residues, 1 model selected
> coulombic sel
Coulombic values for 5mer_A SES surface #7.1: minimum, -26.16, mean -2.94,
maximum 10.22
To also show corresponding color key, enter the above coulombic command and
add key true
> select sequence NPTNAHSTGFE
6724 atoms, 6888 bonds, 902 residues, 14 models selected
> coulombic sel & #12,15#!7
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for copy of copy of 6mer_A SES surface #12.1: minimum,
-16.26, mean -3.03, maximum 11.37
Coulombic values for copy of copy of 6mer_B SES surface #12.2: minimum,
-16.49, mean -3.02, maximum 11.47
Coulombic values for copy of copy of 6mer_C SES surface #12.3: minimum,
-17.56, mean -3.06, maximum 8.24
Coulombic values for copy of copy of 6mer_D SES surface #12.4: minimum,
-18.49, mean -2.99, maximum 12.00
Coulombic values for copy of copy of 6mer_E SES surface #12.5: minimum,
-17.94, mean -3.12, maximum 9.21
Coulombic values for copy of copy of 6mer_F SES surface #12.6: minimum,
-17.72, mean -3.00, maximum 8.52
Coulombic values for 6mer_side_tilt_real_space_refined_053.pdb_A SES surface
#15.1: minimum, -16.54, mean -3.01, maximum 9.13
Coulombic values for 6mer_side_tilt_real_space_refined_053.pdb_B SES surface
#15.2: minimum, -16.53, mean -3.00, maximum 11.32
Coulombic values for 6mer_side_tilt_real_space_refined_053.pdb_C SES surface
#15.3: minimum, -18.46, mean -3.06, maximum 9.04
Coulombic values for 6mer_side_tilt_real_space_refined_053.pdb_D SES surface
#15.4: minimum, -17.60, mean -2.96, maximum 10.67
Coulombic values for 6mer_side_tilt_real_space_refined_053.pdb_E SES surface
#15.5: minimum, -18.88, mean -3.05, maximum 9.19
Coulombic values for 6mer_side_tilt_real_space_refined_053.pdb_F SES surface
#15.6: minimum, -17.41, mean -3.04, maximum 8.47
Coulombic values for 5mer_A SES surface #7.1: minimum, -26.16, mean -2.94,
maximum 10.22
Coulombic values for 5mer_B SES surface #7.2: minimum, -17.53, mean -2.92,
maximum 13.63
Coulombic values for 5mer_C SES surface #7.3: minimum, -21.43, mean -2.91,
maximum 12.24
Coulombic values for 5mer_D SES surface #7.4: minimum, -15.36, mean -2.88,
maximum 11.69
Coulombic values for 5mer_E SES surface #7.5: minimum, -15.67, mean -2.97,
maximum 12.91
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select #7/A:331
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #7/A:331-340
67 atoms, 67 bonds, 10 residues, 1 model selected
> coulombic sel
Coulombic values for 5mer_A SES surface #7.1: minimum, -26.16, mean -2.94,
maximum 10.22
To also show corresponding color key, enter the above coulombic command and
add key true
> select #7/A:319-320
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/A:320-346
188 atoms, 192 bonds, 27 residues, 1 model selected
> coulombic sel
Coulombic values for 5mer_A SES surface #7.1: minimum, -26.16, mean -2.94,
maximum 10.22
To also show corresponding color key, enter the above coulombic command and
add key true
> select #7/A:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:320-322
22 atoms, 22 bonds, 3 residues, 1 model selected
> select #7/A:319-320
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/A:319-330
89 atoms, 91 bonds, 12 residues, 1 model selected
> coulombic sel
Coulombic values for 5mer_A SES surface #7.1: minimum, -26.16, mean -2.94,
maximum 10.22
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> hide #2-6#!7,12,15 surfaces
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/RealSpaceRefine_50/6mer-
> coot-3_real_space_refined_050.pdb"
Chain information for 6mer-coot-3_real_space_refined_050.pdb #16
---
Chain | Description
A B D | No description available
C E F | No description available
> close #16
> open 2u10
Fetching url http://files.rcsb.org/download/2u10.cif failed:
HTTP Error 404: Not Found
> open 7Z46
7z46 title:
Top part (C5) of bacteriophage SU10 capsid [more info...]
Chain information for 7z46 #16
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d | Major head protein | A0A0B4N1Q7_9CAUD 1-352
7z46 mmCIF Assemblies
---
1| author_defined_assembly
> select add #16
80206 atoms, 81725 bonds, 1 pseudobond, 10367 residues, 2 models selected
> select subtract #16
Nothing selected
> hide #!1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #!7 models
> hide #!12 models
> hide #!15 models
> view #16 clip false
> select add #16
80206 atoms, 81725 bonds, 1 pseudobond, 10367 residues, 2 models selected
> ui tool show "Unit Cell"
> hide sel atoms
> show sel cartoons
> select subtract #16
Nothing selected
> hide #!16 cartoons
> show #!16 atoms
> select #16:208@CG2
30 atoms, 30 residues, 1 model selected
> color sel black
> select clear
> select add #16/I:208@CG2
1 atom, 1 residue, 1 model selected
> select add #16/Y:208@CG2
2 atoms, 2 residues, 1 model selected
> select add #16/U:208@CG2
3 atoms, 3 residues, 1 model selected
> select add #16/Q:208@CG2
4 atoms, 4 residues, 1 model selected
> select add #16/M:208@CG2
5 atoms, 5 residues, 1 model selected
> ui tool show Distances
> define centroid sel
Centroid 'centroid' placed at [364.743 487.244 281.1836]
> select clear
> select #!16/M:318@CG
1 atom, 1 residue, 1 model selected
> select add #16.2
2 atoms, 2 residues, 2 models selected
> select add #!16/Y:79@CD1
3 atoms, 3 residues, 2 models selected
> color sel black
> undo
> select #!16/M:318@CG
1 atom, 1 residue, 1 model selected
> select add #!16/M:158@CB
2 atoms, 2 residues, 1 model selected
> define centroid sel
Centroid 'centroid' placed at [410.2235 442.5815 240.104 ]
> select add #!16/Y:76@CG
3 atoms, 3 residues, 1 model selected
> select #!16/Y:76@CG
1 atom, 1 residue, 1 model selected
> select add #!16/Y:143@CD2
2 atoms, 2 residues, 1 model selected
> define centroid sel
Centroid 'centroid' placed at [306.2655 467.7305 282.5425]
> select #16.4
1 atom, 1 residue, 1 model selected
> select add #16.2
2 atoms, 2 residues, 2 models selected
> select add #16.3
3 atoms, 3 residues, 3 models selected
> color (#16.2-4 & sel) black
> select #!16/B:208@CG2
1 atom, 1 residue, 1 model selected
> select add #!16/F:208@CG2
2 atoms, 2 residues, 1 model selected
> select add #!16/E:208@CG2
3 atoms, 3 residues, 1 model selected
> select add #!16/D:208@CG2
4 atoms, 4 residues, 1 model selected
> select add #!16/G:208@CG2
5 atoms, 5 residues, 1 model selected
> select add #!16/C:208@OG1
6 atoms, 6 residues, 1 model selected
> select subtract #!16/C:208@OG1
5 atoms, 5 residues, 1 model selected
> select add #!16/C:208@CG2
6 atoms, 6 residues, 1 model selected
> define centroid sel
Centroid 'centroid' placed at [323.89166667 389.98466667 364.28683333]
> select #16.5
1 atom, 1 residue, 1 model selected
> select #!16/G:103@OH
1 atom, 1 residue, 1 model selected
> select add #16.5
2 atoms, 2 residues, 2 models selected
> select add #!16/F:52@CA
3 atoms, 3 residues, 2 models selected
> select #!16/b:134@NE
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
264 atoms, 266 bonds, 37 residues, 1 model selected
> select up
2676 atoms, 2727 bonds, 346 residues, 1 model selected
> hide sel atoms
> select #!16/X:10@CD2
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
157 atoms, 162 bonds, 19 residues, 1 model selected
> hide sel atoms
> select #!16/L:64@N
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
185 atoms, 186 bonds, 26 residues, 1 model selected
> hide sel atoms
> select add #!16/E:100@CG2
186 atoms, 186 bonds, 27 residues, 1 model selected
> select add #16.5
187 atoms, 186 bonds, 28 residues, 2 models selected
> select add #!16/G:318@OD2
188 atoms, 186 bonds, 29 residues, 2 models selected
Either three or four atoms must be selected!
> select subtract #!16/G:318@OD2
187 atoms, 186 bonds, 28 residues, 2 models selected
> select add #!16/G:318@CG
188 atoms, 186 bonds, 29 residues, 2 models selected
Either three or four atoms must be selected!
> select subtract #!16/E:100@CG2
187 atoms, 186 bonds, 28 residues, 2 models selected
> select add #!16/E:96@CG2
188 atoms, 186 bonds, 29 residues, 2 models selected
> select clear
> select #!16/E:96@CG2
1 atom, 1 residue, 1 model selected
> select add #16.5
2 atoms, 2 residues, 2 models selected
> select add #!16/G:319@CA
3 atoms, 3 residues, 2 models selected
> select add #16
80210 atoms, 81725 bonds, 1 pseudobond, 10371 residues, 6 models selected
> select subtract #16
Nothing selected
> hide #!16 models
> show #!1 models
> view #1 clip false
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #!7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #!12 models
> show #13 models
> show #14 models
> show #!15 models
> hide #!15 models
> show #2-6,8-11,13-14#!7,12 atoms
> select add #14
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select subtract #14
Nothing selected
> hide #2-6,8-11,13-14#!7,12 atoms
> show #2-6,8-11,13-14#!7,12 cartoons
> select add #14
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view matrix models
> #14,0.8292,-0.41431,-0.3752,267.88,0.55455,0.5257,0.64507,-213.1,-0.070009,-0.74296,0.66567,363.61
> ui tool show "Fit in Map"
> fitmap #14 inMap #1
Fit molecule 6mer_side_straight (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3112, steps = 160
shifted from previous position = 0.555
rotated from previous position = 11.5 degrees
atoms outside contour = 6699, contour level = 0.32686
Position of 6mer_side_straight (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.84391861 -0.36293054 -0.39507326 258.59165210
0.52084945 0.37787502 0.76545828 -198.73308416
-0.12851979 -0.85175815 0.50792792 422.31742720
Axis -0.86847933 -0.14314483 0.47460849
Axis point 0.00000000 234.01730097 449.01905951
Rotation angle (degrees) 68.60098583
Shift along axis 4.30154691
> fitmap #14 inMap #1
Fit molecule 6mer_side_straight (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.3112, steps = 124
shifted from previous position = 0.00453
rotated from previous position = 0.0105 degrees
atoms outside contour = 6704, contour level = 0.32686
Position of 6mer_side_straight (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.84390510 -0.36281194 -0.39521103 258.59379671
0.52090948 0.37786983 0.76541999 -198.74318543
-0.12836511 -0.85181098 0.50787844 422.29153741
Axis -0.86847467 -0.14329983 0.47457023
Axis point 0.00000000 233.95386513 449.00328433
Rotation angle (degrees) 68.60308380
Shift along axis 4.30469176
> view matrix models
> #14,0.666,-0.74563,-0.021749,309.25,0.47732,0.40357,0.78057,-194.29,-0.57324,-0.53024,0.62468,463.8
> fitmap #14 inMap #1
Fit molecule 6mer_side_straight (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1568, steps = 96
shifted from previous position = 6.34
rotated from previous position = 7.71 degrees
atoms outside contour = 9753, contour level = 0.32686
Position of 6mer_side_straight (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.70392843 -0.69938292 -0.12388871 307.18410047
0.47407478 0.33275378 0.81518592 -189.00141434
-0.52890261 -0.63256502 0.56579461 472.98688282
Axis -0.75913828 0.21237186 0.61531071
Axis point 0.00000000 363.79895479 534.23874373
Rotation angle (degrees) 72.46800047
Shift along axis 17.70010237
> fitmap #14 inMap #1
Fit molecule 6mer_side_straight (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.1568, steps = 60
shifted from previous position = 0.0225
rotated from previous position = 0.0149 degrees
atoms outside contour = 9754, contour level = 0.32686
Position of 6mer_side_straight (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.70400454 -0.69934710 -0.12365823 307.12830442
0.47386197 0.33286284 0.81526513 -188.99861916
-0.52899202 -0.63254724 0.56573090 473.01130195
Axis -0.75918576 0.21254387 0.61519272
Axis point 0.00000000 363.87508463 534.18906563
Rotation angle (degrees) 72.46435141
Shift along axis 17.65517366
> view matrix models
> #14,-0.042603,-0.99653,0.071443,518.3,0.11228,0.066279,0.99146,-79.094,-0.99276,0.050262,0.10907,550.21
> fitmap #14 inMap #1
Fit molecule 6mer_side_straight (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2815, steps = 264
shifted from previous position = 4.84
rotated from previous position = 22.4 degrees
atoms outside contour = 7065, contour level = 0.32686
Position of 6mer_side_straight (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.28420717 -0.95367709 0.09862239 423.77270927
0.29840149 0.18574143 0.93619268 -136.44589576
-0.91114376 -0.23664355 0.33736765 546.10185839
Axis -0.58915868 0.50724259 0.62896502
Axis point 575.13811251 27.87664059 0.00000000
Rotation angle (degrees) 95.52855782
Shift along axis 24.59842799
> view matrix models
> #14,0.302,-0.94917,0.08872,420.02,0.28987,0.18009,0.93997,-133.9,-0.90817,-0.25816,0.32952,550.23
> view matrix models
> #14,0.302,-0.94917,0.08872,420.77,0.28987,0.18009,0.93997,-137.18,-0.90817,-0.25816,0.32952,549.24
> fitmap #14 inMap #1
Fit molecule 6mer_side_straight (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2814, steps = 100
shifted from previous position = 3.5
rotated from previous position = 1.34 degrees
atoms outside contour = 7067, contour level = 0.32686
Position of 6mer_side_straight (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.28427539 -0.95364521 0.09873400 423.73189784
0.29848206 0.18589672 0.93613617 -136.48195300
-0.91109608 -0.23665009 0.33749179 546.07179055
Axis -0.58912363 0.50726614 0.62897886
Axis point 575.12793492 27.88638374 -0.00000000
Rotation angle (degrees) 95.51855194
Shift along axis 24.60446235
> fitmap #14 inMap #1
Fit molecule 6mer_side_straight (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2815, steps = 48
shifted from previous position = 0.0147
rotated from previous position = 0.0208 degrees
atoms outside contour = 7063, contour level = 0.32686
Position of 6mer_side_straight (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.28413377 -0.95372094 0.09840968 423.84457096
0.29856852 0.18554932 0.93617752 -136.44435373
-0.91111193 -0.23661756 0.33747181 546.07303556
Axis -0.58914264 0.50712373 0.62907589
Axis point 575.08632819 27.95964885 0.00000000
Rotation angle (degrees) 95.53320166
Shift along axis 24.62230264
> view matrix models
> #14,0.33302,-0.93787,0.097442,408.74,0.17533,0.16313,0.9709,-106.49,-0.92648,-0.30625,0.21876,580.8
> view matrix models
> #14,0.36399,-0.92673,0.093152,399.57,0.18889,0.17138,0.96693,-110.74,-0.91205,-0.33436,0.23743,578.85
> fitmap #14 inMap #1
Fit molecule 6mer_side_straight (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2815, steps = 124
shifted from previous position = 0.306
rotated from previous position = 8.09 degrees
atoms outside contour = 7056, contour level = 0.32686
Position of 6mer_side_straight (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.28412966 -0.95370252 0.09859984 423.79683248
0.29846740 0.18570823 0.93617825 -136.45549361
-0.91114634 -0.23656711 0.33741427 546.08311711
Axis -0.58911487 0.50723415 0.62901287
Axis point 575.10353426 27.88852440 0.00000000
Rotation angle (degrees) 95.53040235
Shift along axis 24.61340433
> fitmap #14 inMap #1
Fit molecule 6mer_side_straight (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2815, steps = 60
shifted from previous position = 0.00103
rotated from previous position = 0.00295 degrees
atoms outside contour = 7059, contour level = 0.32686
Position of 6mer_side_straight (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.28415255 -0.95369508 0.09860585 423.78909796
0.29850450 0.18573209 0.93616169 -136.46546105
-0.91112705 -0.23657839 0.33745846 546.07332495
Axis -0.58910962 0.50722523 0.62902498
Axis point 575.09901736 27.89979417 0.00000000
Rotation angle (degrees) 95.52778505
Shift along axis 24.61680531
> view matrix models
> #14,0.28321,-0.9537,0.10125,423.61,0.19019,0.15933,0.96873,-109.34,-0.94001,-0.2551,0.22651,574.41
> fitmap #14 inMap #1
Fit molecule 6mer_side_straight (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2814, steps = 116
shifted from previous position = 0.323
rotated from previous position = 6.65 degrees
atoms outside contour = 7058, contour level = 0.32686
Position of 6mer_side_straight (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.28419588 -0.95367025 0.09872102 423.75200190
0.29835077 0.18582097 0.93619306 -136.44853289
-0.91116389 -0.23660866 0.33733775 546.11142123
Axis -0.58914025 0.50730130 0.62893494
Axis point 575.14672841 27.84152777 0.00000000
Rotation angle (degrees) 95.52745400
Shift along axis 24.59867467
> fitmap #14 inMap #1
Fit molecule 6mer_side_straight (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2814, steps = 48
shifted from previous position = 0.0263
rotated from previous position = 0.026 degrees
atoms outside contour = 7069, contour level = 0.32686
Position of 6mer_side_straight (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.28443196 -0.95360830 0.09863960 423.71421105
0.29868992 0.18591501 0.93606624 -136.51600512
-0.91097909 -0.23678444 0.33771330 546.04113833
Axis -0.58914467 0.50715021 0.62905264
Axis point 575.12300550 27.98060229 0.00000000
Rotation angle (degrees) 95.50714380
Shift along axis 24.62553178
> view matrix models
> #14,0.28443,-0.95361,0.09864,423.6,0.29869,0.18592,0.93607,-136.69,-0.91098,-0.23678,0.33771,546.06
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule 6mer_top (#2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5971, steps = 44
shifted from previous position = 0.00183
rotated from previous position = 0.000677 degrees
atoms outside contour = 1804, contour level = 0.32686
Position of 6mer_top (#2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 0.00009018 -0.00017454 0.01314345
-0.00009017 1.00000000 0.00002365 0.02083789
0.00017454 -0.00002364 0.99999998 -0.05940197
Axis -0.11949859 -0.88206333 -0.45572401
Axis point 321.75464748 0.00000000 80.14423281
Rotation angle (degrees) 0.01133733
Shift along axis 0.00711995
> fitmap #2 inMap #1
Fit molecule 6mer_top (#2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5971, steps = 28
shifted from previous position = 0.00141
rotated from previous position = 0.0171 degrees
atoms outside contour = 1804, contour level = 0.32686
Position of 6mer_top (#2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 -0.00014435 0.00000979 0.02436976
0.00014435 0.99999999 -0.00000077 -0.03505987
-0.00000979 0.00000077 1.00000000 -0.01741032
Axis 0.00534833 0.06765178 0.99769466
Axis point 233.70926252 169.53914702 0.00000000
Rotation angle (degrees) 0.00828950
Shift along axis -0.01961171
> fitmap #14 inMap #1
Fit molecule 6mer_side_straight (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2815, steps = 48
shifted from previous position = 0.194
rotated from previous position = 0.0303 degrees
atoms outside contour = 7052, contour level = 0.32686
Position of 6mer_side_straight (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.28408640 -0.95372696 0.09848799 423.83172562
0.29844549 0.18557703 0.93621126 -136.43106109
-0.91116701 -0.23657153 0.33735536 546.09050738
Axis -0.58914036 0.50719410 0.62902128
Axis point 575.09808891 27.90042545 0.00000000
Rotation angle (degrees) 95.53711925
Shift along axis 24.60914565
> fitmap #14 inMap #1
Fit molecule 6mer_side_straight (#14) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2815, steps = 44
shifted from previous position = 0.00372
rotated from previous position = 0.00455 degrees
atoms outside contour = 7058, contour level = 0.32686
Position of 6mer_side_straight (#14) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.28402650 -0.95374260 0.09850932 423.84784940
0.29840467 0.18556560 0.93622653 -136.42266224
-0.91119905 -0.23651745 0.33730673 546.09425331
Axis -0.58912431 0.50722388 0.62901231
Axis point 575.09223879 27.88161824 0.00000000
Rotation angle (degrees) 95.54057188
Shift along axis 24.60410099
> select subtract #14
Nothing selected
> select #14/E:196
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 3 residues, 1 model selected
> select up
2023 atoms, 2060 bonds, 281 residues, 1 model selected
> view matrix models
> #14,0.28403,-0.95374,0.098509,424.35,0.2984,0.18557,0.93623,-136.06,-0.9112,-0.23652,0.33731,545.98
> close #15-16
> split #14
Split 6mer_side_straight (#14) into 6 models
Chain information for 6mer_side_straight A #14.1
---
Chain | Description
A | No description available
Chain information for 6mer_side_straight B #14.2
---
Chain | Description
B | No description available
Chain information for 6mer_side_straight C #14.3
---
Chain | Description
C | No description available
Chain information for 6mer_side_straight D #14.4
---
Chain | Description
D | No description available
Chain information for 6mer_side_straight E #14.5
---
Chain | Description
E | No description available
Chain information for 6mer_side_straight F #14.6
---
Chain | Description
F | No description available
> select add #14.1
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> fitmap #14.1 inMap #1
Fit molecule 6mer_side_straight A (#14.1) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4129, steps = 108
shifted from previous position = 4.32
rotated from previous position = 13.6 degrees
atoms outside contour = 764, contour level = 0.32686
Position of 6mer_side_straight A (#14.1) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.35566886 -0.93419934 -0.02777318 422.37904967
0.15964873 0.03144831 0.98667286 -83.39857985
-0.92087570 -0.35536270 0.16032888 596.36132355
Axis -0.68888538 0.45844185 0.56148731
Axis point 0.00000000 440.83631404 519.88792960
Rotation angle (degrees) 103.07797999
Shift along axis 5.64516582
> fitmap #14.1 inMap #1
Fit molecule 6mer_side_straight A (#14.1) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4129, steps = 44
shifted from previous position = 0.00183
rotated from previous position = 0.00755 degrees
atoms outside contour = 764, contour level = 0.32686
Position of 6mer_side_straight A (#14.1) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.35576119 -0.93416443 -0.02776498 422.34683655
0.15972032 0.03150158 0.98665958 -83.42498500
-0.92082762 -0.35544975 0.16041203 596.34729006
Axis -0.68890446 0.45840888 0.56149083
Axis point 0.00000000 440.82237223 519.88355047
Rotation angle (degrees) 103.07125227
Shift along axis 5.64416075
> view matrix models
> #14.1,0.35576,-0.93416,-0.027765,422.37,0.15972,0.031502,0.98666,-83.344,-0.92083,-0.35545,0.16041,596.12
> view matrix models
> #14.1,0.35576,-0.93416,-0.027765,422.03,0.15972,0.031502,0.98666,-83.733,-0.92083,-0.35545,0.16041,595.55
> fitmap #14.1 inMap #1
Fit molecule 6mer_side_straight A (#14.1) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4129, steps = 64
shifted from previous position = 0.917
rotated from previous position = 0.0035 degrees
atoms outside contour = 763, contour level = 0.32686
Position of 6mer_side_straight A (#14.1) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.35572297 -0.93417863 -0.02777678 422.36180201
0.15968632 0.03146896 0.98666612 -83.41130938
-0.92084828 -0.35541531 0.16036973 596.35594680
Axis -0.68889943 0.45841961 0.56148823
Axis point 0.00000000 440.82544842 519.88412851
Rotation angle (degrees) 103.07457959
Shift along axis 5.64466421
> fitmap #14.1 inMap #1
Fit molecule 6mer_side_straight A (#14.1) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4128, steps = 44
shifted from previous position = 0.024
rotated from previous position = 0.00307 degrees
atoms outside contour = 765, contour level = 0.32686
Position of 6mer_side_straight A (#14.1) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.35577237 -0.93415973 -0.02777945 422.35971756
0.15967697 0.03147161 0.98666755 -83.39486506
-0.92083082 -0.35546473 0.16036048 596.34798882
Axis -0.68892201 0.45840693 0.56147087
Axis point 0.00000000 440.82109136 519.85451814
Rotation angle (degrees) 103.07332068
Shift along axis 5.63033430
> view matrix models
> #14.1,0.35577,-0.93416,-0.027779,423.24,0.15968,0.031472,0.98667,-83.932,-0.92083,-0.35546,0.16036,596.27
> fitmap #14.1 inMap #1
Fit molecule 6mer_side_straight A (#14.1) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4128, steps = 64
shifted from previous position = 1.03
rotated from previous position = 0.00359 degrees
atoms outside contour = 763, contour level = 0.32686
Position of 6mer_side_straight A (#14.1) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.35571968 -0.93417978 -0.02778027 422.37660574
0.15965518 0.03145265 0.98667168 -83.38841208
-0.92085495 -0.35541374 0.16033492 596.35310200
Axis -0.68890594 0.45842421 0.56147648
Axis point 0.00000000 440.83096648 519.86540891
Rotation angle (degrees) 103.07617978
Shift along axis 5.63322281
> fitmap #14.1 inMap #1
Fit molecule 6mer_side_straight A (#14.1) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4128, steps = 48
shifted from previous position = 0.00299
rotated from previous position = 0.00568 degrees
atoms outside contour = 765, contour level = 0.32686
Position of 6mer_side_straight A (#14.1) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.35579861 -0.93414995 -0.02777242 422.34947727
0.15969485 0.03149077 0.98666405 -83.40301060
-0.92081758 -0.35548875 0.16038326 596.34468755
Axis -0.68892695 0.45840002 0.56147046
Axis point 0.00000000 440.81851546 519.85336251
Rotation angle (degrees) 103.07131579
Shift along axis 5.63005134
> fitmap #14.2 inMap #1
Fit molecule 6mer_side_straight B (#14.2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.3857, steps = 64
shifted from previous position = 0.54
rotated from previous position = 5.75 degrees
atoms outside contour = 806, contour level = 0.32686
Position of 6mer_side_straight B (#14.2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.33107880 -0.92987112 0.16039520 399.01565764
0.22138268 0.24178253 0.94473857 -129.21761997
-0.91726585 -0.27727414 0.28590637 562.74078962
Axis -0.61253549 0.54017903 0.57706749
Axis point 0.00000000 534.69588404 571.92554687
Rotation angle (degrees) 94.04937721
Shift along axis 10.52751665
> fitmap #14.2 inMap #1
Fit molecule 6mer_side_straight B (#14.2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.3858, steps = 48
shifted from previous position = 0.0206
rotated from previous position = 0.0152 degrees
atoms outside contour = 808, contour level = 0.32686
Position of 6mer_side_straight B (#14.2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.33126353 -0.92983109 0.16024580 398.96839219
0.22151468 0.24172917 0.94472128 -129.24427654
-0.91716729 -0.27745485 0.28604724 562.71931931
Axis -0.61261149 0.54004952 0.57710802
Axis point 0.00000000 534.58145450 571.90764658
Rotation angle (degrees) 94.04155876
Shift along axis 10.53890055
> select subtract #14.1
Nothing selected
> select add #14.2
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> view matrix models
> #14.2,0.33126,-0.92983,0.16025,394.75,0.22151,0.24173,0.94472,-129.04,-0.91717,-0.27745,0.28605,561.02
> fitmap #14.2 inMap #1
Fit molecule 6mer_side_straight B (#14.2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.1884, steps = 72
shifted from previous position = 2.08
rotated from previous position = 2.64 degrees
atoms outside contour = 1550, contour level = 0.32686
Position of 6mer_side_straight B (#14.2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.32355594 -0.93908190 0.11591736 403.89735213
0.23431529 0.19821189 0.95173969 -126.19721944
-0.91673770 -0.28077977 0.28417383 562.85776751
Axis -0.61918129 0.51877533 0.58948001
Axis point 0.00000000 511.45082338 572.31738406
Rotation angle (degrees) 95.56812203
Shift along axis 16.23971551
> fitmap #14.2 inMap #1
Fit molecule 6mer_side_straight B (#14.2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.1884, steps = 44
shifted from previous position = 0.00188
rotated from previous position = 0.00449 degrees
atoms outside contour = 1549, contour level = 0.32686
Position of 6mer_side_straight B (#14.2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.32358859 -0.93907796 0.11585814 403.89474111
0.23429463 0.19815581 0.95175646 -126.18385152
-0.91673145 -0.28083253 0.28414183 562.87135313
Axis -0.61921790 0.51874386 0.58946925
Axis point 0.00000000 511.41105382 572.28918294
Rotation angle (degrees) 95.56971754
Shift along axis 16.23940515
> undo
> volume zone #1 nearAtoms sel & #14.2 range 6.37
> view matrix models
> #14.2,0.33126,-0.92983,0.16025,400.69,0.22151,0.24173,0.94472,-130.5,-0.91717,-0.27745,0.28605,563.18
> fitmap #14.2 inMap #1
Fit molecule 6mer_side_straight B (#14.2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.3858, steps = 52
shifted from previous position = 2.18
rotated from previous position = 0.0136 degrees
atoms outside contour = 808, contour level = 0.32686
Position of 6mer_side_straight B (#14.2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.33123223 -0.92986084 0.16013781 398.99296085
0.22174339 0.24167872 0.94468053 -129.28784692
-0.91712332 -0.27739908 0.28624222 562.66800168
Axis -0.61256066 0.53997119 0.57723526
Axis point 0.00000000 534.56390573 572.01135110
Rotation angle (degrees) 94.03830685
Shift along axis 10.57270758
> fitmap #14.2 inMap #1
Fit molecule 6mer_side_straight B (#14.2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.3858, steps = 48
shifted from previous position = 0.00172
rotated from previous position = 0.0131 degrees
atoms outside contour = 807, contour level = 0.32686
Position of 6mer_side_straight B (#14.2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.33124308 -0.92983445 0.16026857 398.96855137
0.22152873 0.24175008 0.94471264 -129.25189463
-0.91717128 -0.27742538 0.28606303 562.70950033
Axis -0.61259203 0.54006263 0.57711642
Axis point 0.00000000 534.59653830 571.92188961
Rotation angle (degrees) 94.04109194
Shift along axis 10.53981677
> view matrix models
> #14.2,0.33116,-0.93411,0.13329,403.56,0.26749,0.22841,0.9361,-136.69,-0.90486,-0.27435,0.32551,553.63
> fitmap #14.2 inMap #1
Fit molecule 6mer_side_straight B (#14.2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.3858, steps = 52
shifted from previous position = 0.187
rotated from previous position = 2.81 degrees
atoms outside contour = 808, contour level = 0.32686
Position of 6mer_side_straight B (#14.2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.33125893 -0.92983658 0.16022343 398.97523627
0.22154535 0.24171427 0.94471790 -129.24773794
-0.91716154 -0.27744943 0.28607093 562.71530081
Axis -0.61260699 0.54003535 0.57712606
Axis point 0.00000000 534.57784724 571.92182388
Rotation angle (degrees) 94.04143857
Shift along axis 10.54430010
> fitmap #14.2 inMap #1
Fit molecule 6mer_side_straight B (#14.2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.3857, steps = 44
shifted from previous position = 0.0208
rotated from previous position = 0.0189 degrees
atoms outside contour = 805, contour level = 0.32686
Position of 6mer_side_straight B (#14.2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.33107851 -0.92986188 0.16044942 399.00836596
0.22134762 0.24182692 0.94473542 -129.21561152
-0.91727442 -0.27726644 0.28588636 562.74531754
Axis -0.61252953 0.54021004 0.57704479
Axis point 0.00000000 534.72108969 571.91720947
Rotation angle (degrees) 94.04868576
Shift along axis 10.52127875
> select subtract #14.2
Nothing selected
> select add #14.3
2023 atoms, 2060 bonds, 281 residues, 1 model selected
> volume zone #1 nearAtoms sel & #14.3 range 6.37
> surface dust #1 size 10.6
> view matrix models
> #14.3,0.28403,-0.95374,0.098509,425.72,0.2984,0.18557,0.93623,-137.32,-0.9112,-0.23652,0.33731,545.93
> view matrix models
> #14.3,0.28403,-0.95374,0.098509,426.53,0.2984,0.18557,0.93623,-139.65,-0.9112,-0.23652,0.33731,546.46
> fitmap #14.3 inMap #1
Fit molecule 6mer_side_straight C (#14.3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms
average map value = 0.4113, steps = 112
shifted from previous position = 2.19
rotated from previous position = 14 degrees
atoms outside contour = 781, contour level = 0.32686
Position of 6mer_side_straight C (#14.3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.39739666 -0.90274926 0.16468084 375.89620264
0.08305365 0.21410665 0.97327307 -90.94832606
-0.91388079 -0.37309806 0.16006185 597.69957563
Axis -0.67762004 0.54283322 0.49614834
Axis point 0.00000000 500.77776301 493.60755769
Rotation angle (degrees) 96.55848878
Shift along axis -7.53691706
> view matrix models
> #14.3,0.3974,-0.90275,0.16468,376.18,0.083054,0.21411,0.97327,-90.344,-0.91388,-0.3731,0.16006,597.1
> fitmap #14.3 inMap #1
Fit molecule 6mer_side_straight C (#14.3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms
average map value = 0.4113, steps = 48
shifted from previous position = 0.89
rotated from previous position = 0.00989 degrees
atoms outside contour = 782, contour level = 0.32686
Position of 6mer_side_straight C (#14.3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.39726040 -0.90281969 0.16462352 375.95671749
0.08313627 0.21405285 0.97327785 -90.96248998
-0.91393252 -0.37295850 0.16009173 597.67684548
Axis -0.67755849 0.54283544 0.49622997
Axis point -0.00000000 500.79466376 493.66755529
Rotation angle (degrees) 96.56310796
Shift along axis -7.52516388
> fitmap #14.3 inMap #1
Fit molecule 6mer_side_straight C (#14.3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms
average map value = 0.4113, steps = 44
shifted from previous position = 0.0125
rotated from previous position = 0.0193 degrees
atoms outside contour = 781, contour level = 0.32686
Position of 6mer_side_straight C (#14.3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.39744895 -0.90270581 0.16479277 375.85713152
0.08288190 0.21416708 0.97327441 -90.91112949
-0.91387364 -0.37316849 0.15993841 597.73345851
Axis -0.67765659 0.54288629 0.49604034
Axis point 0.00000000 500.79198756 493.53768408
Rotation angle (degrees) 96.55879790
Shift along axis -7.55655627
> select subtract #14.3
Nothing selected
> select add #14.4
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> fitmap #14.4 inMap #1
Fit molecule 6mer_side_straight D (#14.4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.3769, steps = 48
shifted from previous position = 0.813
rotated from previous position = 2.51 degrees
atoms outside contour = 809, contour level = 0.32686
Position of 6mer_side_straight D (#14.4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.26616616 -0.95777595 0.10872392 426.94087277
0.33240484 0.19707406 0.92231714 -143.82724690
-0.90479982 -0.20934920 0.37082374 534.75879502
Axis -0.56779077 0.50851510 0.64732220
Axis point 561.29189950 33.85533584 -0.00000000
Rotation angle (degrees) 94.75918786
Shift along axis 30.60982601
> fitmap #14.4 inMap #1
Fit molecule 6mer_side_straight D (#14.4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.3769, steps = 60
shifted from previous position = 0.00332
rotated from previous position = 0.00437 degrees
atoms outside contour = 809, contour level = 0.32686
Position of 6mer_side_straight D (#14.4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.26610244 -0.95779375 0.10872306 426.95958547
0.33244582 0.19705757 0.92230589 -143.83307363
-0.90480350 -0.20928327 0.37085197 534.74196683
Axis -0.56775328 0.50851762 0.64735310
Axis point 561.26579866 33.86026382 0.00000000
Rotation angle (degrees) 94.76068219
Shift along axis 30.61751254
> select add #14.5
4041 atoms, 4115 bonds, 561 residues, 2 models selected
> select subtract #14.4
2023 atoms, 2060 bonds, 281 residues, 1 model selected
> fitmap #14.5 inMap #1
Fit molecule 6mer_side_straight E (#14.5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms
average map value = 0.3953, steps = 68
shifted from previous position = 1.16
rotated from previous position = 3.59 degrees
atoms outside contour = 773, contour level = 0.32686
Position of 6mer_side_straight E (#14.5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.25589965 -0.96570532 0.04391672 442.13135826
0.31812603 0.12702431 0.93950025 -133.55941310
-0.91285887 -0.22644668 0.33972142 544.69277136
Axis -0.58866131 0.48305524 0.64817860
Axis point 567.17335366 38.04723760 0.00000000
Rotation angle (degrees) 97.97131489
Shift along axis 28.27599838
> fitmap #14.5 inMap #1
Fit molecule 6mer_side_straight E (#14.5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms
average map value = 0.3953, steps = 36
shifted from previous position = 0.00243
rotated from previous position = 0.00894 degrees
atoms outside contour = 771, contour level = 0.32686
Position of 6mer_side_straight E (#14.5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.25578878 -0.96573403 0.04393134 442.16414706
0.31803666 0.12697623 0.93953700 -133.53517040
-0.91292108 -0.22635119 0.33961787 544.71367891
Axis -0.58864259 0.48310300 0.64816001
Axis point 567.17199307 38.01406430 -0.00000000
Rotation angle (degrees) 97.97890850
Shift along axis 28.27373524
> select subtract #14.5
Nothing selected
> select add #14.6
2023 atoms, 2060 bonds, 281 residues, 1 model selected
> fitmap #14.6 inMap #1
Fit molecule 6mer_side_straight F (#14.6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms
average map value = 0.3845, steps = 76
shifted from previous position = 0.667
rotated from previous position = 3.52 degrees
atoms outside contour = 766, contour level = 0.32686
Position of 6mer_side_straight F (#14.6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.28063042 -0.95047514 0.13358023 418.60531308
0.33475862 0.22735762 0.91446445 -148.62971337
-0.89954619 -0.21190936 0.38198315 532.21908788
Axis -0.56404109 0.51734668 0.64359153
Axis point 563.03408564 31.80588201 -0.00000000
Rotation angle (degrees) 93.15368538
Shift along axis 29.52801334
> combine #14
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16U0000PTA/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1 (23B74)
Kernel Version: Darwin 23.1.0
Time since boot: 41 days, 1 hour, 18 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403220040
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 9 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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