![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 17 months ago
Closed 17 months ago
#15255 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
Thread 0x00000003159aa000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000002027ae2c0 (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/chimerax/atomic/molc.py", line 333 in pointer
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 251 in set_cvec_pointer
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 133 in __init__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 391 in __init__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2225 in process_changes
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2231 in changes
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 36 in check_for_changes
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 69 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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.mmcif.mmcif_write (total: 53)
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{
"uptime" : 48000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir10,1",
"coalitionID" : 1177,
"osVersion" : {
"train" : "macOS 13.2",
"build" : "22D49",
"releaseType" : "User"
},
"captureTime" : "2024-05-20 12:36:13.8832 +0200",
"incident" : "8B24AA48-F934-4461-9881-88877073018B",
"pid" : 8546,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-05-20 12:29:26.7642 +0200",
"procStartAbsTime" : 1144476048491,
"procExitAbsTime" : 1154247111801,
"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" : 12304,
"sleepWakeUUID" : "67282BB3-5AE7-4780-A74F-B220C930CD41",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140722903891799\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc9ab2c000-7ffca55f8000 [170.8M] r-x\/r-x SM=COW ...t_id=111d9bb1",
"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: 140722903891799\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc9ab2c000-7ffca55f8000 [170.8M] r-x\/r-x SM=COW ...t_id=111d9bb1",
"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=2.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.8G(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 152K 33 \nColorSync 248K 29 \nCoreAnimation 104K 16 \nCoreGraphics 40K 6 \nCoreUI image data 4164K 42 \nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 1.0G 437 \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 1432K 355 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 780K 78 \nRosetta Thread Context 780K 78 \nSTACK GUARD 52K 13 \nStack 179.2M 42 \nStack Guard 56.1M 29 \nVM_ALLOCATE 285.0M 315 \nVM_ALLOCATE (reserved) 160.1M 13 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 48.3M 733 \n__DATA_CONST 39.4M 376 \n__DATA_DIRTY 1829K 223 \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 672K 4 \nmapped file 4.7G 1718 \nshared memory 3044K 34 \nunshared pmap 14.1M 10 \n=========== ======= ======= \nTOTAL 8.8G 5528 \nTOTAL, minus reserved VM space 7.6G 5528 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "61675b89201f677a9a4cbd65",
"factorPackIds" : {
"HEALTH_FEATURE_AVAILABILITY" : "65a855f5f087695cfac03d1f"
},
"deploymentId" : 240000119
},
{
"rolloutId" : "6297d96be2c9387df974efa4",
"factorPackIds" : {
},
"deploymentId" : 240000025
}
],
"experiments" : [
]
},
"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-VLP-B11/helix/PVAVLP-B11_h_P39_J171.mrc
Opened PVAVLP-B11_h_P39_J171.mrc as #1, grid size 350,350,350, pixel 0.947,
shown at level 0.774, step 2, values float32
> open /Users/nezakoritnik/Desktop/PVA-VLP/helix/Coot15/mono15-edit-coot-0.pdb
Chain information for mono15-edit-coot-0.pdb #2
---
Chain | Description
A | No description available
> select add #2
1484 atoms, 1519 bonds, 183 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.48836,-0.60592,-0.62798,247.99,-0.82607,-0.089052,-0.55649,351.37,0.28126,0.79053,-0.54402,66.122
> view matrix models
> #2,-0.47682,0.87841,-0.03233,138.31,0.87687,0.47278,-0.087109,-66.76,-0.061232,-0.069885,-0.99567,293.94
> view matrix models
> #2,0.19874,0.86763,-0.45577,85.973,0.96748,-0.099431,0.23259,-53.482,0.15649,-0.48717,-0.85917,291.79
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.19874,0.86763,-0.45577,68.027,0.96748,-0.099431,0.23259,15.808,0.15649,-0.48717,-0.85917,333.05
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.19744,0.90386,-0.37955,53.161,0.96956,-0.23725,-0.060609,73.285,-0.14483,-0.35603,-0.92318,375.26
> view matrix models
> #2,0.021591,0.87414,-0.4852,100.64,0.96826,-0.13916,-0.20763,81.353,-0.24902,-0.46531,-0.8494,396.19
> view matrix models
> #2,0.23479,0.79619,-0.55764,85.119,0.9346,-0.3426,-0.095658,97.232,-0.26721,-0.49871,-0.82455,400
> view matrix models
> #2,-0.097887,0.87253,-0.47866,119.76,0.95638,-0.050541,-0.28771,83.151,-0.27523,-0.48594,-0.82952,400.4
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.097887,0.87253,-0.47866,122.71,0.95638,-0.050541,-0.28771,71.772,-0.27523,-0.48594,-0.82952,394.51
> view matrix models
> #2,-0.097887,0.87253,-0.47866,106.67,0.95638,-0.050541,-0.28771,84.313,-0.27523,-0.48594,-0.82952,387.62
> view matrix models
> #2,-0.097887,0.87253,-0.47866,111.2,0.95638,-0.050541,-0.28771,99.783,-0.27523,-0.48594,-0.82952,388.32
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.68677,0.68923,-0.23091,-29.884,0.71937,-0.69001,0.079977,169.29,-0.10421,-0.22104,-0.96968,345.77
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.68677,0.68923,-0.23091,-28.988,0.71937,-0.69001,0.079977,171.86,-0.10421,-0.22104,-0.96968,347.21
> view matrix models
> #2,0.68677,0.68923,-0.23091,-23.565,0.71937,-0.69001,0.079977,158.31,-0.10421,-0.22104,-0.96968,349.23
> view matrix models
> #2,0.68677,0.68923,-0.23091,-23.619,0.71937,-0.69001,0.079977,158.69,-0.10421,-0.22104,-0.96968,350.66
> ui tool show "Fit in Map"
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 0.4234, steps = 96
shifted from previous position = 2.2
rotated from previous position = 7.55 degrees
atoms outside contour = 1269, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.76670063 0.59787472 -0.23391441 -25.11522413
0.63665170 -0.75499843 0.15700950 170.09815552
-0.08273301 -0.26930129 -0.95949573 353.03629510
Axis -0.93904617 -0.33301133 0.08541508
Axis point 0.00000000 111.13414392 165.01996193
Rotation angle (degrees) 166.87999333
Shift along axis -2.90563269
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 0.4234, steps = 44
shifted from previous position = 0.00187
rotated from previous position = 0.0115 degrees
atoms outside contour = 1269, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.76677981 0.59777597 -0.23390728 -25.11619568
0.63654218 -0.75511558 0.15689012 170.14904934
-0.08284189 -0.26919203 -0.95951700 353.04345483
Axis -0.93906848 -0.33294225 0.08543922
Axis point 0.00000000 111.14619454 165.02616616
Rotation angle (degrees) 166.88747247
Shift along axis -2.90022121
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 0.4234, steps = 44
shifted from previous position = 0.00166
rotated from previous position = 0.0159 degrees
atoms outside contour = 1269, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.76667248 0.59788715 -0.23397491 -25.10386263
0.63668526 -0.75495901 0.15706293 170.08036794
-0.08273556 -0.26938420 -0.95947224 353.04387194
Axis -0.93903803 -0.33302956 0.08543358
Axis point 0.00000000 111.13147380 165.02153758
Rotation angle (degrees) 166.87560667
Shift along axis -2.90650495
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 0.4234, steps = 44
shifted from previous position = 0.00319
rotated from previous position = 0.0114 degrees
atoms outside contour = 1270, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.76674433 0.59782456 -0.23389938 -25.11834168
0.63659182 -0.75506416 0.15693619 170.12375504
-0.08278873 -0.26922836 -0.95951139 353.03698031
Axis -0.93905856 -0.33297408 0.08542412
Axis point 0.00000000 111.13876296 165.02232037
Rotation angle (degrees) 166.88475046
Shift along axis -2.90133356
> view matrix models
> #2,0.76674,0.59782,-0.2339,-23.675,0.63659,-0.75506,0.15694,165.17,-0.082789,-0.26923,-0.95951,349.03
> view matrix models
> #2,0.76674,0.59782,-0.2339,-24.619,0.63659,-0.75506,0.15694,164.98,-0.082789,-0.26923,-0.95951,351.52
> volume #1 step 1
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 92
shifted from previous position = 1.87
rotated from previous position = 16.4 degrees
atoms outside contour = 551, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80490832 0.59339916 0.00016363 -65.82225434
0.59338876 -0.80489580 0.00570375 200.16824497
0.00351630 -0.00449390 -0.99998372 311.81889999
Axis -0.94997551 -0.31232290 -0.00096843
Axis point 0.00000000 111.34473880 155.66039051
Rotation angle (degrees) 179.69247341
Shift along axis -0.28957278
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 28
shifted from previous position = 0.0253
rotated from previous position = 0.0159 degrees
atoms outside contour = 550, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80504217 0.59321758 0.00001172 -65.81233920
0.59320768 -0.80502885 0.00576202 200.19250029
0.00342757 -0.00463171 -0.99998340 311.83279832
Axis -0.95001072 -0.31221598 -0.00090507
Axis point 0.00000000 111.35958742 155.65967935
Rotation angle (degrees) 179.68657215
Shift along axis -0.26310051
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0202
rotated from previous position = 0.0197 degrees
atoms outside contour = 552, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80488385 0.59343238 0.00004638 -65.80866760
0.59342304 -0.80487162 0.00554747 200.17615295
0.00332938 -0.00443755 -0.99998461 311.84012303
Axis -0.94996908 -0.31234268 -0.00088839
Axis point 0.00000000 111.33806876 155.67409899
Rotation angle (degrees) 179.69888396
Shift along axis -0.28439271
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0182
rotated from previous position = 0.00649 degrees
atoms outside contour = 550, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80488668 0.59342854 -0.00004986 -65.80148910
0.59341982 -0.80487440 0.00548804 200.18575240
0.00321663 -0.00444684 -0.99998494 311.84214752
Axis -0.94996983 -0.31234056 -0.00083339
Axis point 0.00000000 111.33944262 155.67457649
Rotation angle (degrees) 179.70039624
Shift along axis -0.27658597
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0185
rotated from previous position = 0.00847 degrees
atoms outside contour = 551, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80489418 0.59341836 0.00006280 -65.81116175
0.59340883 -0.80488184 0.00558302 200.17288772
0.00336361 -0.00445648 -0.99998441 311.83748100
Axis -0.94997180 -0.31233439 -0.00090172
Axis point 0.00000000 111.33887509 155.67173647
Rotation angle (degrees) 179.69724182
Shift along axis -0.28331879
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 48
shifted from previous position = 0.0159
rotated from previous position = 0.0141 degrees
atoms outside contour = 550, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80499523 0.59328127 0.00011029 -65.82615838
0.59327095 -0.80498228 0.00575377 200.17631583
0.00350238 -0.00456632 -0.99998344 311.81797494
Axis -0.94999837 -0.31225341 -0.00095071
Axis point 0.00000000 111.35201342 155.65591446
Rotation angle (degrees) 179.68878875
Shift along axis -0.26744303
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0183
rotated from previous position = 0.0181 degrees
atoms outside contour = 552, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80486260 0.59346119 0.00006958 -65.81155763
0.59345179 -0.80485050 0.00553507 200.17107176
0.00334085 -0.00441368 -0.99998468 311.83735503
Axis -0.94996349 -0.31235965 -0.00089752
Axis point 0.00000000 111.33508932 155.67404281
Rotation angle (degrees) 179.69997598
Shift along axis -0.28667006
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 28
shifted from previous position = 0.0242
rotated from previous position = 0.0178 degrees
atoms outside contour = 551, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80500603 0.59326663 0.00002654 -65.81460287
0.59325678 -0.80499292 0.00572550 200.18826150
0.00341811 -0.00459332 -0.99998361 311.82638641
Axis -0.95000121 -0.31224489 -0.00090649
Axis point 0.00000000 111.35571405 155.65860206
Rotation angle (degrees) 179.68882814
Shift along axis -0.26647707
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 48
shifted from previous position = 0.0248
rotated from previous position = 0.0232 degrees
atoms outside contour = 552, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80482919 0.59350650 0.00001104 -65.80091093
0.59349763 -0.80481727 0.00545174 200.17841760
0.00324453 -0.00438116 -0.99998514 311.84536635
Axis -0.94995471 -0.31238648 -0.00085677
Axis point 0.00000000 111.33305600 155.67983046
Rotation angle (degrees) 179.70346674
Shift along axis -0.29232754
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.00865
rotated from previous position = 0.0114 degrees
atoms outside contour = 552, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80490560 0.59340287 0.00006262 -65.81089509
0.59339330 -0.80489322 0.00559373 200.17576402
0.00336973 -0.00446527 -0.99998435 311.83814598
Axis -0.94997480 -0.31232524 -0.00090328
Axis point 0.00000000 111.34075873 155.67157995
Rotation angle (degrees) 179.69665480
Shift along axis -0.28292860
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0196
rotated from previous position = 0.016 degrees
atoms outside contour = 549, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80502402 0.59324221 0.00009143 -65.82481629
0.59323186 -0.80501085 0.00578659 200.17944524
0.00350645 -0.00460410 -0.99998325 311.82013077
Axis -0.95000594 -0.31223039 -0.00094681
Axis point 0.00000000 111.35551893 155.65489785
Rotation angle (degrees) 179.68666215
Shift along axis -0.26337370
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0211
rotated from previous position = 0.00877 degrees
atoms outside contour = 550, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80495924 0.59333008 0.00019803 -65.82931959
0.59331928 -0.80494651 0.00577409 200.16721100
0.00358535 -0.00453042 -0.99998331 311.81428881
Axis -0.94998890 -0.31228208 -0.00099564
Axis point 0.00000000 111.34841245 155.65607561
Rotation angle (degrees) 179.68925543
Shift along axis -0.28196585
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.00219
rotated from previous position = 0.0144 degrees
atoms outside contour = 551, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80489549 0.59341659 0.00006893 -65.81259471
0.59340702 -0.80488316 0.00558632 200.17168991
0.00337050 -0.00445550 -0.99998439 311.83743496
Axis -0.94997214 -0.31233333 -0.00090514
Axis point 0.00000000 111.33857155 155.67176958
Rotation angle (degrees) 179.69717159
Shift along axis -0.28241686
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0184
rotated from previous position = 0.00646 degrees
atoms outside contour = 550, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80495390 0.59333735 0.00006793 -65.81680682
0.59332760 -0.80494132 0.00564120 200.18642264
0.00340181 -0.00450060 -0.99998408 311.82073845
Axis -0.94998751 -0.31228657 -0.00091311
Axis point 0.00000000 111.34911624 155.66091303
Rotation angle (degrees) 179.69416154
Shift along axis -0.27511229
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0211
rotated from previous position = 0.0133 degrees
atoms outside contour = 551, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80494940 0.59334341 0.00023972 -65.83601656
0.59333234 -0.80493672 0.00579639 200.16087851
0.00363221 -0.00452357 -0.99998317 311.80772785
Axis -0.94998631 -0.31228989 -0.00101895
Axis point 0.00000000 111.34730746 155.65318577
Rotation angle (degrees) 179.68878851
Shift along axis -0.28261954
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.023
rotated from previous position = 0.0264 degrees
atoms outside contour = 549, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80493426 0.59336398 -0.00010488 -65.79609928
0.59335550 -0.80492179 0.00549162 200.19479211
0.00317411 -0.00448262 -0.99998491 311.85441239
Axis -0.94998235 -0.31230254 -0.00080771
Axis point 0.00000000 111.34332341 155.67871690
Rotation angle (degrees) 179.69921305
Shift along axis -0.26809722
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0218
rotated from previous position = 0.0115 degrees
atoms outside contour = 552, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80484693 0.59348244 0.00003131 -65.80524796
0.59347340 -0.80483496 0.00547778 200.17694813
0.00327617 -0.00439019 -0.99998499 311.84264257
Axis -0.94995938 -0.31237225 -0.00087043
Axis point 0.00000000 111.33399499 155.67797482
Rotation angle (degrees) 179.70241087
Shift along axis -0.28884925
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.017
rotated from previous position = 0.0108 degrees
atoms outside contour = 551, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80494111 0.59335470 0.00000090 -65.80967758
0.59334548 -0.80492861 0.00557376 200.18498855
0.00330794 -0.00448602 -0.99998446 311.83991908
Axis -0.94998415 -0.31229691 -0.00087077
Axis point 0.00000000 111.34411106 155.67130488
Rotation angle (degrees) 179.69663406
Shift along axis -0.27054262
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.00369
rotated from previous position = 0.00958 degrees
atoms outside contour = 551, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80498661 0.59329298 0.00006637 -65.81940353
0.59328301 -0.80497372 0.00570707 200.18264026
0.00343939 -0.00455474 -0.99998371 311.82471857
Axis -0.94999611 -0.31226039 -0.00092258
Axis point 0.00000000 111.35182779 155.65991356
Rotation angle (degrees) 179.69054532
Shift along axis -0.26861348
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0172
rotated from previous position = 0.0111 degrees
atoms outside contour = 551, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80490116 0.59340887 0.00019320 -65.82931886
0.59339825 -0.80488862 0.00572868 200.15605969
0.00355496 -0.00449638 -0.99998357 311.81253346
Axis -0.94997362 -0.31232859 -0.00098639
Axis point 0.00000000 111.34120237 155.65708809
Rotation angle (degrees) 179.69164634
Shift along axis -0.28591120
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.0168
rotated from previous position = 0.0147 degrees
atoms outside contour = 550, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80491035 0.59339643 0.00000920 -65.80957461
0.59338725 -0.80489798 0.00555062 200.18361064
0.00330113 -0.00446229 -0.99998459 311.83293733
Axis -0.94997606 -0.31232152 -0.00087117
Axis point 0.00000000 111.34232315 155.66912656
Rotation angle (degrees) 179.69804486
Shift along axis -0.27578864
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0166
rotated from previous position = 0.00358 degrees
atoms outside contour = 551, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80489644 0.59341529 0.00005927 -65.81114982
0.59340579 -0.80488411 0.00557965 200.17351797
0.00335875 -0.00445587 -0.99998443 311.83853284
Axis -0.94997239 -0.31233258 -0.00089951
Axis point 0.00000000 111.33894782 155.67229524
Rotation angle (degrees) 179.69736205
Shift along axis -0.28243767
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 48
shifted from previous position = 0.00517
rotated from previous position = 0.0166 degrees
atoms outside contour = 551, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80488840 0.59342614 0.00026257 -65.83832024
0.59341501 -0.80487586 0.00578509 200.14535706
0.00364436 -0.00450054 -0.99998323 311.80044101
Axis -0.94997026 -0.31233867 -0.00102818
Axis point 0.00000000 111.34032085 155.65083086
Rotation angle (degrees) 179.68981848
Shift along axis -0.28927612
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.0187
rotated from previous position = 0.0194 degrees
atoms outside contour = 550, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80493678 0.59336058 0.00000762 -65.81133462
0.59335132 -0.80492429 0.00557686 200.18249528
0.00331522 -0.00448450 -0.99998445 311.83787786
Axis -0.94998301 -0.31230037 -0.00087445
Axis point 0.00000000 111.34333573 155.67037178
Rotation angle (degrees) 179.69658623
Shift along axis -0.27010504
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.00296
rotated from previous position = 0.0143 degrees
atoms outside contour = 549, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80503601 0.59322594 0.00006381 -65.82033976
0.59321583 -0.80502290 0.00575326 200.18833171
0.00346435 -0.00459373 -0.99998345 311.82724497
Axis -0.95000910 -0.31222083 -0.00092846
Axis point 0.00000000 111.35697935 155.65901696
Rotation angle (degrees) 179.68798104
Shift along axis -0.26256537
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0185
rotated from previous position = 0.00861 degrees
atoms outside contour = 550, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80498872 0.59329009 0.00018528 -65.83063902
0.59327928 -0.80497587 0.00579147 200.16827002
0.00358517 -0.00455215 -0.99998321 311.81976624
Axis -0.94999665 -0.31225850 -0.00099223
Axis point 0.00000000 111.34994330 155.65761268
Rotation angle (degrees) 179.68807847
Shift along axis -0.27475548
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.00635
rotated from previous position = 0.0094 degrees
atoms outside contour = 551, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80494746 0.59334609 0.00008044 -65.81667322
0.59333613 -0.80493472 0.00568608 200.17211194
0.00343856 -0.00452926 -0.99998383 311.83407887
Axis -0.94998581 -0.31229171 -0.00092607
Axis point 0.00000000 111.34533253 155.66601404
Rotation angle (degrees) 179.69194357
Shift along axis -0.27596603
> fitmap sel inMap #1
Fit molecule mono15-edit-coot-0.pdb (#2) to map PVAVLP-B11_h_P39_J171.mrc (#1)
using 1484 atoms
average map value = 1.083, steps = 28
shifted from previous position = 0.0154
rotated from previous position = 0.0102 degrees
atoms outside contour = 550, contour level = 0.77402
Position of mono15-edit-coot-0.pdb (#2) relative to PVAVLP-B11_h_P39_J171.mrc
(#1) coordinates:
Matrix rotation and translation
0.80503710 0.59322447 0.00003597 -65.81513104
0.59321443 -0.80502383 0.00576825 200.19009582
0.00345083 -0.00462232 -0.99998336 311.82955475
Axis -0.95000938 -0.31222000 -0.00091757
Axis point 0.00000000 111.35885873 155.65858287
Rotation angle (degrees) 179.68666696
Shift along axis -0.26448722
> save /Users/nezakoritnik/Desktop/PVA-VLP-B11/helix/Coot1/mono1.cif
> selectedOnly true
> close #2
> open /Users/nezakoritnik/Desktop/PVA-VLP-B11/helix/Coot1/mono1.cif
Chain information for mono1.cif #2
---
Chain | Description
A | No description available
> open /Users/nezakoritnik/Desktop/PVA-VLP-B11/helix/Coot1/mono1.cif
Chain information for mono1.cif #3
---
Chain | Description
A | No description available
> select add #3
1484 atoms, 1519 bonds, 183 residues, 1 model selected
> volume #1 level 0.9081
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-3.8776,0,1,0,-27.874,0,0,1,-6.8419
> view matrix models #3,1,0,0,-4.2574,0,1,0,-29.568,0,0,1,-3.2964
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.90241,-0.41786,0.10514,74.603,0.41804,0.90818,0.021366,-73.044,-0.10441,0.024671,0.99423,7.2904
> view matrix models
> #3,0.78205,-0.59303,0.19161,111.32,0.59562,0.8017,0.050205,-81.453,-0.18339,0.074864,0.98019,10.675
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.78205,-0.59303,0.19161,104.48,0.59562,0.8017,0.050205,-78.449,-0.18339,0.074864,0.98019,8.1582
> view matrix models
> #3,0.78205,-0.59303,0.19161,104.41,0.59562,0.8017,0.050205,-77.506,-0.18339,0.074864,0.98019,8.1791
> fitmap sel inMap #1
Fit molecule mono1.cif (#3) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 112
shifted from previous position = 2.8
rotated from previous position = 12.7 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#3) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73772654 -0.67509949 -0.00047150 155.42916076
0.67509961 0.73772657 0.00015890 -68.43591661
0.00024057 -0.00043553 0.99999988 -4.68850105
Axis -0.00044025 -0.00052738 0.99999976
Axis point 165.79480345 165.81779105 0.00000000
Rotation angle (degrees) 42.46189386
Shift along axis -4.72083604
> fitmap sel inMap #1
Fit molecule mono1.cif (#3) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.0167
rotated from previous position = 0.0108 degrees
atoms outside contour = 657, contour level = 0.90808
Position of mono1.cif (#3) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73770975 -0.67511783 -0.00049435 155.43962521
0.67511790 0.73770985 -0.00002667 -68.39157202
0.00038269 -0.00031407 0.99999988 -4.72029596
Axis -0.00021286 -0.00064955 0.99999977
Axis point 165.74098871 165.84716311 0.00000000
Rotation angle (degrees) 42.46331616
Shift along axis -4.70895739
> fitmap sel inMap #1
Fit molecule mono1.cif (#3) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.018
rotated from previous position = 0.0133 degrees
atoms outside contour = 657, contour level = 0.90808
Position of mono1.cif (#3) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73774895 -0.67507503 -0.00043658 155.41552530
0.67507515 0.73774895 0.00018977 -68.44310086
0.00019398 -0.00043472 0.99999989 -4.68326060
Axis -0.00046253 -0.00046703 0.99999978
Axis point 165.80114311 165.80648182 0.00000000
Rotation angle (degrees) 42.45999299
Shift along axis -4.72317943
> fitmap sel inMap #1
Fit molecule mono1.cif (#3) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.0188
rotated from previous position = 0.0145 degrees
atoms outside contour = 657, contour level = 0.90808
Position of mono1.cif (#3) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73766909 -0.67516222 -0.00052761 155.45874767
0.67516231 0.73766920 -0.00001390 -68.39046428
0.00039859 -0.00034597 0.99999986 -4.71670457
Axis -0.00024592 -0.00068591 0.99999973
Axis point 165.74141833 165.85420420 0.00000000
Rotation angle (degrees) 42.46676649
Shift along axis -4.70802382
> fitmap sel inMap #1
Fit molecule mono1.cif (#3) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.0158
rotated from previous position = 0.0128 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#3) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73770994 -0.67511763 -0.00047362 155.43470517
0.67511776 0.73770995 0.00019509 -68.43888724
0.00021768 -0.00046366 0.99999987 -4.68013294
Axis -0.00048788 -0.00051199 0.99999975
Axis point 165.79798608 165.81590089 0.00000000
Rotation angle (degrees) 42.46330392
Shift along axis -4.72092553
> fitmap sel inMap #1
Fit molecule mono1.cif (#3) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0173
rotated from previous position = 0.0134 degrees
atoms outside contour = 656, contour level = 0.90808
Position of mono1.cif (#3) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73765023 -0.67518283 -0.00054062 155.47047130
0.67518292 0.73765034 -0.00001051 -68.39246391
0.00040589 -0.00035726 0.99999985 -4.71210516
Axis -0.00025678 -0.00070093 0.99999972
Axis point 165.74627424 165.85991501 0.00000000
Rotation angle (degrees) 42.46836758
Shift along axis -4.70408761
> fitmap sel inMap #1
Fit molecule mono1.cif (#3) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 48
shifted from previous position = 0.0241
rotated from previous position = 0.0237 degrees
atoms outside contour = 660, contour level = 0.90808
Position of mono1.cif (#3) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73762522 -0.67521018 -0.00050272 155.46415699
0.67521036 0.73762512 0.00040006 -68.46339712
0.00010070 -0.00063454 0.99999979 -4.63979277
Axis -0.00076613 -0.00044684 0.99999961
Axis point 165.82684785 165.80281930 0.00000000
Rotation angle (degrees) 42.47050156
Shift along axis -4.72830466
> fitmap sel inMap #1
Fit molecule mono1.cif (#3) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0205
rotated from previous position = 0.0257 degrees
atoms outside contour = 657, contour level = 0.90808
Position of mono1.cif (#3) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73772804 -0.67509786 -0.00047194 155.42959741
0.67509792 0.73772813 -0.00002131 -68.39419269
0.00036255 -0.00030288 0.99999989 -4.71975316
Axis -0.00020854 -0.00061805 0.99999979
Axis point 165.74269904 165.84107279 0.00000000
Rotation angle (degrees) 42.46176355
Shift along axis -4.70989476
> fitmap sel inMap #1
Fit molecule mono1.cif (#3) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.0161
rotated from previous position = 0.0127 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#3) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73772257 -0.67510384 -0.00045847 155.42809946
0.67510396 0.73772258 0.00019911 -68.44169688
0.00020380 -0.00045641 0.99999988 -4.68037007
Axis -0.00048550 -0.00049050 0.99999976
Axis point 165.80061547 165.81160064 0.00000000
Rotation angle (degrees) 42.46223177
Shift along axis -4.72225804
> open /Users/nezakoritnik/Desktop/PVA-VLP-B11/helix/Coot1/mono1.cif
Chain information for mono1.cif #4
---
Chain | Description
A | No description available
> select add #4
2968 atoms, 3038 bonds, 366 residues, 2 models selected
> select subtract #3
1484 atoms, 1519 bonds, 183 residues, 1 model selected
> view matrix models #4,1,0,0,5.5883,0,1,0,-50.17,0,0,1,-12.623
> view matrix models #4,1,0,0,12.937,0,1,0,-55.969,0,0,1,-12.424
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.64422,-0.76445,-0.024441,219.6,0.76443,0.64459,-0.012122,-89.044,0.025022,-0.010874,0.99963,-13.663
> view matrix models
> #4,0.40205,-0.91561,0.0048546,278.41,0.91451,0.40181,0.04712,-71.655,-0.045094,-0.014505,0.99888,-3.0572
> view matrix models
> #4,0.18173,-0.98311,0.021525,319.65,0.96841,0.18273,0.16969,-56.66,-0.17075,-0.0099918,0.98526,15.883
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.18173,-0.98311,0.021525,296.82,0.96841,0.18273,0.16969,-50.37,-0.17075,-0.0099918,0.98526,17.064
> view matrix models
> #4,0.18173,-0.98311,0.021525,298.65,0.96841,0.18273,0.16969,-52.243,-0.17075,-0.0099918,0.98526,16.936
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 124
shifted from previous position = 4.58
rotated from previous position = 11.3 degrees
atoms outside contour = 660, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08873951 -0.99605485 -0.00020177 316.12519560
0.99605483 0.08873956 -0.00025737 -14.00828561
0.00027426 -0.00017814 0.99999995 -9.48698657
Axis 0.00003978 -0.00023896 0.99999997
Axis point 165.71991412 165.76553313 0.00000000
Rotation angle (degrees) 84.90890372
Shift along axis -9.47106459
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.0177
rotated from previous position = 0.00689 degrees
atoms outside contour = 660, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08864277 -0.99606346 -0.00022020 316.13396713
0.99606342 0.08864284 -0.00032575 -13.96818927
0.00034399 -0.00019045 0.99999992 -9.48353636
Axis 0.00006792 -0.00028321 0.99999996
Axis point 165.70200215 165.77346591 0.00000000
Rotation angle (degrees) 84.91446886
Shift along axis -9.45810984
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 36
shifted from previous position = 0.0114
rotated from previous position = 0.00501 degrees
atoms outside contour = 660, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08871077 -0.99605740 -0.00023023 316.13562182
0.99605738 0.08871083 -0.00027189 -13.99433604
0.00029125 -0.00020520 0.99999994 -9.47254690
Axis 0.00003348 -0.00026177 0.99999997
Axis point 165.71736800 165.77306292 0.00000000
Rotation angle (degrees) 84.91055694
Shift along axis -9.45829985
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0169
rotated from previous position = 0.00575 degrees
atoms outside contour = 661, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08877801 -0.99605142 -0.00016629 316.11050060
0.99605141 0.08877805 -0.00023415 -14.01913533
0.00024799 -0.00014485 0.99999996 -9.49342850
Axis 0.00004483 -0.00020796 0.99999998
Axis point 165.71865780 165.75895215 0.00000000
Rotation angle (degrees) 84.90668932
Shift along axis -9.47634307
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 36
shifted from previous position = 0.0172
rotated from previous position = 0.0101 degrees
atoms outside contour = 660, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08863559 -0.99606409 -0.00025120 316.13735457
0.99606407 0.08863566 -0.00029198 -13.97313417
0.00031309 -0.00022434 0.99999993 -9.47643812
Axis 0.00003395 -0.00028326 0.99999996
Axis point 165.70618255 165.77141953 0.00000000
Rotation angle (degrees) 84.91488180
Shift along axis -9.46174554
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 28
shifted from previous position = 0.0164
rotated from previous position = 0.0182 degrees
atoms outside contour = 661, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08883054 -0.99604674 -0.00018863 316.10429614
0.99604675 0.08883056 -0.00005080 -14.05797124
0.00006736 -0.00018337 0.99999998 -9.46295493
Axis -0.00006655 -0.00012850 0.99999999
Axis point 165.73624923 165.74509131 0.00000000
Rotation angle (degrees) 84.90366750
Shift along axis -9.48218506
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0209
rotated from previous position = 0.021 degrees
atoms outside contour = 659, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08855908 -0.99607085 -0.00038759 316.17177093
0.99607090 0.08855916 -0.00019292 -13.97289084
0.00022648 -0.00036898 0.99999991 -9.43291264
Axis -0.00008838 -0.00030825 0.99999995
Axis point 165.72221944 165.77628214 0.00000000
Rotation angle (degrees) 84.91928319
Shift along axis -9.45654820
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.0187
rotated from previous position = 0.00771 degrees
atoms outside contour = 660, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08866927 -0.99606106 -0.00034996 316.15748445
0.99606111 0.08866932 -0.00012632 -14.01574596
0.00015685 -0.00033738 0.99999993 -9.44123810
Axis -0.00010595 -0.00025441 0.99999996
Axis point 165.73898458 165.76639535 0.00000000
Rotation angle (degrees) 84.91294462
Shift along axis -9.47116897
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.00355
rotated from previous position = 0.00565 degrees
atoms outside contour = 659, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08869553 -0.99605871 -0.00038106 316.15664371
0.99605878 0.08869555 -0.00003661 -14.03449605
0.00007026 -0.00037631 0.99999993 -9.42491187
Axis -0.00017053 -0.00022655 0.99999996
Axis point 165.74856674 165.76092951 0.00000000
Rotation angle (degrees) 84.91143524
Shift along axis -9.47564473
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0194
rotated from previous position = 0.0131 degrees
atoms outside contour = 659, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08855184 -0.99607149 -0.00039103 316.17548432
0.99607154 0.08855193 -0.00021270 -13.96912630
0.00024649 -0.00037066 0.99999990 -9.43370323
Axis -0.00007929 -0.00032002 0.99999995
Axis point 165.72206675 165.77892627 0.00000000
Rotation angle (degrees) 84.91969913
Shift along axis -9.45430177
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.00579
rotated from previous position = 0.00942 degrees
atoms outside contour = 661, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08865898 -0.99606200 -0.00026688 316.14138023
0.99606201 0.08865904 -0.00022107 -13.99106127
0.00024386 -0.00024623 0.99999994 -9.46071439
Axis -0.00001263 -0.00025638 0.99999997
Axis point 165.71781254 165.76861691 0.00000000
Rotation angle (degrees) 84.91353606
Shift along axis -9.46111924
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 36
shifted from previous position = 0.0126
rotated from previous position = 0.00444 degrees
atoms outside contour = 660, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08870436 -0.99605795 -0.00029776 316.14651964
0.99605798 0.08870441 -0.00016642 -14.01568402
0.00019218 -0.00028183 0.99999994 -9.45446000
Axis -0.00005793 -0.00024594 0.99999997
Axis point 165.73392149 165.76683122 0.00000000
Rotation angle (degrees) 84.91092601
Shift along axis -9.46932690
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.00353
rotated from previous position = 0.00388 degrees
atoms outside contour = 660, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08865388 -0.99606244 -0.00031118 316.15316690
0.99606246 0.08865395 -0.00020942 -13.99811753
0.00023619 -0.00029139 0.99999993 -9.45923975
Axis -0.00004114 -0.00027476 0.99999996
Axis point 165.72748399 165.77040870 0.00000000
Rotation angle (degrees) 84.91382936
Shift along axis -9.46840116
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.0164
rotated from previous position = 0.00829 degrees
atoms outside contour = 660, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08854721 -0.99607190 -0.00040335 316.17419364
0.99607196 0.08854728 -0.00017865 -13.97333890
0.00021366 -0.00038595 0.99999990 -9.43094088
Axis -0.00010406 -0.00030972 0.99999995
Axis point 165.72351855 165.77522721 0.00000000
Rotation angle (degrees) 84.91996607
Shift along axis -9.45951265
> fitmap sel inMap #1
Fit molecule mono1.cif (#4) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.00635
rotated from previous position = 0.00544 degrees
atoms outside contour = 660, contour level = 0.90808
Position of mono1.cif (#4) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08860622 -0.99606668 -0.00033582 316.15934321
0.99606671 0.08860629 -0.00020946 -13.98096551
0.00023839 -0.00031594 0.99999992 -9.44485258
Axis -0.00005345 -0.00028824 0.99999996
Axis point 165.72084206 165.77393476 0.00000000
Rotation angle (degrees) 84.91657136
Shift along axis -9.45772011
> open /Users/nezakoritnik/Desktop/PVA-VLP-B11/helix/Coot1/mono1.cif
Chain information for mono1.cif #5
---
Chain | Description
A | No description available
> select add #5
2968 atoms, 3038 bonds, 366 residues, 2 models selected
> select add #3
4452 atoms, 4557 bonds, 549 residues, 3 models selected
> select subtract #4
2968 atoms, 3038 bonds, 366 residues, 2 models selected
> select subtract #3
1484 atoms, 1519 bonds, 183 residues, 1 model selected
> view matrix models #5,1,0,0,45.162,0,1,0,-45.202,0,0,1,-14.492
> view matrix models #5,1,0,0,48.971,0,1,0,-65.594,0,0,1,-12.608
> view matrix models #5,1,0,0,45.398,0,1,0,-64.716,0,0,1,-14.685
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.99988,-0.0051745,0.014762,43.88,0.0051836,0.99999,-0.00058138,-65.333,-0.014759,0.00065783,0.99989,-12.746
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.99988,-0.0051745,0.014762,39.174,0.0051836,0.99999,-0.00058138,-65.359,-0.014759,0.00065783,0.99989,-12.107
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.90755,-0.13557,0.39745,11.465,0.14248,0.98972,0.012248,-84.63,-0.39503,0.045513,0.91754,46.131
> view matrix models
> #5,-0.5905,-0.80208,-0.089324,437.86,0.79575,-0.56022,-0.23006,176.81,0.13448,-0.20693,0.96907,14.039
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.5905,-0.80208,-0.089324,415.24,0.79575,-0.56022,-0.23006,176.16,0.13448,-0.20693,0.96907,18.591
> view matrix models
> #5,-0.5905,-0.80208,-0.089324,405.51,0.79575,-0.56022,-0.23006,164.07,0.13448,-0.20693,0.96907,15.122
> view matrix models
> #5,-0.5905,-0.80208,-0.089324,410.48,0.79575,-0.56022,-0.23006,162.94,0.13448,-0.20693,0.96907,13.084
> view matrix models
> #5,-0.5905,-0.80208,-0.089324,410.52,0.79575,-0.56022,-0.23006,162.93,0.13448,-0.20693,0.96907,13.043
> fitmap sel inMap #1
Fit molecule mono1.cif (#5) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 108
shifted from previous position = 1.66
rotated from previous position = 14.4 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#5) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60712665 -0.79460503 -0.00026038 398.05237108
0.79460507 -0.60712658 -0.00031393 134.71780928
0.00009137 -0.00039750 0.99999992 -14.16688624
Axis -0.00005258 -0.00022134 0.99999997
Axis point 165.72260194 165.76085890 0.00000000
Rotation angle (degrees) 127.38203037
Shift along axis -14.21763455
> fitmap sel inMap #1
Fit molecule mono1.cif (#5) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.00405
rotated from previous position = 0.0172 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#5) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60701458 -0.79469070 -0.00000165 398.01483453
0.79469067 -0.60701456 -0.00025499 134.67542111
0.00020164 -0.00015609 0.99999997 -14.22702094
Axis 0.00006223 -0.00012790 0.99999999
Axis point 165.70889044 165.74891007 0.00000000
Rotation angle (degrees) 127.37394964
Shift along axis -14.21947946
> fitmap sel inMap #1
Fit molecule mono1.cif (#5) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.0177
rotated from previous position = 0.0157 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#5) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60718921 -0.79455727 -0.00011285 398.01686485
0.79455724 -0.60718914 -0.00037630 134.74989643
0.00023047 -0.00031815 0.99999992 -14.18918955
Axis 0.00003659 -0.00021604 0.99999998
Axis point 165.70082954 165.75872463 0.00000000
Rotation angle (degrees) 127.38654108
Shift along axis -14.20373693
> fitmap sel inMap #1
Fit molecule mono1.cif (#5) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.00674
rotated from previous position = 0.0129 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#5) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60723430 -0.79452275 -0.00032855 398.04541693
0.79452281 -0.60723417 -0.00040200 134.76598208
0.00011989 -0.00050514 0.99999986 -14.13834703
Axis -0.00006491 -0.00028220 0.99999996
Axis point 165.71302168 165.76598108 0.00000000
Rotation angle (degrees) 127.38979258
Shift along axis -14.20221563
> fitmap sel inMap #1
Fit molecule mono1.cif (#5) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.00713
rotated from previous position = 0.00925 degrees
atoms outside contour = 659, contour level = 0.90808
Position of mono1.cif (#5) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60715934 -0.79458007 -0.00021126 398.03404758
0.79458009 -0.60715926 -0.00034385 134.73515506
0.00014494 -0.00037663 0.99999992 -14.16709471
Axis -0.00002063 -0.00022415 0.99999997
Axis point 165.71111177 165.76000082 0.00000000
Rotation angle (degrees) 127.38438709
Shift along axis -14.20550690
> fitmap sel inMap #1
Fit molecule mono1.cif (#5) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.0142
rotated from previous position = 0.0046 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#5) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60717209 -0.79457030 -0.00028850 398.04918564
0.79457035 -0.60717201 -0.00032861 134.73183749
0.00008593 -0.00042875 0.99999990 -14.16236473
Axis -0.00006302 -0.00023562 0.99999997
Axis point 165.71991460 165.75986689 0.00000000
Rotation angle (degrees) 127.38530687
Shift along axis -14.21919430
> fitmap sel inMap #1
Fit molecule mono1.cif (#5) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 44
shifted from previous position = 0.0167
rotated from previous position = 0.0176 degrees
atoms outside contour = 657, contour level = 0.90808
Position of mono1.cif (#5) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60710784 -0.79461945 0.00000736 397.99631931
0.79461940 -0.60710781 -0.00034996 134.72118331
0.00028255 -0.00020662 0.99999994 -14.21629153
Axis 0.00009020 -0.00017316 0.99999998
Axis point 165.69359416 165.75245682 0.00000000
Rotation angle (degrees) 127.38067469
Shift along axis -14.20372152
> fitmap sel inMap #1
Fit molecule mono1.cif (#5) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.0187
rotated from previous position = 0.00783 degrees
atoms outside contour = 659, contour level = 0.90808
Position of mono1.cif (#5) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60706592 -0.79465147 -0.00009561 398.02318482
0.79465146 -0.60706588 -0.00027726 134.69193414
0.00016228 -0.00024429 0.99999996 -14.20844708
Axis 0.00002074 -0.00016227 0.99999999
Axis point 165.71151538 165.75084263 0.00000000
Rotation angle (degrees) 127.37765107
Shift along axis -14.22204703
> fitmap sel inMap #1
Fit molecule mono1.cif (#5) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.00515
rotated from previous position = 0.00814 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#5) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60712455 -0.79460666 -0.00020663 398.04192404
0.79460667 -0.60712448 -0.00032639 134.71966957
0.00013390 -0.00036235 0.99999992 -14.17737935
Axis -0.00002263 -0.00021428 0.99999998
Axis point 165.71699457 165.75968887 0.00000000
Rotation angle (degrees) 127.38187837
Shift along axis -14.21525238
> fitmap sel inMap #1
Fit molecule mono1.cif (#5) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.0146
rotated from previous position = 0.0106 degrees
atoms outside contour = 657, contour level = 0.90808
Position of mono1.cif (#5) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60711834 -0.79461143 -0.00002399 398.00163726
0.79461138 -0.60711830 -0.00035074 134.72397495
0.00026413 -0.00023201 0.99999994 -14.20967395
Axis 0.00007471 -0.00018130 0.99999998
Axis point 165.69603476 165.75342056 0.00000000
Rotation angle (degrees) 127.38143130
Shift along axis -14.20436427
> fitmap sel inMap #1
Fit molecule mono1.cif (#5) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.083, steps = 40
shifted from previous position = 0.0176
rotated from previous position = 0.00757 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#5) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60704187 -0.79466985 -0.00005505 398.01937341
0.79466983 -0.60704183 -0.00026582 134.68360656
0.00017782 -0.00020511 0.99999996 -14.21610508
Axis 0.00003820 -0.00014652 0.99999999
Axis point 165.71046893 165.74965748 0.00000000
Rotation angle (degrees) 127.37591673
Shift along axis -14.22063653
> open /Users/nezakoritnik/Desktop/PVA-VLP-B11/helix/Coot1/mono1.cif
Chain information for mono1.cif #6
---
Chain | Description
A | No description available
> select add #6
2968 atoms, 3038 bonds, 366 residues, 2 models selected
> select subtract #5
1484 atoms, 1519 bonds, 183 residues, 1 model selected
> view matrix models #6,1,0,0,29.145,0,1,0,13.414,0,0,1,6.3569
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.8543,0.51339,-0.081242,-39.16,-0.51661,0.85589,-0.023868,118.23,0.057281,0.062361,0.99641,-13.458
> view matrix models
> #6,0.87809,0.47481,-0.059231,-38.582,-0.47675,0.87872,-0.023756,108.1,0.040768,0.049098,0.99796,-8.7793
> view matrix models
> #6,0.83377,0.54606,-0.081561,-42.785,-0.54963,0.83491,-0.028891,127.9,0.05232,0.068917,0.99625,-14.052
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.83377,0.54606,-0.081561,-43.135,-0.54963,0.83491,-0.028891,126.62,0.05232,0.068917,0.99625,-13.94
> fitmap sel inMap #1
Fit molecule mono1.cif (#6) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 88
shifted from previous position = 2.3
rotated from previous position = 10.4 degrees
atoms outside contour = 659, contour level = 0.90808
Position of mono1.cif (#6) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73795373 0.67485130 0.00006614 -68.41789363
-0.67485128 0.73795367 0.00036335 155.20072688
0.00019640 -0.00031277 0.99999993 4.78664873
Axis -0.00050094 -0.00009651 -0.99999987
Axis point 165.63452864 165.70197154 0.00000000
Rotation angle (degrees) 42.44260998
Shift along axis -4.76735351
> fitmap sel inMap #1
Fit molecule mono1.cif (#6) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.00595
rotated from previous position = 0.00777 degrees
atoms outside contour = 659, contour level = 0.90808
Position of mono1.cif (#6) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73790417 0.67490551 -0.00003528 -68.40311404
-0.67490547 0.73790414 0.00031108 155.22910631
0.00023598 -0.00020574 0.99999995 4.75580322
Axis -0.00038289 -0.00020096 -0.99999991
Axis point 165.65636284 165.68657189 0.00000000
Rotation angle (degrees) 42.44681593
Shift along axis -4.76080718
> fitmap sel inMap #1
Fit molecule mono1.cif (#6) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 28
shifted from previous position = 0.0145
rotated from previous position = 0.00659 degrees
atoms outside contour = 661, contour level = 0.90808
Position of mono1.cif (#6) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73795237 0.67485279 0.00005127 -68.40382698
-0.67485277 0.73795232 0.00033644 155.20736170
0.00018921 -0.00028288 0.99999994 4.78742344
Axis -0.00045886 -0.00010220 -0.99999989
Axis point 165.64957426 165.68664395 0.00000000
Rotation angle (degrees) 42.44272454
Shift along axis -4.77189785
> fitmap sel inMap #1
Fit molecule mono1.cif (#6) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.00226
rotated from previous position = 0.00923 degrees
atoms outside contour = 661, contour level = 0.90808
Position of mono1.cif (#6) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73803854 0.67475856 0.00003439 -68.39265830
-0.67475851 0.73803846 0.00043320 155.16204900
0.00026692 -0.00034293 0.99999991 4.79007615
Axis -0.00057512 -0.00017231 -0.99999982
Axis point 165.63390942 165.66682291 0.00000000
Rotation angle (degrees) 42.43541126
Shift along axis -4.77747668
> fitmap sel inMap #1
Fit molecule mono1.cif (#6) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.00286
rotated from previous position = 0.00425 degrees
atoms outside contour = 661, contour level = 0.90808
Position of mono1.cif (#6) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73799445 0.67480678 0.00003278 -68.39640912
-0.67480674 0.73799438 0.00039796 155.18135345
0.00024436 -0.00031582 0.99999992 4.79021783
Axis -0.00052888 -0.00015677 -0.99999985
Axis point 165.63775105 165.67252966 0.00000000
Rotation angle (degrees) 42.43915385
Shift along axis -4.77837132
> fitmap sel inMap #1
Fit molecule mono1.cif (#6) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.00214
rotated from previous position = 0.0134 degrees
atoms outside contour = 662, contour level = 0.90808
Position of mono1.cif (#6) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73791084 0.67489819 -0.00015049 -68.37324162
-0.67489813 0.73791085 0.00031986 155.22375895
0.00032692 -0.00013446 0.99999994 4.74246734
Axis -0.00033659 -0.00035369 -0.99999988
Axis point 165.66652281 165.64609266 0.00000000
Rotation angle (degrees) 42.44624835
Shift along axis -4.77435408
> fitmap sel inMap #1
Fit molecule mono1.cif (#6) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 28
shifted from previous position = 0.0192
rotated from previous position = 0.00698 degrees
atoms outside contour = 660, contour level = 0.90808
Position of mono1.cif (#6) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73787175 0.67494095 -0.00005446 -68.40148261
-0.67494091 0.73787173 0.00027228 155.24839045
0.00022396 -0.00016415 0.99999996 4.74555794
Axis -0.00032331 -0.00020626 -0.99999993
Axis point 165.66789633 165.68746770 0.00000000
Rotation angle (degrees) 42.44956692
Shift along axis -4.75546390
> fitmap sel inMap #1
Fit molecule mono1.cif (#6) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.0196
rotated from previous position = 0.00361 degrees
atoms outside contour = 661, contour level = 0.90808
Position of mono1.cif (#6) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73790050 0.67490951 -0.00007356 -68.39158993
-0.67490946 0.73790048 0.00031451 155.22576944
0.00026655 -0.00018243 0.99999995 4.76150777
Axis -0.00036816 -0.00025197 -0.99999990
Axis point 165.65594006 165.66915337 0.00000000
Rotation angle (degrees) 42.44712673
Shift along axis -4.77544095
> fitmap sel inMap #1
Fit molecule mono1.cif (#6) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0191
rotated from previous position = 0.0131 degrees
atoms outside contour = 660, contour level = 0.90808
Position of mono1.cif (#6) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73793020 0.67487702 0.00015111 -68.43441061
-0.67487703 0.73793014 0.00031757 155.21877791
0.00010281 -0.00033633 0.99999994 4.79614718
Axis -0.00048445 0.00003579 -0.99999988
Axis point 165.64003504 165.72792126 0.00000000
Rotation angle (degrees) 42.44460753
Shift along axis -4.75743850
> fitmap sel inMap #1
Fit molecule mono1.cif (#6) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.018
rotated from previous position = 0.0165 degrees
atoms outside contour = 662, contour level = 0.90808
Position of mono1.cif (#6) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73793236 0.67487466 -0.00013579 -68.37416515
-0.67487460 0.73793236 0.00032794 155.21607229
0.00032152 -0.00015035 0.99999994 4.74390867
Axis -0.00035435 -0.00033882 -0.99999988
Axis point 165.66565537 165.64774077 0.00000000
Rotation angle (degrees) 42.44442163
Shift along axis -4.77226937
> fitmap sel inMap #1
Fit molecule mono1.cif (#6) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.0179
rotated from previous position = 0.0101 degrees
atoms outside contour = 661, contour level = 0.90808
Position of mono1.cif (#6) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73784201 0.67497345 -0.00008489 -68.40336095
-0.67497343 0.73784200 0.00022589 155.26299389
0.00021510 -0.00010938 0.99999997 4.73892068
Axis -0.00024836 -0.00022222 -0.99999994
Axis point 165.67279096 165.69094344 0.00000000
Rotation angle (degrees) 42.45209063
Shift along axis -4.75643530
> fitmap sel inMap #1
Fit molecule mono1.cif (#6) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.00453
rotated from previous position = 0.0174 degrees
atoms outside contour = 659, contour level = 0.90808
Position of mono1.cif (#6) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73795163 0.67485360 0.00015070 -68.43045855
-0.67485360 0.73795156 0.00032606 155.21116918
0.00010883 -0.00034231 0.99999994 4.79603970
Axis -0.00049520 0.00003102 -0.99999988
Axis point 165.64156015 165.72322746 0.00000000
Rotation angle (degrees) 42.44278886
Shift along axis -4.75733803
> fitmap sel inMap #1
Fit molecule mono1.cif (#6) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0201
rotated from previous position = 0.00974 degrees
atoms outside contour = 661, contour level = 0.90808
Position of mono1.cif (#6) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.73803021 0.67476766 0.00011785 -68.40495603
-0.67476763 0.73803011 0.00044556 155.16446517
0.00021368 -0.00040836 0.99999989 4.80914852
Axis -0.00063275 -0.00007101 -0.99999980
Axis point 165.62769397 165.68285272 0.00000000
Rotation angle (degrees) 42.43611976
Shift along axis -4.77688217
> open /Users/nezakoritnik/Desktop/PVA-VLP-B11/helix/Coot1/mono1.cif
Chain information for mono1.cif #7
---
Chain | Description
A | No description available
> select add #7
2968 atoms, 3038 bonds, 366 residues, 2 models selected
> select subtract #6
1484 atoms, 1519 bonds, 183 residues, 1 model selected
> view matrix models #7,1,0,0,36.702,0,1,0,-11.242,0,0,1,9.3738
> view matrix models #7,1,0,0,41.135,0,1,0,-12.608,0,0,1,9.7036
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.27073,0.95527,-0.119,-27.859,-0.95952,0.25782,-0.11333,289.02,-0.077584,0.14486,0.98641,-6.123
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.27073,0.95527,-0.119,-15.155,-0.95952,0.25782,-0.11333,285.1,-0.077584,0.14486,0.98641,-5.9979
> view matrix models
> #7,0.27073,0.95527,-0.119,-4.6263,-0.95952,0.25782,-0.11333,292.48,-0.077584,0.14486,0.98641,-5.7174
> view matrix models
> #7,0.27073,0.95527,-0.119,-8.0216,-0.95952,0.25782,-0.11333,293.77,-0.077584,0.14486,0.98641,-6.253
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 0.4682, steps = 124
shifted from previous position = 2.09
rotated from previous position = 14.2 degrees
atoms outside contour = 1220, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.06774323 0.99753361 -0.01837240 -4.27705956
-0.99765813 0.06755449 -0.01070703 319.64114832
-0.00943949 0.01905471 0.99977388 5.52188639
Axis 0.01491492 -0.00447668 -0.99987874
Axis point 168.91120067 162.04068240 0.00000000
Rotation angle (degrees) 86.12753607
Shift along axis -7.01593982
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 0.4683, steps = 40
shifted from previous position = 0.00233
rotated from previous position = 0.00684 degrees
atoms outside contour = 1220, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.06775760 0.99753455 -0.01826803 -4.29861009
-0.99765656 0.06756878 -0.01076347 319.64835819
-0.00950259 0.01895453 0.99977519 5.54982377
Axis 0.01489302 -0.00439276 -0.99987944
Axis point 168.90719691 162.05609191 0.00000000
Rotation angle (degrees) 86.12667567
Shift along axis -7.01731109
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 0.4682, steps = 40
shifted from previous position = 0.00148
rotated from previous position = 0.00739 degrees
atoms outside contour = 1220, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.06783080 0.99753146 -0.01816502 -4.32364521
-0.99765127 0.06764245 -0.01079047 319.63734464
-0.00953511 0.01885428 0.99977677 5.57268500
Axis 0.01485639 -0.00432486 -0.99988028
Axis point 168.90171552 162.06441295 0.00000000
Rotation angle (degrees) 86.12241280
Shift along axis -7.01863757
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 0.4682, steps = 40
shifted from previous position = 0.00082
rotated from previous position = 0.00572 degrees
atoms outside contour = 1220, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.06778690 0.99753294 -0.01824744 -4.30492128
-0.99765465 0.06759845 -0.01075421 319.64065042
-0.00949418 0.01893364 0.99977566 5.55257086
Axis 0.01487794 -0.00438666 -0.99987969
Axis point 168.90498016 162.05574264 0.00000000
Rotation angle (degrees) 86.12496876
Shift along axis -7.01810625
> view matrix models
> #7,0.067787,0.99753,-0.018247,-7.0498,-0.99765,0.067598,-0.010754,320.65,-0.0094942,0.018934,0.99978,7.3836
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 68
shifted from previous position = 2.12
rotated from previous position = 1.74 degrees
atoms outside contour = 662, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08895989 0.99603517 0.00026191 -14.12448624
-0.99603515 0.08895979 0.00036607 315.98798242
0.00034132 -0.00029343 0.99999990 9.50286735
Axis -0.00033106 -0.00003986 -0.99999994
Axis point 165.66994271 165.71663478 0.00000000
Rotation angle (degrees) 84.89623241
Shift along axis -9.51078685
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.0019
rotated from previous position = 0.0104 degrees
atoms outside contour = 662, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08902493 0.99602931 0.00041019 -14.15504286
-0.99602937 0.08902481 0.00028301 315.98765641
0.00024537 -0.00043375 0.99999988 9.54213950
Axis -0.00035981 0.00008274 -0.99999993
Axis point 165.66630253 165.73441642 0.00000000
Rotation angle (degrees) 84.89249246
Shift along axis -9.51090164
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0165
rotated from previous position = 0.0109 degrees
atoms outside contour = 664, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08917570 0.99601579 0.00048519 -14.17865802
-0.99601586 0.08917553 0.00036923 315.93372416
0.00032449 -0.00051618 0.99999981 9.55993811
Axis -0.00044448 0.00008067 -0.99999990
Axis point 165.65083991 165.72197384 0.00000000
Rotation angle (degrees) 84.88382276
Shift along axis -9.52814822
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.00331
rotated from previous position = 0.00605 degrees
atoms outside contour = 662, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08912750 0.99602015 0.00039334 -14.16091392
-0.99602016 0.08912734 0.00038884 315.94136830
0.00035224 -0.00042643 0.99999985 9.53945345
Axis -0.00040927 0.00002063 -0.99999992
Axis point 165.65535918 165.71524695 0.00000000
Rotation angle (degrees) 84.88659416
Shift along axis -9.52713790
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0196
rotated from previous position = 0.0118 degrees
atoms outside contour = 661, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08897069 0.99603421 0.00026317 -14.12581186
-0.99603419 0.08897060 0.00036497 315.98753954
0.00034011 -0.00029460 0.99999990 9.49955348
Axis -0.00033110 -0.00003862 -0.99999994
Axis point 165.67092539 165.71722754 0.00000000
Rotation angle (degrees) 84.89561107
Shift along axis -9.50708026
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0201
rotated from previous position = 0.00636 degrees
atoms outside contour = 662, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08897703 0.99603365 0.00022375 -14.11837757
-0.99603358 0.08897692 0.00046863 315.96003147
0.00044686 -0.00026456 0.99999987 9.49735440
Axis -0.00036805 -0.00011200 -0.99999993
Axis point 165.66014908 165.69930653 0.00000000
Rotation angle (degrees) 84.89524813
Shift along axis -9.52754480
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0178
rotated from previous position = 0.0055 degrees
atoms outside contour = 662, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08894288 0.99603671 0.00021794 -14.11621919
-0.99603666 0.08894279 0.00037912 315.98993906
0.00035824 -0.00025079 0.99999990 9.49099056
Axis -0.00031621 -0.00007043 -0.99999995
Axis point 165.67209765 165.71273922 0.00000000
Rotation angle (degrees) 84.89721076
Shift along axis -9.50878141
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0152
rotated from previous position = 0.00504 degrees
atoms outside contour = 660, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08901811 0.99602998 0.00023822 -14.12185957
-0.99602993 0.08901800 0.00041954 315.95994732
0.00039666 -0.00027462 0.99999988 9.50174706
Axis -0.00034846 -0.00007954 -0.99999994
Axis point 165.66577606 165.70153856 0.00000000
Rotation angle (degrees) 84.89288439
Shift along axis -9.52195583
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.016
rotated from previous position = 0.00488 degrees
atoms outside contour = 661, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08895171 0.99603591 0.00024009 -14.11974770
-0.99603588 0.08895162 0.00036639 315.99049107
0.00034359 -0.00027173 0.99999990 9.49558162
Axis -0.00032033 -0.00005195 -0.99999995
Axis point 165.67224883 165.71512153 0.00000000
Rotation angle (degrees) 84.89670267
Shift along axis -9.50747449
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0195
rotated from previous position = 0.0175 degrees
atoms outside contour = 663, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08917320 0.99601603 0.00044930 -14.17298434
-0.99601607 0.08917303 0.00038972 315.93103952
0.00034810 -0.00048227 0.99999982 9.55056814
Axis -0.00043774 0.00005080 -0.99999990
Axis point 165.65165220 165.71733173 0.00000000
Rotation angle (degrees) 84.88396631
Shift along axis -9.52831258
> fitmap sel inMap #1
Fit molecule mono1.cif (#7) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 28
shifted from previous position = 0.0227
rotated from previous position = 0.0155 degrees
atoms outside contour = 661, contour level = 0.90808
Position of mono1.cif (#7) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
0.08895892 0.99603525 0.00030044 -14.12850140
-0.99603525 0.08895882 0.00032267 315.99772887
0.00029466 -0.00032795 0.99999990 9.50918620
Axis -0.00032661 0.00000290 -0.99999995
Axis point 165.67333650 165.72387407 0.00000000
Rotation angle (degrees) 84.89628810
Shift along axis -9.50365470
> open /Users/nezakoritnik/Desktop/PVA-VLP-B11/helix/Coot1/mono1.cif
Chain information for mono1.cif #8
---
Chain | Description
A | No description available
> select add #8
2968 atoms, 3038 bonds, 366 residues, 2 models selected
> select subtract #7
1484 atoms, 1519 bonds, 183 residues, 1 model selected
> view matrix models #8,1,0,0,51.637,0,1,0,-5.0806,0,0,1,10.439
> view matrix models #8,1,0,0,62.582,0,1,0,-20.961,0,0,1,13.719
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.59445,0.79195,-0.13947,150.13,-0.79387,-0.60559,-0.055081,420.23,-0.12808,0.077978,0.98869,17.896
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.59445,0.79195,-0.13947,155.38,-0.79387,-0.60559,-0.055081,404.44,-0.12808,0.077978,0.98869,18.247
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 72
shifted from previous position = 2.62
rotated from previous position = 8.64 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60657196 0.79502853 0.00030277 134.43734133
-0.79502858 -0.60657194 -0.00015870 398.02083533
0.00005748 -0.00033697 0.99999994 14.28676656
Axis -0.00011212 0.00015426 -0.99999998
Axis point 165.70075502 165.74806764 0.00000000
Rotation angle (degrees) 127.34204561
Shift along axis -14.24043835
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.0194
rotated from previous position = 0.0174 degrees
atoms outside contour = 657, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60664782 0.79497066 0.00026113 134.46143847
-0.79497066 -0.60664786 0.00012640 397.97579168
0.00025890 -0.00013091 0.99999996 14.23841180
Axis -0.00016183 0.00000140 -0.99999999
Axis point 165.68894697 165.72266144 0.00000000
Rotation angle (degrees) 127.34751407
Shift along axis -14.25961378
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0179
rotated from previous position = 0.012 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60664826 0.79497033 0.00022705 134.47210215
-0.79497036 -0.60664826 -0.00008033 398.01432663
0.00007388 -0.00022923 0.99999997 14.26550330
Axis -0.00009365 0.00009634 -0.99999999
Axis point 165.70456553 165.73974898 0.00000000
Rotation angle (degrees) 127.34754414
Shift along axis -14.23975378
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0207
rotated from previous position = 0.022 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60640336 0.79515707 0.00044267 134.36626273
-0.79515718 -0.60640336 -0.00015464 397.99147982
0.00014547 -0.00044576 0.99999989 14.31387850
Axis -0.00018306 0.00018688 -0.99999997
Axis point 165.68382178 165.74259706 0.00000000
Rotation angle (degrees) 127.32989865
Shift along axis -14.26409965
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.00456
rotated from previous position = 0.0136 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60654640 0.79504803 0.00030617 134.43014866
-0.79504808 -0.60654640 -0.00008059 397.99328023
0.00012163 -0.00029230 0.99999995 14.28313065
Axis -0.00013314 0.00011605 -0.99999998
Axis point 165.69403820 165.73452631 0.00000000
Rotation angle (degrees) 127.34020372
Shift along axis -14.25484065
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.0163
rotated from previous position = 0.0107 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60656990 0.79503011 0.00029809 134.43712730
-0.79503016 -0.60656984 -0.00026463 398.03791769
-0.00002958 -0.00039751 0.99999992 14.31272086
Axis -0.00008357 0.00020607 -0.99999998
Axis point 165.70558383 165.75682465 0.00000000
Rotation angle (degrees) 127.34189621
Shift along axis -14.24193089
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.0149
rotated from previous position = 0.0062 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60656058 0.79503721 0.00029523 134.43502380
-0.79503727 -0.60656056 -0.00015705 398.00915943
0.00005421 -0.00032998 0.99999994 14.29942267
Axis -0.00010875 0.00015158 -0.99999998
Axis point 165.69849477 165.74217448 0.00000000
Rotation angle (degrees) 127.34122542
Shift along axis -14.25371453
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.015
rotated from previous position = 0.0076 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60657513 0.79502612 0.00029181 134.43962125
-0.79502617 -0.60657506 -0.00028848 398.04203051
-0.00005234 -0.00040698 0.99999991 14.31725393
Axis -0.00007453 0.00021644 -0.99999997
Axis point 165.70713506 165.75858186 0.00000000
Rotation angle (degrees) 127.34227295
Shift along axis -14.24112086
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.00289
rotated from previous position = 0.011 degrees
atoms outside contour = 659, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60656523 0.79503367 0.00029557 134.43716207
-0.79503372 -0.60656523 -0.00009628 398.00780513
0.00010274 -0.00029338 0.99999995 14.27684024
Axis -0.00012396 0.00012127 -0.99999998
Axis point 165.69828936 165.74104845 0.00000000
Rotation angle (degrees) 127.34156065
Shift along axis -14.24523850
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.00115
rotated from previous position = 0.00799 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60659996 0.79500717 0.00030275 134.44502046
-0.79500722 -0.60659992 -0.00022856 398.03277013
0.00000194 -0.00037933 0.99999993 14.30783254
Axis -0.00009482 0.00018918 -0.99999998
Axis point 165.70343215 165.75379870 0.00000000
Rotation angle (degrees) 127.34406299
Shift along axis -14.24527976
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 48
shifted from previous position = 0.0134
rotated from previous position = 0.0164 degrees
atoms outside contour = 661, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60660980 0.79499971 0.00010938 134.47307443
-0.79499971 -0.60660981 -0.00001774 398.00250495
0.00005225 -0.00009772 0.99999999 14.25772225
Axis -0.00005030 0.00003593 -1.00000000
Axis point 165.70821656 165.73098922 0.00000000
Rotation angle (degrees) 127.34477166
Shift along axis -14.25018551
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 28
shifted from previous position = 0.0205
rotated from previous position = 0.022 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60648643 0.79509375 0.00038019 134.40371651
-0.79509384 -0.60648638 -0.00024092 398.01145798
0.00003903 -0.00044840 0.99999990 14.32131622
Axis -0.00013047 0.00021454 -0.99999997
Axis point 165.69502849 165.74769807 0.00000000
Rotation angle (degrees) 127.33588231
Shift along axis -14.25346237
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.00807
rotated from previous position = 0.00727 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60654351 0.79505023 0.00032303 134.42478176
-0.79505029 -0.60654350 -0.00015340 398.00659144
0.00007398 -0.00034987 0.99999993 14.30266228
Axis -0.00012356 0.00015663 -0.99999998
Axis point 165.69530945 165.74261532 0.00000000
Rotation angle (degrees) 127.33999553
Shift along axis -14.25693141
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 44
shifted from previous position = 0.00127
rotated from previous position = 0.0107 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60658308 0.79502005 0.00028926 134.44253357
-0.79502008 -0.60658311 0.00002327 397.98016414
0.00019396 -0.00021586 0.99999996 14.26072985
Axis -0.00015039 0.00005994 -0.99999999
Axis point 165.69094961 165.72649420 0.00000000
Rotation angle (degrees) 127.34284783
Shift along axis -14.25709404
> fitmap sel inMap #1
Fit molecule mono1.cif (#8) to map PVAVLP-B11_h_P39_J171.mrc (#1) using 1484
atoms
average map value = 1.082, steps = 40
shifted from previous position = 0.0165
rotated from previous position = 0.0133 degrees
atoms outside contour = 658, contour level = 0.90808
Position of mono1.cif (#8) relative to PVAVLP-B11_h_P39_J171.mrc (#1)
coordinates:
Matrix rotation and translation
-0.60657713 0.79502459 0.00030228 134.43781079
-0.79502464 -0.60657709 -0.00020833 398.02949715
0.00001773 -0.00036669 0.99999993 14.30171798
Axis -0.00009959 0.00017896 -0.99999998
Axis point 165.70250464 165.75268769 0.00000000
Rotation angle (degrees) 127.34241769
Shift along axis -14.24387663
> open /Users/nezakoritnik/Desktop/PVA-VLP-B11/helix/Coot1/mono1.cif
Chain information for mono1.cif #9
---
Chain | Description
A | No description available
> select add #9
2968 atoms, 3038 bonds, 366 residues, 2 models selected
> select subtract #8
1484 atoms, 1519 bonds, 183 residues, 1 model selected
> view matrix models #9,1,0,0,29.879,0,1,0,-62.242,0,0,1,23.193
> view matrix models #9,1,0,0,53.22,0,1,0,-77.492,0,0,1,23.535
> view matrix models #9,1,0,0,53.934,0,1,0,-76.204,0,0,1,23.872
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.51088,-0.85936,-0.022243,297.74,-0.83416,-0.48931,-0.25448,382.04,0.2078,0.14856,-0.96682,307.72
> view matrix models
> #9,0.78836,-0.31273,0.52979,53.679,-0.42004,0.35559,0.83494,-34.259,-0.4495,-0.88077,0.14897,410.76
> view matrix models
> #9,-0.082228,-0.33831,0.93744,108.87,-0.34393,0.89247,0.29191,-57.697,-0.93539,-0.29841,-0.18974,420.79
===== 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: 2 days, 23 hours, 34 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
HP E243i:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
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 , 17 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 , 17 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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