![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Closed 16 months ago
#15565 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.2-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x00000002006eb2c0 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 157 in asArray
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2828 in set_matrix
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 817 in set_projection_matrix
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 725 in _use_shader
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 801 in _opengl_shader
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 698 in shader
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 818 in _draw_geometry
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 787 in draw_self
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1554 in draw_opaque
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 258 in _draw_scene
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.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-1.7.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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, 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.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.mmcif.mmcif_write (total: 53)
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{
"uptime" : 190000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir10,1",
"coalitionID" : 896,
"osVersion" : {
"train" : "macOS 13.2",
"build" : "22D49",
"releaseType" : "User"
},
"captureTime" : "2024-07-06 20:06:34.7134 +0200",
"incident" : "EF8FD9C3-B0D1-4875-B544-B1BB057087CE",
"pid" : 36716,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-06 19:31:38.2790 +0200",
"procStartAbsTime" : 4517967289812,
"procExitAbsTime" : 4568282088497,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D82AA68D-AACC-5141-AE12-1309469013C3","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "311D3808-133C-AE77-3A0C-264C8C389551",
"throttleTimeout" : 2147483647,
"wakeTime" : 28869,
"sleepWakeUUID" : "B32C72E8-AE8F-457D-8BBE-3FC5B7B73224",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140723039453015\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffca2c74000-7ffcad740000 [170.8M] r-x\/r-x SM=COW ...t_id=c296771b",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140723039453015\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffca2c74000-7ffcad740000 [170.8M] r-x\/r-x SM=COW ...t_id=c296771b",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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],
"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=3.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 2944K 8 \nCG image 168K 37 \nColorSync 252K 29 \nCoreAnimation 100K 15 \nCoreGraphics 48K 7 \nCoreUI image data 4224K 43 \nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 1.7G 559 \nMALLOC guard page 192K 9 \nMALLOC_MEDIUM (reserved) 744.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1436K 356 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 780K 78 \nRosetta Thread Context 780K 78 \nSTACK GUARD 44K 11 \nStack 170.1M 40 \nStack Guard 56.1M 29 \nVM_ALLOCATE 247.9M 324 \nVM_ALLOCATE (reserved) 160.1M 12 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 48.3M 736 \n__DATA_CONST 39.4M 377 \n__DATA_DIRTY 1829K 224 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 199.4M 151 \n__OBJC_RO 65.4M 1 \n__OBJC_RW 1987K 2 \n__TEXT 897.5M 743 \ndyld private memory 416K 3 \nmapped file 4.7G 1716 \nshared memory 3012K 25 \nunshared pmap 14.0M 10 \n=========== ======= ======= \nTOTAL 9.4G 5653 \nTOTAL, minus reserved VM space 8.2G 5653 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60186475825c62000ccf5450",
"factorPackIds" : {
},
"deploymentId" : 240000074
},
{
"rolloutId" : "6297d96be2c9387df974efa4",
"factorPackIds" : {
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],
"experiments" : [
{
"treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
"experimentId" : "6639bc6ba73d460582162323",
"deploymentId" : 400000006
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{
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"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000002
}
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/nezakoritnik/Desktop/PVA-
> VLPmut/helixWIDE/NEW_PVAhelixWIDE_P98_J234.mrc
Opened NEW_PVAhelixWIDE_P98_J234.mrc as #1, grid size 350,350,350, pixel
0.953, shown at level 1.19, step 2, values float32
> open "/Users/nezakoritnik/Desktop/PVA-VLPmut/helixWIDE/Rigidbodyrefine24 -
> FINAL/BREZ OXT/pdb_extract_21660.cif"
Summary of feedback from opening /Users/nezakoritnik/Desktop/PVA-
VLPmut/helixWIDE/Rigidbodyrefine24 - FINAL/BREZ OXT/pdb_extract_21660.cif
---
warnings | Unknown polymer entity '1' near line 61
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for pdb_extract_21660.cif #2
---
Chain | Description
Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax Ay Az
Ba | No description available
> select /Aa:44-228
1497 atoms, 1531 bonds, 185 residues, 1 model selected
> save /Users/nezakoritnik/Desktop/PVA-VLPmut/helixWIDE/Coot25/mono25.cif
> selectedOnly true relModel #2
Not saving entity_poly_seq for non-authoritative sequences
> select clear
> hide atoms
> show cartoons
> volume #1 step 1
> set bgColor white
> select add #2
40419 atoms, 41337 bonds, 4995 residues, 1 model selected
> open /Users/nezakoritnik/Desktop/PVA-VLPmut/helixWIDE/Coot25/mono25.cif-
> coot-0.pdb
Chain information for mono25.cif-coot-0.pdb #3
---
Chain | Description
Aa | No description available
> select add #3
41916 atoms, 42868 bonds, 5180 residues, 2 models selected
> select subtract #2
1497 atoms, 1531 bonds, 185 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,51.618,0,1,0,-38.668,0,0,1,-55.119
> view matrix models #3,1,0,0,3.52,0,1,0,21.473,0,0,1,-55.748
> view matrix models #3,1,0,0,78.383,0,1,0,21.223,0,0,1,-59.987
> view matrix models #3,1,0,0,67.349,0,1,0,36.498,0,0,1,-50.163
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.21155,-0.97052,-0.11548,371.19,0.9755,-0.20237,-0.086271,82.069,0.060358,-0.13091,0.98956,-39.077
> view matrix models
> #3,-0.48582,-0.85995,-0.15642,399.88,0.87271,-0.46729,-0.14149,139.89,0.048582,-0.20524,0.9775,-25.695
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.48582,-0.85995,-0.15642,414.75,0.87271,-0.46729,-0.14149,112.36,0.048582,-0.20524,0.9775,-29.364
> view matrix models
> #3,-0.48582,-0.85995,-0.15642,421.91,0.87271,-0.46729,-0.14149,123.84,0.048582,-0.20524,0.9775,-29.558
> view matrix models
> #3,-0.48582,-0.85995,-0.15642,421.99,0.87271,-0.46729,-0.14149,124.58,0.048582,-0.20524,0.9775,-28.955
> ui tool show "Fit in Map"
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4154, steps = 60
shifted from previous position = 1.86
rotated from previous position = 1.89 degrees
atoms outside contour = 1236, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.45693745 -0.87553440 -0.15699581 421.19588058
0.88821731 -0.43964501 -0.13335019 117.02498074
0.04773026 -0.20037909 0.97855508 -28.19688823
Axis -0.03772326 -0.11521800 0.99262368
Axis point 176.19484608 185.40352139 0.00000000
Rotation angle (degrees) 117.32348098
Shift along axis -57.36116650
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4154, steps = 28
shifted from previous position = 0.0297
rotated from previous position = 0.0585 degrees
atoms outside contour = 1237, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.45610155 -0.87595818 -0.15706252 421.12147655
0.88866434 -0.43890366 -0.13281293 116.78967876
0.04740325 -0.20015204 0.97861744 -28.18807364
Axis -0.03787981 -0.11501674 0.99264106
Axis point 176.18986619 185.39486369 0.00000000
Rotation angle (degrees) 117.27062346
Shift along axis -57.36541044
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4154, steps = 28
shifted from previous position = 0.0282
rotated from previous position = 0.0595 degrees
atoms outside contour = 1236, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.45695931 -0.87551088 -0.15706334 421.20609270
0.88820885 -0.43966749 -0.13333243 117.02607346
0.04767835 -0.20043255 0.97854666 -28.18101638
Axis -0.03776392 -0.11522856 0.99262091
Axis point 176.20067044 185.40327950 0.00000000
Rotation angle (degrees) 117.32518222
Shift along axis -57.36420672
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4154, steps = 28
shifted from previous position = 0.0271
rotated from previous position = 0.0539 degrees
atoms outside contour = 1238, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.45620014 -0.87588858 -0.15716434 421.14484675
0.88861746 -0.43899891 -0.13281177 116.80738818
0.04733334 -0.20024772 0.97860125 -28.16321665
Axis -0.03793660 -0.11504169 0.99263600
Axis point 176.20071882 185.39447114 0.00000000
Rotation angle (degrees) 117.27739295
Shift along axis -57.37034473
> view matrix models
> #3,-0.4562,-0.87589,-0.15716,420.41,0.88862,-0.439,-0.13281,121.56,0.047333,-0.20025,0.9786,-29.299
> view matrix models
> #3,-0.4562,-0.87589,-0.15716,419.19,0.88862,-0.439,-0.13281,123.07,0.047333,-0.20025,0.9786,-30.51
> view matrix models
> #3,-0.4562,-0.87589,-0.15716,419.14,0.88862,-0.439,-0.13281,121.73,0.047333,-0.20025,0.9786,-27.77
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.45892,-0.87622,-0.14705,417.67,0.88741,-0.46017,-0.027473,105.2,-0.043597,-0.1431,0.98875,-25.285
> view matrix models
> #3,-0.50265,-0.86429,-0.018856,398.14,0.86394,-0.50142,-0.046805,117.15,0.030998,-0.039817,0.99873,-50.165
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 52
shifted from previous position = 1.55
rotated from previous position = 3.44 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52981021 -0.84811610 0.00046989 396.49633017
0.84811622 -0.52981020 0.00015424 113.69510955
0.00011814 0.00048023 0.99999988 -50.13953273
Axis 0.00019219 0.00020737 0.99999996
Axis point 166.73421558 166.76283112 0.00000000
Rotation angle (degrees) 121.99263600
Shift along axis -50.03975155
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 40
shifted from previous position = 0.00957
rotated from previous position = 0.00582 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52975566 -0.84815020 0.00043279 396.50322805
0.84815031 -0.52975561 0.00022341 113.67864013
0.00003979 0.00048543 0.99999988 -50.13456061
Axis 0.00015446 0.00023168 0.99999996
Axis point 166.73855515 166.76493246 0.00000000
Rotation angle (degrees) 121.98894966
Shift along axis -50.04697630
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.00704
rotated from previous position = 0.0127 degrees
atoms outside contour = 727, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52987880 -0.84807322 0.00051481 396.49364660
0.84807336 -0.52987883 0.00007814 113.72489727
0.00020652 0.00047801 0.99999986 -50.15263025
Axis 0.00023575 0.00018176 0.99999996
Axis point 166.72907299 166.76645980 0.00000000
Rotation angle (degrees) 121.99727180
Shift along axis -50.03848437
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.0126
rotated from previous position = 0.0129 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52974870 -0.84815454 0.00043128 396.50519076
0.84815465 -0.52974866 0.00021948 113.68202932
0.00004232 0.00048206 0.99999988 -50.13753644
Axis 0.00015480 0.00022930 0.99999996
Axis point 166.73833380 166.76817923 0.00000000
Rotation angle (degrees) 121.98847982
Shift along axis -50.05008876
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.0197
rotated from previous position = 0.00978 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52985374 -0.84808890 0.00048354 396.49475492
0.84808902 -0.52985375 0.00011432 113.70787870
0.00015926 0.00047066 0.99999988 -50.14152328
Axis 0.00021009 0.00019119 0.99999996
Axis point 166.73247004 166.76196825 0.00000000
Rotation angle (degrees) 121.99557766
Shift along axis -50.03648395
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 36
shifted from previous position = 0.00255
rotated from previous position = 0.00742 degrees
atoms outside contour = 730, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52995983 -0.84802261 0.00048730 396.50127787
0.84802273 -0.52995986 0.00008110 113.73810394
0.00018948 0.00045622 0.99999988 -50.14528305
Axis 0.00022118 0.00017560 0.99999996
Axis point 166.73249903 166.76244028 0.00000000
Rotation angle (degrees) 122.00274565
Shift along axis -50.03761201
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 40
shifted from previous position = 0.0151
rotated from previous position = 0.0186 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52972459 -0.84816960 0.00042875 396.50345621
0.84816971 -0.52972453 0.00024079 113.67159563
0.00002288 0.00049121 0.99999988 -50.13484140
Axis 0.00014762 0.00023926 0.99999996
Axis point 166.73898387 166.76631699 0.00000000
Rotation angle (degrees) 121.98685043
Shift along axis -50.04911131
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.0171
rotated from previous position = 0.0139 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52987585 -0.84807508 0.00049792 396.49371683
0.84807520 -0.52987588 0.00009291 113.71671798
0.00018504 0.00047151 0.99999987 -50.14545488
Axis 0.00022321 0.00018447 0.99999996
Axis point 166.73089307 166.76273398 0.00000000
Rotation angle (degrees) 121.99707214
Shift along axis -50.03597545
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 44
shifted from previous position = 0.00118
rotated from previous position = 0.00149 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52989238 -0.84806476 0.00048129 396.49825006
0.84806488 -0.52989240 0.00008874 113.72154567
0.00017978 0.00045519 0.99999988 -50.14343689
Axis 0.00021605 0.00017777 0.99999996
Axis point 166.73245906 166.76361174 0.00000000
Rotation angle (degrees) 121.99818854
Shift along axis -50.03755506
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 40
shifted from previous position = 0.0171
rotated from previous position = 0.0211 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52964638 -0.84821845 0.00041335 396.50194849
0.84821855 -0.52964630 0.00030561 113.64457058
-0.00004030 0.00051248 0.99999987 -50.12939189
Axis 0.00012194 0.00026741 0.99999996
Axis point 166.74126158 166.76468671 0.00000000
Rotation angle (degrees) 121.98156710
Shift along axis -50.05064952
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.0197
rotated from previous position = 0.0199 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52987340 -0.84807661 0.00048972 396.49445464
0.84807673 -0.52987342 0.00009938 113.71394562
0.00017521 0.00046798 0.99999988 -50.14286669
Axis 0.00021731 0.00018543 0.99999996
Axis point 166.73176156 166.76186919 0.00000000
Rotation angle (degrees) 121.99690638
Shift along axis -50.03561494
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 36
shifted from previous position = 0.0188
rotated from previous position = 0.0119 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52974080 -0.84815948 0.00043161 396.50382349
0.84815959 -0.52974075 0.00022361 113.67830250
0.00003898 0.00048453 0.99999988 -50.13624125
Axis 0.00015381 0.00023146 0.99999996
Axis point 166.73828221 166.76718540 0.00000000
Rotation angle (degrees) 121.98794562
Shift along axis -50.04893957
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.0179
rotated from previous position = 0.00684 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52981366 -0.84811395 0.00046991 396.49470367
0.84811407 -0.52981365 0.00015014 113.69308886
0.00012163 0.00047809 0.99999988 -50.13719177
Axis 0.00019334 0.00020533 0.99999996
Axis point 166.73417091 166.76080641 0.00000000
Rotation angle (degrees) 121.99286938
Shift along axis -50.03718759
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 36
shifted from previous position = 0.00288
rotated from previous position = 0.0114 degrees
atoms outside contour = 730, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52997372 -0.84801393 0.00048320 396.50287415
0.84801404 -0.52997375 0.00008945 113.73975378
0.00018023 0.00045716 0.99999988 -50.14426157
Axis 0.00021681 0.00017864 0.99999996
Axis point 166.73329728 166.76159997 0.00000000
Rotation angle (degrees) 122.00368437
Shift along axis -50.03797614
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 40
shifted from previous position = 0.0132
rotated from previous position = 0.0193 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52972483 -0.84816945 0.00042774 396.50298591
0.84816956 -0.52972478 0.00024323 113.66997389
0.00002028 0.00049164 0.99999988 -50.13361791
Axis 0.00014644 0.00024020 0.99999996
Axis point 166.73916632 166.76534552 0.00000000
Rotation angle (degrees) 121.98686687
Shift along axis -50.04824976
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.0129
rotated from previous position = 0.0105 degrees
atoms outside contour = 730, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52983212 -0.84810240 0.00048642 396.49411822
0.84810253 -0.52983213 0.00012504 113.70374247
0.00015167 0.00047879 0.99999987 -50.14312765
Axis 0.00020855 0.00019735 0.99999996
Axis point 166.73222694 166.76316048 0.00000000
Rotation angle (degrees) 121.99411720
Shift along axis -50.03799665
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 40
shifted from previous position = 0.0155
rotated from previous position = 0.00899 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52974156 -0.84815900 0.00043386 396.50392901
0.84815911 -0.52974151 0.00022716 113.67822755
0.00003716 0.00048832 0.99999988 -50.13693001
Axis 0.00015395 0.00023386 0.99999996
Axis point 166.73835929 166.76712303 0.00000000
Rotation angle (degrees) 121.98799708
Shift along axis -50.04930055
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.0197
rotated from previous position = 0.0159 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52992060 -0.84804711 0.00050315 396.49483329
0.84804724 -0.52992064 0.00006179 113.73032322
0.00021423 0.00045944 0.99999987 -50.14706542
Axis 0.00023445 0.00017035 0.99999996
Axis point 166.73011984 166.76280976 0.00000000
Rotation angle (degrees) 122.00009567
Shift along axis -50.03473100
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.0148
rotated from previous position = 0.00985 degrees
atoms outside contour = 726, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52980261 -0.84812079 0.00056136 396.48328068
0.84812096 -0.52980262 0.00014412 113.70326348
0.00017517 0.00055246 0.99999983 -50.15920086
Axis 0.00024073 0.00022767 0.99999995
Axis point 166.72603643 166.76563242 0.00000000
Rotation angle (degrees) 121.99212506
Shift along axis -50.03786671
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 48
shifted from previous position = 0.0114
rotated from previous position = 0.00772 degrees
atoms outside contour = 730, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52988850 -0.84806717 0.00049770 396.49548000
0.84806730 -0.52988853 0.00008231 113.72227391
0.00019392 0.00046570 0.99999987 -50.14705570
Axis 0.00022603 0.00017910 0.99999996
Axis point 166.73093460 166.76397237 0.00000000
Rotation angle (degrees) 121.99792686
Shift along axis -50.03706450
> open /Users/nezakoritnik/Desktop/PVA-VLPmut/helixWIDE/Coot25/mono25.cif-
> coot-0.pdb
Chain information for mono25.cif-coot-0.pdb #4
---
Chain | Description
Aa | No description available
> close #2
> select add #4
2994 atoms, 3062 bonds, 370 residues, 2 models selected
> select subtract #3
1497 atoms, 1531 bonds, 185 residues, 1 model selected
> view matrix models
> #4,0.94513,0.11589,0.30545,-64.246,0.073123,0.83621,-0.54351,111.99,-0.31841,0.53602,0.78186,11.932
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.94513,0.11589,0.30545,-52.932,0.073123,0.83621,-0.54351,73.827,-0.31841,0.53602,0.78186,-31.933
> view matrix models
> #4,0.94513,0.11589,0.30545,9.9737,0.073123,0.83621,-0.54351,106.6,-0.31841,0.53602,0.78186,-29.217
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.17377,-0.98404,0.038266,301.61,0.91019,0.14566,-0.38773,59.102,0.37597,0.10221,0.92098,-88.465
> view matrix models
> #4,-0.027459,-0.99724,0.069029,323.68,0.98588,-0.038428,-0.16298,31.73,0.16518,0.063579,0.98421,-67.848
> view matrix models
> #4,-0.04289,-0.99878,0.024533,334.08,0.99048,-0.045722,-0.12981,25.965,0.13077,0.018732,0.99124,-58.879
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.04289,-0.99878,0.024533,332.4,0.99048,-0.045722,-0.12981,25.23,0.13077,0.018732,0.99124,-65.021
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 92
shifted from previous position = 1.33
rotated from previous position = 10.8 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08882315 -0.99604726 0.00056592 318.01770707
0.99604741 0.08882308 -0.00015007 -14.09383363
0.00009921 0.00057701 0.99999983 -46.30083984
Axis 0.00036498 0.00023428 0.99999991
Axis point 166.71468259 166.78727390 0.00000000
Rotation angle (degrees) 84.90409954
Shift along axis -46.18806588
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 44
shifted from previous position = 0.0113
rotated from previous position = 0.0117 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08867491 -0.99606048 0.00053102 318.03822295
0.99606060 0.08867477 -0.00028460 -14.05916350
0.00023639 0.00055417 0.99999982 -46.31094459
Axis 0.00042104 0.00014790 0.99999990
Axis point 166.70832425 166.78925810 0.00000000
Rotation angle (degrees) 84.91262885
Shift along axis -46.17911215
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0149
rotated from previous position = 0.0196 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08892520 -0.99603813 0.00059556 318.00012377
0.99603831 0.08892518 -0.00006059 -14.11963049
0.00000739 0.00059859 0.99999982 -46.29269217
Axis 0.00033090 0.00029526 0.99999990
Axis point 166.71845369 166.78320055 0.00000000
Rotation angle (degrees) 84.89822797
Shift along axis -46.19163085
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 36
shifted from previous position = 0.00031
rotated from previous position = 0.00388 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08889089 -0.99604121 0.00056604 318.01064646
0.99604137 0.08889084 -0.00011095 -14.10687033
0.00006019 0.00057366 0.99999984 -46.29692393
Axis 0.00034367 0.00025393 0.99999991
Axis point 166.71781320 166.78868365 0.00000000
Rotation angle (degrees) 84.90020228
Shift along axis -46.19121229
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0145
rotated from previous position = 0.0141 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08870421 -0.99605787 0.00053303 318.03397375
0.99605799 0.08870408 -0.00026600 -14.06540336
0.00021767 0.00055453 0.99999983 -46.30873291
Axis 0.00041189 0.00015830 0.99999990
Axis point 166.70936159 166.78895930 0.00000000
Rotation angle (degrees) 84.91094327
Shift along axis -46.17995989
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0144
rotated from previous position = 0.0159 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08890493 -0.99603995 0.00058503 318.00509107
0.99604012 0.08890490 -0.00008145 -14.11355218
0.00002912 0.00058995 0.99999983 -46.29465990
Axis 0.00033704 0.00027906 0.99999990
Axis point 166.71800865 166.78518191 0.00000000
Rotation angle (degrees) 84.89939437
Shift along axis -46.19141423
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0107
rotated from previous position = 0.0124 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08874254 -0.99605442 0.00060352 318.01982410
0.99605459 0.08874242 -0.00022230 -14.07567166
0.00016787 0.00062086 0.99999980 -46.31080443
Axis 0.00042325 0.00021869 0.99999989
Axis point 166.70693518 166.78449400 0.00000000
Rotation angle (degrees) 84.90873881
Shift along axis -46.17927487
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.011
rotated from previous position = 0.0104 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08888336 -0.99604188 0.00057258 318.01074902
0.99604204 0.08888331 -0.00011214 -14.10570352
0.00006080 0.00058029 0.99999983 -46.29794581
Axis 0.00034759 0.00025691 0.99999991
Axis point 166.71718397 166.78817249 0.00000000
Rotation angle (degrees) 84.90063533
Shift along axis -46.19102872
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0141
rotated from previous position = 0.0135 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08870876 -0.99605747 0.00053331 318.03362636
0.99605759 0.08870863 -0.00026316 -14.06618364
0.00021481 0.00055455 0.99999983 -46.30861580
Axis 0.00041047 0.00015988 0.99999990
Axis point 166.70957689 166.78917720 0.00000000
Rotation angle (degrees) 84.91068153
Shift along axis -46.18031635
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0137
rotated from previous position = 0.0141 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08888808 -0.99604146 0.00057513 318.00922445
0.99604162 0.08888804 -0.00010066 -14.10832080
0.00004914 0.00058181 0.99999983 -46.29625029
Axis 0.00034259 0.00026404 0.99999991
Axis point 166.71759296 166.78689709 0.00000000
Rotation angle (degrees) 84.90036357
Shift along axis -46.19102386
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0113
rotated from previous position = 0.0102 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08875880 -0.99605300 0.00054965 318.02509922
0.99605314 0.08875870 -0.00021872 -14.07849319
0.00016907 0.00056689 0.99999983 -46.30502369
Axis 0.00039436 0.00019104 0.99999990
Axis point 166.71126815 166.78744723 0.00000000
Rotation angle (degrees) 84.90780202
Shift along axis -46.18229226
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.00719
rotated from previous position = 0.00528 degrees
atoms outside contour = 730, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08868411 -0.99605966 0.00053746 318.03315058
0.99605978 0.08868398 -0.00027079 -14.06440505
0.00022206 0.00055935 0.99999982 -46.30791651
Axis 0.00041671 0.00015832 0.99999990
Axis point 166.70835999 166.78560925 0.00000000
Rotation angle (degrees) 84.91209943
Shift along axis -46.17761015
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0171
rotated from previous position = 0.0159 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08889074 -0.99604122 0.00058175 318.00665345
0.99604139 0.08889070 -0.00009300 -14.11063449
0.00004092 0.00058772 0.99999983 -46.29524296
Axis 0.00034171 0.00027149 0.99999990
Axis point 166.71738420 166.78495107 0.00000000
Rotation angle (degrees) 84.90021063
Shift along axis -46.19040313
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.0172
rotated from previous position = 0.0161 degrees
atoms outside contour = 730, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08868080 -0.99605996 0.00053750 318.03356050
0.99606007 0.08868066 -0.00027226 -14.06366607
0.00022352 0.00055953 0.99999982 -46.30796294
Axis 0.00041754 0.00015761 0.99999990
Axis point 166.70817253 166.78562647 0.00000000
Rotation angle (degrees) 84.91229008
Shift along axis -46.17738371
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0209
rotated from previous position = 0.02 degrees
atoms outside contour = 731, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08894260 -0.99603658 0.00059569 317.99918892
0.99603676 0.08894259 -0.00005129 -14.12218954
-0.00000190 0.00059790 0.99999982 -46.29251800
Axis 0.00032588 0.00029999 0.99999990
Axis point 166.71928464 166.78444289 0.00000000
Rotation angle (degrees) 84.89722674
Shift along axis -46.19311921
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0169
rotated from previous position = 0.0165 degrees
atoms outside contour = 730, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08873298 -0.99605531 0.00054114 318.02804472
0.99605543 0.08873287 -0.00023988 -14.07340755
0.00019092 0.00056029 0.99999983 -46.30559231
Axis 0.00040167 0.00017580 0.99999990
Axis point 166.71031551 166.78690655 0.00000000
Rotation angle (degrees) 84.90928760
Shift along axis -46.18031890
> open /Users/nezakoritnik/Desktop/PVA-VLPmut/helixWIDE/Coot25/mono25.cif-
> coot-0.pdb
Chain information for mono25.cif-coot-0.pdb #2
---
Chain | Description
Aa | No description available
> select add #2
2994 atoms, 3062 bonds, 370 residues, 2 models selected
> select subtract #2
1497 atoms, 1531 bonds, 185 residues, 1 model selected
> open /Users/nezakoritnik/Desktop/PVA-VLPmut/helixWIDE/Coot25/mono25.cif-
> coot-0.pdb
Chain information for mono25.cif-coot-0.pdb #5
---
Chain | Description
Aa | No description available
> select subtract #4
Nothing selected
> select add #4
1497 atoms, 1531 bonds, 185 residues, 1 model selected
> select add #3
2994 atoms, 3062 bonds, 370 residues, 2 models selected
> select add #2
4491 atoms, 4593 bonds, 555 residues, 3 models selected
> close #2-5
> open /Users/nezakoritnik/Desktop/PVA-VLPmut/helixWIDE/Coot25/mono25.cif-
> coot-0.pdb
Chain information for mono25.cif-coot-0.pdb #2
---
Chain | Description
Aa | No description available
> select add #2
1497 atoms, 1531 bonds, 185 residues, 1 model selected
> view matrix models #2,1,0,0,12.398,0,1,0,66.188,0,0,1,-51.185
> view matrix models #2,1,0,0,69.038,0,1,0,17.445,0,0,1,-56.712
> view matrix models #2,1,0,0,77.547,0,1,0,39.803,0,0,1,-52.83
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.29034,-0.94193,-0.16871,397.69,0.95574,-0.27668,-0.10006,100.1,0.047569,-0.19029,0.98057,-30.734
> view matrix models
> #2,-0.35418,-0.93258,-0.069682,386.47,0.93274,-0.3469,-0.098226,111.85,0.06743,-0.099785,0.99272,-47.276
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.35418,-0.93258,-0.069682,391.48,0.93274,-0.3469,-0.098226,95.506,0.06743,-0.099785,0.99272,-45.456
> view matrix models
> #2,-0.35418,-0.93258,-0.069682,391.47,0.93274,-0.3469,-0.098226,95.364,0.06743,-0.099785,0.99272,-45.779
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 120
shifted from previous position = 4.09
rotated from previous position = 13.3 degrees
atoms outside contour = 730, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52988782 -0.84806760 0.00049013 396.49710663
0.84806772 -0.52988785 0.00008485 113.72318745
0.00018775 0.00046063 0.99999988 -50.14633281
Axis 0.00022155 0.00017828 0.99999996
Axis point 166.73136356 166.76490163 0.00000000
Rotation angle (degrees) 121.99788058
Shift along axis -50.03821359
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 40
shifted from previous position = 0.0109
rotated from previous position = 0.0127 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52975015 -0.84815364 0.00043292 396.50313289
0.84815375 -0.52975010 0.00022474 113.67771332
0.00003872 0.00048624 0.99999988 -50.13487371
Axis 0.00015416 0.00023239 0.99999996
Axis point 166.73850558 166.76529841 0.00000000
Rotation angle (degrees) 121.98857729
Shift along axis -50.04733083
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.00817
rotated from previous position = 0.00672 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52980830 -0.84811729 0.00047985 396.49528587
0.84811742 -0.52980829 0.00014210 113.69839215
0.00013371 0.00048226 0.99999988 -50.14296325
Axis 0.00020054 0.00020406 0.99999996
Axis point 166.73295537 166.76450770 0.00000000
Rotation angle (degrees) 121.99250720
Shift along axis -50.04024738
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 36
shifted from previous position = 0.00673
rotated from previous position = 0.01 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52994995 -0.84802875 0.00053106 396.49217054
0.84802890 -0.52994997 0.00012925 113.72552077
0.00017182 0.00051885 0.99999985 -50.14941058
Axis 0.00022971 0.00021181 0.99999995
Axis point 166.73071233 166.75616001 0.00000000
Rotation angle (degrees) 122.00207888
Shift along axis -50.03424244
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 36
shifted from previous position = 0.000802
rotated from previous position = 0.00358 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52994395 -0.84803253 0.00049699 396.49836792
0.84803265 -0.52994398 0.00007738 113.73278991
0.00019775 0.00046248 0.99999987 -50.14560915
Axis 0.00022705 0.00017643 0.99999996
Axis point 166.73195660 166.76150551 0.00000000
Rotation angle (degrees) 122.00167281
Shift along axis -50.03551617
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.0243
rotated from previous position = 0.0201 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52969693 -0.84818688 0.00042456 396.50490951
0.84818699 -0.52969687 0.00025872 113.66716446
0.00000545 0.00049715 0.99999988 -50.13677686
Axis 0.00014055 0.00024706 0.99999996
Axis point 166.73944164 166.76882894 0.00000000
Rotation angle (degrees) 121.98498194
Shift along axis -50.05296215
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.0224
rotated from previous position = 0.0127 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52983987 -0.84809757 0.00047831 396.49541623
0.84809769 -0.52983987 0.00012402 113.70440463
0.00014825 0.00047137 0.99999988 -50.14090600
Axis 0.00020478 0.00019459 0.99999996
Axis point 166.73297522 166.76254669 0.00000000
Rotation angle (degrees) 121.99464014
Shift along axis -50.03758340
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 40
shifted from previous position = 0.00275
rotated from previous position = 0.0105 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52978770 -0.84813018 0.00043801 396.50064026
0.84813029 -0.52978762 0.00029212 113.66141422
-0.00001570 0.00052625 0.99999986 -50.12607071
Axis 0.00013803 0.00026748 0.99999995
Axis point 166.74253085 166.75137626 0.00000000
Rotation angle (degrees) 121.99111355
Shift along axis -50.04093831
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 44
shifted from previous position = 0.0193
rotated from previous position = 0.00503 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52972921 -0.84816672 0.00042828 396.50455215
0.84816683 -0.52972915 0.00023854 113.67446214
0.00002456 0.00048962 0.99999988 -50.13595511
Axis 0.00014801 0.00023800 0.99999996
Axis point 166.73896693 166.76732224 0.00000000
Rotation angle (degrees) 121.98716250
Shift along axis -50.05021078
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.0207
rotated from previous position = 0.0141 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52988625 -0.84806858 0.00049155 396.49488216
0.84806870 -0.52988628 0.00008989 113.71823556
0.00018424 0.00046450 0.99999988 -50.14362540
Axis 0.00022086 0.00018119 0.99999996
Axis point 166.73149746 166.76211143 0.00000000
Rotation angle (degrees) 121.99777481
Shift along axis -50.03544884
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.0144
rotated from previous position = 0.00878 degrees
atoms outside contour = 726, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52979573 -0.84812507 0.00058847 396.47803401
0.84812526 -0.52979574 0.00014202 113.70205654
0.00019131 0.00057434 0.99999982 -50.16401581
Axis 0.00025486 0.00023414 0.99999994
Axis point 166.72371182 166.76498417 0.00000000
Rotation angle (degrees) 121.99166065
Shift along axis -50.03634323
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 48
shifted from previous position = 0.00963
rotated from previous position = 0.00925 degrees
atoms outside contour = 730, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52989586 -0.84806257 0.00050346 396.49548480
0.84806269 -0.52989590 0.00007205 113.72697086
0.00020568 0.00046514 0.99999987 -50.14940887
Axis 0.00023176 0.00017556 0.99999996
Axis point 166.73015090 166.76518750 0.00000000
Rotation angle (degrees) 121.99842457
Shift along axis -50.03754904
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 40
shifted from previous position = 0.014
rotated from previous position = 0.0199 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52967251 -0.84820213 0.00041736 396.50245545
0.84820224 -0.52967244 0.00028145 113.65371130
-0.00001766 0.00050308 0.99999987 -50.13087698
Axis 0.00013065 0.00025644 0.99999996
Axis point 166.74049592 166.76525082 0.00000000
Rotation angle (degrees) 121.98333205
Shift along axis -50.04992837
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 28
shifted from previous position = 0.0182
rotated from previous position = 0.0171 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52986646 -0.84808095 0.00049068 396.49414298
0.84808107 -0.52986648 0.00010307 113.71235232
0.00017258 0.00047075 0.99999988 -50.14322220
Axis 0.00021677 0.00018754 0.99999996
Axis point 166.73170011 166.76209258 0.00000000
Rotation angle (degrees) 121.99643733
Shift along axis -50.03594636
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 36
shifted from previous position = 0.00302
rotated from previous position = 0.00559 degrees
atoms outside contour = 730, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52994643 -0.84803098 0.00048997 396.50011229
0.84803110 -0.52994646 0.00007831 113.73589310
0.00019325 0.00045701 0.99999988 -50.14600775
Axis 0.00022328 0.00017495 0.99999996
Axis point 166.73200376 166.76307122 0.00000000
Rotation angle (degrees) 122.00184078
Shift along axis -50.03757751
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#2) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.316, steps = 40
shifted from previous position = 0.0145
rotated from previous position = 0.0177 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#2) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.52972894 -0.84816689 0.00042952 396.50343079
0.84816699 -0.52972889 0.00023784 113.67276140
0.00002580 0.00049030 0.99999988 -50.13493159
Axis 0.00014883 0.00023799 0.99999996
Axis point 166.73888653 166.76621269 0.00000000
Rotation angle (degrees) 121.98714450
Shift along axis -50.04886615
> open /Users/nezakoritnik/Desktop/PVA-VLPmut/helixWIDE/Coot25/mono25.cif-
> coot-0.pdb
Chain information for mono25.cif-coot-0.pdb #3
---
Chain | Description
Aa | No description available
> select add #3
2994 atoms, 3062 bonds, 370 residues, 2 models selected
> select subtract #2
1497 atoms, 1531 bonds, 185 residues, 1 model selected
> view matrix models #3,1,0,0,2.051,0,1,0,-15.996,0,0,1,-44.354
> view matrix models #3,1,0,0,42.185,0,1,0,32.171,0,0,1,-43.274
> view matrix models #3,1,0,0,60.683,0,1,0,-0.69722,0,0,1,-48.71
> view matrix models #3,1,0,0,62.658,0,1,0,14.982,0,0,1,-45.682
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.4635,-0.88288,-0.07539,260.41,0.87965,0.44822,0.15911,-56.629,-0.10669,-0.14007,0.98438,-10.843
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.4635,-0.88288,-0.07539,261.03,0.87965,0.44822,0.15911,-71.579,-0.10669,-0.14007,0.98438,-10.186
> view matrix models
> #3,0.4635,-0.88288,-0.07539,264.2,0.87965,0.44822,0.15911,-67.128,-0.10669,-0.14007,0.98438,-11.203
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4987, steps = 100
shifted from previous position = 3.29
rotated from previous position = 9.94 degrees
atoms outside contour = 1187, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.37007944 -0.92845151 0.03192178 262.62779436
0.92583144 0.37143497 0.06980116 -50.52793756
-0.07666385 0.00372221 0.99705005 -34.28683702
Axis -0.03555242 0.05842226 0.99765869
Axis point 166.00908884 168.45492225 0.00000000
Rotation angle (degrees) 68.32864250
Shift along axis -46.49556957
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4987, steps = 40
shifted from previous position = 0.0112
rotated from previous position = 0.00754 degrees
atoms outside contour = 1185, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.36998661 -0.92848595 0.03199602 262.63040091
0.92586948 0.37134794 0.06975965 -50.51981548
-0.07665251 0.00381400 0.99705057 -34.29026115
Axis -0.03547933 0.05845386 0.99765944
Axis point 166.00144084 168.44428804 0.00000000
Rotation angle (degrees) 68.33417078
Shift along axis -46.48103309
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4988, steps = 36
shifted from previous position = 0.0072
rotated from previous position = 0.0063 degrees
atoms outside contour = 1182, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.36995545 -0.92849795 0.03200811 262.63126532
0.92587351 0.37131819 0.06986445 -50.53673005
-0.07675419 0.00378873 0.99704285 -34.26536782
Axis -0.03554879 0.05851421 0.99765343
Axis point 166.01046496 168.42797480 0.00000000
Rotation angle (degrees) 68.33628644
Shift along axis -46.47830343
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4987, steps = 28
shifted from previous position = 0.017
rotated from previous position = 0.00622 degrees
atoms outside contour = 1185, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.36991633 -0.92851596 0.03193768 262.65492221
0.92588579 0.37127405 0.06993624 -50.53902320
-0.07679454 0.00370009 0.99704007 -34.26343624
Axis -0.03563445 0.05849696 0.99765139
Axis point 166.02056507 168.43125954 0.00000000
Rotation angle (degrees) 68.33893861
Shift along axis -46.49890695
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.23593,-0.96894,0.074073,277.46,0.97016,0.23924,0.039411,-33.523,-0.055908,0.062564,0.99647,-44.492
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.5759, steps = 84
shifted from previous position = 3.74
rotated from previous position = 5.54 degrees
atoms outside contour = 1160, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.20545956 -0.97090468 0.12300598 275.28348302
0.96823229 0.21996102 0.11892595 -47.86077330
-0.14252228 0.09466388 0.98525436 -34.20628577
Axis -0.01239516 0.13565477 0.99067863
Axis point 163.48467087 149.18610823 0.00000000
Rotation angle (degrees) 78.15074492
Shift along axis -43.79216075
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.576, steps = 40
shifted from previous position = 0.0158
rotated from previous position = 0.0136 degrees
atoms outside contour = 1159, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.20522846 -0.97094955 0.12303762 275.30123237
0.96828116 0.21973673 0.11894268 -47.84528540
-0.14252322 0.09472459 0.98524839 -34.20669314
Axis -0.01237208 0.13566471 0.99067756
Axis point 163.47842283 149.16483134 0.00000000
Rotation angle (degrees) 78.16424978
Shift along axis -43.78476865
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.5759, steps = 44
shifted from previous position = 0.0152
rotated from previous position = 0.0131 degrees
atoms outside contour = 1159, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.20540910 -0.97092642 0.12291862 275.30839399
0.96823719 0.21990433 0.11899090 -47.86762674
-0.14256175 0.09457257 0.98525742 -34.18917552
Axis -0.01247486 0.13562879 0.99068118
Axis point 163.49891485 149.18461064 0.00000000
Rotation angle (degrees) 78.15379191
Shift along axis -43.79723371
> view matrix models
> #3,0.0043203,-0.98624,0.16526,295.5,0.9949,0.0209,0.098719,-21.782,-0.10081,0.16399,0.9813,-47.858
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4281, steps = 116
shifted from previous position = 1.84
rotated from previous position = 9.06 degrees
atoms outside contour = 1237, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.01371152 -0.99986601 0.00894160 326.32567820
0.99420016 -0.01267877 0.10679552 -20.49150236
-0.10666784 0.01035407 0.99424080 -29.67827137
Axis -0.04822695 0.05781219 0.99716193
Axis point 171.22927789 150.52541062 0.00000000
Rotation angle (degrees) 90.92105502
Shift along axis -46.51639390
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4282, steps = 40
shifted from previous position = 0.0195
rotated from previous position = 0.0876 degrees
atoms outside contour = 1236, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.01350144 -0.99988027 0.00756063 326.52118562
0.99413457 -0.01261165 0.10741234 -20.59743569
-0.10730412 0.00896650 0.99418581 -29.40544670
Axis -0.04922919 0.05743969 0.99713448
Axis point 171.37911285 150.55320437 0.00000000
Rotation angle (degrees) 90.91468799
Shift along axis -46.57866899
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4282, steps = 40
shifted from previous position = 0.0125
rotated from previous position = 0.0206 degrees
atoms outside contour = 1237, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
-0.01337671 -0.99988237 0.00750375 326.52175539
0.99410043 -0.01249079 0.10774189 -20.66121789
-0.10763548 0.00890071 0.99415058 -29.35437656
Axis -0.04942680 0.05757686 0.99711679
Axis point 171.40659385 150.53680869 0.00000000
Rotation angle (degrees) 90.90866103
Shift along axis -46.59827623
> view matrix models
> #3,0.04049,-0.99787,0.051242,311.23,0.99592,0.044443,0.078517,-22.888,-0.080627,0.047854,0.99559,-38.164
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.04049,-0.99787,0.051242,312.72,0.99592,0.044443,0.078517,-20.749,-0.080627,0.047854,0.99559,-39.614
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4278, steps = 84
shifted from previous position = 2.64
rotated from previous position = 4.96 degrees
atoms outside contour = 1230, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.03107627 -0.99808262 0.05352893 312.27823379
0.98562784 0.03949744 0.16424893 -33.43804468
-0.16604825 0.04765537 0.98496545 -23.77297733
Axis -0.05831927 0.10983095 0.99223789
Axis point 170.17730653 145.01551044 0.00000000
Rotation angle (degrees) 88.40871589
Shift along axis -45.47282014
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4278, steps = 28
shifted from previous position = 0.0333
rotated from previous position = 0.129 degrees
atoms outside contour = 1229, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.03013283 -0.99819243 0.05199897 312.70525579
0.98544012 0.03837633 0.16563519 -33.52311928
-0.16733132 0.04625081 0.98481526 -23.41882150
Axis -0.05971342 0.10970414 0.99216899
Axis point 170.41002807 144.97012763 0.00000000
Rotation angle (degrees) 88.47218686
Shift along axis -45.58575353
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4278, steps = 28
shifted from previous position = 0.0267
rotated from previous position = 0.0515 degrees
atoms outside contour = 1229, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.02924271 -0.99821469 0.05207969 312.79467247
0.98548011 0.03750926 0.16559591 -33.42183698
-0.16725374 0.04648103 0.98481760 -23.44730827
Axis -0.05957725 0.10970319 0.99217728
Axis point 170.39119465 144.93023770 0.00000000
Rotation angle (degrees) 88.52247695
Shift along axis -45.56581421
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4277, steps = 40
shifted from previous position = 0.0229
rotated from previous position = 0.0626 degrees
atoms outside contour = 1230, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.02925178 -0.99825768 0.05124397 312.95922174
0.98536616 0.03741051 0.16629489 -33.51747712
-0.16792221 0.04562965 0.98474365 -23.25217597
Axis -0.06035256 0.10961931 0.99213970
Axis point 170.51727937 144.92841353 0.00000000
Rotation angle (degrees) 88.52716600
Shift along axis -45.63145873
> view matrix models
> #3,0.029252,-0.99826,0.051244,314.71,0.98537,0.037411,0.16629,-30.985,-0.16792,0.04563,0.98474,-25.747
> view matrix models
> #3,0.029252,-0.99826,0.051244,315.46,0.98537,0.037411,0.16629,-34.783,-0.16792,0.04563,0.98474,-24.308
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 100
shifted from previous position = 2.98
rotated from previous position = 10.5 degrees
atoms outside contour = 731, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08873614 -0.99605500 0.00058472 318.02715747
0.99605515 0.08873602 -0.00021881 -14.07347923
0.00016607 0.00060183 0.99999980 -46.31251368
Axis 0.00041195 0.00021016 0.99999989
Axis point 166.70930733 166.78799449 0.00000000
Rotation angle (degrees) 84.90910688
Shift along axis -46.18445560
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.00729
rotated from previous position = 0.00779 degrees
atoms outside contour = 730, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08876283 -0.99605267 0.00048308 318.04443895
0.99605275 0.08876269 -0.00030512 -14.05519925
0.00026104 0.00050825 0.99999984 -46.31514156
Axis 0.00040830 0.00011146 0.99999991
Axis point 166.71057133 166.80887772 0.00000000
Rotation angle (degrees) 84.90757093
Shift along axis -46.18684617
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 44
shifted from previous position = 0.0031
rotated from previous position = 0.0138 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08887576 -0.99604255 0.00057282 318.01132608
0.99604272 0.08887571 -0.00011310 -14.10484342
0.00006174 0.00058061 0.99999983 -46.29769710
Axis 0.00034823 0.00025655 0.99999991
Axis point 166.71696723 166.78759372 0.00000000
Rotation angle (degrees) 84.90107270
Shift along axis -46.19056929
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.012
rotated from previous position = 0.0105 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08874390 -0.99605433 0.00054104 318.02808505
0.99605446 0.08874379 -0.00023447 -14.07449598
0.00018554 0.00055971 0.99999983 -46.30595602
Axis 0.00039867 0.00017846 0.99999990
Axis point 166.71087854 166.78828344 0.00000000
Rotation angle (degrees) 84.90865938
Shift along axis -46.18167657
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0138
rotated from previous position = 0.0146 degrees
atoms outside contour = 731, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08893279 -0.99603746 0.00058599 318.00179505
0.99603763 0.08893277 -0.00006977 -14.11819594
0.00001738 0.00058988 0.99999983 -46.29372121
Axis 0.00033113 0.00028544 0.99999990
Axis point 166.71881745 166.78593992 0.00000000
Rotation angle (degrees) 84.89779135
Shift along axis -46.19244577
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0161
rotated from previous position = 0.016 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08872464 -0.99605605 0.00053823 318.02977643
0.99605617 0.08872452 -0.00024798 -14.07103838
0.00019925 0.00055811 0.99999982 -46.30646051
Axis 0.00040464 0.00017016 0.99999990
Axis point 166.71003322 166.78751974 0.00000000
Rotation angle (degrees) 84.90976770
Shift along axis -46.18016193
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0157
rotated from previous position = 0.0123 degrees
atoms outside contour = 731, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08888140 -0.99604205 0.00057598 318.01096057
0.99604221 0.08888135 -0.00010646 -14.10592079
0.00005485 0.00058316 0.99999983 -46.29759324
Axis 0.00034618 0.00026160 0.99999991
Axis point 166.71724212 166.78790851 0.00000000
Rotation angle (degrees) 84.90074835
Shift along axis -46.19118928
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0175
rotated from previous position = 0.0188 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08863504 -0.99606403 0.00052434 318.04427174
0.99606413 0.08863489 -0.00031500 -14.04997159
0.00026728 0.00055019 0.99999981 -46.31391807
Axis 0.00043430 0.00012904 0.99999990
Axis point 166.70680083 166.79007090 0.00000000
Rotation angle (degrees) 84.91492295
Shift along axis -46.17759819
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0195
rotated from previous position = 0.0225 degrees
atoms outside contour = 731, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08893539 -0.99603723 0.00058326 318.00307038
0.99603740 0.08893537 -0.00007074 -14.11765441
0.00001859 0.00058724 0.99999983 -46.29443162
Axis 0.00033030 0.00028346 0.99999991
Axis point 166.71921009 166.78729689 0.00000000
Rotation angle (degrees) 84.89764168
Shift along axis -46.19339277
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0208
rotated from previous position = 0.018 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08869523 -0.99605867 0.00053581 318.03236608
0.99605879 0.08869510 -0.00026729 -14.06576073
0.00021871 0.00055740 0.99999982 -46.30740583
Axis 0.00041398 0.00015918 0.99999990
Axis point 166.70870973 166.78640114 0.00000000
Rotation angle (degrees) 84.91145984
Shift along axis -46.17798242
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 24
shifted from previous position = 0.00535
rotated from previous position = 0.00896 degrees
atoms outside contour = 731, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08856400 -0.99607035 0.00053064 318.05014454
0.99607044 0.08856382 -0.00035126 -14.03951977
0.00030288 0.00055967 0.99999980 -46.31627054
Axis 0.00045726 0.00011433 0.99999989
Axis point 166.70437995 166.78629591 0.00000000
Rotation angle (degrees) 84.91901064
Shift along axis -46.17243931
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.00692
rotated from previous position = 0.0155 degrees
atoms outside contour = 730, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08868961 -0.99605911 0.00063798 318.01671679
0.99605931 0.08868954 -0.00013796 -14.08814194
0.00008083 0.00064770 0.99999979 -46.30166820
Axis 0.00039438 0.00027968 0.99999988
Axis point 166.70957696 166.76797406 0.00000000
Rotation angle (degrees) 84.91178249
Shift along axis -46.18018261
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 44
shifted from previous position = 0.0172
rotated from previous position = 0.00831 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08872764 -0.99605578 0.00053988 318.04016341
0.99605591 0.08872753 -0.00023780 -14.06571926
0.00018896 0.00055885 0.99999983 -46.31341373
Axis 0.00039990 0.00017616 0.99999990
Axis point 166.71208262 166.79640410 0.00000000
Rotation angle (degrees) 84.90959478
Shift along axis -46.18870148
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0136
rotated from previous position = 0.00414 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08867797 -0.99606021 0.00052731 318.04014293
0.99606032 0.08867783 -0.00028862 -14.05765914
0.00024072 0.00055082 0.99999982 -46.31234562
Axis 0.00042138 0.00014386 0.99999990
Axis point 166.70859577 166.79151098 0.00000000
Rotation angle (degrees) 84.91245282
Shift along axis -46.18034776
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.014
rotated from previous position = 0.0188 degrees
atoms outside contour = 731, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08892262 -0.99603837 0.00058327 318.00379926
0.99603854 0.08892259 -0.00007952 -14.11534713
0.00002734 0.00058803 0.99999983 -46.29485305
Axis 0.00033510 0.00027907 0.99999990
Axis point 166.71843613 166.78662966 0.00000000
Rotation angle (degrees) 84.89837669
Shift along axis -46.19222455
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0169
rotated from previous position = 0.0163 degrees
atoms outside contour = 730, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08870919 -0.99605742 0.00053555 318.03195396
0.99605755 0.08870906 -0.00025992 -14.06757631
0.00021139 0.00055649 0.99999982 -46.30749891
Axis 0.00040982 0.00016272 0.99999990
Axis point 166.70941827 166.78769111 0.00000000
Rotation angle (degrees) 84.91065686
Shift along axis -46.17944692
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0173
rotated from previous position = 0.0163 degrees
atoms outside contour = 731, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08891746 -0.99603882 0.00058734 318.00409236
0.99603900 0.08891743 -0.00007409 -14.11548473
0.00002157 0.00059160 0.99999982 -46.29470604
Axis 0.00033417 0.00028401 0.99999990
Axis point 166.71847141 166.78590819 0.00000000
Rotation angle (degrees) 84.89867341
Shift along axis -46.19244428
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0164
rotated from previous position = 0.0155 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08872074 -0.99605639 0.00053703 318.03062818
0.99605652 0.08872061 -0.00025151 -14.06992858
0.00020287 0.00055723 0.99999982 -46.30689163
Axis 0.00040597 0.00016774 0.99999990
Axis point 166.70991427 166.78783335 0.00000000
Rotation angle (degrees) 84.90999234
Shift along axis -46.18013666
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0153
rotated from previous position = 0.0129 degrees
atoms outside contour = 731, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08888615 -0.99604163 0.00057396 318.01037154
0.99604179 0.08888611 -0.00010511 -14.10689844
0.00005367 0.00058103 0.99999983 -46.29714288
Axis 0.00034443 0.00026117 0.99999991
Axis point 166.71748904 166.78787672 0.00000000
Rotation angle (degrees) 84.90047477
Shift along axis -46.19129091
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0162
rotated from previous position = 0.0155 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08868484 -0.99605959 0.00053081 318.03641206
0.99605971 0.08868471 -0.00027927 -14.06143915
0.00023110 0.00055349 0.99999982 -46.30985211
Axis 0.00041803 0.00015045 0.99999990
Axis point 166.70860502 166.78885347 0.00000000
Rotation angle (degrees) 84.91205750
Shift along axis -46.17901496
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0166
rotated from previous position = 0.0195 degrees
atoms outside contour = 731, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08893256 -0.99603747 0.00059593 317.99984327
0.99603765 0.08893254 -0.00005627 -14.12067903
0.00000305 0.00059857 0.99999982 -46.29271061
Axis 0.00032872 0.00029762 0.99999990
Axis point 166.71883370 166.78381190 0.00000000
Rotation angle (degrees) 84.89780477
Shift along axis -46.19237494
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0133
rotated from previous position = 0.0144 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08875258 -0.99605355 0.00054602 318.02605115
0.99605369 0.08875247 -0.00022434 -14.07717192
0.00017500 0.00056378 0.99999982 -46.30509530
Axis 0.00039562 0.00018625 0.99999990
Axis point 166.71112395 166.78745780 0.00000000
Rotation angle (degrees) 84.90816024
Shift along axis -46.18189463
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0118
rotated from previous position = 0.00915 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08886811 -0.99604323 0.00057640 318.01183563
0.99604340 0.08886806 -0.00011889 -14.10313712
0.00006720 0.00058469 0.99999983 -46.29901139
Axis 0.00035319 0.00025561 0.99999990
Axis point 166.71636869 166.78748876 0.00000000
Rotation angle (degrees) 84.90151272
Shift along axis -46.19029410
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0118
rotated from previous position = 0.0116 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08872282 -0.99605621 0.00053495 318.03237610
0.99605633 0.08872269 -0.00025357 -14.06871440
0.00020510 0.00055534 0.99999982 -46.30815924
Axis 0.00040606 0.00016558 0.99999990
Axis point 166.71019751 166.78971283 0.00000000
Rotation angle (degrees) 84.90987260
Shift along axis -46.18134561
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0113
rotated from previous position = 0.0101 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08884672 -0.99604514 0.00057398 318.01510267
0.99604531 0.08884665 -0.00013391 -14.09830595
0.00008238 0.00058361 0.99999983 -46.30072242
Axis 0.00036018 0.00024678 0.99999990
Axis point 166.71558084 166.78791246 0.00000000
Rotation angle (degrees) 84.90274376
Shift along axis -46.18965405
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0104
rotated from previous position = 0.00962 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08873007 -0.99605556 0.00053713 318.03168382
0.99605569 0.08872994 -0.00024846 -14.06999179
0.00019982 0.00055705 0.99999982 -46.30806673
Axis 0.00040435 0.00016932 0.99999990
Axis point 166.71047169 166.79000950 0.00000000
Rotation angle (degrees) 84.90945564
Shift along axis -46.18184777
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.00168
rotated from previous position = 0.00219 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08869667 -0.99605854 0.00053371 318.03596861
0.99605866 0.08869653 -0.00026635 -14.06383365
0.00021796 0.00055523 0.99999982 -46.30960510
Axis 0.00041241 0.00015850 0.99999990
Axis point 166.70945003 166.78953059 0.00000000
Rotation angle (degrees) 84.91137724
Shift along axis -46.18066772
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.00815
rotated from previous position = 0.0123 degrees
atoms outside contour = 731, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08885022 -0.99604484 0.00056876 318.01247454
0.99604500 0.08885016 -0.00012188 -14.10258823
0.00007087 0.00057734 0.99999983 -46.29657216
Axis 0.00035100 0.00024994 0.99999991
Axis point 166.71634170 166.78478957 0.00000000
Rotation angle (degrees) 84.90254202
Shift along axis -46.18846980
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.0027
rotated from previous position = 0.00391 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08880223 -0.99604912 0.00056310 318.02276339
0.99604927 0.08880215 -0.00016974 -14.08758782
0.00011907 0.00057595 0.99999983 -46.30418212
Axis 0.00037433 0.00022290 0.99999991
Axis point 166.71413885 166.78946665 0.00000000
Rotation angle (degrees) 84.90530333
Shift along axis -46.18827392
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.00921
rotated from previous position = 0.00578 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08873179 -0.99605539 0.00057626 318.02586242
0.99605554 0.08873166 -0.00024033 -14.07159906
0.00018825 0.00059531 0.99999980 -46.30988011
Axis 0.00041948 0.00019478 0.99999989
Axis point 166.70816109 166.78729677 0.00000000
Rotation angle (degrees) 84.90935720
Shift along axis -46.17921163
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 36
shifted from previous position = 0.00474
rotated from previous position = 0.0101 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08859072 -0.99606797 0.00052823 318.05101985
0.99606807 0.08859055 -0.00033217 -14.04140273
0.00028406 0.00055558 0.99999980 -46.31754079
Axis 0.00044563 0.00012257 0.99999989
Axis point 166.70557582 166.79041265 0.00000000
Rotation angle (degrees) 84.91747325
Shift along axis -46.17752476
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0142
rotated from previous position = 0.0219 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08889081 -0.99604121 0.00058134 318.00704476
0.99604137 0.08889077 -0.00010214 -14.10901231
0.00005006 0.00058812 0.99999983 -46.29667840
Axis 0.00034650 0.00026669 0.99999990
Axis point 166.71692597 166.78599797 0.00000000
Rotation angle (degrees) 84.90020674
Shift along axis -46.19024723
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.00955
rotated from previous position = 0.0112 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08874909 -0.99605386 0.00054798 318.02747650
0.99605400 0.08874898 -0.00023058 -14.07503157
0.00018103 0.00056628 0.99999982 -46.30674945
Axis 0.00040001 0.00018420 0.99999990
Axis point 166.71079335 166.78875918 0.00000000
Rotation angle (degrees) 84.90836100
Shift along axis -46.18212462
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 44
shifted from previous position = 0.00774
rotated from previous position = 0.0077 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08884138 -0.99604562 0.00057143 318.01485450
0.99604578 0.08884132 -0.00013613 -14.09830265
0.00008483 0.00058126 0.99999983 -46.29966822
Axis 0.00036012 0.00024427 0.99999991
Axis point 166.71547548 166.78678390 0.00000000
Rotation angle (degrees) 84.90305054
Shift along axis -46.18858391
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 36
shifted from previous position = 0.00222
rotated from previous position = 0.00447 degrees
atoms outside contour = 732, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08891202 -0.99603932 0.00056496 318.00703706
0.99603948 0.08891197 -0.00010421 -14.11087916
0.00005356 0.00057199 0.99999983 -46.29530843
Axis 0.00033944 0.00025672 0.99999991
Axis point 166.71819550 166.78836652 0.00000000
Rotation angle (degrees) 84.89898670
Shift along axis -46.19098183
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#3) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0127
rotated from previous position = 0.0139 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#3) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.08872228 -0.99605626 0.00053585 318.03142908
0.99605638 0.08872216 -0.00025249 -14.06940701
0.00020395 0.00055614 0.99999982 -46.30750596
Axis 0.00040592 0.00016661 0.99999990
Axis point 166.71006910 166.78877532 0.00000000
Rotation angle (degrees) 84.90990341
Shift along axis -46.18075120
> open /Users/nezakoritnik/Desktop/PVA-VLPmut/helixWIDE/Coot25/mono25.cif-
> coot-0.pdb
Chain information for mono25.cif-coot-0.pdb #4
---
Chain | Description
Aa | No description available
> select subtract #3
Nothing selected
> select add #4
1497 atoms, 1531 bonds, 185 residues, 1 model selected
> view matrix models #4,1,0,0,3.1711,0,1,0,12.164,0,0,1,-36.646
> view matrix models #4,1,0,0,40.767,0,1,0,13.602,0,0,1,-41.41
> view matrix models #4,1,0,0,39.07,0,1,0,-2.7317,0,0,1,-44.065
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.36106,-0.91217,-0.19388,275.72,0.90026,0.39517,-0.18268,-7.1088,0.24325,-0.10859,0.96387,-54.796
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.36106,-0.91217,-0.19388,268.92,0.90026,0.39517,-0.18268,-21.522,0.24325,-0.10859,0.96387,-57.429
> view matrix models
> #4,0.36106,-0.91217,-0.19388,267.32,0.90026,0.39517,-0.18268,-22.457,0.24325,-0.10859,0.96387,-58.357
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.57959,-0.8027,-0.14052,215.02,0.79715,0.59427,-0.10675,-48.928,0.1692,-0.050142,0.98431,-60.121
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.57959,-0.8027,-0.14052,220.95,0.79715,0.59427,-0.10675,-48.676,0.1692,-0.050142,0.98431,-56.299
> view matrix models
> #4,0.57959,-0.8027,-0.14052,222.31,0.79715,0.59427,-0.10675,-47.891,0.1692,-0.050142,0.98431,-58.114
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 96
shifted from previous position = 2.08
rotated from previous position = 11.7 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67136038 -0.74113096 0.00037537 178.39772492
0.74113102 0.67136010 -0.00064742 -68.66913233
0.00022781 0.00071285 0.99999972 -42.48929955
Axis 0.00091770 0.00009955 0.99999957
Axis point 166.64313629 166.86799296 0.00000000
Rotation angle (degrees) 47.82787496
Shift along axis -42.33240190
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.0171
rotated from previous position = 0.00889 degrees
atoms outside contour = 727, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67126711 -0.74121547 0.00031003 178.41909828
0.74121546 0.67126681 -0.00071018 -68.65516721
0.00031828 0.00070652 0.99999970 -42.49093871
Axis 0.00095566 -0.00000556 0.99999954
Axis point 166.63075732 166.86447677 0.00000000
Rotation angle (degrees) 47.83508675
Shift along axis -42.32003019
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0141
rotated from previous position = 0.016 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67142316 -0.74107404 0.00045510 178.36562908
0.74107417 0.67142290 -0.00059742 -68.67751945
0.00013716 0.00073839 0.99999972 -42.47821340
Axis 0.00090126 0.00021451 0.99999957
Axis point 166.63955608 166.85226351 0.00000000
Rotation angle (degrees) 47.82302082
Shift along axis -42.33217316
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.0111
rotated from previous position = 0.0163 degrees
atoms outside contour = 727, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67126548 -0.74121694 0.00030404 178.42285666
0.74121694 0.67126518 -0.00071175 -68.65545514
0.00032347 0.00070313 0.99999970 -42.49296307
Axis 0.00095443 -0.00001311 0.99999954
Axis point 166.63306728 166.86775735 0.00000000
Rotation angle (degrees) 47.83521243
Shift along axis -42.32175084
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.00758
rotated from previous position = 0.0155 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67141306 -0.74108319 0.00045021 178.36613250
0.74108331 0.67141281 -0.00060207 -68.67589874
0.00014391 0.00073788 0.99999972 -42.47714254
Axis 0.00090404 0.00020665 0.99999957
Axis point 166.63699129 166.84990811 0.00000000
Rotation angle (degrees) 47.82380113
Shift along axis -42.33006586
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 44
shifted from previous position = 0.0123
rotated from previous position = 0.0175 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67124354 -0.74123683 0.00029085 178.42685828
0.74123680 0.67124323 -0.00072603 -68.65227885
0.00034293 0.00070293 0.99999969 -42.49290188
Axis 0.00096391 -0.00003513 0.99999953
Axis point 166.62964682 166.86579978 0.00000000
Rotation angle (degrees) 47.83690945
Shift along axis -42.31848381
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0201
rotated from previous position = 0.0189 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67143107 -0.74106688 0.00045576 178.36689927
0.74106701 0.67143082 -0.00059294 -68.67906754
0.00013340 0.00073587 0.99999972 -42.47987694
Axis 0.00089655 0.00021750 0.99999957
Axis point 166.64280985 166.85566132 0.00000000
Rotation angle (degrees) 47.82240906
Shift along axis -42.33488151
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 36
shifted from previous position = 0.00121
rotated from previous position = 0.000506 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67143586 -0.74106254 0.00044977 178.36577588
0.74106266 0.67143561 -0.00059256 -68.67891219
0.00013714 0.00073117 0.99999972 -42.47909558
Axis 0.00089313 0.00021093 0.99999958
Axis point 166.64298991 166.85592572 0.00000000
Rotation angle (degrees) 47.82203806
Shift along axis -42.33426030
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.0192
rotated from previous position = 0.0203 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67123230 -0.74124701 0.00027760 178.43194393
0.74124697 0.67123199 -0.00073537 -68.65042657
0.00035876 0.00069937 0.99999969 -42.49432475
Axis 0.00096779 -0.00005474 0.99999953
Axis point 166.62953780 166.86811263 0.00000000
Rotation angle (degrees) 47.83777813
Shift along axis -42.31786200
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0186
rotated from previous position = 0.0225 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67145404 -0.74104605 0.00047624 178.35614908
0.74104620 0.67145380 -0.00057629 -68.68168690
0.00010729 0.00073986 0.99999972 -42.47573420
Axis 0.00088804 0.00024894 0.99999957
Axis point 166.64194552 166.85090654 0.00000000
Rotation angle (degrees) 47.82063249
Shift along axis -42.33442666
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.0182
rotated from previous position = 0.0224 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67123455 -0.74124497 0.00027706 178.43182937
0.74124493 0.67123424 -0.00073396 -68.65064266
0.00035807 0.00069803 0.99999969 -42.49438954
Axis 0.00096593 -0.00005464 0.99999953
Axis point 166.62999649 166.86861275 0.00000000
Rotation angle (degrees) 47.83760428
Shift along axis -42.31826529
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0167
rotated from previous position = 0.0202 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67143146 -0.74106651 0.00046003 178.36352722
0.74106665 0.67143121 -0.00059203 -68.67866377
0.00012985 0.00073842 0.99999972 -42.47784357
Axis 0.00089766 0.00022277 0.99999957
Axis point 166.64049596 166.85236929 0.00000000
Rotation angle (degrees) 47.82237832
Shift along axis -42.33301587
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.0139
rotated from previous position = 0.0188 degrees
atoms outside contour = 727, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67124834 -0.74123248 0.00029054 178.42819047
0.74123246 0.67124803 -0.00072352 -68.65305849
0.00034128 0.00070102 0.99999969 -42.49414313
Axis 0.00096093 -0.00003423 0.99999954
Axis point 166.63176239 166.86854861 0.00000000
Rotation angle (degrees) 47.83653829
Shift along axis -42.32031707
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0114
rotated from previous position = 0.0169 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67141111 -0.74108496 0.00044758 178.36880290
0.74108508 0.67141086 -0.00060492 -68.67593099
0.00014779 0.00073785 0.99999972 -42.47876953
Axis 0.00090595 0.00020227 0.99999957
Axis point 166.63833785 166.85218674 0.00000000
Rotation angle (degrees) 47.82395220
Shift along axis -42.33104910
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0214
rotated from previous position = 0.0242 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67116527 -0.74130771 0.00025226 178.44834938
0.74130764 0.67116495 -0.00077804 -68.64188492
0.00040746 0.00070919 0.99999966 -42.49778117
Axis 0.00100311 -0.00010468 0.99999949
Axis point 166.62180597 166.86695064 0.00000000
Rotation angle (degrees) 47.84296070
Shift along axis -42.31157070
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0216
rotated from previous position = 0.0202 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67137104 -0.74112129 0.00041423 178.38486490
0.74112138 0.67137076 -0.00063216 -68.67118669
0.00019040 0.00073141 0.99999971 -42.48395765
Axis 0.00091993 0.00015100 0.99999957
Axis point 166.63811473 166.85756673 0.00000000
Rotation angle (degrees) 47.82705120
Shift along axis -42.33020672
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.022
rotated from previous position = 0.0216 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67114085 -0.74132979 0.00030747 178.44686820
0.74132975 0.67114048 -0.00081739 -68.63615789
0.00039960 0.00077652 0.99999962 -42.50221865
Axis 0.00107504 -0.00006214 0.99999942
Axis point 166.61067220 166.86352924 0.00000000
Rotation angle (degrees) 47.84485179
Shift along axis -42.30609193
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0237
rotated from previous position = 0.0225 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67138164 -0.74111168 0.00041810 178.38290794
0.74111178 0.67138137 -0.00062592 -68.67256764
0.00018317 0.00073009 0.99999972 -42.48379449
Axis 0.00091485 0.00015850 0.99999957
Axis point 166.63972198 166.85847104 0.00000000
Rotation angle (degrees) 47.82623135
Shift along axis -42.33146791
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.0118
rotated from previous position = 0.0122 degrees
atoms outside contour = 727, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67126466 -0.74121769 0.00030377 178.42293059
0.74121768 0.67126436 -0.00071230 -68.65532418
0.00032406 0.00070330 0.99999970 -42.49293711
Axis 0.00095491 -0.00001369 0.99999954
Axis point 166.63287866 166.86761652 0.00000000
Rotation angle (degrees) 47.83527583
Shift along axis -42.32159950
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.00814
rotated from previous position = 0.015 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67140771 -0.74108804 0.00044653 178.36841931
0.74108816 0.67140745 -0.00060606 -68.67535420
0.00014934 0.00073783 0.99999972 -42.47801888
Axis 0.00090670 0.00020051 0.99999957
Axis point 166.63711597 166.85079415 0.00000000
Rotation angle (degrees) 47.82421514
Shift along axis -42.33004387
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0153
rotated from previous position = 0.0273 degrees
atoms outside contour = 727, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67111344 -0.74135464 0.00022543 178.46901042
0.74135456 0.67111314 -0.00074959 -68.64745887
0.00040442 0.00067018 0.99999969 -42.49561541
Axis 0.00095755 -0.00012072 0.99999953
Axis point 166.63091852 166.86597003 0.00000000
Rotation angle (degrees) 47.84696444
Shift along axis -42.31641522
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0226
rotated from previous position = 0.0252 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67138972 -0.74110436 0.00042191 178.38301890
0.74110446 0.67138945 -0.00062116 -68.67403735
0.00017708 0.00072972 0.99999972 -42.48498651
Axis 0.00091140 0.00016518 0.99999957
Axis point 166.64218191 166.86080152 0.00000000
Rotation angle (degrees) 47.82560648
Shift along axis -42.33373372
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 36
shifted from previous position = 0.000608
rotated from previous position = 0.0043 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67143659 -0.74106188 0.00044998 178.36589055
0.74106200 0.67143634 -0.00059229 -68.67898884
0.00013679 0.00073115 0.99999972 -42.47924639
Axis 0.00089294 0.00021131 0.99999958
Axis point 166.64321380 166.85628160 0.00000000
Rotation angle (degrees) 47.82198198
Shift along axis -42.33447120
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 36
shifted from previous position = 0.000758
rotated from previous position = 0.00151 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67145310 -0.74104691 0.00045949 178.36070215
0.74104704 0.67145286 -0.00058191 -68.68084466
0.00012270 0.00073123 0.99999972 -42.47771550
Axis 0.00088600 0.00022724 0.99999958
Axis point 166.64413254 166.85556000 0.00000000
Rotation angle (degrees) 47.82070508
Shift along axis -42.33527734
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 36
shifted from previous position = 0.00087
rotated from previous position = 0.00137 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67146861 -0.74103286 0.00046575 178.35495238
0.74103299 0.67146837 -0.00057226 -68.68255634
0.00011133 0.00072939 0.99999973 -42.47545864
Axis 0.00087827 0.00023914 0.99999959
Axis point 166.64464267 166.85378606 0.00000000
Rotation angle (degrees) 47.81950557
Shift along axis -42.33522173
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 36
shifted from previous position = 0.00125
rotated from previous position = 0.00133 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67145358 -0.74104648 0.00046004 178.36086290
0.74104661 0.67145334 -0.00058193 -68.68072759
0.00012235 0.00073165 0.99999972 -42.47781799
Axis 0.00088630 0.00022784 0.99999958
Axis point 166.64412631 166.85600341 0.00000000
Rotation angle (degrees) 47.82066793
Shift along axis -42.33536695
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 36
shifted from previous position = 0.00276
rotated from previous position = 0.00208 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67147833 -0.74102405 0.00046085 178.35213816
0.74102418 0.67147810 -0.00056778 -68.68310443
0.00011129 0.00072276 0.99999973 -42.47369161
Axis 0.00087078 0.00023587 0.99999959
Axis point 166.64522160 166.85347324 0.00000000
Rotation angle (degrees) 47.81875336
Shift along axis -42.33456894
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.0172
rotated from previous position = 0.0235 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67123693 -0.74124281 0.00027288 178.43210284
0.74124278 0.67123663 -0.00073338 -68.65079459
0.00036044 0.00069454 0.99999969 -42.49442640
Axis 0.00096319 -0.00005906 0.99999953
Axis point 166.63079287 166.86949357 0.00000000
Rotation angle (degrees) 47.83741991
Shift along axis -42.31848795
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0162
rotated from previous position = 0.0191 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67142072 -0.74107626 0.00045215 178.36738626
0.74107638 0.67142046 -0.00059938 -68.67732145
0.00014060 0.00073752 0.99999972 -42.47904517
Axis 0.00090200 0.00021020 0.99999957
Axis point 166.64008904 166.85339426 0.00000000
Rotation angle (degrees) 47.82320951
Shift along axis -42.33257525
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.0134
rotated from previous position = 0.0177 degrees
atoms outside contour = 727, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67124883 -0.74123203 0.00029001 178.42837154
0.74123201 0.67124852 -0.00072338 -68.65314500
0.00034152 0.00070053 0.99999970 -42.49428396
Axis 0.00096050 -0.00003474 0.99999954
Axis point 166.63203526 166.86885806 0.00000000
Rotation angle (degrees) 47.83650032
Shift along axis -42.32049860
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0108
rotated from previous position = 0.0164 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67140632 -0.74108931 0.00044423 178.37038059
0.74108942 0.67140606 -0.00060803 -68.67534085
0.00015235 0.00073745 0.99999972 -42.47919749
Axis 0.00090777 0.00019693 0.99999957
Axis point 166.63807884 166.85247765 0.00000000
Rotation angle (degrees) 47.82432301
Shift along axis -42.33078334
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.021
rotated from previous position = 0.0225 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67117992 -0.74129444 0.00025713 178.44382073
0.74129438 0.67117960 -0.00076713 -68.64373128
0.00039609 0.00070549 0.99999967 -42.49593292
Axis 0.00099327 -0.00009372 0.99999950
Axis point 166.62295267 166.86604951 0.00000000
Rotation angle (degrees) 47.84182820
Shift along axis -42.31223508
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0229
rotated from previous position = 0.0213 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67139529 -0.74109931 0.00043295 178.37667373
0.74109941 0.67139503 -0.00061555 -68.67437469
0.00016550 0.00073414 0.99999972 -42.48172809
Axis 0.00091060 0.00018045 0.99999957
Axis point 166.63942850 166.85580221 0.00000000
Rotation angle (degrees) 47.82517581
Shift along axis -42.33167263
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 40
shifted from previous position = 0.0115
rotated from previous position = 0.0141 degrees
atoms outside contour = 727, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67126087 -0.74122112 0.00030035 178.42453332
0.74122111 0.67126057 -0.00071497 -68.65486220
0.00032834 0.00070255 0.99999970 -42.49345596
Axis 0.00095621 -0.00001888 0.99999954
Axis point 166.63290092 166.86821757 0.00000000
Rotation angle (degrees) 47.83556886
Shift along axis -42.32152949
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.00816
rotated from previous position = 0.0167 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67142064 -0.74107633 0.00045652 178.36347045
0.74107645 0.67142038 -0.00059729 -68.67691030
0.00013612 0.00073934 0.99999972 -42.47643697
Axis 0.00090182 0.00021617 0.99999957
Axis point 166.63736694 166.84927068 0.00000000
Rotation angle (degrees) 47.82321561
Shift along axis -42.33041349
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0155
rotated from previous position = 0.0285 degrees
atoms outside contour = 727, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67113113 -0.74133863 0.00021997 178.46540856
0.74133853 0.67113081 -0.00079322 -68.63978985
0.00044042 0.00069543 0.99999966 -42.50366017
Axis 0.00100403 -0.00014868 0.99999948
Axis point 166.62528900 166.87383951 0.00000000
Rotation angle (degrees) 47.84559951
Shift along axis -42.31424828
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 28
shifted from previous position = 0.0223
rotated from previous position = 0.0241 degrees
atoms outside contour = 729, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67137932 -0.74111379 0.00041245 178.38699283
0.74111388 0.67137905 -0.00062875 -68.67263475
0.00018906 0.00072781 0.99999972 -42.48618458
Axis 0.00091522 0.00015071 0.99999957
Axis point 166.64189323 166.86204748 0.00000000
Rotation angle (degrees) 47.82641080
Shift along axis -42.33325330
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#4) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.317, steps = 36
shifted from previous position = 0.000596
rotated from previous position = 0.00584 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#4) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.67144203 -0.74105694 0.00045284 178.36458753
0.74105707 0.67144178 -0.00058890 -68.67958966
0.00013235 0.00073099 0.99999972 -42.47898950
Axis 0.00089054 0.00021624 0.99999958
Axis point 166.64372110 166.85649696 0.00000000
Rotation angle (degrees) 47.82156102
Shift along axis -42.33498157
> open /Users/nezakoritnik/Desktop/PVA-VLPmut/helixWIDE/Coot25/mono25.cif-
> coot-0.pdb
Chain information for mono25.cif-coot-0.pdb #5
---
Chain | Description
Aa | No description available
> select subtract #4
Nothing selected
> select add #5
1497 atoms, 1531 bonds, 185 residues, 1 model selected
> view matrix models #5,1,0,0,-1.7014,0,1,0,1.7607,0,0,1,-38.207
> view matrix models #5,1,0,0,6.4057,0,1,0,-0.71879,0,0,1,-39.946
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.97129,-0.23788,-0.0023563,41.39,0.23777,0.97047,0.040566,-35.132,-0.0073628,-0.039961,0.99917,-33.661
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.97129,-0.23788,-0.0023563,43.778,0.23777,0.97047,0.040566,-35.889,-0.0073628,-0.039961,0.99917,-33.455
> view matrix models
> #5,0.97129,-0.23788,-0.0023563,38.511,0.23777,0.97047,0.040566,-37.161,-0.0073628,-0.039961,0.99917,-32.255
> view matrix models
> #5,0.97129,-0.23788,-0.0023563,38.921,0.23777,0.97047,0.040566,-37.122,-0.0073628,-0.039961,0.99917,-32.498
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.439, steps = 96
shifted from previous position = 2.59
rotated from previous position = 5.04 degrees
atoms outside contour = 1230, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98642736 -0.15944621 -0.03921705 33.52005632
0.16109382 0.98599276 0.04320951 -28.81628240
0.03177813 -0.04894066 0.99829603 -33.99778443
Axis -0.27023872 -0.20819980 0.94001270
Axis point 235.51147938 130.83116860 0.00000000
Rotation angle (degrees) 9.81675841
Shift along axis -35.01722214
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4388, steps = 44
shifted from previous position = 0.02
rotated from previous position = 0.177 degrees
atoms outside contour = 1230, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98660720 -0.15783108 -0.04117736 33.64829992
0.15951830 0.98632139 0.04152135 -28.35188119
0.03406075 -0.04753380 0.99828874 -34.50005488
Axis -0.26340967 -0.22254126 0.93866434
Axis point 238.02466021 134.68533409 0.00000000
Rotation angle (degrees) 9.73218511
Shift along axis -34.93779531
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 0.4389, steps = 28
shifted from previous position = 0.0207
rotated from previous position = 0.0521 degrees
atoms outside contour = 1230, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98655199 -0.15816157 -0.04123208 33.70058387
0.15987953 0.98622770 0.04234923 -28.51504523
0.03396620 -0.04837188 0.99825170 -34.37509972
Axis -0.26748097 -0.22171367 0.93770837
Axis point 238.30826606 133.74801566 0.00000000
Rotation angle (degrees) 9.76364630
Shift along axis -34.92590810
> view matrix models
> #5,0.98655,-0.15816,-0.041232,36.389,0.15988,0.98623,0.042349,-29.734,0.033966,-0.048372,0.99825,-36.278
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.315, steps = 64
shifted from previous position = 2.84
rotated from previous position = 3.76 degrees
atoms outside contour = 726, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98246417 -0.18645143 -0.00010361 34.07759780
0.18645133 0.98246400 -0.00063337 -28.08513138
0.00021989 0.00060295 0.99999979 -38.61743276
Axis 0.00331537 -0.00086750 0.99999413
Axis point 166.58934563 167.78574187 0.00000000
Rotation angle (degrees) 10.74582642
Shift along axis -38.47986237
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.314, steps = 44
shifted from previous position = 0.00761
rotated from previous position = 0.0152 degrees
atoms outside contour = 727, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98249925 -0.18626653 0.00006347 34.02492325
0.18626654 0.98249909 -0.00055195 -28.08240356
0.00004045 0.00055411 0.99999985 -38.59088216
Axis 0.00296900 0.00006180 0.99999559
Axis point 166.50245069 167.63766290 0.00000000
Rotation angle (degrees) 10.73503113
Shift along axis -38.49142755
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.315, steps = 40
shifted from previous position = 0.00816
rotated from previous position = 0.0143 degrees
atoms outside contour = 726, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98246688 -0.18643718 -0.00011481 34.07685340
0.18643709 0.98246675 -0.00054269 -28.09867936
0.00021398 0.00051177 0.99999985 -38.60536731
Axis 0.00282790 -0.00088177 0.99999561
Axis point 166.66614127 167.68922031 0.00000000
Rotation angle (degrees) 10.74497963
Shift along axis -38.48405526
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.314, steps = 36
shifted from previous position = 0.00802
rotated from previous position = 0.00942 degrees
atoms outside contour = 727, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98249072 -0.18631154 -0.00001407 34.04501212
0.18631150 0.98249056 -0.00056521 -28.08534318
0.00011913 0.00055269 0.99999984 -38.60150876
Axis 0.00300005 -0.00035747 0.99999544
Axis point 166.57788816 167.69665879 0.00000000
Rotation angle (degrees) 10.73765597
Shift along axis -38.48915612
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.314, steps = 40
shifted from previous position = 0.00417
rotated from previous position = 0.0108 degrees
atoms outside contour = 726, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98247577 -0.18639025 -0.00017274 34.08859794
0.18639014 0.98247568 -0.00050193 -28.10689490
0.00026327 0.00046094 0.99999986 -38.61060211
Axis 0.00258292 -0.00116962 0.99999598
Axis point 166.80826738 167.73853777 0.00000000
Rotation angle (degrees) 10.74223829
Shift along axis -38.48952429
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.315, steps = 40
shifted from previous position = 0.0158
rotated from previous position = 0.0108 degrees
atoms outside contour = 726, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98244187 -0.18656885 -0.00020332 34.11001240
0.18656872 0.98244177 -0.00053711 -28.11256768
0.00029996 0.00048975 0.99999984 -38.61222520
Axis 0.00275195 -0.00134877 0.99999530
Axis point 166.74307968 167.70329847 0.00000000
Rotation angle (degrees) 10.75266068
Shift along axis -38.48025734
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.314, steps = 28
shifted from previous position = 0.0102
rotated from previous position = 0.0115 degrees
atoms outside contour = 727, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98246873 -0.18642746 -0.00006263 34.07006949
0.18642740 0.98246859 -0.00053385 -28.10300230
0.00016106 0.00051281 0.99999986 -38.60149715
Axis 0.00280715 -0.00059995 0.99999588
Axis point 166.63560040 167.66188290 0.00000000
Rotation angle (degrees) 10.74441095
Shift along axis -38.48883791
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.315, steps = 28
shifted from previous position = 0.0153
rotated from previous position = 0.0076 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98245929 -0.18647708 -0.00018399 34.08945347
0.18647697 0.98245920 -0.00051651 -28.10237535
0.00027708 0.00047313 0.99999985 -38.60467053
Axis 0.00265351 -0.00123628 0.99999572
Axis point 166.72864249 167.67218997 0.00000000
Rotation angle (degrees) 10.74730484
Shift along axis -38.47930619
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.314, steps = 28
shifted from previous position = 0.0138
rotated from previous position = 0.0116 degrees
atoms outside contour = 726, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98247984 -0.18636889 -0.00001591 34.05210472
0.18636886 0.98247969 -0.00054572 -28.09343132
0.00011733 0.00053320 0.99999985 -38.59710146
Axis 0.00289458 -0.00035747 0.99999575
Axis point 166.57557886 167.65180395 0.00000000
Rotation angle (degrees) 10.74099753
Shift along axis -38.48832842
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.315, steps = 28
shifted from previous position = 0.0119
rotated from previous position = 0.00999 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98245728 -0.18648770 -0.00014148 34.08494284
0.18648760 0.98245716 -0.00054342 -28.10025699
0.00024034 0.00050750 0.99999984 -38.60444528
Axis 0.00281767 -0.00102373 0.99999551
Axis point 166.66614423 167.67641075 0.00000000
Rotation angle (degrees) 10.74792700
Shift along axis -38.47946445
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.314, steps = 28
shifted from previous position = 0.0225
rotated from previous position = 0.0181 degrees
atoms outside contour = 728, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98250352 -0.18624403 0.00005427 34.02723967
0.18624403 0.98250337 -0.00053996 -28.08644821
0.00004724 0.00054062 0.99999985 -38.59409906
Axis 0.00290097 0.00001887 0.99999579
Axis point 166.55100609 167.65562009 0.00000000
Rotation angle (degrees) 10.73371626
Shift along axis -38.49575461
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.315, steps = 28
shifted from previous position = 0.0213
rotated from previous position = 0.0133 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98246826 -0.18642994 -0.00008032 34.06620960
0.18642987 0.98246812 -0.00055211 -28.09292145
0.00018184 0.00052745 0.99999984 -38.59951273
Axis 0.00289534 -0.00070309 0.99999556
Axis point 166.60083045 167.65988443 0.00000000
Rotation angle (degrees) 10.74455844
Shift along axis -38.48095644
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.314, steps = 28
shifted from previous position = 0.0166
rotated from previous position = 0.007 degrees
atoms outside contour = 726, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98248515 -0.18634089 -0.00000023 34.04863588
0.18634086 0.98248501 -0.00053541 -28.09550985
0.00010000 0.00052599 0.99999986 -38.59705227
Axis 0.00284799 -0.00026893 0.99999591
Axis point 166.58874336 167.65233283 0.00000000
Rotation angle (degrees) 10.73936303
Shift along axis -38.49236833
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.314, steps = 44
shifted from previous position = 0.000118
rotated from previous position = 0.00306 degrees
atoms outside contour = 726, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98249391 -0.18629468 0.00002495 34.03720912
0.18629467 0.98249377 -0.00053849 -28.08970025
0.00007581 0.00053371 0.99999985 -38.59465608
Axis 0.00287768 -0.00013650 0.99999585
Axis point 166.56330530 167.64894772 0.00000000
Rotation angle (degrees) 10.73666920
Shift along axis -38.49271345
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.314, steps = 44
shifted from previous position = 0.00202
rotated from previous position = 0.0029 degrees
atoms outside contour = 727, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98250195 -0.18625228 0.00005116 34.02737716
0.18625228 0.98250180 -0.00054137 -28.08558459
0.00005057 0.00054143 0.99999985 -38.59323228
Axis 0.00290678 0.00000157 0.99999578
Axis point 166.54338923 167.64941904 0.00000000
Rotation angle (degrees) 10.73419792
Shift along axis -38.49420308
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.315, steps = 28
shifted from previous position = 0.0148
rotated from previous position = 0.0121 degrees
atoms outside contour = 725, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98246811 -0.18643070 -0.00005592 34.06433771
0.18643064 0.98246796 -0.00056348 -28.09332610
0.00015998 0.00054317 0.99999984 -38.60053750
Axis 0.00296797 -0.00057903 0.99999543
Axis point 166.57744559 167.66625326 0.00000000
Rotation angle (degrees) 10.74460474
Shift along axis -38.48299210
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.314, steps = 40
shifted from previous position = 0.0136
rotated from previous position = 0.00393 degrees
atoms outside contour = 726, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98247931 -0.18637166 -0.00003430 34.05969585
0.18637161 0.98247918 -0.00053850 -28.09894588
0.00013406 0.00052267 0.99999985 -38.60175305
Axis 0.00284690 -0.00045167 0.99999585
Axis point 166.62482906 167.67515722 0.00000000
Rotation angle (degrees) 10.74115745
Shift along axis -38.49193688
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.315, steps = 28
shifted from previous position = 0.0114
rotated from previous position = 0.0034 degrees
atoms outside contour = 726, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98247247 -0.18640772 -0.00006795 34.06427079
0.18640765 0.98247232 -0.00057062 -28.09089103
0.00017313 0.00054795 0.99999983 -38.60396312
Axis 0.00300031 -0.00064663 0.99999529
Axis point 166.59768678 167.69523822 0.00000000
Rotation angle (degrees) 10.74326592
Shift along axis -38.48341350
> fitmap sel inMap #1
Fit molecule mono25.cif-coot-0.pdb (#5) to map NEW_PVAhelixWIDE_P98_J234.mrc
(#1) using 1497 atoms
average map value = 1.315, steps = 40
shifted from previous position = 0.00166
rotated from previous position = 0.0066 degrees
atoms outside contour = 726, contour level = 1.1907
Position of mono25.cif-coot-0.pdb (#5) relative to
NEW_PVAhelixWIDE_P98_J234.mrc (#1) coordinates:
Matrix rotation and translation
0.98245452 -0.18650229 -0.00011649 34.08592805
0.18650220 0.98245440 -0.00052999 -28.10793632
0.00021330 0.00049897 0.99999985 -38.60266428
Axis 0.00275855 -0.00088414 0.99999580
Axis point 166.66586813 167.65399995 0.00000000
Rotation angle (degrees) 10.74877478
Shift along axis -38.48362302
> open "/Users/nezakoritnik/Desktop/PVA-VLP/helix -
> popravljeno/Rigidbodyrefine16 - FINAL2/pdb_extract_8101.cif"
Summary of feedback from opening /Users/nezakoritnik/Desktop/PVA-VLP/helix -
popravljeno/Rigidbodyrefine16 - FINAL2/pdb_extract_8101.cif
---
warnings | Unknown polymer entity '1' near line 61
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for pdb_extract_8101.cif #6
---
Chain | Description
Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax | No
description available
> hide #!1 models
> hide #2 models
> select subtract #5
Nothing selected
> hide #5 models
> hide #4 models
> hide #3 models
> select add #6
35592 atoms, 36432 bonds, 4392 residues, 1 model selected
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: Z128000N6ZE/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2 (22D49)
Kernel Version: Darwin 22.3.0
Time since boot: 8 days, 23 hours, 19 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
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
ASUS VG27V:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 165.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
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: 2.10.5
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: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
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: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
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
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: 1.1.8
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
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-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.2
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: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 16 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 16 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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