![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Closed 10 months ago
#16548 closed defect (duplicate)
Crash in python_instances_of_class
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000031101e000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socketserver.py", line 233 in serve_forever
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/rest_server/server.py", line 90 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/tasks.py", line 285 in _run_function
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000002012b4240 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 162 in copy
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 65 in combine_cmd
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._flinalg, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 108)
{"app_name":"ChimeraX","timestamp":"2025-01-03 10:51:25.00 +0800","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.1 (23B74)","roots_installed":0,"name":"ChimeraX","incident_id":"FA5459D5-4CE9-4902-8FA0-19D24C259B12"}
{
"uptime" : 100000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 8052,
"osVersion" : {
"train" : "macOS 14.1",
"build" : "23B74",
"releaseType" : "User"
},
"captureTime" : "2025-01-03 10:51:02.2510 +0800",
"codeSigningMonitor" : 1,
"incident" : "FA5459D5-4CE9-4902-8FA0-19D24C259B12",
"pid" : 17566,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-02 15:18:42.6445 +0800",
"procStartAbsTime" : 1923160919078,
"procExitAbsTime" : 2552060574384,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"415EFB2F-9949-5714-8659-B453457E1D4B","thirdParty":true},
"parentProc" : "python",
"parentPid" : 15099,
"coalitionName" : "org.pythonmac.unspecified.phenix-1.21.2-5419",
"crashReporterKey" : "2DB44331-A26E-8CBE-0A9B-01589F89B818",
"responsiblePid" : 15098,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 8941,
"sleepWakeUUID" : "AECDD56E-0C51-4025-9516-E3E1C124A99D",
"sip" : "enabled",
"vmRegionInfo" : "0x218a849 is not in any region. Bytes before following region: 4275963831\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100f6b000-100f6f000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x000000000218a849","rawCodes":[1,35170377],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000218a849"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":17566},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x218a849 is not in any region. Bytes before following region: 4275963831\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100f6b000-100f6f000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
> remotecontrol rest start port 57528
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
REST server started on host 127.0.0.1 port 57528
Visit http://127.0.0.1:57528/cmdline.html for CLI interface
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Tail/cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc"
Opened cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc as #1, grid size
384,384,384, pixel 1.06, shown at level 0.233, step 2, values float32
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> volume #1 level 0.3
> surface dust #1 size 10.6
> lighting soft
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Tail/Refinement/6-mers-
> coot-2_ChainMNOPQR.pdb"
Chain information for 6-mers-coot-2_ChainMNOPQR.pdb #2
---
Chain | Description
M N O P Q R | No description available
> combine #2
> rename #2 1
> rename #3 2
> rename #4 3
Already setting window visible!
> select add #3
12612 atoms, 12942 bonds, 1626 residues, 1 model selected
> combine #2
> rename #5 4
> rename #6 5
> select add #2
25224 atoms, 25884 bonds, 3252 residues, 2 models selected
> select add #4
37836 atoms, 38826 bonds, 4878 residues, 3 models selected
> select add #5
50448 atoms, 51768 bonds, 6504 residues, 4 models selected
> select add #6
63060 atoms, 64710 bonds, 8130 residues, 5 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,1,0,0,1.6747,0,1,0,-5.3079,0,0,1,-78.578,#3,1,0,0,1.6747,0,1,0,-5.3079,0,0,1,-78.578,#4,1,0,0,1.6747,0,1,0,-5.3079,0,0,1,-78.578,#5,1,0,0,1.6747,0,1,0,-5.3079,0,0,1,-78.578,#6,1,0,0,1.6747,0,1,0,-5.3079,0,0,1,-78.578
> select subtract #2
50448 atoms, 51768 bonds, 6504 residues, 4 models selected
> view matrix models
> #3,1,0,0,0.8101,0,1,0,-2.6038,0,0,1,-38.52,#4,1,0,0,0.8101,0,1,0,-2.6038,0,0,1,-38.52,#5,1,0,0,0.8101,0,1,0,-2.6038,0,0,1,-38.52,#6,1,0,0,0.8101,0,1,0,-2.6038,0,0,1,-38.52
> select subtract #3
37836 atoms, 38826 bonds, 4878 residues, 3 models selected
> view matrix models
> #4,1,0,0,0.66111,0,1,0,-0.062037,0,0,1,-2.3631,#5,1,0,0,0.66111,0,1,0,-0.062037,0,0,1,-2.3631,#6,1,0,0,0.66111,0,1,0,-0.062037,0,0,1,-2.3631
> select subtract #4
25224 atoms, 25884 bonds, 3252 residues, 2 models selected
> view matrix models
> #5,1,0,0,1.2779,0,1,0,3.0399,0,0,1,39.965,#6,1,0,0,1.2779,0,1,0,3.0399,0,0,1,39.965
> select subtract #5
12612 atoms, 12942 bonds, 1626 residues, 1 model selected
> view matrix models #6,1,0,0,1.8586,0,1,0,5.8261,0,0,1,77.924
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule 1 (#2) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.5205, steps = 92
shifted from previous position = 5.65
rotated from previous position = 6.7 degrees
atoms outside contour = 2619, contour level = 0.3
Position of 1 (#2) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99316355 -0.11673115 0.00000147 25.17075593
0.11673115 0.99316355 0.00009979 -22.41460045
-0.00001311 -0.00009894 1.00000000 -79.55962146
Axis -0.00085122 0.00006242 0.99999964
Axis point 203.87175985 203.10992408 0.00000000
Rotation angle (degrees) 6.70348768
Shift along axis -79.58241727
> select subtract #6
Nothing selected
> select add #2
12612 atoms, 12942 bonds, 1626 residues, 1 model selected
> select subtract #2
Nothing selected
> hide atoms
> show cartoons
> select add #2
12612 atoms, 12942 bonds, 1626 residues, 1 model selected
> fitmap #2 inMap #1
Fit molecule 1 (#2) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.5204, steps = 40
shifted from previous position = 0.018
rotated from previous position = 0.0181 degrees
atoms outside contour = 2620, contour level = 0.3
Position of 1 (#2) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99319742 -0.11644266 -0.00003693 25.11742008
0.11644266 0.99319742 -0.00001791 -22.32153409
0.00003876 0.00001349 1.00000000 -79.59292740
Axis 0.00013483 -0.00032501 0.99999994
Axis point 203.82893810 203.89079026 0.00000000
Rotation angle (degrees) 6.68684291
Shift along axis -79.58228119
> view matrix models
> #2,0.9932,-0.11644,-3.6928e-05,31.827,0.11644,0.9932,-1.791e-05,-21.073,3.8763e-05,1.3488e-05,1,-79.346
> undo
> view matrix models
> #2,0.99309,-0.11724,-0.0048813,26.28,0.11716,0.99301,-0.014584,-19.488,0.006557,0.013911,0.99988,-83.728
> fitmap #2 inMap #1
Fit molecule 1 (#2) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.5204, steps = 44
shifted from previous position = 0.00954
rotated from previous position = 0.883 degrees
atoms outside contour = 2622, contour level = 0.3
Position of 1 (#2) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99319678 -0.11644807 -0.00002334 25.11634358
0.11644807 0.99319678 0.00001634 -22.32753392
0.00002128 -0.00001895 1.00000000 -79.58264167
Axis -0.00015155 -0.00019156 0.99999997
Axis point 203.76851845 203.67879384 0.00000000
Rotation angle (degrees) 6.68715450
Shift along axis -79.58216856
> fitmap #2 inMap #1
Fit molecule 1 (#2) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.5204, steps = 44
shifted from previous position = 0.00206
rotated from previous position = 0.000363 degrees
atoms outside contour = 2619, contour level = 0.3
Position of 1 (#2) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99319653 -0.11645024 -0.00002389 25.11845604
0.11645024 0.99319653 0.00002227 -22.32771860
0.00002114 -0.00002490 1.00000000 -79.58129389
Axis -0.00020252 -0.00019333 0.99999996
Axis point 203.76673858 203.65795465 0.00000000
Rotation angle (degrees) 6.68728001
Shift along axis -79.58206110
> transparency 50
> fitmap #2 inMap #1
Fit molecule 1 (#2) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.5204, steps = 40
shifted from previous position = 0.0236
rotated from previous position = 0.0109 degrees
atoms outside contour = 2616, contour level = 0.3
Position of 1 (#2) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99317580 -0.11662686 0.00000634 25.14320965
0.11662686 0.99317580 0.00008327 -22.39352757
-0.00001600 -0.00008196 1.00000000 -79.56265435
Axis -0.00070834 0.00009578 0.99999974
Axis point 203.83317285 203.17652580 0.00000000
Rotation angle (degrees) 6.69747039
Shift along axis -79.58258889
> fitmap #2 inMap #1
Fit molecule 1 (#2) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.5204, steps = 28
shifted from previous position = 0.00798
rotated from previous position = 0.016 degrees
atoms outside contour = 2612, contour level = 0.3
Position of 1 (#2) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99320742 -0.11635733 0.00003809 25.07196065
0.11635732 0.99320741 0.00014343 -22.36436041
-0.00005452 -0.00013803 0.99999999 -79.54247109
Axis -0.00120945 0.00039795 0.99999919
Axis point 203.76800027 202.75130021 0.00000000
Rotation angle (degrees) 6.68192497
Shift along axis -79.58162978
> fitmap #3 inMap #1
Fit molecule 2 (#3) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1609, steps = 92
shifted from previous position = 2.7
rotated from previous position = 3.79 degrees
atoms outside contour = 9432, contour level = 0.3
Position of 2 (#3) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99807610 0.05889665 0.01937202 -15.45316141
-0.05844158 0.99801949 -0.02327386 16.60031525
-0.02070440 0.02209696 0.99954142 -37.31657115
Axis 0.34363067 0.30353177 -0.88869929
Axis point 97.71449676 457.47537135 0.00000000
Rotation angle (degrees) 3.78523922
Shift along axis 32.89175323
> fitmap #3 inMap #1
Fit molecule 2 (#3) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.161, steps = 64
shifted from previous position = 0.0128
rotated from previous position = 0.015 degrees
atoms outside contour = 9430, contour level = 0.3
Position of 2 (#3) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99806277 0.05910286 0.01943076 -15.50068471
-0.05864330 0.99800408 -0.02342698 16.66354194
-0.02077657 0.02224211 0.99953670 -37.33308350
Axis 0.34457225 0.30336340 -0.88839215
Axis point 98.49909422 457.18903617 0.00000000
Rotation angle (degrees) 3.79973290
Shift along axis 32.88042136
> select subtract #2
Nothing selected
> select add #3
12612 atoms, 12942 bonds, 1626 residues, 1 model selected
> view matrix models
> #3,0.99806,0.059103,0.019431,-13.243,-0.058643,0.998,-0.023427,17.375,-0.020777,0.022242,0.99954,-37.289
> undo
> view matrix models
> #3,0.97655,0.21527,0.002614,-39.54,-0.21518,0.97638,-0.019581,52.185,-0.0067675,0.018559,0.9998,-39.491
> fitmap #3 inMap #1
Fit molecule 2 (#3) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1834, steps = 64
shifted from previous position = 1.53
rotated from previous position = 3.69 degrees
atoms outside contour = 9159, contour level = 0.3
Position of 2 (#3) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.98787941 0.15522301 -0.00030453 -29.09502596
-0.15522290 0.98787941 0.00034374 34.03970820
0.00035420 -0.00029230 0.99999989 -38.60620622
Axis -0.00204880 -0.00212189 -0.99999565
Axis point 203.98298621 202.85878118 0.00000000
Rotation angle (degrees) 8.92976634
Shift along axis 38.59341979
> view matrix models
> #3,0.89586,0.44381,-0.021448,-64.875,-0.44407,0.89595,-0.0089625,113.5,0.015239,0.017554,0.99973,-45.22
> fitmap #3 inMap #1
Fit molecule 2 (#3) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.7467, steps = 48
shifted from previous position = 1.18
rotated from previous position = 1.37 degrees
atoms outside contour = 1441, contour level = 0.3
Position of 2 (#3) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.89367214 0.44872052 0.00004510 -69.76166407
-0.44872052 0.89367214 0.00000511 113.06530399
-0.00003801 -0.00002481 1.00000000 -39.75635667
Axis -0.00003334 0.00009260 -1.00000000
Axis point 203.68886662 203.73068730 0.00000000
Rotation angle (degrees) 26.66162340
Shift along axis 39.76915225
> select subtract #3
Nothing selected
> select add #4
12612 atoms, 12942 bonds, 1626 residues, 1 model selected
> fitmap #4 inMap #1
Fit molecule 3 (#4) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.8443, steps = 68
shifted from previous position = 2.45
rotated from previous position = 0.00865 degrees
atoms outside contour = 1122, contour level = 0.3
Position of 3 (#4) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00015056 -0.00000409 -0.02446989
-0.00015056 0.99999999 0.00001113 0.02845158
0.00000409 -0.00001113 1.00000000 0.00143351
Axis -0.07368311 -0.02709627 -0.99691353
Axis point 188.89248638 162.73821930 0.00000000
Rotation angle (degrees) 0.00865295
Shift along axis -0.00039700
> fitmap #5 inMap #1
Fit molecule 4 (#5) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1664, steps = 100
shifted from previous position = 4.02
rotated from previous position = 1.65 degrees
atoms outside contour = 9249, contour level = 0.3
Position of 4 (#5) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99962841 -0.02712295 -0.00271842 5.91925520
0.02709631 0.99958865 -0.00939761 -3.98225240
0.00297219 0.00932046 0.99995215 36.16318379
Axis 0.32473569 -0.09872515 0.94063812
Axis point 11.29911916 -216.90782691 0.00000000
Rotation angle (degrees) 1.65151973
Shift along axis 36.33181115
> select subtract #4
Nothing selected
> select add #5
12612 atoms, 12942 bonds, 1626 residues, 1 model selected
> view matrix models
> #5,0.97533,0.21972,-0.021219,-35.686,-0.21957,0.97555,0.0092201,47.411,0.022726,-0.0043335,0.99973,34.965
> fitmap #5 inMap #1
Fit molecule 4 (#5) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1617, steps = 96
shifted from previous position = 1.41
rotated from previous position = 2.63 degrees
atoms outside contour = 9345, contour level = 0.3
Position of 4 (#5) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.97181342 0.22627301 -0.06617557 -26.35255322
-0.22648180 0.97400533 0.00442854 48.99686693
0.06545742 0.01068385 0.99779817 23.77581115
Axis 0.01326560 -0.27915343 -0.96015488
Axis point 155.56861491 133.68182116 0.00000000
Rotation angle (degrees) 13.63711990
Shift along axis -36.85568666
> view matrix models
> #5,0.96541,0.23087,0.12113,-63.794,-0.23956,0.96885,0.062695,40.95,-0.10288,-0.089544,0.99066,79.934
> undo
> view matrix models
> #5,0.90494,0.42086,-0.062981,-53.016,-0.41871,0.90702,0.044762,93.667,0.075963,-0.014136,0.99701,26.851
> fitmap #5 inMap #1
Fit molecule 4 (#5) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.7575, steps = 104
shifted from previous position = 1.88
rotated from previous position = 9.58 degrees
atoms outside contour = 1467, contour level = 0.3
Position of 4 (#5) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.83529916 0.54979570 -0.00001116 -78.44528792
-0.54979570 0.83529916 0.00000556 145.54423565
0.00001238 0.00000149 1.00000000 39.77717447
Axis -0.00000370 -0.00002141 -1.00000000
Axis point 203.69992730 203.70291062 0.00000000
Rotation angle (degrees) 33.35299815
Shift along axis -39.78000070
> fitmap #5 inMap #1
Fit molecule 4 (#5) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.7576, steps = 40
shifted from previous position = 0.0125
rotated from previous position = 0.0112 degrees
atoms outside contour = 1467, contour level = 0.3
Position of 4 (#5) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.83540637 0.54963278 -0.00001504 -78.43417795
-0.54963278 0.83540637 0.00002028 145.49864886
0.00002371 -0.00000868 1.00000000 39.77656332
Axis -0.00002634 -0.00003526 -1.00000000
Axis point 203.71419630 203.70925506 0.00000000
Rotation angle (degrees) 33.34182404
Shift along axis -39.77962710
> select subtract #5
Nothing selected
> select add #6
12612 atoms, 12942 bonds, 1626 residues, 1 model selected
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.5478, steps = 92
shifted from previous position = 6.36
rotated from previous position = 6.75 degrees
atoms outside contour = 2518, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99306057 0.11760403 -0.00004234 -22.53893406
-0.11760403 0.99306056 -0.00013517 25.38720150
0.00002615 0.00013921 0.99999999 79.57534362
Axis 0.00116657 -0.00029122 -0.99999928
Axis point 203.70165287 202.88113068 0.00000000
Rotation angle (degrees) 6.75384941
Shift along axis -79.60897263
> view matrix models
> #6,0.95723,0.28931,-0.003319,-49.56,-0.28929,0.95723,0.0053926,66.551,0.0047371,-0.0042018,0.99998,79.504
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1553, steps = 56
shifted from previous position = 1.14
rotated from previous position = 1.99 degrees
atoms outside contour = 9787, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.94678707 0.32185993 -0.00065164 -54.55362328
-0.32186030 0.94678699 -0.00057600 76.49814431
0.00043157 0.00075509 0.99999962 80.50388161
Axis 0.00206779 -0.00168272 -0.99999645
Axis point 203.74691274 202.66153732 0.00000000
Rotation angle (degrees) 18.77552358
Shift along axis -80.74512614
> view matrix models
> #6,0.86418,0.50318,0.0016395,-75.127,-0.50272,0.86353,-0.039888,138.24,-0.021487,0.033646,0.9992,78.429
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1564, steps = 76
shifted from previous position = 3.19
rotated from previous position = 2.56 degrees
atoms outside contour = 9843, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.86280816 0.50546324 -0.00830557 -73.47893680
-0.50545223 0.86284737 0.00353013 130.28032481
0.00895079 0.00115225 0.99995928 75.51315378
Axis -0.00235186 -0.01706751 -0.99985157
Axis point 200.79938530 200.23091232 0.00000000
Rotation angle (degrees) 30.36672529
Shift along axis -77.55269391
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1564, steps = 48
shifted from previous position = 0.00489
rotated from previous position = 0.00341 degrees
atoms outside contour = 9844, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.86280103 0.50547516 -0.00832131 -73.47998957
-0.50546367 0.86284044 0.00358594 130.27625848
0.00899256 0.00111217 0.99995895 75.51393336
Axis -0.00244663 -0.01712396 -0.99985038
Axis point 200.77327919 200.23856696 0.00000000
Rotation angle (degrees) 30.36754100
Shift along axis -77.55370171
> view matrix models
> #6,0.71606,0.69784,-0.016615,-81.101,-0.69796,0.71613,-0.0023007,200.57,0.010293,0.013244,0.99986,72.798
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.154, steps = 52
shifted from previous position = 0.894
rotated from previous position = 1.03 degrees
atoms outside contour = 9774, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.71809602 0.69594351 0.00085727 -84.51672464
-0.69594403 0.71809527 0.00104721 198.99106436
0.00011320 -0.00134861 0.99999908 76.93930319
Axis -0.00172127 0.00053457 -0.99999838
Axis point 203.35333193 204.00339380 0.00000000
Rotation angle (degrees) 44.10256142
Shift along axis -76.68732624
> view matrix models
> #6,0.57718,0.81662,-0.00023085,-80.173,-0.81652,0.57711,-0.015445,255.61,-0.01248,0.0091032,0.99988,77.399
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1543, steps = 60
shifted from previous position = 1.55
rotated from previous position = 0.963 degrees
atoms outside contour = 9747, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.57628034 0.81725198 0.00042346 -80.20649710
-0.81725167 0.57627944 0.00130583 252.53039931
0.00082317 -0.00109860 0.99999906 78.29419064
Axis -0.00147105 -0.00024454 -0.99999889
Axis point 203.35548361 203.71600244 0.00000000
Rotation angle (degrees) 54.81071997
Shift along axis -78.23787037
> view matrix models
> #6,0.42679,0.90435,-0.00087326,-67.233,-0.90417,0.42668,-0.020611,305.14,-0.018267,0.0095861,0.99979,80.049
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.548, steps = 56
shifted from previous position = 1.37
rotated from previous position = 2.33 degrees
atoms outside contour = 2516, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.39489070 0.91872811 0.00000695 -63.88022937
-0.91872811 0.39489070 -0.00001401 310.42767222
-0.00001562 -0.00000085 1.00000000 79.61262700
Axis 0.00000716 0.00001228 -1.00000000
Axis point 203.71968374 203.70807511 0.00000000
Rotation angle (degrees) 66.74084252
Shift along axis -79.60927144
> select subtract #6
Nothing selected
> select add #6
12612 atoms, 12942 bonds, 1626 residues, 1 model selected
> view matrix models
> #6,0.99586,-0.090705,-0.0065575,20.661,0.090935,0.99231,0.08402,-33.953,-0.001114,-0.084268,0.99644,97.723
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1683, steps = 96
shifted from previous position = 2.72
rotated from previous position = 6.84 degrees
atoms outside contour = 9612, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99997414 -0.00718772 -0.00024804 1.52251197
0.00718758 0.99997401 -0.00055933 -1.33775645
0.00025206 0.00055753 0.99999981 82.16189166
Axis 0.07741273 -0.03466322 0.99639637
Axis point -211.90770871 -670.89096412 0.00000000
Rotation angle (degrees) 0.41331509
Shift along axis 82.03004353
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1683, steps = 48
shifted from previous position = 0.0142
rotated from previous position = 0.00905 degrees
atoms outside contour = 9608, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99997510 -0.00705405 -0.00020072 1.49425985
0.00705392 0.99997492 -0.00062868 -1.30223250
0.00020514 0.00062725 0.99999978 82.14750685
Axis 0.08863595 -0.02864307 0.99565217
Axis point -151.10123088 -817.48669714 0.00000000
Rotation angle (degrees) 0.40593169
Shift along axis 81.96008849
> view matrix models
> #6,0.9687,-0.24823,0.0011659,56.725,0.24813,0.96844,0.023748,-48.913,-0.0070239,-0.022715,0.99972,88.433
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1609, steps = 76
shifted from previous position = 1.77
rotated from previous position = 3.93 degrees
atoms outside contour = 9601, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.98255897 -0.18594231 -0.00182214 41.79297187
0.18594064 0.98256042 -0.00104453 -34.10542917
0.00198458 0.00068751 0.99999779 80.00168934
Axis 0.00465719 -0.01023570 0.99993677
Axis point 198.13594938 204.16110261 0.00000000
Rotation angle (degrees) 10.71671295
Shift along axis 80.54036131
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1609, steps = 40
shifted from previous position = 0.0166
rotated from previous position = 0.00534 degrees
atoms outside contour = 9594, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.98255784 -0.18594738 -0.00191387 41.82020558
0.18594569 0.98255949 -0.00102938 -34.09491124
0.00207190 0.00065555 0.99999764 79.99378389
Axis 0.00453039 -0.01071681 0.99993231
Axis point 197.88692416 204.37899015 0.00000000
Rotation angle (degrees) 10.71705638
Shift along axis 80.54321959
> view matrix models
> #6,0.99994,0.0017398,-0.010859,1.8466,-0.0019287,0.99985,-0.017407,3.966,0.010828,0.017427,0.99979,74.835
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1683, steps = 84
shifted from previous position = 1.77
rotated from previous position = 1.25 degrees
atoms outside contour = 9610, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99997418 -0.00718159 -0.00023586 1.52318911
0.00718144 0.99997401 -0.00063087 -1.32118310
0.00024038 0.00062916 0.99999977 82.14496802
Axis 0.08734373 -0.03301251 0.99563108
Axis point -195.64143289 -784.04527363 0.00000000
Rotation angle (degrees) 0.41327964
Shift along axis 81.96273980
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1683, steps = 72
shifted from previous position = 0.0147
rotated from previous position = 0.00339 degrees
atoms outside contour = 9603, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99997441 -0.00715007 -0.00024421 1.53173465
0.00714990 0.99997421 -0.00068016 -1.30425278
0.00024907 0.00067840 0.99999974 82.13931231
Axis 0.09452298 -0.03431997 0.99493093
Axis point -213.90024340 -867.88017987 0.00000000
Rotation angle (degrees) 0.41175473
Shift along axis 81.91248806
> view matrix models
> #6,0.97929,0.2017,-0.017328,-33.356,-0.20182,0.97941,-0.0057083,46.476,0.01582,0.0090872,0.99983,77.287
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1513, steps = 68
shifted from previous position = 1.51
rotated from previous position = 1.28 degrees
atoms outside contour = 9862, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.97903838 0.20363574 0.00404288 -38.12444152
-0.20363829 0.97904617 0.00022542 45.76840429
-0.00391226 -0.00104398 0.99999180 84.84863170
Axis -0.00311622 0.01952884 -0.99980444
Axis point 211.15880411 210.23751885 0.00000000
Rotation angle (degrees) 11.75205408
Shift along axis -83.81943016
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1514, steps = 48
shifted from previous position = 0.0175
rotated from previous position = 0.0209 degrees
atoms outside contour = 9861, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.97896853 0.20397320 0.00394306 -38.16017282
-0.20397539 0.97897600 0.00015845 45.86849350
-0.00382784 -0.00095940 0.99999221 84.79702533
Axis -0.00273966 0.01904519 -0.99981487
Axis point 211.05535850 209.97155022 0.00000000
Rotation angle (degrees) 11.77167243
Shift along axis -83.80320705
> view matrix models
> #6,0.90969,-0.41418,-0.030445,108.83,0.4153,0.90707,0.069001,-79.545,-0.00096328,-0.075413,0.99715,99.955
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1564, steps = 104
shifted from previous position = 6.23
rotated from previous position = 6.76 degrees
atoms outside contour = 9857, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.86839190 -0.49582838 -0.00705162 129.08669829
0.49581762 0.86842032 -0.00332303 -73.56479082
0.00777142 -0.00061063 0.99996961 76.13568118
Axis 0.00273493 -0.01494620 0.99988456
Axis point 200.86024084 206.60312008 0.00000000
Rotation angle (degrees) 29.72781119
Shift along axis 77.57944946
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.1564, steps = 28
shifted from previous position = 0.0192
rotated from previous position = 0.0221 degrees
atoms outside contour = 9863, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.86831870 -0.49596072 -0.00675283 129.08226364
0.49595122 0.86834473 -0.00313304 -73.60320630
0.00741765 -0.00062860 0.99997229 76.21603764
Axis 0.00252460 -0.01428452 0.99989478
Axis point 200.99290771 206.50704678 0.00000000
Rotation angle (degrees) 29.73625166
Shift along axis 77.58528621
> view matrix models
> #6,0.68331,-0.73011,-0.0046307,214.05,0.72967,0.68265,0.039612,-92.017,-0.02576,-0.030446,0.9992,89.205
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.175, steps = 64
shifted from previous position = 0.82
rotated from previous position = 2.34 degrees
atoms outside contour = 9458, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.68825985 -0.72546425 0.00004632 211.28043517
0.72546422 0.68825980 -0.00033826 -84.21512628
0.00021352 0.00026641 0.99999994 76.68689196
Axis 0.00041675 -0.00011524 0.99999991
Axis point 203.60430805 203.69962698 0.00000000
Rotation angle (degrees) 46.50748615
Shift along axis 76.78464042
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.175, steps = 48
shifted from previous position = 0.021
rotated from previous position = 0.0199 degrees
atoms outside contour = 9452, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.68848122 -0.72525417 -0.00001709 211.18503336
0.72525416 0.68848121 -0.00018426 -84.24444458
0.00014540 0.00011446 0.99999998 76.72881646
Axis 0.00020594 -0.00011202 0.99999997
Axis point 203.64033539 203.69607919 0.00000000
Rotation angle (degrees) 46.48999710
Shift along axis 76.78174372
> view matrix models
> #6,0.93303,0.3432,-0.10799,-34.523,-0.35003,0.9353,-0.051862,94.977,0.083205,0.086189,0.9928,43.724
> view matrix models
> #6,0.60447,0.77986,-0.16257,-45.529,-0.79008,0.61299,0.0028775,239.25,0.1019,0.1267,0.98669,32.894
> view matrix models
> #6,0.38132,0.90814,-0.17283,-24.128,-0.91948,0.39194,0.030794,305.01,0.095705,0.14718,0.98447,30.434
> fitmap #6 inMap #1
Fit molecule 5 (#6) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.548, steps = 88
shifted from previous position = 2.84
rotated from previous position = 10.1 degrees
atoms outside contour = 2518, contour level = 0.3
Position of 5 (#6) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.39495007 0.91870258 0.00002735 -63.89088729
-0.91870258 0.39495007 -0.00003255 310.40886347
-0.00004070 -0.00001228 0.99999999 79.62003957
Axis 0.00001103 0.00003704 -1.00000000
Axis point 203.71830243 203.71092519 0.00000000
Rotation angle (degrees) 66.73713995
Shift along axis -79.60924676
> select add #4
25224 atoms, 25884 bonds, 3252 residues, 2 models selected
> select subtract #6
12612 atoms, 12942 bonds, 1626 residues, 1 model selected
> fitmap #4 inMap #1
Fit molecule 3 (#4) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.8443, steps = 40
shifted from previous position = 0.00289
rotated from previous position = 0.0193 degrees
atoms outside contour = 1120, contour level = 0.3
Position of 3 (#4) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 -0.00018585 -0.00001571 0.04554426
0.00018585 0.99999998 0.00001219 -0.03834880
0.00001571 -0.00001219 1.00000000 0.00123161
Axis -0.06521041 -0.08404977 0.99432552
Axis point 205.69287168 245.55350029 0.00000000
Rotation angle (degrees) 0.01070942
Shift along axis 0.00147787
> fitmap #4 inMap #1
Fit molecule 3 (#4) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.8443, steps = 40
shifted from previous position = 0.00705
rotated from previous position = 0.0182 degrees
atoms outside contour = 1123, contour level = 0.3
Position of 3 (#4) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00013036 0.00000085 -0.01598481
-0.00013036 0.99999999 0.00002172 0.02741381
-0.00000085 -0.00002172 1.00000000 0.00664139
Axis -0.16433333 0.00640676 -0.98638406
Axis point 210.46155735 127.35522878 0.00000000
Rotation angle (degrees) 0.00757244
Shift along axis -0.00374849
> fitmap #3 inMap #1
Fit molecule 2 (#3) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.7466, steps = 44
shifted from previous position = 0.0143
rotated from previous position = 0.00531 degrees
atoms outside contour = 1438, contour level = 0.3
Position of 2 (#3) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.89363310 0.44879826 0.00006476 -69.76589352
-0.44879826 0.89363310 -0.00002030 113.08300315
-0.00006698 -0.00001093 1.00000000 -39.74872065
Axis 0.00001044 0.00014676 -0.99999999
Axis point 203.67243298 203.72252252 0.00000000
Rotation angle (degrees) 26.66660817
Shift along axis 39.76458847
> fitmap #2 inMap #1
Fit molecule 1 (#2) to map cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) using 12612 atoms
average map value = 0.5205, steps = 40
shifted from previous position = 0.0234
rotated from previous position = 0.00871 degrees
atoms outside contour = 2617, contour level = 0.3
Position of 1 (#2) relative to cryosparc_P2_J252_012_volume_map_sharp TAIL
TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99319761 -0.11644098 -0.00002129 25.11307047
0.11644098 0.99319761 0.00003160 -22.33567170
0.00001746 -0.00003386 1.00000000 -79.57902802
Axis -0.00028107 -0.00016638 0.99999995
Axis point 203.82594394 203.57265150 0.00000000
Rotation angle (degrees) 6.68674599
Shift along axis -79.58236600
> select subtract #4
Nothing selected
> combine #2-6
Remapping chain ID 'M' in 2 #3 to 'S'
Remapping chain ID 'N' in 2 #3 to 'T'
Remapping chain ID 'O' in 2 #3 to 'U'
Remapping chain ID 'P' in 2 #3 to 'V'
Remapping chain ID 'Q' in 2 #3 to 'W'
Remapping chain ID 'R' in 2 #3 to 'X'
Remapping chain ID 'M' in 3 #4 to 'Y'
Remapping chain ID 'N' in 3 #4 to 'Z'
Remapping chain ID 'O' in 3 #4 to 'a'
Remapping chain ID 'P' in 3 #4 to 'b'
Remapping chain ID 'Q' in 3 #4 to 'c'
Remapping chain ID 'R' in 3 #4 to 'd'
Remapping chain ID 'M' in 4 #5 to 'e'
Remapping chain ID 'N' in 4 #5 to 'f'
Remapping chain ID 'O' in 4 #5 to 'g'
Remapping chain ID 'P' in 4 #5 to 'h'
Remapping chain ID 'Q' in 4 #5 to 'i'
Remapping chain ID 'R' in 4 #5 to 'j'
Remapping chain ID 'M' in 5 #6 to 'k'
Remapping chain ID 'N' in 5 #6 to 'l'
Remapping chain ID 'O' in 5 #6 to 'm'
Remapping chain ID 'P' in 5 #6 to 'n'
Remapping chain ID 'Q' in 5 #6 to 'o'
Remapping chain ID 'R' in 5 #6 to 'p'
> select add #7
63060 atoms, 64710 bonds, 8130 residues, 1 model selected
> fitmap #7 inMap #1
Fit molecule combination (#7) to map cryosparc_P2_J252_012_volume_map_sharp
TAIL TUBE.mrc (#1) using 63060 atoms
average map value = 0.6834, steps = 44
shifted from previous position = 0.00839
rotated from previous position = 0.0068 degrees
atoms outside contour = 9156, contour level = 0.3
Position of combination (#7) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#1) coordinates:
Matrix rotation and translation
0.99318780 -0.11652460 -0.00009877 25.15614902
0.11652461 0.99318780 0.00006322 -22.35160990
0.00009073 -0.00007430 0.99999999 -79.58682774
Axis -0.00059006 -0.00081312 0.99999950
Axis point 204.27349222 203.54189357 0.00000000
Rotation angle (degrees) 6.69157309
Shift along axis -79.58345673
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Tail/5-stack-ring.pdb" models
> #7 selectedOnly true relModel #1
> hide #7 models
> select subtract #7
Nothing selected
> hide #6 models
> hide #5 models
> hide #3 models
> hide #2 models
> hide #4 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Tail/5-stack-ring.pdb"
Chain information for 5-stack-ring.pdb #8
---
Chain | Description
M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m n o p | No description available
> hide #8 atoms
> show #8 cartoons
> show #7 models
> hide #7 models
> hide #!1 models
> select add #8
63060 atoms, 64710 bonds, 8130 residues, 1 model selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Tail/5-stack-ring.pdb" models
> #8 displayedOnly true selectedOnly true relModel #1
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Tail/5-stack-ring.pdb" models
> #8 selectedOnly true relModel #1
> show #!1 models
Drag select of 1 cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc , 2776
residues
Drag select of 1 cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc , 8130
residues
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Tail/5_stack.pdb" selectedOnly
> true relModel #1
> select add #8
63060 atoms, 64710 bonds, 8130 residues, 3 models selected
> select subtract #8
2 models selected
> hide #8 models
> select subtract #1
Nothing selected
> hide #!1 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Tail/5_stack.pdb"
Chain information for 5_stack.pdb #9
---
Chain | Description
M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m n o p | No description available
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> close #2
> close
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/P2_J332_011_C12_volume_map_sharp.mrc"
Opened P2_J332_011_C12_volume_map_sharp.mrc as #1, grid size 512,512,512,
pixel 1.06, shown at level 0.285, step 2, values float32
> surface dust #1 size 10.6
> volume #1 step 1
> volume #1 level 0.3
> close
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/P2_J357_007_volume_map_sharp_C6.mrc"
Opened P2_J357_007_volume_map_sharp_C6.mrc as #1, grid size 512,512,512, pixel
1.06, shown at level 0.215, step 2, values float32
> surface dust #1 size 10.6
> volume #1 step 1
> volume #1 level 0.3
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper/Stopper_45_1-coot-4_6mer.pdb"
Chain information for Stopper_45_1-coot-4_6mer.pdb #2
---
Chain | Description
A B C D E F | No description available
> hide atoms
> show cartoons
> transparency 50
> select add #2
5496 atoms, 5634 bonds, 714 residues, 1 model selected
> fitmap #2 inMap #1
Fit molecule Stopper_45_1-coot-4_6mer.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc (#1) using 5496 atoms
average map value = 0.9887, steps = 36
shifted from previous position = 0.0353
rotated from previous position = 0.00942 degrees
atoms outside contour = 743, contour level = 0.3
Position of Stopper_45_1-coot-4_6mer.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 -0.00012685 0.00010352 -0.00482203
0.00012685 0.99999999 -0.00001422 -0.03742516
-0.00010352 0.00001423 0.99999999 -0.00305375
Axis 0.08657201 0.62988091 0.77185188
Axis point 164.19591092 -20.04877286 0.00000000
Rotation angle (degrees) 0.00941654
Shift along axis -0.02634789
> select subtract #2
Nothing selected
> hide #2 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Terminator/Terminator_1-coot-1_6mer.pdb"
Chain information for Terminator_1-coot-1_6mer.pdb #3
---
Chain | Description
D E F G H I | No description available
> fitmap #3 inMap #1
Fit molecule Terminator_1-coot-1_6mer.pdb (#3) to map
P2_J357_007_volume_map_sharp_C6.mrc (#1) using 7296 atoms
average map value = 1.093, steps = 40
shifted from previous position = 0.0133
rotated from previous position = 0.0171 degrees
atoms outside contour = 1227, contour level = 0.3
Position of Terminator_1-coot-1_6mer.pdb (#3) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#1) coordinates:
Matrix rotation and translation
0.99999996 -0.00027900 0.00009991 0.06872718
0.00027900 0.99999996 -0.00003770 -0.06846304
-0.00009990 0.00003773 0.99999999 0.01703047
Axis 0.12624778 0.33441324 0.93393216
Axis point 247.44523378 245.53598882 0.00000000
Rotation angle (degrees) 0.01711618
Shift along axis 0.00168701
> hide #3 atoms
> show #3 cartoons
> fitmap #3 inMap #1
Fit molecule Terminator_1-coot-1_6mer.pdb (#3) to map
P2_J357_007_volume_map_sharp_C6.mrc (#1) using 7296 atoms
average map value = 1.093, steps = 28
shifted from previous position = 0.0043
rotated from previous position = 0.00227 degrees
atoms outside contour = 1227, contour level = 0.3
Position of Terminator_1-coot-1_6mer.pdb (#3) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#1) coordinates:
Matrix rotation and translation
0.99999994 -0.00031836 0.00009902 0.08000087
0.00031837 0.99999995 -0.00003317 -0.08130862
-0.00009901 0.00003320 0.99999999 0.02211917
Axis 0.09903531 0.29552580 0.95018762
Axis point 259.99120552 249.71364150 0.00000000
Rotation angle (degrees) 0.01919731
Shift along axis 0.00491148
> color #3 bychain
> color #3 #30e1d1ff
> color #3 bychain
> show #2 models
> select add #2
5496 atoms, 5634 bonds, 714 residues, 1 model selected
> select subtract #2
Nothing selected
> hide #2 models
> hide #3 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/P2_J332_011_C12_volume_map_sharp.mrc"
Opened P2_J332_011_C12_volume_map_sharp.mrc as #4, grid size 512,512,512,
pixel 1.06, shown at level 0.285, step 2, values float32
> surface dust #1 size 10.6
> surface dust #4 size 10.6
> volume #4 level 0.3
> volume #4 step 1
> hide #!4 models
> ui mousemode right "map eraser"
> volume erase #1 center 287.4,250.18,195.08 radius 46.202
Opened P2_J357_007_volume_map_sharp_C6.mrc copy as #6, grid size 512,512,512,
pixel 1.06, shown at step 1, values float32
> surface dust #6 size 10.6
> hide #5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!1 models
> show #2 models
> volume zone #1 nearAtoms #2 range 6.37
> surface dust #1 size 10.6
> ui tool show "Color Zone"
> select add #2
5496 atoms, 5634 bonds, 714 residues, 1 model selected
> color sel lime
> color zone #1 near #2 distance 6.37
> volume splitbyzone #1
Opened P2_J357_007_volume_map_sharp_C6.mrc 0 as #7.1, grid size 512,512,512,
pixel 1.06, shown at level 0.3, step 1, values float32
Opened P2_J357_007_volume_map_sharp_C6.mrc 1 as #7.2, grid size 512,512,512,
pixel 1.06, shown at level 0.3, step 1, values float32
> surface dust #7.1 size 10.6
> surface dust #7.2 size 10.6
> hide #!7.1 models
> select subtract #2
Nothing selected
> hide #2 models
> transparency #7.2.1 50
> volume #7.2 color #c2f5f080
> show #2 models
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected atoms"
> select #2/A:2
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
48 atoms, 49 bonds, 7 residues, 1 model selected
> select #2/A:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
48 atoms, 49 bonds, 7 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #2/B #2/C #2/D #2/E #2/F
Alignment identifier is 1
> select #2/A:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A-F:3
66 atoms, 66 bonds, 6 residues, 1 model selected
> select #2/A-F:3-7
198 atoms, 198 bonds, 30 residues, 1 model selected
> select #2/A-F:6-7
78 atoms, 72 bonds, 12 residues, 1 model selected
> select #2/A-F:6-7
78 atoms, 72 bonds, 12 residues, 1 model selected
> select #2/A-F:5
30 atoms, 24 bonds, 6 residues, 1 model selected
> select #2/A-F:4
24 atoms, 18 bonds, 6 residues, 1 model selected
> select #2/A-F:4
24 atoms, 18 bonds, 6 residues, 1 model selected
> select #2/A-F:3
66 atoms, 66 bonds, 6 residues, 1 model selected
> select #2/A-F:3
66 atoms, 66 bonds, 6 residues, 1 model selected
> select #2/A-F:2
42 atoms, 42 bonds, 6 residues, 1 model selected
> select #2/A-F:2
42 atoms, 42 bonds, 6 residues, 1 model selected
> select #2/A-F:1
48 atoms, 42 bonds, 6 residues, 1 model selected
> select #2/A-F:1
48 atoms, 42 bonds, 6 residues, 1 model selected
> select #2/A-F:1
48 atoms, 42 bonds, 6 residues, 1 model selected
> select #2/A-F:1-2
90 atoms, 90 bonds, 12 residues, 1 model selected
> select #2/A-F:1
48 atoms, 42 bonds, 6 residues, 1 model selected
> select #2/A-F:1
48 atoms, 42 bonds, 6 residues, 1 model selected
> fitmap #2 inMap #1
Fit molecule Stopper_45_1-coot-4_6mer.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc (#1) using 5496 atoms
average map value = 0.9723, steps = 40
shifted from previous position = 0.00968
rotated from previous position = 0.0215 degrees
atoms outside contour = 811, contour level = 0.3
Position of Stopper_45_1-coot-4_6mer.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#1) coordinates:
Matrix rotation and translation
0.99999997 0.00014786 0.00020157 -0.08820161
-0.00014781 0.99999996 -0.00024899 0.07166263
-0.00020161 0.00024896 0.99999995 -0.04127003
Axis 0.70567211 0.57136577 -0.41900840
Axis point 0.00000000 172.56553048 296.96563239
Rotation angle (degrees) 0.02021544
Shift along axis -0.00400335
> fitmap #2 inMap #1
Fit molecule Stopper_45_1-coot-4_6mer.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc (#1) using 5496 atoms
average map value = 0.9722, steps = 28
shifted from previous position = 0.0112
rotated from previous position = 0.0267 degrees
atoms outside contour = 805, contour level = 0.3
Position of Stopper_45_1-coot-4_6mer.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#1) coordinates:
Matrix rotation and translation
0.99999986 -0.00019902 0.00048030 -0.04335928
0.00019907 0.99999997 -0.00010839 -0.05738394
-0.00048028 0.00010849 0.99999988 0.07113122
Axis 0.20418420 0.90434644 0.37478838
Axis point 174.68700346 0.00000000 75.83284001
Rotation angle (degrees) 0.03042914
Shift along axis -0.03408909
> fitmap #2 inMap #1
Fit molecule Stopper_45_1-coot-4_6mer.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc (#1) using 5496 atoms
average map value = 0.9722, steps = 28
shifted from previous position = 0.00555
rotated from previous position = 0.0304 degrees
atoms outside contour = 811, contour level = 0.3
Position of Stopper_45_1-coot-4_6mer.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#1) coordinates:
Matrix rotation and translation
0.99999995 0.00023785 0.00021679 -0.12215567
-0.00023779 0.99999994 -0.00025290 0.08516635
-0.00021685 0.00025284 0.99999994 -0.03719868
Axis 0.61783659 0.52974853 -0.58107180
Axis point 0.00000000 167.28590087 355.03438818
Rotation angle (degrees) 0.02345013
Shift along axis -0.00874039
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Tail/RealSpaceRefine_11/5_stack
> copy_real_space_refined_011.pdb"
Chain information for 5_stack copy_real_space_refined_011.pdb #5
---
Chain | Description
M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m n o p | No description available
> show #!1 models
> hide #!1 models
> hide #!7 models
> show #!7 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Tail/cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc"
Opened cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc as #8, grid size
384,384,384, pixel 1.06, shown at level 0.233, step 2, values float32
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 2 maps.
> surface dust #7.2 size 10.6
> surface dust #8 size 10.6
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.6977, steps = 48
shifted from previous position = 0.00776
rotated from previous position = 0.00837 degrees
atoms outside contour = 13286, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.99999999 -0.00002205 0.00012933 -0.01850076
0.00002206 1.00000000 -0.00006426 0.01475373
-0.00012933 0.00006426 0.99999999 0.01660697
Axis 0.43985956 0.88528827 0.15095778
Axis point 119.72077552 0.00000000 168.32823298
Rotation angle (degrees) 0.00837029
Shift along axis 0.00743052
> hide sel atoms
> show sel cartoons
> select add #5
63108 atoms, 64752 bonds, 8136 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.6978, steps = 28
shifted from previous position = 0.00268
rotated from previous position = 0.00885 degrees
atoms outside contour = 13290, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
1.00000000 -0.00002227 -0.00000455 0.01121654
0.00002227 1.00000000 0.00001273 -0.00157515
0.00000455 -0.00001273 1.00000000 0.00502737
Axis -0.48864305 -0.17481384 0.85479125
Axis point 77.86294545 483.71781396 0.00000000
Rotation angle (degrees) 0.00149279
Shift along axis -0.00090817
> ui mousemode right "translate selected models"
> select add #2
68556 atoms, 70344 bonds, 8844 residues, 2 models selected
> select subtract #2
63060 atoms, 64710 bonds, 8130 residues, 1 model selected
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.6977, steps = 44
shifted from previous position = 0.00768
rotated from previous position = 0.00327 degrees
atoms outside contour = 13307, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
1.00000000 -0.00002020 -0.00004256 0.01429129
0.00002020 1.00000000 -0.00002984 0.01389865
0.00004256 0.00002984 1.00000000 -0.01139070
Axis 0.53505117 -0.76320215 0.36227437
Axis point 207.33066451 -0.00000000 424.90951795
Rotation angle (degrees) 0.00319496
Shift along axis -0.00708747
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.6976, steps = 28
shifted from previous position = 0.00981
rotated from previous position = 0.0121 degrees
atoms outside contour = 13293, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.99999999 -0.00001412 0.00011938 -0.02936264
0.00001411 0.99999999 0.00010442 -0.01024572
-0.00011938 -0.00010442 0.99999999 0.04888396
Axis -0.65579136 0.74972240 0.08862288
Axis point 397.65477414 0.00000000 158.60498280
Rotation angle (degrees) 0.00912333
Shift along axis 0.01590656
> view matrix models
> #5,0.98732,0.1587,0.0047282,-30.706,-0.15874,0.98725,0.011489,32.646,-0.0028447,-0.012093,0.99992,3.0622
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1861, steps = 68
shifted from previous position = 2.79
rotated from previous position = 2.51 degrees
atoms outside contour = 44286, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.99313030 0.11701333 0.00030184 -22.48579368
-0.11701335 0.99313034 0.00006493 25.22978120
-0.00029217 -0.00009980 0.99999995 -2.70919745
Axis -0.00070391 0.00253822 -0.99999653
Axis point 203.57172842 204.09903258 0.00000000
Rotation angle (degrees) 6.71978864
Shift along axis 2.78905472
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1862, steps = 40
shifted from previous position = 0.0177
rotated from previous position = 0.00835 degrees
atoms outside contour = 44316, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.99313088 0.11700866 0.00016733 -22.45187018
-0.11700867 0.99313089 0.00000909 25.25667599
-0.00016512 -0.00002861 0.99999999 -2.75085095
Axis -0.00016109 0.00142059 -0.99999898
Axis point 203.85220386 203.84563977 0.00000000
Rotation angle (degrees) 6.71950230
Shift along axis 2.79034429
> view matrix models
> #5,0.96846,0.24858,0.016977,-47.62,-0.24858,0.96861,-0.0019082,57.456,-0.016919,-0.0023723,0.99985,1.1706
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1741, steps = 72
shifted from previous position = 1.67
rotated from previous position = 3.57 degrees
atoms outside contour = 44698, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.95199268 0.30612071 -0.00020906 -52.51135928
-0.30612071 0.95199270 0.00000012 72.15295257
0.00019906 0.00006388 0.99999998 -1.17241161
Axis 0.00010414 -0.00066661 -0.99999977
Axis point 203.78993420 203.49777766 0.00000000
Rotation angle (degrees) 17.82560548
Shift along axis 1.11884488
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1741, steps = 44
shifted from previous position = 0.0155
rotated from previous position = 0.00948 degrees
atoms outside contour = 44674, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.95200418 0.30608497 -0.00015639 -52.53025587
-0.30608499 0.95200418 -0.00015222 72.17398744
0.00010229 0.00019278 0.99999998 -1.17085759
Axis 0.00056357 -0.00042257 -0.99999975
Axis point 203.87461579 203.59055952 0.00000000
Rotation angle (degrees) 17.82345549
Shift along axis 1.11075384
> view matrix models
> #5,0.89859,0.43863,0.011942,-71.086,-0.43869,0.89863,0.0029189,109.45,-0.009451,-0.0078617,0.99992,2.4323
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1593, steps = 88
shifted from previous position = 0.319
rotated from previous position = 1.35 degrees
atoms outside contour = 45151, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.90641992 0.42236855 -0.00278152 -66.62873024
-0.42237234 0.90642195 -0.00092777 105.20609680
0.00212937 0.00201578 0.99999570 -1.77568616
Axis 0.00348448 -0.00581336 -0.99997703
Axis point 204.12482418 202.98385034 0.00000000
Rotation angle (degrees) 24.98494770
Shift along axis 0.93187803
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1594, steps = 60
shifted from previous position = 0.0185
rotated from previous position = 0.0102 degrees
atoms outside contour = 45135, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.90638034 0.42245443 -0.00263460 -66.66966379
-0.42245800 0.90638199 -0.00096221 105.23929772
0.00198147 0.00198514 0.99999607 -1.72095405
Axis 0.00348827 -0.00546326 -0.99997899
Axis point 204.12526332 203.05856121 0.00000000
Rotation angle (degrees) 24.99031689
Shift along axis 0.91340642
> view matrix models
> #5,0.70122,0.71278,0.015171,-87.593,-0.71294,0.70111,0.012745,203.49,-0.0015518,-0.019753,0.9998,3.4664
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.178, steps = 84
shifted from previous position = 1.93
rotated from previous position = 3.41 degrees
atoms outside contour = 44433, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.74011731 0.67247777 -0.00011935 -84.00686856
-0.67247772 0.74011731 0.00029774 189.88509868
0.00028855 -0.00014010 0.99999995 0.97669934
Axis -0.00032554 -0.00030328 -0.99999990
Axis point 203.67131118 203.63177852 0.00000000
Rotation angle (degrees) 42.25859264
Shift along axis -1.00693996
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.178, steps = 40
shifted from previous position = 0.0151
rotated from previous position = 0.0105 degrees
atoms outside contour = 44434, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.74012101 0.67247370 -0.00003198 -84.03785637
-0.67247370 0.74012101 0.00013723 189.90909785
0.00011595 -0.00008007 0.99999999 0.99875719
Axis -0.00016157 -0.00010999 -0.99999998
Axis point 203.68920120 203.68463632 0.00000000
Rotation angle (degrees) 42.25827542
Shift along axis -1.00606765
> view matrix models
> #5,0.58503,0.81066,0.023608,-85.352,-0.81087,0.58523,-0.0016124,250.02,-0.015123,-0.0182,0.99972,7.8523
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1856, steps = 60
shifted from previous position = 1.84
rotated from previous position = 1.73 degrees
atoms outside contour = 44377, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.60039447 0.79970399 -0.00002423 -81.50250153
-0.79970399 0.60039447 -0.00011821 244.31806079
-0.00007998 0.00009035 0.99999999 2.84382319
Axis 0.00013039 0.00003486 -0.99999999
Axis point 203.71778595 203.71147954 0.00000000
Rotation angle (degrees) 53.10184546
Shift along axis -2.84593448
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1856, steps = 40
shifted from previous position = 0.00861
rotated from previous position = 0.00396 degrees
atoms outside contour = 44386, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.60039468 0.79970384 0.00004349 -81.51793862
-0.79970383 0.60039468 -0.00013161 244.32913545
-0.00013136 0.00004424 0.99999999 2.86360475
Axis 0.00010995 0.00010932 -0.99999999
Axis point 203.72141292 203.73265533 0.00000000
Rotation angle (degrees) 53.10183061
Shift along axis -2.84585709
> view matrix models
> #5,0.40259,0.91513,0.0216,-69.066,-0.91534,0.40269,-0.00039998,308.23,-0.0090642,-0.019611,0.99977,8.7353
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1674, steps = 64
shifted from previous position = 1.22
rotated from previous position = 2.07 degrees
atoms outside contour = 45772, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.42901521 0.90329727 -0.00000757 -67.65107528
-0.90329726 0.42901520 -0.00015011 300.41403150
-0.00013235 0.00007124 0.99999999 4.07532248
Axis 0.00012252 0.00006907 -0.99999999
Axis point 203.80225519 203.71872327 0.00000000
Rotation angle (degrees) 64.59492157
Shift along axis -4.06286112
> view matrix models
> #5,0.49673,0.86775,0.016748,-77.591,-0.86756,0.49698,-0.018617,283.01,-0.024478,-0.0052825,0.99969,10.191
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1602, steps = 76
shifted from previous position = 1.07
rotated from previous position = 1.47 degrees
atoms outside contour = 45903, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.50071131 0.86561423 -0.00043659 -74.55151685
-0.86561431 0.50071137 0.00001927 278.05036233
0.00023528 0.00036827 0.99999990 5.01184068
Axis 0.00020159 -0.00038809 -0.99999990
Axis point 203.75030706 203.64811438 0.00000000
Rotation angle (degrees) 59.95293021
Shift along axis -5.13477818
> view matrix models
> #5,0.27189,0.96198,0.025992,-52.879,-0.96223,0.27215,-0.0069781,345.72,-0.013787,-0.023113,0.99964,12.726
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.156, steps = 68
shifted from previous position = 0.597
rotated from previous position = 2.49 degrees
atoms outside contour = 46683, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.23907541 0.97100100 -0.00012190 -42.76185514
-0.97100099 0.23907538 -0.00019282 352.88113847
-0.00015809 0.00016447 0.99999997 5.73114810
Axis 0.00018398 0.00001863 -0.99999998
Axis point 203.77202764 203.72373325 0.00000000
Rotation angle (degrees) 76.16802506
Shift along axis -5.73244066
> view matrix models
> #5,0.039982,0.99908,0.01567,-11.091,-0.9992,0.039938,0.0031445,398.52,0.0025158,-0.015783,0.99987,8.4606
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1425, steps = 80
shifted from previous position = 2.05
rotated from previous position = 2.3 degrees
atoms outside contour = 47575, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.00245312 0.99963205 0.02701368 -5.60073727
-0.99993576 0.00215315 0.01112795 402.95927909
0.01106569 -0.02703924 0.99957312 10.03389127
Axis -0.01908363 0.00797401 -0.99978609
Axis point 199.07500040 204.39066952 0.00000000
Rotation angle (degrees) 89.88026890
Shift along axis -6.71166036
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1425, steps = 60
shifted from previous position = 0.0262
rotated from previous position = 0.015 degrees
atoms outside contour = 47561, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
0.00230377 0.99963751 0.02682418 -5.52237590
-0.99993723 0.00200868 0.01102244 402.99681399
0.01096456 -0.02684789 0.99957940 9.99456708
Axis -0.01893520 0.00792982 -0.99978927
Axis point 199.10420288 204.36868818 0.00000000
Rotation angle (degrees) 89.88850670
Shift along axis -6.69219990
> view matrix models
> #5,-0.14712,0.98828,0.040612,24.462,-0.98899,-0.14763,0.0098636,431.48,0.015744,-0.038714,0.99913,11.529
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1781, steps = 84
shifted from previous position = 5.95
rotated from previous position = 4.47 degrees
atoms outside contour = 44540, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
-0.21243534 0.97717511 0.00016129 47.91524065
-0.97717512 -0.21243536 0.00008970 446.03394229
0.00012192 -0.00013855 0.99999998 1.01006999
Axis -0.00011679 0.00002014 -0.99999999
Axis point 203.70046094 203.70813069 0.00000000
Rotation angle (degrees) 102.26510889
Shift along axis -1.00668069
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1781, steps = 44
shifted from previous position = 0.023
rotated from previous position = 0.00689 degrees
atoms outside contour = 44509, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
-0.21243821 0.97717450 0.00006047 47.92678214
-0.97717449 -0.21243822 0.00015511 446.00027977
0.00016441 -0.00002614 0.99999999 0.97763250
Axis -0.00009274 -0.00005319 -0.99999999
Axis point 203.69211150 203.68666037 0.00000000
Rotation angle (degrees) 102.26527665
Shift along axis -1.00579876
> view matrix models
> #5,-0.36102,0.93245,0.014514,84.404,-0.93253,-0.36109,0.0022862,466.75,0.0073726,-0.01271,0.99989,2.114
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1856, steps = 72
shifted from previous position = 1.84
rotated from previous position = 2.12 degrees
atoms outside contour = 44385, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
-0.39245336 0.91977188 -0.00023398 96.34255188
-0.91977187 -0.39245340 -0.00016035 471.05769113
-0.00023931 0.00015228 0.99999996 2.86667425
Axis 0.00016995 0.00000290 -0.99999999
Axis point 203.74786922 203.70960998 0.00000000
Rotation angle (degrees) 113.10724379
Shift along axis -2.84893597
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1856, steps = 40
shifted from previous position = 0.0111
rotated from previous position = 0.00782 degrees
atoms outside contour = 44391, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
-0.39244951 0.91977352 -0.00023038 96.33080038
-0.91977354 -0.39244953 -0.00002406 471.02476902
-0.00011254 0.00020245 0.99999997 2.83006974
Axis 0.00012313 -0.00006406 -0.99999999
Axis point 203.73169870 203.69683401 0.00000000
Rotation angle (degrees) 113.10700276
Shift along axis -2.84838014
> view matrix models
> #5,-0.58038,0.8143,0.0088167,154.29,-0.81423,-0.58044,0.010883,485.61,0.01398,-0.00086269,0.9999,0.1947
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1675, steps = 48
shifted from previous position = 1.21
rotated from previous position = 1.2 degrees
atoms outside contour = 45836, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
-0.56783849 0.82313996 -0.00024543 151.82980309
-0.82313995 -0.56783853 -0.00015937 487.09699635
-0.00027055 0.00011153 0.99999996 4.08940830
Axis 0.00016455 0.00001526 -0.99999999
Axis point 203.78206035 203.69183245 0.00000000
Rotation angle (degrees) 124.59963699
Shift along axis -4.05699207
> view matrix models
> #5,-0.70012,0.71309,0.036487,193.79,-0.7139,-0.70003,-0.01728,495.22,0.01322,-0.038147,0.99918,9.2981
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1505, steps = 144
shifted from previous position = 3.73
rotated from previous position = 3.06 degrees
atoms outside contour = 46716, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
-0.72991677 0.68351382 0.00550990 215.20560204
-0.68353564 -0.72988410 -0.00694445 494.76284914
-0.00072504 -0.00883508 0.99996071 4.74784870
Axis -0.00138299 0.00456082 -0.99998864
Axis point 205.34941502 204.87610953 0.00000000
Rotation angle (degrees) 136.87969472
Shift along axis -2.78889684
> view matrix models
> #5,-0.81356,0.5811,0.021106,249.97,-0.58137,-0.81359,-0.009676,491.54,0.011549,-0.020143,0.99973,4.5962
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1445, steps = 88
shifted from previous position = 3.17
rotated from previous position = 2.49 degrees
atoms outside contour = 47207, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
-0.82953204 0.55836098 -0.01046975 261.25810520
-0.55840064 -0.82957071 0.00107999 488.96986606
-0.00808238 0.00674220 0.99994461 3.37984445
Axis 0.00507013 -0.00213773 -0.99998486
Axis point 205.25477158 204.61020766 0.00000000
Rotation angle (degrees) 146.05552256
Shift along axis -3.10046755
> view matrix models
> #5,-0.82953,0.55836,-0.01047,258.58,-0.5584,-0.82957,0.00108,485.45,-0.0080824,0.0067422,0.99994,3.8191
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1445, steps = 72
shifted from previous position = 0.65
rotated from previous position = 0.931 degrees
atoms outside contour = 47204, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
-0.83014838 0.55753234 0.00337003 255.80926482
-0.55754097 -0.83011665 -0.00737592 487.41285425
-0.00131480 -0.00800204 0.99996712 4.93745096
Axis -0.00056150 0.00420133 -0.99999102
Axis point 202.14925738 204.75148596 0.00000000
Rotation angle (degrees) 146.11404269
Shift along axis -3.03326335
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1445, steps = 48
shifted from previous position = 0.00885
rotated from previous position = 0.00456 degrees
atoms outside contour = 47210, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
-0.83018068 0.55748394 0.00342013 255.81380243
-0.55749300 -0.83014905 -0.00735548 487.39792812
-0.00126134 -0.00801308 0.99996710 4.92467924
Axis -0.00058978 0.00419868 -0.99999101
Axis point 202.14145393 204.74736739 0.00000000
Rotation angle (degrees) 146.11736832
Shift along axis -3.02907936
> view matrix models
> #5,-0.91311,0.40751,0.012898,301.35,-0.40758,-0.91317,-0.0029573,472.87,0.010573,-0.0079574,0.99991,2.5123
> view matrix models
> #5,-0.96871,0.24589,0.033762,341.4,-0.24633,-0.96914,-0.00956,452.74,0.030369,-0.017578,0.99938,0.54401
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1467, steps = 60
shifted from previous position = 1.85
rotated from previous position = 1.32 degrees
atoms outside contour = 47149, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
-0.96955824 0.24380726 0.02269026 344.50762310
-0.24441506 -0.96921797 -0.02962786 454.71652080
0.01476832 -0.03427178 0.99930343 7.78945693
Axis -0.00951021 0.01622322 -0.99982317
Axis point 200.40715007 206.06851247 0.00000000
Rotation angle (degrees) 165.86813702
Shift along axis -3.68745302
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.1467, steps = 60
shifted from previous position = 0.0154
rotated from previous position = 0.00625 degrees
atoms outside contour = 47168, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
-0.96957692 0.24372830 0.02274003 344.53070529
-0.24433707 -0.96923921 -0.02957631 454.69968101
0.01483194 -0.03423274 0.99930382 7.76255001
Axis -0.00953890 0.01620006 -0.99982327
Axis point 200.40830208 206.06543991 0.00000000
Rotation angle (degrees) 165.87277583
Shift along axis -3.68145969
> view matrix models
> #5,-0.96958,0.24373,0.02274,344.87,-0.24434,-0.96924,-0.029576,455.04,0.014832,-0.034233,0.9993,7.5113
> view matrix models
> #5,-0.96941,0.24264,0.037104,342.16,-0.24332,-0.96983,-0.014945,452,0.032358,-0.023516,0.9992,1.7771
> view matrix models
> #5,-0.96941,0.24264,0.037104,344.48,-0.24332,-0.96983,-0.014945,454.29,0.032358,-0.023516,0.9992,0.37112
> view matrix models
> #5,-0.99966,-0.0073704,0.025101,404,0.0066504,-0.99957,-0.028647,412.17,0.025301,-0.02847,0.99927,2.8035
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.6977, steps = 64
shifted from previous position = 2.06
rotated from previous position = 2.22 degrees
atoms outside contour = 13307, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
-1.00000000 0.00002084 -0.00005817 407.44030115
-0.00002085 -1.00000000 0.00003636 407.42930522
-0.00005817 0.00003636 1.00000000 0.00766276
Axis 0.00002935 -0.00001804 -1.00000000
Axis point 203.72227380 203.71252937 0.00000000
Rotation angle (degrees) 179.99880573
Shift along axis -0.00305334
> fitmap #5 inMap #8
Fit molecule 5_stack copy_real_space_refined_011.pdb (#5) to map
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) using 63060 atoms
average map value = 0.6977, steps = 44
shifted from previous position = 0.0238
rotated from previous position = 0.0032 degrees
atoms outside contour = 13288, contour level = 0.23292
Position of 5_stack copy_real_space_refined_011.pdb (#5) relative to
cryosparc_P2_J252_012_volume_map_sharp TAIL TUBE.mrc (#8) coordinates:
Matrix rotation and translation
-0.99999999 0.00002183 -0.00011340 407.44060115
-0.00002184 -1.00000000 0.00004465 407.40657627
-0.00011340 0.00004465 0.99999999 0.01733976
Axis 0.00005695 -0.00002219 -1.00000000
Axis point 203.72252494 203.70106388 0.00000000
Rotation angle (degrees) 179.99874898
Shift along axis -0.00317503
> close #5
> close #8
> color #2 #f5536eff
> color #2 #e64d67ff
> hide #!7.2 models
> show #!7.2 models
> fitmap #2 inMap #7.2
Fit molecule Stopper_45_1-coot-4_6mer.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 5496 atoms
average map value = 0.9714, steps = 44
shifted from previous position = 0.0241
rotated from previous position = 0.00595 degrees
atoms outside contour = 818, contour level = 0.3
Position of Stopper_45_1-coot-4_6mer.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999997 0.00020862 0.00013399 -0.09093745
-0.00020860 0.99999996 -0.00019729 0.09002475
-0.00013403 0.00019726 0.99999997 -0.04447836
Axis 0.62261170 0.42293536 -0.65839225
Axis point 409.70250861 468.00384204 0.00000000
Rotation angle (degrees) 0.01815413
Shift along axis 0.01074014
> close #2
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper/Stopper_45_1-coot-4.pdb"
Chain information for Stopper_45_1-coot-4.pdb #2
---
Chain | Description
A | No description available
> color #2 #90bad0ff
> color #2 #d07427ff
> fitmap #2 inMap #7.2
Fit molecule Stopper_45_1-coot-4.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 916 atoms
average map value = 0.9956, steps = 40
shifted from previous position = 0.042
rotated from previous position = 0.165 degrees
atoms outside contour = 124, contour level = 0.3
Position of Stopper_45_1-coot-4.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999620 -0.00273589 0.00033327 0.64702235
0.00273618 0.99999589 -0.00085114 -0.52419070
-0.00033094 0.00085205 0.99999958 -0.14117715
Axis 0.29521339 0.11512694 0.94846974
Axis point 191.79638132 236.57738514 0.00000000
Rotation angle (degrees) 0.16528045
Shift along axis -0.00324107
> fitmap #2 inMap #7.2
Fit molecule Stopper_45_1-coot-4.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 916 atoms
average map value = 0.9954, steps = 28
shifted from previous position = 0.00462
rotated from previous position = 0.0266 degrees
atoms outside contour = 124, contour level = 0.3
Position of Stopper_45_1-coot-4.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999521 -0.00302920 0.00063602 0.67206299
0.00302986 0.99999486 -0.00104695 -0.56494120
-0.00063285 0.00104887 0.99999925 -0.11553468
Axis 0.32067510 0.19414639 0.92707856
Axis point 186.75184142 221.70160588 0.00000000
Rotation angle (degrees) 0.18723288
Shift along axis -0.00127716
> volume zone #7.2 nearAtoms #2 range 6.37
> surface dust #7.2 size 10.6
> volume zone #7.2 nearAtoms #2 range 6.37
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
Already setting window visible!
> ui mousemode right "translate selected atoms"
> select #2/A:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:3
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:3
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:1-2
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:1-2
15 atoms, 15 bonds, 2 residues, 1 model selected
> fitmap #2 inMap #7.2
Fit molecule Stopper_45_1-coot-4.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 916 atoms
average map value = 0.9836, steps = 36
shifted from previous position = 0.034
rotated from previous position = 0.12 degrees
atoms outside contour = 130, contour level = 0.3
Position of Stopper_45_1-coot-4.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999730 -0.00203488 0.00112648 0.32790088
0.00203405 0.99999766 0.00073702 -0.64206141
-0.00112797 -0.00073473 0.99999909 0.46906226
Axis -0.30164958 0.46207124 0.83396505
Axis point 314.83967850 160.06837777 0.00000000
Rotation angle (degrees) 0.13977360
Shift along axis -0.00440775
> fitmap #2 inMap #7.2
Fit molecule Stopper_45_1-coot-4.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 916 atoms
average map value = 0.9837, steps = 40
shifted from previous position = 0.00178
rotated from previous position = 0.00318 degrees
atoms outside contour = 130, contour level = 0.3
Position of Stopper_45_1-coot-4.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999734 -0.00202844 0.00109343 0.33214388
0.00202759 0.99999764 0.00078119 -0.64961152
-0.00109501 -0.00077898 0.99999910 0.47111535
Axis -0.32064843 0.44977150 0.83360074
Axis point 319.25447557 162.38412441 0.00000000
Rotation angle (degrees) 0.13939132
Shift along axis -0.00595605
> select #2/A:4-5
9 atoms, 8 bonds, 2 residues, 1 model selected
> select #2/A:4-5
9 atoms, 8 bonds, 2 residues, 1 model selected
> select #2/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:5
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:5
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:3
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:3
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:2
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:2
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:8
7 atoms, 6 bonds, 1 residue, 1 model selected
> fitmap #2 inMap #7.2
Fit molecule Stopper_45_1-coot-4.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 916 atoms
average map value = 0.996, steps = 40
shifted from previous position = 0.02
rotated from previous position = 0.124 degrees
atoms outside contour = 123, contour level = 0.3
Position of Stopper_45_1-coot-4.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999367 -0.00176121 0.00309036 -0.09265699
0.00176123 0.99999845 -0.00000623 -0.45203499
-0.00309034 0.00001168 0.99999522 0.78490689
Axis 0.00251785 0.86880859 0.49514168
Axis point 254.63272823 0.00000000 30.50030832
Rotation angle (degrees) 0.20380151
Shift along axis -0.00432506
> fitmap #2 inMap #7.2
Fit molecule Stopper_45_1-coot-4.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 916 atoms
average map value = 0.9958, steps = 36
shifted from previous position = 0.0218
rotated from previous position = 0.0397 degrees
atoms outside contour = 123, contour level = 0.3
Position of Stopper_45_1-coot-4.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999526 -0.00181262 0.00248794 0.03010384
0.00181348 0.99999830 -0.00034575 -0.38794493
-0.00248731 0.00035026 0.99999685 0.54044620
Axis 0.11233769 0.80302256 0.58526490
Axis point 215.37610951 0.00000000 -11.32142350
Rotation angle (degrees) 0.17749289
Shift along axis 0.00815745
> select #2/A:46
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:46
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:46-54
73 atoms, 73 bonds, 9 residues, 1 model selected
> select #2/A:46
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:42-46
46 atoms, 46 bonds, 5 residues, 1 model selected
> select #2/A:38
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:38-41
39 atoms, 40 bonds, 4 residues, 1 model selected
> fitmap #2 inMap #7.2
Fit molecule Stopper_45_1-coot-4.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 916 atoms
average map value = 0.9304, steps = 28
shifted from previous position = 0.0595
rotated from previous position = 0.111 degrees
atoms outside contour = 155, contour level = 0.3
Position of Stopper_45_1-coot-4.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999213 -0.00129274 0.00375002 -0.37052399
0.00128887 0.99999863 0.00103530 -0.50277261
-0.00375136 -0.00103045 0.99999243 1.21698624
Axis -0.25199047 0.91505618 0.31491744
Axis point 322.82424841 0.00000000 98.37067109
Rotation angle (degrees) 0.23484821
Shift along axis 0.01655352
> undo
> close #2
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper/Stopper_45_1-coot-4.pdb"
Chain information for Stopper_45_1-coot-4.pdb #2
---
Chain | Description
A | No description available
> color #2 #ec8a3fff
> color #2 #e1833bff
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> close #3
Already setting window visible!
> select /A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:5
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:5-6
11 atoms, 10 bonds, 2 residues, 1 model selected
> select /A:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> undo
> select /A:3
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:3-4
15 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:3
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:3
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:3
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:3
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:2
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:2
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:2
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:2
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2
916 atoms, 939 bonds, 119 residues, 1 model selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper/Stopper_45_1-coot-5.pdb" selectedOnly true relModel #1
> close #2
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper/Stopper_45_1-coot-6.pdb"
Chain information for Stopper_45_1-coot-6.pdb #2
---
Chain | Description
A | No description available
> fitmap #2 inMap #7.2
Fit molecule Stopper_45_1-coot-6.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 908 atoms
average map value = 1.041, steps = 28
shifted from previous position = 0.0293
rotated from previous position = 0.112 degrees
atoms outside contour = 90, contour level = 0.3
Position of Stopper_45_1-coot-6.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999885 -0.00075418 0.00131562 -0.03642632
0.00075579 0.99999896 -0.00122469 0.03621967
-0.00131470 0.00122569 0.99999838 0.01086645
Axis 0.62844851 0.67459764 0.38726024
Axis point 6.53429334 0.00000000 30.43980900
Rotation angle (degrees) 0.11170085
Shift along axis 0.00574978
> color #2 #ec6a20ff
> view #2 clip false
> show atoms
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides fill
> style nucleic stick
Changed 0 atom styles
> nucleotides fill
> style nucleic stick
Changed 0 atom styles
> style stick
Changed 908 atom styles
> hide cartoons
> show cartoons
> hide atoms
> cartoon style #2#7.2#!7 modeHelix tube sides 20
> undo
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 2/A
Already setting window visible!
> select /A:36-37
10 atoms, 9 bonds, 2 residues, 1 model selected
> select /A:36-37
10 atoms, 9 bonds, 2 residues, 1 model selected
> select /A:48-49
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /A:48-49
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /A:48
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:48-65
145 atoms, 148 bonds, 18 residues, 1 model selected
> select /A:47
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:47-64
145 atoms, 148 bonds, 18 residues, 1 model selected
> select /A:46
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:46-47
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:47
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:47
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:47-48
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /A:47-51
38 atoms, 37 bonds, 5 residues, 1 model selected
> select /A:46
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:46
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:47
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:47
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:49
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:49
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:48
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:48
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:49
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:49-55
57 atoms, 57 bonds, 7 residues, 1 model selected
> select /A:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:50-55
48 atoms, 48 bonds, 6 residues, 1 model selected
> select /A:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:50-51
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:46
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:47
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:47
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:48
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:48-53
50 atoms, 50 bonds, 6 residues, 1 model selected
> select /A:49-50
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:49-53
45 atoms, 45 bonds, 5 residues, 1 model selected
> select /A:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:51-52
20 atoms, 20 bonds, 2 residues, 1 model selected
> select /A:51-52
20 atoms, 20 bonds, 2 residues, 1 model selected
> select /A:53-54
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /A:53-63
89 atoms, 90 bonds, 11 residues, 1 model selected
> select /A:52
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:52
11 atoms, 11 bonds, 1 residue, 1 model selected
> surface dust #7.2 size 10.6
> fitmap #2 inMap #7.2
Fit molecule Stopper_45_1-coot-6.pdb (#2) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 908 atoms
average map value = 0.9285, steps = 44
shifted from previous position = 0.075
rotated from previous position = 0.155 degrees
atoms outside contour = 140, contour level = 0.3
Position of Stopper_45_1-coot-6.pdb (#2) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999278 -0.00338513 0.00172735 0.47468356
0.00338638 0.99999401 -0.00071811 -0.72441731
-0.00172491 0.00072396 0.99999825 0.25235521
Axis 0.18640244 0.44623933 0.87528544
Axis point 212.33821451 140.53832456 0.00000000
Rotation angle (degrees) 0.22163051
Shift along axis -0.01389848
> volume zone #7.2 nearAtoms sel & #2 range 6.37
> select add #2
908 atoms, 931 bonds, 118 residues, 1 model selected
> surface dust #7.2 size 10.6
> volume zone #7.2 nearAtoms sel & #2 range 6.37
> select /A:48
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:48-49
14 atoms, 13 bonds, 2 residues, 1 model selected
> select add #2
908 atoms, 931 bonds, 118 residues, 1 model selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper/Stopper_45_1-coot-7.pdb" selectedOnly true relModel #1
> hide #!7 models
> show #!7 models
> show #!1 models
> hide #!1 models
> hide #!7.2 models
> show #!7.2 models
> show #!6 models
> hide #!6 models
> select subtract #2
Nothing selected
> hide #2 models
> hide #!7 models
> hide #!7.2 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Corndog-Head-
> Cap-C5-2_96A/00-C5-Head-Cap-pdbs part 2.pdb"
Chain information for 00-C5-Head-Cap-pdbs part 2.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 3.22/A 3.23/A 3.24/A 3.25/A 3.26/A 3.27/A 3.28/A 3.29/A 3.30/A 3.31/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 3.22/B 3.23/B 3.24/B 3.25/B 3.26/B 3.27/B 3.28/B 3.29/B 3.30/B 3.31/B 3.1/C 3.7/C 3.8/C 3.9/C 3.10/C 3.11/C 3.12/C 3.13/C 3.14/C 3.15/C 3.16/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 3.22/D 3.23/D 3.24/D 3.25/D 3.26/D 3.27/D 3.28/D 3.29/D 3.30/D 3.31/D 3.1/E 3.7/E 3.8/E 3.9/E 3.10/E 3.11/E 3.12/E 3.13/E 3.14/E 3.15/E 3.16/E 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 3.22/F 3.23/F 3.24/F 3.25/F 3.26/F 3.27/F 3.28/F 3.29/F 3.30/F 3.31/F | No description available
3.2/C 3.3/C 3.4/C 3.5/C 3.6/C 3.17/C 3.18/C 3.19/C 3.20/C 3.21/C 3.22/C 3.23/C 3.24/C 3.25/C 3.26/C 3.27/C 3.28/C 3.29/C 3.30/C 3.31/C 3.2/E 3.3/E 3.4/E 3.5/E 3.6/E 3.17/E 3.18/E 3.19/E 3.20/E 3.21/E 3.22/E 3.23/E 3.24/E 3.25/E 3.26/E 3.27/E 3.28/E 3.29/E 3.30/E 3.31/E 3.2/F 3.3/F 3.4/F 3.5/F 3.6/F | No description available
> hide #!3 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /3D/Capsid Assembled.pdb"
Chain information for Capsid Assembled.pdb #5
---
Chain | Description
0 1 2 3 4 5 6 7 8 9 A A0 A1 A2 A4 A6 A7 A8 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Af Ah Ai Aj Al An Ao Ap Ar At Au Av Ax Az B B2 B4 B5 B7 B8 B9 BB BC BD BF BH BI BJ BL BN BO BP BR BT BU BV BX BZ Ba Bb Bd Bf Bg Bh Bj Bl Bm Bn Bp Br Bs Bt Bv Bx By Bz C C0 C2 C3 C4 C6 C8 C9 CA CC CD CF CH CI CJ CL CN CO CP CR CT CU CV CX CZ Ca Cb Cd Cf Cg Ch Cj Cl Cm Cn Cp Cr Cs Ct Cv Cx Cy Cz D D0 D2 D3 D4 D6 D8 D9 DB DD DE DF DH DJ DK DL DN DP DQ DR DT DV DW DY DZ Da Dc De Df Dh Dj Dk Dl Dn Dp Dq Dr Dt Dv Dw Dx Dz E E1 E2 E3 E5 E7 E8 E9 EB ED EE EF EH EJ EK EL EN EP EQ ER ET EV EW EX EZ Eb Ec Ed Ef Eh Ei Ej El En Eo Ep Er Et Eu Ev Ex Ey F0 F2 F4 F5 F6 F8 FA FC FD FE FG FI FJ FK FM FO FP FQ FS FU FV FW FY Fa Fb Fd Ff Fg Fh Fj Fl Fm Fn Fp Fr Fs Ft Fv Fx Fy Fz G G0 G1 G3 G4 G5 G7 G9 GA GB GD GF GG GH GJ GL GM GN GP GR GS GT GV GX GY GZ Gb Gd Ge Gf Gh Gj Gk Gl Gn Gp Gq Gr Gt Gu Gw Gx Gy H H0 H1 H2 H4 H6 H7 H8 HA HC HE HF HG HI HK HL HM HO HQ HR HS HU HW HX HZ Hb Hc Hd Hf Hh Hi Hj Hl Hn Ho Hp Hr Ht Hu Hv Hx Hz I0 I1 I2 I3 I4 I6 I8 I9 IB IC ID IF IH II IJ IL IM IN IP IR IS IT IV IX IY IZ Ib Id Ie If Ih Ij Ik Il In Ip Iq Ir Is It Iu Iv Iw Ix Iy Iz J J0 J1 J2 J4 J6 J8 J9 JB JC JD JE JF JG JH JI JJ JK JL JM JN JO JP JQ JR JS JT JU JV JW JX JY JZ Ja Jb Jc Jd Je Jg Ji Jj Jk Jm Jo Jp Jq Js Ju Jv Jw Jy K1 K2 K4 K6 K7 K9 KB KD KE KF KH KJ KK KL KN KP KQ KR KT KV KW KX KZ Kb Kc Kd Kf Kh Ki Kj Kl Kn Ko Kp Kr Kt Ku Kv Kw Kx Ky L LB LC LE LH LI LK LN LO LQ LT LU LV LW LX LY LZ La Lb Lc Ld Le Lf Lg Lh Li Lj M O R S U X Y a d e g j k l m n o p q r s t u v w x y z | No description available
A3 A5 A9 Ae Ag Ak Am Aq As Aw Ay B0 B1 B3 B6 BA BE BG BK BM BQ BS BW BY Bc Be Bi Bk Bo Bq Bu Bw C1 C5 C7 CB CE CG CK CM CQ CS CW CY Cc Ce Ci Ck Co Cq Cu Cw D1 D5 D7 DA DC DG DI DM DO DS DU DX Db Dd Dg Di Dm Do Ds Du Dy E0 E4 E6 EA EC EG EI EM EO ES EU EY Ea Ee Eg Ek Em Eq Es Ew Ez F F1 F3 F7 F9 FB FF FH FL FN FR FT FX FZ Fc Fe Fi Fk Fo Fq Fu Fw G2 G6 G8 GC GE GI GK GO GQ GU GW Ga Gc Gg Gi Gm Go Gs Gv Gz H3 H5 H9 HB HD HH HJ HN HP HT HV HY Ha He Hg Hk Hm Hq Hs Hw Hy I I5 I7 IA IE IG IK IO IQ IU IW Ia Ic Ig Ii Im Io J3 J5 J7 JA Jf Jh Jl Jn Jr Jt Jx Jz K K0 K3 K5 K8 KA KC KG KI KM KO KS KU KY Ka Ke Kg Kk Km Kq Ks Kz LA LD LF LG LJ LL LM LP LR LS N P Q T V W Z b c f h i | No description available
> color #5 #6fef37ff
> close #5
> show #2 models
> view #2 clip false
> show #!3 models
> hide #!3 models
> show #!7.2 models
> hide #!7.2 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper/Stopper_45_1-coot-8.pdb"
Chain information for Stopper_45_1-coot-8.pdb #5
---
Chain | Description
A | No description available
> hide #!7 models
> show #!7 models
> hide #5 models
> show #5 models
> hide #2 models
> close #3
> fitmap #5 inMap #7.2
Fit molecule Stopper_45_1-coot-8.pdb (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 908 atoms
average map value = 1.099, steps = 44
shifted from previous position = 0.0338
rotated from previous position = 0.0793 degrees
atoms outside contour = 57, contour level = 0.3
Position of Stopper_45_1-coot-8.pdb (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999907 -0.00127123 -0.00048535 0.39267667
0.00127135 0.99999916 0.00025043 -0.34889482
0.00048503 -0.00025105 0.99999985 -0.08809806
Axis -0.18121584 -0.35065936 0.91880294
Axis point 282.83772996 304.44656758 0.00000000
Rotation angle (degrees) 0.07927667
Shift along axis -0.02976076
> show #!7.2 models
> hide #!7.2 models
> show #!7.2 models
> surface dust #7.2 size 10.6
> hide #!7.2 models
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near #5 distance 1.06
> color single #1
> volume zone #1 nearAtoms #5 range 6.37
> hide #!1 models
> show #!7.2 models
> fitmap #5 inMap #7.2
Fit molecule Stopper_45_1-coot-8.pdb (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 908 atoms
average map value = 1.099, steps = 40
shifted from previous position = 0.00656
rotated from previous position = 0.00661 degrees
atoms outside contour = 57, contour level = 0.3
Position of Stopper_45_1-coot-8.pdb (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999907 -0.00131232 -0.00037755 0.38105495
0.00131241 0.99999911 0.00025160 -0.36519841
0.00037722 -0.00025210 0.99999990 -0.05946562
Axis -0.18137234 -0.27177829 0.94511409
Axis point 283.85721789 286.56476408 0.00000000
Rotation angle (degrees) 0.07955960
Shift along axis -0.02606163
> fitmap #5 inMap #7.2
Fit molecule Stopper_45_1-coot-8.pdb (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 908 atoms
average map value = 1.099, steps = 44
shifted from previous position = 0.0101
rotated from previous position = 0.0261 degrees
atoms outside contour = 57, contour level = 0.3
Position of Stopper_45_1-coot-8.pdb (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999890 -0.00148507 0.00003078 0.34718534
0.00148506 0.99999883 0.00035585 -0.43385016
-0.00003131 -0.00035580 0.99999994 0.07455404
Axis -0.23295934 0.02032603 0.97227404
Axis point 292.08948589 230.86722708 0.00000000
Rotation angle (degrees) 0.08751426
Shift along axis -0.01721156
> fitmap #5 inMap #7.2
Fit molecule Stopper_45_1-coot-8.pdb (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) using 908 atoms
average map value = 1.099, steps = 44
shifted from previous position = 0.000543
rotated from previous position = 0.00382 degrees
atoms outside contour = 57, contour level = 0.3
Position of Stopper_45_1-coot-8.pdb (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99999893 -0.00146454 -0.00002897 0.35217576
0.00146454 0.99999887 0.00033458 -0.42538760
0.00002848 -0.00033462 0.99999994 0.05362319
Axis -0.22268971 -0.01911980 0.97470186
Axis point 290.87556964 237.51530849 0.00000000
Rotation angle (degrees) 0.08608990
Shift along axis -0.01802597
> rename #5 id #8
> show #!4 models
> hide #!4 models
> close #4
> rename #6 id #3
> rename #7 id #4
> rename #8 id #5
> combine #5
===== 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: 7 days, 23 hours, 4 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403220040
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 10 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| 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 , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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