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Opened 10 months ago
Closed 10 months ago
#16539 closed defect (duplicate)
Crash in python_instances_of_class
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001dd3b5ec0 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 2636 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in include_state
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 260 in discovery
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 641 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 917 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 60)
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"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":5618},
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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper_45.pdb" format pdb
Chain information for Stopper_45.pdb #1
---
Chain | Description
A | No description available
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/P2_J357_007_volume_map_sharp_C6.mrc"
Opened P2_J357_007_volume_map_sharp_C6.mrc as #2, grid size 512,512,512, pixel
1.06, shown at level 0.215, step 2, values float32
> surface dust #2 size 10.6
> volume #2 step 1
> volume #2 level 0.3
> lighting soft
> view #2 clip false
> hide #1 models
> show #1 models
> show #1 target m
Already setting window visible!
> close #1
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper_45.pdb"
Chain information for Stopper_45.pdb #1
---
Chain | Description
A | No description available
> select add #1
916 atoms, 939 bonds, 119 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,12.37,0,1,0,-0.50522,0,0,1,4.664
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule Stopper_45.pdb (#1) to map P2_J357_007_volume_map_sharp_C6.mrc
(#2) using 916 atoms
average map value = 0.1604, steps = 84
shifted from previous position = 3.98
rotated from previous position = 7.94 degrees
atoms outside contour = 710, contour level = 0.3
Position of Stopper_45.pdb (#1) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.99084811 0.05571136 -0.12294823 24.96437977
-0.05206154 0.99810823 0.03270395 8.35677390
0.12453762 -0.02600378 0.99187408 -18.01115549
Axis -0.21252117 -0.89589528 -0.39013638
Axis point 174.43664815 0.00000000 180.09755970
Rotation angle (degrees) 7.93919379
Shift along axis -5.76544638
> view matrix models
> #1,0.86015,-0.49606,-0.11858,186.79,0.50422,0.86205,0.051253,-94.267,0.076802,-0.10388,0.99162,11.922
> view matrix models
> #1,0.61916,-0.76706,-0.1681,316.86,0.77981,0.62579,0.016728,-97.524,0.092362,-0.14144,0.98563,18.19
> view matrix models
> #1,0.61916,-0.76706,-0.1681,320.28,0.77981,0.62579,0.016728,-91.012,0.092362,-0.14144,0.98563,19.922
> fitmap #1 inMap #2
Fit molecule Stopper_45.pdb (#1) to map P2_J357_007_volume_map_sharp_C6.mrc
(#2) using 916 atoms
average map value = 0.2632, steps = 100
shifted from previous position = 4.84
rotated from previous position = 6.87 degrees
atoms outside contour = 613, contour level = 0.3
Position of Stopper_45.pdb (#1) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.68001259 -0.70245554 -0.21009306 300.76128972
0.72969533 0.67636836 0.10035223 -102.26251465
0.07160732 -0.22154470 0.97251753 47.75567532
Axis -0.21536367 -0.18847035 0.95817400
Axis point 274.54063030 303.17569342 0.00000000
Rotation angle (degrees) 48.35991392
Shift along axis 0.25864206
> fitmap #1 inMap #2
Fit molecule Stopper_45.pdb (#1) to map P2_J357_007_volume_map_sharp_C6.mrc
(#2) using 916 atoms
average map value = 0.2632, steps = 44
shifted from previous position = 0.00397
rotated from previous position = 0.00554 degrees
atoms outside contour = 614, contour level = 0.3
Position of Stopper_45.pdb (#1) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.68002789 -0.70243309 -0.21011860 300.75801964
0.72967275 0.67640485 0.10027041 -102.25141140
0.07169199 -0.22150449 0.97252045 47.72213025
Axis -0.21528903 -0.18855022 0.95817506
Axis point 274.52674714 303.19212907 0.00000000
Rotation angle (degrees) 48.35781651
Shift along axis 0.25577823
> select subtract #1
Nothing selected
> hide #!2 models
> show #!2 models
> select add #1
916 atoms, 939 bonds, 119 residues, 1 model selected
> view matrix models
> #1,0.59836,0.31349,-0.73735,166.26,0.00035208,0.92018,0.39151,-36.173,0.80123,-0.23452,0.55048,-51.508
> view matrix models
> #1,0.59836,0.31349,-0.73735,164.95,0.00035208,0.92018,0.39151,-33.749,0.80123,-0.23452,0.55048,-44.835
> view matrix models
> #1,0.59836,0.31349,-0.73735,153.98,0.00035208,0.92018,0.39151,-37.219,0.80123,-0.23452,0.55048,-42.571
> view matrix models
> #1,0.59836,0.31349,-0.73735,150.31,0.00035208,0.92018,0.39151,-38.343,0.80123,-0.23452,0.55048,-42.011
> view matrix models
> #1,0.59836,0.31349,-0.73735,150.09,0.00035208,0.92018,0.39151,-38.034,0.80123,-0.23452,0.55048,-44.732
> view matrix models
> #1,0.81005,0.30711,-0.4995,61.543,0.10245,0.76464,0.63626,-66.182,0.57734,-0.56658,0.58793,81.272
> view matrix models
> #1,0.82768,0.2717,-0.49104,64.383,0.14929,0.73685,0.65936,-74.539,0.54097,-0.61905,0.56932,105.53
> view matrix models
> #1,0.91195,0.13703,-0.38675,59.029,0.11339,0.82171,0.55852,-69.355,0.39433,-0.55319,0.73381,97.047
> view matrix models
> #1,0.94739,0.065943,-0.31322,55.251,0.10312,0.8635,0.4937,-66.022,0.30302,-0.50002,0.81127,93.05
> view matrix models
> #1,0.94739,0.065943,-0.31322,59.043,0.10312,0.8635,0.4937,-68.553,0.30302,-0.50002,0.81127,92.064
> view matrix models
> #1,0.9705,0.007756,-0.24099,55.33,0.10038,0.89575,0.43308,-65.435,0.21922,-0.4445,0.86854,89.106
> view matrix models
> #1,0.97731,-0.013454,-0.21137,53.807,0.10093,0.90697,0.40893,-64.192,0.1862,-0.42098,0.88775,88.114
> view matrix models
> #1,0.97731,-0.013454,-0.21137,53.275,0.10093,0.90697,0.40893,-64.028,0.1862,-0.42098,0.88775,89.418
> fitmap #1 inMap #2
Fit molecule Stopper_45.pdb (#1) to map P2_J357_007_volume_map_sharp_C6.mrc
(#2) using 916 atoms
average map value = 0.2195, steps = 100
shifted from previous position = 5.62
rotated from previous position = 6.68 degrees
atoms outside contour = 654, contour level = 0.3
Position of Stopper_45.pdb (#1) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.99173980 -0.06730157 -0.10919095 50.66832603
0.10677468 0.90488055 0.41205627 -63.32343309
0.07107273 -0.42031143 0.90459216 115.33724062
Axis -0.95754592 -0.20737320 0.20025525
Axis point 0.00000000 231.82885352 213.37675852
Rotation angle (degrees) 25.76212884
Shift along axis -12.28877800
> fitmap #1 inMap #2
Fit molecule Stopper_45.pdb (#1) to map P2_J357_007_volume_map_sharp_C6.mrc
(#2) using 916 atoms
average map value = 0.2195, steps = 36
shifted from previous position = 0.00566
rotated from previous position = 0.0249 degrees
atoms outside contour = 655, contour level = 0.3
Position of Stopper_45.pdb (#1) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.99178883 -0.06695104 -0.10896086 50.53647826
0.10635363 0.90495148 0.41200937 -63.23014291
0.07101984 -0.42021468 0.90464126 115.32047946
Axis -0.95776676 -0.20713116 0.19944804
Axis point 0.00000000 231.90217111 213.15244471
Rotation angle (degrees) 25.75098283
Shift along axis -12.30478179
> view matrix models
> #1,0.99179,-0.066951,-0.10896,47.989,0.10635,0.90495,0.41201,-63.969,0.07102,-0.42021,0.90464,115.47
> fitmap #1 inMap #2
Fit molecule Stopper_45.pdb (#1) to map P2_J357_007_volume_map_sharp_C6.mrc
(#2) using 916 atoms
average map value = 0.2195, steps = 56
shifted from previous position = 2.65
rotated from previous position = 0.011 degrees
atoms outside contour = 655, contour level = 0.3
Position of Stopper_45.pdb (#1) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.99181248 -0.06681361 -0.10882992 50.46332547
0.10617601 0.90495334 0.41205109 -63.18443964
0.07095538 -0.42023254 0.90463802 115.34359610
Axis -0.95788622 -0.20691728 0.19909604
Axis point 0.00000000 231.96216139 213.02380578
Rotation angle (degrees) 25.74951481
Shift along axis -12.29971864
> fitmap #1 inMap #2
Fit molecule Stopper_45.pdb (#1) to map P2_J357_007_volume_map_sharp_C6.mrc
(#2) using 916 atoms
average map value = 0.2195, steps = 44
shifted from previous position = 0.0255
rotated from previous position = 0.0416 degrees
atoms outside contour = 654, contour level = 0.3
Position of Stopper_45.pdb (#1) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.99172487 -0.06737425 -0.10928170 50.71038307
0.10687133 0.90491629 0.41195269 -63.34007507
0.07113579 -0.42022281 0.90462837 115.29289180
Axis -0.95745500 -0.20757836 0.20047730
Axis point 0.00000000 231.78226618 213.44731061
Rotation angle (degrees) 25.75836949
Shift along axis -12.29127252
> view matrix models
> #1,0.99172,-0.067374,-0.10928,26.81,0.10687,0.90492,0.41195,-50.463,0.071136,-0.42022,0.90463,115.59
> view matrix models
> #1,0.61702,0.73875,0.27116,-140.26,0.78678,-0.57208,-0.23174,248.27,-0.016072,0.35633,-0.93422,259.25
> view matrix models
> #1,0.61702,0.73875,0.27116,-134.45,0.78678,-0.57208,-0.23174,237.99,-0.016072,0.35633,-0.93422,249.77
> view matrix models
> #1,0.61702,0.73875,0.27116,-122.23,0.78678,-0.57208,-0.23174,239.5,-0.016072,0.35633,-0.93422,246.74
> view matrix models
> #1,0.61702,0.73875,0.27116,-119.33,0.78678,-0.57208,-0.23174,239.74,-0.016072,0.35633,-0.93422,246.37
> fitmap #1 inMap #2
Fit molecule Stopper_45.pdb (#1) to map P2_J357_007_volume_map_sharp_C6.mrc
(#2) using 916 atoms
average map value = 0.2013, steps = 92
shifted from previous position = 1.41
rotated from previous position = 6.25 degrees
atoms outside contour = 674, contour level = 0.3
Position of Stopper_45.pdb (#1) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.53916141 0.80374033 0.25160770 -112.20216437
0.83927865 -0.48788049 -0.23996658 208.33704402
-0.07011633 0.34054970 -0.93760844 263.16730990
Axis 0.87340775 0.48404545 0.05346869
Axis point 0.00000000 109.58273426 154.61385744
Rotation angle (degrees) 160.58984337
Shift along axis 16.91757039
> fitmap #1 inMap #2
Fit molecule Stopper_45.pdb (#1) to map P2_J357_007_volume_map_sharp_C6.mrc
(#2) using 916 atoms
average map value = 0.2013, steps = 44
shifted from previous position = 0.017
rotated from previous position = 0.0314 degrees
atoms outside contour = 673, contour level = 0.3
Position of Stopper_45.pdb (#1) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.53905903 0.80378013 0.25169992 -112.19951612
0.83938435 -0.48795824 -0.23943818 208.23440020
-0.06963660 0.34034429 -0.93771877 263.10910264
Axis 0.87338774 0.48406323 0.05363441
Axis point 0.00000000 109.57169246 154.56003857
Rotation angle (degrees) 160.61489864
Shift along axis 16.91663808
> select subtract #1
Nothing selected
> hide #1 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Connector/Corndog_45_stopper_6mer/fold_corndog_45_stopper_6mer_model_0.cif"
Chain information for fold_corndog_45_stopper_6mer_model_0.cif #3
---
Chain | Description
A B C D E F | .
> hide #3 atoms
> show #3 cartoons
> select add #3
5496 atoms, 5634 bonds, 714 residues, 1 model selected
> view matrix models #3,1,0,0,243.51,0,1,0,217.53,0,0,1,167.81
> view matrix models #3,1,0,0,255.81,0,1,0,216.03,0,0,1,176.23
> color #3 #adf258ff
> view matrix models
> #3,0.92192,-0.32855,0.20523,257.21,0.36954,0.90481,-0.21157,215.89,-0.11618,0.27089,0.95557,175.33
> view matrix models
> #3,0.88504,-0.39398,-0.24796,257.11,0.36229,0.91742,-0.16458,215.89,0.29232,0.055824,0.95469,175.75
> view matrix models
> #3,0.85929,-0.40022,-0.3185,257.1,0.30229,0.89968,-0.31497,215.88,0.4126,0.17437,0.89407,175.18
> view matrix models
> #3,0.85929,-0.40022,-0.3185,275.55,0.30229,0.89968,-0.31497,255.7,0.4126,0.17437,0.89407,177.77
> fitmap #1 inMap #2
Fit molecule Stopper_45.pdb (#1) to map P2_J357_007_volume_map_sharp_C6.mrc
(#2) using 916 atoms
average map value = 0.2013, steps = 44
shifted from previous position = 0.00806
rotated from previous position = 0.0079 degrees
atoms outside contour = 672, contour level = 0.3
Position of Stopper_45.pdb (#1) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.53902215 0.80381958 0.25165290 -112.19092058
0.83939712 -0.48788682 -0.23953894 208.23820120
-0.06976795 0.34035352 -0.93770565 263.13854683
Axis 0.87337521 0.48409150 0.05358329
Axis point 0.00000000 109.56461922 154.57587388
Rotation angle (degrees) 160.61078490
Shift along axis 16.92140327
> fitmap #1 inMap #2
Fit molecule Stopper_45.pdb (#1) to map P2_J357_007_volume_map_sharp_C6.mrc
(#2) using 916 atoms
average map value = 0.2013, steps = 64
shifted from previous position = 0.0123
rotated from previous position = 0.0301 degrees
atoms outside contour = 673, contour level = 0.3
Position of Stopper_45.pdb (#1) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.53882117 0.80384434 0.25200397 -112.20686646
0.83956303 -0.48778740 -0.23915967 208.10214902
-0.06932279 0.34043752 -0.93770818 263.00762756
Axis 0.87331963 0.48416551 0.05381984
Axis point 0.00000000 109.53140342 154.50503847
Rotation angle (degrees) 160.61976952
Shift along axis 16.91845274
> color sel bychain
> view matrix models
> #3,0.85929,-0.40022,-0.3185,279.66,0.30229,0.89968,-0.31497,265.36,0.4126,0.17437,0.89407,182.47
> view matrix models
> #3,0.85929,-0.40022,-0.3185,278.75,0.30229,0.89968,-0.31497,265.75,0.4126,0.17437,0.89407,181.81
> close #3
> show #1 models
> select add #1
916 atoms, 939 bonds, 119 residues, 1 model selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper_45_1.pdb" selectedOnly true relModel #2
> select subtract #1
Nothing selected
> hide #1 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper_45_1.pdb"
Chain information for Stopper_45_1.pdb #3
---
Chain | Description
A | No description available
> hide #3 models
> close #1
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper_45_1-coot-0.pdb"
Chain information for Stopper_45_1-coot-0.pdb #1
---
Chain | Description
A | No description available
> fitmap #1 inMap #2
Fit molecule Stopper_45_1-coot-0.pdb (#1) to map
P2_J357_007_volume_map_sharp_C6.mrc (#2) using 916 atoms
average map value = 0.4741, steps = 48
shifted from previous position = 0.0845
rotated from previous position = 0.469 degrees
atoms outside contour = 496, contour level = 0.3
Position of Stopper_45_1-coot-0.pdb (#1) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.99997980 -0.00489309 0.00405761 0.55289249
0.00487211 0.99997479 0.00516451 -2.07076965
-0.00408278 -0.00514464 0.99997843 2.34898436
Axis -0.62984496 0.49734239 0.59661199
Axis point 0.00000000 452.18524104 405.41317006
Rotation angle (degrees) 0.46890721
Shift along axis 0.02331417
> fitmap #1 inMap #2
Fit molecule Stopper_45_1-coot-0.pdb (#1) to map
P2_J357_007_volume_map_sharp_C6.mrc (#2) using 916 atoms
average map value = 0.4745, steps = 40
shifted from previous position = 0.0274
rotated from previous position = 0.0451 degrees
atoms outside contour = 496, contour level = 0.3
Position of Stopper_45_1-coot-0.pdb (#1) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.99998237 -0.00432290 0.00406990 0.40092343
0.00430408 0.99998006 0.00462089 -1.85983556
-0.00408979 -0.00460329 0.99998104 2.21761572
Axis -0.61345992 0.54266579 0.57374278
Axis point 0.00000000 477.93747870 406.55740682
Rotation angle (degrees) 0.43076283
Shift along axis 0.01712142
> select add #1
916 atoms, 939 bonds, 119 residues, 1 model selected
> view matrix models
> #1,0.99998,-0.0043229,0.0040699,-0.5628,0.0043041,0.99998,0.0046209,-1.3282,-0.0040898,-0.0046033,0.99998,3.2489
> transparency 50
> select subtract #1
Nothing selected
> hide #1 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/00-Portal-12mers-Adaptor-12mers.pdb"
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb #4
---
Chain | Description
A B C D E F G H I J K L | No description available
M N O P Q R S T U V W X | No description available
> select add #4
49956 atoms, 51084 bonds, 6396 residues, 1 model selected
> view matrix models #4,1,0,0,-13.65,0,1,0,3.2413,0,0,1,-111.25
> view matrix models #4,1,0,0,-12.663,0,1,0,3.6063,0,0,1,-161.52
> view matrix models #4,1,0,0,-2.1021,0,1,0,2.1821,0,0,1,-180.89
> fitmap #4 inMap #2
Fit molecule 00-Portal-12mers-Adaptor-12mers.pdb (#4) to map
P2_J357_007_volume_map_sharp_C6.mrc (#2) using 49956 atoms
average map value = 0.1491, steps = 2000
shifted from previous position = 4.65
rotated from previous position = 2.68 degrees
atoms outside contour = 46825, contour level = 0.3
Position of 00-Portal-12mers-Adaptor-12mers.pdb (#4) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.99902250 0.03984835 -0.01913526 -4.41006051
-0.03955550 0.99909798 0.01544656 5.67521589
0.01973352 -0.01467456 0.99969758 -181.59115510
Axis -0.32250564 -0.41616639 -0.85017389
Axis point 1782.67463599 -1087.47499142 0.00000000
Rotation angle (degrees) 2.67660581
Shift along axis 153.44449416
> fitmap #4 inMap #2
Fit molecule 00-Portal-12mers-Adaptor-12mers.pdb (#4) to map
P2_J357_007_volume_map_sharp_C6.mrc (#2) using 49956 atoms
average map value = 0.1506, steps = 2000
shifted from previous position = 1.63
rotated from previous position = 1.76 degrees
atoms outside contour = 46733, contour level = 0.3
Position of 00-Portal-12mers-Adaptor-12mers.pdb (#4) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.99906150 0.04242057 0.00875332 -13.88227770
-0.04244644 0.99909485 0.00279037 10.89327941
-0.00862703 -0.00315930 0.99995780 -176.96509860
Axis -0.06851890 0.20015954 -0.97736448
Axis point -574.37745338 30.11890143 0.00000000
Rotation angle (degrees) 2.48835020
Shift along axis 176.09099301
> select subtract #4
Nothing selected
> hide #4 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/P2_J332_011_C12_volume_map_sharp.mrc"
Opened P2_J332_011_C12_volume_map_sharp.mrc as #5, grid size 512,512,512,
pixel 1.06, shown at level 0.285, step 2, values float32
> volume #5 step 1
> surface dust #2 size 10.6
> surface dust #5 size 10.6
> volume #5 level 0.3729
> select add #5
2 models selected
> view matrix models #5,1,0,0,5.2745,0,1,0,-25.536,0,0,1,-189.85
> view matrix models #5,1,0,0,2.1847,0,1,0,-1.2644,0,0,1,-190.61
> view matrix models #5,1,0,0,2.0166,0,1,0,0.13243,0,0,1,-189.72
> fitmap #5 inMap #2
Fit map P2_J332_011_C12_volume_map_sharp.mrc in map
P2_J357_007_volume_map_sharp_C6.mrc using 417458 points
correlation = 0.4743, correlation about mean = 0.1284, overlap = 3.641e+04
steps = 224, shift = 6.16, angle = 2.6 degrees
Position of P2_J332_011_C12_volume_map_sharp.mrc (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.99896818 0.04541547 0.00002290 -12.06778064
-0.04541547 0.99896819 -0.00001621 12.62426489
-0.00002361 0.00001515 1.00000000 -183.89988525
Axis 0.00034521 0.00051212 -0.99999981
Axis point 269.69106120 273.24470985 0.00000000
Rotation angle (degrees) 2.60301056
Shift along axis 183.90214945
> fitmap #4 inMap #5
Fit molecule 00-Portal-12mers-Adaptor-12mers.pdb (#4) to map
P2_J332_011_C12_volume_map_sharp.mrc (#5) using 49956 atoms
average map value = 0.2235, steps = 48
shifted from previous position = 1.17
rotated from previous position = 1.29 degrees
atoms outside contour = 36187, contour level = 0.37288
Position of 00-Portal-12mers-Adaptor-12mers.pdb (#4) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99984293 0.01772282 0.00013963 -4.84230131
-0.01772284 0.99984293 0.00014444 4.81827340
-0.00013705 -0.00014690 0.99999998 4.92764678
Axis -0.00821881 0.00780528 -0.99993576
Axis point 271.54119413 277.87977287 0.00000000
Rotation angle (degrees) 1.01556178
Shift along axis -4.84992430
> select subtract #5
Nothing selected
> show #4 models
> select add #4
49956 atoms, 51084 bonds, 6396 residues, 1 model selected
> view matrix models
> #4,0.99801,0.063113,0.00016895,-17.505,-0.063113,0.99801,0.00012175,17.107,-0.00016093,-0.00013217,1,-183.05
> fitmap #4 inMap #5
Fit molecule 00-Portal-12mers-Adaptor-12mers.pdb (#4) to map
P2_J332_011_C12_volume_map_sharp.mrc (#5) using 49956 atoms
average map value = 1.039, steps = 64
shifted from previous position = 1.23
rotated from previous position = 1.02 degrees
atoms outside contour = 6014, contour level = 0.37288
Position of 00-Portal-12mers-Adaptor-12mers.pdb (#4) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999999 -0.00006951 0.00008457 -0.00906172
0.00006951 1.00000000 0.00001256 -0.02519496
-0.00008457 -0.00001255 1.00000000 0.02894906
Axis -0.11394133 0.76751302 0.63082576
Axis point 342.62047564 0.00000000 107.23234595
Rotation angle (degrees) 0.00631332
Shift along axis -0.00004314
> view matrix models
> #4,0.99897,0.045346,0.00010796,-10.688,-0.045346,0.99897,-7.5021e-06,13.437,-0.00010818,2.5991e-06,1,-183.75
> undo
> select subtract #4
Nothing selected
> hide #!5 models
> select add #4
49956 atoms, 51084 bonds, 6396 residues, 1 model selected
> color sel light sea green
> ui tool show "Color Zone"
> color zone #2 near #4 distance 6.37
> select subtract #4
Nothing selected
> hide #4 models
> volume splitbyzone #2
Opened P2_J357_007_volume_map_sharp_C6.mrc 0 as #6.1, grid size 512,512,512,
pixel 1.06, shown at level 0.3, step 1, values float32
Opened P2_J357_007_volume_map_sharp_C6.mrc 1 as #6.2, grid size 512,512,512,
pixel 1.06, shown at level 0.3, step 1, values float32
> surface dust #6.1 size 10.6
> surface dust #6.2 size 10.6
> show #3 models
> hide #3 models
> show #!5 models
> hide #!5 models
> close #5
> show #4 models
> hide #4 models
> show #3 models
> hide #3 models
> hide #!6.1 models
> show #!6.1 models
> show #!6.2 models
> hide #!6.2 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /Connector/Corndog_45_terminator_6mer/fold_corndog_45_terminator_6mer_model_0.cif"
Chain information for fold_corndog_45_terminator_6mer_model_0.cif #5
---
Chain | Description
A B C D E F | .
> select sequence
> MTEPLDDEEPETPEPPEPEILNEGPADAETFVVKWLGEVYRAANTRRPGDPLPFLLIQQVAGKENLDESTADPVVQVDILCDKVDGEDAARDIKDRVHRRMLLLGRYLEMDGTLDWMKVFESPRRLEYTNDKVIRYTARYQFGQTYEQIA
7296 atoms, 7452 bonds, 900 residues, 1 model selected
> view #5 clip false
> rename #5 fold_corndog_48_terminator_6mer_model_0.cif
> view matrix models #5,1,0,0,16.281,0,1,0,321.78,0,0,1,237.02
> view matrix models #5,1,0,0,203.58,0,1,0,380.64,0,0,1,232.24
> view matrix models #5,1,0,0,185.36,0,1,0,331.68,0,0,1,216.71
> view #6.1 clip false
> view matrix models
> #5,0.90835,0.074213,-0.41157,179.93,-0.16621,0.96713,-0.19244,327.02,0.38376,0.24321,0.89083,222.28
> view matrix models
> #5,0.8689,0.038677,-0.49348,178.33,-0.084818,0.99383,-0.071451,329.63,0.48767,0.10394,0.86682,222.99
> view matrix models
> #5,0.86223,0.034604,-0.50533,178.09,-0.071837,0.99593,-0.054375,330.01,0.50139,0.083186,0.86121,223.05
> view matrix models
> #5,0.86223,0.034604,-0.50533,238.46,-0.071837,0.99593,-0.054375,253.5,0.50139,0.083186,0.86121,218.21
> view matrix models
> #5,0.86223,0.034604,-0.50533,273.76,-0.071837,0.99593,-0.054375,268.53,0.50139,0.083186,0.86121,211.14
> fitmap #5 inMap #6.1
Fit molecule fold_corndog_48_terminator_6mer_model_0.cif (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 7296 atoms
average map value = 0.2316, steps = 76
shifted from previous position = 1.73
rotated from previous position = 2.25 degrees
atoms outside contour = 5025, contour level = 0.3
Position of fold_corndog_48_terminator_6mer_model_0.cif (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.87926920 0.04178526 -0.47448885 272.39433390
-0.06802458 0.99694975 -0.03826035 267.44015756
0.47144282 0.06591805 0.87942963 211.31471206
Axis 0.10874962 -0.98743805 -0.11462817
Axis point -209.70497760 0.00000000 686.72548064
Rotation angle (degrees) 28.61898749
Shift along axis -258.68042628
> view matrix models
> #5,0.27209,-0.19045,-0.94324,257.41,-0.42786,0.85405,-0.29587,258.75,0.86192,0.48408,0.15089,211.14
> view matrix models
> #5,-0.22785,-0.5079,-0.83074,249.84,-0.71296,0.6681,-0.21291,254.61,0.66315,0.54377,-0.51434,201.37
> view matrix models
> #5,-0.43657,-0.85107,-0.2917,251.02,-0.89548,0.44231,0.049695,253.74,0.086729,0.28291,-0.95522,187.02
> view matrix models
> #5,-0.345,-0.89953,0.268,258.12,-0.82386,0.42702,0.37271,258.17,-0.4497,-0.092208,-0.88841,178.18
> view matrix models
> #5,-0.28221,-0.89057,0.35672,260.04,-0.79611,0.42488,0.43091,259.2,-0.53532,-0.16238,-0.82889,177.24
> view matrix models
> #5,-0.27306,-0.88767,0.37077,260.34,-0.81146,0.41954,0.40683,258.69,-0.51669,-0.18978,-0.83488,177.34
> fitmap #5 inMap #6.1
Fit molecule fold_corndog_48_terminator_6mer_model_0.cif (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 7296 atoms
average map value = 0.1283, steps = 144
shifted from previous position = 1.17
rotated from previous position = 3.37 degrees
atoms outside contour = 5937, contour level = 0.3
Position of fold_corndog_48_terminator_6mer_model_0.cif (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.23317112 -0.88181336 0.40992246 260.87210431
-0.80555348 0.41128469 0.42653077 259.58717415
-0.54471536 -0.23075981 -0.80624754 176.81556194
Axis -0.56587758 0.82187111 0.06565400
Axis point 253.25112798 0.00000000 18.70645379
Rotation angle (degrees) 144.49521100
Shift along axis 77.33417411
> view matrix models
> #5,-0.23317,-0.88181,0.40992,259.78,-0.80555,0.41128,0.42653,262.01,-0.54472,-0.23076,-0.80625,214.56
> view matrix models
> #5,-0.23317,-0.88181,0.40992,265.92,-0.80555,0.41128,0.42653,267.13,-0.54472,-0.23076,-0.80625,215.4
> fitmap #5 inMap #6.1
Fit molecule fold_corndog_48_terminator_6mer_model_0.cif (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 7296 atoms
average map value = 0.2482, steps = 160
shifted from previous position = 3.4
rotated from previous position = 9.54 degrees
atoms outside contour = 4951, contour level = 0.3
Position of fold_corndog_48_terminator_6mer_model_0.cif (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.17080050 -0.81912523 0.54759569 266.80468535
-0.81538719 0.42950892 0.38815694 269.04262747
-0.55314638 -0.38020512 -0.74126456 212.69797521
Axis -0.57238102 0.81998306 0.00278460
Axis point 277.25199381 0.00000000 33.96745534
Rotation angle (degrees) 137.84040119
Shift along axis 68.48873789
> view matrix models
> #5,-0.19559,-0.84824,0.49216,265.73,-0.79295,0.43208,0.42957,269.83,-0.57704,-0.30624,-0.75713,212.48
> view matrix models
> #5,-0.28501,-0.85408,0.43511,263.76,-0.81912,0.45277,0.35219,268.7,-0.4978,-0.25603,-0.82864,213.11
> fitmap #5 inMap #6.1
Fit molecule fold_corndog_48_terminator_6mer_model_0.cif (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 7296 atoms
average map value = 0.2379, steps = 224
shifted from previous position = 2.57
rotated from previous position = 11 degrees
atoms outside contour = 5053, contour level = 0.3
Position of fold_corndog_48_terminator_6mer_model_0.cif (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.39004502 -0.87505476 0.28660782 266.23338014
-0.83359680 0.46778201 0.29376242 269.73671562
-0.39112819 -0.12433480 -0.91189890 213.03022882
Axis -0.52432419 0.84993003 0.05199128
Axis point 241.74018070 0.00000000 59.22970439
Rotation angle (degrees) 156.50299962
Shift along axis 100.74044924
> view matrix models
> #5,-0.40577,-0.87306,0.27042,265.84,-0.81906,0.47864,0.3163,270.24,-0.40558,-0.093147,-0.9093,212.97
> view matrix models
> #5,-0.38219,-0.87087,0.30905,266.61,-0.80577,0.4778,0.34992,270.79,-0.4524,-0.11529,-0.88433,212.45
> view matrix models
> #5,-0.38219,-0.87087,0.30905,268.66,-0.80577,0.4778,0.34992,271.96,-0.4524,-0.11529,-0.88433,214.93
> fitmap #5 inMap #6.1
Fit molecule fold_corndog_48_terminator_6mer_model_0.cif (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 7296 atoms
average map value = 0.2236, steps = 96
shifted from previous position = 2.55
rotated from previous position = 3.14 degrees
atoms outside contour = 5093, contour level = 0.3
Position of fold_corndog_48_terminator_6mer_model_0.cif (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.43116624 -0.85036739 0.30161395 269.60737619
-0.79168910 0.51690970 0.32562668 273.09972647
-0.43280948 -0.09838525 -0.89610061 217.04087670
Axis -0.49880062 0.86396357 0.06902817
Axis point 240.62369467 0.00000000 55.30209888
Rotation angle (degrees) 154.84734420
Shift along axis 116.44982451
> hide sel atoms
> show sel cartoons
> select subtract #5
Nothing selected
> color zone #6.2 near #5 distance 6.37
> color zone #6.1 near #5 distance 6.37
> select add #5
7296 atoms, 7452 bonds, 900 residues, 1 model selected
> color sel hot pink
> color zone #6.1 near #5 distance 6.37
> volume splitbyzone #6.1
Opened P2_J357_007_volume_map_sharp_C6.mrc 0 0 as #7.1, grid size 512,512,512,
pixel 1.06, shown at level 0.3, step 1, values float32
Opened P2_J357_007_volume_map_sharp_C6.mrc 0 1 as #7.2, grid size 512,512,512,
pixel 1.06, shown at level 0.3, step 1, values float32
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
> surface dust #7.1 size 10.6
> surface dust #7.2 size 10.6
> select subtract #5
Nothing selected
> hide #5 models
> show #4 models
> hide #4 models
> show #3 models
> show #5 models
> close #7
> show #!6.1 models
> color single #6.1
> select add #5
7296 atoms, 7452 bonds, 900 residues, 1 model selected
> view matrix models
> #5,-0.96472,-0.1168,0.23595,264.27,0.15015,-0.98026,0.12865,278.59,0.21627,0.15954,0.96321,245.84
> view matrix models
> #5,-0.93086,-0.089594,0.35421,266.04,0.057731,-0.99336,-0.099542,274.95,0.36078,-0.072211,0.92985,246.64
> view matrix models
> #5,-0.93086,-0.089594,0.35421,265.05,0.057731,-0.99336,-0.099542,282.86,0.36078,-0.072211,0.92985,218.08
> view matrix models
> #5,-0.93086,-0.089594,0.35421,272.33,0.057731,-0.99336,-0.099542,277.7,0.36078,-0.072211,0.92985,214.65
> view matrix models
> #5,-0.86878,-0.13472,0.47652,274.25,0.16595,-0.98585,0.023858,280.51,0.46656,0.099807,0.87884,216.36
> view matrix models
> #5,-0.87354,-0.14028,0.46609,274.06,0.16243,-0.98669,0.0074734,280.29,0.45884,0.082237,0.8847,216.24
> select subtract #5
Nothing selected
> hide #5 models
> show #5 models
> show #3,5 surfaces
> hide #!6.1 models
> show #!6.1 models
> select add #5
7296 atoms, 7452 bonds, 900 residues, 1 model selected
> view matrix models
> #5,-0.87776,-0.17072,0.44765,273.69,0.17506,-0.98404,-0.032034,280.09,0.44598,0.050247,0.89363,216.01
> view matrix models
> #5,-0.8818,-0.17197,0.43914,273.54,0.17885,-0.98353,-0.026032,280.21,0.43639,0.055584,0.89804,215.94
> view matrix models
> #5,-0.8818,-0.17197,0.43914,263.52,0.17885,-0.98353,-0.026032,275.58,0.43639,0.055584,0.89804,209.31
> view matrix models
> #5,-0.88723,-0.17518,0.42677,263.31,0.18541,-0.9825,-0.017854,275.76,0.42243,0.063286,0.90418,209.2
> view matrix models
> #5,-0.88723,-0.17518,0.42677,266.13,0.18541,-0.9825,-0.017854,278.85,0.42243,0.063286,0.90418,208.69
> view matrix models
> #5,-0.90492,0.075028,0.41891,266.86,0.013959,-0.97857,0.20542,278.62,0.42534,0.19174,0.88449,209.1
> view matrix models
> #5,-0.90492,0.075028,0.41891,265.23,0.013959,-0.97857,0.20542,273.47,0.42534,0.19174,0.88449,208.29
> select subtract #5
6 models selected
> hide #!5 models
> color #6.1 #b2b2b2ff models
> show #!5 models
> hide #!5 models
> show #!5 models
> select add #5
7296 atoms, 7452 bonds, 900 residues, 1 model selected
> view matrix models
> #5,-0.90492,0.075028,0.41891,173.85,0.013959,-0.97857,0.20542,259.42,0.42534,0.19174,0.88449,208.29
> view matrix models
> #5,-0.84919,-0.17986,0.49651,174.36,0.24662,-0.96646,0.071706,261.47,0.46696,0.18334,0.86507,208.66
> view matrix models
> #5,-0.84821,-0.42076,0.32172,171.66,0.063296,0.52253,0.85027,272.61,-0.52587,0.74157,-0.41658,183.97
> view matrix models
> #5,-0.76223,-0.52361,0.38058,173.06,-0.3659,0.83352,0.41396,263.38,-0.53397,0.17628,-0.82692,177.49
> view matrix models
> #5,-0.7296,-0.53887,0.42108,173.87,-0.50907,0.83909,0.19176,259.15,-0.45666,-0.074457,-0.88652,176.99
> view matrix models
> #5,-0.70914,-0.55354,0.43672,174.26,-0.56908,0.81503,0.10897,257.37,-0.41626,-0.17125,-0.89297,177.11
> view matrix models
> #5,-0.87131,-0.32908,0.36405,172.12,0.15111,0.52589,0.83702,273.75,-0.4669,0.78431,-0.40848,185.07
> view matrix models
> #5,-0.8835,-0.1467,0.44488,173.49,0.46844,-0.27929,0.83819,275.05,0.00129,0.94894,0.31547,199.63
> view matrix models
> #5,-0.80882,-0.083521,0.5821,176.18,0.38024,-0.82937,0.40934,267.29,0.44859,0.55242,0.70257,208.28
> view matrix models
> #5,-0.74224,-0.14108,0.65512,177.63,0.29772,-0.94524,0.13375,262.91,0.60037,0.29432,0.7436,209.82
> view matrix models
> #5,-0.70332,-0.16419,0.69165,178.45,0.16654,-0.98394,-0.064229,258.9,0.69109,0.070017,0.71937,209.97
> view matrix models
> #5,-0.76975,-0.17403,0.61417,176.69,0.15684,-0.98419,-0.082308,258.58,0.61878,0.032971,0.78487,209.43
> view matrix models
> #5,-0.78275,-0.21068,0.58559,176.07,0.29851,-0.95275,0.056234,262.12,0.54607,0.21882,0.80865,209.38
> view matrix models
> #5,-0.78275,-0.21068,0.58559,275.51,0.29851,-0.95275,0.056234,281.29,0.54607,0.21882,0.80865,214.61
> view matrix models
> #5,-0.78275,-0.21068,0.58559,273.13,0.29851,-0.95275,0.056234,276.73,0.54607,0.21882,0.80865,214.68
> fitmap #5 inMap #6.1
Fit molecule fold_corndog_48_terminator_6mer_model_0.cif (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 7296 atoms
average map value = 0.2202, steps = 84
shifted from previous position = 3.27
rotated from previous position = 4.23 degrees
atoms outside contour = 5096, contour level = 0.3
Position of fold_corndog_48_terminator_6mer_model_0.cif (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.77963722 -0.21401350 0.58852714 272.68492105
0.26062990 -0.96542135 -0.00580504 275.44566144
0.56941901 0.14886195 0.80845666 211.77800782
Axis 0.30959827 0.03824893 0.95009785
Axis point 84.19843475 145.54750950 0.00000000
Rotation angle (degrees) 165.53511672
Shift along axis 296.16811091
> fitmap #5 inMap #6.1
Fit molecule fold_corndog_48_terminator_6mer_model_0.cif (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 7296 atoms
average map value = 0.2202, steps = 40
shifted from previous position = 0.00301
rotated from previous position = 0.000581 degrees
atoms outside contour = 5094, contour level = 0.3
Position of fold_corndog_48_terminator_6mer_model_0.cif (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.77963468 -0.21402180 0.58852749 272.68559623
0.26063367 -0.96542028 -0.00581438 275.44389975
0.56942076 0.14885698 0.80845634 211.78035117
Axis 0.30959913 0.03824514 0.95009773
Axis point 84.19786875 145.54732022 0.00000000
Rotation angle (degrees) 165.53473905
Shift along axis 296.16964287
> select subtract #5
6 models selected
> color zone #6.1 near #5 distance 6.37
> volume splitbyzone #6.1
Opened P2_J357_007_volume_map_sharp_C6.mrc 0 0 as #7.1, grid size 512,512,512,
pixel 1.06, shown at level 0.3, step 1, values float32
Opened P2_J357_007_volume_map_sharp_C6.mrc 0 1 as #7.2, grid size 512,512,512,
pixel 1.06, shown at level 0.3, step 1, values float32
> surface dust #7.1 size 10.6
> surface dust #7.2 size 10.6
> hide #!5 models
> combine #3
> rename #8 id #9
> rename #3 id #8
> rename #7 id #3
> rename #8 id #7
> combine #7
> turn z 60 models #8-12
> turn z 60 models #9-12
> turn z 60 models #10-12
> turn z 60 models #11-12
> turn z 60 models #12
> select add #7
916 atoms, 939 bonds, 119 residues, 1 model selected
> select subtract #7
1 model selected
> select add #8
916 atoms, 939 bonds, 119 residues, 1 model selected
> view matrix models
> #8,0.50018,0.86582,-0.012828,-91.588,-0.86533,0.50034,0.029569,374.55,0.03202,-0.003689,0.99948,-8.0479
> select subtract #8
Nothing selected
> select add #9
916 atoms, 939 bonds, 119 residues, 1 model selected
> view matrix models
> #9,-0.48957,0.87192,-0.0090195,172.5,-0.85437,-0.4776,0.20484,595.26,0.17429,0.10799,0.97875,-75.922
> select subtract #9
Nothing selected
> select add #10
916 atoms, 939 bonds, 119 residues, 1 model selected
> view matrix models
> #10,-0.98844,0.020109,0.15027,505.87,0.00090298,-0.99037,0.13847,512.54,0.1516,0.13701,0.9789,-77.266
> select add #11
1832 atoms, 1878 bonds, 238 residues, 2 models selected
> select subtract #10
916 atoms, 939 bonds, 119 residues, 1 model selected
> view matrix models
> #11,-0.49702,-0.85043,0.17247,603.31,0.86002,-0.50923,-0.032558,186.77,0.11552,0.13215,0.98448,-67.006
> select subtract #11
Nothing selected
> select add #12
916 atoms, 939 bonds, 119 residues, 1 model selected
> view matrix models
> #12,0.49327,-0.86915,0.035391,363.57,0.86386,0.48468,-0.13723,-68.984,0.10212,0.098264,0.98991,-54.983
> select add #11
1832 atoms, 1878 bonds, 238 residues, 2 models selected
> select add #10
2748 atoms, 2817 bonds, 357 residues, 3 models selected
> select add #9
3664 atoms, 3756 bonds, 476 residues, 4 models selected
> select add #8
4580 atoms, 4695 bonds, 595 residues, 5 models selected
> select add #7
5496 atoms, 5634 bonds, 714 residues, 6 models selected
> hide sel surfaces
> fitmap #8 inMap #3.1
Fit molecule copy of Stopper_45_1.pdb (#8) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) using 916 atoms
average map value = 0.2327, steps = 156
shifted from previous position = 5.53
rotated from previous position = 8.38 degrees
atoms outside contour = 641, contour level = 0.3
Position of copy of Stopper_45_1.pdb (#8) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) coordinates:
Matrix rotation and translation
0.47212474 0.87453555 0.11084146 -103.12562348
-0.88080797 0.46289893 0.09950841 376.24994093
0.03571524 -0.14461042 0.98884392 30.02335487
Axis -0.13762254 0.04235257 -0.98957885
Axis point 259.69367403 274.60758179 0.00000000
Rotation angle (degrees) 62.48803804
Shift along axis 0.41708658
> fitmap #9 inMap #3.1
Fit molecule copy of Stopper_45_1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) using 916 atoms
average map value = 0.214, steps = 140
shifted from previous position = 3.17
rotated from previous position = 15.1 degrees
atoms outside contour = 663, contour level = 0.3
Position of copy of Stopper_45_1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) coordinates:
Matrix rotation and translation
-0.50398526 0.85533118 -0.12003102 201.15585308
-0.80388236 -0.41369926 0.42734774 528.35521998
0.31586710 0.31186778 0.89608398 -144.71883352
Axis -0.06716299 -0.25351775 -0.96499631
Axis point 260.81008887 224.03351265 0.00000000
Rotation angle (degrees) 120.71714996
Shift along axis -7.80451260
> fitmap #10 inMap #3.1
Fit molecule copy of Stopper_45_1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) using 916 atoms
average map value = 0.2443, steps = 116
shifted from previous position = 1.95
rotated from previous position = 17.6 degrees
atoms outside contour = 655, contour level = 0.3
Position of copy of Stopper_45_1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) coordinates:
Matrix rotation and translation
-0.90778679 0.24205663 0.34253715 397.55578552
-0.20024246 -0.96770170 0.15315463 556.30386788
0.36854588 0.07044127 0.92693686 -105.05751752
Axis -0.18351479 -0.05770514 -0.98132178
Axis point 240.94929183 258.13987226 0.00000000
Rotation angle (degrees) 166.97601937
Shift along axis -1.96373061
> fitmap #11 inMap #3.1
Fit molecule copy of Stopper_45_1.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) using 916 atoms
average map value = 0.2156, steps = 88
shifted from previous position = 4.61
rotated from previous position = 8.7 degrees
atoms outside contour = 648, contour level = 0.3
Position of copy of Stopper_45_1.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) coordinates:
Matrix rotation and translation
-0.57878699 -0.77334865 0.25872264 590.26510146
0.80685740 -0.58909375 0.04415425 202.59259803
0.11826527 0.23430819 0.96494193 -87.10269396
Axis 0.11901048 0.08790719 0.98899385
Axis point 249.32152497 253.97578978 0.00000000
Rotation angle (degrees) 126.97521026
Shift along axis 1.91305125
> fitmap #12 inMap #3.1
Fit molecule copy of Stopper_45_1.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) using 916 atoms
average map value = 0.2381, steps = 96
shifted from previous position = 1.15
rotated from previous position = 16.7 degrees
atoms outside contour = 642, contour level = 0.3
Position of copy of Stopper_45_1.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) coordinates:
Matrix rotation and translation
0.31285755 -0.94325609 0.11130125 414.58062102
0.94326923 0.32228399 0.07985023 -86.55250318
-0.11118984 0.08000530 0.99057350 3.62150501
Axis 0.00008163 0.11712523 0.99311715
Axis point 266.99278763 245.02259561 0.00000000
Rotation angle (degrees) 71.76847610
Shift along axis -6.50706069
> fitmap #12 inMap #3.1
Fit molecule copy of Stopper_45_1.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) using 916 atoms
average map value = 0.238, steps = 44
shifted from previous position = 0.0211
rotated from previous position = 0.0281 degrees
atoms outside contour = 644, contour level = 0.3
Position of copy of Stopper_45_1.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) coordinates:
Matrix rotation and translation
0.31301614 -0.94315034 0.11175057 414.44063174
0.94320640 0.32248682 0.07977342 -86.59356291
-0.11127643 0.08043349 0.99052910 3.53977086
Axis 0.00034750 0.11741381 0.99308302
Axis point 266.96206485 244.97074778 0.00000000
Rotation angle (degrees) 71.75891378
Shift along axis -6.50797723
> combine #7-12
Remapping chain ID 'A' in copy of Stopper_45_1.pdb #8 to 'B'
Remapping chain ID 'A' in copy of Stopper_45_1.pdb #9 to 'C'
Remapping chain ID 'A' in copy of Stopper_45_1.pdb #10 to 'D'
Remapping chain ID 'A' in copy of Stopper_45_1.pdb #11 to 'E'
Remapping chain ID 'A' in copy of Stopper_45_1.pdb #12 to 'F'
> select subtract #7
4580 atoms, 4695 bonds, 595 residues, 6 models selected
> select subtract #8
3664 atoms, 3756 bonds, 476 residues, 4 models selected
> select subtract #9
2748 atoms, 2817 bonds, 357 residues, 3 models selected
> select subtract #10
1832 atoms, 1878 bonds, 238 residues, 2 models selected
> select subtract #11
916 atoms, 939 bonds, 119 residues, 1 model selected
> select subtract #12
Nothing selected
> fitmap #13 inMap #3.1
Fit molecule combination (#13) to map P2_J357_007_volume_map_sharp_C6.mrc 0 0
(#3.1) using 5496 atoms
average map value = 0.2221, steps = 40
shifted from previous position = 0.0287
rotated from previous position = 0.0306 degrees
atoms outside contour = 3932, contour level = 0.3
Position of combination (#13) relative to P2_J357_007_volume_map_sharp_C6.mrc
0 0 (#3.1) coordinates:
Matrix rotation and translation
0.99999988 0.00049143 -0.00008750 -0.12500529
-0.00049144 0.99999986 -0.00019180 0.19415338
0.00008741 0.00019184 0.99999998 -0.07595523
Axis 0.35871533 -0.16354368 -0.91900858
Axis point 392.73726650 249.51518543 0.00000000
Rotation angle (degrees) 0.03063862
Shift along axis -0.00679036
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> color #13 #e17083ff
> select add #7
916 atoms, 939 bonds, 119 residues, 1 model selected
> view matrix models
> #7,-0.029671,-0.93437,-0.35505,554.49,0.91573,-0.16781,0.36509,0.51781,-0.40071,-0.3143,0.86061,203.61
> view matrix models
> #7,-0.12912,-0.92866,-0.34773,576.74,0.88585,-0.26561,0.38042,29.933,-0.44565,-0.25892,0.85695,201.6
> view matrix models
> #7,-0.25257,-0.93639,-0.2437,591.66,0.95098,-0.28669,0.11599,64.628,-0.17848,-0.20246,0.96289,102.06
> view matrix models
> #7,-0.24458,-0.95959,-0.13916,577.4,0.94969,-0.26602,0.16528,51.232,-0.19562,-0.091739,0.97638,76.212
> view matrix models
> #7,-0.24458,-0.95959,-0.13916,577.29,0.94969,-0.26602,0.16528,51.153,-0.19562,-0.091739,0.97638,76.683
> view matrix models
> #7,-0.24458,-0.95959,-0.13916,574.19,0.94969,-0.26602,0.16528,43.923,-0.19562,-0.091739,0.97638,76.664
> fitmap #7 inMap #3.1
Fit molecule Stopper_45_1.pdb (#7) to map P2_J357_007_volume_map_sharp_C6.mrc
0 0 (#3.1) using 916 atoms
average map value = 0.2277, steps = 96
shifted from previous position = 3.67
rotated from previous position = 8.32 degrees
atoms outside contour = 645, contour level = 0.3
Position of Stopper_45_1.pdb (#7) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) coordinates:
Matrix rotation and translation
-0.15948673 -0.96044550 -0.22827272 570.94695696
0.94368408 -0.21622104 0.25041730 20.18636060
-0.28986953 -0.17547910 0.94084151 124.87475771
Axis -0.21816782 0.03155331 0.97540104
Axis point 291.11504402 242.53318246 0.00000000
Rotation angle (degrees) 102.55831290
Shift along axis -2.12233542
> fitmap #7 inMap #3.1
Fit molecule Stopper_45_1.pdb (#7) to map P2_J357_007_volume_map_sharp_C6.mrc
0 0 (#3.1) using 916 atoms
average map value = 0.2277, steps = 44
shifted from previous position = 0.0192
rotated from previous position = 0.0275 degrees
atoms outside contour = 646, contour level = 0.3
Position of Stopper_45_1.pdb (#7) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 0 (#3.1) coordinates:
Matrix rotation and translation
-0.15976065 -0.96048356 -0.22792076 570.95633904
0.94360768 -0.21640726 0.25054428 20.22130509
-0.28996737 -0.17504066 0.94089303 124.79793343
Axis -0.21801844 0.03178521 0.97542691
Axis point 291.08888932 242.48615985 0.00000000
Rotation angle (degrees) 102.57030629
Shift along axis -2.10501182
> select subtract #7
1 model selected
> transparency #7.1#3.1.1 50
> hide #!7 models
> show #!5 models
> close #3.1
> show #!6.1 models
> fitmap #5 inMap #6.1
Fit molecule fold_corndog_48_terminator_6mer_model_0.cif (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 7296 atoms
average map value = 0.2202, steps = 40
shifted from previous position = 0.000186
rotated from previous position = 0.00148 degrees
atoms outside contour = 5094, contour level = 0.3
Position of fold_corndog_48_terminator_6mer_model_0.cif (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.77962335 -0.21401239 0.58854591 272.68549344
0.26062272 -0.96542321 -0.00581935 275.44396839
0.56944127 0.14885154 0.80844290 211.78024888
Axis 0.30961029 0.03824245 0.95009420
Axis point 84.19705515 145.54693947 0.00000000
Rotation angle (degrees) 165.53531785
Shift along axis 296.17107224
> fitmap #5 inMap #6.1
Fit molecule fold_corndog_48_terminator_6mer_model_0.cif (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 7296 atoms
average map value = 0.2202, steps = 40
shifted from previous position = 7.15e-05
rotated from previous position = 0.0003 degrees
atoms outside contour = 5094, contour level = 0.3
Position of fold_corndog_48_terminator_6mer_model_0.cif (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.77962106 -0.21401091 0.58854949 272.68553186
0.26062053 -0.96542379 -0.00582101 275.44401492
0.56944541 0.14884990 0.80844028 211.78022303
Axis 0.30961251 0.03824158 0.95009351
Axis point 84.19690225 145.54693214 0.00000000
Rotation angle (degrees) 165.53542158
Shift along axis 296.17128148
> select add #5
7296 atoms, 7452 bonds, 900 residues, 1 model selected
> view matrix models
> #5,-0.77962,-0.21401,0.58855,271.43,0.26062,-0.96542,-0.005821,275.3,0.56945,0.14885,0.80844,209.21
> view matrix models
> #5,-0.77962,-0.21401,0.58855,270.29,0.26062,-0.96542,-0.005821,275.14,0.56945,0.14885,0.80844,210.66
> view matrix models
> #5,-0.8481,-0.23181,0.47644,268.12,0.25248,-0.96737,-0.021241,274.86,0.46582,0.10228,0.87895,209.68
> fitmap #5 inMap #6.1
Fit molecule fold_corndog_48_terminator_6mer_model_0.cif (#5) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 7296 atoms
average map value = 0.2233, steps = 84
shifted from previous position = 1.77
rotated from previous position = 4.29 degrees
atoms outside contour = 5081, contour level = 0.3
Position of fold_corndog_48_terminator_6mer_model_0.cif (#5) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.86183405 -0.20745260 0.46282358 269.54793868
0.25986851 -0.96425934 0.05169450 275.32496824
0.43555777 0.16482535 0.88494186 208.73017033
Axis 0.23491006 0.05661597 0.97036689
Axis point 93.17670303 144.38214654 0.00000000
Rotation angle (degrees) 166.06646934
Shift along axis 281.45215646
[deleted to fit within ticket limits]
> fitmap #9 inMap #6.1
Fit molecule Stopper_45_1-coot-4.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.9068, steps = 28
shifted from previous position = 0.0253
rotated from previous position = 0.0308 degrees
atoms outside contour = 197, contour level = 0.3
Position of Stopper_45_1-coot-4.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99998652 -0.00163976 0.00492581 -0.62844912
0.00187730 0.99881591 -0.04861326 12.27044747
-0.00484027 0.04862185 0.99880553 -11.60789266
Axis 0.99435021 0.09987034 0.03596626
Axis point 0.00000000 244.91861478 246.06782378
Rotation angle (degrees) 2.80252567
Shift along axis 0.18306281
> fitmap #9 inMap #6.1
Fit molecule Stopper_45_1-coot-4.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.9063, steps = 28
shifted from previous position = 0.0303
rotated from previous position = 0.0272 degrees
atoms outside contour = 194, contour level = 0.3
Position of Stopper_45_1-coot-4.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99998787 -0.00167996 0.00462915 -0.56025310
0.00190471 0.99879785 -0.04898186 12.35845540
-0.00454129 0.04899008 0.99878894 -11.78244529
Axis 0.99498783 0.09313357 0.03640542
Axis point 0.00000000 246.70878608 245.93891124
Rotation angle (degrees) 2.82196872
Shift along axis 0.16459714
> fitmap #9 inMap #6.1
Fit molecule Stopper_45_1-coot-4.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.9067, steps = 28
shifted from previous position = 0.0272
rotated from previous position = 0.0178 degrees
atoms outside contour = 196, contour level = 0.3
Position of Stopper_45_1-coot-4.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99998689 -0.00166922 0.00484017 -0.60591077
0.00190324 0.99880899 -0.04875436 12.29280178
-0.00475302 0.04876293 0.99879907 -11.66406271
Axis 0.99453535 0.09783666 0.03643393
Axis point 0.00000000 245.38355812 245.79164355
Rotation angle (degrees) 2.81014126
Shift along axis 0.17511928
> fitmap #9 inMap #6.1
Fit molecule Stopper_45_1-coot-4.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.9068, steps = 28
shifted from previous position = 0.00487
rotated from previous position = 0.0116 degrees
atoms outside contour = 196, contour level = 0.3
Position of Stopper_45_1-coot-4.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99998771 -0.00154878 0.00471074 -0.61879430
0.00177618 0.99881394 -0.04865764 12.30710604
-0.00462979 0.04866541 0.99880441 -11.67326528
Axis 0.99485090 0.09548030 0.03398831
Axis point 0.00000000 246.04023641 246.61595070
Rotation angle (degrees) 2.80364913
Shift along axis 0.16272361
> hide #!15 models
> hide #!15.1 models
> show #!15.1 models
> rename #9 id #10
> rename #15 id #11
> rename #11 id #9
> combine #10
> turn z 60 models #11-15
> turn y 60 models #11-15
> turn z 60 models #11-15
> select add #11
916 atoms, 939 bonds, 119 residues, 1 model selected
> select add #12
1832 atoms, 1878 bonds, 238 residues, 2 models selected
> select add #13
2748 atoms, 2817 bonds, 357 residues, 3 models selected
> select add #14
3664 atoms, 3756 bonds, 476 residues, 4 models selected
> select add #15
4580 atoms, 4695 bonds, 595 residues, 5 models selected
> turn z 60 models #12-15
> undo
> select subtract #11
3664 atoms, 3756 bonds, 476 residues, 4 models selected
> turn z 60 models #13-15
> select subtract #12
2748 atoms, 2817 bonds, 357 residues, 3 models selected
> turn z 60 models #14-15
> select subtract #13
1832 atoms, 1878 bonds, 238 residues, 2 models selected
> turn z 60 models #15
> select subtract #14
916 atoms, 939 bonds, 119 residues, 1 model selected
> select subtract #15
Nothing selected
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2811, steps = 160
shifted from previous position = 4.74
rotated from previous position = 17.8 degrees
atoms outside contour = 615, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.61380492 0.78075523 0.11690121 -115.30556247
-0.78741664 0.59482515 0.16173795 284.45821678
0.05674197 -0.19132540 0.97988568 34.92985362
Axis -0.21949157 0.03739965 -0.97489729
Axis point 227.53329596 259.70011139 0.00000000
Rotation angle (degrees) 53.54028353
Shift along axis 1.89421592
> hide #10 models
> select add #11
916 atoms, 939 bonds, 119 residues, 1 model selected
> select subtract #11
Nothing selected
> select add #11
916 atoms, 939 bonds, 119 residues, 1 model selected
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2811, steps = 48
shifted from previous position = 0.00881
rotated from previous position = 4.03 degrees
atoms outside contour = 616, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.61558521 0.77771282 0.12735276 -116.74467541
-0.78110368 0.58068213 0.22953518 274.97843803
0.10456096 -0.24077404 0.96493309 38.49613120
Axis -0.28882044 0.01399662 -0.95728097
Axis point 214.63144523 255.93731762 0.00000000
Rotation angle (degrees) 54.50725850
Shift along axis 0.71540300
> hide #!9.1 models
> select subtract #11
Nothing selected
> show #10 models
> color #10 #b2f88cff
> select add #11
916 atoms, 939 bonds, 119 residues, 1 model selected
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2521, steps = 80
shifted from previous position = 3.47
rotated from previous position = 7.03 degrees
atoms outside contour = 606, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.58976920 0.76949708 0.24504619 -130.33237397
-0.80734247 0.55456037 0.20164826 291.20704850
0.01927486 -0.31676197 0.94830973 83.92963014
Axis -0.30946997 0.13477637 -0.94130955
Axis point 206.53166889 279.24644582 0.00000000
Rotation angle (degrees) 56.88513560
Shift along axis 0.57802291
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2446, steps = 64
shifted from previous position = 1.04
rotated from previous position = 5.83 degrees
atoms outside contour = 633, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.54137937 0.79472323 0.27445303 -131.31788359
-0.83731097 0.47999489 0.26175623 306.90143393
0.07628769 -0.37151176 0.92528926 87.90776442
Axis -0.35944987 0.11248082 -0.92636054
Axis point 194.31443752 277.24241083 0.00000000
Rotation angle (degrees) 61.74923383
Shift along axis 0.28843769
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2446, steps = 56
shifted from previous position = 0.0238
rotated from previous position = 0.0833 degrees
atoms outside contour = 635, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.54082696 0.79479039 0.27534623 -131.37129103
-0.83778096 0.47978918 0.26062713 307.28163229
0.07503578 -0.37163381 0.92534261 88.23454654
Axis -0.35880116 0.11367399 -0.92646638
Axis point 194.43930643 277.47947449 0.00000000
Rotation angle (degrees) 61.77215172
Shift along axis 0.31976075
> undo
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2675, steps = 120
shifted from previous position = 2.33
rotated from previous position = 16.9 degrees
atoms outside contour = 608, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.32027780 0.89716343 0.30417267 -111.92544657
-0.91604464 0.21147560 0.34079519 379.44471721
0.24142379 -0.38778468 0.88957216 60.48529382
Axis -0.37265248 0.03209466 -0.92741580
Axis point 185.28450232 266.04988810 0.00000000
Rotation angle (degrees) 77.83881169
Shift along axis -2.20757263
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2671, steps = 48
shifted from previous position = 0.0613
rotated from previous position = 0.353 degrees
atoms outside contour = 616, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.31530334 0.89773432 0.30766540 -111.47973679
-0.91770465 0.20587900 0.33975443 381.43076819
0.24166728 -0.38947148 0.88876877 61.04770343
Axis -0.37252246 0.03371491 -0.92741054
Axis point 185.21931763 266.36920859 0.00000000
Rotation angle (degrees) 78.17193889
Shift along axis -2.22767421
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2551, steps = 88
shifted from previous position = 1.92
rotated from previous position = 7.94 degrees
atoms outside contour = 638, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.43725602 0.85767298 0.27056484 -122.43227416
-0.85826476 0.30807409 0.41045466 326.86628080
0.26868175 -0.41168983 0.87081723 62.92537252
Axis -0.43208762 0.00098968 -0.90183109
Axis point 172.88505224 257.95930849 0.00000000
Rotation angle (degrees) 72.05683235
Shift along axis -3.52309282
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2551, steps = 64
shifted from previous position = 0.00263
rotated from previous position = 0.00538 degrees
atoms outside contour = 638, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.43724584 0.85766172 0.27061699 -122.43537156
-0.85825582 0.30801965 0.41051419 326.86615082
0.26872684 -0.41175402 0.87077296 62.93726510
Axis -0.43214464 0.00099337 -0.90180376
Axis point 172.87068015 257.95890235 0.00000000
Rotation angle (degrees) 72.06011113
Shift along axis -3.52257432
> select subtract #11
Nothing selected
> select add #12
916 atoms, 939 bonds, 119 residues, 1 model selected
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2552, steps = 48
shifted from previous position = 0.0205
rotated from previous position = 0.0447 degrees
atoms outside contour = 635, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.43732350 0.85785861 0.26986639 -122.36637295
-0.85812015 0.30829170 0.41059360 326.76610942
0.26903357 -0.41113980 0.87096844 62.68106082
Axis -0.43190365 0.00043773 -0.90191964
Axis point 172.94214730 257.85815596 0.00000000
Rotation angle (degrees) 72.04369345
Shift along axis -3.53976144
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2552, steps = 60
shifted from previous position = 0.00321
rotated from previous position = 0.0165 degrees
atoms outside contour = 637, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.43736993 0.85778334 0.27003038 -122.38597457
-0.85806280 0.30819748 0.41078413 326.74183471
0.26914099 -0.41136743 0.87082777 62.73683373
Axis -0.43210957 0.00046745 -0.90182099
Axis point 172.89306845 257.86331024 0.00000000
Rotation angle (degrees) 72.04936921
Shift along axis -3.54050855
> fitmap #12 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2597, steps = 72
shifted from previous position = 3.3
rotated from previous position = 8.8 degrees
atoms outside contour = 643, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.55576195 0.82432345 0.10779874 176.48618833
-0.83131641 -0.55207259 -0.06426472 620.44549555
0.00653784 -0.12533068 0.99209397 26.66246157
Axis -0.03678989 0.06100579 -0.99745917
Axis point 253.36057267 263.86157664 0.00000000
Rotation angle (degrees) 123.90862601
Shift along axis 4.76314340
> fitmap #12 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2596, steps = 36
shifted from previous position = 0.00501
rotated from previous position = 0.0432 degrees
atoms outside contour = 640, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.55567188 0.82431868 0.10829843 176.37776111
-0.83137047 -0.55205668 -0.06369958 620.35874698
0.00727815 -0.12543211 0.99207600 26.51932230
Axis -0.03719015 0.06085866 -0.99745332
Axis point 253.29257676 263.83723176 0.00000000
Rotation angle (degrees) 123.90558803
Shift along axis 4.74289946
> select subtract #12
Nothing selected
> select add #15
916 atoms, 939 bonds, 119 residues, 1 model selected
> fitmap #15 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#15) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.8971, steps = 116
shifted from previous position = 5.76
rotated from previous position = 8.31 degrees
atoms outside contour = 196, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#15) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.49960361 -0.86625183 0.00225708 347.47334554
0.86534359 0.49895692 -0.04715447 -83.58885052
0.03972147 0.02551169 0.99888555 -15.89569803
Axis 0.04191816 -0.02161169 0.99888728
Axis point 246.40845953 258.75946995 0.00000000
Rotation angle (degrees) 60.08446907
Shift along axis 0.49392974
> select subtract #15
Nothing selected
> select add #14
916 atoms, 939 bonds, 119 residues, 1 model selected
> fitmap #14 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#14) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2453, steps = 60
shifted from previous position = 1.66
rotated from previous position = 7.07 degrees
atoms outside contour = 626, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#14) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.47563495 -0.87496679 0.09058448 589.90746065
0.87963438 -0.47356662 0.04448655 136.66592349
0.00397356 0.10084054 0.99489513 -22.62782574
Axis 0.03206228 0.04927679 0.99827041
Axis point 254.63745551 244.64657794 0.00000000
Rotation angle (degrees) 118.49962597
Shift along axis 3.05955019
> fitmap #14 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#14) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.8979, steps = 60
shifted from previous position = 2.45
rotated from previous position = 7.61 degrees
atoms outside contour = 195, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#14) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.50162400 -0.86508478 0.00164871 610.57586747
0.86401568 -0.50109705 -0.04878202 160.67169372
0.04302676 -0.02304570 0.99880855 -9.03520930
Axis 0.01487832 -0.02392089 0.99960313
Axis point 259.10197051 256.11215834 0.00000000
Rotation angle (degrees) 120.12949544
Shift along axis -3.79069198
> fitmap #14 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#14) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.8979, steps = 40
shifted from previous position = 0.005
rotated from previous position = 0.0193 degrees
atoms outside contour = 195, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#14) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.50157610 -0.86511312 0.00131807 610.63097501
0.86405280 -0.50103563 -0.04875543 160.64525488
0.04283937 -0.02331566 0.99881034 -8.92805207
Axis 0.01470633 -0.02400281 0.99960372
Axis point 259.13232280 256.12854099 0.00000000
Rotation angle (degrees) 120.12581566
Shift along axis -3.80030979
> select subtract #14
Nothing selected
> select add #13
916 atoms, 939 bonds, 119 residues, 1 model selected
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2978, steps = 76
shifted from previous position = 2.46
rotated from previous position = 4.56 degrees
atoms outside contour = 589, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.99687571 -0.03565369 -0.07048898 541.24556010
0.03531481 -0.99935847 0.00604836 492.45537489
-0.07065934 0.00354017 0.99749471 16.95503914
Axis -0.03532019 0.00239901 0.99937317
Axis point 266.54691174 251.01598911 0.00000000
Rotation angle (degrees) 177.96519987
Shift along axis -0.99108169
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2976, steps = 40
shifted from previous position = 0.0203
rotated from previous position = 0.0282 degrees
atoms outside contour = 592, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.99690130 -0.03582079 -0.07004092 541.22268094
0.03547531 -0.99935204 0.00617075 492.40302306
-0.07021651 0.00366691 0.99752553 16.82223992
Axis -0.03509709 0.00246134 0.99938088
Axis point 266.51156996 251.01138881 0.00000000
Rotation angle (degrees) 177.95581883
Shift along axis -0.97154770
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2978, steps = 96
shifted from previous position = 2.83
rotated from previous position = 3.49 degrees
atoms outside contour = 589, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.99913815 -0.00798723 -0.04074595 530.04073837
0.00965152 -0.99912068 -0.04081387 504.57038291
-0.04038408 -0.04117193 0.99833610 17.57992916
Axis -0.02029088 -0.02050697 0.99958379
Axis point 264.08551267 253.63501666 0.00000000
Rotation angle (degrees) 179.49447033
Shift along axis -3.52959209
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2976, steps = 40
shifted from previous position = 0.0214
rotated from previous position = 0.0273 degrees
atoms outside contour = 592, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.99915378 -0.00819065 -0.04031999 530.02676780
0.00983444 -0.99912190 -0.04074046 504.52329922
-0.03995084 -0.04110248 0.99835640 17.46501031
Axis -0.02007591 -0.02047112 0.99958886
Axis point 264.05121340 253.63555728 0.00000000
Rotation angle (degrees) 179.48340004
Shift along axis -3.51109928
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3085, steps = 80
shifted from previous position = 1.34
rotated from previous position = 8.18 degrees
atoms outside contour = 574, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.98443244 0.05721779 -0.16619257 536.74460778
-0.04987191 -0.99759983 -0.04804632 521.10650340
-0.16854267 -0.03900999 0.98492262 50.22976387
Axis 0.08406207 0.02186222 -0.99622066
Axis point 277.52336322 253.86691595 0.00000000
Rotation angle (degrees) 176.91898367
Shift along axis 6.47248140
> hide #12 models
> hide #11 models
> hide #13 models
> select subtract #13
Nothing selected
> show #13 models
> hide #13 models
> show #11 models
> select add #11
916 atoms, 939 bonds, 119 residues, 1 model selected
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2866, steps = 60
shifted from previous position = 2.26
rotated from previous position = 5.91 degrees
atoms outside contour = 606, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.51252062 0.80097257 0.30946191 -133.98288412
-0.83001167 0.36977991 0.41754581 302.17193828
0.22000986 -0.47085759 0.85433590 94.07912912
Axis -0.47779012 0.04810799 -0.87715576
Axis point 161.05413882 267.66232900 0.00000000
Rotation angle (degrees) 68.38807994
Shift along axis -3.96946503
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2866, steps = 76
shifted from previous position = 0.0273
rotated from previous position = 4.02 degrees
atoms outside contour = 606, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.56870711 0.77450255 0.27698219 -134.64554884
-0.79268048 0.42614519 0.43595756 275.53315334
0.21961553 -0.46749029 0.85628434 92.96368868
Axis -0.49918272 0.03169684 -0.86591681
Axis point 156.64806719 264.01393229 0.00000000
Rotation angle (degrees) 64.81337601
Shift along axis -4.55255933
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2866, steps = 44
shifted from previous position = 0.00503
rotated from previous position = 0.0138 degrees
atoms outside contour = 605, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.56884818 0.77446689 0.27679217 -134.63977177
-0.79256710 0.42632045 0.43599235 275.45366760
0.21965939 -0.46738958 0.85632807 92.91645059
Axis -0.49919301 0.03157057 -0.86591549
Axis point 156.64659553 263.98790344 0.00000000
Rotation angle (degrees) 64.80197689
Shift along axis -4.55033114
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.284, steps = 96
shifted from previous position = 2.55
rotated from previous position = 10.4 degrees
atoms outside contour = 601, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.61178825 0.68757651 0.39109435 -142.20569363
-0.78936890 0.49872019 0.35801675 268.52714060
0.05111726 -0.52774788 0.84786215 152.13460764
Axis -0.50458584 0.19367179 -0.84135865
Axis point 153.03416143 296.33688563 0.00000000
Rotation angle (degrees) 61.36781499
Shift along axis -4.23865661
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2671, steps = 92
shifted from previous position = 1.85
rotated from previous position = 6.99 degrees
atoms outside contour = 602, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.58308487 0.68702282 0.43360442 -143.02217276
-0.81022143 0.53092823 0.24830935 286.10408047
-0.05961858 -0.49610076 0.86621630 167.92234110
Axis -0.42700778 0.28292208 -0.85884774
Axis point 172.10667385 313.98798141 0.00000000
Rotation angle (degrees) 60.65190083
Shift along axis -2.20298148
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2671, steps = 64
shifted from previous position = 0.00409
rotated from previous position = 0.0334 degrees
atoms outside contour = 603, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.58297161 0.68682001 0.43407773 -143.02381782
-0.81029561 0.53073444 0.24848152 286.13865482
-0.05971786 -0.49658870 0.86592982 168.12334711
Axis -0.42730467 0.28319634 -0.85860966
Axis point 172.01824912 314.05947060 0.00000000
Rotation angle (degrees) 60.67140576
Shift along axis -2.20416559
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2705, steps = 88
shifted from previous position = 1.45
rotated from previous position = 5.8 degrees
atoms outside contour = 613, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.51285461 0.70166648 0.49461642 -140.36665599
-0.85675232 0.45482829 0.24312090 316.58619307
-0.05437570 -0.54844916 0.83441466 186.19274439
Axis -0.43205265 0.29964941 -0.85061198
Axis point 167.91973583 318.39469906 0.00000000
Rotation angle (degrees) 66.35625696
Shift along axis -2.86712713
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2706, steps = 84
shifted from previous position = 0.0219
rotated from previous position = 0.0439 degrees
atoms outside contour = 610, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.51305039 0.70140131 0.49478944 -140.37602611
-0.85666228 0.45463387 0.24380090 316.51267999
-0.05394572 -0.54894932 0.83411362 186.26322825
Axis -0.43266582 0.29948771 -0.85035722
Axis point 167.78265435 318.38617081 0.00000000
Rotation angle (degrees) 66.36562864
Shift along axis -2.86271248
> select subtract #11
Nothing selected
> hide #11 models
> show #13 models
> select add #13
916 atoms, 939 bonds, 119 residues, 1 model selected
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3086, steps = 64
shifted from previous position = 0.0239
rotated from previous position = 1.35 degrees
atoms outside contour = 572, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.98587051 0.05962581 -0.15654129 534.86135414
-0.04921866 -0.99636481 -0.06953966 524.62824922
-0.16011848 -0.06085231 0.98522081 52.56728900
Axis 0.07951870 0.03274342 -0.99629546
Axis point 276.72160506 255.84916404 0.00000000
Rotation angle (degrees) 176.86868371
Shift along axis 7.33704778
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3085, steps = 44
shifted from previous position = 0.00874
rotated from previous position = 0.0334 degrees
atoms outside contour = 573, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.98589014 0.05905628 -0.15663354 534.99464805
-0.04866499 -0.99640387 -0.06936941 524.46361094
-0.16016686 -0.06076801 0.98521815 52.56205634
Axis 0.07955284 0.03267901 -0.99629485
Axis point 276.71239033 255.83897917 0.00000000
Rotation angle (degrees) 176.90102647
Shift along axis 7.33198974
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2988, steps = 100
shifted from previous position = 2.36
rotated from previous position = 11.1 degrees
atoms outside contour = 567, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.94246283 0.20706552 -0.26246667 514.67592366
-0.20050655 -0.97832036 -0.05184068 555.81535954
-0.26751075 0.00376838 0.96354801 70.87349549
Axis 0.13517715 0.01226138 -0.99074558
Axis point 291.32905981 251.38823805 0.00000000
Rotation angle (degrees) 168.13013436
Shift along axis 6.16988472
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2989, steps = 64
shifted from previous position = 0.0115
rotated from previous position = 0.0125 degrees
atoms outside contour = 568, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.94240255 0.20707740 -0.26267366 514.69459511
-0.20050900 -0.97831782 -0.05187928 555.82380166
-0.26772119 0.00377728 0.96348953 70.94437337
Axis 0.13528581 0.01226915 -0.99073065
Axis point 291.34957385 251.39040404 0.00000000
Rotation angle (degrees) 168.12952964
Shift along axis 6.16359355
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3484, steps = 100
shifted from previous position = 3.3
rotated from previous position = 14.3 degrees
atoms outside contour = 555, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.84528620 0.21428312 -0.48946404 529.47473847
-0.23057746 -0.97266232 -0.02762445 554.67517561
-0.48200242 0.08950877 0.87158639 121.49079894
Axis 0.25459124 -0.01621797 -0.96691276
Axis point 314.17957624 244.52626037 0.00000000
Rotation angle (degrees) 166.70047501
Shift along axis 8.33292239
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3481, steps = 28
shifted from previous position = 0.0297
rotated from previous position = 0.0636 degrees
atoms outside contour = 555, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.84509036 0.21461690 -0.48965593 529.39304171
-0.23137807 -0.97249214 -0.02691251 554.67908451
-0.48196216 0.09055210 0.87150087 121.26996882
Axis 0.25465562 -0.01667959 -0.96688795
Axis point 314.20393961 244.42068668 0.00000000
Rotation angle (degrees) 166.66558806
Shift along axis 8.30662210
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3144, steps = 80
shifted from previous position = 2.58
rotated from previous position = 4.6 degrees
atoms outside contour = 561, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.83731208 0.14580972 -0.52692416 548.61438468
-0.16742128 -0.98586278 -0.00676477 538.60638909
-0.52046100 0.08255406 0.84988596 138.64097456
Axis 0.27416829 -0.01983896 -0.96147707
Axis point 317.04520936 244.55563253 0.00000000
Rotation angle (degrees) 170.62529061
Shift along axis 6.42716258
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.319, steps = 76
shifted from previous position = 0.627
rotated from previous position = 8.3 degrees
atoms outside contour = 552, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.83908943 0.14245375 -0.52501136 549.66400500
-0.08784863 -0.98792102 -0.12765477 542.30062951
-0.53685437 -0.06099221 0.84146795 173.45413722
Axis 0.27770444 0.04933588 -0.95939888
Axis point 316.93809314 258.46975240 0.00000000
Rotation angle (degrees) 173.10649641
Shift along axis 12.98731122
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3189, steps = 48
shifted from previous position = 0.0123
rotated from previous position = 0.0501 degrees
atoms outside contour = 551, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.83870493 0.14213961 -0.52571041 549.75911277
-0.08744859 -0.98796251 -0.12760836 542.21359867
-0.53752009 -0.06105309 0.84103843 173.71243737
Axis 0.27808763 0.04934433 -0.95928745
Axis point 317.00874971 258.48097191 0.00000000
Rotation angle (degrees) 173.12717447
Shift along axis 12.99621234
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3161, steps = 60
shifted from previous position = 1.39
rotated from previous position = 4.5 degrees
atoms outside contour = 567, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.86189499 0.08955422 -0.49911736 562.24158073
-0.06779746 -0.99579643 -0.06159571 526.89749770
-0.50253517 -0.01925013 0.86434299 153.43487413
Axis 0.25981144 0.02096998 -0.96543165
Axis point 312.90004757 253.27992972 0.00000000
Rotation angle (degrees) 175.32561752
Shift along axis 8.99494326
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3162, steps = 44
shifted from previous position = 0.0417
rotated from previous position = 0.268 degrees
atoms outside contour = 567, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.86148822 0.08516662 -0.50058541 563.32425595
-0.06369901 -0.99617286 -0.05985938 525.63635009
-0.50376735 -0.01968134 0.86361570 153.94828707
Axis 0.26051562 0.02063176 -0.96524916
Axis point 312.94708241 253.24277670 0.00000000
Rotation angle (degrees) 175.57738763
Shift along axis 9.00111474
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2878, steps = 68
shifted from previous position = 1.13
rotated from previous position = 5.33 degrees
atoms outside contour = 590, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.87438061 -0.00564124 -0.48520902 582.28184597
0.01330696 -0.99983565 -0.01235560 499.43925098
-0.48505931 -0.01726013 0.87431146 145.93567135
Axis -0.25057388 -0.00764867 0.96806726
Axis point 308.76574002 251.76246148 0.00000000
Rotation angle (degrees) 179.43925960
Shift along axis -8.44912461
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2876, steps = 28
shifted from previous position = 0.0242
rotated from previous position = 0.0369 degrees
atoms outside contour = 589, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.87410580 -0.00574704 -0.48570267 582.32668620
0.01354918 -0.99982993 -0.01255368 499.41442355
-0.48554766 -0.01755410 0.87403450 146.18757543
Axis -0.25084626 -0.00777632 0.96799570
Axis point 308.81942107 251.78798842 0.00000000
Rotation angle (degrees) 179.42891775
Shift along axis -8.44913429
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3205, steps = 88
shifted from previous position = 1.55
rotated from previous position = 8.81 degrees
atoms outside contour = 558, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.91165881 -0.05716558 -0.40695379 587.33567714
0.01086382 -0.99328444 0.11519140 473.61663615
-0.41080562 0.10059414 0.90615702 98.03341004
Axis -0.20947671 0.05527538 0.97625004
Axis point 299.95781714 239.27290730 0.00000000
Rotation angle (degrees) 178.00328552
Shift along axis -1.14868484
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3206, steps = 48
shifted from previous position = 0.00974
rotated from previous position = 0.00795 degrees
atoms outside contour = 558, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.91163965 -0.05712039 -0.40700306 587.32508432
0.01086726 -0.99329939 0.11506208 473.64808780
-0.41084805 0.10047210 0.90615132 98.06408761
Axis -0.20950043 0.05521105 0.97624859
Axis point 299.95931759 239.28767468 0.00000000
Rotation angle (degrees) 178.00450840
Shift along axis -1.15932337
> show #12 models
> hide #12 models
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2969, steps = 96
shifted from previous position = 3.39
rotated from previous position = 9.99 degrees
atoms outside contour = 602, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.89539333 0.05283347 -0.44213174 565.45021973
-0.14723089 -0.97221571 0.18199104 497.33448474
-0.42023197 0.22804891 0.87829367 82.37722529
Axis 0.22308127 -0.10607152 -0.96901165
Axis point 305.47015980 229.02022044 0.00000000
Rotation angle (degrees) 174.07473704
Shift along axis -6.43616290
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2569, steps = 80
shifted from previous position = 1.95
rotated from previous position = 10.2 degrees
atoms outside contour = 638, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.80801887 0.13600245 -0.57324505 548.17364553
-0.25476016 -0.95797836 0.13181727 529.32953278
-0.53122860 0.25255072 0.80871212 118.51796912
Axis 0.29365424 -0.10219463 -0.95043329
Axis point 321.29513504 228.23917936 0.00000000
Rotation angle (degrees) 168.13709005
Shift along axis -5.76454279
> select subtract #13
Nothing selected
> hide #13 models
> show #11 models
> ui tool show Matchmaker
> matchmaker #11 to #10
Parameters
---
Chain pairing | bb
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 Stopper_45_1-coot-4.pdb, chain A (#10) with copy of
Stopper_45_1-coot-4.pdb, chain A (#11), sequence alignment score = 591.5
RMSD between 119 pruned atom pairs is 0.000 angstroms; (across all 119 pairs:
0.000)
> turn z 60 models #11
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2253, steps = 96
shifted from previous position = 2.27
rotated from previous position = 12.8 degrees
atoms outside contour = 654, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.77998485 0.60390427 0.16408646 -114.94547307
-0.28370287 0.10751965 0.95286578 138.59588335
0.55779693 -0.78977229 0.25519293 200.77110593
Axis -0.87354485 -0.19735810 -0.44493728
Axis point 0.00000000 201.26238818 46.42683452
Rotation angle (degrees) 85.90854544
Shift along axis -16.27354444
> select add #11
916 atoms, 939 bonds, 119 residues, 1 model selected
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2253, steps = 56
shifted from previous position = 1.95
rotated from previous position = 0.0109 degrees
atoms outside contour = 652, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.77993225 0.60392683 0.16425341 -114.77445126
-0.28380105 0.10735728 0.95285485 136.72148656
0.55782054 -0.78977713 0.25512633 200.71395900
Axis -0.87353298 -0.19728427 -0.44499331
Axis point 0.00000000 200.31687934 47.49137499
Rotation angle (degrees) 85.91663252
Shift along axis -16.03009948
> fitmap #11 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.8979, steps = 112
shifted from previous position = 5.5
rotated from previous position = 17.2 degrees
atoms outside contour = 194, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.82961822 0.55223625 0.08227903 -93.63177271
-0.34046443 0.38357144 0.85846254 92.81185108
0.44251405 -0.74020888 0.50623436 165.29728213
Axis -0.85667828 -0.19303874 -0.47837053
Axis point 0.00000000 190.71874068 32.60633336
Rotation angle (degrees) 68.91750337
Shift along axis -16.77732454
> select subtract #11
Nothing selected
> show #12 models
> select add #12
916 atoms, 939 bonds, 119 residues, 1 model selected
> fitmap #12 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2596, steps = 48
shifted from previous position = 0.00436
rotated from previous position = 0.0123 degrees
atoms outside contour = 641, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.55577571 0.82427167 0.10812329 176.44318825
-0.83130223 -0.55215219 -0.06376227 620.37186749
0.00714310 -0.12532059 0.99209107 26.52116710
Axis -0.03708796 0.06083904 -0.99745832
Axis point 253.30712842 263.83276302 0.00000000
Rotation angle (degrees) 123.91194882
Shift along axis 4.74515368
> fitmap #12 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2346, steps = 68
shifted from previous position = 1.01
rotated from previous position = 6.95 degrees
atoms outside contour = 639, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.56887306 0.82017144 0.06085493 188.12358980
-0.81926558 -0.57161419 0.04541140 603.05451280
0.07203067 -0.02402301 0.99711356 -12.86978162
Axis -0.04231368 -0.00681055 -0.99908116
Axis point 251.88763755 252.41387411 0.00000000
Rotation angle (degrees) 124.86792273
Shift along axis 0.79062377
> fitmap #12 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2349, steps = 64
shifted from previous position = 0.0263
rotated from previous position = 0.0642 degrees
atoms outside contour = 639, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.56807914 0.82076030 0.06032985 187.91744703
-0.81984365 -0.57078368 0.04542528 602.98829067
0.07171855 -0.02365587 0.99714484 -12.91170541
Axis -0.04206885 -0.00693546 -0.99909064
Axis point 251.95885396 252.37546456 0.00000000
Rotation angle (degrees) 124.81013188
Shift along axis 0.81248974
> fitmap #12 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2185, steps = 88
shifted from previous position = 1.46
rotated from previous position = 9.47 degrees
atoms outside contour = 652, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.64627016 0.76175316 -0.04547614 236.60933338
-0.76100375 -0.64776546 -0.03569703 621.23722417
-0.05665014 0.01153759 0.99832791 5.43152141
Axis 0.03100340 0.00733428 -0.99949237
Axis point 262.04272086 255.96757481 0.00000000
Rotation angle (degrees) 130.37996791
Shift along axis 6.46325827
> fitmap #12 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2184, steps = 68
shifted from previous position = 1.96
rotated from previous position = 0.0374 degrees
atoms outside contour = 652, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.64606129 0.76189658 -0.04603786 236.26453057
-0.76116584 -0.64758626 -0.03549189 623.11707003
-0.05685458 0.01211252 0.99830948 5.53464335
Axis 0.03123967 0.00709831 -0.99948672
Axis point 262.35467090 256.96823701 0.00000000
Rotation angle (degrees) 130.36606813
Shift along axis 6.27209997
> fitmap #12 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2184, steps = 44
shifted from previous position = 0.0134
rotated from previous position = 0.0392 degrees
atoms outside contour = 650, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.64623016 0.76179266 -0.04538279 236.20064656
-0.76105272 -0.64771807 -0.03551241 623.13094560
-0.05644829 0.01158951 0.99833874 5.56022927
Axis 0.03091461 0.00726267 -0.99949564
Axis point 262.29021478 257.00326665 0.00000000
Rotation angle (degrees) 130.37627413
Shift along axis 6.27021889
> fitmap #12 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.8971, steps = 148
shifted from previous position = 5.85
rotated from previous position = 37.6 degrees
atoms outside contour = 195, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.41030438 0.77117643 0.48676306 90.97958730
-0.77392159 -0.57679226 0.26145194 554.90122547
0.48238653 -0.26944142 0.83349000 -16.39767202
Axis -0.32495047 0.00267880 -0.94572724
Axis point 200.30167341 253.62712709 0.00000000
Rotation angle (degrees) 125.22600210
Shift along axis -12.56966684
> fitmap #12 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.8973, steps = 28
shifted from previous position = 0.0112
rotated from previous position = 0.012 degrees
atoms outside contour = 195, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.41029989 0.77126919 0.48661984 90.99004101
-0.77390188 -0.57675207 0.26159890 554.85520770
0.48242197 -0.26926187 0.83352751 -16.45581830
Axis -0.32491898 0.00256936 -0.94573837
Axis point 200.31117746 253.60138303 0.00000000
Rotation angle (degrees) 125.22311993
Shift along axis -12.57587204
> select subtract #12
Nothing selected
> show #13 models
> select add #13
916 atoms, 939 bonds, 119 residues, 1 model selected
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2861, steps = 68
shifted from previous position = 1.59
rotated from previous position = 5.97 degrees
atoms outside contour = 613, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.79955061 0.23257612 -0.55374022 523.81371174
-0.31224325 -0.94855378 0.05244935 556.75606091
-0.51305364 0.21483746 0.83103659 118.25429611
Axis 0.28491184 -0.07138508 -0.95589195
Axis point 321.88587447 234.01802111 0.00000000
Rotation angle (degrees) 163.44237717
Shift along axis -3.54168163
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2862, steps = 60
shifted from previous position = 0.0126
rotated from previous position = 0.0302 degrees
atoms outside contour = 612, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.79933710 0.23233313 -0.55415032 523.88743530
-0.31216901 -0.94857031 0.05259215 556.70775051
-0.51343136 0.21502732 0.83075416 118.36242823
Axis 0.28513823 -0.07147794 -0.95581750
Axis point 321.93153364 233.99590644 0.00000000
Rotation angle (degrees) 163.45096947
Shift along axis -3.54486629
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2689, steps = 100
shifted from previous position = 2.45
rotated from previous position = 17.9 degrees
atoms outside contour = 599, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.70187618 0.48502382 -0.52165389 445.02921791
-0.58467731 -0.81059527 0.03299708 597.28141154
-0.40684558 0.32815891 0.85251944 66.43499514
Axis 0.26457690 -0.10291177 -0.95885777
Axis point 326.49411455 224.02787796 0.00000000
Rotation angle (degrees) 146.09624519
Shift along axis -7.42454616
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2689, steps = 44
shifted from previous position = 0.00213
rotated from previous position = 0.0163 degrees
atoms outside contour = 599, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.70194759 0.48494760 -0.52162867 445.05847466
-0.58449707 -0.81073214 0.03282735 597.29322090
-0.40698136 0.32793335 0.85254142 66.50805327
Axis 0.26459262 -0.10279300 -0.95886618
Axis point 326.49231166 224.05182149 0.00000000
Rotation angle (degrees) 146.10581414
Shift along axis -7.41069756
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2965, steps = 164
shifted from previous position = 3.45
rotated from previous position = 15.7 degrees
atoms outside contour = 587, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.57196065 0.70353986 -0.42177450 349.54136786
-0.75163040 -0.65542097 -0.07400108 624.23998199
-0.32850237 0.27469270 0.90367643 48.87798748
Axis 0.23257586 -0.06221174 -0.97058651
Axis point 325.61372949 229.05905532 0.00000000
Rotation angle (degrees) 131.44129682
Shift along axis -4.98048258
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2965, steps = 48
shifted from previous position = 0.0168
rotated from previous position = 0.0568 degrees
atoms outside contour = 587, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.57131347 0.70419733 -0.42155438 349.19961869
-0.75225900 -0.65468441 -0.07413357 624.27293701
-0.32818956 0.27476445 0.90376828 48.76787111
Axis 0.23251024 -0.06221955 -0.97060173
Axis point 325.62357233 229.05261812 0.00000000
Rotation angle (degrees) 131.38493050
Shift along axis -4.98367454
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2966, steps = 108
shifted from previous position = 2.08
rotated from previous position = 5.81 degrees
atoms outside contour = 587, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.49124101 0.76464379 -0.41713691 315.14022696
-0.80994202 -0.57718211 -0.10419118 629.02332647
-0.32043291 0.28667361 0.90285213 44.35142049
Axis 0.24049473 -0.05950089 -0.96882503
Axis point 329.67330988 229.35409368 0.00000000
Rotation angle (degrees) 125.64668245
Shift along axis -4.60665020
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2966, steps = 44
shifted from previous position = 0.0142
rotated from previous position = 0.00258 degrees
atoms outside contour = 590, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.49127369 0.76463950 -0.41710628 315.14730600
-0.80992996 -0.57720127 -0.10417877 629.02101384
-0.32041329 0.28664645 0.90286772 44.36318836
Axis 0.24047423 -0.05949507 -0.96883047
Axis point 329.67149467 229.35283540 0.00000000
Rotation angle (degrees) 125.64796094
Shift along axis -4.61924946
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3019, steps = 56
shifted from previous position = 1.95
rotated from previous position = 5.48 degrees
atoms outside contour = 582, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.51988525 0.72238227 -0.45594324 336.75035416
-0.80593376 -0.59171630 -0.01853806 616.99389912
-0.28318045 0.35782222 0.88981632 21.27013103
Axis 0.23768703 -0.10910683 -0.96519458
Axis point 327.86332992 221.08600492 0.00000000
Rotation angle (degrees) 127.65405596
Shift along axis -7.80687000
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3018, steps = 40
shifted from previous position = 0.0173
rotated from previous position = 0.0281 degrees
atoms outside contour = 583, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.52008340 0.72246108 -0.45559225 336.71290721
-0.80595407 -0.59169755 -0.01825126 616.93407107
-0.28275848 0.35769409 0.89000201 21.15838141
Axis 0.23742426 -0.10915132 -0.96525422
Axis point 327.80325443 221.07623631 0.00000000
Rotation angle (degrees) 127.65382852
Shift along axis -7.81857227
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2873, steps = 88
shifted from previous position = 0.979
rotated from previous position = 5.38 degrees
atoms outside contour = 592, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.56766144 0.67523487 -0.47097709 359.85263561
-0.78681995 -0.61330896 0.06904738 601.26383171
-0.24223113 0.40976951 0.87943961 2.88145253
Axis 0.22437205 -0.15063360 -0.96279110
Axis point 323.42996620 213.77449517 0.00000000
Rotation angle (degrees) 130.59931604
Shift along axis -12.60389573
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2872, steps = 40
shifted from previous position = 0.0152
rotated from previous position = 0.0164 degrees
atoms outside contour = 591, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.56786574 0.67519386 -0.47078956 359.88733698
-0.78672070 -0.61342014 0.06919057 601.24376874
-0.24207460 0.40967066 0.87952876 2.86017869
Axis 0.22424130 -0.15063243 -0.96282174
Axis point 323.40664094 213.77719463 0.00000000
Rotation angle (degrees) 130.60785607
Shift along axis -12.61904347
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3019, steps = 64
shifted from previous position = 1.79
rotated from previous position = 6.73 degrees
atoms outside contour = 584, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.51558102 0.75411462 -0.40680267 319.59795508
-0.82721070 -0.56185082 0.00686871 609.65609124
-0.22338248 0.34005274 0.91349077 6.20572540
Axis 0.20485722 -0.11277537 -0.97227323
Axis point 321.34011376 219.47660410 0.00000000
Rotation angle (degrees) 125.58924330
Shift along axis -9.31590051
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2581, steps = 80
shifted from previous position = 1.73
rotated from previous position = 6.91 degrees
atoms outside contour = 624, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.47585581 0.71668274 -0.50983149 333.75061734
-0.82453255 -0.56526210 -0.02501807 613.92890758
-0.30611826 0.40846747 0.85991100 21.30468930
Axis 0.26859091 -0.12622225 -0.95494862
Axis point 332.67617265 216.31682112 0.00000000
Rotation angle (degrees) 126.19982646
Shift along axis -8.19399153
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3019, steps = 68
shifted from previous position = 2.22
rotated from previous position = 7.96 degrees
atoms outside contour = 584, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.44698915 0.66496422 -0.59835134 350.12803253
-0.84938440 -0.52533479 0.05070058 599.12834315
-0.28062055 0.53089266 0.79962873 -0.56124270
Axis 0.29639290 -0.19611559 -0.93471382
Axis point 337.92324800 202.91506714 0.00000000
Rotation angle (degrees) 125.89823350
Shift along axis -13.19834312
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3019, steps = 44
shifted from previous position = 0.00306
rotated from previous position = 0.00794 degrees
atoms outside contour = 583, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.44696298 0.66501661 -0.59831266 350.10285241
-0.84943928 -0.52523959 0.05076751 599.10840555
-0.28049610 0.53092123 0.79965342 -0.60115561
Axis 0.29634988 -0.19615573 -0.93471904
Axis point 337.91569334 202.90567449 0.00000000
Rotation angle (degrees) 125.89306766
Shift along axis -13.20369474
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2537, steps = 76
shifted from previous position = 1.15
rotated from previous position = 7.9 degrees
atoms outside contour = 614, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.39017534 0.72536414 -0.56710767 318.61671648
-0.84962873 -0.52099500 -0.08183090 618.93653640
-0.35481726 0.44990236 0.81956914 30.33272626
Axis 0.31729525 -0.12667769 -0.93982790
Axis point 342.70639138 215.00834678 0.00000000
Rotation angle (degrees) 123.07937575
Shift along axis -5.81742023
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2537, steps = 76
shifted from previous position = 1.51
rotated from previous position = 0.00623 degrees
atoms outside contour = 614, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.39018793 0.72530156 -0.56717905 317.25978315
-0.84962777 -0.52100755 -0.08176095 619.32792156
-0.35480572 0.44998872 0.81952673 30.77310059
Axis 0.31731337 -0.12673049 -0.93981466
Axis point 342.17569964 215.48364872 0.00000000
Rotation angle (degrees) 123.08168569
Shift along axis -6.73797184
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2536, steps = 56
shifted from previous position = 1.46
rotated from previous position = 0.0376 degrees
atoms outside contour = 618, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.39036355 0.72541696 -0.56691056 318.31482541
-0.84940282 -0.52130802 -0.08218192 619.97550560
-0.35515098 0.44945438 0.81967038 31.73021740
Axis 0.31728674 -0.12638058 -0.93987078
Axis point 342.98249228 215.43188624 0.00000000
Rotation angle (degrees) 123.09305242
Shift along axis -7.17809588
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.187, steps = 72
shifted from previous position = 1.61
rotated from previous position = 4.39 degrees
atoms outside contour = 707, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.36635919 0.68648483 -0.62810871 329.37452247
-0.84513165 -0.52791276 -0.08403381 620.69840132
-0.38927432 0.50004776 0.77357530 35.88571634
Axis 0.35259659 -0.14417882 -0.92460160
Axis point 349.43140284 212.34251745 0.00000000
Rotation angle (degrees) 124.07987486
Shift along axis -6.53522129
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2612, steps = 80
shifted from previous position = 2.65
rotated from previous position = 9.05 degrees
atoms outside contour = 612, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.44511758 0.57356211 -0.68767571 380.91560577
-0.77023099 -0.63692793 -0.03268166 617.10468707
-0.45674458 0.51512172 0.72528271 59.29366062
Axis 0.37280224 -0.15715792 -0.91450526
Axis point 349.89316294 211.46948998 0.00000000
Rotation angle (degrees) 132.71726979
Shift along axis -9.20106471
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.315, steps = 184
shifted from previous position = 3.94
rotated from previous position = 24.2 degrees
atoms outside contour = 574, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.25947620 0.82338358 -0.50469062 257.52899667
-0.77682435 -0.48843053 -0.39746775 647.72516288
-0.57377442 0.28892241 0.76636006 122.94273860
Axis 0.39389407 0.03964465 -0.91830048
Axis point 361.07522580 246.34648475 0.00000000
Rotation angle (degrees) 119.39140985
Shift along axis 14.21960669
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.9067, steps = 72
shifted from previous position = 1.76
rotated from previous position = 15.7 degrees
atoms outside contour = 196, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.18197226 0.86802725 -0.46196952 224.80220563
-0.91765997 -0.31869561 -0.23734860 619.84782590
-0.35325251 0.38073990 0.85454712 37.74283951
Axis 0.32655448 -0.05743842 -0.94343150
Axis point 353.96051752 223.82647476 0.00000000
Rotation angle (degrees) 108.84809571
Shift along axis 2.19930212
> fitmap #13 inMap #6.1
Fit molecule copy of Stopper_45_1-coot-4.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.9068, steps = 24
shifted from previous position = 0.00467
rotated from previous position = 0.0349 degrees
atoms outside contour = 196, contour level = 0.3
Position of copy of Stopper_45_1-coot-4.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.18194957 0.86786161 -0.46228954 224.88481809
-0.91746703 -0.31897603 -0.23771752 619.92402491
-0.35376500 0.38088264 0.85427147 37.88054436
Axis 0.32685626 -0.05734225 -0.94333284
Axis point 354.01631458 223.85050587 0.00000000
Rotation angle (degrees) 108.86424263
Shift along axis 2.22320815
> select subtract #13
Nothing selected
> color #10 #1f93ffff
> combine #10-15
Remapping chain ID 'A' in copy of Stopper_45_1-coot-4.pdb #11 to 'B'
Remapping chain ID 'A' in copy of Stopper_45_1-coot-4.pdb #12 to 'C'
Remapping chain ID 'A' in copy of Stopper_45_1-coot-4.pdb #13 to 'D'
Remapping chain ID 'A' in copy of Stopper_45_1-coot-4.pdb #14 to 'E'
Remapping chain ID 'A' in copy of Stopper_45_1-coot-4.pdb #15 to 'F'
> fitmap #16 inMap #6.1
Fit molecule combination (#16) to map P2_J357_007_volume_map_sharp_C6.mrc 0
(#6.1) using 5496 atoms
average map value = 0.9004, steps = 28
shifted from previous position = 0.0147
rotated from previous position = 0.0171 degrees
atoms outside contour = 1169, contour level = 0.3
Position of combination (#16) relative to P2_J357_007_volume_map_sharp_C6.mrc
0 (#6.1) coordinates:
Matrix rotation and translation
0.99998788 -0.00125529 0.00476133 -0.69348135
0.00148558 0.99881351 -0.04867616 12.39215446
-0.00469458 0.04868264 0.99880326 -11.65546553
Axis 0.99492604 0.09663152 0.02800939
Axis point 0.00000000 245.62371345 248.23712575
Rotation angle (degrees) 2.80446783
Shift along axis 0.18104758
> select add #16
5496 atoms, 5634 bonds, 714 residues, 1 model selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper/Stopper_45_1-coot-4_6mer.pdb" models #16 selectedOnly true
> relModel #2
> select subtract #16
Nothing selected
> hide #16 models
> close #16
> hide #11 models
> hide #10 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitting_3.cxs"
> includeMaps true
> show #15 models
> hide #15 models
> show #1 models
> hide #1 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/00-Portal-12mers-Adaptor-12mers.pdb"
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb #16
---
Chain | Description
A B C D E F G H I J K L | No description available
M N O P Q R S T U V W X | No description available
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #16
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/P2_J332_011_C12_volume_map_sharp.mrc"
Opened P2_J332_011_C12_volume_map_sharp.mrc as #16, grid size 512,512,512,
pixel 1.06, shown at level 0.285, step 2, values float32
> surface dust #16 size 10.6
> volume #16 step 1
> volume #16 level 0.3
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/00-Portal-12mers-Adaptor-12mers.pdb"
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb #17
---
Chain | Description
A B C D E F G H I J K L | No description available
M N O P Q R S T U V W X | No description available
> select add #17
49956 atoms, 51084 bonds, 6396 residues, 1 model selected
> select add #16
49956 atoms, 51084 bonds, 6396 residues, 3 models selected
> show #!2 models
> undo
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #16,1,0,0,-10.529,0,1,0,9.7588,0,0,1,-164.46,#17,1,0,0,-10.529,0,1,0,9.7588,0,0,1,-164.46
> lighting simple
> view matrix models
> #16,1,0,0,0.81769,0,1,0,5.4558,0,0,1,-172.86,#17,1,0,0,0.81769,0,1,0,5.4558,0,0,1,-172.86
> view matrix models
> #16,1,0,0,0.4092,0,1,0,4.8852,0,0,1,-175.94,#17,1,0,0,0.4092,0,1,0,4.8852,0,0,1,-175.94
> close #17
> fitmap #16 inMap #2
Fit map P2_J332_011_C12_volume_map_sharp.mrc in map
P2_J357_007_volume_map_sharp_C6.mrc using 1068594 points
correlation = 0.3767, correlation about mean = 0.1893, overlap = 4.617e+04
steps = 264, shift = 6.8, angle = 3.71 degrees
Position of P2_J332_011_C12_volume_map_sharp.mrc (#16) relative to
P2_J357_007_volume_map_sharp_C6.mrc (#2) coordinates:
Matrix rotation and translation
0.99910115 0.04238974 -0.00003574 -11.25654070
-0.04238974 0.99910115 -0.00002842 11.77031818
0.00003451 0.00002991 1.00000000 -179.93301452
Axis 0.00068797 -0.00082861 -0.99999942
Axis point 275.36939124 274.30771579 0.00000000
Rotation angle (degrees) 2.42948256
Shift along axis 179.91541298
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/00-Portal-12mers-Adaptor-12mers.pdb"
Chain information for 00-Portal-12mers-Adaptor-12mers.pdb #17
---
Chain | Description
A B C D E F G H I J K L | No description available
M N O P Q R S T U V W X | No description available
> select add #17
49956 atoms, 51084 bonds, 6396 residues, 3 models selected
> select subtract #16
49956 atoms, 51084 bonds, 6396 residues, 1 model selected
> view matrix models #17,1,0,0,64.854,0,1,0,-45.457,0,0,1,-89.053
> view matrix models #17,1,0,0,88.466,0,1,0,-56.532,0,0,1,-82.98
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.49026,-0.75727,-0.43149,552.72,-0.86489,-0.48387,-0.13351,621.21,-0.10769,0.43865,-0.89218,345.99
> view matrix models
> #17,-0.53918,-0.84113,0.042362,725.11,-0.81419,0.53345,0.22919,229.35,-0.21537,0.08908,-0.97246,492.97
> view matrix models
> #17,-0.26026,-0.90801,0.3283,589.12,0.15964,0.29487,0.94211,-165.68,-0.95225,0.2976,0.068217,350.16
> view matrix models
> #17,-0.55721,-0.82944,-0.039365,749.26,-0.82987,0.55789,-0.0083718,292.18,0.028906,0.028003,-0.99919,450.68
> hide sel atoms
> show sel cartoons
> view matrix models
> #17,0.046573,-0.98226,0.18166,566.62,0.58186,0.1745,0.79435,-206.06,-0.81195,0.068706,0.57967,235.17
> view matrix models
> #17,0.27401,-0.96162,-0.014424,552.93,0.92037,0.25785,0.29401,-183.74,-0.279,-0.093836,0.9557,31.957
> view matrix models
> #17,0.39956,-0.89752,-0.18657,548.42,0.90596,0.41769,-0.069133,-124.16,0.13998,-0.1414,0.98001,-75.451
> view matrix models
> #17,0.41213,-0.90664,0.090266,471.64,0.89767,0.38708,-0.21063,-74.729,0.15602,0.16783,0.97339,-162.85
> view matrix models
> #17,0.99946,0.0098899,0.031237,76.797,-0.0079136,0.998,-0.06277,-36.925,-0.031796,0.062489,0.99754,-89.549
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.99946,0.0098899,0.031237,-31.427,-0.0079136,0.998,-0.06277,-8.9214,-0.031796,0.062489,0.99754,-182.81
> view matrix models
> #17,0.99946,0.0098899,0.031237,-24.064,-0.0079136,0.998,-0.06277,33.661,-0.031796,0.062489,0.99754,-190.06
> view matrix models
> #17,0.99946,0.0098899,0.031237,-13.706,-0.0079136,0.998,-0.06277,33.836,-0.031796,0.062489,0.99754,-190.33
> fitmap #17 inMap #16
Fit molecule 00-Portal-12mers-Adaptor-12mers.pdb (#17) to map
P2_J332_011_C12_volume_map_sharp.mrc (#16) using 49956 atoms
average map value = 0.212, steps = 100
shifted from previous position = 6.55
rotated from previous position = 1.89 degrees
atoms outside contour = 34961, contour level = 0.3
Position of 00-Portal-12mers-Adaptor-12mers.pdb (#17) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.99973338 -0.02308991 -0.00012003 6.38086701
0.02308987 0.99973335 -0.00029470 -6.10856515
0.00012681 0.00029185 0.99999995 -4.93296022
Axis 0.01270026 -0.00534466 0.99990506
Axis point 268.85761946 275.89483150 0.00000000
Rotation angle (degrees) 1.32319634
Shift along axis -4.81880505
> view matrix models
> #17,0.99982,0.018717,0.0024108,-7.7246,-0.018574,0.99859,-0.049651,27.306,-0.0033367,0.049598,0.99876,-194.51
> view matrix models
> #17,0.99328,0.11557,-0.0068733,-29.978,-0.11577,0.99205,-0.049393,55.43,0.0011104,0.049856,0.99876,-195.78
> fitmap #17 inMap #16
Fit molecule 00-Portal-12mers-Adaptor-12mers.pdb (#17) to map
P2_J332_011_C12_volume_map_sharp.mrc (#16) using 49956 atoms
average map value = 1.039, steps = 68
shifted from previous position = 3.05
rotated from previous position = 4.27 degrees
atoms outside contour = 4441, contour level = 0.3
Position of 00-Portal-12mers-Adaptor-12mers.pdb (#17) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.99999998 0.00000693 -0.00021674 0.04736051
-0.00000692 1.00000000 0.00002539 -0.00252614
0.00021674 -0.00002539 0.99999998 -0.05672475
Axis -0.11629170 -0.99270833 -0.03172409
Axis point 261.92265071 0.00000000 217.84495557
Rotation angle (degrees) 0.01250926
Shift along axis -0.00120038
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper/Stopper_45_1-coot-4_6mer.pdb"
Chain information for Stopper_45_1-coot-4_6mer.pdb #18
---
Chain | Description
A B C D E F | No description available
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Terminator/Terminator_1-coot-1_6mer.pdb"
Chain information for Terminator_1-coot-1_6mer.pdb #19
---
Chain | Description
D E F G H I | No description available
> hide #!16 models
> select subtract #17
Nothing selected
> select add #18
5496 atoms, 5634 bonds, 714 residues, 1 model selected
> select add #19
12792 atoms, 13086 bonds, 1614 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> color #18 #9c86b8ff
> select subtract #19
5496 atoms, 5634 bonds, 714 residues, 1 model selected
> color sel magenta
> select subtract #18
Nothing selected
> select add #19
7296 atoms, 7452 bonds, 900 residues, 1 model selected
> color sel orange
> hide #!6 models
> hide #!9 models
> hide #!2 models
> select subtract #19
Nothing selected
> lighting flat
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A #5/B #5/C #5/D #5/E #5/F #19/D #19/E #19/F #19/G #19/H
> #19/I
Alignment identifier is 1
> select #5/A-F:1 #19/D-I:1
96 atoms, 84 bonds, 12 residues, 2 models selected
> select #5/A-F:1-18 #19/D-I:1-18
1704 atoms, 1764 bonds, 216 residues, 2 models selected
. [ID: 1] region 12 chains [1-18] RMSD: 15.925
> select #5/A-F:1-25 #19/D-I:1-25
2340 atoms, 2412 bonds, 300 residues, 2 models selected
. [ID: 1] region 12 chains [1-18] + 1 other block RMSD: 15.030
> select #5/A-F:1 #19/D-I:1
96 atoms, 84 bonds, 12 residues, 2 models selected
> select #5/A-F:1-23 #19/D-I:1-23
2208 atoms, 2268 bonds, 276 residues, 2 models selected
. [ID: 1] region 12 chains [1-23] RMSD: 15.244
> hide sel & #19 cartoons
> set bgColor white
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted Models/Crude
> Assembly Connector.png" width 854 height 742 supersample 3
> transparentBackground true
> select #17/J:289
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
114 atoms, 114 bonds, 14 residues, 1 model selected
> select up
2604 atoms, 2666 bonds, 333 residues, 1 model selected
> select up
49956 atoms, 51084 bonds, 6396 residues, 1 model selected
> select down
2604 atoms, 2666 bonds, 333 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A #4/B #4/C #4/D #4/E #4/F #4/G #4/H #4/I #4/J #4/K #4/L
> #17/A #17/B #17/C #17/D #17/E #17/F #17/G #17/H #17/I #17/J #17/K #17/L
Alignment identifier is 2
> select #4/A-L:121-122 #17/A-L:121-122
312 atoms, 288 bonds, 48 residues, 2 models selected
> select #4/A-L:121-160 #17/A-L:121-160
7968 atoms, 8304 bonds, 960 residues, 2 models selected
2 [ID: 2] region 24 chains [46-85] RMSD: 3.964
> select #4/A-L:76 #17/A-L:76
168 atoms, 144 bonds, 24 residues, 2 models selected
> select #4/A-L #17/A-L
62496 atoms, 63984 bonds, 7992 residues, 2 models selected
2 [ID: 2] region 24 chains [1-333] RMSD: 3.968
> color (#17 & sel) yellow
> select add #17
81204 atoms, 83076 bonds, 10392 residues, 2 models selected
> select subtract #17
31248 atoms, 31992 bonds, 3996 residues, 1 model selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted Models/Crude
> Assembly Connector.png" width 854 height 742 supersample 3
> transparentBackground true
> lighting simple
> lighting soft
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted Models/Crude
> Assembly Connector.png" width 854 height 742 supersample 3
> transparentBackground true
> show #17-19 atoms
> select add #19
38544 atoms, 39444 bonds, 4896 residues, 2 models selected
> view matrix models
> #4,0.99899,0.044753,0.0026867,-13.168,-0.044566,0.99779,-0.049341,34.314,-0.0048889,0.049172,0.99878,-194.87,#19,1,0,0,-0.11306,0,1,0,-0.049992,0,0,1,0.50135
> undo
> view matrix models
> #4,0.99594,0.03932,-0.080998,21.367,-0.046195,0.99532,-0.084824,49.092,0.077284,0.088221,0.9931,-226.03,#19,0.99648,-0.0011553,-0.083835,18.037,-0.0018325,0.99937,-0.035552,7.7803,0.083823,0.035581,0.99585,-31.601
> view matrix models
> #4,0.99861,0.04299,-0.030566,0.29124,-0.044862,0.99698,-0.063444,40.077,0.027746,0.064727,0.99752,-207.94,#19,0.99945,-0.00010077,-0.033296,6.8372,-0.00036973,0.9999,-0.014124,2.9524,0.033295,0.014129,0.99935,-12.75
> view matrix models
> #4,0.99953,0.030577,-0.0012878,-7.863,-0.03051,0.99228,-0.12019,59.223,-0.0023971,0.12017,0.99275,-212.83,#19,0.99989,-0.013972,-0.0046693,4.7584,0.013605,0.99738,-0.071097,11.236,0.0056504,0.071026,0.99746,-20.318
> view matrix models
> #4,0.99949,0.030258,-0.010404,-4.2653,-0.031322,0.99168,-0.12489,61.413,0.0065383,0.12515,0.99212,-216.35,#19,0.99981,-0.013839,-0.01379,6.5685,0.012754,0.99704,-0.075822,12.504,0.014798,0.075631,0.99703,-23.967
> view matrix models
> #4,0.99922,0.039519,-0.0026339,-9.6648,-0.039498,0.98931,-0.1404,70.228,-0.0029428,0.14039,0.99009,-217.1,#19,0.99997,-0.0049692,-0.0055725,2.4718,0.0044392,0.99581,-0.091389,18.211,0.0060033,0.091361,0.9958,-25.606
> select subtract #19
31248 atoms, 31992 bonds, 3996 residues, 1 model selected
> combine #17-19
Remapping chain ID 'A' in Stopper_45_1-coot-4_6mer.pdb #18 to 'Y'
Remapping chain ID 'B' in Stopper_45_1-coot-4_6mer.pdb #18 to 'Z'
Remapping chain ID 'C' in Stopper_45_1-coot-4_6mer.pdb #18 to 'a'
Remapping chain ID 'D' in Stopper_45_1-coot-4_6mer.pdb #18 to 'b'
Remapping chain ID 'E' in Stopper_45_1-coot-4_6mer.pdb #18 to 'c'
Remapping chain ID 'F' in Stopper_45_1-coot-4_6mer.pdb #18 to 'd'
Remapping chain ID 'D' in Terminator_1-coot-1_6mer.pdb #19 to 'e'
Remapping chain ID 'E' in Terminator_1-coot-1_6mer.pdb #19 to 'f'
Remapping chain ID 'F' in Terminator_1-coot-1_6mer.pdb #19 to 'g'
Remapping chain ID 'G' in Terminator_1-coot-1_6mer.pdb #19 to 'h'
Remapping chain ID 'H' in Terminator_1-coot-1_6mer.pdb #19 to 'i'
Remapping chain ID 'I' in Terminator_1-coot-1_6mer.pdb #19 to 'j'
> hide #17 models
> hide #18 models
> hide #19 models
> show #17 models
> hide #17 models
> show #!16 models
> show #17 models
> hide #17 models
> close #20
> show #17 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/M #4/N #4/O #4/P #4/Q #4/R #4/S #4/T #4/U #4/V #4/W #4/X
> #17/M #17/N #17/O #17/P #17/Q #17/R #17/S #17/T #17/U #17/V #17/W #17/X
Alignment identifier is 2
> select #4/M-X:2 #17/M-X:2
120 atoms, 96 bonds, 24 residues, 2 models selected
> select #4/M-X #17/M-X
37416 atoms, 38184 bonds, 4800 residues, 2 models selected
2 [ID: 2] region 24 chains [1-200] RMSD: 6.939
> view matrix models
> #4,0.99922,0.039519,-0.0026339,-9.3509,-0.039498,0.98931,-0.1404,70.526,-0.0029428,0.14039,0.99009,-219.81,#17,0.99912,0.041803,0.0023275,-11.862,-0.041638,0.99791,-0.049328,33.639,-0.0043848,0.049188,0.99878,-194.25
> view matrix models
> #4,0.99922,0.039519,-0.0026339,-9.1616,-0.039498,0.98931,-0.1404,70.562,-0.0029428,0.14039,0.99009,-215.36,#17,0.99912,0.041803,0.0023275,-11.673,-0.041638,0.99791,-0.049328,33.675,-0.0043848,0.049188,0.99878,-189.8
> undo
> view matrix models
> #4,0.99922,0.039273,-0.0047101,-8.7077,-0.039544,0.98908,-0.14194,71.027,-0.00091587,0.14202,0.98986,-220.72,#17,0.99913,0.041748,0.0002375,-11.274,-0.041682,0.99783,-0.050886,34.1,-0.0023614,0.050832,0.9987,-195.23
> fitmap #17 inMap #16
Fit molecule 00-Portal-12mers-Adaptor-12mers.pdb (#17) to map
P2_J332_011_C12_volume_map_sharp.mrc (#16) using 49956 atoms
average map value = 1.039, steps = 60
shifted from previous position = 2.76
rotated from previous position = 0.158 degrees
atoms outside contour = 4459, contour level = 0.3
Position of 00-Portal-12mers-Adaptor-12mers.pdb (#17) relative to
P2_J332_011_C12_volume_map_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.99999999 0.00005616 -0.00007541 -0.00047963
-0.00005615 1.00000000 0.00008096 -0.00822730
0.00007541 -0.00008096 0.99999999 0.01567949
Axis -0.65252392 -0.60777924 -0.45256704
Axis point 0.00000000 183.69746377 115.01065299
Rotation angle (degrees) 0.00710893
Shift along axis -0.00178267
> select add #17
68664 atoms, 70176 bonds, 8796 residues, 2 models selected
> select subtract #17
18708 atoms, 19092 bonds, 2400 residues, 1 model selected
> show #18 models
> show #19 models
> ui tool show "Color Zone"
> combine #17-19
Remapping chain ID 'A' in Stopper_45_1-coot-4_6mer.pdb #18 to 'Y'
Remapping chain ID 'B' in Stopper_45_1-coot-4_6mer.pdb #18 to 'Z'
Remapping chain ID 'C' in Stopper_45_1-coot-4_6mer.pdb #18 to 'a'
Remapping chain ID 'D' in Stopper_45_1-coot-4_6mer.pdb #18 to 'b'
Remapping chain ID 'E' in Stopper_45_1-coot-4_6mer.pdb #18 to 'c'
Remapping chain ID 'F' in Stopper_45_1-coot-4_6mer.pdb #18 to 'd'
Remapping chain ID 'D' in Terminator_1-coot-1_6mer.pdb #19 to 'e'
Remapping chain ID 'E' in Terminator_1-coot-1_6mer.pdb #19 to 'f'
Remapping chain ID 'F' in Terminator_1-coot-1_6mer.pdb #19 to 'g'
Remapping chain ID 'G' in Terminator_1-coot-1_6mer.pdb #19 to 'h'
Remapping chain ID 'H' in Terminator_1-coot-1_6mer.pdb #19 to 'i'
Remapping chain ID 'I' in Terminator_1-coot-1_6mer.pdb #19 to 'j'
> color zone #16 near #20 distance 6.37
> hide #17 models
> hide #18 models
> hide #19 models
> hide #20 models
> volume splitbyzone #16
Opened P2_J332_011_C12_volume_map_sharp.mrc 0 as #21.1, grid size 512,512,512,
pixel 1.06, shown at level 0.3, step 1, values float32
Opened P2_J332_011_C12_volume_map_sharp.mrc 1 as #21.2, grid size 512,512,512,
pixel 1.06, shown at level 0.3, step 1, values float32
Opened P2_J332_011_C12_volume_map_sharp.mrc 2 as #21.3, grid size 512,512,512,
pixel 1.06, shown at level 0.3, step 1, values float32
Opened P2_J332_011_C12_volume_map_sharp.mrc 3 as #21.4, grid size 512,512,512,
pixel 1.06, shown at level 0.3, step 1, values float32
Opened P2_J332_011_C12_volume_map_sharp.mrc 4 as #21.5, grid size 512,512,512,
pixel 1.06, shown at level 0.3, step 1, values float32
> surface dust #21.1 size 10.6
> surface dust #21.2 size 10.6
> surface dust #21.3 size 10.6
> surface dust #21.4 size 10.6
> surface dust #21.5 size 10.6
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted Models/Crude
> Assembly Connector_Map.png" width 854 height 819 supersample 3
> transparentBackground true
> close #21.1
> close #21.2
> close #21.3
> close #21.4
> close #21.5
> close #16
> close #21
> close #17-20
> show #1 models
> close #1
> select down
18708 atoms, 19092 bonds, 2400 residues, 1 model selected
> close #7
> show #4 models
> select add #4
49956 atoms, 51084 bonds, 6396 residues, 1 model selected
> select subtract #4
Nothing selected
> show #!3.2 models
> hide #4 models
> close #3
> show #!5 models
> hide #!5 models
> show #!5 models
> close #5
> show #!6 models
> show #!6.1 models
> hide #!6 models
> show #4 models
> close #4
> close #8
> show #!9 models
> show #!9.1 models
> hide #!9 models
> hide #!9.1 models
> show #!6.2 models
> close #6
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitting_4.cxs"
> includeMaps true
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16U0000PTA/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1 (23B74)
Kernel Version: Darwin 23.1.0
Time since boot: 1 day, 2 hours, 35 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403220040
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 10 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class |
comment:2 by , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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