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Opened 9 months ago
Closed 9 months ago
#16822 closed defect (duplicate)
Crash in python_instances_of_class
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.1-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: Bus error
Current thread 0x00000001dd3b5ec0 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 162 in copy
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 65 in combine_cmd
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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.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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 57)
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"procLaunch" : "2025-02-10 08:22:02.0095 +0800",
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"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":57986},
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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
> set bgColor white
Already setting window visible!
> volume #1 level 0.3
> 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/5mer_TOP-
> coot-5.pdb"
Chain information for 5mer_TOP-coot-5.pdb #2
---
Chain | Description
A B C D E | No description available
> hide atoms
> show cartoons
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Fitting/6mer_Fit/6mer-
> coot-3.pdb"
Chain information for 6mer-coot-3.pdb #3
---
Chain | Description
A B D | No description available
C E F | No description available
> combine #3
> hide atoms
> show cartoons
> select add #3
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select add #4
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select subtract #4
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #4
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view orient
> turn x 180
> turn z 72 models #4
> turn z 72 models #5
> turn z 72 models #6
> turn z 72 models #7
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule 5mer_TOP-coot-5.pdb (#2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.5746, steps = 40
shifted from previous position = 0.00495
rotated from previous position = 0.00986 degrees
atoms outside contour = 1532, contour level = 0.3
Position of 5mer_TOP-coot-5.pdb (#2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 -0.00016951 -0.00002828 0.04570487
0.00016951 0.99999999 0.00000850 -0.04784961
0.00002828 -0.00000851 1.00000000 -0.00870823
Axis -0.04944154 -0.16438129 0.98515701
Axis point 285.18770002 268.73749466 0.00000000
Rotation angle (degrees) 0.00985854
Shift along axis -0.00297311
> fitmap #2 inMap #1
Fit molecule 5mer_TOP-coot-5.pdb (#2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.5745, steps = 40
shifted from previous position = 0.0041
rotated from previous position = 0.0188 degrees
atoms outside contour = 1524, contour level = 0.3
Position of 5mer_TOP-coot-5.pdb (#2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999988 -0.00049499 -0.00006232 0.13572348
0.00049499 0.99999988 -0.00000474 -0.13133342
0.00006232 0.00000471 1.00000000 -0.02187583
Axis 0.00947410 -0.12491656 0.99212202
Axis point 266.40584156 274.20415002 0.00000000
Rotation angle (degrees) 0.02858604
Shift along axis -0.00401192
> fitmap #4 inMap #1
Fit molecule copy of 6mer-coot-3.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2185, steps = 52
shifted from previous position = 1.27
rotated from previous position = 0.575 degrees
atoms outside contour = 8456, contour level = 0.3
Position of copy of 6mer-coot-3.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30248328 0.95314427 0.00445783 -71.70669631
-0.95312960 0.30250594 -0.00584140 453.30387080
-0.00691622 -0.00248196 0.99997300 1.48002833
Axis 0.00176227 0.00596652 -0.99998065
Axis point 273.86798326 275.65200666 0.00000000
Rotation angle (degrees) 72.39331450
Shift along axis 1.09828182
> fitmap #4 inMap #1
Fit molecule copy of 6mer-coot-3.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2185, steps = 44
shifted from previous position = 0.0239
rotated from previous position = 0.0186 degrees
atoms outside contour = 8461, contour level = 0.3
Position of copy of 6mer-coot-3.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30268705 0.95307852 0.00467760 -71.79305868
-0.95306368 0.30271152 -0.00594691 453.29025008
-0.00708384 -0.00265800 0.99997138 1.55016020
Axis 0.00172539 0.00617016 -0.99997948
Axis point 273.88514483 275.71563968 0.00000000
Rotation angle (degrees) 72.38105954
Shift along axis 1.12287286
> fitmap #3 inMap #1
Fit molecule 6mer-coot-3.pdb (#3) 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 = 0.00571
rotated from previous position = 0.00747 degrees
atoms outside contour = 1491, contour level = 0.3
Position of 6mer-coot-3.pdb (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 -0.00005683 -0.00011434 0.03059448
0.00005683 1.00000000 -0.00002643 -0.01115520
0.00011434 0.00002642 0.99999999 -0.03857003
Axis 0.20264296 -0.87691092 0.43584753
Axis point 334.18880113 0.00000000 269.02654273
Rotation angle (degrees) 0.00747063
Shift along axis -0.00082878
> fitmap #3 inMap #1
Fit molecule 6mer-coot-3.pdb (#3) 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 = 0.00275
rotated from previous position = 0.00159 degrees
atoms outside contour = 1492, contour level = 0.3
Position of 6mer-coot-3.pdb (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 -0.00003765 -0.00013268 0.02952940
0.00003765 1.00000000 -0.00001844 -0.00585603
0.00013268 0.00001843 0.99999999 -0.04400699
Axis 0.13249791 -0.95353864 0.27057046
Axis point 326.78378083 0.00000000 224.95040954
Rotation angle (degrees) 0.00797223
Shift along axis -0.00241046
> view #4 clip false
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.30269,0.95308,0.0046776,-71.017,-0.95306,0.30271,-0.0059469,449.13,-0.0070838,-0.002658,0.99997,0.74756
> fitmap #4 inMap #1
Fit molecule copy of 6mer-coot-3.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5919, steps = 48
shifted from previous position = 1.87
rotated from previous position = 0.587 degrees
atoms outside contour = 1511, contour level = 0.3
Position of copy of 6mer-coot-3.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30916575 0.95100817 -0.00004905 -70.66463434
-0.95100817 0.30916575 0.00008446 445.96029112
0.00009549 0.00002053 1.00000000 -0.03417099
Axis -0.00003361 -0.00007599 -1.00000000
Axis point 271.62400540 271.61890830 0.00000000
Rotation angle (degrees) 71.99103821
Shift along axis 0.00265651
> fitmap #4 inMap #1
Fit molecule copy of 6mer-coot-3.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5918, steps = 28
shifted from previous position = 0.00874
rotated from previous position = 0.0141 degrees
atoms outside contour = 1522, contour level = 0.3
Position of copy of 6mer-coot-3.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30935380 0.95094701 -0.00001621 -70.70134731
-0.95094701 0.30935380 -0.00005817 445.93230452
-0.00005030 0.00003341 1.00000000 -0.00410100
Axis 0.00004815 0.00001793 -1.00000000
Axis point 271.65021559 271.64030393 0.00000000
Rotation angle (degrees) 71.97970811
Shift along axis 0.00869008
> select subtract #4
Nothing selected
> select add #5
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view #5 clip false
> view matrix models
> #5,-0.80902,0.58779,7.1983e-17,331.65,-0.58779,-0.80902,-2.2154e-16,653.29,-7.1983e-17,-2.2154e-16,1,-3.3824
> fitmap #5 inMap #1
Fit molecule copy of 6mer-coot-3.pdb (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2212, steps = 100
shifted from previous position = 6.5
rotated from previous position = 2.59 degrees
atoms outside contour = 8370, contour level = 0.3
Position of copy of 6mer-coot-3.pdb (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.79861927 0.60182174 0.00422494 325.21260348
-0.60116890 -0.79804422 0.04148938 641.93463776
0.02834090 0.03059431 0.99913001 -14.78059410
Axis -0.00905446 -0.02004182 -0.99975814
Axis point 270.05098621 266.71628557 0.00000000
Rotation angle (degrees) 143.01249563
Shift along axis -1.03314423
> fitmap #5 inMap #1
Fit molecule copy of 6mer-coot-3.pdb (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.2212, steps = 36
shifted from previous position = 0.0175
rotated from previous position = 0.0104 degrees
atoms outside contour = 8367, contour level = 0.3
Position of copy of 6mer-coot-3.pdb (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.79858281 0.60187043 0.00418166 325.20023301
-0.60122357 -0.79801165 0.04132344 641.95488587
0.02820838 0.03048608 0.99913707 -14.73933063
Axis -0.00900575 -0.01996598 -0.99976010
Axis point 270.05880881 266.72185157 0.00000000
Rotation angle (degrees) 143.00887229
Shift along axis -1.01013461
> view matrix models
> #5,-0.79858,0.60187,0.0041817,326.57,-0.60122,-0.79801,0.041323,644.65,0.028208,0.030486,0.99914,-12.49
> fitmap #5 inMap #1
Fit molecule copy of 6mer-coot-3.pdb (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5921, steps = 60
shifted from previous position = 1.57
rotated from previous position = 2.57 degrees
atoms outside contour = 1506, contour level = 0.3
Position of copy of 6mer-coot-3.pdb (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80895617 0.58786895 0.00008586 331.65894423
-0.58786895 -0.80895618 0.00007441 651.01114206
0.00011320 0.00000972 0.99999999 -0.02989363
Axis -0.00005502 -0.00002325 -1.00000000
Axis point 271.61126098 271.61482534 0.00000000
Rotation angle (degrees) 143.99407211
Shift along axis -0.00349167
> fitmap #5 inMap #1
Fit molecule copy of 6mer-coot-3.pdb (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5921, steps = 44
shifted from previous position = 0.00978
rotated from previous position = 0.0147 degrees
atoms outside contour = 1508, contour level = 0.3
Position of copy of 6mer-coot-3.pdb (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80883998 0.58802881 -0.00006016 331.61883628
-0.58802881 -0.80883998 0.00000246 651.04710395
-0.00004721 0.00003736 1.00000000 0.01323287
Axis 0.00002968 -0.00001101 -1.00000000
Axis point 271.63261455 271.62120750 0.00000000
Rotation angle (degrees) 143.98274873
Shift along axis -0.01055792
> select subtract #5
Nothing selected
> select add #6
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view #6 clip false
> view matrix models
> #6,-0.80902,-0.58779,-7.1983e-17,651.89,0.58779,-0.80902,-2.2154e-16,333.35,7.1983e-17,-2.2154e-16,1,-2.5685
> fitmap #6 inMap #1
Fit molecule copy of 6mer-coot-3.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5918, steps = 56
shifted from previous position = 3.17
rotated from previous position = 0.00943 degrees
atoms outside contour = 1506, contour level = 0.3
Position of copy of 6mer-coot-3.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80904523 -0.58774638 0.00012829 650.98869529
0.58774637 -0.80904524 -0.00009120 331.72852030
0.00015740 0.00000161 0.99999999 -0.04945172
Axis 0.00007896 -0.00002476 1.00000000
Axis point 271.60619003 271.61513891 0.00000000
Rotation angle (degrees) 144.00275310
Shift along axis -0.00626316
> fitmap #6 inMap #1
Fit molecule copy of 6mer-coot-3.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5918, steps = 40
shifted from previous position = 0.022
rotated from previous position = 0.0135 degrees
atoms outside contour = 1491, contour level = 0.3
Position of copy of 6mer-coot-3.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80915159 -0.58759995 0.00002427 651.01097365
0.58759995 -0.80915159 0.00001711 331.78233396
0.00000959 0.00002810 1.00000000 -0.00064232
Axis 0.00000936 0.00001250 1.00000000
Axis point 271.62518094 271.61310216 0.00000000
Rotation angle (degrees) 144.01312237
Shift along axis 0.00959453
> select subtract #6
Nothing selected
> select add #7
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view #7 clip false
> view matrix models
> #7,0.30902,-0.95106,-1.1647e-16,447.19,0.95106,0.30902,-8.4621e-17,-70.294,1.1647e-16,-8.4621e-17,1,-1.614
> fitmap #7 inMap #1
Fit molecule copy of 6mer-coot-3.pdb (#7) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5915, steps = 52
shifted from previous position = 2.03
rotated from previous position = 0.00838 degrees
atoms outside contour = 1507, contour level = 0.3
Position of copy of 6mer-coot-3.pdb (#7) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30889570 -0.95109592 -0.00004435 446.05077317
0.95109592 0.30889570 -0.00005639 -70.61719053
0.00006733 -0.00002477 1.00000000 -0.01514902
Axis 0.00001662 -0.00005871 1.00000000
Axis point 271.61698264 271.61835377 0.00000000
Rotation angle (degrees) 72.00730735
Shift along axis -0.00358882
> fitmap #7 inMap #1
Fit molecule copy of 6mer-coot-3.pdb (#7) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5915, steps = 44
shifted from previous position = 0.0127
rotated from previous position = 0.00363 degrees
atoms outside contour = 1510, contour level = 0.3
Position of copy of 6mer-coot-3.pdb (#7) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30894025 -0.95108145 -0.00003705 446.04475647
0.95108144 0.30894025 -0.00009842 -70.61106386
0.00010505 -0.00000483 0.99999999 -0.01985016
Axis 0.00004920 -0.00007470 1.00000000
Axis point 271.61215147 271.63239345 0.00000000
Rotation angle (degrees) 72.00462355
Shift along axis 0.00737139
> rename #2 id #2.1
> rename #3 id #2
> rename #4 id #2
> rename #5 id #2
> rename #6 id #2
> rename #7 id #2
> select add #2
70705 atoms, 72000 bonds, 9815 residues, 7 models selected
> select subtract #2
Nothing selected
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Fitting/5mer_side-
> coot-3.pdb"
Chain information for 5mer_side-coot-3.pdb #3
---
Chain | Description
A B C D E | No description available
> select add #2.2
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select add #2.3
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select add #2.4
36369 atoms, 37035 bonds, 5049 residues, 3 models selected
> select add #2.5
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select add #2.6
60615 atoms, 61725 bonds, 8415 residues, 5 models selected
> color sel yellow
> select subtract #2.2
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select subtract #2.3
36369 atoms, 37035 bonds, 5049 residues, 3 models selected
> select subtract #2.4
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select subtract #2.5
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select subtract #2.6
Nothing selected
> select add #2.1
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> color sel red
> select subtract #2.1
Nothing selected
> combine #3
> view orient
> turn x 180
> turn z 72 models #4
> turn z 72 models #5
> turn z 72 models #6
> turn z 72 models #7
> select add #3
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> select add #4
20180 atoms, 20550 bonds, 2800 residues, 2 models selected
> select add #5
30270 atoms, 30825 bonds, 4200 residues, 3 models selected
> select subtract #5
20180 atoms, 20550 bonds, 2800 residues, 2 models selected
> select subtract #4
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> select subtract #3
Nothing selected
> turn z 72 models #7
> turn z 72 models #6
> turn z 72 models #5
> hide atoms
> show cartoons
> view #3 clip false
> fitmap #3 inMap #1
Fit molecule 5mer_side-coot-3.pdb (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.5473, steps = 44
shifted from previous position = 0.0117
rotated from previous position = 0.0186 degrees
atoms outside contour = 1726, contour level = 0.3
Position of 5mer_side-coot-3.pdb (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00002215 -0.00015301 0.02781714
-0.00002219 0.99999996 -0.00028533 0.06193389
0.00015300 0.00028534 0.99999995 -0.12860248
Axis 0.87923042 -0.47147350 -0.06831255
Axis point 0.00000000 449.77904545 223.67413627
Rotation angle (degrees) 0.01859403
Shift along axis 0.00404265
> fitmap #3 inMap #1
Fit molecule 5mer_side-coot-3.pdb (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.5472, steps = 28
shifted from previous position = 0.00729
rotated from previous position = 0.0167 degrees
atoms outside contour = 1731, contour level = 0.3
Position of 5mer_side-coot-3.pdb (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00013866 -0.00002054 -0.03753810
-0.00013866 0.99999999 -0.00005298 0.02505265
0.00002053 0.00005299 1.00000000 -0.03832388
Axis 0.35358439 -0.13705532 -0.92530747
Axis point 199.18879465 318.56130029 0.00000000
Rotation angle (degrees) 0.00858593
Shift along axis 0.01875489
> select add #4
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> view #4 clip false
> view matrix models
> #4,0.30902,0.95106,1.1647e-16,-71.399,-0.95106,0.30902,-8.4621e-17,447.52,-1.1647e-16,-8.4621e-17,1,-3.2523
> fitmap #4 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.2068, steps = 60
shifted from previous position = 2.48
rotated from previous position = 0.405 degrees
atoms outside contour = 7277, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.31230227 0.94998228 0.00097581 -72.84962326
-0.94996694 0.31229096 0.00609638 443.37861872
0.00548671 -0.00283090 0.99998094 -4.46526791
Axis -0.00469863 -0.00237419 -0.99998614
Axis point 269.83161799 271.99935855 0.00000000
Rotation angle (degrees) 71.80288484
Shift along axis 3.75483522
> fitmap #4 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.2068, steps = 40
shifted from previous position = 0.00993
rotated from previous position = 0.0108 degrees
atoms outside contour = 7274, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.31243725 0.94993776 0.00109783 -72.87342047
-0.94992287 0.31242533 0.00607909 443.33089505
0.00543177 -0.00294219 0.99998092 -4.41103155
Axis -0.00474833 -0.00228116 -0.99998612
Axis point 269.83218637 271.99907544 0.00000000
Rotation angle (degrees) 71.79476277
Shift along axis 3.74569009
> view matrix models
> #4,0.31244,0.94994,0.0010978,-71.488,-0.94992,0.31243,0.0060791,445.25,0.0054318,-0.0029422,0.99998,-1.2928
> fitmap #4 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.5433, steps = 56
shifted from previous position = 2.52
rotated from previous position = 0.413 degrees
atoms outside contour = 1829, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30894669 0.95107936 -0.00001575 -70.64582654
-0.95107936 0.30894669 -0.00001668 446.03336539
-0.00001100 0.00002014 1.00000000 -0.01497848
Axis 0.00001936 -0.00000250 -1.00000000
Axis point 271.60936052 271.63072359 0.00000000
Rotation angle (degrees) 72.00423521
Shift along axis 0.01249650
> fitmap #4 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.5433, steps = 44
shifted from previous position = 0.0109
rotated from previous position = 0.0181 degrees
atoms outside contour = 1818, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30908044 0.95103585 -0.00029432 -70.58437096
-0.95103589 0.30908046 0.00003460 445.97462917
0.00012388 0.00026922 0.99999996 -0.10829380
Axis 0.00012335 -0.00021986 -0.99999997
Axis point 271.64505129 271.56626098 0.00000000
Rotation angle (degrees) 71.99617848
Shift along axis 0.00153335
> select subtract #4
Nothing selected
> select add #5
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> view #5 clip false
> view matrix models
> #5,-0.80902,0.58779,7.1983e-17,330.48,-0.58779,-0.80902,-2.2154e-16,650.48,-7.1983e-17,-2.2154e-16,1,0.48581
> fitmap #5 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.5441, steps = 48
shifted from previous position = 1.43
rotated from previous position = 0.0198 degrees
atoms outside contour = 1776, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80896651 0.58785474 -0.00000886 331.68597169
-0.58785471 -0.80896646 0.00033513 650.93912608
0.00018984 0.00027632 0.99999994 -0.11085507
Axis -0.00005002 -0.00016900 -0.99999998
Axis point 271.60991350 271.57604549 0.00000000
Rotation angle (degrees) 143.99507919
Shift along axis -0.01574870
> fitmap #5 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.5442, steps = 44
shifted from previous position = 0.0105
rotated from previous position = 0.0197 degrees
atoms outside contour = 1781, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80904786 0.58774277 0.00000306 331.72626950
-0.58774277 -0.80904786 0.00002040 651.01415915
0.00001446 0.00001470 1.00000000 -0.00523430
Axis -0.00000484 -0.00000970 -1.00000000
Axis point 271.61734803 271.61969457 0.00000000
Rotation angle (degrees) 144.00300854
Shift along axis -0.00268751
> select subtract #5
Nothing selected
> select add #6
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> view #6 clip false
> view matrix models
> #6,-0.80902,-0.58779,-7.1983e-17,684.94,0.58779,-0.80902,-2.2154e-16,382.22,7.1983e-17,-2.2154e-16,1,-6.1306
> view matrix models
> #6,-0.80902,-0.58779,-7.1983e-17,686.2,0.58779,-0.80902,-2.2154e-16,383.44,7.1983e-17,-2.2154e-16,1,-6.2078
> fitmap #6 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.1401, steps = 56
shifted from previous position = 1.15
rotated from previous position = 1.53 degrees
atoms outside contour = 8571, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.82210615 -0.56920362 -0.01219518 684.88730917
0.56916581 -0.82219537 0.00671256 389.36387799
-0.01384763 -0.00142264 0.99990310 -3.24689355
Axis -0.00714617 0.00145156 0.99997341
Axis point 281.61597640 301.64771083 0.00000000
Rotation angle (degrees) 145.30555247
Shift along axis -7.57594521
> fitmap #6 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.14, steps = 44
shifted from previous position = 0.0091
rotated from previous position = 0.017 degrees
atoms outside contour = 8571, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.82194382 -0.56943956 -0.01212198 684.92676293
0.56940137 -0.82203207 0.00673498 389.28024654
-0.01379982 -0.00136650 0.99990384 -3.27420197
Axis -0.00711360 0.00147325 0.99997361
Axis point 281.61808863 301.66600220 0.00000000
Rotation angle (degrees) 145.28912968
Shift along axis -7.57290576
> view matrix models
> #6,-0.82194,-0.56944,-0.012122,641.92,0.5694,-0.82203,0.006735,359.25,-0.0138,-0.0013665,0.9999,18.711
> view matrix models
> #6,-0.82194,-0.56944,-0.012122,636.61,0.5694,-0.82203,0.006735,355.52,-0.0138,-0.0013665,0.9999,21.459
> view matrix models
> #6,-0.82194,-0.56944,-0.012122,638.09,0.5694,-0.82203,0.006735,356.83,-0.0138,-0.0013665,0.9999,20.635
> fitmap #6 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.1363, steps = 176
shifted from previous position = 4.31
rotated from previous position = 4.56 degrees
atoms outside contour = 10069, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.82234895 -0.56768768 0.03837832 625.61780927
0.56893687 -0.81954557 0.06823416 347.06917970
-0.00728291 0.07794713 0.99693089 -6.60946675
Axis 0.00853825 0.04013882 0.99915763
Axis point 258.71124977 271.35953489 0.00000000
Rotation angle (degrees) 145.33401027
Shift along axis 12.66872999
> fitmap #6 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.1363, steps = 64
shifted from previous position = 0.0113
rotated from previous position = 0.0181 degrees
atoms outside contour = 10069, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.82244034 -0.56754127 0.03858498 625.53733735
0.56880820 -0.81964809 0.06807527 347.16359190
-0.00700942 0.07793530 0.99693378 -6.63439598
Axis 0.00866963 0.04008981 0.99915847
Axis point 258.67301562 271.36527119 0.00000000
Rotation angle (degrees) 145.34363233
Shift along axis 12.71208783
> view matrix models
> #6,-0.82244,-0.56754,0.038585,636.53,0.56881,-0.81965,0.068075,343.84,-0.0070094,0.077935,0.99693,-8.8707
> view matrix models
> #6,-0.82244,-0.56754,0.038585,638.69,0.56881,-0.81965,0.068075,332.74,-0.0070094,0.077935,0.99693,-20.124
> view matrix models
> #6,-0.82244,-0.56754,0.038585,639.63,0.56881,-0.81965,0.068075,323.8,-0.0070094,0.077935,0.99693,-26.047
> fitmap #6 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.5451, steps = 84
shifted from previous position = 2.32
rotated from previous position = 4.66 degrees
atoms outside contour = 1777, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80904595 -0.58774535 0.00023884 650.94578273
0.58774539 -0.80904593 0.00019874 331.67585787
0.00007642 0.00030116 0.99999995 -0.11550121
Axis 0.00008713 0.00013817 0.99999999
Axis point 271.59340445 271.58162342 0.00000000
Rotation angle (degrees) 144.00282413
Shift along axis -0.01295478
> fitmap #6 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.545, steps = 44
shifted from previous position = 0.012
rotated from previous position = 0.00362 degrees
atoms outside contour = 1768, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80903084 -0.58776617 0.00018691 650.96377780
0.58776620 -0.80903082 0.00017364 331.67926666
0.00004916 0.00025034 0.99999997 -0.10489011
Axis 0.00006525 0.00011719 0.99999999
Axis point 271.59948811 271.59087786 0.00000000
Rotation angle (degrees) 144.00135000
Shift along axis -0.02354804
> view #6 clip false
> select subtract #6
Nothing selected
> select add #7
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> view #7 clip false
> view matrix models
> #7,0.30902,-0.95106,-1.1647e-16,456.07,0.95106,0.30902,-8.4621e-17,-63.277,1.1647e-16,-8.4621e-17,1,4.6984
> view matrix models
> #7,0.30902,-0.95106,-1.1647e-16,454.44,0.95106,0.30902,-8.4621e-17,-61.044,1.1647e-16,-8.4621e-17,1,5.3438
> view matrix models
> #7,0.30902,-0.95106,-1.1647e-16,455.63,0.95106,0.30902,-8.4621e-17,-62.455,1.1647e-16,-8.4621e-17,1,5.4122
> fitmap #7 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#7) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.546, steps = 172
shifted from previous position = 13.7
rotated from previous position = 0.00723 degrees
atoms outside contour = 1737, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#7) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30912441 -0.95102161 0.00005389 445.96744065
0.95102161 0.30912441 -0.00001606 -70.67339440
-0.00000139 0.00005622 1.00000000 -0.01270359
Axis 0.00003800 0.00002906 1.00000000
Axis point 271.62628821 271.61051504 0.00000000
Rotation angle (degrees) 71.99352877
Shift along axis 0.00218923
> fitmap #7 inMap #1
Fit molecule copy of 5mer_side-coot-3.pdb (#7) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms
average map value = 0.546, steps = 44
shifted from previous position = 0.0218
rotated from previous position = 0.0172 degrees
atoms outside contour = 1723, contour level = 0.3
Position of copy of 5mer_side-coot-3.pdb (#7) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30899264 -0.95106440 0.00024965 445.95832019
0.95106442 0.30899260 -0.00019515 -70.58645385
0.00010846 0.00029774 0.99999995 -0.12943872
Axis 0.00025912 0.00007423 0.99999996
Axis point 271.55482671 271.60299810 0.00000000
Rotation angle (degrees) 72.00146997
Shift along axis -0.01911988
> select add #6
20180 atoms, 20550 bonds, 2800 residues, 2 models selected
> select add #5
30270 atoms, 30825 bonds, 4200 residues, 3 models selected
> select add #4
40360 atoms, 41100 bonds, 5600 residues, 4 models selected
> select add #3
50450 atoms, 51375 bonds, 7000 residues, 5 models selected
> color sel cyan
> select subtract #3
40360 atoms, 41100 bonds, 5600 residues, 4 models selected
> select subtract #4
30270 atoms, 30825 bonds, 4200 residues, 3 models selected
> select subtract #5
20180 atoms, 20550 bonds, 2800 residues, 2 models selected
> select subtract #6
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> select subtract #7
Nothing selected
> rename #3 id #2
> rename #4 id #2
> rename #5 id #2
> rename #6 id #2
> rename #7 id #2
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/6mer_side_tilt.pdb"
Chain information for 6mer_side_tilt.pdb #3
---
Chain | Description
A B D | No description available
C E F | No description available
> combine #3
> hide atoms
> show cartoons
> view orient
> turn x 180
> turn z 72 models #4
> turn z 72 models #5
> turn z 72 models #6
> turn z 72 models #7
> fitmap #3 inMap #1
Fit molecule 6mer_side_tilt.pdb (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4932, steps = 44
shifted from previous position = 0.0283
rotated from previous position = 0.0168 degrees
atoms outside contour = 2748, contour level = 0.3
Position of 6mer_side_tilt.pdb (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999996 0.00006292 -0.00028620 0.06422893
-0.00006292 1.00000000 0.00001980 0.00341497
0.00028620 -0.00001979 0.99999996 -0.04153750
Axis -0.06739639 -0.97445482 -0.21423241
Axis point 144.23698677 0.00000000 224.69154800
Rotation angle (degrees) 0.01682789
Shift along axis 0.00124215
> fitmap #3 inMap #1
Fit molecule 6mer_side_tilt.pdb (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4932, steps = 44
shifted from previous position = 0.0052
rotated from previous position = 0.00055 degrees
atoms outside contour = 2756, contour level = 0.3
Position of 6mer_side_tilt.pdb (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999996 0.00005646 -0.00028099 0.05940778
-0.00005645 1.00000000 0.00002461 0.00233654
0.00028099 -0.00002460 0.99999996 -0.04233969
Axis -0.08554166 -0.97681294 -0.19626284
Axis point 150.05172261 0.00000000 211.69250221
Rotation angle (degrees) 0.01648147
Shift along axis 0.00094551
> fitmap #4 inMap #1
Fit molecule copy of 6mer_side_tilt.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.206, steps = 124
shifted from previous position = 11.4
rotated from previous position = 0.463 degrees
atoms outside contour = 8610, contour level = 0.3
Position of copy of 6mer_side_tilt.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30210051 0.95327238 0.00265637 -71.92273194
-0.95327126 0.30210667 -0.00233876 452.55592822
-0.00303198 -0.00182570 0.99999374 0.79783891
Axis 0.00026910 0.00298358 -0.99999551
Axis point 273.11701354 275.39988126 0.00000000
Rotation angle (degrees) 72.41619455
Shift along axis 0.53304780
> fitmap #4 inMap #1
Fit molecule copy of 6mer_side_tilt.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.206, steps = 48
shifted from previous position = 0.0247
rotated from previous position = 0.0168 degrees
atoms outside contour = 8609, contour level = 0.3
Position of copy of 6mer_side_tilt.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30201805 0.95329823 0.00275381 -71.91595471
-0.95329645 0.30202501 -0.00260201 452.61995671
-0.00331221 -0.00183935 0.99999282 0.86901866
Axis 0.00040001 0.00318158 -0.99999486
Axis point 273.13623925 275.42308163 0.00000000
Rotation angle (degrees) 72.42115428
Shift along axis 0.54226748
> view #4 clip false
> select add #4
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view matrix models
> #4,0.30202,0.9533,0.0027538,-71.605,-0.9533,0.30203,-0.002602,447.85,-0.0033122,-0.0018393,0.99999,0.92881
> fitmap #4 inMap #1
Fit molecule copy of 6mer_side_tilt.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4943, steps = 68
shifted from previous position = 1.74
rotated from previous position = 0.477 degrees
atoms outside contour = 2741, contour level = 0.3
Position of copy of 6mer_side_tilt.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30897093 0.95107148 -0.00001681 -70.62524876
-0.95107144 0.30897092 0.00027734 445.94374148
0.00026897 -0.00006971 0.99999996 -0.05107193
Axis -0.00018245 -0.00015024 -0.99999997
Axis point 271.56620362 271.57305768 0.00000000
Rotation angle (degrees) 72.00277649
Shift along axis -0.00303963
> fitmap #4 inMap #1
Fit molecule copy of 6mer_side_tilt.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4943, steps = 40
shifted from previous position = 0.00604
rotated from previous position = 0.00301 degrees
atoms outside contour = 2750, contour level = 0.3
Position of copy of 6mer_side_tilt.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30897855 0.95106901 0.00000870 -70.63370923
-0.95106896 0.30897853 0.00032265 445.93619772
0.00030417 -0.00010797 0.99999995 -0.05755084
Axis -0.00022639 -0.00015534 -0.99999996
Axis point 271.55936931 271.57551689 0.00000000
Rotation angle (degrees) 72.00231807
Shift along axis 0.00427142
> select subtract #4
Nothing selected
> select add #5
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view #6 clip false
> select subtract #5
Nothing selected
> select add #6
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view matrix models
> #6,-0.80902,-0.58779,-7.1983e-17,658.82,0.58779,-0.80902,-2.2154e-16,341.37,7.1983e-17,-2.2154e-16,1,-4.0386
> fitmap #6 inMap #1
Fit molecule copy of 6mer_side_tilt.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4967, steps = 120
shifted from previous position = 13.1
rotated from previous position = 0.0142 degrees
atoms outside contour = 2717, contour level = 0.3
Position of copy of 6mer_side_tilt.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80901313 -0.58779054 0.00020469 650.96066810
0.58779052 -0.80901315 -0.00013915 331.72862387
0.00024739 0.00000774 0.99999997 -0.04790015
Axis 0.00012495 -0.00003632 0.99999999
Axis point 271.58715559 271.62045827 0.00000000
Rotation angle (degrees) 143.99962567
Shift along axis 0.02139052
> select subtract #6
Nothing selected
> select add #5
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view #5 clip false
> view matrix models
> #5,-0.80902,0.58779,7.1983e-17,336.9,-0.58779,-0.80902,-2.2154e-16,654,-7.1983e-17,-2.2154e-16,1,-0.34927
> view matrix models
> #5,-0.80902,0.58779,7.1983e-17,337.66,-0.58779,-0.80902,-2.2154e-16,654.61,-7.1983e-17,-2.2154e-16,1,-0.0069747
> view matrix models
> #5,-0.80902,0.58779,7.1983e-17,332.01,-0.58779,-0.80902,-2.2154e-16,650.79,-7.1983e-17,-2.2154e-16,1,-0.57263
> fitmap #6 inMap #1
Fit molecule copy of 6mer_side_tilt.pdb (#6) 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 = 0.0111
rotated from previous position = 0.0129 degrees
atoms outside contour = 2710, contour level = 0.3
Position of copy of 6mer_side_tilt.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80903995 -0.58775365 0.00004295 651.00116667
0.58775365 -0.80903995 0.00001049 331.70265119
0.00002858 0.00003373 1.00000000 -0.00655130
Axis 0.00001977 0.00001222 1.00000000
Axis point 271.61580231 271.60584774 0.00000000
Rotation angle (degrees) 144.00223811
Shift along axis 0.01037327
> fitmap #6 inMap #1
Fit molecule copy of 6mer_side_tilt.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4967, steps = 60
shifted from previous position = 0.00553
rotated from previous position = 0.000212 degrees
atoms outside contour = 2714, contour level = 0.3
Position of copy of 6mer_side_tilt.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80904105 -0.58775214 0.00004612 651.00168158
0.58775214 -0.80904105 0.00001081 331.70368923
0.00003096 0.00003585 1.00000000 -0.00201656
Axis 0.00002131 0.00001290 1.00000000
Axis point 271.61606232 271.60611434 0.00000000
Rotation angle (degrees) 144.00234511
Shift along axis 0.01613125
> fitmap #5 inMap #1
Fit molecule copy of 6mer_side_tilt.pdb (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4947, steps = 48
shifted from previous position = 0.682
rotated from previous position = 0.0185 degrees
atoms outside contour = 2735, contour level = 0.3
Position of copy of 6mer_side_tilt.pdb (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80897568 0.58784205 0.00028980 331.61903574
-0.58784204 -0.80897573 0.00012483 650.98037001
0.00030782 -0.00006937 0.99999995 -0.06536667
Axis -0.00016518 -0.00001533 -0.99999999
Axis point 271.58032900 271.60897152 0.00000000
Rotation angle (degrees) 143.99597744
Shift along axis 0.00060910
> fitmap #5 inMap #1
Fit molecule copy of 6mer_side_tilt.pdb (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4947, steps = 40
shifted from previous position = 0.0266
rotated from previous position = 0.0164 degrees
atoms outside contour = 2726, contour level = 0.3
Position of copy of 6mer_side_tilt.pdb (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80891994 0.58791881 0.00002481 331.67479975
-0.58791880 -0.80891994 0.00007042 651.02057321
0.00006147 0.00004238 1.00000000 0.00548588
Axis -0.00002385 -0.00003118 -1.00000000
Axis point 271.63180992 271.61131435 0.00000000
Rotation angle (degrees) 143.99054102
Shift along axis -0.03369280
> select subtract #5
Nothing selected
> select add #7
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view #7 clip false
> view matrix models
> #7,0.30902,-0.95106,-1.1647e-16,446.65,0.95106,0.30902,-8.4621e-17,-70.746,1.1647e-16,-8.4621e-17,1,-3.4766
> view matrix models
> #7,0.30902,-0.95106,-1.1647e-16,447.4,0.95106,0.30902,-8.4621e-17,-70.177,1.1647e-16,-8.4621e-17,1,-0.94653
> fitmap #7 inMap #1
Fit molecule copy of 6mer_side_tilt.pdb (#7) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4947, steps = 72
shifted from previous position = 1.76
rotated from previous position = 0.0194 degrees
atoms outside contour = 2721, contour level = 0.3
Position of copy of 6mer_side_tilt.pdb (#7) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30916082 -0.95100977 -0.00007333 445.97824713
0.95100972 0.30916083 -0.00029450 -70.57235918
0.00030274 0.00002132 0.99999995 -0.06070336
Axis 0.00016604 -0.00019772 0.99999997
Axis point 271.56410866 271.68082171 0.00000000
Rotation angle (degrees) 71.99133638
Shift along axis 0.02730226
> fitmap #7 inMap #1
Fit molecule copy of 6mer_side_tilt.pdb (#7) 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 = 0.0152
rotated from previous position = 0.00113 degrees
atoms outside contour = 2717, contour level = 0.3
Position of copy of 6mer_side_tilt.pdb (#7) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30917795 -0.95100420 -0.00007160 445.98116595
0.95100416 0.30917796 -0.00028664 -70.56478416
0.00029473 0.00002053 0.99999996 -0.05067148
Axis 0.00016150 -0.00019260 0.99999997
Axis point 271.56127256 271.69243470 0.00000000
Rotation angle (degrees) 71.99030391
Shift along axis 0.03494343
> select add #6
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select add #5
36369 atoms, 37035 bonds, 5049 residues, 3 models selected
> select add #4
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select add #3
60615 atoms, 61725 bonds, 8415 residues, 5 models selected
> color sel cornflower blue
> color sel blue
> select subtract #3
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select subtract #4
36369 atoms, 37035 bonds, 5049 residues, 3 models selected
> select subtract #5
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select subtract #6
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select subtract #7
Nothing selected
> rename #3 id #2
> rename #4 id #2
> rename #5 id #2
> rename #6 id #2
> rename #7 id #2
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/6mer_side_straight1.pdb"
Chain information for 6mer_side_straight1.pdb #3
---
Chain | Description
A B D | No description available
C E F | No description available
> hide atoms
> show cartoons
> fitmap #3 inMap #1
Fit molecule 6mer_side_straight1.pdb (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4117, steps = 44
shifted from previous position = 0.0138
rotated from previous position = 0.000918 degrees
atoms outside contour = 3904, contour level = 0.3
Position of 6mer_side_straight1.pdb (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00000348 -0.00001068 0.00363308
0.00000348 1.00000000 0.00001142 -0.00639869
0.00001068 -0.00001142 1.00000000 0.01125876
Axis -0.71283470 -0.66678837 0.21739354
Axis point -0.00000000 907.22367503 319.44989715
Rotation angle (degrees) 0.00091805
Shift along axis 0.00412437
> fitmap #3 inMap #1
Fit molecule 6mer_side_straight1.pdb (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4117, steps = 60
shifted from previous position = 0.0181
rotated from previous position = 0.0131 degrees
atoms outside contour = 3910, contour level = 0.3
Position of 6mer_side_straight1.pdb (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00000700 0.00017224 -0.05617344
-0.00000703 0.99999999 0.00014727 -0.04565547
-0.00017224 -0.00014727 0.99999997 0.07360516
Axis -0.64956245 0.75967840 -0.03094108
Axis point 427.20994172 -0.00000000 327.95476081
Rotation angle (degrees) 0.01299048
Shift along axis -0.00047275
> combine #3
> view orient
> turn x 180
> turn z 72 models #4
> turn z 72 models #5
> turn z 72 models #6
> turn z 72 models #7
> view #3 clip false
> select add #3
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> fitmap #3 inMap #1
Fit molecule 6mer_side_straight1.pdb (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4117, steps = 44
shifted from previous position = 0.0147
rotated from previous position = 0.00147 degrees
atoms outside contour = 3907, contour level = 0.3
Position of 6mer_side_straight1.pdb (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 0.00000501 0.00019418 -0.06155462
-0.00000503 0.99999999 0.00013425 -0.04156282
-0.00019418 -0.00013425 0.99999997 0.09445635
Axis -0.56856333 0.82236490 -0.02125319
Axis point 486.27068369 0.00000000 320.53350503
Rotation angle (degrees) 0.01352865
Shift along axis -0.00118960
> fitmap #3 inMap #1
Fit molecule 6mer_side_straight1.pdb (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4117, steps = 28
shifted from previous position = 0.0207
rotated from previous position = 0.00695 degrees
atoms outside contour = 3910, contour level = 0.3
Position of 6mer_side_straight1.pdb (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 -0.00011008 0.00018399 -0.05731283
0.00011005 0.99999998 0.00017105 -0.10156491
-0.00018401 -0.00017103 0.99999997 0.08051164
Axis -0.62360887 0.67087243 0.40130058
Axis point 437.67017639 0.00000000 311.84316297
Rotation angle (degrees) 0.01571474
Shift along axis -0.00008694
> select subtract #3
Nothing selected
> select add #4
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view #4 clip false
> view matrix models
> #4,0.30901,0.95106,0.00019329,-70.367,-0.95106,0.30901,-0.0001183,447.45,-0.00017224,-0.00014727,1,0.52031
> fitmap #4 inMap #1
Fit molecule copy of 6mer_side_straight1.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4136, steps = 52
shifted from previous position = 1.51
rotated from previous position = 0.00596 degrees
atoms outside contour = 3898, contour level = 0.3
Position of copy of 6mer_side_straight1.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30899677 0.95106306 0.00020902 -70.70683889
-0.95106308 0.30899678 -0.00001641 446.02160378
-0.00008019 -0.00019372 0.99999998 0.06434696
Axis -0.00009322 0.00015205 -0.99999998
Axis point 271.58775317 271.66952613 0.00000000
Rotation angle (degrees) 72.00121856
Shift along axis 0.01006120
> fitmap #4 inMap #1
Fit molecule copy of 6mer_side_straight1.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4136, steps = 44
shifted from previous position = 0.019
rotated from previous position = 0.00187 degrees
atoms outside contour = 3887, contour level = 0.3
Position of copy of 6mer_side_straight1.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30897763 0.95106928 0.00022338 -70.69985108
-0.95106930 0.30897763 0.00000492 446.01369415
-0.00006434 -0.00021397 0.99999998 0.04379612
Axis -0.00011508 0.00015127 -0.99999998
Axis point 271.57930451 271.65972906 0.00000000
Rotation angle (degrees) 72.00237224
Shift along axis 0.03180616
> select subtract #4
Nothing selected
> select add #5
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view #4 clip false
> view #5 clip false
> view matrix models
> #5,-0.80902,0.58778,-5.278e-05,325.51,-0.58778,-0.80902,-0.00022039,653.96,-0.00017224,-0.00014727,1,0.79208
> fitmap #5 inMap #1
Fit molecule copy of 6mer_side_straight1.pdb (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4121, steps = 96
shifted from previous position = 6.9
rotated from previous position = 0.0072 degrees
atoms outside contour = 3946, contour level = 0.3
Position of copy of 6mer_side_straight1.pdb (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80905265 0.58773617 0.00005914 331.71008018
-0.58773616 -0.80905262 -0.00023994 651.07655959
-0.00009317 -0.00022888 0.99999997 0.07117226
Axis 0.00000941 0.00012958 -0.99999999
Axis point 271.61792281 271.65427679 0.00000000
Rotation angle (degrees) 144.00347598
Shift along axis 0.01631185
> fitmap #5 inMap #1
Fit molecule copy of 6mer_side_straight1.pdb (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.412, steps = 48
shifted from previous position = 0.0218
rotated from previous position = 0.0149 degrees
atoms outside contour = 3939, contour level = 0.3
Position of copy of 6mer_side_straight1.pdb (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80908180 0.58769602 0.00019244 331.67529022
-0.58769603 -0.80908181 -0.00002190 650.98235445
0.00014283 -0.00013082 0.99999998 -0.04022438
Axis -0.00009266 0.00004221 -0.99999999
Axis point 271.57629945 271.61736789 0.00000000
Rotation angle (degrees) 144.00631866
Shift along axis 0.03696783
> select add #6
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select subtract #5
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view #6 clip false
> view matrix models
> #6,-0.80901,-0.58779,-0.00022591,651.73,0.58779,-0.80901,-1.7906e-05,333.18,-0.00017224,-0.00014727,1,0.024087
> fitmap #6 inMap #1
Fit molecule copy of 6mer_side_straight1.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4091, steps = 76
shifted from previous position = 1.61
rotated from previous position = 0.0091 degrees
atoms outside contour = 3967, contour level = 0.3
Position of copy of 6mer_side_straight1.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80896621 -0.58785508 -0.00029919 651.09603464
0.58785513 -0.80896621 -0.00013440 331.71456469
-0.00016303 -0.00028460 0.99999995 0.10201758
Axis -0.00012776 -0.00011581 0.99999999
Axis point 271.64980837 271.64979242 0.00000000
Rotation angle (degrees) 143.99505236
Shift along axis -0.01958025
> fitmap #6 inMap #1
Fit molecule copy of 6mer_side_straight1.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4091, steps = 44
shifted from previous position = 0.0145
rotated from previous position = 0.0171 degrees
atoms outside contour = 3972, contour level = 0.3
Position of copy of 6mer_side_straight1.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
-0.80896716 -0.58785384 -0.00000594 651.00390936
0.58785383 -0.80896715 -0.00019175 331.73307327
0.00010792 -0.00015861 0.99999998 -0.02239254
Axis 0.00002819 -0.00009684 0.99999999
Axis point 271.60087767 271.64378633 0.00000000
Rotation angle (degrees) 143.99514281
Shift along axis -0.03616666
> select subtract #6
Nothing selected
> select add #7
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> view #7 clip false
> view matrix models
> #7,0.30902,-0.95105,-8.6839e-05,447.98,0.95105,0.30902,0.00020932,-67.762,-0.00017224,-0.00014727,1,0.85769
> view matrix models
> #7,0.30902,-0.95105,-8.6839e-05,448.51,0.95105,0.30902,0.00020932,-70.163,-0.00017224,-0.00014727,1,0.97804
> fitmap #7 inMap #1
Fit molecule copy of 6mer_side_straight1.pdb (#7) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4101, steps = 64
shifted from previous position = 2.7
rotated from previous position = 0.00556 degrees
atoms outside contour = 3950, contour level = 0.3
Position of copy of 6mer_side_straight1.pdb (#7) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30900829 -0.95105933 -0.00017662 446.06455192
0.95105933 0.30900825 0.00024245 -70.73183698
-0.00017601 -0.00024289 0.99999996 0.10639615
Axis -0.00025516 -0.00000032 0.99999997
Axis point 271.70883134 271.60871477 0.00000000
Rotation angle (degrees) 72.00052681
Shift along axis -0.00739789
> select add #6
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select add #5
36369 atoms, 37035 bonds, 5049 residues, 3 models selected
> select add #4
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select add #3
60615 atoms, 61725 bonds, 8415 residues, 5 models selected
> color sel hot pink
> select subtract #7
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select subtract #6
36369 atoms, 37035 bonds, 5049 residues, 3 models selected
> select subtract #5
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select subtract #4
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select subtract #3
Nothing selected
> rename #3 id #2
> rename #4 id #2
> rename #5 id #2
> rename #6 id #2
> rename #7 id #2
> hide #!1 models
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/Capsid_Top.pdb" selectedOnly true relModel #1
> hide #!2 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/Capsid_Top.pdb"
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #2
242385 atoms, 246825 bonds, 33645 residues, 22 models selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/Capsid_Top.pdb" selectedOnly true relModel #1
> select subtract #2
Nothing selected
> hide #!2 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/Capsid_Top.pdb"
Chain information for Capsid_Top.pdb
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A 3.13/A 3.14/A 3.15/A 3.16/A 3.17/A 3.18/A 3.19/A 3.20/A 3.21/A 3.1/B 3.2/B 3.3/B 3.4/B 3.5/B 3.6/B 3.7/B 3.8/B 3.9/B 3.10/B 3.11/B 3.12/B 3.13/B 3.14/B 3.15/B 3.16/B 3.17/B 3.18/B 3.19/B 3.20/B 3.21/B 3.1/C 3.7/C 3.8/C 3.9/C 3.10/C 3.11/C 3.1/D 3.2/D 3.3/D 3.4/D 3.5/D 3.6/D 3.7/D 3.8/D 3.9/D 3.10/D 3.11/D 3.12/D 3.13/D 3.14/D 3.15/D 3.16/D 3.17/D 3.18/D 3.19/D 3.20/D 3.21/D 3.1/E 3.7/E 3.8/E 3.9/E 3.10/E 3.11/E | No description available
3.2/C 3.3/C 3.4/C 3.5/C 3.6/C 3.12/C 3.13/C 3.14/C 3.15/C 3.16/C 3.17/C 3.18/C 3.19/C 3.20/C 3.21/C 3.2/E 3.3/E 3.4/E 3.5/E 3.6/E 3.12/E 3.13/E 3.14/E 3.15/E 3.16/E 3.17/E 3.18/E 3.19/E 3.20/E 3.21/E 3.2/F 3.3/F 3.4/F 3.5/F 3.6/F 3.12/F 3.13/F 3.14/F 3.15/F 3.16/F 3.17/F 3.18/F 3.19/F 3.20/F 3.21/F | No description available
> hide #3.1-21 atoms
> show #3.1-21 cartoons
> show #!2 models
> select add #3
242385 atoms, 246825 bonds, 33645 residues, 22 models selected
> select subtract #3
Nothing selected
> hide #!2 models
> lighting flat
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/6mer_side_tilt-coot-1.pdb"
Chain information for 6mer_side_tilt-coot-1.pdb #4
---
Chain | Description
A B D | No description available
C E F | No description available
> hide #!2 models
> show #!1 models
> hide #4 atoms
> show #4 cartoons
> fitmap #4 inMap #1
Fit molecule 6mer_side_tilt-coot-1.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.526, steps = 48
shifted from previous position = 0.022
rotated from previous position = 0.0103 degrees
atoms outside contour = 2271, contour level = 0.3
Position of 6mer_side_tilt-coot-1.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00000973 0.00013685 -0.02991728
-0.00000971 0.99999999 -0.00011588 0.03153964
-0.00013686 0.00011588 0.99999998 0.00070070
Axis 0.64526408 0.76204020 -0.05412026
Axis point 6.94722392 0.00000000 240.73008819
Rotation angle (degrees) 0.01028975
Shift along axis 0.00469201
> fitmap #2.13 inMap #1
Fit molecule copy of 6mer_side_tilt.pdb (#2.13) 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 = 0.00283
rotated from previous position = 0.0182 degrees
atoms outside contour = 2748, contour level = 0.3
Position of copy of 6mer_side_tilt.pdb (#2.13) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30904065 0.95104883 0.00002692 -70.65311634
-0.95104883 0.30904065 0.00001302 446.00761869
0.00000406 -0.00002962 1.00000000 0.00996369
Axis -0.00002242 0.00001202 -1.00000000
Axis point 271.61987983 271.62791696 0.00000000
Rotation angle (degrees) 71.99857504
Shift along axis -0.00302035
> fitmap #2.13 inMap #1
Fit molecule copy of 6mer_side_tilt.pdb (#2.13) 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 = 0.0253
rotated from previous position = 0.00162 degrees
atoms outside contour = 2748, contour level = 0.3
Position of copy of 6mer_side_tilt.pdb (#2.13) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.30901689 0.95105655 0.00001822 -70.64807980
-0.95105655 0.30901689 0.00002311 445.99243890
0.00001635 -0.00002447 1.00000000 0.02507277
Axis -0.00002502 0.00000098 -1.00000000
Axis point 271.60389034 271.61558431 0.00000000
Rotation angle (degrees) 72.00000610
Shift along axis -0.02286670
> fitmap #4 inMap #1
Fit molecule 6mer_side_tilt-coot-1.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5261, steps = 36
shifted from previous position = 0.0188
rotated from previous position = 0.0162 degrees
atoms outside contour = 2276, contour level = 0.3
Position of 6mer_side_tilt-coot-1.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999991 -0.00005062 0.00041037 -0.10073495
0.00005068 0.99999999 -0.00014836 0.02310279
-0.00041037 0.00014838 0.99999990 0.08272392
Axis 0.33775081 0.93414767 0.11529315
Axis point 202.34528280 0.00000000 243.12310910
Rotation angle (degrees) 0.02516996
Shift along axis -0.00290439
> fitmap #4 inMap #1
Fit molecule 6mer_side_tilt-coot-1.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.526, steps = 40
shifted from previous position = 0.0141
rotated from previous position = 0.00242 degrees
atoms outside contour = 2269, contour level = 0.3
Position of 6mer_side_tilt-coot-1.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999990 -0.00006508 0.00044993 -0.11415221
0.00006515 0.99999999 -0.00014636 0.02208143
-0.00044992 0.00014638 0.99999989 0.07976850
Axis 0.30647131 0.94206508 0.13634046
Axis point 178.23270166 0.00000000 251.49774612
Rotation angle (degrees) 0.02736437
Shift along axis -0.00330656
> hide #4 models
> close #3
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> hide #2.6 models
> select add #2.2
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select add #2.3
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select add #2.4
36369 atoms, 37035 bonds, 5049 residues, 3 models selected
> select add #2.5
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select add #2.6
60615 atoms, 61725 bonds, 8415 residues, 5 models selected
> color #1#2.7-21#!2 orange
> undo
> show #2.2 models
> show #2.3 models
> show #2.4 models
> show #2.5 models
> show #2.6 models
> color sel orange
> select subtract #2.2
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select subtract #2.3
36369 atoms, 37035 bonds, 5049 residues, 3 models selected
> select subtract #2.4
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select subtract #2.5
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select subtract #2.6
Nothing selected
> select add #2.7
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> select add #2.8
20180 atoms, 20550 bonds, 2800 residues, 2 models selected
> select add #2.9
30270 atoms, 30825 bonds, 4200 residues, 3 models selected
> select add #2.10
40360 atoms, 41100 bonds, 5600 residues, 4 models selected
> select add #2.11
50450 atoms, 51375 bonds, 7000 residues, 5 models selected
> color sel yellow
> select subtract #2.7
40360 atoms, 41100 bonds, 5600 residues, 4 models selected
> select subtract #2.8
30270 atoms, 30825 bonds, 4200 residues, 3 models selected
> select subtract #2.9
20180 atoms, 20550 bonds, 2800 residues, 2 models selected
> select subtract #2.10
10090 atoms, 10275 bonds, 1400 residues, 1 model selected
> select subtract #2.11
Nothing selected
> select add #2.12
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select add #2.13
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select add #2.14
36369 atoms, 37035 bonds, 5049 residues, 3 models selected
> select add #2.15
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select add #2.16
60615 atoms, 61725 bonds, 8415 residues, 5 models selected
> color sel forest green
> select subtract #2.16
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select add #2.16
60615 atoms, 61725 bonds, 8415 residues, 5 models selected
> select subtract #2.15
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select subtract #2.16
36369 atoms, 37035 bonds, 5049 residues, 3 models selected
> select subtract #2.14
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select subtract #2.13
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select subtract #2.12
Nothing selected
> select add #2.17
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select add #2.18
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select add #2.19
36369 atoms, 37035 bonds, 5049 residues, 3 models selected
> select add #2.20
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select add #2.21
60615 atoms, 61725 bonds, 8415 residues, 5 models selected
> color sel blue
> color sel cyan
> select subtract #2.17
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select subtract #2.18
36369 atoms, 37035 bonds, 5049 residues, 3 models selected
> select subtract #2.19
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select subtract #2.20
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select subtract #2.21
Nothing selected
> hide #2.11 models
> hide #2.9 models
> hide #2.10 models
> hide #2.8 models
> hide #2.7 models
> hide #2.4 models
> hide #2.5 models
> hide #2.6 models
> hide #2.3 models
> hide #2.2 models
> hide #2.13 models
> hide #2.14 models
> hide #2.15 models
> hide #2.16 models
> hide #2.20 models
> hide #2.21 models
> hide #2.19 models
> show #2.19 models
> hide #2.17 models
> hide #2.19 models
> hide #2.18 models
> show #2.13 models
> show #2.14 models
> show #2.15 models
> show #2.16 models
> hide #2.13 models
> hide #2.14 models
> hide #2.15 models
> hide #2.16 models
> show #2.17 models
> show #2.18 models
> show #2.19 models
> show #2.20 models
> show #2.21 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Tail/ValidationCryoEM_68/6mer_side_tilt-coot-2.pdb"
Chain information for 6mer_side_tilt-coot-2.pdb #3
---
Chain | Description
A B D | No description available
C E F | No description available
> hide #3#2.12,17-21 atoms
> show #3#2.12,17-21 cartoons
> hide #3 models
> show #3 models
> fitmap #3 inMap #1
Fit molecule 6mer_side_tilt-coot-2.pdb (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5261, steps = 48
shifted from previous position = 0.019
rotated from previous position = 0.0301 degrees
atoms outside contour = 2278, contour level = 0.3
Position of 6mer_side_tilt-coot-2.pdb (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999988 -0.00008820 0.00047934 -0.11806765
0.00008829 0.99999998 -0.00019429 0.02759661
-0.00047933 0.00019433 0.99999987 0.07902974
Axis 0.37033273 0.91354660 0.16818523
Axis point 166.64115701 0.00000000 242.31786352
Rotation angle (degrees) 0.03006294
Shift along axis -0.00522189
> close #3
> show #2.16 models
> hide #2.16 models
> show #4 models
> hide #4 models
> fitmap #4 inMap #1
Fit molecule 6mer_side_tilt-coot-1.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.526, steps = 48
shifted from previous position = 0.00755
rotated from previous position = 0.00275 degrees
atoms outside contour = 2265, contour level = 0.3
Position of 6mer_side_tilt-coot-1.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999987 -0.00006473 0.00049669 -0.11988880
0.00006481 0.99999999 -0.00015750 0.02324241
-0.00049668 0.00015753 0.99999986 0.09341524
Axis 0.29998036 0.94593535 0.12336164
Axis point 188.62353708 0.00000000 239.94071559
Rotation angle (degrees) 0.03008445
Shift along axis -0.00245461
> fitmap #4 inMap #1
Fit molecule 6mer_side_tilt-coot-1.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5261, steps = 44
shifted from previous position = 0.00313
rotated from previous position = 0.00458 degrees
atoms outside contour = 2269, contour level = 0.3
Position of 6mer_side_tilt-coot-1.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999991 -0.00005188 0.00041855 -0.10383628
0.00005194 0.99999999 -0.00014653 0.02409803
-0.00041854 0.00014655 0.99999990 0.07556880
Axis 0.32821222 0.93742066 0.11627232
Axis point 181.24491448 0.00000000 246.00304164
Rotation angle (degrees) 0.02558193
Shift along axis -0.00270379
> hide #2.18 models
> hide #2.17 models
> hide #2.19 models
> show #2.17 models
> show #2.19 models
> show #2.18 models
> hide #2.19 models
> hide #2.17 models
> hide #2.18 models
> hide #2.21 models
> hide #2.20 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/6mer_side_straight1-coot-0.pdb"
Chain information for 6mer_side_straight1-coot-0.pdb #3
---
Chain | Description
A B D | No description available
C E F | No description available
> hide #3#2.12 atoms
> show #3#2.12 cartoons
> fitmap #4 inMap #1
Fit molecule 6mer_side_tilt-coot-1.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.5261, steps = 44
shifted from previous position = 0.0128
rotated from previous position = 0.0095 degrees
atoms outside contour = 2283, contour level = 0.3
Position of 6mer_side_tilt-coot-1.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999997 0.00000119 0.00026140 -0.06453009
-0.00000115 0.99999999 -0.00014719 0.03444334
-0.00026140 0.00014719 0.99999995 0.04848789
Axis 0.49064556 0.87135055 -0.00389211
Axis point 185.42249966 0.00000000 243.43632451
Rotation angle (degrees) 0.01718851
Shift along axis -0.00183790
> fitmap #3 inMap #1
Fit molecule 6mer_side_straight1-coot-0.pdb (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4505, steps = 48
shifted from previous position = 0.0422
rotated from previous position = 0.0553 degrees
atoms outside contour = 3073, contour level = 0.3
Position of 6mer_side_straight1-coot-0.pdb (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 -0.00008292 0.00011253 -0.00502884
0.00008281 0.99999954 0.00095415 -0.36768399
-0.00011261 -0.00095414 0.99999954 0.12860168
Axis -0.98943881 0.11673248 0.08593233
Axis point 0.00000000 137.01954552 382.12671396
Rotation angle (degrees) 0.05525222
Shift along axis -0.02689389
> fitmap #3 inMap #1
Fit molecule 6mer_side_straight1-coot-0.pdb (#3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms
average map value = 0.4504, steps = 44
shifted from previous position = 0.0187
rotated from previous position = 0.0169 degrees
atoms outside contour = 3077, contour level = 0.3
Position of 6mer_side_straight1-coot-0.pdb (#3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 -0.00004757 -0.00015764 0.09259589
0.00004770 0.99999964 0.00084162 -0.31024068
0.00015760 -0.00084163 0.99999963 0.02964269
Axis -0.98139348 -0.18379876 0.05554139
Axis point 0.00000000 37.18216973 375.67040753
Rotation angle (degrees) 0.04913595
Shift along axis -0.03220475
> select add #3
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select subtract #3
Nothing selected
> view #3 clip false
> select #3/A:410
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
48 atoms, 48 bonds, 7 residues, 1 model selected
> select up
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> close #3
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/6mer_side_straight1-coot-1.pdb"
Chain information for 6mer_side_straight1-coot-1.pdb #3
---
Chain | Description
A B D | No description available
C E F | No description available
> hide #3#2.12 atoms
> show #3#2.12 cartoons
> color #3#2.12 bychain
> hide #!1 models
> show #!1 models
> hide #!2 models
> volume zone #1 nearAtoms #3 range 6.37
> surface dust #1 size 10.6
> hide #3 models
> show #4 models
> hide #4 models
> show #!2 models
> show #2.2 models
> view #2.2 clip false
Cell requested for row 1 is out of bounds for table with 25 rows! Resizing
table model.
> save "/Users/melvinshen/Desktop/Docking of Capsid.cxs"
> hide #!2 models
> show #3 models
> close #4
> split #3
Split 6mer_side_straight1-coot-1.pdb (#3) into 6 models
Chain information for 6mer_side_straight1-coot-1.pdb A #3.1
---
Chain | Description
A | No description available
Chain information for 6mer_side_straight1-coot-1.pdb B #3.2
---
Chain | Description
B | No description available
Chain information for 6mer_side_straight1-coot-1.pdb C #3.3
---
Chain | Description
C | No description available
Chain information for 6mer_side_straight1-coot-1.pdb D #3.4
---
Chain | Description
D | No description available
Chain information for 6mer_side_straight1-coot-1.pdb E #3.5
---
Chain | Description
E | No description available
Chain information for 6mer_side_straight1-coot-1.pdb F #3.6
---
Chain | Description
F | No description available
> hide #3.1 models
> show #3.1 models
> fitmap #3.1 inMap #1
Fit molecule 6mer_side_straight1-coot-1.pdb A (#3.1) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.437, steps = 44
shifted from previous position = 0.0423
rotated from previous position = 0.112 degrees
atoms outside contour = 557, contour level = 0.3
Position of 6mer_side_straight1-coot-1.pdb A (#3.1) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999928 0.00015041 0.00118713 -0.38066480
-0.00014857 0.99999880 -0.00154468 0.57846321
-0.00118736 0.00154450 0.99999810 0.22283529
Axis 0.79052326 0.60763421 -0.07650910
Axis point 0.00000000 -145.49278027 361.41449616
Rotation angle (degrees) 0.11194948
Shift along axis 0.03352073
> fitmap #3.1 inMap #1
Fit molecule 6mer_side_straight1-coot-1.pdb A (#3.1) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.437, steps = 48
shifted from previous position = 0.00374
rotated from previous position = 0.0034 degrees
atoms outside contour = 557, contour level = 0.3
Position of 6mer_side_straight1-coot-1.pdb A (#3.1) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999934 0.00015190 0.00114294 -0.36738685
-0.00015009 0.99999873 -0.00158417 0.59125924
-0.00114318 0.00158400 0.99999809 0.19702520
Axis 0.80851167 0.58341194 -0.07706741
Axis point 0.00000000 -125.54183552 361.27720989
Rotation angle (degrees) 0.11225741
Shift along axis 0.03272692
> fitmap #3.2 inMap #1
Fit molecule 6mer_side_straight1-coot-1.pdb B (#3.2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.5, steps = 44
shifted from previous position = 0.111
rotated from previous position = 0.169 degrees
atoms outside contour = 406, contour level = 0.3
Position of 6mer_side_straight1-coot-1.pdb B (#3.2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999891 0.00017271 0.00146337 -0.41601897
-0.00016897 0.99999672 -0.00255470 0.70205449
-0.00146380 0.00255445 0.99999567 0.17175619
Axis 0.86622559 0.49628343 -0.05793079
Axis point 0.00000000 -66.26775200 279.14779184
Rotation angle (degrees) 0.16897064
Shift along axis -0.02189824
> fitmap #3.2 inMap #1
Fit molecule 6mer_side_straight1-coot-1.pdb B (#3.2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.5, steps = 40
shifted from previous position = 0.0143
rotated from previous position = 0.0152 degrees
atoms outside contour = 408, contour level = 0.3
Position of 6mer_side_straight1-coot-1.pdb B (#3.2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999923 0.00023910 0.00121608 -0.35242617
-0.00023591 0.99999653 -0.00262447 0.74466709
-0.00121670 0.00262418 0.99999582 0.09375116
Axis 0.90423613 0.41911852 -0.08183324
Axis point 0.00000000 -34.82559865 286.06055392
Rotation angle (degrees) 0.16628749
Shift along axis -0.01424466
> fitmap #3.3 inMap #1
Fit molecule 6mer_side_straight1-coot-1.pdb C (#3.3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms
average map value = 0.4855, steps = 44
shifted from previous position = 0.118
rotated from previous position = 0.13 degrees
atoms outside contour = 435, contour level = 0.3
Position of 6mer_side_straight1-coot-1.pdb C (#3.3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999869 -0.00115311 -0.00113240 0.54252872
0.00115492 0.99999805 0.00159884 -0.97636010
0.00113055 -0.00160015 0.99999808 -0.29594100
Axis -0.70343238 -0.49760424 0.50751641
Axis point 0.00000000 -171.11015342 624.77147385
Rotation angle (degrees) 0.13028164
Shift along axis -0.04598626
> fitmap #3.3 inMap #1
Fit molecule 6mer_side_straight1-coot-1.pdb C (#3.3) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms
average map value = 0.4855, steps = 28
shifted from previous position = 0.0213
rotated from previous position = 0.0128 degrees
atoms outside contour = 436, contour level = 0.3
Position of 6mer_side_straight1-coot-1.pdb C (#3.3) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999848 -0.00120494 -0.00126364 0.57657629
0.00120674 0.99999825 0.00142621 -0.95663914
0.00126192 -0.00142773 0.99999818 -0.35423721
Axis -0.63280900 -0.55999847 0.53474712
Axis point 0.00000000 -242.01735017 677.75406265
Rotation angle (degrees) 0.12920070
Shift along axis -0.01857353
> fitmap #3.4 inMap #1
Fit molecule 6mer_side_straight1-coot-1.pdb D (#3.4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4141, steps = 44
shifted from previous position = 0.0444
rotated from previous position = 0.124 degrees
atoms outside contour = 569, contour level = 0.3
Position of 6mer_side_straight1-coot-1.pdb D (#3.4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999786 -0.00189416 -0.00082903 0.49378425
0.00189362 0.99999799 -0.00065435 -0.39949289
0.00083026 0.00065278 0.99999944 -0.29872385
Axis 0.30139391 -0.38259304 0.87337522
Axis point 202.99968297 253.97098105 0.00000000
Rotation angle (degrees) 0.12424465
Shift along axis 0.04076875
> fitmap #3.4 inMap #1
Fit molecule 6mer_side_straight1-coot-1.pdb D (#3.4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4141, steps = 40
shifted from previous position = 0.0163
rotated from previous position = 0.0031 degrees
atoms outside contour = 568, contour level = 0.3
Position of 6mer_side_straight1-coot-1.pdb D (#3.4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999797 -0.00185278 -0.00079712 0.48973015
0.00185227 0.99999808 -0.00064026 -0.38800231
0.00079830 0.00063878 0.99999948 -0.29774096
Axis 0.30224104 -0.37700265 0.87551091
Axis point 202.89970862 258.61518296 0.00000000
Rotation angle (degrees) 0.12123412
Shift along axis 0.03361899
> fitmap #3.5 inMap #1
Fit molecule 6mer_side_straight1-coot-1.pdb E (#3.5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms
average map value = 0.4055, steps = 40
shifted from previous position = 0.0409
rotated from previous position = 0.0856 degrees
atoms outside contour = 616, contour level = 0.3
Position of 6mer_side_straight1-coot-1.pdb E (#3.5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999934 -0.00054964 0.00100775 -0.26291649
0.00055061 0.99999939 -0.00095716 0.15876004
-0.00100722 0.00095771 0.99999903 0.26717818
Axis 0.64052261 0.67400453 0.36803353
Axis point 251.49543161 0.00000000 284.53339285
Rotation angle (degrees) 0.08564421
Shift along axis 0.03693156
> fitmap #3.6 inMap #1
Fit molecule 6mer_side_straight1-coot-1.pdb F (#3.6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms
average map value = 0.4629, steps = 48
shifted from previous position = 0.0359
rotated from previous position = 0.0209 degrees
atoms outside contour = 470, contour level = 0.3
Position of 6mer_side_straight1-coot-1.pdb F (#3.6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999994 -0.00030487 0.00018331 -0.04075075
0.00030485 0.99999995 0.00007925 -0.13925991
-0.00018333 -0.00007919 0.99999998 0.09502872
Axis -0.21737300 0.50300526 0.83650146
Axis point 486.98873224 -120.71948308 0.00000000
Rotation angle (degrees) 0.02088121
Shift along axis 0.01830131
> fitmap #3.6 inMap #1
Fit molecule 6mer_side_straight1-coot-1.pdb F (#3.6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms
average map value = 0.4628, steps = 28
shifted from previous position = 0.00944
rotated from previous position = 0.00352 degrees
atoms outside contour = 470, contour level = 0.3
Position of 6mer_side_straight1-coot-1.pdb F (#3.6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999994 -0.00031683 0.00013660 -0.02033363
0.00031683 0.99999995 0.00004127 -0.13237802
-0.00013661 -0.00004123 0.99999999 0.08461148
Axis -0.11870250 0.39312464 0.91179095
Axis point 451.96403591 -53.95209620 0.00000000
Rotation angle (degrees) 0.01990916
Shift along axis 0.02752057
> fitmap #3.2 inMap #1
Fit molecule 6mer_side_straight1-coot-1.pdb B (#3.2) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.5, steps = 40
shifted from previous position = 0.0108
rotated from previous position = 0.0124 degrees
atoms outside contour = 406, contour level = 0.3
Position of 6mer_side_straight1-coot-1.pdb B (#3.2) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999898 0.00019203 0.00141853 -0.40533668
-0.00018839 0.99999669 -0.00256548 0.71173180
-0.00141902 0.00256521 0.99999570 0.15874346
Axis 0.87324874 0.48295383 -0.06474757
Axis point 0.00000000 -60.89431212 281.36465168
Rotation angle (degrees) 0.16831833
Shift along axis -0.02050440
> select add #3.2
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> save /Users/melvinshen/Desktop/Monomer_side_straight1.pdb models #3.2
> selectedOnly true relModel #1
> select subtract #3.2
Nothing selected
> hide #3.2 models
> open /Users/melvinshen/Desktop/Monomer_side_straight1.pdb
Chain information for Monomer_side_straight1.pdb #4
---
Chain | Description
B | No description available
> open /Users/melvinshen/Desktop/Monomer_side_straight1-coot-0.pdb
Chain information for Monomer_side_straight1-coot-0.pdb #5
---
Chain | Description
B | No description available
> fitmap #5 inMap #1
Fit molecule Monomer_side_straight1-coot-0.pdb (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.5056, steps = 28
shifted from previous position = 0.0323
rotated from previous position = 0.0702 degrees
atoms outside contour = 409, contour level = 0.3
Position of Monomer_side_straight1-coot-0.pdb (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999972 -0.00068085 -0.00029814 0.14577918
0.00068114 0.99999929 0.00097466 -0.52468195
0.00029748 -0.00097486 0.99999948 -0.02188757
Axis -0.79519980 -0.24295240 0.55554604
Axis point -0.00000000 -22.39100891 538.45900886
Rotation angle (degrees) 0.07023357
Shift along axis -0.00061039
> fitmap #5 inMap #1
Fit molecule Monomer_side_straight1-coot-0.pdb (#5) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.5056, steps = 36
shifted from previous position = 0.0157
rotated from previous position = 0.0121 degrees
atoms outside contour = 406, contour level = 0.3
Position of Monomer_side_straight1-coot-0.pdb (#5) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999969 -0.00063823 -0.00045391 0.18632471
0.00063861 0.99999944 0.00083799 -0.47121580
0.00045338 -0.00083828 0.99999955 -0.07454433
Axis -0.73065356 -0.39547111 0.55655007
Axis point 0.00000000 -95.02120348 558.13731478
Rotation angle (degrees) 0.06572400
Shift along axis 0.00872578
> fitmap #4 inMap #1
Fit molecule Monomer_side_straight1.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.5, steps = 40
shifted from previous position = 0.0127
rotated from previous position = 0.0125 degrees
atoms outside contour = 407, contour level = 0.3
Position of Monomer_side_straight1.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 0.00005007 -0.00020496 0.05327346
-0.00005008 1.00000000 -0.00005805 0.03347037
0.00020496 0.00005806 0.99999998 -0.06389558
Axis 0.26528006 -0.93662212 -0.22883507
Axis point 314.67801034 0.00000000 263.24627490
Rotation angle (degrees) 0.01253787
Shift along axis -0.00259515
> fitmap #4 inMap #1
Fit molecule Monomer_side_straight1.pdb (#4) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.5, steps = 40
shifted from previous position = 0.0141
rotated from previous position = 0.0124 degrees
atoms outside contour = 406, contour level = 0.3
Position of Monomer_side_straight1.pdb (#4) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00000061 -0.00000188 0.00068200
0.00000061 1.00000000 -0.00000042 -0.00002207
0.00000188 0.00000042 1.00000000 -0.00214976
Axis 0.20816097 -0.93014162 0.30249889
Axis point 1063.89232921 0.00000000 416.34300259
Rotation angle (degrees) 0.00011593
Shift along axis -0.00048781
> hide #5 models
> hide #4 models
> show #4 models
> show #5 models
> hide #4 models
> view #5 clip false
> combine #5
> hide #3.1 models
> show #3.1 models
> hide #3.3 models
> show #3.3 models
> hide #3.3 models
> select add #6
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> view matrix models
> #6,0.93892,-0.033931,-0.34247,124.48,-0.043039,0.97574,-0.21467,79.976,0.34144,0.2163,0.91468,-114.96
> view matrix models
> #6,0.93892,-0.033931,-0.34247,142.78,-0.043039,0.97574,-0.21467,91.566,0.34144,0.2163,0.91468,-114.76
> view matrix models
> #6,0.95995,-0.099497,-0.2619,119.38,0.010079,0.94647,-0.32263,108.31,0.27998,0.30707,0.90957,-102.48
> view matrix models
> #6,0.93168,-0.11922,-0.34315,154.89,0.054093,0.97961,-0.19346,51.979,0.35922,0.16169,0.91914,-116.04
> view matrix models
> #6,0.93168,-0.11922,-0.34315,154.87,0.054093,0.97961,-0.19346,51.968,0.35922,0.16169,0.91914,-116.05
> view matrix models
> #6,0.81503,-0.17036,-0.55381,261.65,-0.02304,0.94552,-0.32475,120.26,0.57897,0.27744,0.7667,-158.94
> view matrix models
> #6,0.81503,-0.17036,-0.55381,266.85,-0.02304,0.94552,-0.32475,123.54,0.57897,0.27744,0.7667,-157.65
> fitmap #6 inMap #1
Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.2044, steps = 84
shifted from previous position = 2.36
rotated from previous position = 8.59 degrees
atoms outside contour = 1437, contour level = 0.3
Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.82085740 -0.23415757 -0.52092548 263.05237063
0.10961917 0.95972686 -0.25866580 55.35184890
0.56051473 0.15522432 0.81346705 -152.34785664
Axis 0.34265522 -0.89531283 0.28460910
Axis point 393.95927097 0.00000000 371.32038387
Rotation angle (degrees) 37.15299510
Shift along axis -2.78053997
> fitmap #6 inMap #1
Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.2044, steps = 40
shifted from previous position = 0.0128
rotated from previous position = 0.00459 degrees
atoms outside contour = 1436, contour level = 0.3
Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.82087891 -0.23410646 -0.52091456 263.03436240
0.10961112 0.95974705 -0.25859428 55.33660322
0.56048481 0.15517656 0.81349678 -152.35267786
Axis 0.34258321 -0.89534889 0.28458234
Axis point 393.96226657 0.00000000 371.31551944
Rotation angle (degrees) 37.14960680
Shift along axis -2.79129083
> view matrix models
> #6,0.82088,-0.23411,-0.52091,267.54,0.10961,0.95975,-0.25859,58.333,0.56048,0.15518,0.8135,-152.26
> fitmap #6 inMap #1
Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.2131, steps = 80
shifted from previous position = 4.32
rotated from previous position = 5.14 degrees
atoms outside contour = 1390, contour level = 0.3
Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.79706764 -0.31996333 -0.51215881 281.54700629
0.17737611 0.93473412 -0.30791208 50.71174493
0.57725288 0.15458202 0.80180017 -150.60790463
Axis 0.36026246 -0.84860355 0.38740544
Axis point 395.82453886 0.00000000 392.85328241
Rotation angle (degrees) 39.93251920
Shift along axis 0.05032707
> fitmap #6 inMap #1
Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.2131, steps = 60
shifted from previous position = 0.00116
rotated from previous position = 0.00204 degrees
atoms outside contour = 1390, contour level = 0.3
Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.79704644 -0.31997599 -0.51218389 281.56237176
0.17738579 0.93473251 -0.30791138 50.70942425
0.57727918 0.15456553 0.80178441 -150.61045749
Axis 0.36023614 -0.84861312 0.38740894
Axis point 395.81957821 0.00000000 392.85096972
Rotation angle (degrees) 39.93424008
Shift along axis 0.04842121
> view matrix models
> #6,0.71314,-0.33187,-0.61749,342.11,0.1107,0.9231,-0.36827,92.257,0.69223,0.19427,0.69504,-162.85
> view matrix models
> #6,0.71314,-0.33187,-0.61749,344.73,0.1107,0.9231,-0.36827,93.911,0.69223,0.19427,0.69504,-161.79
> view matrix models
> #6,0.71314,-0.33187,-0.61749,341.99,0.1107,0.9231,-0.36827,91.682,0.69223,0.19427,0.69504,-165.9
> view matrix models
> #6,0.71314,-0.33187,-0.61749,342.67,0.1107,0.9231,-0.36827,92.032,0.69223,0.19427,0.69504,-166.09
> view matrix models
> #6,0.63138,-0.37067,-0.68115,393.3,0.077771,0.9042,-0.41997,120.4,0.77156,0.21218,0.59972,-167.16
> view matrix models
> #6,0.63138,-0.37067,-0.68115,395.46,0.077771,0.9042,-0.41997,121.82,0.77156,0.21218,0.59972,-165.91
> fitmap #6 inMap #1
Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4003, steps = 76
shifted from previous position = 3.31
rotated from previous position = 7.46 degrees
atoms outside contour = 709, contour level = 0.3
Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.58689173 -0.44065636 -0.67924964 419.13040141
0.03811572 0.85303287 -0.52046337 172.71149149
0.80876776 0.27956556 0.51743387 -160.67916205
Axis 0.45560260 -0.84740011 0.27265239
Axis point 415.87944292 0.00000000 363.58724462
Rotation angle (degrees) 61.40082400
Shift along axis 0.79160636
> fitmap #6 inMap #1
Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4003, steps = 36
shifted from previous position = 0.000931
rotated from previous position = 0.0107 degrees
atoms outside contour = 710, contour level = 0.3
Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.58690544 -0.44063957 -0.67924869 419.12309219
0.03795795 0.85298755 -0.52054917 172.79464093
0.80876523 0.27973025 0.51734881 -160.67134051
Axis 0.45572874 -0.84736743 0.27254312
Axis point 415.90019722 0.00000000 363.56965736
Rotation angle (degrees) 61.40463076
Shift along axis 0.79602061
> view matrix models
> #6,0.58691,-0.44064,-0.67925,418.92,0.037958,0.85299,-0.52055,172.52,0.80877,0.27973,0.51735,-160.82
> fitmap #6 inMap #1
Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4004, steps = 44
shifted from previous position = 0.367
rotated from previous position = 0.0106 degrees
atoms outside contour = 707, contour level = 0.3
Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.58679042 -0.44063777 -0.67934922 419.18046826
0.03784352 0.85297983 -0.52057014 172.83248517
0.80885405 0.27975660 0.51719567 -160.65245021
Axis 0.45571668 -0.84740271 0.27245360
Axis point 415.88247035 0.00000000 363.53904513
Rotation angle (degrees) 61.41363133
Shift along axis 0.79847554
> fitmap #6 inMap #1
Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4003, steps = 28
shifted from previous position = 0.0174
rotated from previous position = 0.0128 degrees
atoms outside contour = 710, contour level = 0.3
Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.58690275 -0.44065349 -0.67924197 419.12466053
0.03801033 0.85299570 -0.52053198 172.77191519
0.80876472 0.27968345 0.51737491 -160.67420099
Axis 0.45569677 -0.84737162 0.27258354
Axis point 415.89635255 0.00000000 363.57725016
Rotation angle (degrees) 61.40360055
Shift along axis 0.79459358
> select subtract #6
Nothing selected
> select add #7
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #6
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> close #2
> show #4 models
> hide #4 models
> save /Users/melvinshen/Desktop/Monomer_side_straight2-coot-0.pdb models #6
> selectedOnly true relModel #1
> open /Users/melvinshen/Desktop/Monomer_side_straight2-coot-1.pdb
Chain information for Monomer_side_straight2-coot-1.pdb #2
---
Chain | Description
B | No description available
> close #3
> close #4
> rename #2 id #8
> rename #5 id #2
> color #2 #0433ffff
> select subtract #6
Nothing selected
> select add #6
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #8
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select subtract #8
Nothing selected
> fitmap #6 inMap #1
Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4004, steps = 28
shifted from previous position = 0.0215
rotated from previous position = 0.0244 degrees
atoms outside contour = 708, contour level = 0.3
Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.58671199 -0.44066026 -0.67940237 419.22261349
0.03769000 0.85293029 -0.52066245 172.91475289
0.80891811 0.27987223 0.51703291 -160.63802185
Axis 0.45579397 -0.84739302 0.27235443
Axis point 415.89230056 0.00000000 363.51625513
Rotation angle (degrees) 61.42311646
Shift along axis 0.80190822
> fitmap #6 inMap #1
Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.4003, steps = 28
shifted from previous position = 0.0232
rotated from previous position = 0.0215 degrees
atoms outside contour = 711, contour level = 0.3
Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.58690614 -0.44062006 -0.67926073 419.12672897
0.03793988 0.85299606 -0.52053653 172.79784811
0.80876557 0.27973502 0.51734570 -160.67268808
Axis 0.45572513 -0.84737609 0.27252223
Axis point 415.90206430 0.00000000 363.56859088
Rotation angle (degrees) 61.40443132
Shift along axis 0.79493773
> fitmap #8 inMap #1
Fit molecule Monomer_side_straight2-coot-1.pdb (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.493, steps = 48
shifted from previous position = 0.033
rotated from previous position = 0.0603 degrees
atoms outside contour = 425, contour level = 0.3
Position of Monomer_side_straight2-coot-1.pdb (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999948 0.00062603 -0.00080026 0.15726136
-0.00062581 0.99999977 0.00027749 0.15407411
0.00080043 -0.00027699 0.99999964 -0.29775941
Axis -0.26323900 -0.75993338 -0.59431177
Axis point 358.36840956 0.00000000 202.36012461
Rotation angle (degrees) 0.06034277
Shift along axis 0.01847854
> fitmap #8 inMap #1
Fit molecule Monomer_side_straight2-coot-1.pdb (#8) to map
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms
average map value = 0.493, steps = 28
shifted from previous position = 0.0186
rotated from previous position = 0.0058 degrees
atoms outside contour = 429, contour level = 0.3
Position of Monomer_side_straight2-coot-1.pdb (#8) relative to
cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999957 0.00058051 -0.00071753 0.13406403
-0.00058028 0.99999978 0.00031392 0.13225338
0.00071771 -0.00031350 0.99999969 -0.24506049
Axis -0.32181446 -0.73616458 -0.59539665
Axis point 337.04560150 0.00000000 189.06541714
Rotation angle (degrees) 0.05585234
Shift along axis 0.00540419
> rename #8 id #3
> select add #3
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> view #3 clip false
> hide #6 models
> select subtract #3
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B
Alignment identifier is 3/B
> select #3/B:208-209
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B:201-209
72 atoms, 71 bonds, 9 residues, 1 model selected
> view #2 clip false
> select sequence ELDSQKMVI
288 atoms, 284 bonds, 36 residues, 4 models selected
> select clear
> select #3/B:201
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:201-208
64 atoms, 63 bonds, 8 residues, 1 model selected
> select #3/B:264
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:264-265
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B:202-264
461 atoms, 464 bonds, 63 residues, 1 model selected
> select #3/B:191
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:191-208
128 atoms, 127 bonds, 18 residues, 1 model selected
> volume zone #1 nearAtoms sel & #3 range 6.37
> surface dust #1 size 10.6
> close #3
> open /Users/melvinshen/Desktop/Monomer_side_straight2-coot-1.pdb
Chain information for Monomer_side_straight2-coot-1.pdb #3
---
Chain | Description
B | No description available
> view #3 clip false
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/Capsid_Top.pdb"
Chain information for Capsid_Top.pdb
---
Chain | Description
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A 4.13/A 4.14/A 4.15/A 4.16/A 4.17/A 4.18/A 4.19/A 4.20/A 4.21/A 4.1/B 4.2/B 4.3/B 4.4/B 4.5/B 4.6/B 4.7/B 4.8/B 4.9/B 4.10/B 4.11/B 4.12/B 4.13/B 4.14/B 4.15/B 4.16/B 4.17/B 4.18/B 4.19/B 4.20/B 4.21/B 4.1/C 4.7/C 4.8/C 4.9/C 4.10/C 4.11/C 4.1/D 4.2/D 4.3/D 4.4/D 4.5/D 4.6/D 4.7/D 4.8/D 4.9/D 4.10/D 4.11/D 4.12/D 4.13/D 4.14/D 4.15/D 4.16/D 4.17/D 4.18/D 4.19/D 4.20/D 4.21/D 4.1/E 4.7/E 4.8/E 4.9/E 4.10/E 4.11/E | No description available
4.2/C 4.3/C 4.4/C 4.5/C 4.6/C 4.12/C 4.13/C 4.14/C 4.15/C 4.16/C 4.17/C 4.18/C 4.19/C 4.20/C 4.21/C 4.2/E 4.3/E 4.4/E 4.5/E 4.6/E 4.12/E 4.13/E 4.14/E 4.15/E 4.16/E 4.17/E 4.18/E 4.19/E 4.20/E 4.21/E 4.2/F 4.3/F 4.4/F 4.5/F 4.6/F 4.12/F 4.13/F 4.14/F 4.15/F 4.16/F 4.17/F 4.18/F 4.19/F 4.20/F 4.21/F | No description available
> hide #2-3,7#4.1-21 cartoons
> show #2-3,7#4.1-21 cartoons
> hide #2-3,7#4.1-21 atoms
> show #6 models
> hide #6 models
> select add #3
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select add #4.4
14141 atoms, 14400 bonds, 1963 residues, 2 models selected
> select subtract #4.4
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select add #4.8
12108 atoms, 12330 bonds, 1680 residues, 2 models selected
> select subtract #4.8
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select add #4.19
14141 atoms, 14400 bonds, 1963 residues, 2 models selected
> select subtract #4.19
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select add #4.19
14141 atoms, 14400 bonds, 1963 residues, 2 models selected
> select add #4.20
26264 atoms, 26745 bonds, 3646 residues, 3 models selected
> select add #4.21
38387 atoms, 39090 bonds, 5329 residues, 4 models selected
> close #4.21
> close #4.19
> close #4.20
> select add #4.18
14141 atoms, 14400 bonds, 1963 residues, 2 models selected
> select subtract #4.18
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select add #4.16
14141 atoms, 14400 bonds, 1963 residues, 2 models selected
> select subtract #4.16
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select add #4.17
14141 atoms, 14400 bonds, 1963 residues, 2 models selected
> close #4.16
> close #4.17
> select add #4.18
14141 atoms, 14400 bonds, 1963 residues, 2 models selected
> close #4.18
> close #4
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Capsid/Fitting/6mer_Fit/Capsid_Top.pdb"
Chain information for Capsid_Top.pdb
---
Chain | Description
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A 4.13/A 4.14/A 4.15/A 4.16/A 4.17/A 4.18/A 4.19/A 4.20/A 4.21/A 4.1/B 4.2/B 4.3/B 4.4/B 4.5/B 4.6/B 4.7/B 4.8/B 4.9/B 4.10/B 4.11/B 4.12/B 4.13/B 4.14/B 4.15/B 4.16/B 4.17/B 4.18/B 4.19/B 4.20/B 4.21/B 4.1/C 4.7/C 4.8/C 4.9/C 4.10/C 4.11/C 4.1/D 4.2/D 4.3/D 4.4/D 4.5/D 4.6/D 4.7/D 4.8/D 4.9/D 4.10/D 4.11/D 4.12/D 4.13/D 4.14/D 4.15/D 4.16/D 4.17/D 4.18/D 4.19/D 4.20/D 4.21/D 4.1/E 4.7/E 4.8/E 4.9/E 4.10/E 4.11/E | No description available
4.2/C 4.3/C 4.4/C 4.5/C 4.6/C 4.12/C 4.13/C 4.14/C 4.15/C 4.16/C 4.17/C 4.18/C 4.19/C 4.20/C 4.21/C 4.2/E 4.3/E 4.4/E 4.5/E 4.6/E 4.12/E 4.13/E 4.14/E 4.15/E 4.16/E 4.17/E 4.18/E 4.19/E 4.20/E 4.21/E 4.2/F 4.3/F 4.4/F 4.5/F 4.6/F 4.12/F 4.13/F 4.14/F 4.15/F 4.16/F 4.17/F 4.18/F 4.19/F 4.20/F 4.21/F | No description available
> hide sel atoms
> show sel cartoons
> select subtract #3
Nothing selected
> hide #2-3,7#4.1-21 atoms
> show #2-3,7#4.1-21 cartoons
> select add #4.21
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select add #4.20
24246 atoms, 24690 bonds, 3366 residues, 2 models selected
> select add #4.19
36369 atoms, 37035 bonds, 5049 residues, 3 models selected
> select add #4.18
48492 atoms, 49380 bonds, 6732 residues, 4 models selected
> select add #4.17
60615 atoms, 61725 bonds, 8415 residues, 5 models selected
> close #4.21
> close #4.17-20
> select add #4.16
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
> select subtract #4.16
Nothing selected
> select add #3
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #2
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> hide #!4 models
> hide #7 models
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #6 models
> close #6
> show #7 models
> select subtract #2
Nothing selected
> select add #7
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> view #7 clip false
> turn z 30 models #7
> turn y 30 models #7
> turn x 30 models #7
> turn z 30 models #7
> turn z 52 models #7
> turn z 72 models #7
> view orient
> view sel
> view orient
> turn x 180
> turn x 90
> turn x 180
> turn y 180
> turn y 30
> turn z 72 models #7
> turn z 70 models #7
> turn z -70 models #7
> turn x 72
> turn x 72 models #7
> view matrix models
> #7,0.51736,0.80053,-0.30249,153.66,0.80002,-0.32693,0.50308,-279.25,0.30384,-0.50227,-0.80958,504.58
> view matrix models
> #7,0.64059,0.75597,-0.13477,67.803,0.73298,-0.54966,0.40077,-201.92,0.22889,-0.35551,-0.90621,541.96
> view matrix models
> #7,0.81789,0.56845,0.089027,-36.929,0.5721,-0.81993,-0.02048,5.6588,0.061354,0.067682,-0.99582,578.06
> view matrix models
> #7,0.65826,0.48291,0.57749,-115.91,0.45933,-0.86543,0.20012,-15.443,0.59641,0.13353,-0.79149,329.51
> view matrix models
> #7,0.65826,0.48291,0.57749,-124.59,0.45933,-0.86543,0.20012,-21.173,0.59641,0.13353,-0.79149,352.68
> view matrix models
> #7,0.65826,0.48291,0.57749,-122.98,0.45933,-0.86543,0.20012,-20.26,0.59641,0.13353,-0.79149,350.62
> view matrix models
> #7,0.45091,0.66089,0.59992,-78.89,0.66034,-0.69921,0.27396,-128.47,0.60053,0.27262,-0.75169,322.17
> view matrix models
> #7,0.3075,0.58085,0.7537,-66.251,0.58096,-0.74191,0.33474,-114.55,0.75361,0.33494,-0.56559,208.97
> view #7 clip false
> view matrix models
> #7,0.3075,0.58085,0.7537,-66.749,0.58096,-0.74191,0.33474,-114.6,0.75361,0.33494,-0.56559,206.88
> view matrix models
> #7,0.29412,0.69051,0.66083,-47.247,0.30515,-0.72306,0.61973,-106.31,0.90575,0.019378,-0.42338,148.71
> view matrix models
> #7,0.29412,0.69051,0.66083,-42.413,0.30515,-0.72306,0.61973,-104.64,0.90575,0.019378,-0.42338,140.37
> undo
> close #7
> rename #4 id #10
> combine #2
===== 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: 46 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
| 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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