![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16981 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.3.1-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 0x0000700018d11000 (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 0x00007ff846fb9b00 (most recent call first):
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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, 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.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite (total: 62)
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{
"uptime" : 250000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 2785,
"osVersion" : {
"train" : "macOS 15.3.1",
"build" : "24D70",
"releaseType" : "User"
},
"captureTime" : "2025-02-27 14:17:49.7749 -0800",
"codeSigningMonitor" : 0,
"incident" : "4C7D4487-8CBA-422F-8C3A-6FF9AB1A6E3F",
"pid" : 81180,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-25 17:56:12.1177 -0800",
"procStartAbsTime" : 179258615330418,
"procExitAbsTime" : 255703267798509,
"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":"D8767BF8-46D5-5622-8B47-86ACB089778F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "EDC31B47-E55E-A1A5-DE71-2E12D2B7CCD0",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "4B449E58-3EFE-495A-9693-72506AD45040",
"wakeTime" : 1474,
"bridgeVersion" : {"build":"22P3051","train":"9.3"},
"sleepWakeUUID" : "1FFDF925-5FA5-42B2-A26A-8714226C1134",
"sip" : "enabled",
"vmRegionInfo" : "0x59e is not in any region. Bytes before following region: 4406893154\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 106abe000-106ac2000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x000000000000059e","rawCodes":[1,1438],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000059e"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":81180},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x59e is not in any region. Bytes before following region: 4406893154\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 106abe000-106ac2000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"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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===== Log before crash start =====
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
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/bsingal/Downloads/cryosparc_P11_J79_class_00_02000_volume.mrc
Opened cryosparc_P11_J79_class_00_02000_volume.mrc as #1, grid size 64,64,64,
pixel 4.31, shown at level 0.0875, step 1, values float32
> open /Users/bsingal/Downloads/CDK19_CCNC_MED12_docked.pdb
CDK19_CCNC_MED12_docked.pdb title:
Alphafold monomer V2.0 prediction for mediator of RNA polymerase II
transcription subunit 12 (Q93074) [more info...]
Chain information for CDK19_CCNC_MED12_docked.pdb #2
---
Chain | Description
A | No description available
B | No description available
D | No description available
Non-standard residues in CDK19_CCNC_MED12_docked.pdb #2
---
ACE — (ACE)
NMA — (NMA)
> color bychain
> select add #2
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,128.08,0,1,0,127.29,0,0,1,163.13
> select subtract #2
Nothing selected
> volume #1 level 0.3285
> select add #2
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> view matrix models #2,1,0,0,182.27,0,1,0,167.56,0,0,1,136.4
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.3415,-0.62402,0.70283,187.97,-0.039208,0.73768,0.67401,182.71,-0.93906,-0.25773,0.22745,102.96
> view matrix models
> #2,0.79196,-0.30621,0.52824,191.24,0.096673,0.91712,0.3867,178.2,-0.60288,-0.25518,0.75592,120.83
> view matrix models
> #2,0.21521,-0.69111,0.68997,185.6,-0.099321,0.68737,0.71948,182.79,-0.9715,-0.22337,0.079286,98.959
> view matrix models
> #2,-0.16629,-0.93427,0.31543,168.91,0.14581,0.29307,0.94491,187.31,-0.97524,0.20312,0.087495,103.62
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.16629,-0.93427,0.31543,143,0.14581,0.29307,0.94491,162.53,-0.97524,0.20312,0.087495,131
> fitmap #2 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 14210 atoms
average map value = 0.3518, steps = 292
shifted from previous position = 16.4
rotated from previous position = 49.2 degrees
atoms outside contour = 8085, contour level = 0.32851
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.25750926 -0.90061712 0.35011111 152.90944005
0.81836740 -0.01061971 0.57459727 153.46626381
-0.51377406 0.43448363 0.73977036 137.99854559
Axis -0.07263736 0.44785320 0.89115168
Axis point 51.00905486 113.12628181 0.00000000
Rotation angle (degrees) 105.31819254
Shift along axis 180.60105541
> volume #1 level 0.4002
> volume #1 level 0.1657
> open /Users/bsingal/Downloads/CDK19_CCNC_MED12_docked.pdb
CDK19_CCNC_MED12_docked.pdb title:
Alphafold monomer V2.0 prediction for mediator of RNA polymerase II
transcription subunit 12 (Q93074) [more info...]
Chain information for CDK19_CCNC_MED12_docked.pdb #3
---
Chain | Description
A | No description available
B | No description available
D | No description available
Non-standard residues in CDK19_CCNC_MED12_docked.pdb #3
---
ACE — (ACE)
NMA — (NMA)
> select subtract #2
Nothing selected
> volume #1 color #b2b2b28a
> ui tool show Matchmaker
> matchmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CDK19_CCNC_MED12_docked.pdb, chain B (#2) with
CDK19_CCNC_MED12_docked.pdb, chain B (#3), sequence alignment score = 2573.2
RMSD between 502 pruned atom pairs is 0.000 angstroms; (across all 502 pairs:
0.000)
> volume #1 level 0.4653
> select #3/B
7942 atoms, 8048 bonds, 504 residues, 1 model selected
> select #3/D
1571 atoms, 1588 bonds, 102 residues, 1 model selected
> select #2/A
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> hide #3 models
> select ~sel & ##selected
9513 atoms, 9636 bonds, 606 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> volume #1 level 0.335
> volume #1 level 0.537
> show #3 models
> color bychain
> volume #1 level 0.6282
> volume #1 level 0.309
> select add #3
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #2
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #3
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #3
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> hide #2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.85796,0.40937,0.31036,177.18,0.23508,0.22432,-0.94574,108.58,-0.45677,0.88436,0.096221,125.84
> view matrix models
> #3,0.14424,0.9706,-0.1927,162,0.43728,-0.23721,-0.86748,107.96,-0.88768,0.040858,-0.45864,97.428
> view matrix models
> #3,0.57408,0.53411,-0.62061,150.26,-0.39765,-0.4807,-0.78154,99.062,-0.71575,0.69545,-0.063571,116.82
> view matrix models
> #3,0.34385,0.27554,-0.89769,137.62,-0.77487,-0.45673,-0.437,104.75,-0.53041,0.84586,0.056465,123.59
> fitmap #3 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 14210 atoms
average map value = 0.3426, steps = 116
shifted from previous position = 30.6
rotated from previous position = 22.2 degrees
atoms outside contour = 8081, contour level = 0.30897
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.44124508 0.54908155 -0.70979731 120.60528354
-0.75514973 -0.20013280 -0.62425615 124.99002488
-0.48482126 0.81145321 0.32633117 127.39844751
Axis 0.73525691 -0.11521496 -0.66792423
Axis point 0.00000000 6.34454495 186.02845408
Rotation angle (degrees) 102.49053172
Shift along axis -10.81736260
> select subtract #3
Nothing selected
> ui mousemode right translate
> show #2 models
> hide #3 models
> show #3 models
> select add #2
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CDK19_CCNC_MED12_docked.pdb, chain A (#3) with
CDK19_CCNC_MED12_docked.pdb, chain A (#2), sequence alignment score = 1495.7
RMSD between 283 pruned atom pairs is 0.000 angstroms; (across all 283 pairs:
0.000)
> hide #3 models
> show #3 models
> hide #3 models
> fitmap #2 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 4697 atoms
average map value = 0.512, steps = 232
shifted from previous position = 9.61
rotated from previous position = 87.7 degrees
atoms outside contour = 1441, contour level = 0.30897
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.78193111 0.10069471 -0.61517828 130.15425470
-0.14585862 -0.98902610 0.02350814 176.61574577
-0.60606023 0.10811080 0.78803747 154.05441833
Axis 0.32436654 -0.03495859 -0.94528527
Axis point 97.49328745 79.71975822 0.00000000
Rotation angle (degrees) 172.50659186
Shift along axis -109.58192598
> volume #1 level 0.5174
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.76945,0.25369,-0.58617,130.28,-0.29718,-0.95455,-0.023026,172.85,-0.56536,0.15648,0.80986,155
> fitmap #2 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 4697 atoms
average map value = 0.512, steps = 68
shifted from previous position = 3.18
rotated from previous position = 9.47 degrees
atoms outside contour = 2349, contour level = 0.51743
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.78104613 0.10181027 -0.61611817 130.10802888
-0.14690641 -0.98888705 0.02282327 176.57933784
-0.60694764 0.10833774 0.78732299 154.02294605
Axis 0.32494388 -0.03484683 -0.94509109
Axis point 97.57204089 79.65847167 0.00000000
Rotation angle (degrees) 172.43889706
Shift along axis -109.44113735
> volume #1 level 0.3285
> show #3 models
> select subtract #2
Nothing selected
> hide #2 models
> select #3/A
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #3
9513 atoms, 9636 bonds, 606 residues, 1 model selected
> fitmap #3 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 9513 atoms
average map value = 0.3241, steps = 104
shifted from previous position = 4.71
rotated from previous position = 24.1 degrees
atoms outside contour = 5992, contour level = 0.32851
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.74224927 0.41434310 -0.52667430 119.06802456
-0.61862279 0.12151703 -0.77623415 122.26616376
-0.25762737 0.90197195 0.34651801 128.38599685
Axis 0.84377995 -0.13527326 -0.51936166
Axis point 0.00000000 -19.76745610 182.88924863
Rotation angle (degrees) 83.96464318
Shift along axis 17.24910494
> volume #1 level 0.1358
> view matrix models
> #3,0.69112,0.41784,-0.58971,117.89,-0.58315,-0.15963,-0.79653,119.46,-0.42696,0.89439,0.13334,124.25
> fitmap #3 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 9513 atoms
average map value = 0.3528, steps = 412
shifted from previous position = 8
rotated from previous position = 47 degrees
atoms outside contour = 4147, contour level = 0.13579
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.84403375 0.50439171 0.18219780 123.93241240
0.01483001 0.31765571 -0.94809014 127.05417532
-0.53608498 0.80292207 0.26063200 126.62675480
Axis 0.89570300 0.36742636 -0.25042765
Axis point 0.00000000 -71.30065224 136.50370826
Rotation angle (degrees) 77.80961748
Shift along axis 125.97884528
> view matrix models
> #3,0.78515,0.51977,-0.33672,117.89,-0.38001,-0.024993,-0.92465,119.61,-0.48902,0.85394,0.17789,126.76
> open /Users/bsingal/Downloads/CDK19_CCNC_MED12_docked.pdb
CDK19_CCNC_MED12_docked.pdb title:
Alphafold monomer V2.0 prediction for mediator of RNA polymerase II
transcription subunit 12 (Q93074) [more info...]
Chain information for CDK19_CCNC_MED12_docked.pdb #4
---
Chain | Description
A | No description available
B | No description available
D | No description available
Non-standard residues in CDK19_CCNC_MED12_docked.pdb #4
---
ACE — (ACE)
NMA — (NMA)
> view matrix models
> #3,0.62458,0.54477,-0.55957,114.08,-0.71519,0.1112,-0.69002,120.09,-0.31368,0.83118,0.45907,131.37
> fitmap #3 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 9513 atoms
average map value = 0.3241, steps = 60
shifted from previous position = 4.86
rotated from previous position = 10.6 degrees
atoms outside contour = 4454, contour level = 0.13579
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.74045923 0.41423804 -0.52927022 119.01670052
-0.62064805 0.11924759 -0.77496839 122.31429283
-0.25790719 0.90232303 0.34539401 128.30954946
Axis 0.84309065 -0.13640065 -0.52018556
Axis point 0.00000000 -19.34150864 182.78986035
Rotation angle (degrees) 84.11394615
Shift along axis 16.91334344
> show #2 models
> volume #1 level 0.2465
> ui tool show Matchmaker
> matchmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CDK19_CCNC_MED12_docked.pdb, chain B (#3) with
CDK19_CCNC_MED12_docked.pdb, chain B (#4), sequence alignment score = 2573.2
RMSD between 502 pruned atom pairs is 0.000 angstroms; (across all 502 pairs:
0.000)
> select #4/A
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #3 models
> show #3 models
> hide #3 models
> select #4/B
7942 atoms, 8048 bonds, 504 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #3 models
> hide #4 models
> show #4 models
> hide #4 models
> select #3/D
1571 atoms, 1588 bonds, 102 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #4 models
> select add #3
7942 atoms, 8048 bonds, 504 residues, 1 model selected
> view matrix models
> #3,0.43092,0.67172,-0.60258,120.07,-0.84944,0.076567,-0.5221,121.83,-0.30457,0.73684,0.60358,127.36
> fitmap #3 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 7942 atoms
average map value = 0.3612, steps = 76
shifted from previous position = 3.57
rotated from previous position = 22.8 degrees
atoms outside contour = 4119, contour level = 0.24654
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.70056477 0.43753328 -0.56371414 118.99439964
-0.65505444 0.08097435 -0.75123021 122.48643683
-0.28304183 0.89554887 0.34333589 128.50993324
Axis 0.82499922 -0.14061050 -0.54736183
Axis point 0.00000000 -15.27119242 183.71514276
Rotation angle (degrees) 86.42026591
Shift along axis 10.60597511
> select subtract #3
Nothing selected
> select add #4
1571 atoms, 1588 bonds, 102 residues, 1 model selected
> view matrix models
> #4,-0.40302,0.87757,-0.25971,105.85,-0.11602,-0.33048,-0.93665,136.26,-0.90781,-0.34736,0.235,170.99
> fitmap #4 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 1571 atoms
average map value = 0.547, steps = 68
shifted from previous position = 17.6
rotated from previous position = 11.8 degrees
atoms outside contour = 481, contour level = 0.24654
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.26569445 0.94593468 -0.18604848 91.64800648
-0.26190012 -0.25655000 -0.93037112 136.05320032
-0.92780105 -0.19846833 0.31590432 153.28661464
Axis 0.45880844 0.46498298 -0.75715629
Axis point 138.60915009 83.36341886 0.00000000
Rotation angle (degrees) 127.09727574
Shift along axis -10.75062290
> view matrix models
> #4,-0.32931,0.94178,-0.0679,92.344,-0.25419,-0.15768,-0.95421,132.6,-0.90936,-0.29697,0.29131,156.5
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.32931,0.94178,-0.0679,93.498,-0.25419,-0.15768,-0.95421,141.54,-0.90936,-0.29697,0.29131,162.6
> volume #1 level 0.3899
> fitmap #4 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 1571 atoms
average map value = 0.5472, steps = 56
shifted from previous position = 11
rotated from previous position = 7.99 degrees
atoms outside contour = 593, contour level = 0.38986
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.26694297 0.94560821 -0.18592087 91.72531239
-0.26279967 -0.25703647 -0.92998311 136.02167480
-0.92718811 -0.19939251 0.31711960 153.33873601
Axis 0.45809876 0.46479328 -0.75770227
Axis point 138.52446424 83.29443336 0.00000000
Rotation angle (degrees) 127.11594478
Shift along axis -10.94389478
> select subtract #4
Nothing selected
> select add #3
7942 atoms, 8048 bonds, 504 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #4
1571 atoms, 1588 bonds, 102 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #2
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> view matrix models
> #2,-0.78105,0.10181,-0.61612,126.33,-0.14691,-0.98889,0.022823,178.23,-0.60695,0.10834,0.78732,156.08
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.57285,-0.71823,-0.39497,144.62,0.36168,-0.65391,0.66452,208.23,-0.73555,0.23782,0.63436,147.15
> fitmap #2 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 4697 atoms
average map value = 0.5188, steps = 168
shifted from previous position = 25.2
rotated from previous position = 40.8 degrees
atoms outside contour = 1658, contour level = 0.38986
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.38059191 -0.90571656 -0.18662077 176.44247248
-0.02418396 -0.19199073 0.98109872 186.01780060
-0.92442681 0.37791147 0.05116631 119.71841768
Axis -0.46463779 0.56833524 0.67904844
Axis point 94.88925856 104.05191207 0.00000000
Rotation angle (degrees) 139.52666820
Shift along axis 105.03323441
> view matrix models
> #2,-0.37995,-0.92349,-0.052915,182.39,0.29666,-0.17584,0.93866,187.16,-0.87615,0.34094,0.34077,133.03
> fitmap #2 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 4697 atoms
average map value = 0.5188, steps = 84
shifted from previous position = 2.77
rotated from previous position = 18.7 degrees
atoms outside contour = 1660, contour level = 0.38986
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.38019389 -0.90602730 -0.18592240 176.47649294
-0.02487391 -0.19092873 0.98128870 185.99469147
-0.92457227 0.37770459 0.05005350 119.67325265
Axis -0.46479785 0.56880700 0.67854370
Axis point 94.90613352 104.05726405 0.00000000
Rotation angle (degrees) 139.51134667
Shift along axis 104.97272138
> volume #1 level 0.5071
> view matrix models
> #2,-0.38147,-0.89003,-0.24966,173.57,-0.045665,-0.2516,0.96675,185.66,-0.92325,0.38018,0.055336,119.89
> fitmap #2 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 4697 atoms
average map value = 0.5189, steps = 60
shifted from previous position = 1.26
rotated from previous position = 3.74 degrees
atoms outside contour = 2274, contour level = 0.50712
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.37921851 -0.90632461 -0.18646454 176.44788606
-0.02253134 -0.19241205 0.98105552 186.01801698
-0.92503279 0.37623571 0.05254550 119.75696200
Axis -0.46491868 0.56772970 0.67936266
Axis point 94.79912976 104.24987128 0.00000000
Rotation angle (degrees) 139.42388453
Shift along axis 104.93244245
> view matrix models
> #2,-0.30949,-0.39394,-0.86546,143.53,-0.3572,-0.79533,0.48975,166.41,-0.88126,0.46072,0.10544,121.78
> fitmap #2 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 4697 atoms
average map value = 0.5363, steps = 164
shifted from previous position = 15.6
rotated from previous position = 61.9 degrees
atoms outside contour = 2135, contour level = 0.50712
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.59775516 -0.11638861 -0.79318501 133.43140185
-0.80080274 0.04044786 0.59756083 159.62490708
-0.03746664 0.99237980 -0.11738223 107.87470739
Axis 0.36110929 -0.69119508 -0.62597879
Axis point 102.66628995 0.00000000 20.45296247
Rotation angle (degrees) 146.86078649
Shift along axis -129.67591011
> select subtract #2
Nothing selected
> select add #3
7942 atoms, 8048 bonds, 504 residues, 1 model selected
> view matrix models
> #3,0.67231,0.4647,-0.57624,119.1,-0.68022,0.080694,-0.72855,122.46,-0.29206,0.88178,0.37035,128.44
> view matrix models
> #3,0.64102,0.48742,-0.59288,119.04,-0.66674,-0.02902,-0.74473,120.27,-0.3802,0.87269,0.30638,126.65
> ui mousemode right translate
> volume #1 level 0.4355
> volume #1 level 0.3768
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.64102,0.48742,-0.59288,108.05,-0.66674,-0.02902,-0.74473,120.92,-0.3802,0.87269,0.30638,128.41
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.52301,0.40326,-0.75089,103.47,-0.79185,-0.096036,-0.60311,119.83,-0.31532,0.91003,0.26909,129.41
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.52301,0.40326,-0.75089,109.68,-0.79185,-0.096036,-0.60311,127.47,-0.31532,0.91003,0.26909,135.45
> view matrix models
> #3,0.52301,0.40326,-0.75089,114.81,-0.79185,-0.096036,-0.60311,124.63,-0.31532,0.91003,0.26909,132.34
> fitmap #3 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 7942 atoms
average map value = 0.3612, steps = 100
shifted from previous position = 5.63
rotated from previous position = 15.6 degrees
atoms outside contour = 4850, contour level = 0.37683
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.70059516 0.43777354 -0.56348980 118.99003042
-0.65486224 0.08081500 -0.75141492 122.48638602
-0.28341114 0.89544585 0.34329996 128.50886911
Axis 0.82503588 -0.14031237 -0.54738308
Axis point 0.00000000 -15.29438179 183.70387290
Rotation angle (degrees) 86.42499917
Shift along axis 10.64110868
> select subtract #3
Nothing selected
> select add #4
1571 atoms, 1588 bonds, 102 residues, 1 model selected
> view matrix models
> #4,-0.26694,0.94561,-0.18592,94.456,-0.2628,-0.25704,-0.92998,148.45,-0.92719,-0.19939,0.31712,168
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.89984,-0.43622,-0.0027325,140.51,0.43623,0.89983,0.0038361,112.16,0.00078545,-0.0046439,0.99999,162.99
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.89984,-0.43622,-0.0027325,128.86,0.43623,0.89983,0.0038361,115.7,0.00078545,-0.0046439,0.99999,158.88
> fitmap #4 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 1571 atoms
average map value = 0.4985, steps = 152
shifted from previous position = 35.5
rotated from previous position = 38.1 degrees
atoms outside contour = 583, contour level = 0.37683
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.82684007 -0.43008932 0.36243436 163.86619584
0.21919800 0.83986284 0.49657088 118.95541828
-0.51796499 -0.33113982 0.78870697 158.83973607
Axis -0.60338416 0.64179312 0.47331717
Axis point 400.65456173 0.00000000 -348.36186149
Rotation angle (degrees) 43.30566497
Shift along axis 52.65207595
> view matrix models
> #4,0.82684,-0.43009,0.36243,125.63,0.2192,0.83986,0.49657,114.57,-0.51796,-0.33114,0.78871,174.37
> open /Users/bsingal/Downloads/CDK19_CCNC_MED12_docked.pdb
CDK19_CCNC_MED12_docked.pdb title:
Alphafold monomer V2.0 prediction for mediator of RNA polymerase II
transcription subunit 12 (Q93074) [more info...]
Chain information for CDK19_CCNC_MED12_docked.pdb #5
---
Chain | Description
A | No description available
B | No description available
D | No description available
Non-standard residues in CDK19_CCNC_MED12_docked.pdb #5
---
ACE — (ACE)
NMA — (NMA)
> ui tool show Matchmaker
> matchmaker #3-4 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CDK19_CCNC_MED12_docked.pdb, chain B (#5) with
CDK19_CCNC_MED12_docked.pdb, chain B (#3), sequence alignment score = 2573.2
RMSD between 502 pruned atom pairs is 0.000 angstroms; (across all 502 pairs:
0.000)
Matchmaker CDK19_CCNC_MED12_docked.pdb, chain D (#5) with
CDK19_CCNC_MED12_docked.pdb, chain D (#4), sequence alignment score = 504.9
RMSD between 100 pruned atom pairs is 0.000 angstroms; (across all 100 pairs:
0.000)
> undo
> select subtract #4
Nothing selected
> ui tool show Matchmaker
> matchmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CDK19_CCNC_MED12_docked.pdb, chain A (#2) with
CDK19_CCNC_MED12_docked.pdb, chain A (#5), sequence alignment score = 1495.7
RMSD between 283 pruned atom pairs is 0.000 angstroms; (across all 283 pairs:
0.000)
> ui tool show Matchmaker
> matchmaker #3 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CDK19_CCNC_MED12_docked.pdb, chain B (#5) with
CDK19_CCNC_MED12_docked.pdb, chain B (#3), sequence alignment score = 2573.2
RMSD between 502 pruned atom pairs is 0.000 angstroms; (across all 502 pairs:
0.000)
> color #5 #7580efff
> color #5 #1b2eefff
> select add #3
7942 atoms, 8048 bonds, 504 residues, 1 model selected
> view matrix models
> #3,-0.59776,-0.11639,-0.79319,92.041,-0.8008,0.040448,0.59756,112.76,-0.037467,0.99238,-0.11738,148.93
> view matrix models
> #3,-0.59776,-0.11639,-0.79319,103.98,-0.8008,0.040448,0.59756,120.17,-0.037467,0.99238,-0.11738,143.27
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.3988,0.68013,-0.61512,131.9,-0.41003,-0.46774,-0.783,99.36,-0.82026,0.56448,0.092343,128.99
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.3988,0.68013,-0.61512,104.93,-0.41003,-0.46774,-0.783,116.08,-0.82026,0.56448,0.092343,136.39
> fitmap #3 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 7942 atoms
average map value = 0.3612, steps = 160
shifted from previous position = 19.3
rotated from previous position = 40.9 degrees
atoms outside contour = 4846, contour level = 0.37683
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.70077623 0.43733637 -0.56360410 118.93744920
-0.65496463 0.08131981 -0.75127121 122.47567786
-0.28272605 0.89561375 0.34342684 128.45547689
Axis 0.82506905 -0.14071644 -0.54722933
Axis point 0.00000000 -15.25827761 183.66885741
Rotation angle (degrees) 86.40166946
Shift along axis 10.60266283
> select subtract #3
Nothing selected
> select #3/B:1-390
6392 atoms, 6476 bonds, 390 residues, 1 model selected
> select ~sel & ##selected
1550 atoms, 1572 bonds, 114 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #3
6392 atoms, 6476 bonds, 390 residues, 1 model selected
> view matrix models
> #3,0.70078,0.43734,-0.5636,110.1,-0.65496,0.08132,-0.75127,120.26,-0.28273,0.89561,0.34343,132.74
> fitmap #3 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 6392 atoms
average map value = 0.4262, steps = 72
shifted from previous position = 10
rotated from previous position = 4.26 degrees
atoms outside contour = 3380, contour level = 0.37683
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.64599486 0.46900638 -0.60226544 118.34441437
-0.70232973 0.05609962 -0.70963778 122.15047893
-0.29903778 0.88141128 0.36563719 128.06968437
Axis 0.79598112 -0.15170085 -0.58600419
Axis point 0.00000000 -11.10353974 187.03232086
Rotation angle (degrees) 88.05925945
Shift along axis 0.62021606
> hide #4 models
> hide #3 models
> select subtract #3
Nothing selected
> hide #2 models
> select add #5
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> color sel byhetero
> color sel bychain
> view matrix models
> #5,-0.59776,-0.11639,-0.79319,36.638,-0.8008,0.040448,0.59756,112.65,-0.037467,0.99238,-0.11738,136.47
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.46473,-0.83607,-0.29156,44.082,-0.60652,0.06067,0.79275,120.18,-0.64511,0.54525,-0.53529,114.11
> view matrix models
> #5,-0.34258,0.79564,-0.49959,56.845,-0.45641,-0.60575,-0.65174,75.504,-0.82118,0.0047489,0.57065,136.64
> view matrix models
> #5,-0.33024,0.94275,-0.046457,70.827,-0.41393,-0.18888,-0.8905,73.84,-0.84829,-0.27485,0.45261,130.21
> show #4 models
> show #3 models
> show #2 models
> select subtract #5
Nothing selected
> select add #5
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #2
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> view matrix models
> #2,-0.41696,0.10296,-0.90308,128.63,-0.87384,0.22798,0.42945,150.1,0.2501,0.96821,-0.0050879,115.73
> view matrix models
> #2,-0.39714,0.1199,-0.90989,128.39,-0.87602,0.24606,0.41478,149.3,0.27362,0.96181,0.0073117,116.54
> view matrix models
> #2,-0.60947,0.17188,-0.77395,131.8,-0.79161,-0.078262,0.606,161.05,0.043589,0.982,0.18376,121.79
> fitmap #2 inMap #1
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 4697 atoms
average map value = 0.5366, steps = 68
shifted from previous position = 6.56
rotated from previous position = 17.5 degrees
atoms outside contour = 1437, contour level = 0.37683
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.56906739 -0.08321795 -0.81806912 131.92754373
-0.82209437 0.07932660 0.56379796 157.38316527
0.01797653 0.99336905 -0.11355519 108.41380849
Axis 0.35929550 -0.69927294 -0.61800009
Axis point 99.68507031 0.00000000 27.01303688
Rotation angle (degrees) 143.28776318
Shift along axis -129.65255882
> volume flip #1 flip z
Expected a keyword
> volume flip #1 axis z
Opened cryosparc_P11_J79_class_00_02000_volume.mrc z flip as #6, grid size
64,64,64, pixel 4.31, shown at step 1, values float32
> select add #5
18907 atoms, 19152 bonds, 1176 residues, 2 models selected
> view matrix models
> #2,-0.59529,-0.030471,-0.80293,132.6,-0.80307,-0.010412,0.59579,157.73,-0.026515,0.99948,-0.018272,111.45,#5,-0.38641,0.92073,-0.054174,69.841,-0.32381,-0.19043,-0.92676,74.367,-0.86362,-0.34057,0.37173,128.79
> select subtract #2
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> view matrix models
> #5,0.079878,0.94769,-0.30905,68.044,-0.21099,-0.28694,-0.93442,74.317,-0.97422,0.13985,0.17704,127.4
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.079878,0.94769,-0.30905,35.609,-0.21099,-0.28694,-0.93442,54.36,-0.97422,0.13985,0.17704,113.81
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.092989,0.99073,-0.099043,39.97,-0.43366,-0.12984,-0.89167,54.86,-0.89626,-0.039965,0.44172,119.92
> view matrix models
> #5,-0.070764,0.98852,-0.13349,39.242,-0.4004,-0.15072,-0.90386,54.655,-0.91361,-0.01051,0.40647,119.09
> view matrix models
> #5,-0.12847,0.99103,-0.036817,41.295,-0.49127,-0.095847,-0.86572,55.323,-0.86148,-0.093133,0.49918,121.28
> view matrix models
> #5,-0.85652,0.46903,-0.21539,23.398,0.37888,0.288,-0.87949,68.02,-0.35047,-0.83491,-0.42438,93.713
> view matrix models
> #5,-0.69882,0.33376,-0.63266,12.281,-0.048636,0.86025,0.50755,107.27,0.71365,0.38545,-0.58492,113.23
> view matrix models
> #5,-0.066242,0.70402,-0.70708,20.72,-0.26582,0.67058,0.69258,108.04,0.96174,0.23383,0.14272,133.97
> view matrix models
> #5,-0.27023,0.70857,-0.65185,20.15,-0.28588,0.58745,0.75708,108.71,0.91937,0.39094,0.043819,132.5
> select subtract #5
Nothing selected
> select add #5
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #3
6392 atoms, 6476 bonds, 390 residues, 1 model selected
> view matrix models
> #3,0.11776,-0.099053,-0.98809,98.489,-0.96328,0.23038,-0.1379,130.57,0.24129,0.96805,-0.068286,128.57
> fitmap #3 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 6392 atoms
average map value = 0.4247, steps = 128
shifted from previous position = 21
rotated from previous position = 55.6 degrees
atoms outside contour = 3433, contour level = 0.37683
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.76620720 -0.47208815 -0.43595792 119.11881488
-0.54640858 -0.12160563 -0.82864331 122.14346552
0.33817775 0.87312362 -0.35112813 138.97033487
Axis 0.90952612 -0.41374444 -0.03972129
Axis point 0.00000000 34.56203414 126.72677265
Rotation angle (degrees) 110.68704222
Shift along axis 52.28541277
> volume #6 level 0.2726
> view matrix models
> #3,0.58796,-0.33264,-0.73733,117.86,-0.78219,-0.0015106,-0.62304,125.57,0.20613,0.94305,-0.26107,140.68
> fitmap #3 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 6392 atoms
average map value = 0.4248, steps = 76
shifted from previous position = 4.7
rotated from previous position = 21.8 degrees
atoms outside contour = 2881, contour level = 0.2726
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.76675635 -0.47206965 -0.43501143 119.07882501
-0.54565548 -0.12232451 -0.82903366 122.12993048
0.33814907 0.87303319 -0.35138049 139.00038020
Axis 0.90976394 -0.41325847 -0.03933202
Axis point 0.00000000 34.52889861 126.68975656
Rotation angle (degrees) 110.69996817
Shift along axis 52.39522651
> select subtract #3
Nothing selected
> select add #2
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> view matrix models
> #2,-0.59867,-0.019468,-0.80076,132.57,-0.80083,-0.0058877,0.59887,157.84,-0.016374,0.99979,-0.012066,111.81
> view matrix models
> #2,-0.34225,0.91027,-0.23299,152.06,0.93836,0.34393,-0.034699,144.41,0.048546,-0.2305,-0.97186,80.904
> view matrix models
> #2,-0.20552,0.85179,-0.48188,143.09,0.97859,0.18451,-0.091222,143.66,0.011211,-0.49031,-0.87148,87.01
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.20552,0.85179,-0.48188,126.05,0.97859,0.18451,-0.091222,153.02,0.011211,-0.49031,-0.87148,119.55
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99182,0.071579,0.10571,169.48,0.0012634,-0.8335,0.55252,179.74,0.12766,-0.54786,-0.82677,123.08
> view matrix models
> #2,0.86064,0.43586,0.26328,172.07,0.13197,-0.69029,0.71139,186.72,0.49181,-0.57751,-0.65162,134.44
> fitmap #2 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 4697 atoms
average map value = 0.5199, steps = 116
shifted from previous position = 8.48
rotated from previous position = 48.5 degrees
atoms outside contour = 1056, contour level = 0.2726
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.94732583 0.18409636 -0.26207310 156.65963153
0.24253946 -0.94677421 0.21164404 183.95774975
-0.20916115 -0.26405893 -0.94155430 107.81527733
Axis -0.98654379 -0.10973223 0.12120311
Axis point 0.00000000 91.16712297 53.22370146
Rotation angle (degrees) 166.04878008
Shift along axis -161.67013472
> view matrix models
> #2,0.039685,-0.82972,0.55676,191.6,-0.9987,-0.050769,-0.004473,155.25,0.031977,-0.55586,-0.83066,117.34
> view matrix models
> #2,0.11453,-0.63158,0.76681,199.81,-0.97231,-0.22956,-0.043859,155.26,0.20373,-0.74055,-0.64038,128.75
> fitmap #2 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 4697 atoms
average map value = 0.5389, steps = 196
shifted from previous position = 13.4
rotated from previous position = 76.4 degrees
atoms outside contour = 908, contour level = 0.2726
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.59243244 -0.77630090 -0.21536181 169.23891461
-0.77098123 0.62387081 -0.12795759 122.13554935
0.23369155 0.09023369 -0.96811474 104.35685669
Axis 0.43700824 -0.89939440 0.01065459
Axis point 106.90766912 0.00000000 65.90612373
Rotation angle (degrees) 165.54366724
Shift along axis -34.77734995
> view matrix models
> #2,-0.72019,-0.6344,-0.28083,164.01,-0.6341,0.76614,-0.10458,123.31,0.28151,0.10276,-0.95404,105.33
> fitmap #2 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 4697 atoms
average map value = 0.5389, steps = 52
shifted from previous position = 3.23
rotated from previous position = 11.6 degrees
atoms outside contour = 907, contour level = 0.2726
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.59194733 -0.77586230 -0.21825683 169.16162702
-0.77027923 0.62429100 -0.13011787 122.11259485
0.23720933 0.09109578 -0.96717801 104.41364369
Axis 0.43685700 -0.89946340 0.01102556
Axis point 106.73810856 0.00000000 66.14370612
Rotation angle (degrees) 165.33377504
Shift along axis -34.78514977
> select subtract #2
Nothing selected
> select add #3
6392 atoms, 6476 bonds, 390 residues, 1 model selected
> view matrix models
> #3,-0.87346,-0.14917,-0.46348,115.94,-0.033031,0.96787,-0.24926,155.47,0.48577,-0.20241,-0.85033,110.86
> view matrix models
> #3,-0.27698,0.028359,-0.96046,118.1,0.17052,0.98515,-0.020087,159.55,0.94562,-0.16934,-0.2777,120.55
> fitmap #3 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 6392 atoms
average map value = 0.4506, steps = 144
shifted from previous position = 42.5
rotated from previous position = 56.2 degrees
atoms outside contour = 2231, contour level = 0.2726
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.34828153 0.55083369 -0.75847361 161.10236671
-0.29489094 0.83243568 0.46913768 148.86296801
0.88979734 0.06027500 0.45235784 138.18651110
Axis -0.21551302 -0.86880968 -0.44578456
Axis point 32.06094859 0.00000000 120.73740715
Rotation angle (degrees) 71.54634196
Shift along axis -225.65465897
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.34828,0.55083,-0.75847,116.99,-0.29489,0.83244,0.46914,131.18,0.8898,0.060275,0.45236,137.8
> fitmap #3 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 6392 atoms
average map value = 0.4398, steps = 132
shifted from previous position = 11
rotated from previous position = 54.7 degrees
atoms outside contour = 2637, contour level = 0.2726
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.27385769 -0.33410786 -0.90187244 119.63308563
0.20648412 0.93628010 -0.28415468 127.09476010
0.93934353 -0.10840439 0.32539547 146.31328695
Axis 0.09120562 -0.95549919 0.28054025
Axis point -48.28278131 0.00000000 178.55109296
Rotation angle (degrees) 74.46858838
Shift along axis -69.48096360
> volume #6 level 0.1293
> view matrix models
> #3,0.27386,-0.33411,-0.90187,117.59,0.20648,0.93628,-0.28415,125.56,0.93934,-0.1084,0.3254,143.65
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.0062301,-0.44972,-0.89315,113.52,-0.09318,0.88902,-0.44829,120.94,0.99563,0.086017,-0.036367,144.37
> fitmap #3 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 6392 atoms
average map value = 0.4415, steps = 104
shifted from previous position = 7.29
rotated from previous position = 20.2 degrees
atoms outside contour = 1642, contour level = 0.12928
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.34851824 -0.43271245 -0.83144150 121.49312937
-0.03952146 0.87948518 -0.47428248 125.48548706
0.93646841 0.19815587 0.28941520 145.69159036
Axis 0.34806911 -0.91510966 0.20352444
Axis point -25.33306278 0.00000000 183.92989413
Rotation angle (degrees) 75.00650904
Shift along axis -42.89317693
> select subtract #3
Nothing selected
> select add #2
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> view matrix models
> #2,-0.1394,-0.9547,0.26289,195.85,-0.94872,0.052695,-0.31169,117.18,0.28372,-0.29286,-0.91309,110.34
> fitmap #2 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 4697 atoms
average map value = 0.5389, steps = 136
shifted from previous position = 13.6
rotated from previous position = 41.6 degrees
atoms outside contour = 491, contour level = 0.12928
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.59187362 -0.77631919 -0.21682743 169.22585252
-0.77075734 0.62381795 -0.12955422 122.14078826
0.23583628 0.09044161 -0.96757510 104.39593243
Axis 0.43708722 -0.89935124 0.01105028
Axis point 106.84342132 0.00000000 66.05960539
Rotation angle (degrees) 165.42416191
Shift along axis -34.72740711
> select add #4
6268 atoms, 6346 bonds, 387 residues, 2 models selected
> view matrix models
> #2,-0.64216,-0.76393,-0.063528,175.73,0.068616,0.025258,-0.99732,91.166,0.76349,-0.6448,0.036198,162.5,#4,-0.12296,0.9581,-0.2587,92.52,-0.97769,-0.07222,0.19723,144.47,0.17029,0.27718,0.94561,138.78
> undo
> select subtract #4
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> select add #4
6268 atoms, 6346 bonds, 387 residues, 2 models selected
> select subtract #2
1571 atoms, 1588 bonds, 102 residues, 1 model selected
> view matrix models
> #4,-0.87536,0.18481,0.44675,123.53,0.2934,-0.53136,0.79472,163.98,0.38426,0.82674,0.41091,131.98
> view matrix models
> #4,-0.94709,0.16779,0.2736,123.5,0.20382,-0.34408,0.91655,158.24,0.24793,0.92383,0.29168,128.39
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.94709,0.16779,0.2736,113.37,0.20382,-0.34408,0.91655,157.87,0.24793,0.92383,0.29168,87.887
> view matrix models
> #4,-0.94709,0.16779,0.2736,117.58,0.20382,-0.34408,0.91655,159.75,0.24793,0.92383,0.29168,92.181
> fitmap #4 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 1571 atoms
average map value = 0.5086, steps = 168
shifted from previous position = 19
rotated from previous position = 72.5 degrees
atoms outside contour = 327, contour level = 0.12928
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.94367554 0.14999873 0.29491839 121.17658543
-0.15906115 -0.98724505 -0.00683787 164.74034115
0.29013104 -0.05336279 0.95549798 140.64941635
Axis -0.14884221 0.01531563 -0.98874235
Axis point 56.64629106 79.55616406 0.00000000
Rotation angle (degrees) 171.00841534
Shift along axis -154.57912290
> view matrix models
> #4,-0.94368,0.15,0.29492,100.12,-0.15906,-0.98725,-0.0068379,176.36,0.29013,-0.053363,0.9555,120.89
> fitmap #4 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 1571 atoms
average map value = 0.5088, steps = 80
shifted from previous position = 31.1
rotated from previous position = 0.0454 degrees
atoms outside contour = 329, contour level = 0.12928
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.94393589 0.14971606 0.29422803 121.16407740
-0.15876966 -0.98729094 -0.00698462 164.75449785
0.28944296 -0.05330752 0.95570973 140.62975605
Axis -0.14847987 0.01533770 -0.98879648
Axis point 56.65529550 79.57028214 0.00000000
Rotation angle (degrees) 171.02575313
Shift along axis -154.51767942
> select subtract #4
Nothing selected
> select add #6
2 models selected
> select subtract #6
Nothing selected
> select add #5
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> view matrix models
> #5,-0.27023,0.70857,-0.65185,125.85,-0.28588,0.58745,0.75708,129.63,0.91937,0.39094,0.043819,142.64
> fitmap #5 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 14210 atoms
average map value = 0.3489, steps = 308
shifted from previous position = 12.9
rotated from previous position = 57.8 degrees
atoms outside contour = 6137, contour level = 0.12928
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.10075600 0.11813920 -0.98787213 121.92959700
0.28335668 0.95521060 0.08533284 129.85083000
0.95370709 -0.27132237 -0.12971874 143.91012320
Axis -0.18004098 -0.98011697 0.08340244
Axis point -19.96351737 0.00000000 120.66292222
Rotation angle (degrees) 97.91084745
Shift along axis -137.21887045
> hide #4 models
> hide #3 models
> hide #2 models
> select subtract #5
Nothing selected
> select add #5
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> view matrix models
> #5,-0.10076,0.11814,-0.98787,121.55,0.28336,0.95521,0.085333,129.42,0.95371,-0.27132,-0.12972,143.91
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.18599,-0.12396,-0.9747,118.48,0.41752,0.88802,-0.1926,122.55,0.88943,-0.44278,-0.11341,141.88
> view matrix models
> #5,-0.42712,-0.20056,-0.88167,117.7,0.31778,0.87959,-0.35403,117.05,0.84652,-0.43139,-0.31196,136.16
> fitmap #5 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 14210 atoms
average map value = 0.3489, steps = 120
shifted from previous position = 12.7
rotated from previous position = 28.6 degrees
atoms outside contour = 6144, contour level = 0.12928
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.10088128 0.11817536 -0.98785502 121.92584433
0.28351941 0.95516425 0.08531118 129.86624040
0.95364548 -0.27146978 -0.12986320 143.92007042
Axis -0.18010845 -0.98009898 0.08346819
Axis point -19.97044526 0.00000000 120.66026515
Rotation angle (degrees) 97.91998987
Shift along axis -137.22889659
> volume #6 level 0.09019
> volume #6 level 0.1293
> select subtract #5
Nothing selected
> select add #5
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> view matrix models
> #5,-0.42471,-0.02548,0.90497,168.47,-0.49046,-0.83373,-0.25365,93.824,0.76097,-0.55158,0.3416,151.78
> fitmap #5 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 14210 atoms
average map value = 0.3572, steps = 280
shifted from previous position = 51.9
rotated from previous position = 72 degrees
atoms outside contour = 5867, contour level = 0.12928
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.49257165 -0.40898316 0.76818353 156.13155170
-0.84238223 -0.44573739 0.30283716 141.35839549
0.21855283 -0.79627316 -0.56407776 137.82473178
Axis -0.84348236 0.42179915 -0.33260034
Axis point 0.00000000 131.37295868 -3.83670555
Rotation angle (degrees) 139.34284476
Shift along axis -117.90991047
> view matrix models
> #5,0.35949,-0.51167,0.78036,154,-0.87821,-0.46823,0.097558,135.17,0.31547,-0.72039,-0.61767,138.17
> fitmap #5 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 14210 atoms
average map value = 0.3571, steps = 88
shifted from previous position = 4.58
rotated from previous position = 12.2 degrees
atoms outside contour = 5870, contour level = 0.12928
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.49306255 -0.40891607 0.76790426 156.10935619
-0.84211818 -0.44596732 0.30323277 141.41789668
0.21846345 -0.79617887 -0.56424545 137.82515080
Axis -0.84364328 0.42161828 -0.33242148
Axis point 0.00000000 131.37723827 -3.81305664
Rotation angle (degrees) 139.33874310
Shift along axis -117.89227932
> view matrix models
> #5,0.76539,-0.23583,0.5988,156.16,-0.61907,-0.52408,0.58489,150.56,0.17588,-0.81837,-0.54712,137.61
> fitmap #5 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 14210 atoms
average map value = 0.3571, steps = 88
shifted from previous position = 3.88
rotated from previous position = 21.2 degrees
atoms outside contour = 5868, contour level = 0.12928
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.49282648 -0.40864415 0.76820050 156.10783456
-0.84211687 -0.44620387 0.30288823 141.41895598
0.21900053 -0.79618595 -0.56402722 137.80063336
Axis -0.84357608 0.42152929 -0.33270476
Axis point 0.00000000 131.35249875 -3.84526581
Rotation angle (degrees) 139.34992895
Shift along axis -117.92352987
> select subtract #5
Nothing selected
> volume #6 level 0.2531
> fitmap #5 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 14210 atoms
average map value = 0.3571, steps = 40
shifted from previous position = 0.022
rotated from previous position = 0.0795 degrees
atoms outside contour = 7359, contour level = 0.25305
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.49374732 -0.40865262 0.76760447 156.10155099
-0.84183257 -0.44591700 0.30409858 141.45463281
0.21801720 -0.79634230 -0.56418741 137.79432070
Axis -0.84383555 0.42143225 -0.33216927
Axis point 0.00000000 131.38339063 -3.82847646
Rotation angle (degrees) 139.30388452
Shift along axis -117.88153370
> fitmap #5 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 14210 atoms
average map value = 0.3571, steps = 40
shifted from previous position = 0.0441
rotated from previous position = 0.0397 degrees
atoms outside contour = 7353, contour level = 0.25305
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.49315040 -0.40876126 0.76793028 156.11073973
-0.84213785 -0.44570783 0.30355949 141.41073983
0.21818918 -0.79640364 -0.56403433 137.82719437
Axis -0.84364576 0.42163845 -0.33238962
Axis point 0.00000000 131.39135618 -3.83550858
Rotation angle (degrees) 139.31419587
Shift along axis -117.89028621
> select add #5
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> view matrix models
> #5,0.5812,-0.53763,0.61088,151.41,-0.80139,-0.24771,0.54444,150.46,-0.14139,-0.80598,-0.57481,133.7
> fitmap #5 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 14210 atoms
average map value = 0.3572, steps = 104
shifted from previous position = 9.45
rotated from previous position = 21.5 degrees
atoms outside contour = 7354, contour level = 0.25305
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.49285341 -0.40898936 0.76799949 156.11851311
-0.84213882 -0.44622153 0.30280116 141.39262221
0.21885546 -0.79599877 -0.56434762 137.81046051
Axis -0.84360027 0.42160364 -0.33254917
Axis point 0.00000000 131.34574058 -3.80629172
Rotation angle (degrees) 139.36361371
Shift along axis -117.91872991
> select subtract #5
Nothing selected
> select add #5
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> view matrix models
> #5,0.35948,0.2395,-0.90189,116.19,0.66523,0.61202,0.42768,171.56,0.6544,-0.75371,0.060688,159.76
> fitmap #5 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 14210 atoms
average map value = 0.3489, steps = 152
shifted from previous position = 33.2
rotated from previous position = 40.8 degrees
atoms outside contour = 7501, contour level = 0.25305
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.10083428 0.11872123 -0.98779437 121.91631423
0.28444191 0.95485278 0.08572614 129.90076429
0.95337571 -0.27232598 -0.13005118 143.94639582
Axis -0.18075591 -0.97996334 0.08366098
Axis point -20.04238074 0.00000000 120.63567917
Rotation angle (degrees) 97.93307672
Shift along axis -137.29238391
> view matrix models
> #5,-0.097845,0.063427,-0.99318,121.22,-0.045483,0.99664,0.068129,126.44,0.99416,0.051839,-0.094631,148.74
> fitmap #5 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 14210 atoms
average map value = 0.3489, steps = 80
shifted from previous position = 8.01
rotated from previous position = 19.1 degrees
atoms outside contour = 7507, contour level = 0.25305
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.10103591 0.11808868 -0.98784958 121.92799053
0.28343871 0.95519850 0.08519581 129.85968682
0.95365310 -0.27138698 -0.12998025 143.91152815
Axis -0.18001142 -0.98011643 0.08347260
Axis point -19.94845116 0.00000000 120.65802261
Rotation angle (degrees) 97.92685752
Shift along axis -137.21337311
> select subtract #5
Nothing selected
> show #3 models
> select add #3
6392 atoms, 6476 bonds, 390 residues, 1 model selected
> view matrix models
> #3,0.3489,-0.59737,-0.72209,119.05,-0.022308,0.765,-0.64365,121.25,0.93689,0.24068,0.25358,146.24
> fitmap #3 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 6392 atoms
average map value = 0.4538, steps = 68
shifted from previous position = 10.3
rotated from previous position = 24.9 degrees
atoms outside contour = 2419, contour level = 0.25305
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.64846626 -0.46172119 -0.60523140 127.65775891
0.16218749 0.86060059 -0.48276480 130.08517438
0.74376524 0.21489572 0.63295585 142.80443750
Axis 0.42491453 -0.82161490 0.37999552
Axis point -68.11912256 0.00000000 249.34569275
Rotation angle (degrees) 55.17921983
Shift along axis 1.62876536
> view matrix models
> #3,0.4464,-0.68062,-0.58093,121.88,-0.32936,0.47866,-0.81388,115.14,0.83201,0.55466,-0.010498,143.87
> fitmap #3 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 6392 atoms
average map value = 0.4454, steps = 68
shifted from previous position = 8.48
rotated from previous position = 26 degrees
atoms outside contour = 2529, contour level = 0.25305
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.25638915 -0.40987823 -0.87536532 119.06150827
-0.42335119 0.76652955 -0.48291430 123.68295731
0.86892944 0.49440094 0.02300742 141.46686685
Axis 0.48878650 -0.87237741 -0.00673826
Axis point 11.41526856 0.00000000 154.60158109
Rotation angle (degrees) 88.68419816
Shift along axis -50.65579972
> view matrix models
> #3,0.25512,-0.46437,-0.8481,118.15,-0.31774,0.78815,-0.52712,124.32,0.91321,0.40395,0.053526,140.07
> fitmap #3 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 6392 atoms
average map value = 0.4454, steps = 56
shifted from previous position = 1.88
rotated from previous position = 6.75 degrees
atoms outside contour = 2533, contour level = 0.25305
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.25663865 -0.41125378 -0.87464675 119.08286070
-0.42232501 0.76627427 -0.48421619 123.67946095
0.86935504 0.49365379 0.02297284 141.46645955
Axis 0.48906372 -0.87223048 -0.00553707
Axis point 11.40197236 0.00000000 154.65244125
Rotation angle (degrees) 88.68535433
Shift along axis -50.42119922
> select subtract #3
Nothing selected
> show #2 models
> hide #3 models
> show #3 models
> hide #5 models
> select add #2
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> view matrix models
> #2,-0.57872,-0.79025,-0.20147,170.13,-0.78006,0.60846,-0.14591,121.47,0.23789,0.072718,-0.96857,104.52
> fitmap #2 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 4697 atoms
average map value = 0.5389, steps = 44
shifted from previous position = 0.558
rotated from previous position = 1.6 degrees
atoms outside contour = 837, contour level = 0.25305
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.59175820 -0.77608966 -0.21796117 169.17964245
-0.77047892 0.62403539 -0.13016172 122.11599621
0.23703265 0.09091022 -0.96723878 104.41480295
Axis 0.43699695 -0.89939461 0.01109086
Axis point 106.76637185 0.00000000 66.13698005
Rotation angle (degrees) 165.34817912
Shift along axis -34.74143002
> show #5 models
> show #4 models
> select subtract #2
Nothing selected
> select add #4
1571 atoms, 1588 bonds, 102 residues, 1 model selected
> view matrix models
> #4,0.053273,0.96614,0.25245,92.098,-0.8194,-0.1022,0.56404,137.92,0.57075,-0.23691,0.78621,145.81
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.053273,0.96614,0.25245,103.87,-0.8194,-0.1022,0.56404,146.22,0.57075,-0.23691,0.78621,138.18
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.14005,0.86735,-0.47759,104.52,-0.70186,0.25327,0.66577,134.45,0.69841,0.42845,0.57328,114.63
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.14005,0.86735,-0.47759,105.81,-0.70186,0.25327,0.66577,133.54,0.69841,0.42845,0.57328,122.87
> view matrix models
> #4,-0.14005,0.86735,-0.47759,101.67,-0.70186,0.25327,0.66577,136.97,0.69841,0.42845,0.57328,120.47
> view matrix models
> #4,-0.14005,0.86735,-0.47759,104.45,-0.70186,0.25327,0.66577,138.13,0.69841,0.42845,0.57328,123.69
> view matrix models
> #4,-0.14005,0.86735,-0.47759,103.91,-0.70186,0.25327,0.66577,140.25,0.69841,0.42845,0.57328,122.63
> fitmap #4 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 1571 atoms
average map value = 0.5339, steps = 108
shifted from previous position = 8.78
rotated from previous position = 48.7 degrees
atoms outside contour = 586, contour level = 0.25305
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.60168106 0.24516766 -0.76017940 122.67073884
-0.69843198 0.30025715 0.64964485 131.10474328
0.38752120 0.92181260 -0.00942611 107.94058676
Axis 0.18018143 -0.75980471 -0.62468508
Axis point 71.65691981 0.00000000 44.74560083
Rotation angle (degrees) 130.95188433
Shift along axis -144.93988642
> view matrix models
> #4,-0.60168,0.24517,-0.76018,116.63,-0.69843,0.30026,0.64964,132.19,0.38752,0.92181,-0.0094261,106.75
> view matrix models
> #4,-0.60168,0.24517,-0.76018,116.15,-0.69843,0.30026,0.64964,132.03,0.38752,0.92181,-0.0094261,117.78
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.17987,0.90877,-0.37655,94.696,-0.25883,0.32558,0.9094,131.67,0.94903,0.26104,0.17666,140.2
> view matrix models
> #4,0.0090138,-0.025135,-0.99964,123.57,0.45327,0.89119,-0.018321,107.88,0.89133,-0.45294,0.019426,163.81
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.0090138,-0.025135,-0.99964,132.65,0.45327,0.89119,-0.018321,113.51,0.89133,-0.45294,0.019426,147.92
> view matrix models
> #4,0.0090138,-0.025135,-0.99964,137.53,0.45327,0.89119,-0.018321,125.58,0.89133,-0.45294,0.019426,151.28
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.11656,0.26056,-0.9584,127.89,0.069517,0.96047,0.26957,124.87,0.99075,-0.098047,0.093842,139.44
> view matrix models
> #4,-0.16488,0.47784,-0.86283,121.27,-0.036346,0.87127,0.48946,128.91,0.98564,0.11206,-0.12629,131.45
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.16488,0.47784,-0.86283,114.75,-0.036346,0.87127,0.48946,126.25,0.98564,0.11206,-0.12629,134.73
> hide #5 models
> volume #6 level 0.1684
> view matrix models
> #4,-0.16488,0.47784,-0.86283,129.98,-0.036346,0.87127,0.48946,113.23,0.98564,0.11206,-0.12629,113.64
> view matrix models
> #4,-0.16488,0.47784,-0.86283,117.37,-0.036346,0.87127,0.48946,106.92,0.98564,0.11206,-0.12629,108.42
> view matrix models
> #4,-0.16488,0.47784,-0.86283,152.59,-0.036346,0.87127,0.48946,116.93,0.98564,0.11206,-0.12629,95.179
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.086632,0.60941,-0.78811,148.12,0.096719,0.7822,0.61547,120.29,0.99153,-0.12954,0.0088225,103.9
> view matrix models
> #4,-0.26939,0.54355,-0.79497,150.77,-0.19992,0.77594,0.59829,120.8,0.94205,0.32011,-0.10037,88.294
> view matrix models
> #4,0.98954,-0.10819,0.095448,174.84,0.10671,0.10355,-0.98888,136.79,0.097101,0.98872,0.11401,67.583
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.98954,-0.10819,0.095448,153,0.10671,0.10355,-0.98888,122.32,0.097101,0.98872,0.11401,75.121
> view matrix models
> #4,0.98954,-0.10819,0.095448,153.26,0.10671,0.10355,-0.98888,123.24,0.097101,0.98872,0.11401,75.167
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.26393,0.73576,-0.6237,122.7,0.89241,-0.43163,-0.13153,143.82,-0.36598,-0.52188,-0.77052,123.33
> fitmap #4 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 1571 atoms
average map value = 0.4148, steps = 76
shifted from previous position = 14.5
rotated from previous position = 36.7 degrees
atoms outside contour = 674, contour level = 0.16837
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.00731696 0.96997330 -0.24310133 112.32357433
0.99932163 0.01586772 0.03323418 130.77518833
0.03609374 -0.24269325 -0.96943140 123.38910317
Axis -0.70097587 -0.70927710 0.07455753
Axis point -17.95254915 0.00000000 68.46709525
Rotation angle (degrees) 168.64913389
Shift along axis -162.29237522
> view matrix models
> #4,0.88793,0.45897,-0.03034,129.35,0.2348,-0.39556,0.88792,149.11,0.39553,-0.79554,-0.459,143.71
> view matrix models
> #4,0.85651,0.19427,-0.47817,136.55,0.5161,-0.33144,0.7898,146.19,-0.0050461,-0.92326,-0.38415,148.84
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.85651,0.19427,-0.47817,130.42,0.5161,-0.33144,0.7898,139.3,-0.0050461,-0.92326,-0.38415,139.49
> volume #6 level 0.09019
> view matrix models
> #4,0.85651,0.19427,-0.47817,129.67,0.5161,-0.33144,0.7898,132.44,-0.0050461,-0.92326,-0.38415,131.25
> fitmap #4 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 1571 atoms
average map value = 0.5603, steps = 92
shifted from previous position = 40.8
rotated from previous position = 62.9 degrees
atoms outside contour = 188, contour level = 0.090193
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.71700699 0.63261183 0.29275118 128.94214384
0.49580784 -0.75804091 0.42373172 173.63185629
0.48997507 -0.15867027 -0.85717453 127.68056899
Axis -0.92455864 -0.31309139 -0.21717527
Axis point 0.00000000 72.32089953 39.03060577
Rotation angle (degrees) 161.64146998
Shift along axis -201.30627540
> view matrix models
> #4,0.71701,0.63261,0.29275,129.64,0.49581,-0.75804,0.42373,148.09,0.48998,-0.15867,-0.85717,97.721
> fitmap #4 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 1571 atoms
average map value = 0.5343, steps = 180
shifted from previous position = 37.9
rotated from previous position = 61.9 degrees
atoms outside contour = 274, contour level = 0.090193
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.14832468 0.98621251 0.07338037 130.36788757
0.47435800 0.00584188 0.88031265 149.29136904
0.86774667 0.16538065 -0.46868428 114.33054862
Axis -0.60333627 -0.67037145 -0.43195771
Axis point -5.86223240 0.00000000 7.28844538
Rotation angle (degrees) 143.66664860
Shift along axis -228.12230870
> view matrix models
> #4,-0.14832,0.98621,0.07338,123.2,0.47436,0.0058419,0.88031,124.26,0.86775,0.16538,-0.46868,83.327
> fitmap #4 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 1571 atoms
average map value = 0.5252, steps = 116
shifted from previous position = 40.6
rotated from previous position = 35.6 degrees
atoms outside contour = 269, contour level = 0.090193
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.15506444 0.96594272 0.20714655 128.00398448
0.84522042 -0.23826946 0.47836190 149.02013793
0.51142689 0.10090757 -0.85338163 120.05485368
Axis -0.75546463 -0.60900887 -0.24162241
Axis point 0.00000000 28.60688511 38.11341763
Rotation angle (degrees) 165.53337452
Shift along axis -216.46501154
> view matrix models
> #4,0.15506,0.96594,0.20715,99.207,0.84522,-0.23827,0.47836,143.42,0.51143,0.10091,-0.85338,112.66
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.10162,0.63956,-0.76199,106.42,0.86707,-0.43245,-0.24734,147.05,-0.48771,-0.63557,-0.59849,139.88
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.10162,0.63956,-0.76199,113.24,0.86707,-0.43245,-0.24734,145.61,-0.48771,-0.63557,-0.59849,117.63
> volume #6 level 0.06414
> fitmap #4 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 1571 atoms
average map value = 0.4148, steps = 112
shifted from previous position = 25.1
rotated from previous position = 46.6 degrees
atoms outside contour = 517, contour level = 0.064135
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.00712401 0.96998201 -0.24307233 112.31969423
0.99933089 0.01562661 0.03306951 130.78341499
0.03587523 -0.24267410 -0.96944430 123.39198834
Axis -0.70105095 -0.70919667 0.07461664
Axis point -17.96723590 0.00000000 68.47446138
Rotation angle (degrees) 168.65802722
Shift along axis -162.28589612
> volume #6 level 0.1684
> select subtract #4
Nothing selected
> open /Users/bsingal/Downloads/5bnj.pdb
5bnj.pdb title:
CDK8/cycc In complex with 8-{3-chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)-
phenyl]-pyridin- 4-yl}-2,8-diaza-spiro[4.5]decan-1-one [more info...]
Chain information for 5bnj.pdb #7
---
Chain | Description | UniProt
A | cyclin-dependent kinase 8 | CDK8_HUMAN 1-403
B | cyclin-C | CCNC_HUMAN 1-283
Non-standard residues in 5bnj.pdb #7
---
4TV —
8-{3-chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]pyridin-4-yl}-2,8-diazaspiro[4.5]decan-1-one
FMT — formic acid
> select add #7
4929 atoms, 5004 bonds, 669 residues, 1 model selected
> color sel bychain
> view matrix models #7,1,0,0,74.016,0,1,0,87.955,0,0,1,92.613
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.63558,0.34658,0.68987,67.046,0.7097,0.61405,0.34535,57.48,-0.30392,0.7091,-0.63625,183
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.63558,0.34658,0.68987,92.181,0.7097,0.61405,0.34535,45.936,-0.30392,0.7091,-0.63625,149.89
> fitmap #7 inMap #6
Fit molecule 5bnj.pdb (#7) to map cryosparc_P11_J79_class_00_02000_volume.mrc
z flip (#6) using 4929 atoms
average map value = 0.4765, steps = 80
shifted from previous position = 6.2
rotated from previous position = 45.7 degrees
atoms outside contour = 1303, contour level = 0.16837
Position of 5bnj.pdb (#7) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.69162825 0.68772000 0.22066166 107.92628240
0.56073590 0.31872387 0.76419261 44.96679037
0.45522040 0.65227011 -0.60606772 122.97179755
Axis -0.38693146 -0.81090181 -0.43900148
Axis point 40.32438273 0.00000000 51.85867261
Rotation angle (degrees) 171.68424289
Shift along axis -132.20852678
> view matrix models
> #7,-0.69163,0.68772,0.22066,106.03,0.56074,0.31872,0.76419,43.511,0.45522,0.65227,-0.60607,123.33
> fitmap #7 inMap #6
Fit molecule 5bnj.pdb (#7) to map cryosparc_P11_J79_class_00_02000_volume.mrc
z flip (#6) using 4929 atoms
average map value = 0.4765, steps = 56
shifted from previous position = 2.4
rotated from previous position = 0.0886 degrees
atoms outside contour = 1302, contour level = 0.16837
Position of 5bnj.pdb (#7) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.69055473 0.68880402 0.22064266 107.81035985
0.56149684 0.31824775 0.76383222 44.97785764
0.45591167 0.65135812 -0.60652877 123.02351802
Axis -0.38759054 -0.81074699 -0.43870592
Axis point 40.22962462 0.00000000 51.88679143
Rotation angle (degrees) 171.65727861
Shift along axis -132.22308466
> volume #6 level 0.3182
> view matrix models
> #7,-0.69055,0.6888,0.22064,104.9,0.5615,0.31825,0.76383,43.427,0.45591,0.65136,-0.60653,122.35
> fitmap #7 inMap #6
Fit molecule 5bnj.pdb (#7) to map cryosparc_P11_J79_class_00_02000_volume.mrc
z flip (#6) using 4929 atoms
average map value = 0.4766, steps = 68
shifted from previous position = 3.31
rotated from previous position = 0.0184 degrees
atoms outside contour = 1948, contour level = 0.3182
Position of 5bnj.pdb (#7) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.69076216 0.68857931 0.22069474 107.80719397
0.56135622 0.31829512 0.76391584 44.91677917
0.45577058 0.65157253 -0.60640450 122.96641675
Axis -0.38746588 -0.81076358 -0.43878539
Axis point 40.25034721 0.00000000 51.87256682
Rotation angle (degrees) 171.66434905
Shift along axis -132.14436457
> hide #4 models
> hide #3 models
> hide #2 models
> show #2 models
> hide #2 models
> show #3 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> volume #6 level 0.5071
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> select subtract #7
Nothing selected
> volume #6 level 0.3182
> select add #3
6392 atoms, 6476 bonds, 390 residues, 1 model selected
> view matrix models
> #3,0.25664,-0.41125,-0.87465,118.4,-0.42233,0.76627,-0.48422,122.98,0.86936,0.49365,0.022973,142.1
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.31353,-0.48643,-0.81552,117.73,-0.39772,0.7126,-0.57795,120.94,0.86227,0.50556,0.029959,142.39
> fitmap #3 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 6392 atoms
average map value = 0.4454, steps = 52
shifted from previous position = 3.28
rotated from previous position = 6.45 degrees
atoms outside contour = 2887, contour level = 0.3182
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.25693706 -0.41010459 -0.87509861 119.05200600
-0.42265269 0.76662984 -0.48336673 123.72938220
0.86910762 0.49405760 0.02364381 141.50193052
Axis 0.48884838 -0.87234619 -0.00627580
Axis point 11.33854131 0.00000000 154.69624301
Rotation angle (degrees) 88.64738700
Shift along axis -50.62451217
> volume #6 level 0.2205
> view matrix models
> #3,0.26676,-0.53946,-0.79864,117.09,-0.36082,0.7125,-0.6018,121.64,0.89367,0.4487,-0.0045854,140.35
> fitmap #3 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 6392 atoms
average map value = 0.4454, steps = 52
shifted from previous position = 3.18
rotated from previous position = 8.76 degrees
atoms outside contour = 2317, contour level = 0.22048
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.25691827 -0.41042115 -0.87495570 119.04931606
-0.42249958 0.76654784 -0.48363055 123.73623521
0.86918761 0.49392194 0.02353739 141.50759092
Axis 0.48891128 -0.87231260 -0.00604088
Axis point 11.33987746 0.00000000 154.69970893
Rotation angle (degrees) 88.65332482
Shift along axis -50.58695320
> show #2 models
> save /Users/bsingal/Documents/Ashley_cdk19-ccnc/P11_krios_CCMD.cxs
> includeMaps true
> open /Users/bsingal/Downloads/cryosparc_P11_J78_class_00_final_volume.mrc
Opened cryosparc_P11_J78_class_00_final_volume.mrc as #8, grid size
128,128,128, pixel 2.16, shown at level 0.0247, step 1, values float32
> volume flip #8 axis z
Opened cryosparc_P11_J78_class_00_final_volume.mrc z flip as #9, grid size
128,128,128, pixel 2.16, shown at step 1, values float32
> view matrix models
> #3,0.27177,-0.32061,-0.90739,120.77,-0.3458,0.84737,-0.40297,126.85,0.89809,0.42329,0.11942,141.16
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 2 maps.
> hide #!9 models
> fitmap #3 inMap #6
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) using 6392 atoms
average map value = 0.4454, steps = 56
shifted from previous position = 2.96
rotated from previous position = 8.43 degrees
atoms outside contour = 2318, contour level = 0.22048
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.25693306 -0.41034612 -0.87498655 119.04697204
-0.42249588 0.76658677 -0.48357208 123.74059173
0.86918504 0.49392387 0.02359194 141.51108502
Axis 0.48888363 -0.87232785 -0.00607656
Axis point 11.33338206 0.00000000 154.70417577
Rotation angle (degrees) 88.65022227
Shift along axis -50.60214979
> show #!9 models
> volume #9 level 0.07657
> select subtract #3
Nothing selected
> select add #9
2 models selected
> view matrix models
> #9,-0.79771,-0.60192,-0.036657,349.84,-0.11108,0.20642,-0.97214,257.91,0.59272,-0.77142,-0.23152,187.64
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.79771,-0.60192,-0.036657,284.61,-0.11108,0.20642,-0.97214,238.36,0.59272,-0.77142,-0.23152,143.51
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.041013,0.41732,0.90783,-94.516,0.88468,0.43746,-0.16113,-51.884,-0.46438,0.79654,-0.38714,110.83
> view matrix models
> #9,-0.39426,0.60584,0.69103,-37.612,0.85997,-0.021946,0.50988,-80.279,0.32407,0.79529,-0.51235,12.552
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.39426,0.60584,0.69103,8.6179,0.85997,-0.021946,0.50988,-53.661,0.32407,0.79529,-0.51235,38.734
> volume #9 level 0.1171
> hide #2 models
> hide #3 models
> fitmap #9 inMap #6
Fit map cryosparc_P11_J78_class_00_final_volume.mrc z flip in map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip using 9308 points
correlation = 0.7683, correlation about mean = 0.1607, overlap = 982
steps = 76, shift = 8.29, angle = 13.7 degrees
Position of cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) relative
to cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.43178985 0.40137090 0.80774929 26.89295899
0.87671627 -0.02368231 0.48042453 -47.41525450
0.21195779 0.91560938 -0.34166262 21.66202648
Axis 0.49584047 0.67883230 0.54159851
Axis point 35.10773763 0.00000000 24.56631860
Rotation angle (degrees) 153.97039117
Shift along axis -7.12026762
> view matrix models
> #9,-0.43179,0.40137,0.80775,26.757,0.87672,-0.023682,0.48042,-49.237,0.21196,0.91561,-0.34166,17.725
> fitmap #9 inMap #6
Fit map cryosparc_P11_J78_class_00_final_volume.mrc z flip in map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip using 9308 points
correlation = 0.7679, correlation about mean = 0.1598, overlap = 981.8
steps = 56, shift = 4.42, angle = 0.0984 degrees
Position of cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) relative
to cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.43320854 0.40149864 0.80692577 27.24519617
0.87590207 -0.02347096 0.48191771 -47.48959474
0.21242863 0.91555882 -0.34150567 21.64975282
Axis 0.49529717 0.67902407 0.54185517
Axis point 35.26312916 0.00000000 24.55827031
Rotation angle (degrees) 154.03904695
Shift along axis -7.02107889
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.31041,0.33492,0.88965,7.6879,0.85078,-0.31959,0.41716,4.5917,0.42404,0.88639,-0.18574,-25.335
> fitmap #9 inMap #6
Fit map cryosparc_P11_J78_class_00_final_volume.mrc z flip in map
cryosparc_P11_J79_class_00_02000_volume.mrc z flip using 9308 points
correlation = 0.7682, correlation about mean = 0.1606, overlap = 982
steps = 104, shift = 1.57, angle = 17.7 degrees
Position of cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) relative
to cryosparc_P11_J79_class_00_02000_volume.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.43222772 0.40089349 0.80775219 27.04998589
0.87674285 -0.02272331 0.48042233 -47.56788355
0.21095298 0.91584281 -0.34165886 21.77337061
Axis 0.49550262 0.67914942 0.54151013
Axis point 35.24402640 0.00000000 24.64065111
Rotation angle (degrees) 153.93614649
Shift along axis -7.11186084
> select subtract #9
Nothing selected
> volume #9 color #b2ffff7e
> volume #9 color #b2ffff80
> show #3 models
> show #2 models
> hide #!6 models
> select add #2
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> fitmap #2 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 4697 atoms
average map value = 0.1539, steps = 316
shifted from previous position = 8.73
rotated from previous position = 83 degrees
atoms outside contour = 2004, contour level = 0.11706
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
0.66559860 0.73385627 -0.13576995 122.56673948
-0.61902076 0.44124278 -0.64970618 107.45528256
-0.41688345 0.51648794 0.74796284 169.43219768
Axis 0.64497489 0.15547253 -0.74822168
Axis point 252.77158060 -79.09292529 0.00000000
Rotation angle (degrees) 64.69719602
Shift along axis -31.01402955
> volume #9 level 0.07333
> view matrix models
> #2,0.85504,0.38597,-0.34632,137.44,0.51414,-0.54393,0.66318,169.29,0.067591,-0.7451,-0.66352,110.11
> fitmap #2 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 4697 atoms
average map value = 0.1521, steps = 168
shifted from previous position = 29.6
rotated from previous position = 25.7 degrees
atoms outside contour = 1386, contour level = 0.073329
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.01550559 -0.95557025 0.29435536 174.47962891
0.62086000 -0.23996312 -0.74629121 136.32456776
0.78376811 0.17118178 0.59699611 183.27904678
Axis 0.48582227 -0.25915489 0.83475473
Axis point -46.42109616 129.00728957 0.00000000
Rotation angle (degrees) 109.22242850
Shift along axis 202.42996269
> select add #3
11089 atoms, 11234 bonds, 675 residues, 2 models selected
> select subtract #2
6392 atoms, 6476 bonds, 390 residues, 1 model selected
> view matrix models
> #3,0.2602,-0.51512,-0.81667,117.39,-0.3881,0.71868,-0.57696,121.89,0.88412,0.46707,-0.012913,140.62
> fitmap #3 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 6392 atoms
average map value = 0.1725, steps = 180
shifted from previous position = 3.59
rotated from previous position = 38.1 degrees
atoms outside contour = 1641, contour level = 0.073329
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.71816898 0.60723167 -0.33985736 132.93381057
0.64466271 0.39669301 -0.65348653 141.92685890
-0.26199867 -0.68840712 -0.67635223 112.99469909
Axis -0.37476501 -0.83557324 0.40170705
Axis point 32.37374579 0.00000000 91.82449869
Rotation angle (degrees) 177.32962393
Shift along axis -123.01845865
> view matrix models
> #3,0.039467,-0.56103,-0.82685,116.22,-0.13724,0.81661,-0.56063,138.11,0.98975,0.1356,-0.044765,135.24
> fitmap #3 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 6392 atoms
average map value = 0.1725, steps = 228
shifted from previous position = 16.4
rotated from previous position = 54 degrees
atoms outside contour = 1644, contour level = 0.073329
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.71837681 0.60711520 -0.33962613 132.94202166
0.64433459 0.39665733 -0.65383171 141.93332121
-0.26223597 -0.68853039 -0.67613475 113.00395640
Axis -0.37463374 -0.83556373 0.40184924
Axis point 32.40058070 0.00000000 91.83637136
Rotation angle (degrees) 177.34567487
Shift along axis -122.98834852
> view matrix models
> #3,-0.19353,0.28041,-0.94017,132.1,0.044839,0.95981,0.27704,151.41,0.98007,0.01146,-0.19833,130.81
> view matrix models
> #3,0.22358,-0.64869,-0.72747,116.49,-0.48966,0.57059,-0.65929,129.51,0.84276,0.50361,-0.19006,140.89
> fitmap #3 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 6392 atoms
average map value = 0.1725, steps = 124
shifted from previous position = 8.01
rotated from previous position = 27.7 degrees
atoms outside contour = 1641, contour level = 0.073329
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.71819274 0.60725968 -0.33975708 132.93896627
0.64452428 0.39650335 -0.65373814 141.92370213
-0.26227399 -0.68849167 -0.67615944 112.98788334
Axis -0.37475506 -0.83551739 0.40183246
Axis point 32.38638594 0.00000000 91.82777629
Rotation angle (degrees) 177.34233754
Shift along axis -122.99707363
> view matrix models
> #3,0.4149,-0.72844,-0.54519,117.84,-0.26291,0.47765,-0.83829,126.9,0.87105,0.49114,0.0066698,142.9
> fitmap #3 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 6392 atoms
average map value = 0.1677, steps = 116
shifted from previous position = 4.03
rotated from previous position = 28 degrees
atoms outside contour = 1670, contour level = 0.073329
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.24714336 0.95111655 -0.18519579 138.88409959
0.95264244 0.27344503 0.13304212 146.73052818
0.17717943 -0.14354489 -0.97365411 120.30611649
Axis -0.60672191 -0.79490712 0.00334720
Axis point 4.65710824 0.00000000 61.71414167
Rotation angle (degrees) 166.82443919
Shift along axis -200.49847802
> view matrix models
> #3,-0.1306,-0.46309,-0.87664,114.99,-0.29614,0.86206,-0.41128,132.46,0.94617,0.2059,-0.24973,131.84
> fitmap #3 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 6392 atoms
average map value = 0.1725, steps = 176
shifted from previous position = 14.5
rotated from previous position = 51.6 degrees
atoms outside contour = 1641, contour level = 0.073329
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.71784949 0.60772202 -0.33965580 132.98524126
0.64473165 0.39620459 -0.65371479 141.93260676
-0.26270368 -0.68825567 -0.67623288 112.99034734
Axis -0.37499240 -0.83542926 0.40179429
Axis point 32.39877075 0.00000000 91.82348270
Rotation angle (degrees) 177.36028404
Shift along axis -123.04423015
> select subtract #3
Nothing selected
> select add #2
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> view matrix models
> #2,0.71406,0.292,0.63629,179.11,-0.15304,-0.82179,0.54886,185.51,0.68316,-0.48929,-0.54211,136.9
> fitmap #2 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 4697 atoms
average map value = 0.1532, steps = 60
shifted from previous position = 5.85
rotated from previous position = 7.39 degrees
atoms outside contour = 1278, contour level = 0.073329
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.33973227 -0.92167206 0.18735689 168.43517536
0.86960329 -0.38370654 -0.31074010 156.36503314
0.35829053 0.05735773 0.93184655 192.20058984
Axis 0.20041514 -0.09306680 0.97528065
Axis point 5.23972363 130.19678949 0.00000000
Rotation angle (degrees) 113.31563590
Shift along axis 206.65408044
> volume #9 level 0.05389
> volume #9 level 0.1041
> show #4 models
> view matrix models
> #2,0.74146,0.36155,0.56526,171.97,-0.26081,-0.62089,0.73924,191.75,0.61823,-0.69554,-0.36607,144.61
> undo
> select subtract #2
Nothing selected
> select add #4
1571 atoms, 1588 bonds, 102 residues, 1 model selected
> view matrix models
> #4,0.40215,-0.34436,-0.84835,153.87,-0.0096364,-0.92812,0.37217,165.37,-0.91552,-0.14149,-0.37656,123.55
> view matrix models
> #4,0.49004,-0.52924,-0.69265,160.64,0.56004,0.80006,-0.21508,103.78,0.66799,-0.28252,0.68846,130.62
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.49004,-0.52924,-0.69265,143.58,0.56004,0.80006,-0.21508,98.195,0.66799,-0.28252,0.68846,104.59
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.61439,0.26717,-0.74239,116.26,-0.28597,0.95235,0.10607,95.396,0.73536,0.14713,0.66152,89.85
> view matrix models
> #4,0.29005,0.68273,-0.67064,102.89,-0.6884,0.63565,0.34937,107.61,0.66482,0.36033,0.65436,82.692
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.29005,0.68273,-0.67064,110.96,-0.6884,0.63565,0.34937,108.21,0.66482,0.36033,0.65436,96.932
> view matrix models
> #4,0.29005,0.68273,-0.67064,110.52,-0.6884,0.63565,0.34937,109.37,0.66482,0.36033,0.65436,94.712
> fitmap #4 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 1571 atoms
average map value = 0.1617, steps = 156
shifted from previous position = 14.8
rotated from previous position = 73.8 degrees
atoms outside contour = 672, contour level = 0.1041
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
0.20824297 -0.34740881 0.91429863 145.86039199
0.29175862 0.91429766 0.28095676 88.85567046
-0.93354795 0.20824724 0.29175558 132.99140916
Axis -0.03716079 0.94440788 0.32666930
Axis point 135.53554631 0.00000000 -47.11869126
Rotation angle (degrees) 78.04472379
Shift along axis 121.93991889
> view matrix models
> #4,-0.72712,0.68491,-0.046885,121.59,-0.27255,-0.22532,0.93539,135.58,0.63009,0.69292,0.35051,94.023
> fitmap #4 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 1571 atoms
average map value = 0.2001, steps = 92
shifted from previous position = 23.4
rotated from previous position = 25.4 degrees
atoms outside contour = 410, contour level = 0.1041
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
0.48859625 -0.08166104 0.86868014 137.28415085
0.35354751 0.92874167 -0.11154852 100.10445208
-0.79767028 0.36162189 0.48265075 115.65697653
Axis 0.26492372 0.93297413 0.24366923
Axis point 121.58000753 0.00000000 -38.29239333
Rotation angle (degrees) 63.25667960
Shift along axis 157.94673835
> view matrix models
> #4,-0.71377,0.69972,-0.030325,110.14,0.037121,0.081031,0.99602,128.06,0.6994,0.7098,-0.083812,86.992
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.20878,0.56803,-0.79609,110.36,-0.4479,0.77917,0.4385,102.79,0.86937,0.26502,0.41709,103.85
> view matrix models
> #4,0.30817,0.48905,-0.816,112.83,-0.57509,0.77905,0.24971,102.2,0.75782,0.39233,0.52133,100.1
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.30817,0.48905,-0.816,118.63,-0.57509,0.77905,0.24971,107.77,0.75782,0.39233,0.52133,90.178
> view matrix models
> #4,0.30817,0.48905,-0.816,118.53,-0.57509,0.77905,0.24971,107.66,0.75782,0.39233,0.52133,90.712
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.82774,0.3434,-0.44375,124.31,0.49614,-0.81731,0.29299,160.53,-0.26207,-0.46268,-0.8469,115.44
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.82774,0.3434,-0.44375,120.54,0.49614,-0.81731,0.29299,158.24,-0.26207,-0.46268,-0.8469,122.42
> show #5 models
> view matrix models
> #4,0.82774,0.3434,-0.44375,126.77,0.49614,-0.81731,0.29299,162.55,-0.26207,-0.46268,-0.8469,117.86
> volume #9 level 0.07171
> select subtract #4
Nothing selected
> hide #5 models
> show #5 models
> ui tool show Matchmaker
> matchmaker #5 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CDK19_CCNC_MED12_docked.pdb, chain B (#3) with
CDK19_CCNC_MED12_docked.pdb, chain B (#5), sequence alignment score = 2436.4
RMSD between 390 pruned atom pairs is 0.000 angstroms; (across all 390 pairs:
0.000)
> select add #5
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> view matrix models
> #5,0.35654,-0.65978,-0.66149,131.37,-0.77023,0.19316,-0.60781,130.25,0.5288,0.72621,-0.43931,123.3
> view matrix models
> #5,0.35654,-0.65978,-0.66149,156.38,-0.77023,0.19316,-0.60781,133.43,0.5288,0.72621,-0.43931,117.83
> view matrix models
> #5,0.35654,-0.65978,-0.66149,127.34,-0.77023,0.19316,-0.60781,86.013,0.5288,0.72621,-0.43931,128.7
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.30616,0.2993,-0.90371,130.32,-0.7301,0.68301,-0.021142,107.51,0.61091,0.66627,0.42763,152.47
> view matrix models
> #5,0.34973,0.31088,-0.88377,131.43,0.082945,-0.94991,-0.30132,91.189,-0.93317,0.032078,-0.358,108.43
> select subtract #5
Nothing selected
> hide #5 models
> select add #2
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> view matrix models
> #2,0.50756,0.071704,0.85863,184.78,-0.72801,-0.49731,0.47188,174.63,0.46084,-0.8646,-0.20022,151.65
> fitmap #2 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 4697 atoms
average map value = 0.1601, steps = 140
shifted from previous position = 5.72
rotated from previous position = 22.9 degrees
atoms outside contour = 1236, contour level = 0.071709
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.88682251 -0.45198506 0.09620475 145.91441772
0.44350865 -0.77400340 0.45190576 184.38250300
-0.12979184 0.44342784 0.88686292 175.14354158
Axis -0.00917912 0.24468836 0.96955833
Axis point 57.11169507 88.75369125 0.00000000
Rotation angle (degrees) 152.49635967
Shift along axis 213.58876556
> view matrix models
> #2,0.63779,0.31903,0.70103,173.8,-0.33407,-0.70552,0.62501,175.13,0.69399,-0.63282,-0.3434,142.56
> fitmap #2 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 4697 atoms
average map value = 0.1599, steps = 252
shifted from previous position = 8.01
rotated from previous position = 42.8 degrees
atoms outside contour = 1215, contour level = 0.071709
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.84337445 -0.49343410 0.21270247 151.13658502
0.52775992 -0.68632975 0.50042076 184.12893942
-0.10094064 0.53429792 0.83924771 171.48946269
Axis 0.03169612 0.29345049 0.95544867
Axis point 54.72069742 87.56588759 0.00000000
Rotation angle (degrees) 147.69639819
Shift along axis 222.67255007
> view matrix models
> #2,0.5261,0.83534,0.15944,143.4,0.71422,-0.53578,0.45037,175.35,0.46164,-0.12307,-0.87849,110.99
> fitmap #2 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 4697 atoms
average map value = 0.1521, steps = 132
shifted from previous position = 9.47
rotated from previous position = 32.7 degrees
atoms outside contour = 1364, contour level = 0.071709
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.01552142 -0.95557963 0.29432406 174.48067165
0.62089265 -0.23994096 -0.74627117 136.32501370
0.78374193 0.17116046 0.59703660 183.28467159
Axis 0.48579617 -0.25915536 0.83476978
Axis point -46.41963161 129.01021648 0.00000000
Rotation angle (degrees) 109.22100823
Shift along axis 202.43318796
> view matrix models
> #2,0.93867,0.25052,0.23694,164.33,0.055351,-0.7877,0.61356,190.06,0.34034,-0.56282,-0.75326,125.03
> fitmap #2 inMap #9
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) using 4697 atoms
average map value = 0.1532, steps = 124
shifted from previous position = 1.5
rotated from previous position = 21 degrees
atoms outside contour = 1258, contour level = 0.071709
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.33738744 -0.92230131 0.18849408 168.50716147
0.87028460 -0.38192498 -0.31102738 156.34004580
0.35885155 0.05910677 0.93152131 192.15217600
Axis 0.20134475 -0.09267068 0.97512688
Axis point 5.07427176 130.19633980 0.00000000
Rotation angle (degrees) 113.19711021
Shift along axis 206.81264645
> ui mousemode right "tape measure"
> select subtract #2
Nothing selected
> marker segment #10 position 95,109.6,142.7 toPosition 187.2,151.5,127.8
> color yellow radius 1.078 label 102.3 labelHeight 10.23 labelColor yellow
> marker segment #10 position 123.9,136,91.05 toPosition 175,146.4,160.9 color
> yellow radius 0.5391 label 87.18 labelHeight 8.718 labelColor yellow
> close #10
> hide #!6 models
> open /Users/bsingal/Downloads/cryosparc_P11_J82_class_04_02800_volume.mrc
Opened cryosparc_P11_J82_class_04_02800_volume.mrc as #10, grid size 64,64,64,
pixel 4.31, shown at level 0.134, step 1, values float32
> open /Users/bsingal/Downloads/cryosparc_P11_J82_class_01_02800_volume.mrc
Opened cryosparc_P11_J82_class_01_02800_volume.mrc as #11, grid size 64,64,64,
pixel 4.31, shown at level 0.132, step 1, values float32
> volume #10 level 0.1747
> volume #11 level 0.1945
> select add #10
2 models selected
> select add #11
4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #10,1,0,0,60.904,0,1,0,45.596,0,0,1,-15.824,#11,1,0,0,60.904,0,1,0,45.596,0,0,1,-15.824
> select subtract #10
2 models selected
> view matrix models #11,1,0,0,37.092,0,1,0,2.5635,0,0,1,-72.405
> volume #11 level 0.3514
> volume flip #11 axis z
Opened cryosparc_P11_J82_class_01_02800_volume.mrc z flip as #12, grid size
64,64,64, pixel 4.31, shown at step 1, values float32
> select subtract #11
Nothing selected
> select add #12
2 models selected
> view matrix models #12,1,0,0,9.851,0,1,0,-23.98,0,0,1,-54.529
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.40256,-0.51965,0.7536,175.6,-0.251,0.85436,0.45505,-30.691,-0.88031,-0.0059738,-0.47436,270.72
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 3 atomic models, 3 maps.
> view matrix models
> #12,-0.29144,-0.51472,0.8063,152.17,-0.56223,0.77411,0.29095,46.432,-0.77393,-0.36853,-0.515,311.91
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.29144,-0.51472,0.8063,146.67,-0.56223,0.77411,0.29095,60.485,-0.77393,-0.36853,-0.515,359.99
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #3 models
> hide #2 models
> fitmap #12 inMap #9
Fit map cryosparc_P11_J82_class_01_02800_volume.mrc z flip in map
cryosparc_P11_J78_class_00_final_volume.mrc z flip using 917 points
correlation = 0.8098, correlation about mean = 0.2996, overlap = 129
steps = 116, shift = 11.9, angle = 34.5 degrees
Position of cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) relative
to cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.32048662 0.66354635 -0.67601374 181.15119746
-0.67055428 -0.66299126 -0.33286566 366.94618255
-0.66906300 0.34662491 0.65742367 95.73097941
Axis 0.45384368 -0.00464252 -0.89106922
Axis point 207.63391260 136.91841441 0.00000000
Rotation angle (degrees) 131.53114761
Shift along axis -4.79215919
> select subtract #12
Nothing selected
> show #!10 models
> volume flip #10 axis z
Opened cryosparc_P11_J82_class_04_02800_volume.mrc z flip as #13, grid size
64,64,64, pixel 4.31, shown at step 1, values float32
> select add #13
2 models selected
> view matrix models #13,1,0,0,-20.597,0,1,0,4.2333,0,0,1,-59.477
> view matrix models #13,1,0,0,36.883,0,1,0,33.581,0,0,1,-30.15
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.020091,0.25334,0.96717,15.54,0.68076,0.71194,-0.17234,-0.31595,-0.73223,0.65495,-0.18677,145.93
> hide #!12 models
> fitmap #13 inMap #9
Fit map cryosparc_P11_J82_class_04_02800_volume.mrc z flip in map
cryosparc_P11_J78_class_00_final_volume.mrc z flip using 1904 points
correlation = 0.6289, correlation about mean = 0.2405, overlap = 106.7
steps = 768, shift = 51, angle = 106 degrees
Position of cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) relative
to cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
0.66152240 -0.10331870 0.74277410 -22.97717594
0.21670338 0.97454617 -0.05744048 -15.58127403
-0.71793298 0.19895982 0.66707364 127.12100232
Axis 0.16899848 0.96278079 0.21093286
Axis point 131.71909734 0.00000000 92.76201159
Rotation angle (degrees) 49.33983863
Shift along axis 7.92953695
> view matrix models
> #13,0.027133,0.039475,0.99885,-14.647,0.65209,0.75664,-0.047616,-35.659,-0.75765,0.65264,-0.0052118,156.91
> volume #13 level 0.2566
> fitmap #13 inMap #9
Fit map cryosparc_P11_J82_class_04_02800_volume.mrc z flip in map
cryosparc_P11_J78_class_00_final_volume.mrc z flip using 1412 points
correlation = 0.7724, correlation about mean = 0.3419, overlap = 138.5
steps = 116, shift = 21.4, angle = 3.4 degrees
Position of cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) relative
to cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
0.41516049 0.76070649 -0.49896634 43.15447657
-0.65538104 0.63047796 0.41590053 84.94532784
0.63096550 0.15434761 0.76030215 -80.29423188
Axis -0.14289182 -0.61730535 -0.77363818
Axis point 115.30069686 31.25470050 -0.00000000
Rotation angle (degrees) 66.23600210
Shift along axis 3.51505595
> view matrix models
> #13,-0.067116,0.49558,0.86596,-49.431,0.95398,0.2861,-0.089792,-25.058,-0.29225,0.82009,-0.49198,122.94
> fitmap #13 inMap #9
Fit map cryosparc_P11_J82_class_04_02800_volume.mrc z flip in map
cryosparc_P11_J78_class_00_final_volume.mrc z flip using 1412 points
correlation = 0.7723, correlation about mean = 0.3416, overlap = 138.5
steps = 172, shift = 3.33, angle = 40.7 degrees
Position of cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) relative
to cryosparc_P11_J78_class_00_final_volume.mrc z flip (#9) coordinates:
Matrix rotation and translation
0.41492115 0.76062988 -0.49928210 43.23741229
-0.65516813 0.63054509 0.41613413 84.87807239
0.63134394 0.15445087 0.75996695 -80.30121345
Axis -0.14294559 -0.61760926 -0.77338565
Axis point 115.27632866 31.16860566 0.00000000
Rotation angle (degrees) 66.25188365
Shift along axis 3.50172582
> volume #13 color #ffb2ff85
> show #5 models
> hide #5 models
> show #5 models
> view matrix models
> #13,0.050133,0.035264,0.99812,-18.344,0.69481,0.71667,-0.060219,-53.351,-0.71744,0.69653,0.011427,133.61
> select subtract #13
Nothing selected
> select add #5
14210 atoms, 14394 bonds, 891 residues, 1 model selected
> view matrix models
> #5,0.084239,0.67577,-0.73228,136.62,-0.39006,-0.65388,-0.6483,79.962,-0.91693,0.34025,0.20851,127.23
> view matrix models
> #5,-0.86525,0.48274,0.13528,148.3,-0.10522,0.088964,-0.99046,81.432,-0.49017,-0.87123,-0.02618,112.55
> view matrix models
> #5,0.34263,-0.29639,-0.89149,124.77,-0.18968,0.90756,-0.37464,105.88,0.92012,0.29746,0.25474,147.11
> fitmap #5 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 14210 atoms
average map value = 0.328, steps = 80
shifted from previous position = 7.9
rotated from previous position = 16.9 degrees
atoms outside contour = 7780, contour level = 0.25664
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.59752640 0.63605008 -0.48826478 112.59313496
0.72359505 0.69009369 0.01344968 138.69677928
0.34550312 -0.34526944 -0.87259189 133.90262217
Axis -0.39338714 -0.91434647 0.09600565
Axis point 6.79200963 0.00000000 80.87324349
Rotation angle (degrees) 152.87479227
Shift along axis -158.25419319
> view matrix models
> #5,0.39513,-0.21412,-0.89332,127.24,0.071917,0.97668,-0.20229,118.34,0.9158,0.015685,0.40132,152.1
> fitmap #5 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 14210 atoms
average map value = 0.3278, steps = 68
shifted from previous position = 2.57
rotated from previous position = 5.51 degrees
atoms outside contour = 7803, contour level = 0.25664
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.59426681 0.64679176 -0.47802445 112.61031740
0.73121680 0.68200632 0.01376121 138.87087369
0.33491634 -0.34136168 -0.87823872 133.51956482
Axis -0.39850854 -0.91225841 0.09473931
Axis point 6.82875420 0.00000000 80.32094542
Rotation angle (degrees) 153.54050874
Shift along axis -158.91274411
> view matrix models
> #5,-0.23441,0.20475,-0.95033,123.37,0.54619,0.83642,0.045484,128.37,0.80419,-0.5084,-0.3079,126.58
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.23441,0.20475,-0.95033,105.27,0.54619,0.83642,0.045484,127.38,0.80419,-0.5084,-0.3079,139.17
> volume #13 level 0.3659
> fitmap #5 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 14210 atoms
average map value = 0.3383, steps = 212
shifted from previous position = 14.4
rotated from previous position = 69.7 degrees
atoms outside contour = 8824, contour level = 0.3659
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.82937600 0.48989103 -0.26859305 121.18592557
0.31385601 0.80626828 0.50142383 143.27086379
0.46220109 0.33156935 -0.82245481 129.58536355
Axis -0.22040464 -0.94828478 -0.22842456
Axis point 34.88892331 0.00000000 55.86654750
Rotation angle (degrees) 157.33613163
Shift along axis -192.17199876
> view matrix models
> #5,0.43082,0.38394,-0.81669,124.69,-0.37916,0.89824,0.22226,125.76,0.81892,0.21391,0.53256,156.7
> view matrix models
> #5,0.43082,0.38394,-0.81669,130.39,-0.37916,0.89824,0.22226,117.96,0.81892,0.21391,0.53256,153.45
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.55726,-0.2278,-0.79848,114.2,0.64003,0.49478,-0.58784,102.3,0.52898,-0.83863,-0.12992,121.38
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.55726,-0.2278,-0.79848,99.375,0.64003,0.49478,-0.58784,115.07,0.52898,-0.83863,-0.12992,130.81
> fitmap #5 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 14210 atoms
average map value = 0.3417, steps = 156
shifted from previous position = 33.5
rotated from previous position = 39 degrees
atoms outside contour = 8572, contour level = 0.3659
Position of CDK19_CCNC_MED12_docked.pdb (#5) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.57513805 0.73370579 -0.36179004 126.11542058
0.42756581 -0.64664763 -0.63169163 147.31518370
-0.69742647 0.20862084 -0.68561917 125.41556709
Axis 0.87968000 0.35136056 -0.32048222
Axis point 0.00000000 24.67323787 100.74915915
Rotation angle (degrees) 151.46966697
Shift along axis 122.50849869
> select subtract #5
Nothing selected
> ui tool show "Fit in Map"
> select #4/D
1571 atoms, 1588 bonds, 102 residues, 1 model selected
> select #5/D
1571 atoms, 1588 bonds, 102 residues, 1 model selected
> select #5/B
7942 atoms, 8048 bonds, 504 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules false
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 7942 atoms
average map value = 0.3513, steps = 100
shifted from previous position = 13.7
rotated from previous position = 44.1 degrees
atoms outside contour = 4810, contour level = 0.37683
> view matrix models
> #5,-0.6522,0.22221,-0.72474,113.48,0.74803,0.033795,-0.6628,121.15,-0.12279,-0.97441,-0.18826,154.16
> fitmap sel inMap #1 moveWholeMolecules false
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 7942 atoms
average map value = 0.3514, steps = 96
shifted from previous position = 14
rotated from previous position = 0.0325 degrees
atoms outside contour = 4812, contour level = 0.37683
> view matrix models
> #5,-0.6522,0.22221,-0.72474,112.92,0.74803,0.033795,-0.6628,108.32,-0.12279,-0.97441,-0.18826,161.94
> fitmap sel inMap #1 moveWholeMolecules false
Fit molecule CDK19_CCNC_MED12_docked.pdb (#5) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 7942 atoms
average map value = 0.3514, steps = 72
shifted from previous position = 15
rotated from previous position = 0.0257 degrees
atoms outside contour = 4815, contour level = 0.37683
> undo
> close #5
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #2 models
> show #3 models
> show #4 models
> hide #4 models
> volume #13 level 0.2627
> select add #3
6392 atoms, 6476 bonds, 390 residues, 1 model selected
> view matrix models
> #3,0.35654,-0.65978,-0.66149,109.23,-0.77023,0.19316,-0.60781,113.38,0.5288,0.72621,-0.43931,136.91
> fitmap sel inMap #1 moveWholeMolecules false
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J79_class_00_02000_volume.mrc (#1) using 6392 atoms
average map value = 0.4408, steps = 144
shifted from previous position = 12.9
rotated from previous position = 78.7 degrees
atoms outside contour = 3311, contour level = 0.37683
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.93051,-0.17725,-0.32053,115.8,-0.1097,0.70006,-0.70561,110.65,0.34946,0.69174,0.63197,159.57
> view matrix models
> #3,0.61035,-0.44253,-0.657,109.24,0.0051649,0.83161,-0.55534,113.94,0.79212,0.33556,0.50985,150
> fitmap #3 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 6392 atoms
average map value = 0.4829, steps = 128
shifted from previous position = 18.1
rotated from previous position = 55.3 degrees
atoms outside contour = 2086, contour level = 0.26267
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.45118930 0.83137212 -0.32442044 118.91987696
0.43268372 0.52172851 0.73524428 158.37371722
0.78052099 0.19136291 -0.59511950 134.14633826
Axis -0.42015728 -0.85358536 -0.30799332
Axis point 6.62831813 0.00000000 43.61406389
Rotation angle (degrees) 139.66651009
Shift along axis -226.46671537
> view matrix models
> #3,0.60066,0.15477,-0.78439,123.62,-0.58155,0.75782,-0.29581,124.76,0.54864,0.63384,0.54519,165.2
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.60066,0.15477,-0.78439,106.61,-0.58155,0.75782,-0.29581,118.45,0.54864,0.63384,0.54519,152.08
> fitmap #3 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 6392 atoms
average map value = 0.4828, steps = 108
shifted from previous position = 18.1
rotated from previous position = 52.9 degrees
atoms outside contour = 2088, contour level = 0.26267
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.45149595 0.83115755 -0.32454358 118.89945063
0.43195956 0.52186642 0.73557214 158.38294241
0.78074474 0.19191814 -0.59464703 134.17054932
Axis -0.41986563 -0.85361751 -0.30830181
Axis point 6.65091455 0.00000000 43.60676470
Rotation angle (degrees) 139.65306814
Shift along axis -226.48526825
> view matrix models
> #3,0.77187,0.25163,-0.58386,115.88,-0.05115,0.93995,0.33747,122.41,0.63371,-0.23062,0.73839,158.41
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.68396,-0.11453,-0.72048,110.41,-0.45574,0.7041,-0.54456,105.9,0.56966,0.7008,0.42938,161.6
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.68396,-0.11453,-0.72048,111.11,-0.45574,0.7041,-0.54456,104.3,0.56966,0.7008,0.42938,149.36
> view matrix models
> #3,0.68396,-0.11453,-0.72048,113.4,-0.45574,0.7041,-0.54456,107.93,0.56966,0.7008,0.42938,150.28
> volume #13 level 0.2192
> fitmap #3 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 6392 atoms
average map value = 0.4829, steps = 136
shifted from previous position = 16.4
rotated from previous position = 62.1 degrees
atoms outside contour = 1809, contour level = 0.21921
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.45129439 0.83133953 -0.32435776 118.92459291
0.43235419 0.52166308 0.73548452 158.37468073
0.78064283 0.19168260 -0.59485675 134.14965374
Axis -0.42006066 -0.85355945 -0.30819686
Axis point 6.64650888 0.00000000 43.60083479
Rotation angle (degrees) 139.66242821
Shift along axis -226.48225024
> view matrix models
> #3,0.7718,0.2514,-0.58406,113.23,-0.050721,0.93994,0.33755,119.3,0.63384,-0.2309,0.73819,148.22
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.56392,-0.077115,-0.82222,107.09,-0.59623,0.65088,-0.46997,104.97,0.57141,0.75526,0.32107,149.75
> view matrix models
> #3,0.51672,0.085699,-0.85186,108.44,-0.74788,0.52951,-0.40038,106.5,0.41675,0.84397,0.3377,152.24
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.51672,0.085699,-0.85186,106.18,-0.74788,0.52951,-0.40038,104.51,0.41675,0.84397,0.3377,148.59
> view matrix models
> #3,0.51672,0.085699,-0.85186,98.846,-0.74788,0.52951,-0.40038,115.46,0.41675,0.84397,0.3377,134.73
> fitmap #3 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 6392 atoms
average map value = 0.4319, steps = 104
shifted from previous position = 21.5
rotated from previous position = 48.3 degrees
atoms outside contour = 2312, contour level = 0.21921
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.47069003 -0.05505584 -0.88057920 106.63768169
-0.66540201 0.67755186 0.31331072 143.18311434
0.57938849 0.73341141 -0.35555118 125.19343712
Axis 0.25659280 -0.89173192 -0.37279260
Axis point 53.39480310 0.00000000 74.75417185
Rotation angle (degrees) 125.05375265
Shift along axis -146.98967963
> show #!12 models
> hide #!13 models
> volume #12 color #ffb2b27d
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.30753,0.48539,-0.81842,107.73,-0.69567,0.70152,0.15466,127.88,0.64921,0.52179,0.55341,145.93
> fitmap #3 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 6392 atoms
average map value = 0.4427, steps = 84
shifted from previous position = 5.58
rotated from previous position = 20.3 degrees
atoms outside contour = 3160, contour level = 0.35136
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.20193388 -0.97697044 0.06893048 148.61667911
-0.92828612 0.21336011 0.30456904 130.58884097
-0.31226197 -0.00248440 -0.94999276 103.76294631
Axis -0.62422690 0.77494844 0.09897321
Axis point 135.11564681 0.00000000 30.62615582
Rotation angle (degrees) 165.76219549
Shift along axis 18.69884084
> select subtract #3
Nothing selected
> select add #2
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> view matrix models
> #2,0.16362,0.87661,-0.45253,118.06,0.81554,0.13791,0.56203,188.3,0.55509,-0.46101,-0.69234,127.95
> view matrix models
> #2,0.42978,0.57537,-0.69587,112.56,0.61176,0.38129,0.69309,190.02,0.66411,-0.72358,-0.18812,152.99
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.42978,0.57537,-0.69587,124.99,0.61176,0.38129,0.69309,188.81,0.66411,-0.72358,-0.18812,156.86
> view matrix models
> #2,0.42978,0.57537,-0.69587,126.74,0.61176,0.38129,0.69309,169.11,0.66411,-0.72358,-0.18812,138.86
> view matrix models
> #2,0.42978,0.57537,-0.69587,119.78,0.61176,0.38129,0.69309,166.04,0.66411,-0.72358,-0.18812,142.36
> fitmap #2 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 4697 atoms
average map value = 0.5134, steps = 128
shifted from previous position = 5.51
rotated from previous position = 56.8 degrees
atoms outside contour = 1822, contour level = 0.35136
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.71279283 -0.65949504 -0.23873137 123.57929111
-0.03359504 -0.30788239 0.95083111 178.30748141
-0.70056959 0.68576579 0.19730060 128.13939345
Axis -0.32255438 0.56200463 0.76164918
Axis point 76.28881859 66.50311622 0.00000000
Rotation angle (degrees) 155.73957687
Shift along axis 157.94585280
> volume #12 level 0.2615
> view matrix models
> #2,0.0040117,0.99931,0.037019,132.27,0.58155,-0.032447,0.81287,178.88,0.8135,0.018267,-0.58127,113.65
> fitmap #2 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 4697 atoms
average map value = 0.5134, steps = 52
shifted from previous position = 3.95
rotated from previous position = 0.0811 degrees
atoms outside contour = 1369, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.71334752 -0.65858154 -0.23959480 123.52648680
-0.03460560 -0.30836325 0.95063903 178.31384966
-0.69995554 0.68642731 0.19717955 128.12131280
Axis -0.32252474 0.56196498 0.76169098
Axis point 76.29755372 66.42539837 0.00000000
Rotation angle (degrees) 155.82034412
Shift along axis 157.95464018
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.37252,0.90671,-0.19774,117,0.71579,0.41635,0.56063,164.68,0.59066,0.067304,-0.80411,104.59
> fitmap #2 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 4697 atoms
average map value = 0.5242, steps = 76
shifted from previous position = 6.75
rotated from previous position = 34.5 degrees
atoms outside contour = 1304, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
0.00471287 -0.95168721 0.30703297 155.15586498
0.67917925 0.22840041 0.69753050 163.80839737
-0.73395731 0.20524305 0.64744263 155.48696143
Axis -0.24658386 0.52142586 0.81689135
Axis point 58.96216145 146.49701115 0.00000000
Rotation angle (degrees) 93.42385843
Shift along axis 174.17095525
> view matrix models
> #2,-0.011065,0.93875,-0.34442,119.43,0.65866,0.266,0.70386,166.59,0.75236,-0.21907,-0.62126,117.75
> view matrix models
> #2,0.297,0.73947,-0.60413,112.8,0.68903,0.27205,0.67173,165.45,0.66108,-0.61577,-0.42872,128.44
> fitmap #2 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 4697 atoms
average map value = 0.5134, steps = 100
shifted from previous position = 10
rotated from previous position = 44.3 degrees
atoms outside contour = 1367, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.71277598 -0.65963165 -0.23840405 123.66529205
-0.03329587 -0.30769649 0.95090181 178.37093561
-0.70060102 0.68571784 0.19735566 128.14967774
Axis -0.32247437 0.56205011 0.76164950
Axis point 76.31235368 66.55792750 0.00000000
Rotation angle (degrees) 155.72160814
Shift along axis 157.97965331
> view matrix models
> #2,0.96501,0.25853,-0.043681,141.89,0.066713,-0.08099,0.99448,181.22,0.25357,-0.9626,-0.095404,140.35
> fitmap #2 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 4697 atoms
average map value = 0.5522, steps = 100
shifted from previous position = 18.7
rotated from previous position = 47.2 degrees
atoms outside contour = 1069, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.37540917 0.21526106 -0.90151574 81.47203862
-0.91688711 0.05604496 0.39519236 143.81669168
0.13559494 0.97494699 0.17633030 129.03055536
Axis 0.35325464 -0.63192968 -0.68983769
Axis point 92.06263027 -38.22891714 0.00000000
Rotation angle (degrees) 124.85607572
Shift along axis -151.11180024
> view matrix models
> #2,0.667,0.73654,-0.11233,135.55,0.23168,-0.061741,0.97083,189.15,0.70812,-0.67357,-0.21182,143.75
> fitmap #2 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 4697 atoms
average map value = 0.5521, steps = 120
shifted from previous position = 8.16
rotated from previous position = 48.7 degrees
atoms outside contour = 1073, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.37535580 0.21522648 -0.90154622 81.52393826
-0.91692255 0.05597348 0.39512025 143.89009313
0.13550302 0.97495873 0.17633604 129.02288727
Axis 0.35330759 -0.63189556 -0.68984183
Axis point 92.11745832 -38.20893461 0.00000000
Rotation angle (degrees) 124.85650734
Shift along axis -151.12586968
> view matrix models
> #2,0.85802,0.37212,0.354,160.51,-0.29464,-0.20792,0.93271,183.62,0.42069,-0.9046,-0.068759,148.98
> fitmap #2 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 4697 atoms
average map value = 0.5522, steps = 68
shifted from previous position = 7.61
rotated from previous position = 23 degrees
atoms outside contour = 1070, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.37499478 0.21543642 -0.90164631 81.47366725
-0.91704284 0.05615375 0.39481539 143.81125197
0.13568844 0.97490200 0.17650707 129.04267983
Axis 0.35335201 -0.63187860 -0.68983461
Axis point 92.08896225 -38.26410178 0.00000000
Rotation angle (degrees) 124.83164303
Shift along axis -151.10047612
> view matrix models
> #2,0.74982,0.59514,0.28909,154.89,0.11953,-0.55159,0.82551,185.77,0.65076,-0.58443,-0.48473,130.63
> fitmap #2 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 4697 atoms
average map value = 0.5521, steps = 92
shifted from previous position = 4.37
rotated from previous position = 39.8 degrees
atoms outside contour = 1075, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.37515881 0.21548639 -0.90156613 81.51881177
-0.91691725 0.05651739 0.39505512 143.87874949
0.13608317 0.97486994 0.17638019 129.03342864
Axis 0.35317556 -0.63205072 -0.68976728
Axis point 92.10222080 -38.26951722 0.00000000
Rotation angle (degrees) 124.82910461
Shift along axis -151.15125282
> show #!13 models
> hide #!12 models
> view matrix models
> #2,0.83646,0.5102,-0.20008,135.18,0.41092,-0.34234,0.84495,187.75,0.3626,-0.78899,-0.49601,128.97
> fitmap #2 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 4697 atoms
average map value = 0.4284, steps = 124
shifted from previous position = 13
rotated from previous position = 40.4 degrees
atoms outside contour = 1305, contour level = 0.21921
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.01649135 -0.22215470 0.97487196 188.19726150
0.20969685 -0.95408923 -0.21387139 171.10885064
0.97762737 0.20090055 0.06231936 164.30398965
Axis 0.69269348 -0.00460170 0.72121742
Axis point -3.09996474 87.81603208 0.00000000
Rotation angle (degrees) 162.57899034
Shift along axis 248.07452376
> select subtract #2
Nothing selected
> select add #3
6392 atoms, 6476 bonds, 390 residues, 1 model selected
> view matrix models
> #3,0.53232,0.076666,-0.84306,100.34,-0.47955,0.848,-0.22568,120.71,0.69761,0.52442,0.48818,154.17
> fitmap #3 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 6392 atoms
average map value = 0.4829, steps = 116
shifted from previous position = 21.8
rotated from previous position = 47.6 degrees
atoms outside contour = 1813, contour level = 0.21921
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.45064720 0.83168017 -0.32438427 118.92241736
0.43368267 0.52157531 0.73476425 158.37267837
0.78027969 0.19043962 -0.59573174 134.13649081
Axis -0.42058519 -0.85354452 -0.30752211
Axis point 6.56904446 0.00000000 43.63221782
Rotation angle (degrees) 139.67639752
Shift along axis -226.44507626
> view matrix models
> #3,0.75555,0.087103,-0.64928,124.38,-0.48436,0.7416,-0.46415,120.43,0.44108,0.66517,0.6025,167.56
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.75555,0.087103,-0.64928,117.53,-0.48436,0.7416,-0.46415,107.18,0.44108,0.66517,0.6025,155.98
> fitmap #3 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 6392 atoms
average map value = 0.4829, steps = 124
shifted from previous position = 15.3
rotated from previous position = 55.9 degrees
atoms outside contour = 1809, contour level = 0.21921
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.45104480 0.83141041 -0.32452316 118.97225150
0.43300135 0.52179971 0.73500672 158.33988263
0.78042834 0.19100199 -0.59535690 134.10369412
Axis -0.42026087 -0.85361001 -0.30778361
Axis point 6.65195338 -0.00000000 43.62794542
Rotation angle (degrees) 139.66747107
Shift along axis -226.43480992
> view matrix models
> #3,0.77162,0.25072,-0.58459,120.22,-0.050071,0.94013,0.33712,127.17,0.63411,-0.23086,0.73797,160.28
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.56479,-0.42009,-0.71031,113.08,-0.26315,0.72412,-0.6375,107.38,0.78215,0.54697,0.29843,157.6
> fitmap #3 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 6392 atoms
average map value = 0.4829, steps = 100
shifted from previous position = 14.1
rotated from previous position = 66 degrees
atoms outside contour = 1811, contour level = 0.21921
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.45074595 0.83164012 -0.32434975 118.92078848
0.43242619 0.52130409 0.73569669 158.37977849
0.78091975 0.19135498 -0.59459869 134.15355422
Axis -0.42030659 -0.85341991 -0.30824800
Axis point 6.60734776 0.00000000 43.58157620
Rotation angle (degrees) 139.64262672
Shift along axis -226.50021217
> view matrix models
> #3,0.77172,0.2523,-0.58377,127.12,-0.050245,0.93925,0.33952,134.73,0.63397,-0.23269,0.73752,160.1
> view matrix models
> #3,0.96253,-0.10376,-0.25052,128.81,-0.26888,-0.48474,-0.8323,99.566,-0.035074,0.86848,-0.49448,151.51
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.96253,-0.10376,-0.25052,116.27,-0.26888,-0.48474,-0.8323,103.6,-0.035074,0.86848,-0.49448,120.76
> view matrix models
> #3,0.96253,-0.10376,-0.25052,103.55,-0.26888,-0.48474,-0.8323,105.79,-0.035074,0.86848,-0.49448,123.23
> view matrix models
> #3,0.96253,-0.10376,-0.25052,113.54,-0.26888,-0.48474,-0.8323,116,-0.035074,0.86848,-0.49448,123.4
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.93539,0.23693,0.26252,127.29,0.13346,0.45094,-0.88252,120.48,-0.32748,0.86053,0.39019,143.53
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.93539,0.23693,0.26252,118.69,0.13346,0.45094,-0.88252,111.23,-0.32748,0.86053,0.39019,143.36
> fitmap #3 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 6392 atoms
average map value = 0.4837, steps = 120
shifted from previous position = 12.6
rotated from previous position = 47.8 degrees
atoms outside contour = 1913, contour level = 0.21921
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.75901444 0.33078954 -0.56078101 118.15657180
-0.30530066 0.94158035 0.14218978 141.13686822
0.57505527 0.06328273 0.81566336 142.78059487
Axis -0.06050184 -0.87090051 -0.48772106
Axis point -16.06925715 0.00000000 196.05994143
Rotation angle (degrees) 40.70046161
Shift along axis -199.70196354
> select subtract #3
Nothing selected
> show #4 models
> select add #4
1571 atoms, 1588 bonds, 102 residues, 1 model selected
> view matrix models
> #4,0.82774,0.3434,-0.44375,93.612,0.49614,-0.81731,0.29299,140.93,-0.26207,-0.46268,-0.8469,115.27
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.82952,-0.34485,0.43928,120.47,-0.54932,-0.64563,0.53048,137.39,0.10068,-0.68135,-0.725,122.71
> view matrix models
> #4,0.095036,-0.29996,0.9492,121.93,-0.98765,-0.1477,0.052211,119.16,0.12453,-0.94245,-0.3103,133.19
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.095036,-0.29996,0.9492,121.88,-0.98765,-0.1477,0.052211,134.2,0.12453,-0.94245,-0.3103,127.84
> fitmap #4 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 1571 atoms
average map value = 0.4674, steps = 92
shifted from previous position = 28.6
rotated from previous position = 39.4 degrees
atoms outside contour = 667, contour level = 0.21921
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.47267663 0.87575962 0.09809119 119.41039139
-0.78059284 -0.46774903 0.41459095 156.20236127
0.40896407 0.11939818 0.90470572 115.36275026
Axis -0.17253344 -0.18169811 -0.96810021
Axis point 86.39592479 40.58561210 0.00000000
Rotation angle (degrees) 121.18881184
Shift along axis -160.66666099
> view matrix models
> #4,0.35697,0.14658,0.92254,102.4,-0.91247,0.26608,0.3108,133.89,-0.19991,-0.95274,0.22874,146.82
> fitmap #4 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 1571 atoms
average map value = 0.4673, steps = 76
shifted from previous position = 12.7
rotated from previous position = 0.142 degrees
atoms outside contour = 666, contour level = 0.21921
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.47243548 0.87570880 0.09969356 119.34971743
-0.78112387 -0.46840742 0.41284378 156.23297560
0.40822814 0.11716904 0.90532933 115.40576150
Axis -0.17280253 -0.18031826 -0.96831018
Axis point 86.42501173 40.70756636 0.00000000
Rotation angle (degrees) 121.18190131
Shift along axis -160.54416438
> view matrix models
> #4,0.35623,0.14433,0.92318,93.414,-0.91264,0.26571,0.31062,125.68,-0.20046,-0.95319,0.22638,147.52
> view matrix models
> #4,0.35623,0.14433,0.92318,95.158,-0.91264,0.26571,0.31062,129.23,-0.20046,-0.95319,0.22638,144.31
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.83349,0.48271,0.26886,80.466,-0.5513,0.69415,0.46285,114.88,0.036792,-0.534,0.84468,132.31
> view matrix models
> #4,0.4915,0.70642,0.50931,74.29,-0.86222,0.31247,0.39868,127.94,0.12249,-0.63508,0.76267,135.29
> fitmap #4 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 1571 atoms
average map value = 0.4672, steps = 100
shifted from previous position = 18.5
rotated from previous position = 41.6 degrees
atoms outside contour = 666, contour level = 0.21921
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.47284513 0.87560472 0.09866029 119.35220853
-0.78095715 -0.46830051 0.41328023 156.23519716
0.40807279 0.11836809 0.90524338 115.37707644
Axis -0.17238054 -0.18085621 -0.96828507
Axis point 86.42012726 40.66516107 0.00000000
Rotation angle (degrees) 121.19491726
Shift along axis -160.54800451
> view matrix models
> #4,0.51651,0.23371,-0.82377,98.089,-0.80803,0.4514,-0.37858,125.4,0.28337,0.86117,0.42199,96.869
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.51651,0.23371,-0.82377,88.305,-0.80803,0.4514,-0.37858,125.76,0.28337,0.86117,0.42199,84.638
> fitmap #4 inMap #13
Fit molecule CDK19_CCNC_MED12_docked.pdb (#4) to map
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) using 1571 atoms
average map value = 0.5157, steps = 104
shifted from previous position = 23.3
rotated from previous position = 40.1 degrees
atoms outside contour = 388, contour level = 0.21921
Position of CDK19_CCNC_MED12_docked.pdb (#4) relative to
cryosparc_P11_J82_class_04_02800_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
-0.85614362 -0.05331405 -0.51398025 137.33028878
0.17801176 0.90334983 -0.39021902 101.27571385
0.48510813 -0.42557806 -0.76390667 124.70749283
Axis -0.03445869 -0.97364851 0.22543554
Axis point 46.78773450 0.00000000 93.18131450
Rotation angle (degrees) 149.13184893
Shift along axis -75.22566776
> view matrix models
> #4,0.44755,-0.39559,-0.802,113.18,-0.4965,0.63598,-0.59077,111.51,0.74377,0.66259,0.088224,73.014
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.52435,-0.40998,-0.7463,113.8,-0.36313,0.68509,-0.63149,109.52,0.77019,0.60213,0.21035,75.519
> view matrix models
> #4,0.54394,-0.41522,-0.7292,114.02,-0.32483,0.69706,-0.63922,109.03,0.77371,0.58456,0.24428,76.246
> view matrix models
> #4,0.64094,-0.4555,-0.61783,115.71,-0.095695,0.7512,-0.6531,106.86,0.7616,0.47772,0.43788,80.658
> view matrix models
> #4,-0.70543,0.3402,0.62179,95.455,-0.70665,-0.4054,-0.57991,147.08,0.054791,-0.84848,0.52639,126.81
> view matrix models
> #4,0.047918,0.8283,0.55823,77.724,-0.76213,0.39157,-0.51559,120.42,-0.64565,-0.40074,0.65004,113.03
> view matrix models
> #4,0.05736,0.79548,0.60326,79.005,-0.81003,0.39029,-0.43763,120.84,-0.58357,-0.46356,0.66675,115.14
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.05736,0.79548,0.60326,85.004,-0.81003,0.39029,-0.43763,120.95,-0.58357,-0.46356,0.66675,127.22
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!6 models
> hide #!6 models
> show #!12 models
> select subtract #4
Nothing selected
> hide #4 models
> select add #2
4697 atoms, 4758 bonds, 285 residues, 1 model selected
> view matrix models
> #2,0.98236,0.15574,0.10353,164.93,0.079953,-0.85022,0.52033,188.48,0.16906,-0.50287,-0.84767,112.27
> fitmap #2 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#2) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 4697 atoms
average map value = 0.5028, steps = 176
shifted from previous position = 3.63
rotated from previous position = 30.1 degrees
atoms outside contour = 1336, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#2) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.76849861 0.45598200 0.44887672 112.55686257
-0.08749385 -0.76983071 0.63222268 181.78514206
0.63384124 0.44658829 0.63150945 161.06431632
Axis -0.30766994 -0.30655971 -0.90075544
Axis point 38.16754362 60.04525505 0.00000000
Rotation angle (degrees) 162.44159592
Shift along axis -235.43792145
> show #!6 models
> show #4 models
> hide #!6 models
> hide #4 models
> hide #3 models
> show #3 models
> select add #3
11089 atoms, 11234 bonds, 675 residues, 2 models selected
> select subtract #2
6392 atoms, 6476 bonds, 390 residues, 1 model selected
> view matrix models
> #3,0.60126,0.11295,0.79103,134.88,0.27395,0.90082,-0.33685,120.88,-0.75063,0.41924,0.51069,148.48
> view matrix models
> #3,0.60126,0.11295,0.79103,132.75,0.27395,0.90082,-0.33685,129.66,-0.75063,0.41924,0.51069,148.17
> fitmap #3 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 6392 atoms
average map value = 0.413, steps = 88
shifted from previous position = 6.88
rotated from previous position = 37.2 degrees
atoms outside contour = 2835, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.72717165 -0.56223738 -0.39384069 138.37270055
0.16362696 0.41522657 -0.89488161 124.27373982
0.66666902 -0.71517550 -0.20994381 116.33715557
Axis 0.13848751 -0.81726408 0.55937522
Axis point 51.30678096 0.00000000 132.43030258
Rotation angle (degrees) 139.54752951
Shift along axis -17.32545032
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.71564,0.12158,-0.6878,110.59,-0.69647,0.19858,-0.68956,128.24,0.05274,0.97251,0.22679,139.61
> view matrix models
> #3,0.30739,-0.15167,-0.93942,106.4,-0.68219,0.65314,-0.32867,139.67,0.66342,0.7419,0.097297,129.67
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.30739,-0.15167,-0.93942,108.61,-0.68219,0.65314,-0.32867,116.18,0.66342,0.7419,0.097297,139.91
> fitmap #3 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 6392 atoms
average map value = 0.4427, steps = 116
shifted from previous position = 7.33
rotated from previous position = 52.4 degrees
atoms outside contour = 2565, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.20193511 -0.97690081 0.06990716 148.61431959
-0.92807988 0.21366787 0.30498163 130.63344045
-0.31287370 -0.00329294 -0.94978903 103.73526662
Axis -0.62416307 0.77501587 0.09884768
Axis point 135.15396702 0.00000000 30.56586838
Rotation angle (degrees) 165.70287800
Shift along axis 18.73740995
> view matrix models
> #3,0.17263,0.59472,-0.78518,109.15,-0.50563,0.73761,0.44752,134.12,0.84531,0.31975,0.42804,150.5
> fitmap #3 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 6392 atoms
average map value = 0.4426, steps = 64
shifted from previous position = 1.08
rotated from previous position = 0.0898 degrees
atoms outside contour = 2566, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.20048020 -0.97716317 0.07042599 148.64347370
-0.92832647 0.21244850 0.30508293 130.70909482
-0.31307769 -0.00421523 -0.94971817 103.77614944
Axis -0.62471673 0.77459615 0.09863978
Axis point 135.30395374 0.00000000 30.55750157
Rotation angle (degrees) 165.66737606
Shift along axis 18.62315327
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.30904,0.43293,-0.8468,105.51,-0.77222,0.63394,0.042278,126.6,0.55513,0.64085,0.53023,157.23
> fitmap #3 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 6392 atoms
average map value = 0.4644, steps = 104
shifted from previous position = 15.5
rotated from previous position = 40.4 degrees
atoms outside contour = 2497, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.09520008 -0.95647904 -0.27583474 136.29132155
-0.89093852 0.20546803 -0.40498326 119.84946530
0.44403322 0.20719735 -0.87172459 116.59368584
Axis 0.64627575 -0.75996071 0.06919077
Axis point 99.84627756 0.00000000 85.79151323
Rotation angle (degrees) 151.73034497
Shift along axis 5.06809850
> view matrix models
> #3,0.76837,0.019678,-0.6397,114.79,-0.50362,0.63537,-0.58538,113.19,0.39493,0.77195,0.49811,148.61
> fitmap #3 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 6392 atoms
average map value = 0.4502, steps = 156
shifted from previous position = 8.24
rotated from previous position = 80.7 degrees
atoms outside contour = 2484, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.46081193 -0.49055415 0.73960057 160.13016141
0.09679225 -0.85616281 -0.50755938 125.25536275
0.88220384 -0.16230181 0.44201187 131.34449409
Axis 0.49600942 -0.20486899 0.84380291
Axis point 24.53947313 86.92707242 0.00000000
Rotation angle (degrees) 159.63280812
Shift along axis 164.59399477
> view matrix models
> #3,0.96086,0.15298,-0.23096,115.25,-0.21444,-0.11708,-0.96969,119.21,-0.17539,0.98127,-0.079694,133.44
> view matrix models
> #3,0.8427,-0.1812,-0.50698,107.54,-0.47719,0.18465,-0.85918,126.51,0.24929,0.96596,0.069141,132.69
> fitmap #3 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 6392 atoms
average map value = 0.4495, steps = 128
shifted from previous position = 15.4
rotated from previous position = 44.8 degrees
atoms outside contour = 2540, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.50270321 -0.41434988 0.75868547 159.90329772
-0.13443660 -0.82949197 -0.54209766 123.04936706
0.85394160 -0.37450932 0.36128448 130.61190979
Axis 0.49309666 -0.28027298 0.82359137
Axis point 32.24555287 88.16469190 0.00000000
Rotation angle (degrees) 170.21598519
Shift along axis 151.93121126
> fitmap #3 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 6392 atoms
average map value = 0.4496, steps = 48
shifted from previous position = 0.0179
rotated from previous position = 0.284 degrees
atoms outside contour = 2545, contour level = 0.26151
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.50278627 -0.41182523 0.76000390 159.91558711
-0.13930724 -0.82911972 -0.54143695 123.04544341
0.85311162 -0.37810111 0.35949977 130.56867024
Axis 0.49334312 -0.28122458 0.82311925
Axis point 32.43886752 88.13314906 -0.00000000
Rotation angle (degrees) 170.47140593
Shift along axis 151.76343857
> view matrix models
> #3,0.63361,0.11854,-0.76452,111.03,-0.64475,0.62708,-0.43712,137.99,0.4276,0.76988,0.47375,138.63
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.63361,0.11854,-0.76452,113.69,-0.64475,0.62708,-0.43712,117.21,0.4276,0.76988,0.47375,144.16
> volume #12 level 0.1717
> fitmap #3 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 6392 atoms
average map value = 0.4644, steps = 116
shifted from previous position = 9.3
rotated from previous position = 50.9 degrees
atoms outside contour = 1912, contour level = 0.17166
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.09483544 -0.95647697 -0.27596744 136.29112728
-0.89080287 0.20528445 -0.40537453 119.84237245
0.44438324 0.20738871 -0.87150069 116.60015569
Axis 0.64637725 -0.75986655 0.06927675
Axis point 99.83718430 0.00000000 85.82000356
Rotation angle (degrees) 151.70586032
Shift along axis 5.10895396
> view matrix models
> #3,0.61297,0.72863,-0.30554,125.4,-0.74398,0.66248,0.087282,127.5,0.26601,0.17381,0.94817,153.58
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.68787,0.27386,-0.67218,113.1,-0.58142,0.76226,-0.28443,119.62,0.43448,0.58648,0.68357,150.77
> volume #12 level 0.4312
> fitmap #3 inMap #12
Fit molecule CDK19_CCNC_MED12_docked.pdb (#3) to map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) using 6392 atoms
average map value = 0.4644, steps = 104
shifted from previous position = 11
rotated from previous position = 36.6 degrees
atoms outside contour = 3450, contour level = 0.43123
Position of CDK19_CCNC_MED12_docked.pdb (#3) relative to
cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.09525261 -0.95654999 -0.27557039 136.29891478
-0.89086595 0.20543357 -0.40516030 119.84928745
0.44416750 0.20690369 -0.87172592 116.58583920
Axis 0.64626473 -0.75995519 0.06935431
Axis point 99.85484979 0.00000000 85.79517253
Rotation angle (degrees) 151.73568792
Shift along axis 5.09082405
> open /Users/bsingal/Downloads/cryosparc_P11_J93_class_00_final_volume.mrc
Opened cryosparc_P11_J93_class_00_final_volume.mrc as #5, grid size
128,128,128, pixel 2.16, shown at level 0.027, step 1, values float32
> select subtract #3
Nothing selected
> hide #3 models
> hide #2 models
> show #!13 models
> hide #!13 models
> select add #5
2 models selected
> volume flip #5 axis z
Opened cryosparc_P11_J93_class_00_final_volume.mrc z flip as #14, grid size
128,128,128, pixel 2.16, shown at step 1, values float32
> select subtract #5
Nothing selected
> select add #14
2 models selected
> fitmap #14 inMap #12
Fit map cryosparc_P11_J93_class_00_final_volume.mrc z flip in map
cryosparc_P11_J82_class_01_02800_volume.mrc z flip using 20967 points
correlation = 0.6903, correlation about mean = 0.3395, overlap = 1099
steps = 196, shift = 9.91, angle = 75.5 degrees
Position of cryosparc_P11_J93_class_00_final_volume.mrc z flip (#14) relative
to cryosparc_P11_J82_class_01_02800_volume.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.73420665 -0.15415460 0.66119358 166.04292231
-0.47800403 0.80896483 -0.34218131 144.46049425
-0.48213353 -0.56728499 -0.66763388 370.84000143
Axis -0.18612212 0.94533534 -0.26776791
Axis point 163.57143251 0.00000000 176.10568893
Rotation angle (degrees) 142.79127586
Shift along axis 6.36029752
> volume #14 level 0.08379
> show #3 models
> show #2 models
> hide #!12 models
> volume #14 color #99bfe597
> volume #14 color #99bfe596
> select add #3
6392 atoms, 6476 bonds, 390 residues, 3 models selected
> hide #2 models
> select subtract #14
6392 atoms, 6476 bonds, 390 residues, 1 model selected
> view matrix models
> #3,-0.69289,0.66451,-0.27989,140.46,0.48193,0.71552,0.50574,127.51,0.53634,0.21554,-0.81602,115.79
> view matrix models
> #3,-0.092037,0.37916,0.92074,156.75,0.22502,-0.89283,0.39016,112.09,0.97,0.24309,-0.0031447,128.68
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
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 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
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 Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13051.0.0,0)
OS Loader Version: 582~3311
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 6 days, 9 hours, 50 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-020
Option ROM Version: 113-D32207P1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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-Clipper: 0.22.4
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-ISOLDE: 1.7.1
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 , 8 months ago
| Component: | Unassigned → Core |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 8 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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