![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15854 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001e8f88c00 (most recent call first):
File "/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, 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._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.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, 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._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.morph._morph, lxml._elementpath, lxml.etree (total: 120)
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{
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"procRole" : "Background",
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"codeSigningMonitor" : 1,
"incident" : "CA8930C1-90C1-4C70-93E4-131D772589B6",
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"procLaunch" : "2024-08-29 14:34:14.0574 -0400",
"procStartAbsTime" : 2569332497667,
"procExitAbsTime" : 3586076289588,
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"procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "601EFD1A-7C31-028E-F125-8C968238879B",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sip" : "enabled",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J905_AMP-PnP-ATP_F-chain.pdb format pdb
Chain information for J905_AMP-PnP-ATP_F-chain.pdb #1
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> open /Users/nicholasferraro/Replicase/Rep_F-chain.pdb format pdb
No such file/path: /Users/nicholasferraro/Replicase/Rep_F-chain.pdb
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/Rep_F-chain.pdb
Rep_F-chain.pdb title:
Cryo-em structure of PCV2 replicase bound to ssDNA [more info...]
Chain information for Rep_F-chain.pdb #2
---
Chain | Description | UniProt
F | atp-dependent helicase rep | Q6TC59_PCV2 1-314
> hide #2 models
> select protein
17548 atoms, 17813 bonds, 1109 residues, 2 models selected
> show sel & #!1 cartoons
> hide sel & #!1 atoms
> select clear
> show #2 models
> select #2/F
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> select clear
Drag select of 1 residues
> select #2/F
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.97823,0.20421,0.037036,-21.434,-0.11479,0.68105,-0.72319,125.49,-0.1729,0.70319,0.68966,-13.254
> view matrix models
> #2,0.9942,0.081095,0.070677,-14.717,-0.010294,0.72573,-0.6879,100.67,-0.10708,0.68318,0.72236,-24.991
> view matrix models
> #2,0.97981,-0.090329,0.17839,-5.8148,0.15712,-0.204,-0.96628,198.71,0.12367,0.97479,-0.18569,1.6759
> view matrix models
> #2,0.9939,-0.051726,0.097408,-3.7085,0.10322,0.12502,-0.98677,175.41,0.038864,0.99081,0.1296,-18.943
> view matrix models
> #2,0.99261,0.10768,-0.056012,-4.1831,-0.098629,0.44661,-0.88927,164.2,-0.070739,0.88822,0.45393,-24.32
> view matrix models
> #2,0.9732,0.21246,-0.087956,-8.6371,-0.22994,0.90125,-0.36725,84.42,0.0012461,0.37763,0.92596,-31.564
> view matrix models
> #2,0.95821,0.27598,-0.075235,-14.125,0.2328,-0.59953,0.76575,49.453,0.16623,-0.75127,-0.63872,219.68
> view matrix models
> #2,0.89615,0.1669,0.41117,-43.033,0.25916,0.55531,-0.79023,86.051,-0.36022,0.81472,0.45439,29.13
> view matrix models
> #2,0.84581,0.20749,0.49149,-47.497,0.30579,0.56636,-0.76533,74.955,-0.43715,0.79761,0.41558,47.088
> view matrix models
> #2,0.84319,0.17978,0.50667,-45.783,0.35333,0.52501,-0.77429,72.605,-0.40521,0.83189,0.37916,42.228
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.84319,0.17978,0.50667,-52.163,0.35333,0.52501,-0.77429,66.244,-0.40521,0.83189,0.37916,52.44
> view matrix models
> #2,0.84319,0.17978,0.50667,-55.088,0.35333,0.52501,-0.77429,73.009,-0.40521,0.83189,0.37916,64.294
> view matrix models
> #2,0.84319,0.17978,0.50667,-55.039,0.35333,0.52501,-0.77429,75.322,-0.40521,0.83189,0.37916,59.161
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.84972,0.17855,0.49607,-54.859,0.35354,0.50505,-0.78736,78.692,-0.39112,0.84442,0.36603,56.985
> view matrix models
> #2,0.66796,0.62915,0.39749,-62.408,0.19932,0.36337,-0.91008,130.39,-0.71701,0.68712,0.11731,150.48
> view matrix models
> #2,0.66022,0.63257,0.40492,-62.298,0.23425,0.33881,-0.91123,127.51,-0.71361,0.69646,0.075512,153.27
> view matrix models
> #2,0.76323,0.54577,0.34587,-63.602,0.22216,0.28101,-0.93364,137.7,-0.60674,0.78941,0.093226,124.91
> ui mousemode right "move picked models"
> view matrix models
> #2,0.76323,0.54577,0.34587,-60.262,0.22216,0.28101,-0.93364,139.38,-0.60674,0.78941,0.093226,122.78
> view matrix models
> #2,0.76323,0.54577,0.34587,-60.982,0.22216,0.28101,-0.93364,138.47,-0.60674,0.78941,0.093226,123.88
> open /Users/nicholasferraro/Replicase/AMP-PnP-
> ATP/J905/cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc format
> mrc
Opened cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc as #3, grid
size 300,300,300, pixel 0.844, shown at level 0.107, step 2, values float32
> surface dust #3 size 8.44
> transparency 50
> view matrix models
> #2,0.76323,0.54577,0.34587,-48.845,0.22216,0.28101,-0.93364,142.67,-0.60674,0.78941,0.093226,134.31
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.75544,0.56456,0.33252,-48.179,0.20803,0.27458,-0.93879,146.11,-0.62131,0.77838,0.089981,138.09
> view matrix models
> #2,0.46987,0.80087,0.37125,-31.262,0.78067,-0.18069,-0.59825,67.268,-0.41204,0.57092,-0.71012,208.58
> ui mousemode right "move picked models"
> view matrix models #3,1,0,0,0.10035,0,1,0,0.274,0,0,1,-0.95049
> view matrix models
> #2,0.46987,0.80087,0.37125,-29.616,0.78067,-0.18069,-0.59825,67.792,-0.41204,0.57092,-0.71012,200.32
> view matrix models
> #2,0.46987,0.80087,0.37125,-35.519,0.78067,-0.18069,-0.59825,65.281,-0.41204,0.57092,-0.71012,198.46
> view matrix models #3,1,0,0,-0.17391,0,1,0,0.12879,0,0,1,-0.85748
> view matrix models
> #2,0.46987,0.80087,0.37125,-34.756,0.78067,-0.18069,-0.59825,65.58,-0.41204,0.57092,-0.71012,198.99
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.35332,0.90227,0.24713,-13.976,0.74448,-0.11122,-0.65831,70.325,-0.56649,0.41657,-0.71102,239.51
> view matrix models
> #2,0.69394,0.70751,0.1337,-36.231,0.26375,-0.076982,-0.96152,174.21,-0.66999,0.70249,-0.24002,177.99
> ui mousemode right "move picked models"
> view matrix models
> #2,0.69394,0.70751,0.1337,-32.11,0.26375,-0.076982,-0.96152,175.48,-0.66999,0.70249,-0.24002,183.52
> ui tool show "Fit in Map"
> hide #!1 models
Opened Rep_F-chain.pdb map 5 as #4, grid size 50,39,43, pixel 1.67, shown at
level 0.0982, step 1, values float32
> fitmap #2 inMap #3 resolution 5
Fit map Rep_F-chain.pdb map 5 in map
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc using 4834 points
correlation = 0.6136, correlation about mean = 0.09847, overlap = 259.3
steps = 128, shift = 14.9, angle = 10.8 degrees
Position of Rep_F-chain.pdb map 5 (#4) relative to
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) coordinates:
Matrix rotation and translation
0.64300027 0.70128731 0.30780961 -48.78083241
0.41710681 0.01641218 -0.90870927 137.23661534
-0.64231811 0.71268979 -0.28195868 195.46827478
Axis 0.85308013 0.49989857 -0.14951824
Axis point 0.00000000 0.02321171 152.22842263
Rotation angle (degrees) 108.13597115
Shift along axis -2.23564317
Average map value = 0.1444 for 2301 atoms, 1024 outside contour
> view matrix models #3,1,0,0,-6.2892,0,1,0,-4.0999,0,0,1,8.6324
> show #!1 models
Opened J905_AMP-PnP-ATP_F-chain.pdb map 5 as #5, grid size 68,72,79, pixel
1.67, shown at level 0.107, step 1, values float32
> fitmap #1 inMap #3 resolution 5
Fit map J905_AMP-PnP-ATP_F-chain.pdb map 5 in map
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc using 32348 points
correlation = 0.7747, correlation about mean = 0.6944, overlap = 3924
steps = 116, shift = 11.4, angle = 0.135 degrees
Position of J905_AMP-PnP-ATP_F-chain.pdb map 5 (#5) relative to
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) coordinates:
Matrix rotation and translation
0.99999727 -0.00152767 0.00176773 0.04566317
0.00152726 0.99999881 0.00023406 -0.15390765
-0.00176809 -0.00023136 0.99999841 0.27377555
Axis -0.09911389 0.75296278 0.65055629
Axis point 133.64046404 0.00000000 -28.85992112
Rotation angle (degrees) 0.13452723
Shift along axis 0.05769382
Average map value = 0.3812 for 15646 atoms, 2501 outside contour
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.65834,0.67803,0.32691,-50.95,0.38528,0.069564,-0.92018,138.11,-0.64664,0.73174,-0.21543,186.49
> view matrix models
> #2,0.88419,0.43034,0.18172,-46.274,0.26527,-0.14235,-0.95361,182.45,-0.38451,0.89137,-0.24002,130.97
> ui mousemode right "move picked models"
> view matrix models #3,1,0,0,-6.5278,0,1,0,-4.0479,0,0,1,8.4528
> view matrix models #3,1,0,0,-6.152,0,1,0,-4.0428,0,0,1,8.6224
> view matrix models #3,1,0,0,-5.0878,0,1,0,-4.2701,0,0,1,9.4175
> view matrix models #3,1,0,0,-4.8834,0,1,0,-4.1728,0,0,1,9.3867
> view matrix models #3,1,0,0,-4.5536,0,1,0,-4.4886,0,0,1,9.9525
> view matrix models
> #2,0.88419,0.43034,0.18172,-54.194,0.26527,-0.14235,-0.95361,175.15,-0.38451,0.89137,-0.24002,129.43
> view matrix models
> #2,0.88419,0.43034,0.18172,-54.404,0.26527,-0.14235,-0.95361,174.94,-0.38451,0.89137,-0.24002,129.82
> view matrix models #3,1,0,0,-4.3608,0,1,0,-4.4807,0,0,1,9.7115
> view matrix models
> #2,0.88419,0.43034,0.18172,-54.102,0.26527,-0.14235,-0.95361,175.1,-0.38451,0.89137,-0.24002,127.31
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.87678,0.4387,0.197,-55.36,0.29597,-0.16938,-0.94006,171.63,-0.37903,0.88253,-0.27835,131.29
> view matrix models
> #2,0.93973,0.27287,0.20601,-49.155,0.27132,-0.22851,-0.93497,181.12,-0.20805,0.93452,-0.28878,99.882
> fitmap #2 inMap #3
Fit molecule Rep_F-chain.pdb (#2) to map
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) using 2301
atoms
average map value = 0.1186, steps = 112
shifted from previous position = 2.65
rotated from previous position = 7.93 degrees
atoms outside contour = 1145, contour level = 0.10709
Position of Rep_F-chain.pdb (#2) relative to
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) coordinates:
Matrix rotation and translation
0.96244220 0.26220683 0.07037457 -32.48738924
0.14420491 -0.27411606 -0.95082350 214.52295222
-0.23002162 0.92526102 -0.30163238 94.62985232
Axis 0.98552346 0.15780072 -0.06198743
Axis point 0.00000000 74.98227012 125.80983045
Rotation angle (degrees) 107.85764699
Shift along axis -4.03106931
> select clear
> select protein
17548 atoms, 17813 bonds, 1109 residues, 2 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
> select clear
> hide #!3 models
> select clear
> select #2/F:199
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/F:219
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/F:199
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/F:195
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #2/F:227
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/F:228
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/F:212
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/F:251
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/F:193
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/F:194
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/F:234
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/F:157
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2/F:158
18 atoms, 16 bonds, 2 residues, 2 models selected
> ui tool show "Build Structure"
> build join peptide sel length 1.33 omega 180 phi -120 move small
> show #!3 models
> fitmap #1/F:158-301 inMap #3
Fit molecule J905_AMP-PnP-ATP_F-chain.pdb (#1) to map
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) using 2301
atoms
average map value = 0.1473, steps = 140
shifted from previous position = 12
rotated from previous position = 23.4 degrees
atoms outside contour = 1030, contour level = 0.10709
Position of J905_AMP-PnP-ATP_F-chain.pdb (#1) relative to
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) coordinates:
Matrix rotation and translation
0.98548521 -0.02528075 -0.16786838 20.79408241
0.08446934 0.93077082 0.35571141 -43.22013628
0.14725434 -0.36472807 0.91939632 29.58457982
Axis -0.90739448 -0.39689749 0.13823037
Axis point 0.00000000 51.72310976 128.91980738
Rotation angle (degrees) 23.38967573
Shift along axis 2.37501573
> fitmap #1 inMap #3
Fit molecule J905_AMP-PnP-ATP_F-chain.pdb (#1) to map
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) using 17947
atoms
average map value = 0.1275, steps = 72
shifted from previous position = 2.8
rotated from previous position = 5.02 degrees
atoms outside contour = 10544, contour level = 0.10709
Position of J905_AMP-PnP-ATP_F-chain.pdb (#1) relative to
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) coordinates:
Matrix rotation and translation
0.97649167 -0.00108788 -0.21555238 25.29628792
0.06579771 0.95376518 0.29326207 -33.02083947
0.20526732 -0.30055082 0.93141534 12.60962435
Axis -0.81246969 -0.57577608 0.09151454
Axis point 0.00000000 15.64232947 115.82216674
Rotation angle (degrees) 21.43447575
Shift along axis -0.38589391
> undo
> select #1/F:158-301
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> select clear
> select #1/F:158-301
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> delete atoms sel
> close
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix_2/Round_000_real_space_refined_m6_J905_F-chain_001.pdb
Chain information for Round_000_real_space_refined_m6_J905_F-chain_001.pdb #1
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> open /Users/nicholasferraro/Replicase/AMP-PnP-
> ATP/J905/cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc format
> mrc
Opened cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc as #2, grid
size 300,300,300, pixel 0.844, shown at level 0.107, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> surface dust #2 size 8.44
> style ball
Changed 17950 atom styles
> show cartoons
> hide atoms
> ui tool show "Map Filter"
> volume gaussian #2 sDev 0.76
Opened cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc gaussian as
#3, grid size 300,300,300, pixel 0.844, shown at step 1, values float32
> volume gaussian #2 sDev 1.39 modelId #3
Opened cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc gaussian as
#3, grid size 300,300,300, pixel 0.844, shown at step 1, values float32
> transparency #3.1 50
> close
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J905_AMP-PnP-ATP_F-chain.pdb
Chain information for J905_AMP-PnP-ATP_F-chain.pdb #1
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> show cartoons
> hide atoms
> show atoms
> hide atoms
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/Rep_F-chain.pdb
Rep_F-chain.pdb title:
Cryo-em structure of PCV2 replicase bound to ssDNA [more info...]
Chain information for Rep_F-chain.pdb #2
---
Chain | Description | UniProt
F | atp-dependent helicase rep | Q6TC59_PCV2 1-314
> select #2/F
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> open /Users/nicholasferraro/Replicase/AMP-PnP-
> ATP/J905/cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc format
> mrc
Opened cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc as #3, grid
size 300,300,300, pixel 0.844, shown at level 0.107, step 2, values float32
> surface dust #3 size 8.44
> select clear
> hide #2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #1 inMap #3
Fit molecule J905_AMP-PnP-ATP_F-chain.pdb (#1) to map
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) using 15646
atoms
average map value = 0.3812, steps = 48
shifted from previous position = 0.124
rotated from previous position = 0.177 degrees
atoms outside contour = 2503, contour level = 0.10709
Position of J905_AMP-PnP-ATP_F-chain.pdb (#1) relative to
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) coordinates:
Matrix rotation and translation
0.99999542 -0.00243404 0.00179942 0.17598289
0.00243298 0.99999686 0.00059298 -0.29408400
-0.00180085 -0.00058860 0.99999821 0.33565761
Axis -0.19156142 0.58368756 0.78905833
Axis point 135.24453505 76.72786250 0.00000000
Rotation angle (degrees) 0.17670461
Shift along axis 0.05948873
> transparency 50
> volume gaussian #3 sDev 1.39
Opened cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc gaussian as
#4, grid size 300,300,300, pixel 0.844, shown at step 1, values float32
> transparency #4.1 50
> show #2 models
> select add #2
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> ui mousemode right "move picked models"
Drag select of 5 residues
> select add #2
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> view matrix models #2,1,0,0,1.5068,0,1,0,2.2802,0,0,1,15.38
> view matrix models #2,1,0,0,1.2791,0,1,0,3.2749,0,0,1,25.757
> view matrix models #2,1,0,0,-0.18983,0,1,0,14.812,0,0,1,23.838
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99873,-0.017665,-0.047249,6.6937,0.016424,0.99951,-0.026542,14.987,0.047695,0.025733,0.99853,13.769
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99873,-0.017665,-0.047249,2.7487,0.016424,0.99951,-0.026542,12.487,0.047695,0.025733,0.99853,12.857
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99939,-0.027994,-0.02093,1.0038,0.027057,0.99867,-0.043806,12.663,0.022129,0.043213,0.99882,15.077
> view matrix models
> #2,0.98232,-0.1785,-0.056455,22.9,0.17837,0.98394,-0.0074561,-13.551,0.056879,-0.0027456,0.99838,14.356
> fitmap #2 inMap #4
Fit molecule Rep_F-chain.pdb (#2) to map
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc gaussian (#4)
using 2301 atoms
average map value = 0.1539, steps = 64
shifted from previous position = 0.797
rotated from previous position = 6.05 degrees
atoms outside contour = 675, contour level = 0.11785
Position of Rep_F-chain.pdb (#2) relative to
cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.99133997 -0.13046432 0.01497075 9.92324272
0.12948941 0.99011553 0.05388618 -12.88758147
-0.02185299 -0.05148097 0.99843485 31.99752721
Axis -0.37244959 0.13016380 0.91887904
Axis point 134.04284684 135.75984104 -0.00000000
Rotation angle (degrees) 8.13185002
Shift along axis 24.02845280
> select clear
> select #2/F
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> view matrix models
> #2,0.9911,-0.1315,0.020838,9.4648,0.13043,0.99038,0.046314,-12.284,-0.026728,-0.043183,0.99871,31.886
> ui mousemode right "move picked models"
> view matrix models
> #2,0.9911,-0.1315,0.020838,8.4969,0.13043,0.99038,0.046314,-13.015,-0.026728,-0.043183,0.99871,32.385
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99122,-0.1299,-0.024746,13,0.13023,0.99141,0.012021,-9.5644,0.022972,-0.015137,0.99962,21.514
> select clear
> hide #!4 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/Rep_F-chain.pdb models #2 relModel #1
> close #1
> close #3
> close #4
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb
Summary of feedback from opening /Users/nicholasferraro/Replicase/AMP-PnP-
ATP/AMP-PnP-ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb
---
warnings | Cannot find LINK/SSBOND residue LYS (180 )
Cannot find LINK/SSBOND residue SER (181 )
Chain information for J906_AMP-PnP-ATP_F-chain.pdb #1
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> open /Users/nicholasferraro/Replicase/AMP-PnP-
> ATP/J906/cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc
Opened cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc as #3, grid
size 300,300,300, pixel 0.844, shown at level 0.102, step 2, values float32
> surface dust #3 size 8.44
> volume gaussian #3 sDev 1.39
Opened cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc gaussian as #4,
grid size 300,300,300, pixel 0.844, shown at step 1, values float32
> style ball
Changed 17948 atom styles
> show cartoons
> hide atoms
> volume #!4 style image
> volume #!4 style surface
> transparency #4.1 50
> select #2/F
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> fitmap #2 inMap #4
Fit molecule Rep_F-chain.pdb (#2) to map
cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc gaussian (#4) using
2301 atoms
average map value = 0.1512, steps = 148
shifted from previous position = 13.4
rotated from previous position = 11.3 degrees
atoms outside contour = 694, contour level = 0.11036
Position of Rep_F-chain.pdb (#2) relative to
cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.95170411 -0.29988927 0.06577020 18.86607318
0.29806581 0.95385834 0.03620833 -39.77252537
-0.07359394 -0.01485577 0.99717764 28.17895433
Axis -0.08288271 0.22620348 0.97054750
Axis point 152.82341965 42.93857940 0.00000000
Rotation angle (degrees) 17.94177732
Shift along axis 16.78865879
> view matrix models
> #2,0.94285,-0.32663,0.065855,23.021,0.331,0.94085,-0.072441,-32.481,-0.038298,0.090099,0.9952,11.951
> fitmap #2 inMap #4
Fit molecule Rep_F-chain.pdb (#2) to map
cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc gaussian (#4) using
2301 atoms
average map value = 0.1512, steps = 80
shifted from previous position = 0.255
rotated from previous position = 6.54 degrees
atoms outside contour = 694, contour level = 0.11036
Position of Rep_F-chain.pdb (#2) relative to
cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.95166220 -0.30016098 0.06513401 18.95505007
0.29835014 0.95377072 0.03617461 -39.79295834
-0.07298111 -0.01499327 0.99722062 28.08533074
Axis -0.08301514 0.22407900 0.97102888
Axis point 152.67497169 43.20409743 0.00000000
Rotation angle (degrees) 17.94982358
Shift along axis 16.78134491
> hide #!4 models
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/Rep_F-chain.pdb models #2 relModel #1
> close #1
> hide #2 models
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb
Summary of feedback from opening /Users/nicholasferraro/Replicase/AMP-PnP-
ATP/AMP-PnP-ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 121 LEU A 127 1 7
Start residue of secondary structure not found: HELIX 2 2 LEU A 132 GLN A 138
1 7
Start residue of secondary structure not found: HELIX 3 3 VAL A 141 VAL A 144
1 4
Start residue of secondary structure not found: HELIX 4 4 ARG A 148 SER A 157
1 10
Start residue of secondary structure not found: HELIX 5 5 SER A 181 ASN A 186
1 6
2 messages similar to the above omitted
End residue of secondary structure not found: HELIX 39 39 ARG F 148 SER F 157
1 10
Start residue of secondary structure not found: SHEET 1 1 1 ASN A 168 VAL A
173 0
Start residue of secondary structure not found: SHEET 1 2 1 THR A 193 TRP A
195 0
Start residue of secondary structure not found: SHEET 1 3 1 VAL A 212 PHE A
217 0
Start residue of secondary structure not found: SHEET 1 4 1 SER A 250 SER A
255 0
Start residue of secondary structure not found: SHEET 1 5 1 SER A 280 PHE A
283 0
notes | Combining 3 symmetry atoms into MG /C:401 MG
Combining 3 symmetry atoms into MG /B:401 MG
Combining 3 symmetry atoms into MG /D:401 MG
Combining 3 symmetry atoms into MG /A:401 MG
Chain information for J906_AMP-PnP-ATP_F-chain.pdb #1
---
Chain | Description
B C E I J K N O P Q T | No description available
D L R | No description available
F | No description available
G | No description available
M S | No description available
> style #!1 ball
Changed 46286 atom styles
> select #1/I
2969 atoms, 3015 bonds, 186 residues, 1 model selected
> select #1/T
2958 atoms, 3004 bonds, 186 residues, 1 model selected
> select #1/E:235@CG
1 atom, 1 residue, 1 model selected
> select #1/T
2958 atoms, 3004 bonds, 186 residues, 1 model selected
> view matrix models
> #1,1,0.00051083,0.00089905,-0.1864,-0.00050689,0.99999,-0.0043795,0.6425,-0.00090128,0.004379,0.99999,-0.46758
> view matrix models
> #1,1,0.00051083,0.00089905,-0.15951,-0.00050689,0.99999,-0.0043795,0.65177,-0.00090128,0.004379,0.99999,-0.50336
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #1/S
589 atoms, 592 bonds, 38 residues, 1 model selected
> select #1/D:156@CG2
1 atom, 1 residue, 1 model selected
> select #1/S
589 atoms, 592 bonds, 38 residues, 1 model selected
> view matrix models
> #1,1,0.00052342,0.0014962,-0.2394,-0.00051361,0.99998,-0.0065486,0.93866,-0.0014996,0.0065478,0.99998,-0.71387
> select add #1/F:128@HB3
590 atoms, 592 bonds, 39 residues, 1 model selected
> view matrix models
> #1,1,-0.0015512,0.0013835,0.054038,0.0015635,0.99996,-0.0089234,0.9783,-0.0013696,0.0089255,0.99996,-1.0479
> view matrix models
> #1,1,-0.00057657,-0.00023451,0.13508,0.00057417,0.99995,-0.010146,1.2707,0.00024035,0.010146,0.99995,-1.423
> view matrix models
> #1,0.9999,0.0065703,-0.012238,0.76213,-0.0068038,0.99979,-0.019138,3.4451,0.01211,0.01922,0.99974,-4.182
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/S
589 atoms, 592 bonds, 38 residues, 1 model selected
> select #1/F:120@C
1 atom, 1 residue, 1 model selected
> select #1/S
589 atoms, 592 bonds, 38 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #1/F:120@C
590 atoms, 592 bonds, 39 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #1/R
2983 atoms, 3031 bonds, 187 residues, 1 model selected
> select add #1/D:121@OG1
2984 atoms, 3031 bonds, 188 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #1/Q
2969 atoms, 3015 bonds, 186 residues, 1 model selected
> select add #1/C:121@OG1
2970 atoms, 3015 bonds, 187 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #1/P
2970 atoms, 3016 bonds, 186 residues, 1 model selected
> select add #1/B:140@CG
2971 atoms, 3016 bonds, 187 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #1/O
2969 atoms, 3015 bonds, 186 residues, 1 model selected
> select add #1/I:119@CG
2970 atoms, 3015 bonds, 187 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #1/N
2958 atoms, 3004 bonds, 186 residues, 1 model selected
> select add #1/E:120@OG
2959 atoms, 3004 bonds, 187 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #1/M
589 atoms, 592 bonds, 38 residues, 1 model selected
> select add #1/F:119@HG
590 atoms, 592 bonds, 39 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #1/L
2983 atoms, 3031 bonds, 187 residues, 1 model selected
> select add #1/D:121@CG2
2984 atoms, 3031 bonds, 188 residues, 1 model selected
> select subtract #1/D:121@CG2
2983 atoms, 3031 bonds, 187 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #1/D:121@CG2
2984 atoms, 3031 bonds, 188 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #1/I
2967 atoms, 3011 bonds, 186 residues, 1 model selected
> select #1/K
2969 atoms, 3015 bonds, 186 residues, 1 model selected
> select add #1/C:289@OE2
2970 atoms, 3015 bonds, 187 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #1/J
2970 atoms, 3016 bonds, 186 residues, 1 model selected
> select add #1/B:145@CZ
2971 atoms, 3016 bonds, 187 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete bonds sel
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete bonds sel
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb models #1 relModel #1
> select #1/G
582 atoms, 615 bonds, 2 pseudobonds, 18 residues, 2 models selected
> select #1/I
2967 atoms, 3011 bonds, 186 residues, 1 model selected
> select subtract #1/I:119@CD2
2966 atoms, 3008 bonds, 186 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #1/I:119@CD2
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #1/A:303@CB
1 atom, 1 bond, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #1/A:303@HB3
2 atoms, 1 bond, 1 residue, 1 model selected
> select add #1/A:303@N
3 atoms, 1 bond, 1 residue, 1 model selected
> select add #1/A:303@C
4 atoms, 1 bond, 1 residue, 1 model selected
> select add #1/A:303@O
5 atoms, 1 bond, 1 residue, 1 model selected
> select add #1/A:303@CA
6 atoms, 1 bond, 1 residue, 1 model selected
> select add #1/A:303@HA
7 atoms, 2 bonds, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb models #1 relModel #1
> close #1
> close #3-4
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb
Chain information for J906_AMP-PnP-ATP_F-chain.pdb #1
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> style #!1 ball
Changed 18314 atom styles
> select protein
19827 atoms, 20128 bonds, 1 pseudobond, 1253 residues, 3 models selected
> show sel & #!1 cartoons
> hide sel & #!1 atoms
> select clear
> select #1/F:180
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/F:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> view matrix models
> #1,1,1.1084e-05,-0.00078809,0.10147,-9.4237e-06,1,0.0021073,-0.27362,0.00078811,-0.0021073,1,0.178
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete bonds sel
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete bonds sel
> select ligand
202 atoms, 212 bonds, 5 residues, 1 model selected
> select nucleic-acid
582 atoms, 615 bonds, 2 pseudobonds, 18 residues, 2 models selected
> color sel byhetero
> color (#!1 & sel) dim gray
> color sel byhetero
> select clear
> close #1
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J907_AMP-PnP-ATP_F-chain.pdb
Chain information for J907_AMP-PnP-ATP_F-chain.pdb #1
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> select protein
17548 atoms, 17813 bonds, 1109 residues, 2 models selected
> style sel & #!1 ball
Changed 15247 atom styles
> show sel & #!1 cartoons
> hide sel & #!1 atoms
> select clear
> show #2 models
> open /Users/nicholasferraro/Replicase/AMP-PnP-
> ATP/J907/cryosparc_P5_cryosparc_P5_J907_006_volume_map_sharp.mrc
Opened cryosparc_P5_cryosparc_P5_J907_006_volume_map_sharp.mrc as #3, grid
size 300,300,300, pixel 0.844, shown at level 0.128, step 2, values float32
> surface dust #3 size 8.44
> volume gaussian #3 sDev 1.39
Opened cryosparc_P5_cryosparc_P5_J907_006_volume_map_sharp.mrc gaussian as #4,
grid size 300,300,300, pixel 0.844, shown at step 1, values float32
> transparency #4.1 50
> select #2/F
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "move picked models"
Drag select of 4 residues, 4
cryosparc_P5_cryosparc_P5_J907_006_volume_map_sharp.mrc gaussian
> select clear
> select #2/F
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> view matrix models
> #2,0.95166,-0.30016,0.065134,23.953,0.29835,0.95377,0.036175,-37.253,-0.072981,-0.014993,0.99722,27.614
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.94317,-0.3102,0.11918,20.779,0.30644,0.95062,0.049143,-39.544,-0.12854,-0.0098279,0.99166,36.465
> fitmap #2 inMap #4
Fit molecule Rep_F-chain.pdb (#2) to map
cryosparc_P5_cryosparc_P5_J907_006_volume_map_sharp.mrc gaussian (#4) using
2301 atoms
average map value = 0.2168, steps = 64
shifted from previous position = 4.29
rotated from previous position = 4.89 degrees
atoms outside contour = 620, contour level = 0.13548
Position of Rep_F-chain.pdb (#2) relative to
cryosparc_P5_cryosparc_P5_J907_006_volume_map_sharp.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.93427765 -0.35235322 0.05452054 29.32605372
0.34699294 0.93371156 0.08819650 -48.95454813
-0.08198278 -0.06348177 0.99460992 36.00893891
Axis -0.20820387 0.18737370 0.95996992
Axis point 163.74077607 64.08526484 0.00000000
Rotation angle (degrees) 21.36169254
Shift along axis 19.28890544
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/Rep_F-chain.pdb models #2 relModel #1
> close #4
> close #3
> close #1
> hide #2 models
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J907_AMP-PnP-ATP_F-chain.pdb
Summary of feedback from opening /Users/nicholasferraro/Replicase/AMP-PnP-
ATP/AMP-PnP-ATP_Models_Phenix/J907_AMP-PnP-ATP_F-chain.pdb
---
warnings | Start residue of secondary structure not found: HELIX 36 36 THR F 121 LEU F 127 1 7
Start residue of secondary structure not found: HELIX 37 37 LEU F 132 GLN F
138 1 7
Start residue of secondary structure not found: HELIX 38 38 VAL F 141 VAL F
144 1 4
Start residue of secondary structure not found: HELIX 39 39 ARG F 148 SER F
157 1 10
Chain information for J907_AMP-PnP-ATP_F-chain.pdb #1
---
Chain | Description
A B C E | No description available
D | No description available
G | No description available
f | No description available
> select protein
19844 atoms, 20150 bonds, 1253 residues, 2 models selected
> style sel & #!1 ball
Changed 17543 atom styles
> show sel & #!1 cartoons
> hide sel & #!1 atoms
> select clear
> show #2 models
> hide #2 models
> close #1
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J908_AMP-PnP-ATP_F-chain.pdb
Chain information for J908_AMP-PnP-ATP_F-chain.pdb #1
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> select protein
17541 atoms, 17806 bonds, 1109 residues, 2 models selected
> style sel & #!1 ball
Changed 15240 atom styles
> hide sel & #!1 atoms
> show sel & #!1 cartoons
> show #2 models
> select clear
> open /Users/nicholasferraro/Replicase/AMP-PnP-
> ATP/J908/cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc
Opened cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc as #3, grid
size 300,300,300, pixel 0.844, shown at level 0.109, step 2, values float32
> surface dust #3 size 8.44
> volume gaussian #3 sDev 1.39
Opened cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian as #4,
grid size 300,300,300, pixel 0.844, shown at step 1, values float32
> volume gaussian #3 sDev 1.99 modelId #4
Opened cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian as #4,
grid size 300,300,300, pixel 0.844, shown at step 1, values float32
> transparency #4.1 50
> volume #4 level 0.1774
> select add #2
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> fitmap #2 inMap #4
Fit molecule Rep_F-chain.pdb (#2) to map
cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian (#4) using
2301 atoms
average map value = 0.1902, steps = 68
shifted from previous position = 1.83
rotated from previous position = 1.73 degrees
atoms outside contour = 975, contour level = 0.17737
Position of Rep_F-chain.pdb (#2) relative to
cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.94045145 -0.33383660 0.06406395 24.53146002
0.32978649 0.94173541 0.06614591 -45.91724457
-0.08241322 -0.04107959 0.99575124 32.61711383
Axis -0.15585028 0.21290186 0.96456389
Axis point 160.17273027 53.25130062 0.00000000
Rotation angle (degrees) 20.12086339
Shift along axis 17.86218855
> volume #4 level 0.1225
> ui mousemode right "move picked models"
> view matrix models #4,1,0,0,0.25077,0,1,0,0.11398,0,0,1,0.13124
> view matrix models
> #2,0.94045,-0.33384,0.064064,26.5,0.32979,0.94174,0.066146,-44.84,-0.082413,-0.04108,0.99575,30.444
> view matrix models
> #2,0.94045,-0.33384,0.064064,25.836,0.32979,0.94174,0.066146,-44.589,-0.082413,-0.04108,0.99575,31.493
> fitmap #2 inMap #4
Fit molecule Rep_F-chain.pdb (#2) to map
cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian (#4) using
2301 atoms
average map value = 0.1902, steps = 88
shifted from previous position = 2.04
rotated from previous position = 0.00579 degrees
atoms outside contour = 452, contour level = 0.12253
Position of Rep_F-chain.pdb (#2) relative to
cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.94044719 -0.33386547 0.06397604 24.54360099
0.32981553 0.94172227 0.06618827 -45.92387749
-0.08234564 -0.04114628 0.99575408 32.61095523
Axis -0.15599976 0.21266355 0.96459229
Axis point 160.17382780 53.28833140 0.00000000
Rotation angle (degrees) 20.12207655
Shift along axis 17.86114518
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J908_AMP-PnP-ATP_F-chain.pdb models #2 relModel #1
> close #1
> close #3
> close #4
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix_2/Round_000_real_space_refined_m5_J908_F-chain_001.pdb
Chain information for Round_000_real_space_refined_m5_J908_F-chain_001.pdb #1
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> hide #2 models
> select #1/F:158-301
2237 atoms, 2277 bonds, 144 residues, 1 model selected
> select subtract #1/F:187@CZ
2236 atoms, 2274 bonds, 144 residues, 1 model selected
> select subtract #1/F:275@H
2235 atoms, 2273 bonds, 144 residues, 1 model selected
> select subtract #1/F:301@C
2234 atoms, 2271 bonds, 144 residues, 1 model selected
> select subtract #1/F:301@H
2233 atoms, 2270 bonds, 144 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #1/F:187@CZ
1 atom, 1 residue, 1 model selected
> select subtract #1/F:187@CZ
Nothing selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/F:187@CZ
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select add #1/F:301@C
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select protein
17541 atoms, 17806 bonds, 1109 residues, 2 models selected
> style sel & #!1 ball
Changed 15240 atom styles
> hide sel & #!1 atoms
> show sel & #!1 cartoons
> select clear
> hide #!1 models
> show #2 models
> show #!1 models
> hide #2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J908_AMP-PnP-ATP_F-chain.pdb models #1 relModel #1
> open /Users/nicholasferraro/Replicase/AMP-PnP-
> ATP/J908/cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc
Opened cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc as #3, grid
size 300,300,300, pixel 0.844, shown at level 0.109, step 2, values float32
> surface dust #3 size 8.44
> volume gaussian #3 sDev 1.99
Opened cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian as #4,
grid size 300,300,300, pixel 0.844, shown at step 1, values float32
> volume #4 level 0.08933
> transparency #4.1 50
> volume #4 level 0.1168
> show #2 models
> select #2/F
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> fitmap #2 inMap #4
Fit molecule Rep_F-chain.pdb (#2) to map
cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian (#4) using
2301 atoms
average map value = 0.1902, steps = 48
shifted from previous position = 0.305
rotated from previous position = 0.0154 degrees
atoms outside contour = 404, contour level = 0.11684
Position of Rep_F-chain.pdb (#2) relative to
cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.94043423 -0.33395056 0.06372200 24.57937352
0.32990985 0.94168804 0.06620525 -45.93622576
-0.08211552 -0.04123916 0.99576924 32.58286412
Axis -0.15613959 0.21193296 0.96473045
Axis point 160.14850085 53.38733438 0.00000000
Rotation angle (degrees) 20.12474429
Shift along axis 17.86046749
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/Rep_F-chain.pdb models #2 relModel #1
> close #1
> close #4
> close #3
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J909_AMP-PnP-ATP_F-chain.pdb
Chain information for J909_AMP-PnP-ATP_F-chain.pdb #1
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> open /Users/nicholasferraro/Replicase/AMP-PnP-
> ATP/J909/cryosparc_P5_cryosparc_P5_J909_005_volume_map_sharp.mrc
Opened cryosparc_P5_cryosparc_P5_J909_005_volume_map_sharp.mrc as #3, grid
size 300,300,300, pixel 0.844, shown at level 0.112, step 2, values float32
> surface dust #3 size 8.44
> volume gaussian #3 sDev 1.99
Opened cryosparc_P5_cryosparc_P5_J909_005_volume_map_sharp.mrc gaussian as #4,
grid size 300,300,300, pixel 0.844, shown at step 1, values float32
> transparency #4.1 50
> select #2/F
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> fitmap #2 inMap #4
Fit molecule Rep_F-chain.pdb (#2) to map
cryosparc_P5_cryosparc_P5_J909_005_volume_map_sharp.mrc gaussian (#4) using
2301 atoms
average map value = 0.1186, steps = 72
shifted from previous position = 3.6
rotated from previous position = 3.5 degrees
atoms outside contour = 1348, contour level = 0.12932
Position of Rep_F-chain.pdb (#2) relative to
cryosparc_P5_cryosparc_P5_J909_005_volume_map_sharp.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.95235909 -0.30219235 0.04113324 23.49737932
0.29631370 0.94876734 0.10972113 -43.63966789
-0.07218276 -0.09230557 0.99311094 38.86709029
Axis -0.31479762 0.17656878 0.93259097
Axis point 172.42758410 72.59977955 0.00000000
Rotation angle (degrees) 18.71636147
Shift along axis 21.14477536
> view matrix models
> #2,0.95236,-0.30219,0.041133,22.889,0.29631,0.94877,0.10972,-47.041,-0.072183,-0.092306,0.99311,46.721
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.94819,-0.31675,0.024549,26.758,0.31147,0.94205,0.12463,-50.284,-0.062602,-0.11052,0.9919,47.207
> view matrix models
> #2,0.96067,-0.24914,-0.12267,32.937,0.25357,0.96707,0.021704,-33.102,0.11322,-0.051955,0.99221,13.245
> ui mousemode right "move picked models"
> view matrix models #4,1,0,0,0.18634,0,1,0,-0.01177,0,0,1,0.3745
> view matrix models
> #2,0.96067,-0.24914,-0.12267,32.915,0.25357,0.96707,0.021704,-31.626,0.11322,-0.051955,0.99221,9.3094
> view matrix models
> #2,0.96067,-0.24914,-0.12267,35.94,0.25357,0.96707,0.021704,-28.517,0.11322,-0.051955,0.99221,7.8589
> volume #4 level 0.086
> view matrix models
> #2,0.96067,-0.24914,-0.12267,36.429,0.25357,0.96707,0.021704,-30.474,0.11322,-0.051955,0.99221,6.4883
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.95181,-0.29273,-0.091415,39.12,0.29757,0.95366,0.044463,-38.408,0.074164,-0.069523,0.99482,14.228
> view matrix models
> #2,0.95143,-0.30018,0.068362,23.521,0.30763,0.93563,-0.17307,-15.776,-0.012011,0.18569,0.98253,2.8138
> view matrix models
> #2,0.95953,-0.27955,0.033907,23.649,0.2781,0.92178,-0.27014,0.31878,0.044263,0.26864,0.96222,-12.585
> view matrix models
> #2,0.95996,-0.27835,0.031671,23.688,0.27605,0.92062,-0.27613,1.3785,0.047704,0.27382,0.9606,-13.498
> view matrix models
> #2,0.9647,-0.26333,0.00085811,24.553,0.24646,0.90172,-0.35518,16.151,0.092757,0.34286,0.9348,-25.117
> view matrix models
> #2,0.96312,-0.26906,-0.0033581,25.829,0.24991,0.89907,-0.35947,16.317,0.099735,0.34537,0.93315,-26.314
> view matrix models
> #2,0.96313,-0.26902,-0.0032043,25.807,0.24991,0.899,-0.35965,16.344,0.099633,0.34559,0.93308,-26.313
> volume #4 level 0.1072
> hide #2 models
> select protein
17540 atoms, 17805 bonds, 1109 residues, 2 models selected
> style sel & #!1 ball
Changed 15239 atom styles
> hide sel & #!1 atoms
> show sel & #!1 cartoons
> show #2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[deleted to fit within ticket limits]
> morph #1,7,6,3,10,5,4 frames 7
Computed 43 frame morph #11
> coordset #11 1,43
> hide #!8 models
> show #!8 models
> hide #!11 models
> show #!11 models
> hide #!8 models
> hide #!11 models
> show #!5 models
> show #!4 models
> show #!10 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!10 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> morph #1,7,6,3,5,4,10 frames 7
Computed 43 frame morph #12
> coordset #12 1,43
> morph #1,7,6,3,frames 4
Missing or invalid "structures" argument: only initial part "#1,7,6,3" of atom
specifier valid
> morph #1,7,6,3 frames 4
Computed 13 frame morph #13
> coordset #13 1,13
> hide #!12 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> hide #!13 models
> show #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!3 models
> hide #!6 models
> morph #1,7,6,5,3 frames 4
Computed 17 frame morph #14
> coordset #14 1,17
> show #!3 models
> hide #!14 models
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!10 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> morph #1,7,6,5,3,4,10 frames 4
Computed 25 frame morph #15
> coordset #15 1,25
> morph #1,7,6,5,3,4,10 frames 7
Computed 43 frame morph #16
> coordset #16 1,43
> morph #1,7,6,5,3,10,4 frames 7
Computed 43 frame morph #17
> coordset #17 1,43
> morph #1,7,6,5,3,4,10frames 7
Missing or invalid "structures" argument: only initial part "#1,7,6,5,3,4" of
atom specifier valid
> morph #1,7,6,5,3,4,10 frames 7
Computed 43 frame morph #18
> coordset #18 1,43
> hide #!18 models
> hide #!17 models
> hide #!16 models
> show #!3 models
> hide #!15 models
> show #!10 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!10 models
> show #!4 models
> hide #!4 models
> show #!10 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> hide #!10 models
> show #!3 models
> show #!10 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!10 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> morph #1,7,6,5,4,3,10 frames 7
Computed 43 frame morph #19
> coordset #19 1,43
> morph #1,7,6,5,4,10,3 frames 7
Computed 43 frame morph #20
> coordset #20 1,43
> hide #!19 models
> show #!19 models
> hide #!20 models
> hide #!19 models
> show #!20 models
> select nucleic-acid
4254 atoms, 4454 bonds, 2 pseudobonds, 132 residues, 21 models selected
> hide sel & #!20 cartoons
> select clear
> morph #1,7,6,5,3,4,10frames 7
Missing or invalid "structures" argument: only initial part "#1,7,6,5,3,4" of
atom specifier valid
> morph #1,7,6,5,3,4,10 frames 7
Computed 43 frame morph #21
> coordset #21 1,43
> hide #!20 models
> morph #7,1,6,5,3,4,10 frames 7
Computed 43 frame morph #22
> coordset #22 1,43
> hide #!21 models
> morph #7,6,1,5,3,4,10 frames 7
Computed 43 frame morph #23
> coordset #23 1,43
> hide #!22 models
> morph #7,1,6,5,3,4,10 frames 7
Computed 43 frame morph #24
> coordset #24 1,43
> hide #!23 models
> select nucleic-acid
5026 atoms, 5258 bonds, 2 pseudobonds, 156 residues, 25 models selected
> hide sel & #!24 cartoons
> select clear
> morph #1,7,6,5,3,4,10 frames 7
Computed 43 frame morph #25
> coordset #25 1,43
> hide #!24 models
> close #2,11-25
> close #8-9
> show #!10 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!10 models
> show #!10 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!10 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> show #!10 models
> hide #!10 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> morph #1,7,6,5,4,3,10 frames 7
Computed 43 frame morph #2
> coordset #2 1,43
> hide #!2 models
> show #!3 models
> show #!10 models
> hide #!10 models
> hide #!3 models
> show #!10 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> morph #1,7,6,5,4,10,3 frames 7
Computed 43 frame morph #8
> coordset #8 1,43
> morph #1,7,6,5,4,10 frames 7
Computed 36 frame morph #9
> coordset #9 1,36
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!1 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!10 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!10 models
> show #!10 models
> morph #1,7,6,5,3,4,10 frames 7
Computed 43 frame morph #11
> coordset #11 1,43
> morph #1,7,6,5,3,4,10 frames 7
Computed 43 frame morph #12
> coordset #12 1,43
> morph #1,7,6,5,3,4 frames 7
Computed 36 frame morph #13
> coordset #13 1,36
> hide #!11 models
> hide #!12 models
> morph #1,7,6,5,4,3,10 frames 7
Computed 43 frame morph #14
> coordset #14 1,43
> hide #!13 models
> hide #!14 models
> show #!5 models
> show #!4 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!10 models
> morph #1,7,6,5,3,4,10 frames 7
Computed 43 frame morph #15
> coordset #15 1,43
> morph #1,7,6,5,3,4 frames 7
Computed 36 frame morph #16
> coordset #16 1,36
> hide #!15 models
> show #!15 models
> hide #!16 models
> hide #!15 models
> show #!5 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> close #2,8-9,11-16
> hide #!10 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!4 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!4 models
> hide #!10 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> show #!10 models
> hide #!10 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> show #!10 models
> hide #!10 models
> hide #!4 models
> hide #!3 models
> show #!7 models
> hide #!7 models
> show #!1 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> ui tool show Matchmaker
> matchmaker #7/C to #1/C pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J905_AMP-PnP-ATP_F-chain.pdb, chain C (#1) with J922_AMP-PnP-ATP_F-
chain.pdb, chain C (#7), sequence alignment score = 870.8
RMSD between 183 pruned atom pairs is 0.650 angstroms; (across all 185 pairs:
0.694)
> show #!7 models
> ui tool show Matchmaker
> matchmaker #7/C to #1/C pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J905_AMP-PnP-ATP_F-chain.pdb, chain C (#1) with J922_AMP-PnP-ATP_F-
chain.pdb, chain C (#7), sequence alignment score = 870.8
RMSD between 183 pruned atom pairs is 0.650 angstroms; (across all 185 pairs:
0.694)
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!1 models
> show #!7 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!4 models
> show #!10 models
> hide #!4 models
> hide #!10 models
> hide #!3 models
> show #!4 models
> show #!3 models
> show #!10 models
> morph #1,7,6,5,4,3,10 frames 7
Computed 43 frame morph #2
> coordset #2 1,43
> show #!1 models
> hide #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> select nucleic-acid
1938 atoms, 2042 bonds, 2 pseudobonds, 60 residues, 9 models selected
> hide sel & #!2 cartoons
> select clear
> ui tool show "Side View"
> ui tool show "Show Sequence Viewer"
> sequence chain #1/F #4/F #5/F #6/F #7/F #3/F #10/F #2/F
Alignment identifier is 1
> hide #!2 models
> show #!1 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!7 models
> hide #!7 models
> show #!2 models
> morph #7,1,5,4,3 frames 7
Computed 29 frame morph #8
> coordset #8 1,29
> hide #!2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!8 models
> open /Users/nicholasferraro/Replicase/AMP-
> PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968-RSR-Regclash-out-
> coot-2.pdb
Summary of feedback from opening /Users/nicholasferraro/Replicase/AMP-
PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968-RSR-Regclash-out-
coot-2.pdb
---
warnings | Duplicate atom serial number found: 9340
Duplicate atom serial number found: 12880
Duplicate atom serial number found: 13463
Chain information for J968-RSR-Regclash-out-coot-2.pdb #9
---
Chain | Description
A B C D E | No description available
F | No description available
G | No description available
> select #9/F:119-157
600 atoms, 603 bonds, 39 residues, 1 model selected
> select subtract #9/F:128@HB2
599 atoms, 602 bonds, 39 residues, 1 model selected
> select subtract #9/F:128@CA
598 atoms, 598 bonds, 39 residues, 1 model selected
> select subtract #9/F:128@O
597 atoms, 597 bonds, 39 residues, 1 model selected
> select subtract #9/F:154@CA
596 atoms, 593 bonds, 39 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #9/F:154@CA
1 atom, 1 residue, 1 model selected
> select subtract #9/F:154@CA
Nothing selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #9/F:154@CA
1 atom, 1 residue, 1 model selected
> select subtract #9/F:154@CA
Nothing selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #9/F:154@CA
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #9/F:128@O
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> select #9/F:128@CA
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> open /Users/nicholasferraro/Replicase/AMP-
> PnP/ssDNA/J968_with_FOD/cryosparc_P5_J968_004_volume_map_sharp_inv.mrc
Opened cryosparc_P5_J968_004_volume_map_sharp_inv.mrc as #11, grid size
300,300,300, pixel 0.844, shown at level 0.166, step 2, values float32
> surface dust #11 size 8.44
> fitmap #9 inMap #11
Fit molecule J968-RSR-Regclash-out-coot-2.pdb (#9) to map
cryosparc_P5_J968_004_volume_map_sharp_inv.mrc (#11) using 15253 atoms
average map value = 0.5132, steps = 44
shifted from previous position = 0.0145
rotated from previous position = 0.0499 degrees
atoms outside contour = 2472, contour level = 0.16566
Position of J968-RSR-Regclash-out-coot-2.pdb (#9) relative to
cryosparc_P5_J968_004_volume_map_sharp_inv.mrc (#11) coordinates:
Matrix rotation and translation
0.99999976 -0.00052808 -0.00044255 0.11393674
0.00052832 0.99999972 0.00053171 -0.13591873
0.00044227 -0.00053194 0.99999976 0.01360411
Axis -0.61102746 -0.50829386 0.60686307
Axis point 0.00000000 16.65081026 248.25080303
Rotation angle (degrees) 0.04986914
Shift along axis 0.00772401
> fitmap #9 inMap #11
Fit molecule J968-RSR-Regclash-out-coot-2.pdb (#9) to map
cryosparc_P5_J968_004_volume_map_sharp_inv.mrc (#11) using 15253 atoms
average map value = 0.5132, steps = 40
shifted from previous position = 0.0164
rotated from previous position = 0.0151 degrees
atoms outside contour = 2457, contour level = 0.16566
Position of J968-RSR-Regclash-out-coot-2.pdb (#9) relative to
cryosparc_P5_J968_004_volume_map_sharp_inv.mrc (#11) coordinates:
Matrix rotation and translation
0.99999980 -0.00035946 -0.00051458 0.11169757
0.00035983 0.99999967 0.00072154 -0.15049025
0.00051432 -0.00072173 0.99999961 0.02863936
Axis -0.75450829 -0.53788310 0.37603060
Axis point 0.00000000 35.69548994 203.03796385
Rotation angle (degrees) 0.05479953
Shift along axis 0.00743869
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Opened J968-RSR-Regclash-out-coot-2.pdb map 5 as #12, grid size 65,67,76,
pixel 1.67, shown at level 0.114, step 1, values float32
> fitmap #9 inMap #11 resolution 5
Fit map J968-RSR-Regclash-out-coot-2.pdb map 5 in map
cryosparc_P5_J968_004_volume_map_sharp_inv.mrc using 30785 points
correlation = 0.8206, correlation about mean = 0.6727, overlap = 5513
steps = 40, shift = 0.068, angle = 0.0282 degrees
Position of J968-RSR-Regclash-out-coot-2.pdb map 5 (#12) relative to
cryosparc_P5_J968_004_volume_map_sharp_inv.mrc (#11) coordinates:
Matrix rotation and translation
0.99999989 -0.00047232 -0.00003471 0.01200406
0.00047234 0.99999963 0.00072238 -0.20737148
0.00003437 -0.00072239 0.99999974 0.08331265
Axis -0.83629942 -0.03998769 0.54681283
Axis point 0.00000000 82.06384152 284.68493080
Rotation angle (degrees) 0.04949148
Shift along axis 0.04380974
Average map value = 0.5129 for 15253 atoms, 2459 outside contour
> ui tool show "Map Filter"
> volume gaussian #11 sDev 1.1
Opened cryosparc_P5_J968_004_volume_map_sharp_inv.mrc gaussian as #13, grid
size 300,300,300, pixel 0.844, shown at step 1, values float32
> transparency #13.1 50
> volume #13 level 0.1404
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/Rep_F-chain.pdb
Rep_F-chain.pdb title:
Cryo-em structure of PCV2 replicase bound to ssDNA [more info...]
Chain information for Rep_F-chain.pdb #14
---
Chain | Description | UniProt
F | atp-dependent helicase rep | Q6TC59_PCV2 1-314
> hide #14 models
> show #!12 models
> hide #!12 models
> close #12
> close #9
> open /Users/nicholasferraro/Replicase/AMP-
> PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968-RSR-Regclash-out-
> coot-2.pdb
Summary of feedback from opening /Users/nicholasferraro/Replicase/AMP-
PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968-RSR-Regclash-out-
coot-2.pdb
---
warnings | Duplicate atom serial number found: 9340
Duplicate atom serial number found: 12880
Duplicate atom serial number found: 13463
Chain information for J968-RSR-Regclash-out-coot-2.pdb #9
---
Chain | Description
A B C D E | No description available
F | No description available
G | No description available
Opened J968-RSR-Regclash-out-coot-2.pdb map 5 as #12, grid size 65,70,76,
pixel 1.67, shown at level 0.115, step 1, values float32
> fitmap #9 inMap #11 resolution 5
Fit map J968-RSR-Regclash-out-coot-2.pdb map 5 in map
cryosparc_P5_J968_004_volume_map_sharp_inv.mrc using 31951 points
correlation = 0.8218, correlation about mean = 0.6725, overlap = 5770
steps = 44, shift = 0.0803, angle = 0.0559 degrees
Position of J968-RSR-Regclash-out-coot-2.pdb map 5 (#12) relative to
cryosparc_P5_J968_004_volume_map_sharp_inv.mrc (#11) coordinates:
Matrix rotation and translation
0.99999999 -0.00015335 -0.00007506 -0.02388188
0.00015342 0.99999953 0.00096011 -0.20291118
0.00007491 -0.00096012 0.99999954 0.11236664
Axis -0.98455494 -0.07689316 0.15728641
Axis point 0.00000000 107.63107755 206.84718171
Rotation angle (degrees) 0.05587336
Shift along axis 0.05678925
Average map value = 0.5147 for 15853 atoms, 2515 outside contour
> show #14 models
> select #14/F
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> fitmap #14 inMap #13
Fit molecule Rep_F-chain.pdb (#14) to map
cryosparc_P5_J968_004_volume_map_sharp_inv.mrc gaussian (#13) using 2301 atoms
average map value = 0.2469, steps = 80
shifted from previous position = 4.56
rotated from previous position = 11.8 degrees
atoms outside contour = 530, contour level = 0.14036
Position of Rep_F-chain.pdb (#14) relative to
cryosparc_P5_J968_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates:
Matrix rotation and translation
0.98020244 0.06268018 0.18781474 -28.48538168
-0.07257796 0.99628804 0.04628801 4.07138667
-0.18421624 -0.05900283 0.98111317 34.60542112
Axis -0.25704560 0.90823595 -0.33020450
Axis point 169.68189378 0.00000000 170.11070766
Rotation angle (degrees) 11.81835657
Shift along axis -0.40704422
> hide #!13 models
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/nicholasferraro/Replicase/AMP-
> PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968_F-chain_in.pdb
> models #14 relModel #9
> show #!12 models
> show #!11 models
> close #9,11-13
> hide #14 models
> open /Users/nicholasferraro/Replicase/AMP-
> PnP/ssDNA/J981_with_FOD/Round_000_real_space_refined_m5_001.pdb
Chain information for Round_000_real_space_refined_m5_001.pdb #9
---
Chain | Description
A B C D E F | No description available
G | No description available
> open /Users/nicholasferraro/Replicase/AMP-
> PnP/ssDNA/J981_with_FOD/cryosparc_P5_J981_004_volume_map_sharp_inv.mrc
Opened cryosparc_P5_J981_004_volume_map_sharp_inv.mrc as #11, grid size
300,300,300, pixel 0.844, shown at level 0.187, step 2, values float32
Opened Round_000_real_space_refined_m5_001.pdb map 5 as #12, grid size
73,69,75, pixel 1.67, shown at level 0.116, step 1, values float32
> fitmap #9 inMap #11 resolution 5
Fit map Round_000_real_space_refined_m5_001.pdb map 5 in map
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc using 36757 points
correlation = 0.7533, correlation about mean = 0.7276, overlap = 7851
steps = 60, shift = 0.0451, angle = 0.00889 degrees
Position of Round_000_real_space_refined_m5_001.pdb map 5 (#12) relative to
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc (#11) coordinates:
Matrix rotation and translation
1.00000000 0.00000938 0.00008330 -0.04567419
-0.00000939 0.99999999 0.00013050 -0.04439060
-0.00008330 -0.00013050 0.99999999 0.02084044
Axis -0.84137711 0.53705038 -0.06050981
Axis point 0.00000000 165.83812057 395.01508720
Rotation angle (degrees) 0.00888684
Shift along axis 0.01332818
Average map value = 0.7111 for 18135 atoms, 2551 outside contour
> surface dust #11 size 8.44
> fitmap #9 inMap #11 resolution 5
Fit map Round_000_real_space_refined_m5_001.pdb map 5 in map
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc using 36757 points
correlation = 0.7533, correlation about mean = 0.7275, overlap = 7851
steps = 44, shift = 0.0162, angle = 0.0139 degrees
Position of Round_000_real_space_refined_m5_001.pdb map 5 (#12) relative to
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc (#11) coordinates:
Matrix rotation and translation
0.99999996 -0.00007697 0.00026666 -0.05894520
0.00007697 1.00000000 -0.00000131 -0.03510633
-0.00026666 0.00000133 0.99999996 0.01245642
Axis 0.00476551 0.96076267 0.27733081
Axis point 78.46177691 0.00000000 220.51661181
Rotation angle (degrees) 0.01590236
Shift along axis -0.03055520
Average map value = 0.7111 for 18135 atoms, 2557 outside contour
> ui tool show "Map Filter"
Window position QRect(954,1009 807x134) outside any known screen, using
primary screen
> volume gaussian #11 sDev 1.1
Opened cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian as #13, grid
size 300,300,300, pixel 0.844, shown at step 1, values float32
> volume gaussian #11 sDev 1.16 modelId #13
Opened cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian as #13, grid
size 300,300,300, pixel 0.844, shown at step 1, values float32
> volume gaussian #11 sDev 0.95 modelId #13
Opened cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian as #13, grid
size 300,300,300, pixel 0.844, shown at step 1, values float32
> volume gaussian #11 sDev 1.02 modelId #13
Opened cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian as #13, grid
size 300,300,300, pixel 0.844, shown at step 1, values float32
> select protein
177836 atoms, 180553 bonds, 8 pseudobonds, 11235 residues, 14 models selected
> fitmap #9 inMap #13
Fit molecule Round_000_real_space_refined_m5_001.pdb (#9) to map
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) using 18135
atoms
average map value = 0.4741, steps = 44
shifted from previous position = 0.0191
rotated from previous position = 0.0385 degrees
atoms outside contour = 2855, contour level = 0.19564
Position of Round_000_real_space_refined_m5_001.pdb (#9) relative to
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates:
Matrix rotation and translation
0.99999994 -0.00020620 -0.00028703 0.01396351
0.00020630 0.99999991 0.00035738 -0.08792908
0.00028696 -0.00035744 0.99999989 -0.00958410
Axis -0.71106260 -0.57097381 0.41033996
Axis point 0.00000000 -68.59145060 187.95862302
Rotation angle (degrees) 0.02879897
Shift along axis 0.03634354
> fitmap #9 inMap #13
Fit molecule Round_000_real_space_refined_m5_001.pdb (#9) to map
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) using 18135
atoms
average map value = 0.4741, steps = 44
shifted from previous position = 0.013
rotated from previous position = 0.0117 degrees
atoms outside contour = 2847, contour level = 0.19564
Position of Round_000_real_space_refined_m5_001.pdb (#9) relative to
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates:
Matrix rotation and translation
0.99999997 -0.00020659 -0.00012645 0.00160601
0.00020662 0.99999995 0.00023118 -0.08004404
0.00012640 -0.00023120 0.99999997 -0.01048149
Axis -0.69045057 -0.37756311 0.61702844
Axis point 0.00000000 -105.81681497 309.23968334
Rotation angle (degrees) 0.01918482
Shift along axis 0.02264543
> fitmap #9 inMap #13
Fit molecule Round_000_real_space_refined_m5_001.pdb (#9) to map
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) using 18135
atoms
average map value = 0.4741, steps = 44
shifted from previous position = 0.00852
rotated from previous position = 0.00996 degrees
atoms outside contour = 2852, contour level = 0.19564
Position of Round_000_real_space_refined_m5_001.pdb (#9) relative to
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates:
Matrix rotation and translation
0.99999996 -0.00026473 0.00002971 -0.01301395
0.00026473 0.99999995 0.00018158 -0.07654306
-0.00002976 -0.00018157 0.99999998 -0.00260143
Axis -0.56321959 0.09223704 0.82114312
Axis point 288.47831851 -53.16852251 0.00000000
Rotation angle (degrees) 0.01847172
Shift along axis -0.00186653
> fitmap #9 inMap #13
Fit molecule Round_000_real_space_refined_m5_001.pdb (#9) to map
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) using 18135
atoms
average map value = 0.4741, steps = 44
shifted from previous position = 0.0148
rotated from previous position = 0.0105 degrees
atoms outside contour = 2846, contour level = 0.19564
Position of Round_000_real_space_refined_m5_001.pdb (#9) relative to
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates:
Matrix rotation and translation
0.99999998 -0.00015172 -0.00011330 -0.00693700
0.00015175 0.99999997 0.00020271 -0.07132349
0.00011327 -0.00020272 0.99999997 -0.00634114
Axis -0.73076374 -0.40839385 0.54699069
Axis point 0.00000000 -114.23166267 289.92981066
Rotation angle (degrees) 0.01589387
Shift along axis 0.03072884
> fitmap #9 inMap #13
Fit molecule Round_000_real_space_refined_m5_001.pdb (#9) to map
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) using 18135
atoms
average map value = 0.4741, steps = 44
shifted from previous position = 0.00758
rotated from previous position = 0.00383 degrees
atoms outside contour = 2847, contour level = 0.19564
Position of Round_000_real_space_refined_m5_001.pdb (#9) relative to
cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates:
Matrix rotation and translation
0.99999997 -0.00020319 -0.00013563 0.00239800
0.00020322 0.99999995 0.00023892 -0.08048452
0.00013558 -0.00023895 0.99999996 -0.01177430
Axis -0.69922219 -0.39683366 0.59465232
Axis point 0.00000000 -107.20814946 298.20661583
Rotation angle (degrees) 0.01957906
Shift along axis 0.02326062
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/nicholasferraro/Replicase/AMP-PnP/ssDNA/J981_with_FOD/J981_F-
> chain.pdb models #9 relModel #11
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #13
> close #12
> close #9
> close #11
> open /Users/nicholasferraro/Replicase/AMP-
> PnP/ssDNA/J983/Round_001_J983_with_FOD_real_space_refined_m4_001.pdb
Chain information for Round_001_J983_with_FOD_real_space_refined_m4_001.pdb #9
---
Chain | Description
A | No description available
B C D E | No description available
F | No description available
G | No description available
> open /Users/nicholasferraro/Replicase/AMP-
> PnP/ssDNA/J983/cryosparc_P5_J983_006_volume_map_sharp_inv.mrc
Opened cryosparc_P5_J983_006_volume_map_sharp_inv.mrc as #11, grid size
300,300,300, pixel 0.844, shown at level 0.181, step 2, values float32
> surface dust #11 size 8.44
> volume gaussian #11 sDev 1.02
Opened cryosparc_P5_J983_006_volume_map_sharp_inv.mrc gaussian as #12, grid
size 300,300,300, pixel 0.844, shown at step 1, values float32
> volume gaussian #11 sDev 1.09 modelId #12
Opened cryosparc_P5_J983_006_volume_map_sharp_inv.mrc gaussian as #12, grid
size 300,300,300, pixel 0.844, shown at step 1, values float32
> transparency #12.1 50
> show #14 models
> select #14/F
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> fitmap #14 inMap #12
Fit molecule Rep_F-chain.pdb (#14) to map
cryosparc_P5_J983_006_volume_map_sharp_inv.mrc gaussian (#12) using 2301 atoms
average map value = 0.2597, steps = 52
shifted from previous position = 1.77
rotated from previous position = 3.69 degrees
atoms outside contour = 753, contour level = 0.18978
Position of Rep_F-chain.pdb (#14) relative to
cryosparc_P5_J983_006_volume_map_sharp_inv.mrc gaussian (#12) coordinates:
Matrix rotation and translation
0.98620852 0.00495050 0.16543353 -19.12819427
-0.01182260 0.99910630 0.04058109 -3.82838013
-0.16508478 -0.04197727 0.98538567 29.67738027
Axis -0.24204566 0.96901788 -0.04917560
Axis point 168.06391931 0.00000000 130.42443323
Rotation angle (degrees) 9.81938803
Shift along axis -0.53927530
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/nicholasferraro/Replicase/AMP-PnP/ssDNA/J983/J983_F-
> chain_fit.pdb models #14 relModel #9
> close #9,11-12
> open /Users/nicholasferraro/Replicase/AMP-
> PnP/ssDNA/J985/Phenix/Round_000_real_space_refined_m6_001_with_FOD.pdb
Summary of feedback from opening /Users/nicholasferraro/Replicase/AMP-
PnP/ssDNA/J985/Phenix/Round_000_real_space_refined_m6_001_with_FOD.pdb
---
warning | Cannot find LINK/SSBOND residue ARG (232 )
Chain information for Round_000_real_space_refined_m6_001_with_FOD.pdb #9
---
Chain | Description
A B C D E | No description available
F | No description available
G | No description available
> open /Users/nicholasferraro/Replicase/AMP-
> PnP/ssDNA/J985/cryosparc_P5_J985_004_volume_map_sharp_inv.mrc
Opened cryosparc_P5_J985_004_volume_map_sharp_inv.mrc as #11, grid size
300,300,300, pixel 0.844, shown at level 0.175, step 2, values float32
> surface dust #11 size 8.44
Opened Round_000_real_space_refined_m6_001_with_FOD.pdb map 5 as #12, grid
size 68,69,77, pixel 1.67, shown at level 0.115, step 1, values float32
> fitmap #9 inMap #11 resolution 5
Fit map Round_000_real_space_refined_m6_001_with_FOD.pdb map 5 in map
cryosparc_P5_J985_004_volume_map_sharp_inv.mrc using 31939 points
correlation = 0.8776, correlation about mean = 0.7267, overlap = 6126
steps = 40, shift = 0.0315, angle = 0.0772 degrees
Position of Round_000_real_space_refined_m6_001_with_FOD.pdb map 5 (#12)
relative to cryosparc_P5_J985_004_volume_map_sharp_inv.mrc (#11) coordinates:
Matrix rotation and translation
0.99999917 0.00090400 0.00091545 -0.24954701
-0.00090436 0.99999951 0.00040005 0.04446861
-0.00091509 -0.00040087 0.99999950 0.15237744
Axis -0.29719846 0.67925838 -0.67102990
Axis point 167.92359338 0.00000000 272.05824455
Rotation angle (degrees) 0.07720340
Shift along axis 0.00212085
Average map value = 0.5315 for 15766 atoms, 1934 outside contour
> fitmap #9 inMap #11 resolution 5
Fit map Round_000_real_space_refined_m6_001_with_FOD.pdb map 5 in map
cryosparc_P5_J985_004_volume_map_sharp_inv.mrc using 31939 points
correlation = 0.8776, correlation about mean = 0.7266, overlap = 6126
steps = 48, shift = 0.0131, angle = 0.0099 degrees
Position of Round_000_real_space_refined_m6_001_with_FOD.pdb map 5 (#12)
relative to cryosparc_P5_J985_004_volume_map_sharp_inv.mrc (#11) coordinates:
Matrix rotation and translation
0.99999924 0.00092810 0.00080995 -0.24170122
-0.00092853 0.99999943 0.00053479 0.03031724
-0.00080945 -0.00053555 0.99999953 0.16947538
Axis -0.39847339 0.60288161 -0.69119659
Axis point 34.14579185 261.55015794 0.00000000
Rotation angle (degrees) 0.07695128
Shift along axis -0.00255159
Average map value = 0.5315 for 15766 atoms, 1944 outside contour
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume gaussian #11 sDev 1.09
Opened cryosparc_P5_J985_004_volume_map_sharp_inv.mrc gaussian as #13, grid
size 300,300,300, pixel 0.844, shown at step 1, values float32
> volume gaussian #11 sDev 1.19 modelId #13
Opened cryosparc_P5_J985_004_volume_map_sharp_inv.mrc gaussian as #13, grid
size 300,300,300, pixel 0.844, shown at step 1, values float32
> select #14/F
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> fitmap #14 inMap #13
Fit molecule Rep_F-chain.pdb (#14) to map
cryosparc_P5_J985_004_volume_map_sharp_inv.mrc gaussian (#13) using 2301 atoms
average map value = 0.2611, steps = 88
shifted from previous position = 7.75
rotated from previous position = 14.7 degrees
atoms outside contour = 682, contour level = 0.18452
Position of Rep_F-chain.pdb (#14) relative to
cryosparc_P5_J985_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates:
Matrix rotation and translation
0.99359813 -0.10944935 -0.02799292 21.44980875
0.10713511 0.99149326 -0.07391332 -3.06923684
0.03584456 0.07044111 0.99687172 -12.21693772
Axis 0.53864251 -0.23820244 0.80816078
Axis point 37.72983201 181.90388082 0.00000000
Rotation angle (degrees) 7.70070461
Shift along axis 2.41162853
> transparency #13.1 50
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/nicholasferraro/Replicase/AMP-PnP/ssDNA/J985/J985_F-
> chain_fit.pdb models #14 relModel #9
> hide #!11 models
> select #14/F
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> fitmap #14 inMap #13
Fit molecule Rep_F-chain.pdb (#14) to map
cryosparc_P5_J985_004_volume_map_sharp_inv.mrc gaussian (#13) using 2301 atoms
average map value = 0.2611, steps = 40
shifted from previous position = 0.00972
rotated from previous position = 0.0105 degrees
atoms outside contour = 683, contour level = 0.18452
Position of Rep_F-chain.pdb (#14) relative to
cryosparc_P5_J985_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates:
Matrix rotation and translation
0.99361681 -0.10930159 -0.02790687 21.42339856
0.10699614 0.99151328 -0.07384602 -3.06644058
0.03574152 0.07038872 0.99687912 -12.19650890
Axis 0.53888196 -0.23779967 0.80811976
Axis point 37.71253902 181.88069652 0.00000000
Rotation angle (degrees) 7.69084086
Shift along axis 2.41764162
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #12
> close #11,13
> close #14
> close #9
> open /Users/nicholasferraro/Replicase/AMP-
> PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968_F-chain_in.pdb
J968_F-chain_in.pdb title:
Cryo-em structure of PCV2 replicase bound to ssDNA [more info...]
Chain information for J968_F-chain_in.pdb #9
---
Chain | Description | UniProt
F | atp-dependent helicase rep | Q6TC59_PCV2 1-314
> open /Users/nicholasferraro/Replicase/AMP-
> PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968_F-chain.pdb
Chain information for J968_F-chain.pdb #11
---
Chain | Description
A B C D E | No description available
F | No description available
G | No description available
> hide #!11 models
> close #9
> show #!11 models
> open /Users/nicholasferraro/Replicase/AMP-PnP/ssDNA/J981_with_FOD/J981_F-
> chain.pdb
Chain information for J981_F-chain.pdb #9
---
Chain | Description
A B C D E F | No description available
G | No description available
> hide #!11 models
> select #9/F
2964 atoms, 3014 bonds, 1 pseudobond, 185 residues, 2 models selected
> select clear
> hide #!9 models
> open /Users/nicholasferraro/Replicase/AMP-PnP/ssDNA/J983/J983_with_F-
> chain.pdb
Chain information for J983_with_F-chain.pdb #12
---
Chain | Description
A | No description available
B C D E | No description available
F | No description available
G | No description available
> open /Users/nicholasferraro/Replicase/AMP-PnP/ssDNA/J985/J985_with_F-
> chain.pdb
Chain information for J985_with_F-chain.pdb #13
---
Chain | Description
A B C D E | No description available
F | No description available
G | No description available
> show #!9 models
> show #!11 models
> select #1/A#2/A#3/A#4/A#5/A#6/A#7/A#8/A#9/A#10/A#11/A#12/A#13/A
38676 atoms, 39283 bonds, 11 pseudobonds, 2427 residues, 24 models selected
> color (#!9,11-13 & sel) #ff85ffff
> select #1/B#2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B
38655 atoms, 39255 bonds, 11 pseudobonds, 2426 residues, 23 models selected
> color (#!9,11-13 & sel) #73fa79ff
> select #1/C#2/C#3/C#4/C#5/C#6/C#7/C#8/C#9/C#10/C#11/C#12/C#13/C
38654 atoms, 39260 bonds, 9 pseudobonds, 2426 residues, 21 models selected
> color (#!9,11-13 & sel) #fffc79ff
> color (#!9,11-13 & sel) #7a81ffff
> select #1/D#2/D#3/D#4/D#5/D#6/D#7/D#8/D#9/D#10/D#11/D#12/D#13/D
38790 atoms, 39414 bonds, 7 pseudobonds, 2435 residues, 19 models selected
> color (#!9,11-13 & sel) #76d6ffff
> select #1/E#2/E#3/E#4/E#5/E#6/E#7/E#8/E#9/E#10/E#11/E#12/E#13/E
38530 atoms, 39145 bonds, 3 pseudobonds, 2413 residues, 16 models selected
> color (#!9,11-13 & sel) #fffc79ff
> select #1/F#2/F#3/F#4/F#5/F#6/F#7/F#8/F#9/F#10/F#11/F#12/F#13/F
37674 atoms, 38238 bonds, 3 pseudobonds, 2381 residues, 16 models selected
> color (#!9,11-13 & sel) #ff7e79ff
> select clear
> select ligand
4457 atoms, 4694 bonds, 126 residues, 13 models selected
> color (#!9,11-13 & sel) dim gray
> color sel & #!9,11-13 byhetero
> select clear
> select protein
228689 atoms, 232243 bonds, 25 pseudobonds, 14411 residues, 19 models selected
> style sel & #!9,11-13 ball
Changed 70948 atom styles
> show sel & #!9,11-13 cartoons
> hide sel & #!9,11-13 atoms
> select clear
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!9 models
> hide #!12 models
> hide #!13 models
> hide #!11 models
> show #!11 models
> show #!9 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!9 models
> show #!9 models
> show #!12 models
> show #!11 models
> hide #!11 models
> hide #!9 models
> hide #!12 models
> show #!12 models
> show #!11 models
> show #!9 models
> hide #!9 models
> hide #!11 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!12 models
> show #!9 models
> show #!12 models
> hide #!12 models
> show #!12 models
> show #!11 models
> hide #!11 models
> hide #!12 models
> hide #!9 models
> show #!12 models
> hide #!12 models
> show #!9 models
> show #!12 models
> show #!11 models
> morph #13,9,12,11 frames 10
Computed 31 frame morph #14
> coordset #14 1,31
> movie record
> movie encode /Users/nicholasferraro/Desktop/movie8.mp4 framerate 25.0
Movie saved to /Users/nicholasferraro/Desktop/movie8.mp4
> morph #13,9,12,11 frames 25
Computed 76 frame morph #15
> coordset #15 1,76
> close #14-15
> show #!13 models
> show #!12 models
> show #!11 models
> show #!9 models
> matchmaker #9/C to #13/C pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J985_with_F-chain.pdb, chain C (#13) with J981_F-chain.pdb, chain C
(#9), sequence alignment score = 949.9
RMSD between 185 pruned atom pairs is 0.307 angstroms; (across all 185 pairs:
0.307)
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #11/C to #13/C pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J985_with_F-chain.pdb, chain C (#13) with J968_F-chain.pdb, chain C
(#11), sequence alignment score = 955.9
RMSD between 185 pruned atom pairs is 0.473 angstroms; (across all 185 pairs:
0.473)
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #12/C to #13/C pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J985_with_F-chain.pdb, chain C (#13) with J983_with_F-chain.pdb,
chain C (#12), sequence alignment score = 959.1
RMSD between 184 pruned atom pairs is 0.332 angstroms; (across all 184 pairs:
0.332)
> morph #13,9,12,11 frames 25
Computed 76 frame morph #14
> coordset #14 1,76
> movie record
> movie encode /Users/nicholasferraro/Desktop/movie8.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> movie record
> movie encode /Users/nicholasferraro/Desktop/movie8.mp4 framerate 25.0
Movie saved to /Users/nicholasferraro/Desktop/movie8.mp4
> hide #!14 models
> open
> /Users/nicholasferraro/Desktop/fold_2024_08_12_15_49/fold_2024_08_12_15_49_full_data_0.json
Traceback (most recent call last):
File
"/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/__init__.py", line 129, in open
structs = [m for m in session.models.list(type = AtomicStructure)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/__init__.py", line 130, in
if hasattr(m, 'filename') and dirname(m.filename) == dirname(path)]
^^^^^^^^^^^^^^^^^^^
File "", line 152, in dirname
TypeError: expected str, bytes or os.PathLike object, not NoneType
TypeError: expected str, bytes or os.PathLike object, not NoneType
File "", line 152, in dirname
See log for complete Python traceback.
> show #!13 models
> show #!12 models
> show #!11 models
> show #!9 models
> hide #!11 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!12 models
> show #!11 models
> show #!12 models
> show #!13 models
> morph #13,9,12,11 frames 4
Computed 13 frame morph #15
> coordset #15 1,13
> hide #!15 models
> show #!13 models
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!13 models
> show #!9 models
> hide #!11 models
> show #!11 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!13 models
> hide #!11 models
> hide #!13 models
> show #!12 models
Cell requested for row 11 is out of bounds for table with 17 rows! Resizing
table model.
> close #9,11-13
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: MK1A3LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 4 days, 20 hours, 53 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 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: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 15 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Mac Qt 6.6 bug, crash in _NSViewHierarchyDidChangeBackingProperties.
Unfortunately the Qt window toolkit version used by ChimeraX 1.8 has a bug where plugging in or unplugging an external monitor, or sometimes waking the computer from sleep causes it to crash while it is configuring the displays. Nothing we can do to fix this. Save a ChimeraX session before changing external displays or leaving the computer. The ChimeraX daily builds use a newer Qt version 6.7 and the crash has never been reported with that Qt version so you might try the daily build.
Note:
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Reported by Nicholas Ferraro