![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Last modified 12 months ago
#16539 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 1353,
"osVersion" : {
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"build" : "23B74",
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"captureTime" : "2024-12-27 14:21:51.7292 +0800",
"codeSigningMonitor" : 1,
"incident" : "3B0ED7B4-BC69-4022-B432-2BCE33A55210",
"pid" : 5618,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-12-27 09:03:00.2772 +0800",
"procStartAbsTime" : 609007687099,
"procExitAbsTime" : 1068160200017,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"415EFB2F-9949-5714-8659-B453457E1D4B","thirdParty":true},
"parentProc" : "launchd",
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"crashReporterKey" : "2DB44331-A26E-8CBE-0A9B-01589F89B818",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 21703,
"sleepWakeUUID" : "328A1D88-DC23-497B-A7A9-78B131037433",
"sip" : "enabled",
"vmRegionInfo" : "0x477223d is not in any region. Bytes before following region: 4261338563\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102760000-102764000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x000000000477223d","rawCodes":[1,74916413],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000477223d"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":5618},
"vmregioninfo" : "0x477223d is not in any region. Bytes before following region: 4261338563\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102760000-102764000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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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
> 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 = 44
shifted from previous position = 0.00593
rotated from previous position = 0.00158 degrees
atoms outside contour = 5079, 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
-0.86184779 -0.20744754 0.46280025 269.54484210
0.25986052 -0.96426121 0.05169967 275.32840609
0.43553533 0.16482076 0.88495375 208.72644804
Axis 0.23489711 0.05661588 0.97037003
Axis point 93.17741397 144.38368842 0.00000000
Rotation angle (degrees) 166.06691234
Shift along axis 281.44515292
> view matrix models
> #5,-0.6789,-0.60094,0.42186,270.17,0.57928,-0.79142,-0.19516,278.17,0.45115,0.11188,0.88541,208.74
> 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 = 0.2285, steps = 72
shifted from previous position = 2.83
rotated from previous position = 2.98 degrees
atoms outside contour = 5068, 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
-0.64688894 -0.63756517 0.41838440 271.12509035
0.60302050 -0.76350950 -0.23112672 280.16175904
0.46679878 0.10278106 0.87837065 210.65682837
Axis 0.25971941 -0.03765757 0.96494960
Axis point 52.50293709 182.43808619 0.00000000
Rotation angle (degrees) 139.99727452
Shift along axis 263.13946110
> view matrix models
> #5,-0.5086,-0.78441,0.355,271.89,0.71132,-0.61512,-0.34007,281.24,0.48513,0.079561,0.87082,210.75
> color single #6.1
> view matrix models
> #5,-0.66603,-0.60539,0.43577,271.15,0.57055,-0.78979,-0.22518,279.65,0.48049,0.098657,0.87143,210.77
> view matrix models
> #5,-0.23072,-0.92547,0.30045,274.76,0.85683,-0.33957,-0.38798,283.98,0.46109,0.16792,0.87132,210.77
> hide sel atoms
> show sel surfaces
> 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 = 0.2064, steps = 92
shifted from previous position = 2.63
rotated from previous position = 3.2 degrees
atoms outside contour = 5292, 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
-0.27053927 -0.92321025 0.27293118 273.07213866
0.83794118 -0.36539768 -0.40538775 282.15665118
0.47398652 0.11902696 0.87245024 209.94673637
Axis 0.28369179 -0.10876459 0.95272726
Axis point -3.19686248 224.34573591 0.00000000
Rotation angle (degrees) 112.44171112
Shift along axis 246.80165072
> 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 = 0.2064, steps = 40
shifted from previous position = 0.00692
rotated from previous position = 0.0052 degrees
atoms outside contour = 5297, 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
-0.27052944 -0.92322124 0.27290375 273.06781387
0.83790712 -0.36538624 -0.40546845 282.15753646
0.47405233 0.11897684 0.87242132 209.95217338
Axis 0.28370881 -0.10881521 0.95271641
Axis point -3.20720533 224.35050580 0.00000000
Rotation angle (degrees) 112.44194808
Shift along axis 246.79359358
> view matrix models
> #5,0.026707,-0.98737,0.15619,275.92,0.88851,-0.04815,-0.45632,283.7,0.45807,0.15096,0.876,209.89
> 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 = 0.1963, steps = 56
shifted from previous position = 1.1
rotated from previous position = 2.11 degrees
atoms outside contour = 5413, 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
0.02718220 -0.99142806 0.12779507 276.68679327
0.89853831 -0.03178953 -0.43774249 283.58282842
0.43805271 0.12672757 0.88997191 210.68315932
Axis 0.28269978 -0.15538426 0.94653926
Axis point -52.66755409 264.15549349 0.00000000
Rotation angle (degrees) 93.28586355
Shift along axis 233.57486771
> view matrix models
> #5,0.36536,-0.93084,-0.0065788,280.45,0.83791,0.33194,-0.43327,284.24,0.40549,0.15279,0.90124,210.43
> 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 = 0.204, steps = 76
shifted from previous position = 2.21
rotated from previous position = 3.58 degrees
atoms outside contour = 5381, 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
0.37987730 -0.92335842 -0.05570006 279.57310710
0.80936592 0.36092833 -0.46331169 283.40449551
0.44790645 0.13091986 0.88444325 212.32153790
Axis 0.31279398 -0.26509041 0.91207839
Axis point -152.67752638 335.54057558 0.00000000
Rotation angle (degrees) 71.78253833
Shift along axis 205.97485855
> view matrix models
> #5,0.69598,-0.6886,-0.20357,283.6,0.59494,0.71173,-0.37348,282.64,0.40207,0.13882,0.90503,211.9
> 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 = 0.1951, steps = 76
shifted from previous position = 3.29
rotated from previous position = 2.37 degrees
atoms outside contour = 5454, 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
0.67704411 -0.70505448 -0.21097276 280.85024903
0.59526748 0.69320935 -0.40634662 283.15120944
0.43274477 0.14952936 0.88902924 213.70456301
Axis 0.35775903 -0.41429342 0.83688078
Axis point -344.23595019 473.80908714 0.00000000
Rotation angle (degrees) 50.97633601
Shift along axis 162.01427229
> view matrix models
> #5,0.83735,-0.41047,-0.36106,282.86,0.2975,0.89625,-0.32897,280.47,0.45863,0.16804,0.87259,213.99
> 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 = 0.2013, steps = 84
shifted from previous position = 2.38
rotated from previous position = 4.59 degrees
atoms outside contour = 5354, 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
0.84895330 -0.44251715 -0.28888919 281.25036229
0.33577695 0.87380339 -0.35174078 281.58522318
0.40808366 0.20160915 0.89040526 215.39147688
Axis 0.46804917 -0.58953213 0.65831744
Axis point -736.57337244 773.35801332 0.00000000
Rotation angle (degrees) 36.23678869
Shift along axis 107.43142637
> 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 = 0.2013, steps = 48
shifted from previous position = 0.00089
rotated from previous position = 0.00397 degrees
atoms outside contour = 5353, 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
0.84891744 -0.44255881 -0.28893076 281.25049233
0.33580874 0.87378995 -0.35174384 281.58454266
0.40813210 0.20157599 0.89039057 215.39106164
Axis 0.46798914 -0.58956472 0.65833093
Axis point -736.44716202 773.34096837 0.00000000
Rotation angle (degrees) 36.23989064
Shift along axis 107.40846204
> view matrix models
> #5,0.84892,-0.44256,-0.28893,276.65,0.33581,0.87379,-0.35174,278.45,0.40813,0.20158,0.89039,215.52
> view matrix models
> #5,0.89284,-0.32015,-0.31676,277.5,0.21934,0.92339,-0.31503,277.35,0.39335,0.21179,0.89466,215.39
> 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 = 0.2216, steps = 84
shifted from previous position = 2.03
rotated from previous position = 2.71 degrees
atoms outside contour = 5076, 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
0.90218851 -0.31201571 -0.29782916 276.67350252
0.23143169 0.93282061 -0.27619771 275.45677762
0.36399918 0.18025529 0.91379028 215.03841020
Axis 0.47036989 -0.68200696 0.56001668
Axis point -276.24953855 0.00000000 920.66698705
Rotation angle (degrees) 29.02599687
Shift along axis 62.70054124
> view matrix models
> #5,0.86609,-0.32292,-0.38159,275.28,0.19903,0.92299,-0.32935,274.42,0.45855,0.20929,0.86367,216.02
> 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 = 0.2302, steps = 112
shifted from previous position = 1.79
rotated from previous position = 4.15 degrees
atoms outside contour = 4999, 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
0.83536176 -0.32134947 -0.44598809 276.97769827
0.17839127 0.92589719 -0.33300305 275.01292300
0.51994945 0.19861763 0.83078497 215.73876503
Axis 0.43916151 -0.79794221 0.41282611
Axis point -193.67900632 0.00000000 701.15030179
Rotation angle (degrees) 37.24811585
Shift along axis -8.74388201
> view matrix models
> #5,0.87194,-0.31269,-0.37675,278.22,0.20973,0.93386,-0.28969,275.92,0.44241,0.17358,0.87985,215.01
> view matrix models
> #5,0.88596,-0.2279,-0.4039,278.5,0.13536,0.96008,-0.24481,275.41,0.44357,0.16222,0.88144,215
> view matrix models
> #5,0.88787,-0.22739,-0.39997,278.57,0.13694,0.96054,-0.2421,275.46,0.43924,0.16018,0.88397,214.95
> view matrix models
> #5,0.87701,-0.23031,-0.42166,278.19,0.12799,0.9579,-0.257,275.17,0.4631,0.17143,0.86957,215.2
> 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 = 0.2137, steps = 88
shifted from previous position = 0.999
rotated from previous position = 1.81 degrees
atoms outside contour = 5103, 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
0.88091123 -0.20271490 -0.42767067 279.17604893
0.09660782 0.96162023 -0.25681419 275.19398071
0.46331681 0.18491417 0.86668584 215.03556861
Axis 0.42533367 -0.85791859 0.28821340
Axis point -273.01656401 0.00000000 783.87914541
Rotation angle (degrees) 31.28347901
Shift along axis -55.37492847
> view matrix models
> #5,0.87055,0.14336,-0.47074,280.09,-0.20679,0.97463,-0.085608,272.58,0.44653,0.17187,0.87811,214.85
> 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 = 0.2189, steps = 64
shifted from previous position = 2.32
rotated from previous position = 2.81 degrees
atoms outside contour = 5184, 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
0.86819724 0.12611174 -0.47992660 281.51228225
-0.21364095 0.96793504 -0.13213382 272.67927531
0.44787412 0.21725018 0.86730109 212.99487619
Axis 0.33337997 -0.88530150 -0.32418984
Axis point -92.85272933 0.00000000 762.53715408
Rotation angle (degrees) 31.60112633
Shift along axis -216.60358880
> 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 = 0.2189, steps = 48
shifted from previous position = 0.0135
rotated from previous position = 0.0221 degrees
atoms outside contour = 5186, 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
0.86838142 0.12601041 -0.47961991 281.50397368
-0.21353283 0.96793495 -0.13230912 272.67516860
0.44756852 0.21730937 0.86744401 212.98449013
Axis 0.33377306 -0.88516634 -0.32415444
Axis point -93.10031564 0.00000000 763.10639364
Rotation angle (degrees) 31.58324436
Shift along axis -216.44430575
> view matrix models
> #5,0.86838,0.12601,-0.47962,275.82,-0.21353,0.96793,-0.13231,268.42,0.44757,0.21731,0.86744,212.33
> view matrix models
> #5,0.87623,0.12768,-0.46468,276.08,-0.20619,0.97088,-0.12202,268.64,0.43556,0.20273,0.87703,212.19
> 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 = 0.2328, steps = 80
shifted from previous position = 0.939
rotated from previous position = 4.77 degrees
atoms outside contour = 4978, 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
0.88205945 0.05810053 -0.46754211 275.27467971
-0.12558239 0.98545811 -0.11446141 269.07765819
0.45409287 0.15967682 0.87652897 212.42706787
Axis 0.28003889 -0.94147264 -0.18763658
Axis point -171.46403197 0.00000000 761.45845571
Rotation angle (degrees) 29.30539257
Shift along axis -216.10072571
> 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 = 0.2327, steps = 64
shifted from previous position = 0.0235
rotated from previous position = 0.0177 degrees
atoms outside contour = 4985, 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
0.88208159 0.05786262 -0.46752983 275.26378002
-0.12546106 0.98544058 -0.11474510 269.09161802
0.45408339 0.15987133 0.87649843 212.41111279
Axis 0.28051415 -0.94140598 -0.18726078
Axis point -171.61695001 0.00000000 761.57602984
Rotation angle (degrees) 29.30691049
Shift along axis -215.88534243
> hide sel surfaces
> show sel cartoons
> select #5/D:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
208 atoms, 214 bonds, 27 residues, 2 models selected
> select up
1216 atoms, 1242 bonds, 150 residues, 2 models selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Terminator_1.pdb"
> models #5 selectedOnly true relModel #6.1.1
> hide #!5 models
> show #!5 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Terminator_1.pdb"
Summary of feedback from opening /Users/melvinshen/Desktop/Sinica /Protein
Purification/New Phage Proteins/Structure/CryoEM/cryosparc/Corndog
/Connector/Terminator_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 28 TRP A 35 1 8
Start residue of secondary structure not found: HELIX 2 2 LEU A 36 GLU A 38 1
3
Start residue of secondary structure not found: HELIX 3 3 LYS A 83 ASP A 85 1
3
Start residue of secondary structure not found: HELIX 4 4 GLU A 87 LEU A 108 1
22
Start residue of secondary structure not found: HELIX 5 5 ALA B 28 GLY B 37 1
10
44 messages similar to the above omitted
Chain information for Terminator_1.pdb #14
---
Chain | Description
D | No description available
> hide #!5 models
> fitmap #14 inMap #6.1
Fit molecule Terminator_1.pdb (#14) to map P2_J357_007_volume_map_sharp_C6.mrc
0 (#6.1) using 1216 atoms
average map value = 0.2799, steps = 140
shifted from previous position = 3.1
rotated from previous position = 8.3 degrees
atoms outside contour = 785, contour level = 0.3
Position of Terminator_1.pdb (#14) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99255496 -0.11767376 0.03142502 24.59341301
0.11976623 0.98988095 -0.07610362 -12.10150393
-0.02215163 0.07930068 0.99660459 -12.63875860
Axis 0.53812525 0.18552224 0.82219384
Axis point 118.76094476 198.74932954 0.00000000
Rotation angle (degrees) 8.30219832
Shift along axis 0.59772883
> hide #14 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Terminator_1-coot-0.pdb"
Summary of feedback from opening /Users/melvinshen/Desktop/Sinica /Protein
Purification/New Phage Proteins/Structure/CryoEM/cryosparc/Corndog
/Connector/Fitted Models/Terminator_1-coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 28 TRP A 35 1 8
Start residue of secondary structure not found: HELIX 2 2 LEU A 36 GLU A 38 1
3
Start residue of secondary structure not found: HELIX 3 3 LYS A 83 ASP A 85 1
3
Start residue of secondary structure not found: HELIX 4 4 GLU A 87 LEU A 108 1
22
Start residue of secondary structure not found: HELIX 5 5 ALA B 28 GLY B 37 1
10
44 messages similar to the above omitted
Chain information for Terminator_1-coot-0.pdb #15
---
Chain | Description
D | No description available
> fitmap #15 inMap #6.1
Fit molecule Terminator_1-coot-0.pdb (#15) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.6509, steps = 76
shifted from previous position = 0.0592
rotated from previous position = 0.112 degrees
atoms outside contour = 539, contour level = 0.3
Position of Terminator_1-coot-0.pdb (#15) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99999964 0.00080783 -0.00027481 -0.18021335
-0.00080831 0.99999813 -0.00175660 0.57662811
0.00027339 0.00175682 0.99999842 -0.53635474
Axis 0.89950081 -0.14034861 -0.41376388
Axis point 0.00000000 310.56361631 326.24756224
Rotation angle (degrees) 0.11189757
Shift along axis -0.02110679
> hide #!3 models
> volume zone #6.1 nearAtoms #15 range 6.37
> transparency #6.1.1 50
> view matrix models
> #5,0.88208,0.057863,-0.46753,283.63,-0.12546,0.98544,-0.11475,276.26,0.45408,0.15987,0.8765,210.98
> volume #!6.1 region all imageMode "full region"
> volume unzone #!6.1
> mousemode rightMode "crop volume"
> volume #!6.1 style surface
> surface dust #6.1 size 10.6
> fitmap #15 inMap #6.1
Fit molecule Terminator_1-coot-0.pdb (#15) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.6509, steps = 48
shifted from previous position = 0.00473
rotated from previous position = 0.00878 degrees
atoms outside contour = 539, contour level = 0.3
Position of Terminator_1-coot-0.pdb (#15) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99999956 0.00090030 -0.00025597 -0.20529067
-0.00090078 0.99999783 -0.00187734 0.63305720
0.00025428 0.00187757 0.99999821 -0.56022086
Axis 0.89494936 -0.12161480 -0.42927321
Axis point 0.00000000 303.32051713 335.54900728
Rotation angle (degrees) 0.12019715
Shift along axis -0.02022607
> fitmap #15 inMap #6.1
Fit molecule Terminator_1-coot-0.pdb (#15) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.6509, steps = 64
shifted from previous position = 0.00516
rotated from previous position = 0.00514 degrees
atoms outside contour = 538, contour level = 0.3
Position of Terminator_1-coot-0.pdb (#15) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99999962 0.00081760 -0.00029087 -0.17980925
-0.00081814 0.99999790 -0.00187840 0.60527184
0.00028933 0.00187864 0.99999819 -0.56948079
Axis 0.90781413 -0.14019494 -0.39524535
Axis point 0.00000000 308.28290075 320.16592816
Rotation angle (degrees) 0.11856090
Shift along axis -0.02300480
> fitmap #15 inMap #6.1
Fit molecule Terminator_1-coot-0.pdb (#15) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.6509, steps = 60
shifted from previous position = 0.00196
rotated from previous position = 0.00671 degrees
atoms outside contour = 538, contour level = 0.3
Position of Terminator_1-coot-0.pdb (#15) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99999963 0.00080634 -0.00030619 -0.17438195
-0.00080688 0.99999812 -0.00176290 0.57910944
0.00030477 0.00176315 0.99999840 -0.54663126
Axis 0.89826479 -0.15564211 -0.41096945
Axis point 0.00000000 315.48536202 326.20850427
Rotation angle (degrees) 0.11245438
Shift along axis -0.02212623
> volume zone #6.1 nearAtoms #15 range 6.37
> hide #15 models
> show #15 models
> hide #15 models
> show #14 models
> surface dust #6.1 size 10.6
> select add #14
2432 atoms, 2484 bonds, 300 residues, 3 models selected
> volume #6.1 region 0,0,0,511,511,511
> select subtract #14
1216 atoms, 1242 bonds, 150 residues, 2 models selected
> volume #6.1 region 0,7,0,511,511,511
> ui mousemode right "translate selected models"
> select add #14
2432 atoms, 2484 bonds, 300 residues, 3 models selected
> ui mousemode right "map eraser"
> volume erase #6.1 center 241.17,301.83,217.62 radius 46.56
Opened P2_J357_007_volume_map_sharp_C6.mrc 0 copy as #17, grid size
512,505,512, pixel 1.06, shown at step 1, values float32
> surface dust #17 size 10.6
> ui mousemode right "translate selected models"
> close #16
> view matrix models
> #5,0.88208,0.057863,-0.46753,284.17,-0.12546,0.98544,-0.11475,276.69,0.45408,0.15987,0.8765,210.53,#14,0.99255,-0.11767,0.031425,25.129,0.11977,0.98988,-0.076104,-11.673,-0.022152,0.079301,0.9966,-13.09
> select subtract #14
1216 atoms, 1242 bonds, 150 residues, 2 models selected
> hide #14 models
> show #15 models
> fitmap #15 inMap #6.1
Fit molecule Terminator_1-coot-0.pdb (#15) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.6509, steps = 48
shifted from previous position = 0.0167
rotated from previous position = 0.0128 degrees
atoms outside contour = 538, contour level = 0.3
Position of Terminator_1-coot-0.pdb (#15) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99999975 0.00068214 -0.00016968 -0.16298491
-0.00068246 0.99999799 -0.00188727 0.58247684
0.00016839 0.00188739 0.99999820 -0.54377751
Axis 0.93711372 -0.08393220 -0.33878202
Axis point 0.00000000 291.52765521 307.54958272
Rotation angle (degrees) 0.11539261
Shift along axis -0.01740192
> fitmap #15 inMap #6.1
Fit molecule Terminator_1-coot-0.pdb (#15) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.6508, steps = 60
shifted from previous position = 0.021
rotated from previous position = 0.00501 degrees
atoms outside contour = 539, contour level = 0.3
Position of Terminator_1-coot-0.pdb (#15) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99999972 0.00072007 -0.00019713 -0.17364246
-0.00072046 0.99999782 -0.00196121 0.59045724
0.00019572 0.00196135 0.99999806 -0.56290461
Axis 0.93458057 -0.09359841 -0.34321785
Axis point 0.00000000 291.55653375 299.58176703
Rotation angle (degrees) 0.12023896
Shift along axis -0.02434982
> select add #15
2432 atoms, 2484 bonds, 300 residues, 3 models selected
> view matrix models
> #5,0.88208,0.057863,-0.46753,284.46,-0.12546,0.98544,-0.11475,276.91,0.45408,0.15987,0.8765,209.54,#15,1,0.00072007,-0.00019713,0.12109,-0.00072046,1,-0.0019612,0.80733,0.00019572,0.0019613,1,-1.553
> fitmap #15 inMap #6.1
Fit molecule Terminator_1-coot-0.pdb (#15) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.6509, steps = 68
shifted from previous position = 1.04
rotated from previous position = 0.0105 degrees
atoms outside contour = 537, contour level = 0.3
Position of Terminator_1-coot-0.pdb (#15) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99999984 0.00055598 -0.00013484 -0.14289270
-0.00055623 0.99999803 -0.00190699 0.55137617
0.00013378 0.00190707 0.99999817 -0.53944650
Axis 0.95782836 -0.06745947 -0.27930997
Axis point 0.00000000 286.56892204 288.01025969
Rotation angle (degrees) 0.11407549
Shift along axis -0.02338944
> view matrix models
> #5,0.88208,0.057863,-0.46753,288.4,-0.12546,0.98544,-0.11475,276.4,0.45408,0.15987,0.8765,207.8,#15,1,0.00055598,-0.00013484,3.7983,-0.00055623,1,-0.001907,0.040964,0.00013378,0.0019071,1,-2.2802
> fitmap #15 inMap #6.1
Fit molecule Terminator_1-coot-0.pdb (#15) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3049, steps = 72
shifted from previous position = 1.54
rotated from previous position = 1.56 degrees
atoms outside contour = 780, contour level = 0.3
Position of Terminator_1-coot-0.pdb (#15) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99969796 0.01954014 0.01490547 -2.73136661
-0.01969365 0.99975379 0.01022311 2.53123760
-0.01470204 -0.01051356 0.99983664 5.84527170
Axis -0.38871275 0.55499841 -0.73544488
Axis point 177.93083596 178.98324570 0.00000000
Rotation angle (degrees) 1.52846079
Shift along axis -1.83232528
> view matrix models
> #5,0.88208,0.057863,-0.46753,285.74,-0.12546,0.98544,-0.11475,277.73,0.45408,0.15987,0.8765,205.63,#15,0.9997,0.01954,0.014905,-5.3922,-0.019694,0.99975,0.010223,3.8678,-0.014702,-0.010514,0.99984,3.6758
> fitmap #15 inMap #6.1
Fit molecule Terminator_1-coot-0.pdb (#15) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.329, steps = 88
shifted from previous position = 2.8
rotated from previous position = 7.01 degrees
atoms outside contour = 761, contour level = 0.3
Position of Terminator_1-coot-0.pdb (#15) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99688931 -0.07881254 -0.00052767 21.37333943
0.07859023 0.99352831 0.08200660 -37.64237425
-0.00593889 -0.08179297 0.99663165 16.71731549
Axis -0.72084151 0.02381344 0.69269072
Axis point 0.00000000 224.80907140 475.38603800
Rotation angle (degrees) 6.52385712
Shift along axis -4.72325536
> view matrix models
> #5,0.88208,0.057863,-0.46753,281.61,-0.12546,0.98544,-0.11475,278.98,0.45408,0.15987,0.8765,205.07,#15,0.99689,-0.078813,-0.00052767,17.235,0.07859,0.99353,0.082007,-36.398,-0.0059389,-0.081793,0.99663,16.158
> fitmap #15 inMap #6.1
Fit molecule Terminator_1-coot-0.pdb (#15) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.5171, steps = 96
shifted from previous position = 3.73
rotated from previous position = 4.51 degrees
atoms outside contour = 594, contour level = 0.3
Position of Terminator_1-coot-0.pdb (#15) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99970891 -0.01592240 0.01812631 -2.47732586
0.01354115 0.99210784 0.12465419 -28.18319504
-0.01996805 -0.12437245 0.99203466 28.03557348
Axis -0.98180911 0.15019030 0.11616260
Axis point 0.00000000 208.61818508 241.05355332
Rotation angle (degrees) 7.28588775
Shift along axis 1.45610383
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Terminator_1-coot-0.pdb" models #15 selectedOnly true relModel #2
> select subtract #15
1216 atoms, 1242 bonds, 150 residues, 2 models selected
> close #14
> close #8-13
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Terminator_1-coot-1.pdb"
Chain information for Terminator_1-coot-1.pdb #8
---
Chain | Description
D | No description available
> hide #8 models
> show #8 models
> hide #15 models
> fitmap #8 inMap #6.1
Fit molecule Terminator_1-coot-1.pdb (#8) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.099, steps = 44
shifted from previous position = 0.0205
rotated from previous position = 0.136 degrees
atoms outside contour = 208, contour level = 0.3
Position of Terminator_1-coot-1.pdb (#8) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99999807 -0.00067575 -0.00184331 0.53667755
0.00067327 0.99999887 -0.00134483 0.07777271
0.00184422 0.00134359 0.99999740 -0.86179772
Axis 0.56494727 -0.77490139 0.28348266
Axis point 467.49607740 0.00000000 291.08147954
Rotation angle (degrees) 0.13632716
Shift along axis -0.00137637
> combine #8
> turn z 60 models #9-13
> undo
> turn z 1 60 models #9-13
> turn z -1 60 models #9-13
> ui tool show "Side View"
> view orient
> turn x 90
> zoom 0.5
> move y -300
> move y 150
> zoom 1.3
> zoom 0.5
> turn x 90
> select add #1
2132 atoms, 2181 bonds, 269 residues, 3 models selected
> select subtract #1
1216 atoms, 1242 bonds, 150 residues, 2 models selected
> select
67596 atoms, 69108 bonds, 8584 residues, 24 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,1,-0.00059359,0.0025787,-0.49537,0.00072009,0.99878,-0.049334,12.717,-0.0025463,0.049336,0.99878,-12.378,#1,0.99997,-0.0049283,0.0066458,-1.049,0.0052207,0.99899,-0.044715,11.23,-0.0064187,0.044748,0.99898,-9.1967,#4,0.99899,0.044753,0.0026867,-13.055,-0.044566,0.99779,-0.049341,34.364,-0.0048889,0.049172,0.99878,-195.37,#6,1,-0.00059359,0.0025787,-0.49537,0.00072009,0.99878,-0.049334,12.717,-0.0025463,0.049336,0.99878,-12.378,#5,0.88332,0.05769,-0.4652,281.47,-0.14707,0.97639,-0.15818,281.44,0.44509,0.20815,0.87096,205.49,#3,1,-0.00059359,0.0025787,-0.49537,0.00072009,0.99878,-0.049334,12.717,-0.0025463,0.049336,0.99878,-12.378,#7,-0.16107,-0.9608,-0.22564,570.77,0.95665,-0.2082,0.20366,27.168,-0.24265,-0.18306,0.95269,111.81,#15,0.99965,-0.016832,0.02061,-2.8837,0.01523,0.99702,0.075575,-16.816,-0.021821,-0.075234,0.99693,14.24,#17,1,-0.00059359,0.0025787,-0.49537,0.00072009,0.99878,-0.049334,12.717,-0.0025463,0.049336,0.99878,-12.378,#8,1,-0.0012659,0.00073622,0.039039,0.0013016,0.99871,-0.050678,12.838,-0.00067112,0.050679,0.99871,-13.236,#9,1,-0.0012659,0.00073622,0.039038,0.0013016,0.99871,-0.050678,12.838,-0.00067112,0.050679,0.99871,-13.236,#10,1,-0.0012659,0.00073622,0.039038,0.0013016,0.99871,-0.050678,12.838,-0.00067112,0.050679,0.99871,-13.236,#11,1,-0.0012659,0.00073622,0.039038,0.0013016,0.99871,-0.050678,12.838,-0.00067112,0.050679,0.99871,-13.236,#12,1,-0.0012659,0.00073622,0.039038,0.0013016,0.99871,-0.050678,12.838,-0.00067112,0.050679,0.99871,-13.236,#13,1,-0.0012659,0.00073622,0.039038,0.0013016,0.99871,-0.050678,12.838,-0.00067112,0.050679,0.99871,-13.236
> select clear
> turn z 60 models #9-13
> turn z 30 models #9-13
> turn z 60 models #9-13
> select add #9
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> select add #10
2432 atoms, 2484 bonds, 300 residues, 2 models selected
> select add #11
3648 atoms, 3726 bonds, 450 residues, 3 models selected
> select add #12
4864 atoms, 4968 bonds, 600 residues, 4 models selected
> select subtract #12
3648 atoms, 3726 bonds, 450 residues, 3 models selected
> select add #13
4864 atoms, 4968 bonds, 600 residues, 4 models selected
> select add #12
6080 atoms, 6210 bonds, 750 residues, 5 models selected
> view matrix models
> #9,0.48045,0.8259,-0.29506,-42.072,-0.86631,0.49934,-0.012945,382.49,0.13665,0.26184,0.95539,-95.726,#10,0.48045,0.8259,-0.29506,-42.072,-0.86631,0.49934,-0.012945,382.49,0.13665,0.26184,0.95539,-95.726,#11,0.48045,0.8259,-0.29506,-42.072,-0.86631,0.49934,-0.012945,382.49,0.13665,0.26184,0.95539,-95.726,#12,0.48045,0.8259,-0.29506,-42.072,-0.86631,0.49934,-0.012945,382.49,0.13665,0.26184,0.95539,-95.726,#13,0.48045,0.8259,-0.29506,-42.072,-0.86631,0.49934,-0.012945,382.49,0.13665,0.26184,0.95539,-95.726
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.50113,0.86428,-0.043521,-96.502,-0.86537,0.50045,-0.025977,385.16,-0.00067112,0.050679,0.99871,-13.114,#10,0.50113,0.86428,-0.043521,-96.502,-0.86537,0.50045,-0.025977,385.16,-0.00067112,0.050679,0.99871,-13.114,#11,0.50113,0.86428,-0.043521,-96.502,-0.86537,0.50045,-0.025977,385.16,-0.00067112,0.050679,0.99871,-13.114,#12,0.50113,0.86428,-0.043521,-96.502,-0.86537,0.50045,-0.025977,385.16,-0.00067112,0.050679,0.99871,-13.114,#13,0.50113,0.86428,-0.043521,-96.502,-0.86537,0.50045,-0.025977,385.16,-0.00067112,0.050679,0.99871,-13.114
> turn z 60 models #10-13
> select subtract #9
4864 atoms, 4968 bonds, 600 residues, 4 models selected
> view matrix models
> #10,-0.49881,0.86586,-0.038458,185.05,-0.86665,-0.49883,0.0097862,653.83,-0.01071,0.038211,0.99921,-6.9353,#11,-0.49881,0.86586,-0.038458,185.05,-0.86665,-0.49883,0.0097862,653.83,-0.01071,0.038211,0.99921,-6.9353,#12,-0.49881,0.86586,-0.038458,185.05,-0.86665,-0.49883,0.0097862,653.83,-0.01071,0.038211,0.99921,-6.9353,#13,-0.49881,0.86586,-0.038458,185.05,-0.86665,-0.49883,0.0097862,653.83,-0.01071,0.038211,0.99921,-6.9353
> turn z 60 models #11-13
> view matrix models
> #10,-0.49881,0.86586,-0.038458,195.15,-0.86665,-0.49883,0.0097862,652.51,-0.01071,0.038211,0.99921,-6.8505,#11,-0.99999,0.0012209,-0.0049537,548.74,-0.0013359,-0.99973,0.02328,546.26,-0.0049239,0.023286,0.99972,-4.6334,#12,-0.99999,0.0012209,-0.0049537,548.74,-0.0013359,-0.99973,0.02328,546.26,-0.0049239,0.023286,0.99972,-4.6334,#13,-0.99999,0.0012209,-0.0049537,548.74,-0.0013359,-0.99973,0.02328,546.26,-0.0049239,0.023286,0.99972,-4.6334
> select subtract #10
3648 atoms, 3726 bonds, 450 residues, 3 models selected
> view matrix models
> #11,-0.99999,0.0012209,-0.0049537,553.38,-0.0013359,-0.99973,0.02328,544.45,-0.0049239,0.023286,0.99972,-4.6096,#12,-0.99999,0.0012209,-0.0049537,553.38,-0.0013359,-0.99973,0.02328,544.45,-0.0049239,0.023286,0.99972,-4.6096,#13,-0.99999,0.0012209,-0.0049537,553.38,-0.0013359,-0.99973,0.02328,544.45,-0.0049239,0.023286,0.99972,-4.6096
> turn z 60 models #12-13
> view matrix models
> #11,-0.99999,0.0012209,-0.0049537,557.32,-0.0013359,-0.99973,0.02328,544.99,-0.0049239,0.023286,0.99972,-4.5634,#12,-0.50123,-0.865,0.023488,632.06,0.86525,-0.50135,0.00101,174.47,0.010902,0.020829,0.99972,-8.4431,#13,-0.50123,-0.865,0.023488,632.06,0.86525,-0.50135,0.00101,174.47,0.010902,0.020829,0.99972,-8.4431
> select subtract #11
2432 atoms, 2484 bonds, 300 residues, 2 models selected
> view matrix models
> #12,-0.50123,-0.865,0.023488,637.88,0.86525,-0.50135,0.00101,174.95,0.010902,0.020829,0.99972,-8.3787,#13,-0.50123,-0.865,0.023488,637.88,0.86525,-0.50135,0.00101,174.95,0.010902,0.020829,0.99972,-8.3787
> turn z 60 models #13
> select subtract #12
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> view matrix models
> #13,0.49871,-0.86658,0.018425,369.59,0.86652,0.49793,-0.034753,-81.25,0.020941,0.033297,0.99923,-14.269
> select subtract #13
Nothing selected
> fitmap #8 inMap #6.1
Fit molecule Terminator_1-coot-1.pdb (#8) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.099, steps = 28
shifted from previous position = 0.0212
rotated from previous position = 0.0164 degrees
atoms outside contour = 205, contour level = 0.3
Position of Terminator_1-coot-1.pdb (#8) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99999872 -0.00147524 0.00061364 0.09538511
0.00150436 0.99872152 -0.05052781 12.75427863
-0.00053832 0.05052867 0.99872247 -13.23195415
Axis 0.99950074 0.01139343 0.02946979
Axis point 0.00000000 267.99459589 245.67368385
Rotation angle (degrees) 2.89773636
Shift along axis -0.14929044
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3428, steps = 108
shifted from previous position = 5.32
rotated from previous position = 8.81 degrees
atoms outside contour = 742, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.43089544 0.88896660 -0.15513708 -56.04300734
-0.90224705 0.42122296 -0.09231193 425.68138049
-0.01671492 0.17974876 0.98357054 -34.84055779
Axis 0.14972764 -0.07618015 -0.98578812
Axis point 305.89250341 257.78072247 0.00000000
Rotation angle (degrees) 65.30142568
Shift along axis -6.47425108
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3134, steps = 84
shifted from previous position = 4.17
rotated from previous position = 2.1 degrees
atoms outside contour = 772, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.50910096 0.86068642 -0.00592361 183.37185538
-0.86069151 -0.50912088 -0.00245774 654.98288999
-0.00513118 0.00384717 0.99997942 3.18066853
Axis 0.00366268 -0.00046035 -0.99999319
Axis point 278.47035966 275.19632380 0.00000000
Rotation angle (degrees) 120.60531178
Shift along axis -2.81053322
> fitmap #11 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3116, steps = 92
shifted from previous position = 6.11
rotated from previous position = 2.72 degrees
atoms outside contour = 795, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.99946855 -0.02385160 -0.02221897 556.86280051
0.02414152 -0.99962565 -0.01287300 545.05238118
-0.02190362 -0.01340256 0.99967021 10.22890834
Axis -0.01103319 -0.00657037 0.99991755
Axis point 275.21695775 275.90156086 0.00000000
Rotation angle (degrees) 178.62485290
Shift along axis 0.50289463
> fitmap #12 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.092, steps = 72
shifted from previous position = 1.37
rotated from previous position = 3.12 degrees
atoms outside contour = 203, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.50126985 -0.86527793 0.00475183 641.71944700
0.86407830 -0.50085043 -0.05017453 185.68606634
0.04579488 -0.02104503 0.99872910 -6.37232512
Axis 0.01683700 -0.02372309 0.99957678
Axis point 267.40877785 277.67516582 0.00000000
Rotation angle (degrees) 120.11224339
Shift along axis 0.02995634
> fitmap #13 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3338, steps = 152
shifted from previous position = 5.35
rotated from previous position = 17.4 degrees
atoms outside contour = 768, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.47979274 -0.84118695 -0.24940600 423.83509211
0.87668597 0.47095394 0.09810211 -109.81333965
0.03493653 -0.26571944 0.96341707 61.42730654
Axis -0.20452637 -0.15984635 0.96572155
Axis point 312.89490423 307.96764284 0.00000000
Rotation angle (degrees) 62.80103230
Shift along axis -9.81051758
> hide #!17 models
> show #!6.1 models
> select add #13
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> view matrix models
> #13,0.54156,-0.8043,-0.24459,395.8,0.83989,0.53011,0.11648,-116.87,0.035973,-0.26851,0.96261,61.954
> view matrix models
> #13,0.54156,-0.8043,-0.24459,396.14,0.83989,0.53011,0.11648,-118.91,0.035973,-0.26851,0.96261,62.037
> view matrix models
> #13,0.60389,-0.76069,-0.23805,365.99,0.7962,0.58967,0.1355,-124.16,0.037294,-0.27136,0.96175,62.505
> fitmap #13 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3336, steps = 88
shifted from previous position = 1.27
rotated from previous position = 8.47 degrees
atoms outside contour = 773, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.48034216 -0.84102686 -0.24888783 423.55854223
0.87637600 0.47160290 0.09775342 -109.80384255
0.03516298 -0.26507444 0.96358650 61.17009123
Axis -0.20404846 -0.15974554 0.96583932
Axis point 312.77407388 307.98334397 0.00000000
Rotation angle (degrees) 62.75696725
Shift along axis -9.80531455
> view matrix models
> #13,0.6421,-0.73044,-0.23272,346.08,0.76565,0.62627,0.14685,-124.19,0.03848,-0.27248,0.96139,62.411
> view matrix models
> #13,0.6421,-0.73044,-0.23272,345.49,0.76565,0.62627,0.14685,-131.29,0.03848,-0.27248,0.96139,62.714
> fitmap #13 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.087, steps = 152
shifted from previous position = 1.95
rotated from previous position = 20.4 degrees
atoms outside contour = 204, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.49912899 -0.86652455 0.00231866 370.78582202
0.86542880 0.49835954 -0.05167876 -85.78260167
0.04362539 0.02780100 0.99866098 -19.04999284
Axis 0.04582899 -0.02381796 0.99866531
Axis point 260.02851543 277.59691230 0.00000000
Rotation angle (degrees) 60.12728957
Shift along axis 0.01134024
> fitmap #13 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.087, steps = 40
shifted from previous position = 0.0189
rotated from previous position = 0.0192 degrees
atoms outside contour = 204, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.49930887 -0.86642017 0.00257966 370.66972956
0.86533337 0.49852880 -0.05164421 -85.79161903
0.04345956 0.02801868 0.99866213 -19.06310065
Axis 0.04593992 -0.02357458 0.99866599
Axis point 259.99682742 277.56855279 0.00000000
Rotation angle (degrees) 60.11571631
Shift along axis 0.01336938
> select subtract #13
Nothing selected
> select add #11
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> fitmap #11 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3116, steps = 44
shifted from previous position = 0.00236
rotated from previous position = 0.012 degrees
atoms outside contour = 795, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.99947172 -0.02373333 -0.02220304 556.83023074
0.02401931 -0.99963076 -0.01270348 545.05161281
-0.02189335 -0.01323007 0.99967273 10.18278161
Axis -0.01102662 -0.00648484 0.99991818
Axis point 275.21678758 275.88364197 0.00000000
Rotation angle (degrees) 178.63174546
Shift along axis 0.50742332
> fitmap #11 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3116, steps = 44
shifted from previous position = 0.0027
rotated from previous position = 0.00493 degrees
atoms outside contour = 795, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.99947331 -0.02368165 -0.02218661 556.81464165
0.02396597 -0.99963287 -0.01263789 545.05102840
-0.02187917 -0.01316296 0.99967393 10.16215633
Axis -0.01101895 -0.00645165 0.99991848
Axis point 275.21600577 275.87570473 0.00000000
Rotation angle (degrees) 178.63475581
Shift along axis 0.50933655
> view matrix models
> #11,-0.99665,-0.021918,-0.078841,566.94,0.017619,-0.99834,0.054818,533.06,-0.079912,0.053245,0.99538,12.175
> fitmap #11 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3116, steps = 76
shifted from previous position = 1.12
rotated from previous position = 5.06 degrees
atoms outside contour = 795, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.99947541 -0.02358161 -0.02219848 556.79247633
0.02386406 -0.99963646 -0.01254651 545.06661096
-0.02189454 -0.01306967 0.99967481 10.14251938
Axis -0.01102575 -0.00640546 0.99991870
Axis point 275.21852564 275.86900120 0.00000000
Rotation angle (degrees) 178.64054362
Shift along axis 0.51123700
> view matrix models
> #11,-0.97147,-0.23472,-0.033909,601.54,0.23507,-0.97196,-0.0067023,475.1,-0.031385,-0.014482,0.9994,13.329
> fitmap #11 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.099, steps = 116
shifted from previous position = 2.49
rotated from previous position = 14 degrees
atoms outside contour = 206, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.99998832 0.00163278 0.00454588 541.77882908
-0.00184993 -0.99883687 -0.04818144 555.77601262
0.00446193 -0.04818929 0.99882822 12.19990376
Axis -0.00225345 0.02409966 -0.99970702
Axis point 271.11775703 277.79906105 0.00000000
Rotation angle (degrees) 179.90019867
Shift along axis -0.02318708
> fitmap #11 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.099, steps = 44
shifted from previous position = 0.00304
rotated from previous position = 0.0103 degrees
atoms outside contour = 206, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.99998773 0.00154473 0.00470243 541.76771131
-0.00176948 -0.99883745 -0.04817242 555.75195661
0.00462255 -0.04818015 0.99882793 12.15576823
Axis -0.00233281 0.02409512 -0.99970695
Axis point 271.10004357 277.79789496 0.00000000
Rotation angle (degrees) 179.90502684
Shift along axis -0.02513986
> select subtract #11
Nothing selected
> select add #10
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> view matrix models
> #10,-0.50926,0.86061,-0.0022379,180.97,-0.86061,-0.50926,-0.00081188,651.48,-0.0018384,0.0015125,1,2.9095
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3446, steps = 108
shifted from previous position = 2.78
rotated from previous position = 8.57 degrees
atoms outside contour = 741, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.56411444 0.81735667 -0.11705967 228.22371176
-0.82564006 -0.56003750 0.06838474 638.09093116
-0.00966308 0.13522598 0.99076764 -26.03476052
Axis 0.04056247 -0.06517340 -0.99704920
Axis point 281.75661285 259.63872126 0.00000000
Rotation angle (degrees) 124.51987957
Shift along axis -6.37130311
> view matrix models
> #10,-0.55556,0.7754,-0.30018,272.56,-0.83116,-0.52786,0.17476,610.62,-0.022942,0.34659,0.93774,-62.244
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3221, steps = 64
shifted from previous position = 2.1
rotated from previous position = 4.25 degrees
atoms outside contour = 766, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.52185329 0.81586936 -0.24905081 243.79426094
-0.85303381 -0.49858054 0.15411280 612.84609118
0.00156403 0.29287303 0.95615004 -61.37817518
Axis 0.08194613 -0.14800289 -0.98558611
Axis point 290.72544512 242.45154040 0.00000000
Rotation angle (degrees) 122.15028860
Shift along axis -10.23152103
> view matrix models
> #10,-0.51393,0.72819,-0.45345,303.57,-0.85756,-0.4228,0.29297,568.09,0.021619,0.53943,0.84175,-103.54
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2869, steps = 84
shifted from previous position = 2.37
rotated from previous position = 5.4 degrees
atoms outside contour = 796, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.51929146 0.76644630 -0.37801644 279.67998981
-0.85406589 -0.44984241 0.26117666 581.39783217
0.03013006 0.45847776 0.88819496 -97.52295330
Axis 0.11725079 -0.24255059 -0.96302724
Axis point 297.78669781 223.19518845 0.00000000
Rotation angle (degrees) 122.71560274
Shift along axis -14.30842800
> view matrix models
> #10,-0.4831,0.82131,-0.30343,240.86,-0.83542,-0.53612,-0.12103,673.38,-0.26208,0.19502,0.94514,40.442
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2941, steps = 76
shifted from previous position = 0.93
rotated from previous position = 3.91 degrees
atoms outside contour = 783, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.53726010 0.79748703 -0.27452870 255.18391760
-0.80302940 -0.58319434 -0.12258927 676.14326973
-0.25786695 0.15459230 0.95373258 46.83046305
Axis 0.17063354 -0.01025701 -0.98528117
Axis point 307.63211646 270.97611265 0.00000000
Rotation angle (degrees) 125.68728164
Shift along axis -9.53344801
> view matrix models
> #10,-0.49655,0.76293,-0.41396,279.49,-0.86429,-0.47868,0.15452,613.44,-0.080264,0.43451,0.89708,-61.374
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3221, steps = 92
shifted from previous position = 4.37
rotated from previous position = 10 degrees
atoms outside contour = 764, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.52195619 0.81575564 -0.24920765 243.87425257
-0.85297135 -0.49874983 0.15391059 612.90804051
0.00126116 0.29290158 0.95614175 -61.30062854
Axis 0.08209095 -0.14793206 -0.98558469
Axis point 290.74842440 242.46497021 0.00000000
Rotation angle (degrees) 122.15977967
Shift along axis -10.23191967
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3221, steps = 44
shifted from previous position = 0.000826
rotated from previous position = 0.00605 degrees
atoms outside contour = 763, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.52197079 0.81571939 -0.24929574 243.90576950
-0.85296254 -0.49877626 0.15387374 612.91990517
0.00117500 0.29295753 0.95612472 -61.28646879
Axis 0.08214753 -0.14793639 -0.98557933
Axis point 290.76020774 242.46335596 0.00000000
Rotation angle (degrees) 122.16174455
Shift along axis -10.23422465
> view matrix models
> #10,-0.54327,0.80552,-0.23664,250.09,-0.79156,-0.3975,0.46415,508.18,0.27982,0.43947,0.85356,-158
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2839, steps = 120
shifted from previous position = 1.63
rotated from previous position = 8.74 degrees
atoms outside contour = 807, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.57196665 0.81555205 -0.08791466 225.56770462
-0.74726253 -0.47385037 0.46590184 512.42092722
0.33830882 0.33217565 0.88045809 -153.90673974
Axis -0.08227258 -0.26222615 -0.96149294
Axis point 255.85456029 217.07285927 0.00000000
Rotation angle (degrees) 125.63922358
Shift along axis -4.94796352
> view matrix models
> #10,-0.58442,0.6555,-0.47829,346.08,-0.81109,-0.45441,0.3683,546.16,0.024077,0.60318,0.79724,-109.69
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2899, steps = 116
shifted from previous position = 2.78
rotated from previous position = 11.1 degrees
atoms outside contour = 786, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.42861694 0.77120496 -0.47067016 270.92889924
-0.90103053 -0.32648394 0.28557348 556.10078675
0.06656944 0.54648982 0.83481576 -113.48973204
Axis 0.14693800 -0.30255257 -0.94173837
Axis point 304.03376463 207.79244421 0.00000000
Rotation angle (degrees) 117.39630725
Shift along axis -21.56233616
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2899, steps = 44
shifted from previous position = 0.00521
rotated from previous position = 0.0236 degrees
atoms outside contour = 786, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.42869861 0.77111911 -0.47073645 270.98691077
-0.90096918 -0.32633538 0.28593660 555.96976345
0.06687322 0.54669966 0.83465408 -113.58955406
Axis 0.14685574 -0.30276935 -0.94168153
Axis point 304.01494842 207.73863065 0.00000000
Rotation angle (degrees) 117.39936584
Shift along axis -21.56943796
> view matrix models
> #10,-0.4206,0.52373,-0.74081,382.26,-0.89972,-0.34577,0.26638,564.2,-0.11664,0.77856,0.61664,-71.421
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.246, steps = 96
shifted from previous position = 3.82
rotated from previous position = 2.96 degrees
atoms outside contour = 845, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.43160175 0.53323354 -0.72758635 381.23781340
-0.89960814 -0.31391644 0.30358138 547.38878731
-0.06652154 0.78556887 0.61518811 -90.27255016
Axis 0.29212147 -0.40065609 -0.86841220
Axis point 337.96242813 176.20176629 0.00000000
Rotation angle (degrees) 124.41375274
Shift along axis -29.55311763
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2461, steps = 76
shifted from previous position = 0.00571
rotated from previous position = 0.0313 degrees
atoms outside contour = 844, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.43135077 0.53352903 -0.72751856 381.08696666
-0.89976185 -0.31345927 0.30359822 547.31799657
-0.06606897 0.78555079 0.61525997 -90.40720756
Axis 0.29200578 -0.40075957 -0.86840336
Axis point 337.94254991 176.18084813 0.00000000
Rotation angle (degrees) 124.38667095
Shift along axis -29.55340535
> view matrix models
> #10,-0.39501,0.82248,-0.40926,237.05,-0.8645,-0.18206,0.46851,472.24,0.31083,0.53887,0.78295,-175.9
> view matrix models
> #10,-0.39501,0.82248,-0.40926,238.73,-0.8645,-0.18206,0.46851,471.32,0.31083,0.53887,0.78295,-179.98
> view matrix models
> #10,-0.39501,0.82248,-0.40926,242.01,-0.8645,-0.18206,0.46851,472.02,0.31083,0.53887,0.78295,-180.62
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2487, steps = 80
shifted from previous position = 1.95
rotated from previous position = 4.26 degrees
atoms outside contour = 841, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.39069891 0.82529720 -0.40772401 241.24608448
-0.88663339 -0.21831931 0.40769829 499.17587279
0.24745824 0.52078901 0.81703317 -164.12523079
Axis 0.06157923 -0.35675447 -0.93216642
Axis point 290.03404501 195.65516058 0.00000000
Rotation angle (degrees) 113.32788972
Shift along axis -10.23544793
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2487, steps = 44
shifted from previous position = 0.0191
rotated from previous position = 0.0284 degrees
atoms outside contour = 839, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.39038866 0.82541996 -0.40777270 241.15345742
-0.88684882 -0.21824276 0.40727050 499.29942650
0.24717577 0.52062652 0.81722221 -164.05681558
Axis 0.06171535 -0.35657898 -0.93222457
Axis point 290.07345115 195.69518465 0.00000000
Rotation angle (degrees) 113.30992574
Shift along axis -10.21901373
> view matrix models
> #10,-0.39994,0.81,-0.42889,252,-0.87511,-0.19837,0.44141,484.09,0.27246,0.55186,0.78817,-173.18
> view matrix models
> #10,-0.39994,0.81,-0.42889,252.32,-0.87511,-0.19837,0.44141,483.66,0.27246,0.55186,0.78817,-173.17
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2486, steps = 72
shifted from previous position = 0.794
rotated from previous position = 2.86 degrees
atoms outside contour = 840, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.39039241 0.82550613 -0.40759463 241.09728069
-0.88687341 -0.21838853 0.40713878 499.36841820
0.24708156 0.52042874 0.81737666 -164.01413773
Axis 0.06167931 -0.35643033 -0.93228380
Axis point 290.06550140 195.73173824 0.00000000
Rotation angle (degrees) 113.30977230
Shift along axis -10.21161326
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2487, steps = 44
shifted from previous position = 0.022
rotated from previous position = 0.0277 degrees
atoms outside contour = 841, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.39050976 0.82538880 -0.40771981 241.16781420
-0.88673496 -0.21822667 0.40752694 499.21761402
0.24739284 0.52068267 0.81712075 -164.09770887
Axis 0.06160929 -0.35668565 -0.93219078
Axis point 290.04204853 195.67494192 0.00000000
Rotation angle (degrees) 113.31636695
Shift along axis -10.23520872
> view matrix models
> #10,-0.39051,0.82539,-0.40772,238.09,-0.88673,-0.21823,0.40753,499.18,0.24739,0.52068,0.81712,-164.25
> view matrix models
> #10,-0.38271,0.78478,-0.4875,261.57,-0.91832,-0.38086,0.10782,607.74,-0.10106,0.48895,0.86644,-63.844
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3912, steps = 192
shifted from previous position = 1.43
rotated from previous position = 17.2 degrees
atoms outside contour = 703, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.38415824 0.88268930 -0.27070654 194.17102206
-0.90608508 -0.41674231 -0.07304560 651.18350031
-0.17729144 0.21722209 0.95988660 5.13507008
Axis 0.15996424 -0.05148033 -0.98577950
Axis point 308.33466951 262.16389054 0.00000000
Rotation angle (degrees) 114.86659928
Shift along axis -7.52476573
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3912, steps = 64
shifted from previous position = 0.0223
rotated from previous position = 0.178 degrees
atoms outside contour = 703, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.38625846 0.88241186 -0.26861439 194.38184510
-0.90520478 -0.41858542 -0.07342025 651.47296257
-0.17722497 0.21479183 0.96044560 5.59067273
Axis 0.15896917 -0.05040767 -0.98599588
Axis point 308.09199672 262.38182226 0.00000000
Rotation angle (degrees) 114.97350686
Shift along axis -7.45089225
> view matrix models
> #10,-0.35807,0.8393,-0.4091,224.64,-0.89692,-0.43095,-0.09909,657.16,-0.25947,0.33145,0.90709,12.52
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3912, steps = 148
shifted from previous position = 1.77
rotated from previous position = 8.6 degrees
atoms outside contour = 705, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.38363437 0.88276240 -0.27121063 194.11507508
-0.90628641 -0.41630247 -0.07305596 651.13258939
-0.17739671 0.21776773 0.95974350 5.05872898
Axis 0.16023708 -0.05168928 -0.98572425
Axis point 308.40089541 262.12153388 0.00000000
Rotation angle (degrees) 114.84069102
Shift along axis -7.53865347
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3912, steps = 60
shifted from previous position = 0.0236
rotated from previous position = 0.181 degrees
atoms outside contour = 706, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.38578165 0.88248193 -0.26906903 194.32935009
-0.90540455 -0.41816598 -0.07334719 651.41154052
-0.17724309 0.21532033 0.96032391 5.48985806
Axis 0.15918871 -0.05063837 -0.98594863
Axis point 308.14689609 262.33598385 0.00000000
Rotation angle (degrees) 114.94903073
Shift along axis -7.46409953
> view matrix models
> #10,-0.37576,0.84954,-0.37026,219.61,-0.91741,-0.39748,0.01904,631.43,-0.131,0.34684,0.92873,-33.386
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3911, steps = 112
shifted from previous position = 0.78
rotated from previous position = 8.19 degrees
atoms outside contour = 705, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.38601574 0.88239376 -0.26902247 194.40452500
-0.90538468 -0.41829150 -0.07287520 651.33365737
-0.17683444 0.21543785 0.96037289 5.35802419
Axis 0.15900591 -0.05084210 -0.98596765
Axis point 308.10345626 262.28802347 0.00000000
Rotation angle (degrees) 114.95884628
Shift along axis -7.48654276
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3911, steps = 44
shifted from previous position = 0.0254
rotated from previous position = 0.0607 degrees
atoms outside contour = 704, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.38629303 0.88243609 -0.26848508 194.35604557
-0.90515598 -0.41864934 -0.07365715 651.52782017
-0.17739883 0.21456763 0.96046361 5.68813230
Axis 0.15897946 -0.05024149 -0.98600270
Axis point 308.09346920 262.41945954 0.00000000
Rotation angle (degrees) 114.97604970
Shift along axis -7.44362302
> view matrix models
> #10,-0.37618,0.74884,-0.54564,279.13,-0.92611,-0.32189,0.19673,580.16,-0.028312,0.57933,0.8146,-96.577
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2869, steps = 132
shifted from previous position = 3.63
rotated from previous position = 12.7 degrees
atoms outside contour = 796, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.51939459 0.76649282 -0.37778036 279.65114671
-0.85399897 -0.44994084 0.26122591 581.39319466
0.03024897 0.45830337 0.88828092 -97.53069307
Axis 0.11712306 -0.24249167 -0.96305762
Axis point 297.75929452 223.20842306 0.00000000
Rotation angle (degrees) 122.71953879
Shift along axis -14.30173141
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2869, steps = 44
shifted from previous position = 0.00687
rotated from previous position = 0.0298 degrees
atoms outside contour = 796, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.51952806 0.76620147 -0.37818765 279.83642706
-0.85392539 -0.45002348 0.26132410 581.37034031
0.03003359 0.45870924 0.88807870 -97.53082012
Axis 0.11732466 -0.24264448 -0.96299459
Axis point 297.79576132 223.17019331 0.00000000
Rotation angle (degrees) 122.73378409
Shift along axis -14.31294072
> view matrix models
> #10,-0.50664,0.77992,-0.3675,270.6,-0.77546,-0.22592,0.5896,438.49,0.37681,0.58369,0.71925,-195.84
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2559, steps = 88
shifted from previous position = 2.37
rotated from previous position = 6.1 degrees
atoms outside contour = 816, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.41857814 0.81681629 -0.39699303 244.65205732
-0.83286488 -0.17095206 0.52641378 455.65528484
0.36211658 0.55098687 0.75185439 -190.46341273
Axis 0.01353053 -0.41798382 -0.90835371
Axis point 279.34731668 185.39376296 0.00000000
Rotation angle (degrees) 114.76124124
Shift along axis -14.13811665
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2561, steps = 64
shifted from previous position = 0.0161
rotated from previous position = 0.0129 degrees
atoms outside contour = 819, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.41873385 0.81673870 -0.39698848 244.72186579
-0.83275253 -0.17099239 0.52657840 455.61398935
0.36219495 0.55108937 0.75174151 -190.48792413
Axis 0.01349738 -0.41805727 -0.90832040
Axis point 279.34558325 185.37659962 0.00000000
Rotation angle (degrees) 114.77098771
Shift along axis -14.14556970
> view matrix models
> #10,-0.41873,0.81674,-0.39699,243.33,-0.83275,-0.17099,0.52658,450.56,0.36219,0.55109,0.75174,-190.66
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2848, steps = 132
shifted from previous position = 2.27
rotated from previous position = 5.49 degrees
atoms outside contour = 814, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.34177341 0.82609238 -0.44806506 232.13817932
-0.85934901 -0.08172413 0.50481721 440.50451842
0.38040793 0.55757738 0.73783280 -194.81986193
Axis 0.02808195 -0.44096019 -0.89708724
Axis point 282.54868069 177.47931562 0.00000000
Rotation angle (degrees) 110.04953171
Shift along axis -12.95565045
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2849, steps = 76
shifted from previous position = 0.00999
rotated from previous position = 0.0187 degrees
atoms outside contour = 812, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.34182437 0.82622931 -0.44777361 232.05058378
-0.85929692 -0.08188629 0.50487961 440.51399090
0.38047982 0.55735065 0.73796703 -194.81462851
Axis 0.02792848 -0.44085008 -0.89714615
Axis point 282.50960891 177.51273883 -0.00000000
Rotation angle (degrees) 110.05193761
Shift along axis -12.94261544
> view matrix models
> #10,-0.34182,0.82623,-0.44777,229.72,-0.8593,-0.081886,0.50488,437.34,0.38048,0.55735,0.73797,-195
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2599, steps = 156
shifted from previous position = 1.14
rotated from previous position = 9.04 degrees
atoms outside contour = 833, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.45872163 0.81212497 -0.36059324 247.48067508
-0.82174281 -0.23330803 0.51990970 459.99493705
0.33810235 0.53480874 0.77438129 -184.41354908
Axis 0.00838412 -0.39317631 -0.91942487
Axis point 274.05877206 187.43100939 0.00000000
Rotation angle (degrees) 117.31126040
Shift along axis -9.22980119
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2598, steps = 44
shifted from previous position = 0.00633
rotated from previous position = 0.0311 degrees
atoms outside contour = 834, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.45896836 0.81212458 -0.36028002 247.49162144
-0.82169925 -0.23380150 0.51975685 460.13276877
0.33787331 0.53459378 0.77462964 -184.34467270
Axis 0.00835037 -0.39292734 -0.91953161
Axis point 274.05090813 187.48722626 0.00000000
Rotation angle (degrees) 117.32711985
Shift along axis -9.22134789
> select subtract #10
Nothing selected
> select add #9
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3429, steps = 48
shifted from previous position = 0.00482
rotated from previous position = 0.0297 degrees
atoms outside contour = 743, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.43081558 0.88894856 -0.15546189 -55.95005334
-0.90228110 0.42106768 -0.09268672 425.80064604
-0.01693375 0.18020121 0.98348400 -34.87414002
Axis 0.15017068 -0.07623227 -0.98571670
Axis point 305.98064381 257.76012713 0.00000000
Rotation angle (degrees) 65.31156844
Shift along axis -6.48578615
> view matrix models
> #9,0.4316,0.89467,-0.11531,-65.618,-0.89754,0.41312,-0.15414,438.65,-0.090268,0.17002,0.9813,-10.378
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3431, steps = 64
shifted from previous position = 1.09
rotated from previous position = 4.24 degrees
atoms outside contour = 742, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.43055940 0.88906107 -0.15552817 -55.89625549
-0.90240047 0.42078031 -0.09282959 425.91491378
-0.01708798 0.18031735 0.98346005 -34.86764887
Axis 0.15029165 -0.07617294 -0.98570285
Axis point 305.98630048 257.75976176 0.00000000
Rotation angle (degrees) 65.32946065
Shift along axis -6.47479083
> view matrix models
> #9,0.43056,0.88906,-0.15553,-54.331,-0.9024,0.42078,-0.09283,423.75,-0.017088,0.18032,0.98346,-34.882
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3431, steps = 80
shifted from previous position = 2.68
rotated from previous position = 0.0172 degrees
atoms outside contour = 743, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.43071344 0.88901482 -0.15536599 -55.96059835
-0.90232909 0.42096990 -0.09266369 425.81899077
-0.01697499 0.18010275 0.98350133 -34.85342199
Axis 0.15009690 -0.07615328 -0.98573404
Axis point 305.95098058 257.77200239 0.00000000
Rotation angle (degrees) 65.31732552
Shift along axis -6.47082065
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3428, steps = 44
shifted from previous position = 0.0224
rotated from previous position = 0.0238 degrees
atoms outside contour = 742, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.43075065 0.88903334 -0.15515669 -56.01434867
-0.90231565 0.42107410 -0.09232048 425.73733288
-0.01674352 0.17976741 0.98356664 -34.83608674
Axis 0.14973134 -0.07616946 -0.98578838
Axis point 305.89070127 257.77776616 0.00000000
Rotation angle (degrees) 65.31080747
Shift along axis -6.47427740
> view matrix models
> #9,0.43075,0.88903,-0.15516,-52.084,-0.90232,0.42107,-0.09232,420.48,-0.016744,0.17977,0.98357,-34.866
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.092, steps = 72
shifted from previous position = 3.1
rotated from previous position = 10.3 degrees
atoms outside contour = 201, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.50141154 0.86520879 0.00048075 -99.84074559
-0.86418861 0.50084714 -0.04827203 382.71666870
-0.04200616 0.02378869 0.99883412 5.27911260
Axis 0.04161944 0.02453878 -0.99883215
Axis point 282.26220433 278.05067915 0.00000000
Rotation angle (degrees) 59.96384426
Shift along axis -0.03686481
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.092, steps = 40
shifted from previous position = 0.00281
rotated from previous position = 0.00699 degrees
atoms outside contour = 201, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.50138790 0.86522248 0.00048859 -99.83717711
-0.86419711 0.50082103 -0.04839061 382.74779744
-0.04211334 0.02384023 0.99882837 5.29653833
Axis 0.04171693 0.02460475 -0.99882646
Axis point 282.28124064 278.06078612 0.00000000
Rotation angle (degrees) 59.96568043
Shift along axis -0.03780880
> select subtract #9
Nothing selected
> hide #!6.1 models
> color #9 #fa7d41ff
> hide #10 models
> show #10 models
> select add #10
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> view matrix models
> #10,-0.45897,0.81212,-0.36028,247.43,-0.8217,-0.2338,0.51976,459.7,0.33787,0.53459,0.77463,-181.58
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2599, steps = 76
shifted from previous position = 2.81
rotated from previous position = 0.00998 degrees
atoms outside contour = 832, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.45907437 0.81210356 -0.36019233 247.49908529
-0.82160065 -0.23385719 0.51988765 460.10057019
0.33796905 0.53460136 0.77458265 -184.36844023
Axis 0.00828152 -0.39295572 -0.91952010
Axis point 274.03289274 187.48709972 0.00000000
Rotation angle (degrees) 117.33384960
Shift along axis -9.21899693
> view matrix models
> #10,-0.48466,0.74828,-0.45297,289.01,-0.84682,-0.27169,0.45725,489.2,0.21908,0.6052,0.76534,-164.43
> view matrix models
> #10,-0.54275,0.73639,-0.40391,299.13,-0.81584,-0.34798,0.46186,497.47,0.19955,0.58021,0.78964,-157.56
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2626, steps = 92
shifted from previous position = 3.08
rotated from previous position = 11.8 degrees
atoms outside contour = 823, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.46991203 0.84532728 -0.25417409 222.73768167
-0.84409672 -0.34608621 0.40954248 518.30839037
0.25823129 0.40699646 0.87616805 -148.38916888
Axis -0.00144216 -0.29024506 -0.95695127
Axis point 273.31109525 211.77385464 0.00000000
Rotation angle (degrees) 118.02878544
Shift along axis -8.75647093
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2626, steps = 48
shifted from previous position = 0.00437
rotated from previous position = 0.0141 degrees
atoms outside contour = 824, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.46994686 0.84537908 -0.25393729 222.68269933
-0.84405198 -0.34618769 0.40954892 518.32028108
0.25831413 0.40680250 0.87623370 -148.37999222
Axis -0.00155570 -0.29016404 -0.95697566
Axis point 273.28563242 211.79406149 0.00000000
Rotation angle (degrees) 118.03107852
Shift along axis -8.74829333
> view matrix models
> #10,-0.5163,0.83012,-0.21056,231.3,-0.82382,-0.41423,0.38696,533.24,0.234,0.37325,0.89773,-137.47
> view matrix models
> #10,-0.52315,0.81421,-0.25175,245.41,-0.83166,-0.42321,0.35948,543.23,0.18615,0.39744,0.89855,-129.35
> view matrix models
> #10,-0.52481,0.80915,-0.26429,249.63,-0.83377,-0.4261,0.35109,546.23,0.17147,0.40461,0.89827,-126.68
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2636, steps = 76
shifted from previous position = 2.44
rotated from previous position = 2.54 degrees
atoms outside contour = 809, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.49235645 0.82007490 -0.29165437 243.10432160
-0.85363344 -0.38951910 0.34581036 545.08387355
0.16998545 0.41922789 0.89182560 -130.64623661
Axis 0.04224843 -0.26565261 -0.96314265
Axis point 282.44675723 217.10127815 0.00000000
Rotation angle (degrees) 119.67139738
Shift along axis -8.70121670
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2626, steps = 144
shifted from previous position = 0.342
rotated from previous position = 2.13 degrees
atoms outside contour = 808, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.47505739 0.81838272 -0.32337313 245.35142587
-0.86714010 -0.37289473 0.33017805 547.80974109
0.14962788 0.43726334 0.88679887 -128.50019801
Axis 0.06105534 -0.26968444 -0.96101121
Axis point 286.64086834 216.15142582 0.00000000
Rotation angle (degrees) 118.72306907
Shift along axis -9.26561666
> view matrix models
> #10,-0.47506,0.81838,-0.32337,246.01,-0.86714,-0.37289,0.33018,546.24,0.14963,0.43726,0.8868,-128.94
> view matrix models
> #10,-0.50135,0.778,-0.37863,274.56,-0.86039,-0.402,0.31324,554.64,0.091494,0.48281,0.87093,-119.57
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2915, steps = 168
shifted from previous position = 1.55
rotated from previous position = 13 degrees
atoms outside contour = 806, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.62646300 0.73647792 -0.25523395 293.39321320
-0.77894435 -0.57973324 0.23907123 590.59453011
0.02810308 0.34858233 0.93685674 -81.62535318
Axis 0.07085497 -0.18332239 -0.98049604
Axis point 285.79567182 232.07102359 0.00000000
Rotation angle (degrees) 129.39549496
Shift along axis -7.44749726
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2915, steps = 60
shifted from previous position = 0.0197
rotated from previous position = 0.031 degrees
atoms outside contour = 805, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.62645079 0.73651144 -0.25516721 293.37930862
-0.77893728 -0.57953661 0.23957049 590.44525285
0.02856767 0.34883838 0.93674737 -81.77946703
Axis 0.07069387 -0.18357010 -0.98046132
Axis point 285.76935571 232.01630242 0.00000000
Rotation angle (degrees) 129.39180697
Shift along axis -7.46637011
> view matrix models
> #10,-0.65507,0.68109,-0.32711,329.57,-0.75517,-0.6042,0.25429,586.41,-0.024443,0.4136,0.91013,-76.368
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2915, steps = 92
shifted from previous position = 1.03
rotated from previous position = 5.47 degrees
atoms outside contour = 807, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.62641848 0.73654460 -0.25515080 293.35888586
-0.77897050 -0.57960331 0.23930095 590.52659984
0.02836958 0.34865749 0.93682074 -81.69670194
Axis 0.07074976 -0.18342752 -0.98048397
Axis point 285.78130656 232.04734436 0.00000000
Rotation angle (degrees) 129.39036260
Shift along axis -7.46145472
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2915, steps = 60
shifted from previous position = 0.0144
rotated from previous position = 0.0247 degrees
atoms outside contour = 807, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.62665400 0.73642867 -0.25490696 293.39145875
-0.77878367 -0.57991394 0.23915645 590.57759405
0.02829757 0.34838573 0.93692401 -81.63909936
Axis 0.07068407 -0.18326632 -0.98051885
Axis point 285.75804624 232.08178944 0.00000000
Rotation angle (degrees) 129.40678125
Shift along axis -7.44620260
> view matrix models
> #10,-0.73425,0.64301,-0.21773,340.08,-0.6787,-0.68812,0.2566,583.57,0.01517,0.33619,0.94167,-75.794
> view matrix models
> #10,-0.78664,0.58479,-0.19805,365.55,-0.61733,-0.73953,0.26832,575.48,0.01044,0.33333,0.94275,-73.93
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2679, steps = 160
shifted from previous position = 1.35
rotated from previous position = 19.1 degrees
atoms outside contour = 821, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.69045958 0.64215276 -0.33302461 352.74236478
-0.71064280 -0.51616834 0.47807640 503.74426218
0.13510132 0.56675398 0.81273460 -140.14317458
Axis 0.06182871 -0.32639167 -0.94321031
Axis point 283.86454132 196.95419443 0.00000000
Rotation angle (degrees) 134.18254447
Shift along axis -10.42383908
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2679, steps = 44
shifted from previous position = 0.00825
rotated from previous position = 0.0144 degrees
atoms outside contour = 820, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.69035378 0.64220159 -0.33314977 352.73387407
-0.71072859 -0.51596128 0.47817237 503.69515483
0.13519067 0.56688718 0.81262684 -140.17962089
Axis 0.06184608 -0.32649587 -0.94317311
Axis point 283.87303177 196.92757566 0.00000000
Rotation angle (degrees) 134.17435145
Shift along axis -10.42553272
> fitmap #11 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#11) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.099, steps = 40
shifted from previous position = 0.0172
rotated from previous position = 0.0183 degrees
atoms outside contour = 208, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#11) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.99998905 0.00137221 0.00446927 541.84223356
-0.00158534 -0.99884422 -0.04803821 555.67989885
0.00439819 -0.04804478 0.99883546 12.17812607
Axis -0.00221850 0.02402764 -0.99970883
Axis point 271.11315612 277.78586494 0.00000000
Rotation angle (degrees) 179.91524754
Shift along axis -0.02497863
> fitmap #12 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#12) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.092, steps = 44
shifted from previous position = 0.0164
rotated from previous position = 0.00859 degrees
atoms outside contour = 201, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#12) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.50132805 -0.86524467 0.00466751 641.74373238
0.86404208 -0.50090249 -0.05027849 185.71392730
0.04584117 -0.02117310 0.99872427 -6.35037358
Axis 0.01682372 -0.02379950 0.99957518
Axis point 267.41670156 277.68219195 0.00000000
Rotation angle (degrees) 120.11605473
Shift along axis 0.02894002
> fitmap #13 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#13) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.087, steps = 40
shifted from previous position = 0.0183
rotated from previous position = 0.0171 degrees
atoms outside contour = 204, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#13) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.49920594 -0.86648021 0.00232134 370.75408935
0.86538213 0.49843470 -0.05173525 -85.77682652
0.04367054 0.02783539 0.99865805 -19.07094375
Axis 0.04588366 -0.02384363 0.99866219
Axis point 260.01625020 277.60467430 0.00000000
Rotation angle (degrees) 60.12236081
Shift along axis 0.01135631
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2679, steps = 44
shifted from previous position = 0.0174
rotated from previous position = 0.0197 degrees
atoms outside contour = 816, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.69024690 0.64220296 -0.33336849 352.75449235
-0.71082104 -0.51570778 0.47830839 503.64299014
0.13525034 0.56711623 0.81245707 -140.20608389
Axis 0.06190294 -0.32664778 -0.94311678
Axis point 283.89184618 196.89436903 0.00000000
Rotation angle (degrees) 134.16673888
Shift along axis -10.44661410
> select subtract #10
Nothing selected
> select add #9
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> view matrix models
> #9,0.48988,0.86797,-0.081577,-80.623,-0.86965,0.49309,0.024099,371.65,0.061142,0.059137,0.99638,-33.119
> view matrix models
> #9,0.13841,0.99024,-0.016474,-19.49,-0.98967,0.13892,0.0354,489.83,0.037343,0.011404,0.99924,-15.214
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2608, steps = 80
shifted from previous position = 2.13
rotated from previous position = 6.17 degrees
atoms outside contour = 828, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.19350872 0.97870791 0.06844856 -50.76105780
-0.98103281 0.19383195 0.00195088 482.30821138
-0.01135818 -0.06752779 0.99765274 18.60428476
Axis -0.03540142 0.04066388 -0.99854554
Axis point 267.70278809 272.35986583 0.00000000
Rotation angle (degrees) 78.90147495
Shift along axis 2.83231072
> view matrix models
> #9,0.34838,0.93735,0.00019153,-72.761,-0.93723,0.34833,0.01608,429.45,0.015006,-0.0057815,0.99987,-4.4431
> view matrix models
> #9,-0.07083,0.98835,0.13469,11.521,-0.99665,-0.064593,-0.050131,559.45,-0.040847,-0.13779,0.98962,45.786
> view matrix models
> #9,-0.082764,0.92067,0.38147,-18.263,-0.99186,-0.11325,0.058137,547.98,0.096727,-0.37355,0.92255,75.345
> view matrix models
> #9,-0.082764,0.92067,0.38147,-28.594,-0.99186,-0.11325,0.058137,545.63,0.096727,-0.37355,0.92255,74.582
> view matrix models
> #9,-0.01802,0.99918,0.036272,2.7902,-0.95957,-0.0070909,-0.28139,578.8,-0.2809,-0.039877,0.95891,98.414
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2966, steps = 164
shifted from previous position = 1.63
rotated from previous position = 13.3 degrees
atoms outside contour = 790, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.18236024 0.98156913 0.05715579 -53.35272309
-0.96842839 0.18936012 -0.16213948 507.56709544
-0.16997414 -0.02578350 0.98511117 58.88840412
Axis 0.06928973 0.11541681 -0.99089752
Axis point 282.35559943 289.30986437 0.00000000
Rotation angle (degrees) 79.72250403
Shift along axis -3.46739635
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2967, steps = 44
shifted from previous position = 0.00915
rotated from previous position = 0.0335 degrees
atoms outside contour = 794, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.18248685 0.98155722 0.05695588 -53.34015310
-0.96832063 0.18946449 -0.16266030 507.62380575
-0.17045151 -0.02546819 0.98503688 58.96504355
Axis 0.06971562 0.11555947 -0.99085102
Axis point 282.45228044 289.34202550 0.00000000
Rotation angle (degrees) 79.71794177
Shift along axis -3.48347831
> select add #10
2432 atoms, 2484 bonds, 300 residues, 2 models selected
> select subtract #9
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> view matrix models
> #10,-0.69025,0.6422,-0.33337,343.6,-0.71082,-0.51571,0.47831,508.21,0.13525,0.56712,0.81246,-141.16
> select add #9
2432 atoms, 2484 bonds, 300 residues, 2 models selected
> select subtract #10
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2966, steps = 48
shifted from previous position = 0.0117
rotated from previous position = 0.0314 degrees
atoms outside contour = 792, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.18236893 0.98156873 0.05713505 -53.34662037
-0.96842224 0.18936594 -0.16216940 507.58189140
-0.16999984 -0.02575619 0.98510745 58.90480670
Axis 0.06931888 0.11541944 -0.99089517
Axis point 282.37246944 289.31421476 0.00000000
Rotation angle (degrees) 79.72219004
Shift along axis -3.48159856
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2967, steps = 40
shifted from previous position = 0.0196
rotated from previous position = 0.00654 degrees
atoms outside contour = 790, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.18237174 0.98156839 0.05713184 -53.35036884
-0.96840242 0.18937110 -0.16228170 507.58662104
-0.17010971 -0.02573102 0.98508914 58.91753852
Axis 0.06938867 0.11547353 -0.99088399
Axis point 282.37709621 289.32178302 0.00000000
Rotation angle (degrees) 79.72249095
Shift along axis -3.46953848
> view matrix models
> #9,0.18463,0.98239,-0.028556,-37.005,-0.98053,0.18215,-0.073349,495.04,-0.066856,0.041543,0.9969,9.957
> view matrix models
> #9,0.33228,0.94318,-0.0029871,-76.233,-0.94314,0.33223,-0.010903,435.42,-0.0092912,0.0064401,0.99994,0.81422
> view matrix models
> #9,0.29519,0.95541,0.0078788,-70.423,-0.95541,0.29524,-0.005384,446.82,-0.00747,-0.0059381,0.99995,3.2472
> view matrix models
> #9,0.29519,0.95541,0.0078788,-67.908,-0.95541,0.29524,-0.005384,445.03,-0.00747,-0.0059381,0.99995,3.2741
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2932, steps = 96
shifted from previous position = 1.5
rotated from previous position = 7.15 degrees
atoms outside contour = 790, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.37850249 0.92312660 -0.06762514 -67.81548525
-0.92533707 0.37564134 -0.05142862 424.97423632
-0.02207233 0.08204191 0.99638444 -12.88995694
Axis 0.07199695 -0.02457219 -0.99710212
Axis point 281.76416990 262.96849039 0.00000000
Rotation angle (degrees) 67.95936125
Shift along axis -2.47245310
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2932, steps = 48
shifted from previous position = 0.0167
rotated from previous position = 0.029 degrees
atoms outside contour = 790, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.37811322 0.92327563 -0.06776810 -67.71751520
-0.92549179 0.37522990 -0.05164758 425.14705679
-0.02225634 0.08224746 0.99636340 -12.88996285
Axis 0.07221299 -0.02454565 -0.99708716
Axis point 281.79393111 262.95813903 0.00000000
Rotation angle (degrees) 67.98475639
Shift along axis -2.47317902
> view matrix models
> #9,0.46694,0.87982,-0.088792,-79.234,-0.88402,0.46198,-0.071253,396.03,-0.02167,0.11176,0.9935,-19.578
> view matrix models
> #9,0.46714,0.87606,-0.11956,-72.213,-0.87254,0.43489,-0.2226,429.54,-0.14302,0.20831,0.96755,-1.7957
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2726, steps = 104
shifted from previous position = 4.08
rotated from previous position = 7.33 degrees
atoms outside contour = 819, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.52861284 0.84736378 -0.05042905 -93.47253152
-0.84306236 0.51714009 -0.14768880 386.88489880
-0.09906725 0.12058503 0.98774741 5.79986235
Axis 0.15667706 0.02840564 -0.98724132
Axis point 301.09903826 276.07616257 0.00000000
Rotation angle (degrees) 58.88548948
Shift along axis -9.38115114
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2726, steps = 48
shifted from previous position = 0.00526
rotated from previous position = 0.0113 degrees
atoms outside contour = 819, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.52875268 0.84728075 -0.05035813 -93.50177990
-0.84298030 0.51729559 -0.14761267 386.81183468
-0.09901934 0.12050150 0.98776240 5.80309068
Axis 0.15660096 0.02842219 -0.98725292
Axis point 301.08838830 276.08362951 0.00000000
Rotation angle (degrees) 58.87510479
Shift along axis -9.37754635
> view matrix models
> #9,0.52875,0.84728,-0.050358,-94.387,-0.84298,0.5173,-0.14761,388.49,-0.099019,0.1205,0.98776,5.7968
> view matrix models
> #9,0.53691,0.83688,-0.10662,-82.994,-0.82929,0.50033,-0.24889,408.87,-0.15495,0.22205,0.96265,2.9303
> view matrix models
> #9,0.42189,0.89582,-0.1397,-56.611,-0.89353,0.3847,-0.23151,452.08,-0.15365,0.2225,0.96275,2.4184
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3016, steps = 452
shifted from previous position = 2.86
rotated from previous position = 17.5 degrees
atoms outside contour = 774, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.65070841 0.72139481 -0.23699809 -55.77446810
-0.75542240 0.58340782 -0.29828227 378.24989778
-0.07691274 0.37312845 0.92458618 -46.83676724
Axis 0.41186899 -0.09820247 -0.90593610
Axis point 364.12003956 243.52037284 0.00000000
Rotation angle (degrees) 54.59507746
Shift along axis -17.68572882
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3016, steps = 44
shifted from previous position = 0.00789
rotated from previous position = 0.0253 degrees
atoms outside contour = 774, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.65085681 0.72137615 -0.23664715 -55.88025383
-0.75525706 0.58348907 -0.29854194 378.23934814
-0.07728002 0.37303748 0.92459226 -46.72000903
Axis 0.41201483 -0.09777194 -0.90591635
Axis point 364.16735498 243.62085686 0.00000000
Rotation angle (degrees) 54.58679194
Shift along axis -17.68026647
> view matrix models
> #9,0.65086,0.72138,-0.23665,-55.21,-0.75526,0.58349,-0.29854,377.45,-0.07728,0.37304,0.92459,-52.35
> view matrix models
> #9,0.60727,0.78847,-0.09765,-86.396,-0.79426,0.5995,-0.098748,344.97,-0.019318,0.13753,0.99031,-26.056
> view matrix models
> #9,0.82625,0.55523,-0.095062,-95.421,-0.56174,0.79958,-0.21242,251.22,-0.041931,0.22891,0.97254,-37.776
> view matrix models
> #9,0.82625,0.55523,-0.095062,-98.321,-0.56174,0.79958,-0.21242,253.58,-0.041931,0.22891,0.97254,-35.909
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2964, steps = 144
shifted from previous position = 4.76
rotated from previous position = 15.7 degrees
atoms outside contour = 785, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.87382541 0.41097136 -0.25986864 -38.84217653
-0.48359780 0.79018468 -0.37648551 269.61831477
0.05061946 0.45465451 0.88922829 -99.23943565
Axis 0.65966598 -0.24643072 -0.71000894
Axis point 459.36752043 200.86831609 0.00000000
Rotation angle (degrees) 39.04793494
Shift along axis -21.60421234
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2963, steps = 44
shifted from previous position = 0.0225
rotated from previous position = 0.0512 degrees
atoms outside contour = 789, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.87424076 0.41036199 -0.25943428 -38.89353517
-0.48284537 0.79064968 -0.37647502 269.31425568
0.05063059 0.45439644 0.88935956 -99.20712069
Axis 0.66010675 -0.24633884 -0.70963107
Axis point 459.64464863 200.86957404 0.00000000
Rotation angle (degrees) 39.00190882
Shift along axis -21.61599166
> view matrix models
> #9,0.87164,0.40575,-0.27496,-33.903,-0.48906,0.75718,-0.433,290.54,0.032503,0.5119,0.85843,-101.47
> view matrix models
> #9,0.87164,0.40575,-0.27496,-33.077,-0.48906,0.75718,-0.433,292.01,0.032503,0.5119,0.85843,-101.67
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2964, steps = 60
shifted from previous position = 1.56
rotated from previous position = 3.86 degrees
atoms outside contour = 787, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.87403962 0.41046181 -0.25995358 -38.75680993
-0.48319192 0.79030271 -0.37675882 269.54277613
0.05079691 0.45490959 0.88908770 -99.32466259
Axis 0.66020918 -0.24668524 -0.70941542
Axis point 459.69243100 200.71990375 0.00000000
Rotation angle (degrees) 39.03921901
Shift along axis -21.61737932
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2963, steps = 28
shifted from previous position = 0.00931
rotated from previous position = 0.0285 degrees
atoms outside contour = 785, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.87412613 0.41051109 -0.25958458 -38.87051865
-0.48305185 0.79050531 -0.37651331 269.39535569
0.05064009 0.45451294 0.88929949 -99.22799153
Axis 0.66002318 -0.24638870 -0.70969149
Axis point 459.56207150 200.85735684 0.00000000
Rotation angle (degrees) 39.01643054
Shift along axis -21.61015327
> view matrix models
> #9,0.86966,0.42026,-0.25899,-40.015,-0.4936,0.73294,-0.46814,304.74,-0.0069178,0.53496,0.84485,-92.664
> view matrix models
> #9,0.86966,0.42026,-0.25899,-39.554,-0.4936,0.73294,-0.46814,310.59,-0.0069178,0.53496,0.84485,-93.244
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2845, steps = 96
shifted from previous position = 4.61
rotated from previous position = 3.25 degrees
atoms outside contour = 800, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.85829272 0.45540789 -0.23651061 -45.02496671
-0.50982452 0.70427961 -0.49403360 326.71496768
-0.05841720 0.54460435 0.83665617 -78.63861079
Axis 0.72680740 -0.12462437 -0.67544042
Axis point 0.00000000 310.64589441 470.24655168
Rotation angle (degrees) 45.60393708
Shift along axis -20.32543118
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2845, steps = 80
shifted from previous position = 0.00597
rotated from previous position = 0.00779 degrees
atoms outside contour = 799, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.85824688 0.45544509 -0.23660530 -45.00503405
-0.50991175 0.70427802 -0.49394583 326.72259472
-0.05832928 0.54457529 0.83668122 -78.65616062
Axis 0.72671450 -0.12475025 -0.67551714
Axis point 0.00000000 310.70041242 470.30534774
Rotation angle (degrees) 45.60483405
Shift along axis -20.33095204
> view matrix models
> #9,0.85825,0.45545,-0.23661,-45.841,-0.50991,0.70428,-0.49395,328.22,-0.058329,0.54458,0.83668,-78.787
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2845, steps = 72
shifted from previous position = 1.72
rotated from previous position = 0.00491 degrees
atoms outside contour = 800, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.85828442 0.45540488 -0.23654650 -45.01645152
-0.50984779 0.70432874 -0.49393953 326.69166231
-0.05833597 0.54454332 0.83670156 -78.65351926
Axis 0.72674180 -0.12471370 -0.67549452
Axis point 0.00000000 310.68757470 470.29049083
Rotation angle (degrees) 45.60047993
Shift along axis -20.32824311
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2847, steps = 100
shifted from previous position = 0.0197
rotated from previous position = 0.0206 degrees
atoms outside contour = 804, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.85843020 0.45512416 -0.23655780 -44.99122021
-0.50962906 0.70454365 -0.49385877 326.57190588
-0.05810176 0.54450001 0.83674604 -78.70135014
Axis 0.72685685 -0.12492021 -0.67533255
Axis point 0.00000000 310.75495296 470.20629564
Rotation angle (degrees) 45.58423187
Shift along axis -20.34802237
> view matrix models
> #9,0.85843,0.45512,-0.23656,-48.101,-0.50963,0.70454,-0.49386,329.4,-0.058102,0.5445,0.83675,-79.186
> view matrix models
> #9,0.83391,0.37053,-0.40903,14.082,-0.52037,0.7748,-0.35902,288.61,0.18389,0.51224,0.83893,-143.19
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2835, steps = 72
shifted from previous position = 1.57
rotated from previous position = 2.46 degrees
atoms outside contour = 790, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.82039865 0.35631052 -0.44720115 27.85382955
-0.52879941 0.77032412 -0.35633123 291.20657185
0.21752526 0.52881337 0.82038966 -151.96013636
Axis 0.62452526 -0.46900635 -0.62450080
Axis point 0.00000000 478.08972049 477.11779617
Rotation angle (degrees) 45.12550301
Shift along axis -24.28308347
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2836, steps = 52
shifted from previous position = 0.00347
rotated from previous position = 0.0314 degrees
atoms outside contour = 791, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.82030677 0.35655833 -0.44717219 27.81591077
-0.52888322 0.77049558 -0.35583578 291.08973449
0.21766798 0.52839636 0.82062046 -151.94585108
Axis 0.62401756 -0.46918893 -0.62487105
Axis point 476.85500616 119.82783789 0.00000000
Rotation angle (degrees) 45.11295401
Shift along axis -24.27190075
> view matrix models
> #9,0.82031,0.35656,-0.44717,28.566,-0.52888,0.7705,-0.35584,290.16,0.21767,0.5284,0.82062,-150.64
> ui tool show Matchmaker
> matchmaker #9 to #8
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 Terminator_1-coot-1.pdb, chain D (#8) with copy of
Terminator_1-coot-1.pdb, chain D (#9), sequence alignment score = 777.7
RMSD between 150 pruned atom pairs is 0.000 angstroms; (across all 150 pairs:
0.000)
> turn z 60 models #9
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.1677, steps = 420
shifted from previous position = 7.09
rotated from previous position = 13.4 degrees
atoms outside contour = 982, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.56963481 0.79976643 -0.18944621 -72.53753216
-0.81537486 0.52091432 -0.25261062 405.12765871
-0.10334425 0.29836547 0.94884037 -43.45015243
Axis 0.32245261 -0.05039021 -0.94524343
Axis point 337.37722345 271.14360437 0.00000000
Rotation angle (degrees) 58.68822239
Shift along axis -2.73341279
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.1675, steps = 48
shifted from previous position = 0.0273
rotated from previous position = 0.102 degrees
atoms outside contour = 983, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.56996062 0.79914813 -0.19106853 -72.12202875
-0.81530023 0.52113495 -0.25239636 405.00457503
-0.10212959 0.29963419 0.94857205 -44.03862139
Axis 0.32310172 -0.05205568 -0.94493147
Axis point 337.54338256 270.76747665 0.00000000
Rotation angle (degrees) 58.67889616
Shift along axis -2.77206004
> view matrix models
> #9,0.56996,0.79915,-0.19107,-69.217,-0.8153,0.52113,-0.2524,401.38,-0.10213,0.29963,0.94857,-38.621
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2879, steps = 116
shifted from previous position = 5.26
rotated from previous position = 13.8 degrees
atoms outside contour = 812, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.72621253 0.67216504 -0.14425516 -88.38813154
-0.68738927 0.70673980 -0.16737641 305.45158949
-0.01055371 0.22071029 0.97528233 -46.95505767
Axis 0.27326829 -0.09414485 -0.95731979
Axis point 331.02969677 263.09740749 -0.00000000
Rotation angle (degrees) 45.24172258
Shift along axis -7.95936268
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.288, steps = 44
shifted from previous position = 0.000721
rotated from previous position = 0.00988 degrees
atoms outside contour = 811, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.72626314 0.67209237 -0.14433892 -88.36754610
-0.68733561 0.70676135 -0.16750574 305.45707733
-0.01056617 0.22086252 0.97524773 -46.98211077
Axis 0.27347372 -0.09419753 -0.95725595
Axis point 331.07595834 263.08416842 0.00000000
Rotation angle (degrees) 45.24020712
Shift along axis -7.96559993
> view matrix models
> #9,0.86877,0.44852,-0.20993,-63.488,-0.49175,0.83142,-0.2587,236.19,0.058505,0.32798,0.94287,-86.567
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2731, steps = 68
shifted from previous position = 4.06
rotated from previous position = 8.17 degrees
atoms outside contour = 831, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.87209312 0.44144456 -0.21114051 -59.16373811
-0.48927201 0.77943411 -0.39127407 277.24652285
-0.00815569 0.44453256 0.89572558 -85.64382959
Axis 0.65952588 -0.16017310 -0.73441827
Axis point 454.03354337 234.90676290 0.00000000
Rotation angle (degrees) 39.31933795
Shift along axis -20.52905875
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2731, steps = 48
shifted from previous position = 0.00637
rotated from previous position = 0.0326 degrees
atoms outside contour = 829, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.87214986 0.44159046 -0.21060037 -59.33030744
-0.48916339 0.77952748 -0.39122385 277.18299952
-0.00859194 0.44422381 0.89587467 -85.48030473
Axis 0.65943275 -0.15944861 -0.73465951
Axis point 453.97429122 235.14592031 0.00000000
Rotation angle (degrees) 39.30580902
Shift along axis -20.52187435
> view matrix models
> #9,0.87215,0.44159,-0.2106,-54.621,-0.48916,0.77953,-0.39122,276.07,-0.0085919,0.44422,0.89587,-88.246
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2823, steps = 68
shifted from previous position = 3.09
rotated from previous position = 4.42 degrees
atoms outside contour = 810, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.84497009 0.48677063 -0.22153991 -57.34830762
-0.53273653 0.72960606 -0.42879692 310.65541680
-0.04708889 0.48034297 0.87581579 -82.87911959
Axis 0.66019151 -0.12668136 -0.74033709
Axis point 456.66000456 241.74807084 0.00000000
Rotation angle (degrees) 43.51484831
Shift along axis -15.85663127
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2825, steps = 44
shifted from previous position = 0.0212
rotated from previous position = 0.0185 degrees
atoms outside contour = 808, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.84512991 0.48650280 -0.22151860 -57.31753650
-0.53249549 0.72978543 -0.42879110 310.55024436
-0.04694703 0.48034183 0.87582403 -82.93391013
Axis 0.66036197 -0.12680261 -0.74016428
Axis point 456.76755768 241.71346750 0.00000000
Rotation angle (degrees) 43.50039119
Shift along axis -15.84418556
> view matrix models
> #9,0.85034,0.45117,-0.27085,-40.459,-0.5241,0.67993,-0.51285,336.93,-0.04722,0.57805,0.81463,-94.036
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2803, steps = 60
shifted from previous position = 1.12
rotated from previous position = 3.2 degrees
atoms outside contour = 804, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.87127114 0.42097914 -0.25231566 -41.74099644
-0.49011974 0.71918506 -0.49249925 314.23889954
-0.02587025 0.55276526 0.83293537 -97.69771533
Axis 0.74397340 -0.16117390 -0.64848019
Axis point 0.00000000 332.06762050 442.70608712
Rotation angle (degrees) 44.62694393
Shift along axis -18.34626804
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.28, steps = 44
shifted from previous position = 0.0315
rotated from previous position = 0.0259 degrees
atoms outside contour = 801, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.87139966 0.42093037 -0.25195292 -41.82036406
-0.48987251 0.71917247 -0.49276354 314.25193048
-0.02622154 0.55281878 0.83288886 -97.60506954
Axis 0.74423686 -0.16067373 -0.64830197
Axis point 0.00000000 331.86525418 442.62301020
Rotation angle (degrees) 44.62411282
Shift along axis -18.33872631
> undo
> ui tool show "Show Sequence Viewer"
> ui tool show Matchmaker
> matchmaker #9 to #8
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 Terminator_1-coot-1.pdb, chain D (#8) with copy of
Terminator_1-coot-1.pdb, chain D (#9), sequence alignment score = 777.7
RMSD between 150 pruned atom pairs is 0.000 angstroms; (across all 150 pairs:
0.000)
> turn y 60 models #9
> view matrix models
> #9,0.50177,0.86496,0.0088708,-105.52,-0.8609,0.50036,-0.092178,391.82,-0.084169,0.038615,0.9957,14.983
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3106, steps = 72
shifted from previous position = 1.92
rotated from previous position = 2 degrees
atoms outside contour = 798, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.48179358 0.87611114 -0.01744252 -98.17094522
-0.87334741 0.47845502 -0.09135158 400.83369178
-0.07168867 0.05924599 0.99566595 4.79931456
Axis 0.08572430 0.03087841 -0.99584028
Axis point 289.77010375 283.36766147 0.00000000
Rotation angle (degrees) 61.44792719
Shift along axis -0.81788015
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.3106, steps = 40
shifted from previous position = 0.0165
rotated from previous position = 0.0255 degrees
atoms outside contour = 801, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.48167561 0.87616762 -0.01785848 -98.05488327
-0.87342180 0.47830231 -0.09144000 400.91911608
-0.07157502 0.05964241 0.99565046 4.67982080
Axis 0.08599267 0.03057423 -0.99582653
Axis point 289.83788405 283.29415936 0.00000000
Rotation angle (degrees) 61.45725999
Shift along axis -0.83449797
> view matrix models
> #9,0.50873,0.85929,-0.05312,-94.891,-0.85475,0.49674,-0.15051,402.85,-0.10295,0.12198,0.98718,0.65318
> view matrix models
> #9,0.42842,0.90166,-0.058939,-83.802,-0.89718,0.41672,-0.14635,435.92,-0.10739,0.11558,0.98748,4.0277
> view matrix models
> #9,0.42842,0.90166,-0.058939,-73.62,-0.89718,0.41672,-0.14635,429.54,-0.10739,0.11558,0.98748,4.0274
> view matrix models
> #9,0.41581,0.90155,-0.11966,-57.683,-0.89387,0.38087,-0.23651,455.28,-0.16765,0.2053,0.96423,4.8988
> view matrix models
> #9,0.41581,0.90155,-0.11966,-59.401,-0.89387,0.38087,-0.23651,456.64,-0.16765,0.2053,0.96423,1.8008
> select subtract #9
Nothing selected
> select add #8
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> rainbow sel
> select subtract #8
Nothing selected
> select add #9
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> rainbow sel
> select subtract #9
Nothing selected
> select add #9
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> view matrix models
> #9,0.53418,0.84272,-0.066862,-90.76,-0.8435,0.52608,-0.10834,381.18,-0.056128,0.11427,0.99186,-14.747
> view matrix models
> #9,0.32005,0.92062,-0.22367,-14.877,-0.94608,0.29809,-0.12682,469.89,-0.05008,0.2522,0.96638,-44.542
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2797, steps = 124
shifted from previous position = 2.18
rotated from previous position = 9.88 degrees
atoms outside contour = 793, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.47689231 0.85509059 -0.20345473 -45.24040802
-0.87842241 0.45554844 -0.14439429 415.01249606
-0.03078671 0.24757971 0.96837828 -50.00828911
Axis 0.21951405 -0.09669788 -0.97080539
Axis point 318.83950491 247.57095156 0.00000000
Rotation angle (degrees) 63.23003935
Shift along axis -1.51341926
> view matrix models
> #9,0.47689,0.85509,-0.20345,-46.061,-0.87842,0.45555,-0.14439,418.32,-0.030787,0.24758,0.96838,-49.561
> view matrix models
> #9,0.41274,0.87803,-0.24229,-24.868,-0.9038,0.36178,-0.22859,465.23,-0.11305,0.31333,0.94289,-35.993
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2591, steps = 84
shifted from previous position = 2.64
rotated from previous position = 5.52 degrees
atoms outside contour = 818, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.47844475 0.85965167 -0.17913585 -49.36966714
-0.87098137 0.43862204 -0.22136436 436.80286910
-0.11172331 0.26193460 0.95859700 -28.03649982
Axis 0.26878108 -0.03749070 -0.96247139
Axis point 334.21888808 259.37013068 0.00000000
Rotation angle (degrees) 64.03437118
Shift along axis -2.66134735
> view matrix models
> #9,0.44748,0.88587,-0.12249,-57.917,-0.88417,0.4588,0.088054,373.7,0.1342,0.068899,0.98856,-60.158
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2831, steps = 80
shifted from previous position = 2.89
rotated from previous position = 6.46 degrees
atoms outside contour = 779, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.44217438 0.89645661 -0.02911000 -79.39401058
-0.88458880 0.44122620 0.15106989 363.57936861
0.14827169 -0.04104885 0.98809439 -39.07953317
Axis -0.10672446 -0.09853783 -0.98939385
Axis point 256.40015975 246.76411798 0.00000000
Rotation angle (degrees) 64.16713327
Shift along axis 11.31200995
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.283, steps = 44
shifted from previous position = 0.0116
rotated from previous position = 0.0105 degrees
atoms outside contour = 778, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.44203170 0.89652658 -0.02912189 -79.37065916
-0.88464409 0.44108329 0.15116343 363.59938187
0.14836721 -0.04105653 0.98807974 -39.09937354
Axis -0.10677206 -0.09858954 -0.98938356
Axis point 256.37903803 246.74589980 0.00000000
Rotation angle (degrees) 64.17668900
Shift along axis 11.31175116
> view matrix models
> #9,0.44203,0.89653,-0.029122,-81.646,-0.88464,0.44108,0.15116,363.69,0.14837,-0.041057,0.98808,-39.238
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2831, steps = 60
shifted from previous position = 2.27
rotated from previous position = 0.0065 degrees
atoms outside contour = 777, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.44207861 0.89650150 -0.02918172 -79.37548068
-0.88460493 0.44113523 0.15124106 363.56340350
0.14846091 -0.04104615 0.98806609 -39.10951224
Axis -0.10681186 -0.09867708 -0.98937054
Axis point 256.36791191 246.73913536 0.00000000
Rotation angle (degrees) 64.17397749
Shift along axis 11.29666659
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2831, steps = 44
shifted from previous position = 0.0304
rotated from previous position = 0.0255 degrees
atoms outside contour = 779, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.44226769 0.89640798 -0.02918996 -79.38623444
-0.88457018 0.44133930 0.15084843 363.59468286
0.14810441 -0.04089482 0.98812587 -39.08091895
Axis -0.10652268 -0.09849562 -0.98941979
Axis point 256.44745224 246.77418600 0.00000000
Rotation angle (degrees) 64.15956164
Shift along axis 11.31138380
> hide #9 models
> hide #10 models
> select subtract #9
Nothing selected
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #9 models
> select add #9
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> view matrix models
> #9,0.44227,0.89641,-0.02919,-80.48,-0.88457,0.44134,0.15085,364.93,0.1481,-0.040895,0.98813,-39.046
> view matrix models
> #9,0.44227,0.89641,-0.02919,-82.04,-0.88457,0.44134,0.15085,364.41,0.1481,-0.040895,0.98813,-39.367
> view matrix models
> #9,0.39645,0.87508,-0.27761,-13.524,-0.90563,0.42236,0.03805,397.83,0.15055,0.23633,0.95994,-101.02
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2687, steps = 76
shifted from previous position = 2.36
rotated from previous position = 4.99 degrees
atoms outside contour = 810, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.44400524 0.85759882 -0.25958359 -26.22735910
-0.87290833 0.47938157 0.09068830 362.25387651
0.20221377 0.18632659 0.96145308 -102.10541343
Axis 0.05332150 -0.25746723 -0.96481472
Axis point 286.83762301 216.78276377 0.00000000
Rotation angle (degrees) 63.74161493
Shift along axis 3.84582079
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2686, steps = 48
shifted from previous position = 0.0217
rotated from previous position = 0.0178 degrees
atoms outside contour = 807, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.44408888 0.85747345 -0.25985452 -26.14416945
-0.87283521 0.47951966 0.09066214 362.20926292
0.20234573 0.18654812 0.96138236 -102.18584723
Axis 0.05346181 -0.25770256 -0.96474412
Axis point 286.88294494 216.71931271 0.00000000
Rotation angle (degrees) 63.73679118
Shift along axis 3.84322630
> view matrix models
> #9,0.44409,0.85747,-0.25985,-28.853,-0.87284,0.47952,0.090662,366.38,0.20235,0.18655,0.96138,-102.49
> view matrix models
> #9,0.32139,0.82796,-0.45957,54.506,-0.82471,0.48323,0.29384,310.5,0.46536,0.28458,0.83813,-178.79
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2713, steps = 92
shifted from previous position = 1.48
rotated from previous position = 6.04 degrees
atoms outside contour = 817, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.37396301 0.77217877 -0.51370384 64.99282454
-0.81671843 0.53663982 0.21210547 312.38422595
0.43945727 0.34023179 0.83133608 -182.47613265
Axis 0.06898562 -0.51319989 -0.85549217
Axis point 294.79951706 154.86251144 0.00000000
Rotation angle (degrees) 68.22458195
Shift along axis 0.27492383
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2713, steps = 64
shifted from previous position = 0.00124
rotated from previous position = 0.00549 degrees
atoms outside contour = 817, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.37389577 0.77222209 -0.51368766 64.99765599
-0.81672682 0.53659394 0.21218923 312.38183038
0.43949889 0.34020583 0.83132470 -182.47859108
Axis 0.06892470 -0.51319985 -0.85549711
Axis point 294.78556130 154.86195461 0.00000000
Rotation angle (degrees) 68.22842261
Shift along axis 0.27554440
> view matrix models
> #9,0.3739,0.77222,-0.51369,67.447,-0.81673,0.53659,0.21219,313.04,0.4395,0.34021,0.83132,-181.98
> view matrix models
> #9,0.3739,0.77222,-0.51369,67.222,-0.81673,0.53659,0.21219,312.38,0.4395,0.34021,0.83132,-182.06
> view matrix models
> #9,0.40662,0.79224,-0.45499,40.98,-0.81646,0.53859,0.20813,312.63,0.40994,0.28685,0.86583,-167.46
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2714, steps = 76
shifted from previous position = 2.08
rotated from previous position = 4.06 degrees
atoms outside contour = 817, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.37362644 0.77195161 -0.51428982 65.28256538
-0.81672132 0.53662374 0.21213502 312.38334595
0.43973809 0.34077220 0.83096615 -182.62006849
Axis 0.06924992 -0.51358682 -0.85523858
Axis point 294.87169750 154.71937115 0.00000000
Rotation angle (degrees) 68.24687067
Shift along axis 0.26857181
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2714, steps = 64
shifted from previous position = 0.0223
rotated from previous position = 0.0447 degrees
atoms outside contour = 817, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.37391451 0.77225081 -0.51363085 64.97443527
-0.81673165 0.53658433 0.21219494 312.38325809
0.43947397 0.34015579 0.83135834 -182.46718198
Axis 0.06889532 -0.51316056 -0.85552304
Axis point 294.77883212 154.87391266 0.00000000
Rotation angle (degrees) 68.22710297
Shift along axis 0.27854481
> view matrix models
> #9,0.42561,0.78486,-0.45038,34.007,-0.77603,0.57258,0.26445,281.25,0.46544,0.23695,0.85277,-169.63
> view matrix models
> #9,0.42561,0.78486,-0.45038,33.498,-0.77603,0.57258,0.26445,280.12,0.46544,0.23695,0.85277,-161.33
> view matrix models
> #9,0.36084,0.91143,-0.19772,-28.557,-0.79113,0.41141,0.45262,285.49,0.49387,-0.0068984,0.86951,-114.5
> view matrix models
> #9,0.68765,0.39349,-0.61017,82.377,-0.38178,0.9108,0.15711,104.24,0.61756,0.12492,0.77654,-163.94
> view matrix models
> #9,0.83018,0.39946,-0.38889,-5.4977,-0.47691,0.87012,-0.12429,198.56,0.28873,0.28865,0.91286,-133.74
> view matrix models
> #9,0.51091,0.85828,-0.048254,-90.033,-0.83419,0.50856,0.21329,322.91,0.20761,-0.068721,0.9758,-36.626
> view matrix models
> #9,0.47328,0.8806,-0.023355,-89.306,-0.85839,0.46698,0.21237,340.21,0.19792,-0.080462,0.97691,-31.175
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.092, steps = 128
shifted from previous position = 4.27
rotated from previous position = 15.2 degrees
atoms outside contour = 203, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.50125546 0.86529923 0.00048124 -99.82211090
-0.86427135 0.50068698 -0.04845202 382.79646238
-0.04216645 0.02387091 0.99882541 5.30129247
Axis 0.04176636 0.02462896 -0.99882380
Axis point 282.27238890 278.05688394 0.00000000
Rotation angle (degrees) 59.97459682
Shift along axis -0.03638333
> fitmap #9 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#9) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.092, steps = 28
shifted from previous position = 0.0192
rotated from previous position = 0.00928 degrees
atoms outside contour = 201, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#9) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.50131252 0.86526619 0.00045419 -99.82249484
-0.86424512 0.50074629 -0.04830675 382.76366393
-0.04202563 0.02382425 0.99883246 5.27650862
Axis 0.04165724 0.02453303 -0.99883072
Axis point 282.26801228 278.04672129 0.00000000
Rotation angle (degrees) 59.97051301
Shift along axis -0.03831592
> select subtract #9
Nothing selected
> color #8 #fade4aff
> show #10 models
> rainbow #8-13
> undo
> select add #10
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> rainbow sel
> ui tool show Matchmaker
> matchmaker #10 to #9
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 copy of Terminator_1-coot-1.pdb, chain D (#9) with copy of
Terminator_1-coot-1.pdb, chain D (#10), sequence alignment score = 777.7
RMSD between 150 pruned atom pairs is 0.000 angstroms; (across all 150 pairs:
0.000)
> view #10 clip false
> turn y 60 models #10
> undo
> turn z 60 models #10
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 0.2823, steps = 64
shifted from previous position = 1.27
rotated from previous position = 1.1 degrees
atoms outside contour = 793, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.49745039 0.86453558 -0.07156334 186.76840147
-0.85557576 -0.50257131 -0.12414576 663.07557047
-0.14329411 -0.00052850 0.98968000 41.81615979
Axis 0.07161905 0.04155803 -0.99656592
Axis point 285.64439149 278.66624920 0.00000000
Rotation angle (degrees) 120.34269498
Shift along axis -0.74026892
> view matrix models
> #10,-0.49745,0.86454,-0.071563,186.57,-0.85558,-0.50257,-0.12415,666.53,-0.14329,-0.0005285,0.98968,41.992
> fitmap #10 inMap #6.1
Fit molecule copy of Terminator_1-coot-1.pdb (#10) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 1216 atoms
average map value = 1.087, steps = 72
shifted from previous position = 1.82
rotated from previous position = 6.15 degrees
atoms outside contour = 204, contour level = 0.3
Position of copy of Terminator_1-coot-1.pdb (#10) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.49916936 0.86650072 0.00253528 171.19651970
-0.86560108 -0.49851327 -0.04710910 654.27593302
-0.03955620 -0.02570997 0.99888652 18.03256359
Axis 0.01234985 0.02429179 -0.99962863
Axis point 274.80478327 277.87878760 0.00000000
Rotation angle (degrees) 119.96018387
Shift along axis -0.01808304
> select add #8
2432 atoms, 2484 bonds, 300 residues, 2 models selected
> select add #9
3648 atoms, 3726 bonds, 450 residues, 3 models selected
> select add #11
4864 atoms, 4968 bonds, 600 residues, 4 models selected
> select add #12
6080 atoms, 6210 bonds, 750 residues, 5 models selected
> select add #13
7296 atoms, 7452 bonds, 900 residues, 6 models selected
> color sel yellow
> select subtract #8
6080 atoms, 6210 bonds, 750 residues, 5 models selected
> select subtract #9
4864 atoms, 4968 bonds, 600 residues, 4 models selected
> select subtract #10
3648 atoms, 3726 bonds, 450 residues, 3 models selected
> select subtract #12
2432 atoms, 2484 bonds, 300 residues, 2 models selected
> select subtract #13
1216 atoms, 1242 bonds, 150 residues, 1 model selected
> select subtract #11
Nothing selected
> combine #8-13
Remapping chain ID 'D' in copy of Terminator_1-coot-1.pdb #9 to 'E'
Remapping chain ID 'D' in copy of Terminator_1-coot-1.pdb #10 to 'F'
Remapping chain ID 'D' in copy of Terminator_1-coot-1.pdb #11 to 'G'
Remapping chain ID 'D' in copy of Terminator_1-coot-1.pdb #12 to 'H'
Remapping chain ID 'D' in copy of Terminator_1-coot-1.pdb #13 to 'I'
> select add #14
7296 atoms, 7452 bonds, 900 residues, 1 model selected
> show #!6.1 models
> hide #!6.1 models
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Terminator_1-coot-1_6mer.pdb" models #14 selectedOnly true relModel
> #2
> select subtract #14
Nothing selected
> hide #14 models
> hide #13 models
> hide #12 models
> hide #11 models
> hide #10 models
> show #10 models
> hide #9 models
> show #9 models
> hide #8 models
> hide #10 models
> hide #9 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Terminator_1-coot-1_6mer.pdb"
Chain information for Terminator_1-coot-1_6mer.pdb #16
---
Chain | Description
D E F G H I | No description available
> hide #16 atoms
> show #16 cartoons
> rainbow #16
> fitmap #14 inMap #6.1
Fit molecule combination (#14) to map P2_J357_007_volume_map_sharp_C6.mrc 0
(#6.1) using 7296 atoms
average map value = 1.093, steps = 28
shifted from previous position = 0.00645
rotated from previous position = 0.00684 degrees
atoms outside contour = 1224, contour level = 0.3
Position of combination (#14) relative to P2_J357_007_volume_map_sharp_C6.mrc
0 (#6.1) coordinates:
Matrix rotation and translation
0.99999860 -0.00151691 0.00070204 0.08460115
0.00155049 0.99871799 -0.05059619 12.76073646
-0.00062439 0.05059721 0.99871895 -13.22915984
Axis 0.99945512 0.01310065 0.03029577
Axis point 0.00000000 267.58590245 245.46594319
Rotation angle (degrees) 2.90179805
Shift along axis -0.14905856
> hide #!6 models
> show #!6 models
> hide #16 models
> show #16 models
> close #16
> close #15
> show #14 models
> show #!17 models
> close #17
> show #!6.1 models
> ui tool show "Color Zone"
> color zone #6.1 near #14 distance 6.37
> volume splitbyzone #6.1
Opened P2_J357_007_volume_map_sharp_C6.mrc 0 0 as #15.1, grid size
512,505,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened P2_J357_007_volume_map_sharp_C6.mrc 0 1 as #15.2, grid size
512,505,512, pixel 1.06, shown at level 0.3, step 1, values float32
> surface dust #15.1 size 10.6
> surface dust #15.2 size 10.6
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitting_2.cxs"
> includeMaps true
> hide #14 models
> close #8-14
> undo
> show #!7 models
> hide #!7 models
> show #!7 models
> fitmap #7 inMap #6.1
Fit molecule Stopper_45_1.pdb (#7) to map P2_J357_007_volume_map_sharp_C6.mrc
0 (#6.1) using 916 atoms
average map value = 0.2456, steps = 176
shifted from previous position = 0.849
rotated from previous position = 3.28 degrees
atoms outside contour = 622, contour level = 0.3
Position of Stopper_45_1.pdb (#7) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.18153211 -0.96798647 -0.17334443 568.51505895
0.95324795 -0.21651827 0.21080366 28.56985457
-0.24158732 -0.12697259 0.96203614 96.91361406
Axis -0.17305048 0.03496239 0.98429221
Axis point 281.11979904 243.82400751 0.00000000
Rotation angle (degrees) 102.59200851
Shift along axis -1.99161634
> select add #7
916 atoms, 939 bonds, 119 residues, 1 model selected
> view matrix models
> #7,-0.18153,-0.96799,-0.17334,567.32,0.95325,-0.21652,0.2108,30.018,-0.24159,-0.12697,0.96204,96.992
> view matrix models
> #7,-0.18153,-0.96799,-0.17334,568,0.95325,-0.21652,0.2108,28.339,-0.24159,-0.12697,0.96204,97.863
> view matrix models
> #7,0.9961,-0.042696,-0.077202,23.457,-0.032435,0.63657,-0.77054,231.04,0.082043,0.77004,0.6327,-151.73
> view matrix models
> #7,0.84688,0.49972,0.18187,-120.2,-0.32152,0.75356,-0.57339,240.07,-0.42358,0.42711,0.79884,32.539
> view matrix models
> #7,0.30881,0.63367,0.7093,-110.09,0.55995,0.48169,-0.67412,104.65,-0.76883,0.60534,-0.20607,248.19
> view matrix models
> #7,-0.70691,-0.014394,0.70716,307.93,0.46011,0.74998,0.47521,-136.5,-0.5372,0.6613,-0.52355,230.94
> view matrix models
> #7,-0.88698,-0.19435,0.41892,448.17,0.24853,0.56368,0.78772,-90.667,-0.38923,0.80281,-0.45167,145.83
> view matrix models
> #7,-0.88698,-0.19435,0.41892,451.78,0.24853,0.56368,0.78772,-96.606,-0.38923,0.80281,-0.45167,145.38
> view matrix models
> #7,0.44325,0.18292,0.87753,-56.06,0.89283,-0.17727,-0.41403,135.77,0.079824,0.96702,-0.24189,-49.833
> view matrix models
> #7,0.57841,0.16192,0.79952,-71.197,0.80889,-0.24063,-0.53646,193.92,0.10553,0.95702,-0.27015,-48.88
> fitmap #7 inMap #6.1
Fit molecule Stopper_45_1.pdb (#7) to map P2_J357_007_volume_map_sharp_C6.mrc
0 (#6.1) using 916 atoms
average map value = 0.173, steps = 104
shifted from previous position = 4.11
rotated from previous position = 10.7 degrees
atoms outside contour = 708, contour level = 0.3
Position of Stopper_45_1.pdb (#7) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.58503650 -0.01082136 0.81093477 -33.52940855
0.79699909 -0.17736908 -0.57734968 192.27871230
0.15008246 0.98408491 -0.09514277 -96.85513582
Axis 0.83137664 0.35186691 0.43011924
Axis point 0.00000000 143.60287392 41.33724165
Rotation angle (degrees) 110.10475777
Shift along axis -1.87830688
> view matrix models
> #7,-0.36273,-0.083538,0.92814,202.24,0.9291,0.044654,0.36712,-60.007,-0.072114,0.9955,0.061418,-71.059
> view matrix models
> #7,-0.93746,-0.34483,-0.047465,580.83,-0.075488,0.068292,0.99481,77.517,-0.3398,0.93618,-0.090052,37.203
> view matrix models
> #7,-0.84739,-0.45408,-0.27521,625.07,-0.2483,-0.11926,0.96131,173.79,-0.46934,0.88294,-0.011689,69.522
> view matrix models
> #7,-0.74584,-0.53592,-0.39563,640.98,-0.26596,-0.30495,0.91448,232.97,-0.61073,0.78727,0.084911,112.32
> view matrix models
> #7,-0.67324,-0.64293,-0.36522,644.4,-0.29766,-0.21649,0.9298,216.05,-0.67686,0.73469,-0.045624,164.7
> fitmap #7 inMap #6.1
Fit molecule Stopper_45_1.pdb (#7) to map P2_J357_007_volume_map_sharp_C6.mrc
0 (#6.1) using 916 atoms
average map value = 0.2128, steps = 84
shifted from previous position = 2.73
rotated from previous position = 12.4 degrees
atoms outside contour = 650, contour level = 0.3
Position of Stopper_45_1.pdb (#7) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.77223501 -0.53172675 -0.34773518 638.14417915
-0.36744148 -0.07272263 0.92719911 200.94715164
-0.51830478 0.84378794 -0.13921950 115.42842215
Axis -0.33220979 0.67934422 0.65431498
Axis point 373.55781750 -0.00000000 -68.65688695
Rotation angle (degrees) 172.78806472
Shift along axis 0.04108536
> fitmap #7 inMap #6.1
Fit molecule Stopper_45_1.pdb (#7) to map P2_J357_007_volume_map_sharp_C6.mrc
0 (#6.1) using 916 atoms
average map value = 0.2125, steps = 60
shifted from previous position = 0.0248
rotated from previous position = 0.0354 degrees
atoms outside contour = 650, contour level = 0.3
Position of Stopper_45_1.pdb (#7) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
-0.77231948 -0.53141484 -0.34802428 638.13934064
-0.36787024 -0.07248885 0.92704739 201.04713147
-0.51787461 0.84400453 -0.13950715 115.32267163
Axis -0.33219247 0.67944434 0.65421980
Axis point 373.54020642 0.00000000 -68.59512745
Rotation angle (degrees) 172.81970104
Shift along axis 0.06163044
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper_45_1-coot-1.pdb" models #7 selectedOnly true relModel #2
> select subtract #7
1 model selected
> hide #!7 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper_45_1-coot-1.pdb"
Chain information for Stopper_45_1-coot-1.pdb #8
---
Chain | Description
A | No description available
> close #8
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper_45_1-coot-2.pdb"
Chain information for Stopper_45_1-coot-2.pdb #8
---
Chain | Description
A | No description available
> fitmap #8 inMap #6.1
Fit molecule Stopper_45_1-coot-2.pdb (#8) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2416, steps = 76
shifted from previous position = 2.81
rotated from previous position = 5.69 degrees
atoms outside contour = 613, contour level = 0.3
Position of Stopper_45_1-coot-2.pdb (#8) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99603941 -0.08341334 0.03078486 16.53076653
0.08198082 0.99560918 0.04518299 -26.43588346
-0.03441855 -0.04248027 0.99850428 22.40508070
Axis -0.44225017 0.32894299 0.83439277
Axis point 343.75308559 196.10859657 0.00000000
Rotation angle (degrees) 5.68795107
Shift along axis 2.68800441
> select add #8
916 atoms, 939 bonds, 119 residues, 1 model selected
> ui mousemode right "translate selected atoms"
> fitmap #8 inMap #6.1
Fit molecule Stopper_45_1-coot-2.pdb (#8) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.4002, steps = 56
shifted from previous position = 2
rotated from previous position = 0.404 degrees
atoms outside contour = 519, contour level = 0.3
Position of Stopper_45_1-coot-2.pdb (#8) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99610739 -0.08010536 0.03678597 13.31621226
0.07849236 0.99597047 0.04337942 -23.94051992
-0.04011266 -0.04032314 0.99838120 23.81493401
Axis -0.42897465 0.39410453 0.81281140
Axis point 334.99637541 172.49832643 0.00000000
Rotation angle (degrees) 5.59875090
Shift along axis 4.20966486
> select #8/A:44
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
31 atoms, 31 bonds, 3 residues, 1 model selected
> color zone #6.1 near #8 distance 6.37
> color single #6.1
> color zone #15.1 near #8 distance 6.37
> select add #8
916 atoms, 939 bonds, 119 residues, 1 model selected
> color sel yellow
> color single #15.1
> color zone #15.1 near #8 distance 6.37
> color single #15.1
> rainbow sel
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
Already setting window visible!
> select subtract #8
Nothing selected
> select #8/A:21
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
74 atoms, 76 bonds, 11 residues, 1 model selected
> select #8/A:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:8-15
64 atoms, 65 bonds, 8 residues, 1 model selected
> select #8/A:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:27-34
59 atoms, 58 bonds, 8 residues, 1 model selected
> select #8/A:16
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/A:16-19
23 atoms, 23 bonds, 4 residues, 1 model selected
> select #8/A:16
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/A:16-26
74 atoms, 76 bonds, 11 residues, 1 model selected
> fitmap #8 inMap #6.1
Fit molecule Stopper_45_1-coot-2.pdb (#8) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3604, steps = 48
shifted from previous position = 0.207
rotated from previous position = 1.94 degrees
atoms outside contour = 559, contour level = 0.3
Position of Stopper_45_1-coot-2.pdb (#8) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99694464 -0.06849311 0.03755115 10.12297075
0.06555064 0.99505174 0.07466692 -25.43997213
-0.04247951 -0.07197728 0.99650126 32.78897434
Axis -0.68464691 0.37364416 0.62581839
Axis point 0.00000000 401.19159414 387.73605137
Rotation angle (degrees) 6.14786817
Shift along axis 4.08378528
> select #8/A:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:8-15
64 atoms, 65 bonds, 8 residues, 1 model selected
> fitmap #8 inMap #6.1
Fit molecule Stopper_45_1-coot-2.pdb (#8) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3377, steps = 68
shifted from previous position = 0.226
rotated from previous position = 2.66 degrees
atoms outside contour = 593, contour level = 0.3
Position of Stopper_45_1-coot-2.pdb (#8) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99533281 -0.09099092 0.03214408 17.06278739
0.08985284 0.99533152 0.03523675 -25.38667083
-0.03520024 -0.03218405 0.99886192 20.41710196
Axis -0.32982397 0.32944982 0.88469145
Axis point 307.15568915 186.52529576 0.00000000
Rotation angle (degrees) 5.86628782
Shift along axis 4.07148510
> fitmap #8 inMap #6.1
Fit molecule Stopper_45_1-coot-2.pdb (#8) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.3378, steps = 44
shifted from previous position = 0.0172
rotated from previous position = 0.0248 degrees
atoms outside contour = 591, contour level = 0.3
Position of Stopper_45_1-coot-2.pdb (#8) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99529842 -0.09126146 0.03244072 17.08034056
0.09011909 0.99531269 0.03508856 -25.43981493
-0.03549090 -0.03200006 0.99885754 20.44930297
Axis -0.32730247 0.33141519 0.88489382
Axis point 306.94490874 185.95590636 0.00000000
Rotation angle (degrees) 5.88241146
Shift along axis 4.07388294
> select #8/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1-7
48 atoms, 49 bonds, 7 residues, 1 model selected
> select #8/A:37
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:37-46
91 atoms, 93 bonds, 10 residues, 1 model selected
> select #8/A:37
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:37-54
155 atoms, 158 bonds, 18 residues, 1 model selected
> select #8/A:55-56
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #8/A:55-59
43 atoms, 44 bonds, 5 residues, 1 model selected
> select #8/A:38
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:38-63
223 atoms, 228 bonds, 26 residues, 1 model selected
> fitmap #8 inMap #6.1
Fit molecule Stopper_45_1-coot-2.pdb (#8) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2906, steps = 64
shifted from previous position = 0.442
rotated from previous position = 1.86 degrees
atoms outside contour = 604, contour level = 0.3
Position of Stopper_45_1-coot-2.pdb (#8) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99399572 -0.10911283 0.00817865 25.64220567
0.10889540 0.99377564 0.02348974 -27.76895518
-0.01069078 -0.02245809 0.99969062 11.86059920
Axis -0.20549554 0.08439099 0.97501269
Axis point 271.07350788 227.53149565 0.00000000
Rotation angle (degrees) 6.41895192
Shift along axis 3.95142619
> select #8/A:35
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:35-38
28 atoms, 28 bonds, 4 residues, 1 model selected
> select #8/A:42-43
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/A:42-55
115 atoms, 116 bonds, 14 residues, 1 model selected
> fitmap #8 inMap #6.1
Fit molecule Stopper_45_1-coot-2.pdb (#8) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2941, steps = 64
shifted from previous position = 0.274
rotated from previous position = 1.97 degrees
atoms outside contour = 595, contour level = 0.3
Position of Stopper_45_1-coot-2.pdb (#8) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99548296 -0.09048207 0.02875190 16.97681714
0.08919315 0.99507135 0.04333108 -26.45323088
-0.03253088 -0.04057088 0.99864696 22.08301571
Axis -0.40424330 0.29526311 0.86568300
Axis point 321.87015241 191.40983093 -0.00000000
Rotation angle (degrees) 5.95668389
Shift along axis 4.44346352
> fitmap #8 inMap #6.1
Fit molecule Stopper_45_1-coot-2.pdb (#8) to map
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) using 916 atoms
average map value = 0.2941, steps = 44
shifted from previous position = 0.00411
rotated from previous position = 0.00967 degrees
atoms outside contour = 595, contour level = 0.3
Position of Stopper_45_1-coot-2.pdb (#8) relative to
P2_J357_007_volume_map_sharp_C6.mrc 0 (#6.1) coordinates:
Matrix rotation and translation
0.99549307 -0.09035452 0.02880308 16.93131273
0.08906053 0.99507915 0.04342467 -26.43820711
-0.03258496 -0.04066374 0.99864142 22.12352547
Axis -0.40537309 0.29593921 0.86492349
Axis point 322.20359280 191.26969057 0.00000000
Rotation angle (degrees) 5.95326956
Shift along axis 4.44755592
> select add #8
916 atoms, 939 bonds, 119 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
916 atoms, 939 bonds, 119 residues, 1 model selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper/Stopper_45_1-coot-3.pdb" models #8 selectedOnly true relModel
> #2
> select subtract #8
Nothing selected
> hide #8 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper/Stopper_45_1-coot-3.pdb"
Chain information for Stopper_45_1-coot-3.pdb #9
---
Chain | Description
A | No description available
> close #9
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper/Stopper_45_1-coot-4.pdb"
Chain information for Stopper_45_1-coot-4.pdb #9
---
Chain | Description
A | No description available
> 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 = 0.9066, steps = 76
shifted from previous position = 4.31
rotated from previous position = 2.83 degrees
atoms outside contour = 195, 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
0.99998878 -0.00165271 0.00444027 -0.53652593
0.00186894 0.99879000 -0.04914314 12.38716759
-0.00435368 0.04915089 0.99878188 -11.86586289
Axis 0.99538822 0.08905324 0.03566252
Axis point 0.00000000 247.61224516 245.70191070
Rotation angle (degrees) 2.83011369
Shift along axis 0.14589924
> select add #9
916 atoms, 939 bonds, 119 residues, 1 model selected
> 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 = 56
shifted from previous position = 2.77
rotated from previous position = 0.0233 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
0.99998807 -0.00154974 0.00463339 -0.42827439
0.00177403 0.99880695 -0.04880083 15.03300112
-0.00455223 0.04880847 0.99879778 -11.06755944
Axis 0.99502957 0.09363829 0.03388247
Axis point 0.00000000 234.59364008 301.14909209
Rotation angle (degrees) 2.81139679
Shift along axis 0.60652254
> 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 = 64
shifted from previous position = 0.41
rotated from previous position = 8.56 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
0.99363048 0.10264051 0.04651239 -31.50835306
-0.10480455 0.99339325 0.04675323 27.53534136
-0.04140632 -0.05133015 0.99782300 22.79562012
Axis -0.39915013 0.35778500 -0.84419729
Axis point 232.37979572 309.01531263 0.00000000
Rotation angle (degrees) 7.05749476
Shift along axis 3.18429456
> 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 = 36
shifted from previous position = 0.00875
rotated from previous position = 0.022 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
0.99363103 0.10247723 0.04685922 -31.53451562
-0.10466085 0.99340649 0.04679376 27.48518390
-0.04175496 -0.05140005 0.99780487 22.90150633
Axis -0.39954269 0.36056393 -0.84282815
Axis point 232.05489383 309.63878139 0.00000000
Rotation angle (degrees) 7.05850365
Shift along axis 3.20751680
> 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 = 0.2434, steps = 64
shifted from previous position = 1.95
rotated from previous position = 6.78 degrees
atoms outside contour = 630, 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
0.99134972 0.11210214 -0.06825565 -12.05044408
-0.10717022 0.99162426 0.07208244 23.73010592
0.07576456 -0.06414393 0.99506044 -2.92412366
Axis -0.46084577 -0.48721191 -0.74178550
Axis point 193.17166540 138.18357904 0.00000000
Rotation angle (degrees) 8.49947699
Shift along axis -3.83912137
> 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 = 0.2434, steps = 40
shifted from previous position = 0.00635
rotated from previous position = 0.00449 degrees
atoms outside contour = 630, 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
0.99135085 0.11207039 -0.06829145 -12.03885371
-0.10714104 0.99163207 0.07201834 23.73763516
0.07579111 -0.06407863 0.99506263 -2.94652898
Axis -0.46052398 -0.48754557 -0.74176612
Axis point 193.27741062 138.13193473 0.00000000
Rotation angle (degrees) 8.49732112
Shift along axis -3.84336275
> undo
> 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 = 0.2485, steps = 80
shifted from previous position = 2.33
rotated from previous position = 7.2 degrees
atoms outside contour = 616, 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
0.98049727 0.19644182 0.00597577 -43.10986304
-0.19652265 0.98030121 0.01970738 58.89626124
-0.00198670 -0.02049741 0.99978793 7.50543461
Axis -0.10175951 0.02015325 -0.99460487
Axis point 275.05321296 247.74049165 0.00000000
Rotation angle (degrees) 11.39361126
Shift along axis -1.89115211
> 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 = 0.286, steps = 120
shifted from previous position = 2.51
rotated from previous position = 8.29 degrees
atoms outside contour = 593, 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
0.99551759 0.07449111 -0.05827349 -6.31468898
-0.07116064 0.99581877 0.05728119 18.63194411
0.06229678 -0.05287765 0.99665594 1.36739008
Axis -0.50339902 -0.55097675 -0.66559300
Axis point 191.07820417 150.31195357 0.00000000
Rotation angle (degrees) 6.28159556
Shift along axis -7.99708501
> 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 = 0.2481, steps = 76
shifted from previous position = 2.53
rotated from previous position = 8.22 degrees
atoms outside contour = 613, 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
0.98056440 0.19613975 0.00475943 -43.27036552
-0.19619676 0.98033824 0.02106569 62.59484585
-0.00053403 -0.02159005 0.99976677 9.59363230
Axis -0.10807565 0.01341189 -0.99405220
Axis point 294.06554965 251.96439449 0.00000000
Rotation angle (degrees) 11.38156938
Shift along axis -4.02058319
> 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 = 0.9064, steps = 88
shifted from previous position = 4.46
rotated from previous position = 20 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
0.96394944 0.00558817 0.26602679 -35.43599628
-0.05138556 0.98486890 0.16550762 3.04913866
-0.26107663 -0.17321091 0.94965098 117.83981345
Axis -0.53838535 0.83781883 -0.09055844
Axis point 422.70555403 0.00000000 168.30365370
Rotation angle (degrees) 18.33478806
Shift along axis 10.96145756
> 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 = 0.0234
rotated from previous position = 0.0366 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
0.96384217 0.00550877 0.26641683 -35.46414005
-0.05150511 0.98478443 0.16597241 3.00107032
-0.26144884 -0.17369304 0.94946049 118.08800480
Axis -0.53890352 0.83749663 -0.09045660
Axis point 422.90595617 0.00000000 168.37570285
Rotation angle (degrees) 18.36956483
Shift along axis 10.94329695
> select subtract #9
Nothing selected
> select add #9
916 atoms, 939 bonds, 119 residues, 1 model selected
> 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 = 116
shifted from previous position = 0.00623
rotated from previous position = 28.9 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
0.83152977 -0.10197232 0.54604019 -22.95500990
-0.21100519 0.85133809 0.48031267 22.83163520
-0.51384342 -0.51461160 0.68639628 308.15525095
Axis -0.68249383 0.72705436 -0.07479389
Axis point 490.13191991 0.00000000 181.73785601
Rotation angle (degrees) 46.79332164
Shift along axis 9.21836142
> 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 = 24
shifted from previous position = 0.00587
rotated from previous position = 0.0354 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
0.83135753 -0.10220999 0.54625798 -22.89156230
-0.21121047 0.85107517 0.48068825 22.87804983
-0.51403774 -0.51499920 0.68595993 308.37168534
Axis -0.68263427 0.72692910 -0.07472974
Axis point 490.21394721 0.00000000 181.73375794
Rotation angle (degrees) 46.82756559
Shift along axis 9.21274983
> 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 = 0.9064, steps = 120
shifted from previous position = 0.0259
rotated from previous position = 29 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
0.82803450 -0.09573857 0.55244276 -24.61847151
-0.44134639 0.49638404 0.74754013 121.59486495
-0.34579219 -0.86280763 0.36876924 401.76938757
Axis -0.85838034 0.47879547 -0.18422292
Axis point 0.00000000 390.71829465 103.98362892
Rotation angle (degrees) 69.72087719
Shift along axis 5.33595516
> 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 = 0.00552
rotated from previous position = 0.014 degrees
atoms outside contour = 195, 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
0.82801598 -0.09598125 0.55242841 -24.54838425
-0.44124585 0.49636896 0.74760950 121.56290722
-0.34596481 -0.86278935 0.36865010 401.83075371
Axis -0.85838175 0.47886543 -0.18403443
Axis point 0.00000000 390.74117925 104.03893053
Rotation angle (degrees) 69.72554177
Shift along axis 5.33346647
> 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 = 76
shifted from previous position = 0.029
rotated from previous position = 13.9 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
0.72744524 -0.19738184 0.65716348 7.75308376
-0.56898629 0.36176947 0.73849675 187.84403111
-0.38350753 -0.91113295 0.15085992 459.54414875
Axis -0.83082221 0.52412525 -0.18715548
Axis point 0.00000000 409.14416376 103.49706392
Rotation angle (degrees) 83.10574372
Shift along axis 6.00616277
> select subtract #9
Nothing selected
> select add #9
916 atoms, 939 bonds, 119 residues, 1 model selected
> 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 = 0.1606, steps = 252
shifted from previous position = 1.07
rotated from previous position = 14.9 degrees
atoms outside contour = 725, 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
0.54281469 -0.13782653 0.82846609 12.48098161
-0.73896719 0.39037855 0.54911936 255.58567637
-0.39909860 -0.91027932 0.11005393 469.26870655
Axis -0.72987000 0.61392589 -0.30064063
Axis point -0.00000000 462.95865761 56.03406926
Rotation angle (degrees) 88.76096323
Shift along axis 6.71993150
> 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 = 0.1606, steps = 84
shifted from previous position = 0.00483
rotated from previous position = 0.0446 degrees
atoms outside contour = 725, 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
0.54235976 -0.13733501 0.82884558 12.42255095
-0.73931907 0.39058871 0.54849592 255.72344796
-0.39906541 -0.91026345 0.11030521 469.21524516
Axis -0.72955032 0.61409912 -0.30106245
Axis point 0.00000000 463.11557667 55.83855011
Rotation angle (degrees) 88.76077680
Shift along axis 6.71357949
> 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 = 0.2191, steps = 76
shifted from previous position = 2.5
rotated from previous position = 10.8 degrees
atoms outside contour = 670, 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
0.44748585 -0.01290420 0.89419791 -1.76073653
-0.84390955 0.32477968 0.42700682 317.59911970
-0.29592749 -0.94570167 0.13444433 448.64933686
Axis -0.68710214 0.59571111 -0.41595543
Axis point 0.00000000 470.72073868 5.85058388
Rotation angle (degrees) 92.67353563
Shift along axis 3.78900228
> 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 = 0.2191, steps = 44
shifted from previous position = 0.00244
rotated from previous position = 0.00195 degrees
atoms outside contour = 670, 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
0.44747174 -0.01289895 0.89420504 -1.76086100
-0.84392580 0.32475178 0.42699592 317.60985205
-0.29590248 -0.94571132 0.13443149 448.64651888
Axis -0.68710239 0.59570293 -0.41596673
Axis point 0.00000000 470.71541919 5.84784759
Rotation angle (degrees) 92.67510873
Shift along axis 3.78898865
> undo
> close #9
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted
> Models/Stopper/Stopper_45_1-coot-4.pdb"
Chain information for Stopper_45_1-coot-4.pdb #9
---
Chain | Description
A | No description available
> 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 = 0.9066, steps = 76
shifted from previous position = 4.31
rotated from previous position = 2.83 degrees
atoms outside contour = 195, 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
0.99998878 -0.00165271 0.00444027 -0.53652593
0.00186894 0.99879000 -0.04914314 12.38716759
-0.00435368 0.04915089 0.99878188 -11.86586289
Axis 0.99538822 0.08905324 0.03566252
Axis point 0.00000000 247.61224516 245.70191070
Rotation angle (degrees) 2.83011369
Shift along axis 0.14589924
> 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 = 0.9064, steps = 28
shifted from previous position = 0.00555
rotated from previous position = 0.011 degrees
atoms outside contour = 195, 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
0.99998802 -0.00166174 0.00460471 -0.55917319
0.00188559 0.99879488 -0.04904308 12.36929059
-0.00451767 0.04905118 0.99878605 -11.80053844
Axis 0.99505887 0.09253656 0.03598373
Axis point 0.00000000 246.78025237 245.84007410
Rotation angle (degrees) 2.82529290
Shift along axis 0.16357397
> 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
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