![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Last modified 15 months ago
#15854 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: 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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{
"uptime" : 140000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,2",
"coalitionID" : 5611,
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"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-08-30 13:56:58.2110 -0400",
"codeSigningMonitor" : 1,
"incident" : "CA8930C1-90C1-4C70-93E4-131D772589B6",
"pid" : 84283,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-29 14:34:14.0574 -0400",
"procStartAbsTime" : 2569332497667,
"procExitAbsTime" : 3586076289588,
"procName" : "ChimeraX",
"procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "601EFD1A-7C31-028E-F125-8C968238879B",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 11890,
"sleepWakeUUID" : "009503F0-BF26-415C-A532-5CA253E7F922",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4330913431\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102248000-10224c000 [ 16K] r-x\/r-x SM=COW \/var\/folders\/*\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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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.
> save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/Rep_F-chain.pdb models #2 relModel #1
> close #1
> show #!3 models
> hide #!3 models
> close #4
> close #3
> hide #2 models
> 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
> 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
> select protein
19841 atoms, 20146 bonds, 1253 residues, 2 models selected
> select clear
> style #!1 ball
Changed 17940 atom styles
> show #!1 cartoons
> hide #!1 atoms
> select ligand
396 atoms, 417 bonds, 11 residues, 1 model selected
> show sel atoms
> select clear
> select #1/A:402@N7
1 atom, 1 residue, 1 model selected
> select add #1/A:402@C5
2 atoms, 1 residue, 1 model selected
> select add #1/A:402@C2'
3 atoms, 1 residue, 1 model selected
> select add #1/A:402@C4'
4 atoms, 1 residue, 1 model selected
> select add #1/A:402@O3A
5 atoms, 1 bond, 1 residue, 1 model selected
> select add #1/A:402@PB
6 atoms, 1 bond, 1 residue, 1 model selected
> select add #1/A:402@O2B
7 atoms, 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:402@N3B
8 atoms, 2 bonds, 1 residue, 1 model selected
> select add #1/A:402@O3G
9 atoms, 2 bonds, 1 residue, 1 model selected
> select add #1/A:402@PG
10 atoms, 2 bonds, 1 residue, 1 model selected
> select add #1/A:402@O2G
11 atoms, 2 bonds, 1 residue, 1 model selected
> select subtract #1/A:402@N3B
10 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 bonds sel
> select subtract #1/A:402@O2G
9 atoms, 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/A:402@N6
1 atom, 1 residue, 1 model selected
> select add #1/A:402@C6
2 atoms, 1 residue, 1 model selected
> select add #1/A:402@C2
3 atoms, 1 bond, 1 residue, 1 model selected
> select add #1/A:402@C4
4 atoms, 2 bonds, 1 residue, 1 model selected
> select add #1/A:402@C1'
5 atoms, 3 bonds, 1 residue, 1 model selected
> select add #1/A:402@O4'
6 atoms, 3 bonds, 1 residue, 1 model selected
> select add #1/A:402@C8
7 atoms, 3 bonds, 1 residue, 1 model selected
> select add #1/A:402@C3'
8 atoms, 3 bonds, 1 residue, 1 model selected
> select add #1/A:402@O2'
9 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:402@O2A
10 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:402@C5'
11 atoms, 4 bonds, 1 residue, 1 model selected
> select subtract #1/A:402@C5'
10 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:402@O5'
11 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:402@O1A
12 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:402@PA
13 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:402@O1B
14 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:402@N3B
15 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:402@O1G
16 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:402@O2G
17 atoms, 4 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
> select #1/A:402@C5'
1 atom, 1 residue, 1 model selected
> select #1/A:402@N9
1 atom, 1 residue, 1 model selected
> select #1/A:402@O3'
1 atom, 1 residue, 1 model selected
> select #1/A:402@N3
1 atom, 1 residue, 1 model selected
> select #1/A:402@N1
1 atom, 1 residue, 1 model selected
> select add #1/A:402@N9
2 atoms, 1 residue, 1 model selected
> select add #1/A:402@N3
3 atoms, 1 residue, 1 model selected
> select add #1/A:402@O3'
4 atoms, 1 residue, 1 model selected
> select add #1/A:402@C5'
5 atoms, 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/J909_AMP-PnP-ATP_F-chain.pdb models #1 relModel #1
> close #1
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J921_AMP-PnP-ATP_F-chain.pdb
Chain information for J921_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 15652 atom styles
> show #!1 cartoons
> hide #!1 atoms
> select ligand
409 atoms, 430 bonds, 11 residues, 1 model selected
> show sel atoms
> select clear
> show #2 models
> open /Users/nicholasferraro/Replicase/AMP-PnP-
> ATP/J921/cryosparc_P5_crypsparc_P5_J921_005_volume_map_sharp_flip.mrc
Opened cryosparc_P5_crypsparc_P5_J921_005_volume_map_sharp_flip.mrc as #3,
grid size 300,300,300, pixel 0.844, shown at level 0.105, step 2, values
float32
> surface dust #3 size 8.44
> volume gaussian #3 sDev 1.99
Opened cryosparc_P5_crypsparc_P5_J921_005_volume_map_sharp_flip.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 0.0982
> volume gaussian #3 sDev 1.32 modelId #4
Opened cryosparc_P5_crypsparc_P5_J921_005_volume_map_sharp_flip.mrc gaussian
as #4, grid size 300,300,300, pixel 0.844, shown at step 1, values float32
> 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_crypsparc_P5_J921_005_volume_map_sharp_flip.mrc gaussian (#4)
using 2301 atoms
average map value = 0.1807, steps = 132
shifted from previous position = 5.76
rotated from previous position = 31.2 degrees
atoms outside contour = 565, contour level = 0.11632
Position of Rep_F-chain.pdb (#2) relative to
cryosparc_P5_crypsparc_P5_J921_005_volume_map_sharp_flip.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.99393118 -0.07549020 0.08001275 -3.77635388
0.06509498 0.98996930 0.12539308 -11.72745979
-0.08867611 -0.11942366 0.98887539 50.60538444
Axis -0.74441838 0.51293505 0.42747972
Axis point -0.00000000 339.51702968 196.06899964
Rotation angle (degrees) 9.46440891
Shift along axis 18.42853776
> select clear
> hide #!4 models
> select #1/F:157
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/F:158
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1/F:157
18 atoms, 16 bonds, 2 residues, 2 models selected
> ui tool show "Build Structure"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> build join peptide sel length 1.33 omega 180 phi -120 move small
> undo
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Undo failed, probably because structures have been modified.
> select subtract /F:157
Nothing selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select /F:157
11 atoms, 10 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.
> select clear
> close #1
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/Rep_F-chain.pdb /Users/nicholasferraro/Replicase/AMP-PnP-
> ATP/AMP-PnP-ATP_Models_Phenix/J921_AMP-PnP-ATP_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 #1
---
Chain | Description | UniProt
F | atp-dependent helicase rep | Q6TC59_PCV2 1-314
Chain information for J921_AMP-PnP-ATP_F-chain.pdb #2
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> show #!4 models
> select add #1
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> fitmap #1 inMap #4
Fit molecule Rep_F-chain.pdb (#1) to map
cryosparc_P5_crypsparc_P5_J921_005_volume_map_sharp_flip.mrc gaussian (#4)
using 2301 atoms
average map value = 0.1807, steps = 132
shifted from previous position = 5.76
rotated from previous position = 31.2 degrees
atoms outside contour = 565, contour level = 0.11632
Position of Rep_F-chain.pdb (#1) relative to
cryosparc_P5_crypsparc_P5_J921_005_volume_map_sharp_flip.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.97734944 0.15170661 0.14755737 -27.58756758
-0.20396675 0.86117966 0.46558259 -8.29435040
-0.05644144 -0.48513368 0.87261657 82.94464458
Axis -0.91824271 0.19703083 -0.34352465
Axis point 0.00000000 151.56591880 60.97711541
Rotation angle (degrees) 31.17692320
Shift along axis -4.79568996
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 #1 relModel #2
> close #2
> hide #1 models
> close #4
> close #3
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J921_AMP-PnP-ATP_F-chain.pdb
Chain information for J921_AMP-PnP-ATP_F-chain.pdb #2
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> close #2
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J922_AMP-PnP-ATP_F-chain.pdb
Chain information for J922_AMP-PnP-ATP_F-chain.pdb #2
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> color #!2 byhetero
> style #!2 ball
Changed 15653 atom styles
> undo
> style #!2 ball
Changed 15653 atom styles
> show #!2 cartoons
> hide #!2 atoms
> select ligand
409 atoms, 430 bonds, 11 residues, 1 model selected
> show sel atoms
> select clear
> show #1 models
> open /Users/nicholasferraro/Replicase/AMP-PnP-
> ATP/J922/cryosparc_P5_cryosparc_P5_J922_004_volume_map_sharp.mrc
Opened cryosparc_P5_cryosparc_P5_J922_004_volume_map_sharp.mrc as #3, grid
size 300,300,300, pixel 0.844, shown at level 0.101, step 2, values float32
> surface dust #3 size 8.44
> volume gaussian #3 sDev 1.32
Opened cryosparc_P5_cryosparc_P5_J922_004_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 1.06 modelId #4
Opened cryosparc_P5_cryosparc_P5_J922_004_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 1.22 modelId #4
Opened cryosparc_P5_cryosparc_P5_J922_004_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 add #1
2301 atoms, 2341 bonds, 144 residues, 1 model selected
> fitmap #1 inMap #4
Fit molecule Rep_F-chain.pdb (#1) to map
cryosparc_P5_cryosparc_P5_J922_004_volume_map_sharp.mrc gaussian (#4) using
2301 atoms
average map value = 0.2179, steps = 76
shifted from previous position = 2.37
rotated from previous position = 5.04 degrees
atoms outside contour = 390, contour level = 0.11147
Position of Rep_F-chain.pdb (#1) relative to
cryosparc_P5_cryosparc_P5_J922_004_volume_map_sharp.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.99014328 0.12126500 0.07007907 -15.37877976
-0.13987418 0.88179397 0.45041603 -16.99984171
-0.00717561 -0.45577866 0.89006422 70.74496544
Axis -0.95768990 0.08164474 -0.27597861
Axis point 0.00000000 134.14835181 71.82714793
Rotation angle (degrees) 28.23668115
Shift along axis -6.18394292
> 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 #1 relModel #2
> close
> open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J905_AMP-PnP-ATP_F-chain.pdb
> /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb
> /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J907_AMP-PnP-ATP_F-chain.pdb
> /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J908_AMP-PnP-ATP_F-chain.pdb
> /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J909_AMP-PnP-ATP_F-chain.pdb
> /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J921_AMP-PnP-ATP_F-chain.pdb
> /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP-
> ATP_Models_Phenix/J922_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 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
Chain information for J906_AMP-PnP-ATP_F-chain.pdb #2
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
Chain information for J907_AMP-PnP-ATP_F-chain.pdb #3
---
Chain | Description
A B C E | No description available
D | No description available
G | No description available
f | No description available
Chain information for J908_AMP-PnP-ATP_F-chain.pdb #4
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
Chain information for J909_AMP-PnP-ATP_F-chain.pdb #5
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
Chain information for J921_AMP-PnP-ATP_F-chain.pdb #6
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
Chain information for J922_AMP-PnP-ATP_F-chain.pdb #7
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> style ball
Changed 125942 atom styles
> show cartoons
> hide atoms
> select ligand
2572 atoms, 2706 bonds, 70 residues, 7 models selected
> show sel 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.
> matchmaker #2/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 J906_AMP-PnP-ATP_F-
chain.pdb, chain C (#2), sequence alignment score = 951.8
RMSD between 185 pruned atom pairs is 0.186 angstroms; (across all 185 pairs:
0.186)
> 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 #3/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 J907_AMP-PnP-ATP_F-
chain.pdb, chain C (#3), sequence alignment score = 948.2
RMSD between 185 pruned atom pairs is 0.256 angstroms; (across all 185 pairs:
0.256)
> 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 #4/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 J908_AMP-PnP-ATP_F-
chain.pdb, chain C (#4), sequence alignment score = 890.6
RMSD between 184 pruned atom pairs is 0.587 angstroms; (across all 185 pairs:
0.610)
> 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 #5/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 J909_AMP-PnP-ATP_F-
chain.pdb, chain C (#5), sequence alignment score = 864.2
RMSD between 184 pruned atom pairs is 0.600 angstroms; (across all 185 pairs:
0.625)
> 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 #5/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 J909_AMP-PnP-ATP_F-
chain.pdb, chain C (#5), sequence alignment score = 864.2
RMSD between 184 pruned atom pairs is 0.600 angstroms; (across all 185 pairs:
0.625)
> 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 #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)
> cartoon style modeHelix tube sides 20
> 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 #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)
> select #1/A#2/A#3/A#4/A#5/A#6/A#7/A
20789 atoms, 21104 bonds, 7 pseudobonds, 1309 residues, 14 models selected
> color (#!1-7 & sel) #ff85ffff
> select #1/B#2/B#3/B#4/B#5/B#6/B#7/B
20783 atoms, 21095 bonds, 6 pseudobonds, 1309 residues, 13 models selected
> color (#!1-7 & sel) #73fa79ff
> select #1/C#2/C#3/C#4/C#5/C#6/C#7/C
20780 atoms, 21095 bonds, 4 pseudobonds, 1309 residues, 11 models selected
> color (#!1-7 & sel) #7a81ffff
> color (#!1-7 & sel) #76d6ffff
> select #1/C#2/C#3/C#4/C#5/C#6/C#7/C
20780 atoms, 21095 bonds, 4 pseudobonds, 1309 residues, 11 models selected
> color (#!1-7 & sel) #7a81ffff
> select #1/D#2/D#3/D#4/D#5/D#6/D#7/D
20879 atoms, 21208 bonds, 2 pseudobonds, 1316 residues, 9 models selected
> color (#!1-7 & sel) #76d6ffff
> select #1/E#2/E#3/E#4/E#5/E#6/E#7/E
20654 atoms, 20972 bonds, 1300 residues, 7 models selected
> color sel #fffc79ff
> select #1/F#2/F#4/F#5/F#6/F#7/F
17378 atoms, 17635 bonds, 1 pseudobond, 1098 residues, 7 models selected
> color (#!1-2,4-7 & sel) #ff7e79ff
> select clear
> select ligand
2572 atoms, 2706 bonds, 70 residues, 7 models selected
> color sel byhetero
> color sel #919191ff
> color sel byhetero
> select clear
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!7 models
> hide #!6 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!1 models
> show #!7 models
> hide #!7 models
> hide #!1 models
> show #!7 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!2 models
> select nucleic-acid
1745 atoms, 1843 bonds, 54 residues, 7 models selected
> show sel & #!2 atoms
> hide sel & #!2 cartoons
> view matrix models
> #1,0.99309,-0.093215,-0.071231,22.664,0.088214,0.99361,-0.070392,-1.601,0.077338,0.063622,0.99497,-18.052,#2,0.99324,-0.094897,-0.066797,22.364,0.090523,0.99372,-0.065731,-2.3817,0.072615,0.059241,0.9956,-16.997,#3,0.99355,-0.091618,-0.066891,21.636,0.087175,0.99397,-0.066571,-2.1157,0.072587,0.06031,0.99554,-17.17,#4,0.99185,-0.097372,-0.082187,24.641,0.091886,0.99344,-0.068099,-2.4964,0.088279,0.059992,0.99429,-18.739,#5,0.99106,-0.099347,-0.089052,25.852,0.093935,0.99358,-0.06304,-3.3804,0.094743,0.054111,0.99403,-18.61,#6,0.99309,-0.093215,-0.071231,22.664,0.088214,0.99361,-0.070392,-1.601,0.077338,0.063622,0.99497,-18.052,#7,0.99212,-0.093933,-0.082878,23.44,0.08437,0.9901,-0.11219,4.7428,0.092596,0.10431,0.99022,-24.949
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete bonds sel
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete bonds sel
> show #!3 models
> hide #!2 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 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 #!1 models
> show #!7 models
> morph start #2,#3,#4,#5,#6,#1,#7
Missing or invalid "structures" argument: invalid structures specifier
> morph start #2 #3 #4 #5 #6 #1 #7
Missing or invalid "structures" argument: invalid structures specifier
> morph start #2,3,4,5,6,1,7
Missing or invalid "structures" argument: invalid structures specifier
> morph #2,3,4,5,6,1,7
models have different number of chains, 5 (Morph - J906_AMP-PnP-ATP_F-
chain.pdb #/A,Morph - J906_AMP-PnP-ATP_F-chain.pdb #/B,Morph - J906_AMP-PnP-
ATP_F-chain.pdb #/C,Morph - J906_AMP-PnP-ATP_F-chain.pdb #/D,Morph - J906_AMP-
PnP-ATP_F-chain.pdb #/E) and 7 (J908_AMP-PnP-ATP_F-chain.pdb #4/A,J908_AMP-
PnP-ATP_F-chain.pdb #4/B,J908_AMP-PnP-ATP_F-chain.pdb #4/C,J908_AMP-PnP-ATP_F-
chain.pdb #4/D,J908_AMP-PnP-ATP_F-chain.pdb #4/E,J908_AMP-PnP-ATP_F-chain.pdb
#4/F,J908_AMP-PnP-ATP_F-chain.pdb #4/G)
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!5 models
> hide #!4 models
> hide #!6 models
> hide #!7 models
> show #!2 models
> select #3/f
2896 atoms, 2940 bonds, 183 residues, 1 model selected
> hide #!2 models
> show #!3 models
> close #3
> 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 #3
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> show #!1 models
> show #!2 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> select #1/A#2/A#3/A#4/A#5/A#6/A#7/A
20789 atoms, 21104 bonds, 7 pseudobonds, 1309 residues, 14 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color (#!1-7 & sel) #ff85ffff
> select #1/B#2/B#3/B#4/B#5/B#6/B#7/B
20783 atoms, 21095 bonds, 6 pseudobonds, 1309 residues, 13 models selected
> color (#!1-7 & sel) #73fa79ff
> select #1/C#2/C#3/C#4/C#5/C#6/C#7/C
20780 atoms, 21095 bonds, 4 pseudobonds, 1309 residues, 11 models selected
> color (#!1-7 & sel) #7a81ffff
> select #1/D#2/D#3/D#4/D#5/D#6/D#7/D
20879 atoms, 21208 bonds, 2 pseudobonds, 1316 residues, 9 models selected
> color (#!1-7 & sel) #76d6ffff
> select #1/E#2/E#3/E#4/E#5/E#6/E#7/E
20654 atoms, 20972 bonds, 1300 residues, 7 models selected
> color sel #fffc79ff
> select #1/F#2/F#3/F#4/F#5/F#6/F#7/F
20274 atoms, 20575 bonds, 1 pseudobond, 1281 residues, 8 models selected
> color (#!1-7 & sel) #ff7e79ff
> style sel ball
Changed 20274 atom styles
> select clear
> style ball
Changed 125942 atom styles
> show cartoons
> hide atoms
> select nucleic-acid
1745 atoms, 1841 bonds, 2 pseudobonds, 54 residues, 8 models selected
> show sel atoms
> select clear
> select ligand
2572 atoms, 2706 bonds, 70 residues, 7 models selected
> show sel atoms
> color sel dim gray
> color sel byhetero
> select clear
> ui tool show Matchmaker
> matchmaker #3/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 J907_AMP-PnP-ATP_F-
chain.pdb, chain C (#3), sequence alignment score = 948.2
RMSD between 185 pruned atom pairs is 0.256 angstroms; (across all 185 pairs:
0.256)
> morph #2,3,4,5,6,1,7
Computed 301 frame morph #8
> coordset #8 1,301
> close #8
> morph #2,3,4,5,7,1,6
Computed 301 frame morph #8
> coordset #8 1,301
> select ligand
2572 atoms, 2706 bonds, 70 residues, 7 models selected
> show #!8 atoms
> hide #!8 atoms
> hide #!8 models
> show #!6 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!2 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!1 models
> hide #!1 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!1 models
> show #!3 models
> show #!2 models
> morph #2,4,3,5,6,7,1
Computed 301 frame morph #9
> coordset #9 1,301
> hide #!9 models
> show #!8 models
> show #!7 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> show #!8 models
> hide #!7 models
> cartoon style #8 modeHelix tube sides 20
> select #1/A#2/A#3/A#4/A#5/A#6/A#7/A#8/A#9/A
26631 atoms, 27034 bonds, 7 pseudobonds, 1679 residues, 16 models selected
> cartoon style (#!8 & sel) modeHelix tube sides 20
> hide #!8 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> select clear
> select #7/A
2970 atoms, 3015 bonds, 1 pseudobond, 187 residues, 2 models selected
> cartoon style #8 modeHelix tube sides 20
> select #7/A
2970 atoms, 3015 bonds, 1 pseudobond, 187 residues, 2 models selected
> hide #!8 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> show #!9 models
> hide #!9 models
> close #8
> show #!9 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> morph #2,4,3,5,6,7,1 frames 40
Computed 241 frame morph #8
> coordset #8 1,241
> hide #!8 models
> close #8
> close #9
> morph #2,4,3,5,6,7,1 frames 40
Computed 241 frame morph #8
> coordset #8 1,241
> select ligand
2572 atoms, 2706 bonds, 70 residues, 7 models selected
> show #!8 atoms
> hide #!8 atoms
> select nucleic-acid
1938 atoms, 2042 bonds, 2 pseudobonds, 60 residues, 9 models selected
> show sel & #!8 atoms
> hide #!8 models
> show #!1 models
> hide #!1 models
> show #!2 models
> select clear
> show #!1 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> select nucleic-acid
1938 atoms, 2042 bonds, 2 pseudobonds, 60 residues, 9 models selected
> color (#!1-7 & sel) dim gray
> color sel & #!1-7 byhetero
> select clear
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!2 models
Drag select of 123 atoms, 40 residues, 2 pseudobonds, 129 bonds
> select clear
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> select #2/A
2970 atoms, 3015 bonds, 1 pseudobond, 187 residues, 2 models selected
> cartoon style (#!2 & sel) modeHelix tube sides 20
> hide #!2 models
> cartoon style #3 modeHelix tube sides 20
> hide #!3 models
> show #!2 models
> select clear
> cartoon style #2 modeHelix tube sides 20
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> morph #3,2,4,5,6,7,1 frames 40
Computed 241 frame morph #9
> coordset #9 1,241
> morph #3,2,4,5,6,7,1 frames 30
Computed 181 frame morph #10
> coordset #10 1,181
> hide #!9 models
> hide #!10 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!2 models
> close #2
> show #!8 models
> hide #!8 models
> morph #1,7,6,5,4,2,3 frames 40
Computed 201 frame morph #2
> coordset #2 1,201
> morph #1,7,6,5,4,2,3 frames 15
Computed 91 frame morph #11
> coordset #11 1,91
> morph #1,7,6,5, frames 15
Missing or invalid "structures" argument: only initial part "#1,7,6,5" of atom
specifier valid
> morph #1,7,6,5 frames 15
Computed 46 frame morph #12
> coordset #12 1,46
> hide #!11 models
> hide #!12 models
> show #!4 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> show #!1 models
> hide #!1 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 #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> close #10-11
> hide #!4 models
> show #!12 models
> select #1/E#3/E#4/E#5/E#6/E#7/E#8/E#9/E#12/E
26463 atoms, 26867 bonds, 1669 residues, 9 models selected
> select subtract #12/E:185
26453 atoms, 26856 bonds, 1668 residues, 9 models selected
> hide sel atoms
> select clear
> morph #15,6,7,1 frames 5
Computed 11 frame morph #2
> coordset #2 1,11
> hide #!2 models
> show #!2 models
> hide #!12 models
> close #2
> close #12
> morph #5,6,7,1 frames 10
Computed 31 frame morph #2
> coordset #2 1,31
> 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 #10
---
Chain | Description
A B C E | No description available
D | No description available
F | No description available
G | No description available
> hide #!2 models
> style #!10 ball
Changed 18314 atom styles
> select #10/A
2970 atoms, 3015 bonds, 1 pseudobond, 187 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!10 & sel) #ff85ffff
> select #10/B
2967 atoms, 3009 bonds, 1 pseudobond, 187 residues, 2 models selected
> color (#!10 & sel) #73fa79ff
> select #10/C
2967 atoms, 3012 bonds, 187 residues, 1 model selected
> color sel #7a81ffff
> select #10/D
2978 atoms, 3025 bonds, 1 pseudobond, 188 residues, 2 models selected
> color (#!10 & sel) #76d6ffff
> select #10/E
2956 atoms, 3002 bonds, 186 residues, 1 model selected
> color sel #fffc79ff
> select #10/F
2894 atoms, 2936 bonds, 1 pseudobond, 183 residues, 2 models selected
> color (#!10 & sel) #ff7e79ff
> select clear
> delete bonds sel
> select ligand
2958 atoms, 3108 bonds, 82 residues, 9 models selected
> color (#!10 & sel) #929292ff
> color sel & #!10 byhetero
> select nucleic-acid
2324 atoms, 2444 bonds, 2 pseudobonds, 72 residues, 11 models selected
> color (#!10 & sel) #a9a9a9ff
> color (#!10 & sel) #929292ff
> color sel & #!10 byhetero
> select clear
> close #9
> close #8
> close #2
> show #!7 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!1 models
> show surfaces
> hide #!10 models
> hide #!1 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> show #!1 models
> show #!10 models
> ui tool show Matchmaker
> matchmaker #10/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 J906_AMP-PnP-ATP_F-
chain.pdb, chain C (#10), sequence alignment score = 951.8
RMSD between 185 pruned atom pairs is 0.186 angstroms; (across all 185 pairs:
0.186)
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!10 models
> hide #!10 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!10 models
> morph #7,6,5,4,3,2,1,10 frames 20
Computed 121 frame morph #2
> coordset #2 1,121
> select protein
140239 atoms, 142351 bonds, 2 pseudobonds, 8872 residues, 10 models selected
> show sel & #!2 surfaces
> select clear
> show #!1 models
> hide #!1 models
> close #2
> show #!4 models
> show #!3 models
> show #!5 models
> hide #!4 models
> hide #!3 models
> show #!6 models
> show #!7 models
> show #!10 models
> hide #!10 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!1 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!10 models
> hide #!10 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!7 models
> show #!10 models
> hide #!7 models
> hide #!10 models
> show #!3 models
> hide #!3 models
> show #!10 models
> hide #!10 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!5 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!6 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!5 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> select ligand
2572 atoms, 2706 bonds, 70 residues, 7 models selected
> show sel & #!7 atoms
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> show #!10 models
> hide #!10 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!6 models
> hide #!5 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!1 models
> show #!10 models
> hide #!10 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!1 models
> show #!6 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!5 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!10 models
> hide #!10 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> show #!10 models
> morph #7,6,5,4,1,3,10 frames 20
Computed 121 frame morph #2
> coordset #2 1,121
> hide #!2 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> show #!10 models
> hide surfaces
> show cartoons
> hide atoms
> select ligand
2765 atoms, 2907 bonds, 76 residues, 8 models selected
> show sel atoms
> select clear
> hide #!10 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> show #!10 models
> hide #!10 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!10 models
> hide #!7 models
> cartoon style #10 modeHelix tube sides 20
> show #!7 models
> hide #!10 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> morph #7,5,4,3,2 frames 20
Computed 81 frame morph #8
> coordset #8 1,81
> show #!8 surfaces
> close #8
> close #2
> morph #7,5,4,3,2 frames 20
Computed 61 frame morph #2
> coordset #2 1,61
> movie record
> movie encode /Users/nicholasferraro/Desktop/movie6.mp4 framerate 25.0
Movie saved to /Users/nicholasferraro/Desktop/movie6.mp4
> morph #7,5,4,3,2 frames 10
Computed 41 frame morph #8
> coordset #8 1,41
> morph #2,3,4,5,7 frames 10
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/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
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/morph/morph.py", line 84, in morph
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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/morph/motion.py", line 28, in compute_morph
motion.interpolate(res_groups, atom_map, res_interp)
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/morph/motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
~~~~~~~^^^^^^^^^^^
IndexError: index 17696 is out of bounds for axis 0 with size 17696
Window position QRect(2198,402 600x300) outside any known screen, using
primary screen
IndexError: index 17696 is out of bounds for axis 0 with size 17696
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/morph/motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
> morph #2,3,4,5,7 frames 10
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/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
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/morph/morph.py", line 84, in morph
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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/morph/motion.py", line 28, in compute_morph
motion.interpolate(res_groups, atom_map, res_interp)
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/morph/motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
~~~~~~~^^^^^^^^^^^
IndexError: index 17696 is out of bounds for axis 0 with size 17696
IndexError: index 17696 is out of bounds for axis 0 with size 17696
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/morph/motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
> morph #2,3,4,5, frames 10
Missing or invalid "structures" argument: only initial part "#2,3,4,5" of atom
specifier valid
> morph #2,3,4,5, frames 10
Missing or invalid "structures" argument: only initial part "#2,3,4,5" of atom
specifier valid
> morph #2,3,4,5,7 frames 10
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/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
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/morph/morph.py", line 84, in morph
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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/morph/motion.py", line 28, in compute_morph
motion.interpolate(res_groups, atom_map, res_interp)
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/morph/motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
~~~~~~~^^^^^^^^^^^
IndexError: index 17696 is out of bounds for axis 0 with size 17696
IndexError: index 17696 is out of bounds for axis 0 with size 17696
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/morph/motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
> hide #!8 models
> morph #2,3,4,5,7 frames 20
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/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
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/morph/morph.py", line 84, in morph
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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/morph/motion.py", line 28, in compute_morph
motion.interpolate(res_groups, atom_map, res_interp)
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/morph/motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
~~~~~~~^^^^^^^^^^^
IndexError: index 17696 is out of bounds for axis 0 with size 17696
IndexError: index 17696 is out of bounds for axis 0 with size 17696
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/morph/motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
> morph #2,3 frames 20
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/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
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/morph/morph.py", line 84, in morph
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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/morph/motion.py", line 28, in compute_morph
motion.interpolate(res_groups, atom_map, res_interp)
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/morph/motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
~~~~~~~^^^^^^^^^^^
IndexError: index 17696 is out of bounds for axis 0 with size 17696
IndexError: index 17696 is out of bounds for axis 0 with size 17696
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/morph/motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
> close #2
> close #8
> show #!1 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!10 models
> morph #2,3,4,5,7 frames 20
Computed 61 frame morph #2
> coordset #2 1,61
> hide #!1 models
> hide #!6 models
> hide #!10 models
> morph #7,6,5,4,3,2 frames 20
Computed 101 frame morph #8
> coordset #8 1,101
> morph #7,,5,4,3,2 frames 20
Missing or invalid "structures" argument: only initial part "#7" of atom
specifier valid
> morph #7,5,4,3,2 frames 20
Computed 81 frame morph #9
> coordset #9 1,81
> hide #!8 models
> morph #,5,4,3,2 frames 20
Missing or invalid "structures" argument: invalid structures specifier
> morph #5,4,3,2 frames 20
Computed 61 frame morph #11
> coordset #11 1,61
> hide #!9 models
> hide #!11 models
> show #!5 models
Drag select of 9 atoms, 2 residues, 7 bonds
> select clear
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
Drag select of 17 residues
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> close #2
> close #11
> close #9
> close #8
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> hide #!7 models
> show #!4 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> show #!6 models
> show #!7 models
> hide #!7 models
> hide #!5 models
> hide #!1 models
> show #!7 models
> show #!5 models
> show #!1 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!7 models
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #!6 models
> hide #!7 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> show #!10 models
> hide #!10 models
> show #!4 models
> show #!3 models
> show #!10 models
> morph #6,7,1,5,4,3,10 frames 20
Computed 121 frame morph #2
> coordset #2 1,121
> select clear
Drag select of 5 residues
> select clear
> morph #6,7,1,5,4,3,10 frames 10
Computed 61 frame morph #8
> coordset #8 1,61
> hide #!2 models
> movie record
> movie encode /Users/nicholasferraro/Desktop/movie7.mp4 framerate 25.0
Movie saved to /Users/nicholasferraro/Desktop/movie7.mp4
> hide #!8 models
> show #!6 models
> show #!8 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> hide #!8 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!6 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
> morph #1,7,6,5,4,3,10 frames 10
Computed 61 frame morph #2
> coordset #2 1,61
> hide #!2 models
> show #!1 models
> show #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> ui tool show Matchmaker
> matchmaker #6/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 J921_AMP-PnP-ATP_F-
chain.pdb, chain C (#6), sequence alignment score = 876.2
RMSD between 183 pruned atom pairs is 0.699 angstroms; (across all 185 pairs:
0.759)
> hide #!6 models
> hide #!1 models
> show #!6 models
> show #!1 models
> hide #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> ui tool show Matchmaker
> matchmaker #5/G to #1/C pairing ss
Match chain (J909_AMP-PnP-ATP_F-chain.pdb (#5) chain G) not compatible with
BLOSUM-62 similarity matrix
> ui tool show Matchmaker
> matchmaker #5/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 J909_AMP-PnP-ATP_F-
chain.pdb, chain C (#5), sequence alignment score = 864.2
RMSD between 184 pruned atom pairs is 0.600 angstroms; (across all 185 pairs:
0.625)
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!10 models
> morph #1,7,6,5,4,3,10 frames 10
Computed 61 frame morph #9
> coordset #9 1,61
> select clear
> ui tool show "Side View"
> hide #!9 models
> show #!1 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!6 models
> hide #!1 models
> hide #!6 models
> show #!6 models
> show #!1 models
> show #!5 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!7 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!7 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> hide #!7 models
> hide #!5 models
> show #!5 models
> show #!7 models
> show #!6 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> show #!2 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!1 models
> hide #!10 models
> show #!10 models
> hide #!2 models
> hide #!10 models
> show #!10 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> show #!9 models
> close #8
> hide #!9 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!3 models
> hide #!10 models
> show #!3 models
> show #!10 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!10 models
> show #!1 models
> show #!10 models
> hide #!1 models
> hide #!10 models
> show #!1 models
> show #!10 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!10 models
> show #!10 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!10 models
> show #!10 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> select nucleic-acid
1938 atoms, 2042 bonds, 2 pseudobonds, 60 residues, 9 models selected
> show sel & #!10 atoms
> select clear
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!7 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!10 models
> show #!10 models
> show #!7 models
> hide #!10 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!7 models
> show #!7 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!5 models
> hide #!7 models
> show #!4 models
> show #!10 models
> show #!7 models
> hide #!7 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 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
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!10 models
> show #!4 models
> show #!10 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> hide #!10 models
> show #!1 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!6 models
> morph #1,7,6,5,3,4,10 frames 10
Computed 61 frame morph #2
> coordset #2 1,61
> show #!1 models
> hide #!2 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!1 models
> show #!7 models
> show #!1 models
> show #!5 models
> hide #!5 models
> show #!3 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!10 models
> show #!5 models
> show #!4 models
> hide #!4 models
> hide #!10 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!3 models
> hide #!1 models
> show #!5 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!10 models
> show #!5 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> hide #!10 models
> show #!7 models
> show #!6 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> hide #!7 models
> show #!1 models
> show #!7 models
> show #!6 models
> show #!3 models
> show #!10 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> morph #1,7,6,3,10,5,4 frames 10
Computed 61 frame morph #8
> coordset #8 1,61
> 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
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