![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Last modified 13 months ago
#16044 feedback defect
Unknown crash
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.6-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff853245dc0 (most recent call first):
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.coulombic._esp (total: 61)
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{
"uptime" : 37000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,4",
"coalitionID" : 5577,
"osVersion" : {
"train" : "macOS 14.6",
"build" : "23G80",
"releaseType" : "User"
},
"captureTime" : "2024-09-30 13:26:17.6671 -0400",
"codeSigningMonitor" : 0,
"incident" : "6B9C08D8-3C20-41E3-9E64-D371AD0C8039",
"pid" : 26695,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-30 10:44:58.9487 -0400",
"procStartAbsTime" : 27808912585639,
"procExitAbsTime" : 37487454607638,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"FAD1F7A5-AFC8-5CA0-970D-04CC3EEAC657","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "2145464F-803C-5923-4D0A-4BF9FED76F62",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 12102,
"bridgeVersion" : {"build":"21P6074","train":"8.6"},
"sleepWakeUUID" : "14E263A2-A73A-4E25-8402-F12A13CBBA69",
"sip" : "enabled",
"vmRegionInfo" : "0x6c is not in any region. Bytes before following region: 4403027860\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10670e000-106712000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x000000000000006c","rawCodes":[1,108],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000006c"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":26695},
"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" : "0x6c is not in any region. Bytes before following region: 4403027860\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10670e000-106712000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_4.cxs
Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83,
shown at level 0.047, step 1, values float32
Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.38, shown at level 0.0748, step 1, values float32
Opened cryosparc_P30_J276_map_sharp.mrc z flip as #7, grid size 300,300,300,
pixel 0.83, shown at level 0.00111, step 1, values float32
Opened cryosparc_P30_J366_003_volume_map_sharp.mrc z flip as #9, grid size
300,300,300, pixel 0.83, shown at level 0.0455, step 1, values float32
Log from Fri Sep 27 17:28:16 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs
Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83,
shown at level 0.047, step 1, values float32
Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32
Log from Thu Sep 26 13:21:30 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs
Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83,
shown at level 0.047, step 1, values float32
Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid
size 180,180,180, pixel 1.38, shown at level 0.0903, step 1, values float32
Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size
180,180,180, pixel 1.38, shown at level 0.0709, step 1, values float32
Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size
180,180,180, pixel 1.38, shown at level 0.0781, step 1, values float32
Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size
180,180,180, pixel 1.38, shown at level 0.0892, step 1, values float32
Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32
Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size
180,180,180, pixel 1.38, shown at level 0.0708, step 1, values float32
Log from Thu Sep 26 13:06:28 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/ruchigautamsharma/Desktop/25HepE525K/interaction
> 25HepE525K.cxs"
Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83,
shown at level 0.047, step 1, values float32
Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid
size 180,180,180, pixel 1.38, shown at level 0.0903, step 1, values float32
Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size
180,180,180, pixel 1.38, shown at level 0.0709, step 1, values float32
Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size
180,180,180, pixel 1.38, shown at level 0.0781, step 1, values float32
Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size
180,180,180, pixel 1.38, shown at level 0.0892, step 1, values float32
Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32
Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size
180,180,180, pixel 1.38, shown at level 0.0708, step 1, values float32
Log from Wed Sep 25 04:14:14 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_20240903.cxs
Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83,
shown at level 0.033, step 1, values float32
Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid
size 180,180,180, pixel 1.38, shown at level 0.0903, step 1, values float32
Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size
180,180,180, pixel 1.38, shown at level 0.0709, step 1, values float32
Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size
180,180,180, pixel 1.38, shown at level 0.0781, step 1, values float32
Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size
180,180,180, pixel 1.38, shown at level 0.0892, step 1, values float32
Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32
Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size
180,180,180, pixel 1.38, shown at level 0.0708, step 1, values float32
Log from Tue Sep 3 19:15:56 2024 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: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ruchigautamsharma/Downloads/cryosparc_P30_J277_005_volume_map_sharp.mrc
Opened cryosparc_P30_J277_005_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.83, shown at level 0.061, step 2, values float32
> set bgColor white
> color #1 #699dbfff models
> color #1 #6b98bfff models
> surface dust #1 size 8.3
> transparency 50
> volume #1 level 0.04162
> volume #1 step 1
> volume #1 level 0.04802
> open /Users/ruchigautamsharma/Desktop/pdbs/8g4l.pdb
Summary of feedback from opening
/Users/ruchigautamsharma/Desktop/pdbs/8g4l.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER CONTRACTILE PROTEIN 2023-02-10 XXXX
Chain information for 8g4l.pdb #2
---
Chain | Description
A B | No description available
C D | No description available
E F | No description available
G H | No description available
I J | No description available
K L | No description available
M N | No description available
> ui mousemode right select
Drag select of 62714 atoms, 4 pseudobonds
> ui mousemode right translate
> select /E
5809 atoms, 5816 bonds, 355 residues, 1 model selected
> hide sel atoms
> select /F
5809 atoms, 5816 bonds, 355 residues, 1 model selected
> hide sel atoms
> select /G
5820 atoms, 5829 bonds, 357 residues, 1 model selected
> hide sel atoms
> select /H
5820 atoms, 5829 bonds, 357 residues, 1 model selected
> hide sel atoms
> select /I
5683 atoms, 5699 bonds, 350 residues, 1 model selected
> hide sel atoms
> select /J
5683 atoms, 5699 bonds, 350 residues, 1 model selected
> hide sel atoms
> select /K
5823 atoms, 5842 bonds, 359 residues, 1 model selected
> hide sel atoms
> select /L
5823 atoms, 5842 bonds, 359 residues, 1 model selected
> hide sel atoms
> select /L
5823 atoms, 5842 bonds, 359 residues, 1 model selected
> select /M
5809 atoms, 5829 bonds, 358 residues, 1 model selected
> hide sel atoms
> select /M
5809 atoms, 5829 bonds, 358 residues, 1 model selected
> select /N
5809 atoms, 5829 bonds, 358 residues, 1 model selected
> hide sel atoms
> ui mousemode right select
Drag select of 39683 atoms, 4 pseudobonds
> select clear
Drag select of 31714 atoms, 4 pseudobonds
> select clear
Drag select of 41883 atoms, 4 pseudobonds
> show sel cartoons
> hide sel atoms
> ui mousemode right "translate selected models"
> select add #2
99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 2 models selected
> view matrix models #2,1,0,0,-145.97,0,1,0,-273.41,0,0,1,-71.128
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.33201,0.77488,0.53789,-305.02,0.61793,-0.25218,0.7447,-219.31,0.7127,0.57962,-0.39509,36.051
> view matrix models
> #2,0.68978,-0.71496,0.11413,226.44,-0.050952,0.10931,0.9927,-277.33,-0.72222,-0.69057,0.038968,877.43
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.68978,-0.71496,0.11413,251.77,-0.050952,0.10931,0.9927,-152.19,-0.72222,-0.69057,0.038968,779.18
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.78513,-0.60169,0.14676,156.66,0.1682,0.43522,0.88447,-322.45,-0.59606,-0.66974,0.44291,558.11
> view matrix models
> #2,-0.50413,0.63042,0.59027,-182.3,0.83794,0.19158,0.51104,-264.56,0.20909,0.75224,-0.62484,116.61
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.50413,0.63042,0.59027,-238.07,0.83794,0.19158,0.51104,-324.86,0.20909,0.75224,-0.62484,-90.886
> view matrix models
> #2,-0.50413,0.63042,0.59027,-157.14,0.83794,0.19158,0.51104,-349.51,0.20909,0.75224,-0.62484,-89.187
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.64055,0.44273,0.62745,-45.163,0.76397,0.28458,0.57911,-397.18,0.077832,0.8503,-0.52052,-136.51
> view matrix models
> #2,-0.53777,0.61178,0.58011,-133.79,0.81962,0.21814,0.52975,-363.7,0.19755,0.76035,-0.61874,-91.81
> ui mousemode right select
Drag select of 57 atoms, 260 residues
> hide sel cartoons
> hide sel atoms
Drag select of 68 residues
Drag select of 120 residues
> hide sel cartoons
> select add #2
99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.53777,0.61178,0.58011,-133.74,0.81962,0.21814,0.52975,-360.37,0.19755,0.76035,-0.61874,-108
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.82313,0.40245,0.40062,100.33,0.56745,0.60968,0.55344,-466.49,-0.021518,0.68288,-0.73021,26.515
> open /Users/ruchigautamsharma/Desktop/pdbs/8act.pdb
8act.pdb title:
Structure of the human β-cardiac myosin folded-back off state [more info...]
Chain information for 8act.pdb #3
---
Chain | Description | UniProt
A B | myosin-7 | MYH7_HUMAN 3-906
C D | myosin light chain 3 | MYL3_HUMAN 39-195
E F | myosin regulatory light chain 2, ventricular/cardiac muscle isoform |
MLRV_HUMAN 20-163
Non-standard residues in 8act.pdb #3
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
PO4 — phosphate ion
> select add #3
118674 atoms, 119507 bonds, 23 pseudobonds, 8474 residues, 5 models selected
> select subtract #2
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,4.2373,0,1,0,-97.37,0,0,1,-63.243
> view matrix models #3,1,0,0,2.676,0,1,0,-7.5822,0,0,1,-6.9289
> view matrix models #3,1,0,0,-28.537,0,1,0,-116.48,0,0,1,-73.257
> view matrix models #3,1,0,0,-74.431,0,1,0,-86.716,0,0,1,-91.941
> view matrix models #3,1,0,0,-77.549,0,1,0,-89.295,0,0,1,-82.343
> hide #!1 models
> open /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J279_map.mrc
Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83,
shown at level 0.0557, step 2, values float32
> select subtract #3
Nothing selected
> select add #4
2 models selected
> view matrix models #4,1,0,0,-3.5551,0,1,0,1.2444,0,0,1,9.7098
> view matrix models #4,1,0,0,-29.5,0,1,0,31.846,0,0,1,74.225
> volume #4 level 0.03328
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.91868,-0.12918,-0.37327,255.55,-0.23246,-0.5872,0.77534,174.17,-0.31934,0.79907,0.50942,65.389
> view matrix models
> #4,-0.91602,-0.1276,-0.38031,255.91,-0.21581,-0.6424,0.73535,184.54,-0.33814,0.75567,0.56091,66.973
> view matrix models
> #4,-0.8978,-0.097493,-0.42947,255.87,-0.045054,-0.94974,0.30978,258.35,-0.43809,0.29747,0.84829,104
> view matrix models
> #4,0.93714,0.02002,0.34839,-67.977,0.070672,-0.98855,-0.1333,304.93,0.34173,0.14954,-0.92782,253.19
> transparency sel 50
> view matrix models
> #4,0.98946,0.13009,0.063575,-53.463,0.13724,-0.98257,-0.1254,295.46,0.046154,0.13281,-0.99007,297.27
> surface dust #4 size 8.3
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.98946,0.13009,0.063575,-55.693,0.13724,-0.98257,-0.1254,243.61,0.046154,0.13281,-0.99007,230.84
> select subtract #4
Nothing selected
> select add #4
2 models selected
> hide #!2 models
> view matrix models
> #4,0.98946,0.13009,0.063575,-17.14,0.13724,-0.98257,-0.1254,238.58,0.046154,0.13281,-0.99007,218.87
> view matrix models
> #4,0.98946,0.13009,0.063575,-14.137,0.13724,-0.98257,-0.1254,247.93,0.046154,0.13281,-0.99007,226.91
> fitmap #3 inMap #4
Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834
atoms
average map value = 0.06921, steps = 132
shifted from previous position = 3.77
rotated from previous position = 11.1 degrees
atoms outside contour = 3445, contour level = 0.033285
Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99530642 -0.04985030 0.08294620 -93.88397645
-0.05708112 -0.99455248 0.08721873 330.44446938
0.07814647 -0.09154402 -0.99272998 332.89917405
Axis -0.99882356 0.02681814 -0.04040165
Axis point 0.00000000 171.51399022 160.98585768
Rotation angle (degrees) 174.86592494
Shift along axis 89.18575633
> color #4 #a1d7ff80 models
> color #4 #76ffcf80 models
> view matrix models
> #4,0.98946,0.13009,0.063575,-14.422,0.13724,-0.98257,-0.1254,247.38,0.046154,0.13281,-0.99007,228.5
> fitmap #3 inMap #4
Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834
atoms
average map value = 0.06921, steps = 72
shifted from previous position = 1.7
rotated from previous position = 0.0115 degrees
atoms outside contour = 3448, contour level = 0.033285
Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99528837 -0.04999379 0.08307632 -93.87652160
-0.05723957 -0.99453995 0.08725781 330.47220450
0.07826037 -0.09160194 -0.99271567 332.89509969
Axis -0.99881903 0.02689404 -0.04046312
Axis point 0.00000000 171.52859786 160.98201658
Rotation angle (degrees) 174.86310814
Shift along axis 89.18341503
> ui mousemode right translate
> show #!2 models
> hide #!3 models
> select add #2
99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 4 models selected
> select subtract #2
2 models selected
> select add #2
99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 4 models selected
> select subtract #4
99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.82313,0.40245,0.40062,100.26,0.56745,0.60968,0.55344,-467.99,-0.021518,0.68288,-0.73021,28.334
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.98302,0.15318,0.10103,348.35,0.18276,0.76793,0.61391,-438.53,0.016457,0.62195,-0.78289,59.345
> view matrix models
> #2,-0.8026,0.36897,0.46871,89.465,0.5558,0.74787,0.36301,-472.01,-0.2166,0.55187,-0.80531,169.18
> fitmap #2 inMap #4
Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840
atoms
average map value = 0.03324, steps = 1916
shifted from previous position = 40
rotated from previous position = 19.9 degrees
atoms outside contour = 75314, contour level = 0.033285
Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.89768062 0.39496708 0.19537273 171.38448995
-0.43446605 -0.71933681 -0.54202750 713.12497930
-0.07354423 -0.57145040 0.81733450 187.01973679
Axis -0.03372507 0.30823754 -0.95071144
Axis point 167.14028490 366.03689970 0.00000000
Rotation angle (degrees) 154.13723635
Shift along axis 36.23013114
> volume #4 step 1
> select subtract #2
Nothing selected
> color #4 #7cc1f980 models
> show #!3 models
> save /Users/ruchigautamsharma/Desktop/image5.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie4.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie4.mp4
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:524-525
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #2/A:524-526
56 atoms, 55 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 56 atom styles
> rainbow sel
> select #2/A:940
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/A:939-940
44 atoms, 43 bonds, 2 residues, 1 model selected
> select
> #2/A:10-16,20-27,82-84,90-92,98-111,136-142,154-168,184-199,216-231,271-273,284-291,295-301,307-309,311-314,325-338,343-359,379-388,393-400,417-447,473-504,518-524,530-539,545-555,604-611,615-618,647-662,686-696,698-707,715-723,738-748,753-755,769-826,829-836,842-919,922-1171
11821 atoms, 11850 bonds, 720 residues, 1 model selected
> ui mousemode right translate
> select #2/A:903
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:903-904
39 atoms, 38 bonds, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> select #2/B:903
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/B:903-904
39 atoms, 38 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 39 atom styles
> rainbow sel
> close #1
> volume #4 level 0.04236
> ui mousemode right distance
> distance #2/B:903@OE2 #2/A:525@CD
Distance between 8g4l.pdb #2/B GLU 903 OE2 and /A GLU 525 CD: 7.678Å
> save /Users/ruchigautamsharma/Desktop/image6.png supersample 3
> open
> "/Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_00_00027_volume
> (1).mrc"
Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc as #5, grid size
180,180,180, pixel 1.38, shown at level 0.123, step 1, values float32
> flip volume #5
Unknown command: flip volume #5
> volume flip #5
Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid
size 180,180,180, pixel 1.38, shown at step 1, values float32
> select add #6
39 atoms, 38 bonds, 2 residues, 3 models selected
> select add #2
99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 5 models selected
> select subtract #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-12.543,0,1,0,-4.9141,0,0,1,-59.886
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.97719,-0.1898,-0.095255,24.452,0.21213,0.85157,0.47941,-74.838,-0.0098755,-0.48869,0.8724,14.37
> view matrix models
> #6,0.9436,-0.26902,-0.193,50.243,0.32425,0.63294,0.70303,-91.715,-0.066973,-0.72595,0.68448,72.907
> view matrix models
> #6,0.94098,-0.27295,-0.20014,51.932,0.33074,0.6159,0.71504,-92.063,-0.071902,-0.73903,0.66983,76.899
> view matrix models
> #6,-0.96802,-0.2488,0.032094,272.71,-0.24873,0.93529,-0.25172,66.645,0.032612,-0.25166,-0.96727,208.41
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.96802,-0.2488,0.032094,298.35,-0.24873,0.93529,-0.25172,67.863,0.032612,-0.25166,-0.96727,270.44
> view matrix models
> #6,-0.96802,-0.2488,0.032094,280.09,-0.24873,0.93529,-0.25172,73.622,0.032612,-0.25166,-0.96727,274.5
> view matrix models
> #6,-0.96802,-0.2488,0.032094,279.77,-0.24873,0.93529,-0.25172,74.716,0.032612,-0.25166,-0.96727,273.45
> close #5
> hide #!2 models
> hide #!3 models
> hide #!4 models
> volume #6 level 0.09029
> surface dust #6 size 13.8
> ui mousemode right translate
> select subtract #6
Nothing selected
> save /Users/ruchigautamsharma/Desktop/image7.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!3 models
> fitmap #4 inMap #6
Fit map cryosparc_P30_J279_map.mrc in map
cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip using 398148 points
correlation = 0.9513, correlation about mean = 0.6514, overlap = 4478
steps = 120, shift = 2.21, angle = 10.5 degrees
Position of cryosparc_P30_J279_map.mrc (#4) relative to
cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.99999913 -0.00034252 -0.00127077 249.21336620
0.00034239 -0.99999993 0.00010594 248.98589046
-0.00127081 0.00010551 0.99999919 -1.22511845
Axis -0.00063596 0.00005334 0.99999980
Axis point 124.58497705 124.51431379 0.00000000
Rotation angle (degrees) 179.98037890
Shift along axis -1.37032688
> show #!2 models
> show #!3 models
> undo
[Repeated 3 time(s)]
> select add #6
2 models selected
> hide #!3 models
> hide #!2 models
> ui mousemode right "translate selected models"
> fitmap #6 inMap #4
Fit map cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip in map
cryosparc_P30_J279_map.mrc using 102014 points
correlation = 0.9277, correlation about mean = 0.6892, overlap = 1011
steps = 48, shift = 0.0317, angle = 0.033 degrees
Position of cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip (#6)
relative to cryosparc_P30_J279_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.99999934 -0.00020646 -0.00113078 249.17086350
0.00020623 -0.99999996 0.00020732 248.95988727
-0.00113082 0.00020709 0.99999934 1.49527864
Axis -0.00056633 0.00010440 0.99999983
Axis point 124.57301229 124.49271938 0.00000000
Rotation angle (degrees) 179.98817733
Shift along axis 1.38015468
> select subtract #6
Nothing selected
> show #!2 models
> hide #!6 models
> fitmap #2 inMap #4
Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840
atoms
average map value = 0.03324, steps = 796
shifted from previous position = 21.2
rotated from previous position = 10.5 degrees
atoms outside contour = 78980, contour level = 0.04236
Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.89772325 0.39491741 0.19527728 171.44427967
-0.43436867 -0.71936134 -0.54207299 713.11865308
-0.07359913 -0.57145385 0.81732715 187.04031769
Axis -0.03368282 0.30824538 -0.95071039
Axis point 167.15705533 366.03494475 0.00000000
Rotation angle (degrees) 154.14213016
Shift along axis 36.21962762
> show #!3 models
> hide #!2 models
> fitmap #3 inMap #4
Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834
atoms
average map value = 0.06921, steps = 156
shifted from previous position = 2.77
rotated from previous position = 10.5 degrees
atoms outside contour = 5343, contour level = 0.04236
Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99530058 -0.04986346 0.08300844 -93.89354486
-0.05710589 -0.99454449 0.08729358 330.43411156
0.07820282 -0.09162362 -0.99271820 332.90953349
Axis -0.99882208 0.02682778 -0.04043159
Axis point 0.00000000 171.51509590 160.98648532
Rotation angle (degrees) 174.86146946
Shift along axis 89.18769933
> show #!2 models
> show #!6 models
> hide #!6 models
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_01_00027_volume.mrc
Opened cryosparc_P30_J280_class_01_00027_volume.mrc as #5, grid size
180,180,180, pixel 1.38, shown at level 0.12, step 1, values float32
> volume flip #6
Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip z flip as #7,
grid size 180,180,180, pixel 1.38, shown at step 1, values float32
> undo
> hide #!6 models
> show #!6 models
> hide #!7 models
> close #7
> volume flip #5
Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size
180,180,180, pixel 1.38, shown at step 1, values float32
> hide #!6 models
> close #5
> select add #7
2 models selected
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.84223,-0.48294,-0.23962,106.87,0.48671,0.48999,0.7232,-95.43,-0.23185,-0.72572,0.64774,158.93
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.84223,-0.48294,-0.23962,105.38,0.48671,0.48999,0.7232,-78.575,-0.23185,-0.72572,0.64774,170.33
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.95159,-0.22068,-0.21396,309.08,-0.18623,0.96771,-0.16985,66.446,0.24453,-0.12179,-0.96196,238.05
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.95159,-0.22068,-0.21396,310.5,-0.18623,0.96771,-0.16985,52.678,0.24453,-0.12179,-0.96196,229.62
> volume #7 level 0.07479
> surface dust #7 size 13.8
> fitmap #7 inMap #4
Fit map cryosparc_P30_J280_class_01_00027_volume.mrc z flip in map
cryosparc_P30_J279_map.mrc using 113502 points
correlation = 0.9643, correlation about mean = 0.8414, overlap = 1130
steps = 208, shift = 5.04, angle = 14.9 degrees
Position of cryosparc_P30_J280_class_01_00027_volume.mrc z flip (#7) relative
to cryosparc_P30_J279_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.99999966 -0.00026364 -0.00078820 249.12543022
0.00026376 -0.99999995 -0.00015099 248.98160004
-0.00078816 -0.00015120 0.99999968 1.49763888
Axis -0.00039360 -0.00007449 0.99999992
Axis point 124.54659569 124.50727948 0.00000000
Rotation angle (degrees) 179.98489106
Shift along axis 1.38103566
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> select subtract #7
Nothing selected
> volume #7 level 0.0619
> volume #7 level 0.07092
> save /Users/ruchigautamsharma/Desktop/image7.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4
> show #!6 models
> show #!4 models
> show #!3 models
> show #!2 models
> save
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_classes.cxs
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_02_00027_volume.mrc
Opened cryosparc_P30_J280_class_02_00027_volume.mrc as #5, grid size
180,180,180, pixel 1.38, shown at level 0.119, step 1, values float32
> volume flip #5
Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size
180,180,180, pixel 1.38, shown at step 1, values float32
> close #5
> select add #8
2 models selected
> hide #!3 models
> hide #!2 models
> hide #!6 models
> hide #!7 models
> view matrix models #8,1,0,0,2.8324,0,1,0,-4.8659,0,0,1,8.6713
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.96696,-0.17515,-0.18521,304.59,-0.10484,0.93554,-0.33731,57.912,0.23235,-0.30675,-0.92299,250.36
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.96696,-0.17515,-0.18521,302.83,-0.10484,0.93554,-0.33731,66.738,0.23235,-0.30675,-0.92299,248.15
> surface dust #8 size 13.8
> fitmap #8 inMap #4
Fit map cryosparc_P30_J280_class_02_00027_volume.mrc z flip in map
cryosparc_P30_J279_map.mrc using 58302 points
correlation = 0.9609, correlation about mean = 0.7291, overlap = 874.3
steps = 144, shift = 5.03, angle = 14.4 degrees
Position of cryosparc_P30_J280_class_02_00027_volume.mrc z flip (#8) relative
to cryosparc_P30_J279_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.99999916 0.00002492 -0.00129399 249.16805302
-0.00002528 -0.99999996 0.00027762 248.99198953
-0.00129399 0.00027765 0.99999912 1.50291671
Axis 0.00064340 -0.00013133 -0.99999978
Axis point 124.58607228 124.49433268 0.00000000
Rotation angle (degrees) 179.99856201
Shift along axis -1.37530370
> show #!7 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> select subtract #8
Nothing selected
> hide #!4 models
> volume #8 level 0.07811
> surface dust #8 size 13.8
> save /Users/ruchigautamsharma/Desktop/image7.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4
> show #!4 models
> show #!3 models
> show #!2 models
> hide #!8 models
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_04_00027_volume.mrc
Opened cryosparc_P30_J280_class_04_00027_volume.mrc as #5, grid size
180,180,180, pixel 1.38, shown at level 0.122, step 1, values float32
> volume flip #5
Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size
180,180,180, pixel 1.38, shown at step 1, values float32
> close #5
> select add #9
2 models selected
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.94987,-0.3125,-0.0095436,296.08,-0.29326,0.90112,-0.31935,89.841,0.1084,-0.30054,-0.94759,261.2
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.94987,-0.3125,-0.0095436,296.29,-0.29326,0.90112,-0.31935,94.465,0.1084,-0.30054,-0.94759,265.66
> surface dust #9 size 13.8
> fitmap #9 inMap #4
Fit map cryosparc_P30_J280_class_04_00027_volume.mrc z flip in map
cryosparc_P30_J279_map.mrc using 58281 points
correlation = 0.9434, correlation about mean = 0.6496, overlap = 833.5
steps = 116, shift = 5.59, angle = 6.08 degrees
Position of cryosparc_P30_J280_class_04_00027_volume.mrc z flip (#9) relative
to cryosparc_P30_J279_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.99999961 -0.00086803 -0.00014872 249.12096554
0.00086814 -0.99999934 -0.00074800 249.01468160
-0.00014807 -0.00074812 0.99999971 1.52412702
Axis -0.00007408 -0.00037371 0.99999993
Axis point 124.50649781 124.56168997 0.00000000
Rotation angle (degrees) 179.95026257
Shift along axis 1.41261188
> hide #!4 models
> select subtract #9
Nothing selected
> volume #9 level 0.07975
> show #!4 models
> hide #!4 models
> volume #9 level 0.08919
> save /Users/ruchigautamsharma/Desktop/image7.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4
> show #!4 models
> show #!3 models
> show #!2 models
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_05_00027_volume.mrc
Opened cryosparc_P30_J280_class_05_00027_volume.mrc as #5, grid size
180,180,180, pixel 1.38, shown at level 0.125, step 1, values float32
> volume flip #5
Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.38, shown at step 1, values float32
> close #5
> color #10 #4ab7ffff models
> color #10 #fbd6ffff models
> color #10 #ffb5b1ff models
> color #10 #f7b45cff models
> color #10 #30bdf7ff models
> hide #!9 models
> hide #!2 models
> hide #!3 models
> volume #10 level 0.09708
> select add #10
2 models selected
> view matrix models #10,1,0,0,3.1115,0,1,0,-2.0096,0,0,1,8.118
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.79927,-0.55558,-0.2291,334.52,-0.51624,0.8299,-0.21156,112.19,0.30768,-0.050826,-0.95013,212.13
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.79927,-0.55558,-0.2291,333.19,-0.51624,0.8299,-0.21156,115.1,0.30768,-0.050826,-0.95013,210.7
> surface dust #10 size 13.8
> fitmap #10 inMap #4
Fit map cryosparc_P30_J280_class_05_00027_volume.mrc z flip in map
cryosparc_P30_J279_map.mrc using 84424 points
correlation = 0.9741, correlation about mean = 0.8468, overlap = 1111
steps = 276, shift = 5.07, angle = 25.6 degrees
Position of cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) relative
to cryosparc_P30_J279_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.99999922 0.00035517 0.00119687 248.79666503
-0.00035522 -0.99999994 -0.00003695 249.05630070
0.00119686 -0.00003738 0.99999928 1.23988110
Axis -0.00059829 0.00001925 -0.99999982
Axis point 124.42007755 124.50606948 0.00000000
Rotation angle (degrees) 179.97964879
Shift along axis -1.38393827
> hide #!4 models
> save /Users/ruchigautamsharma/Desktop/image7.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4
> show #!4 models
> show #!2 models
> show #!3 models
> select subtract #10
Nothing selected
> hide #!10 models
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_08_00027_volume.mrc
Opened cryosparc_P30_J280_class_08_00027_volume.mrc as #5, grid size
180,180,180, pixel 1.38, shown at level 0.121, step 1, values float32
> volume flip #5
Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size
180,180,180, pixel 1.38, shown at step 1, values float32
> close #5
> volume #11 level 0.08441
> hide #!3 models
> hide #!2 models
> select add #11
2 models selected
> view matrix models #11,1,0,0,1.1155,0,1,0,-3.8677,0,0,1,5.8448
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.99209,-0.0053981,-0.12542,17.552,0.081093,0.7902,0.60746,-62.634,0.095827,-0.61282,0.78439,87.413
> view matrix models
> #11,0.99729,-0.013338,-0.072294,11.493,0.039229,0.92824,0.36991,-44.599,0.062172,-0.37174,0.92625,48.066
> view matrix models
> #11,0.96616,0.092495,-0.24077,23.583,0.23126,0.10267,0.96746,-47.711,0.1142,-0.99041,0.077802,210.68
> view matrix models
> #11,-0.87555,-0.41067,0.25448,270.56,-0.45727,0.87442,-0.16216,91.081,-0.15593,-0.25834,-0.95338,285.91
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.87555,-0.41067,0.25448,270.16,-0.45727,0.87442,-0.16216,97.04,-0.15593,-0.25834,-0.95338,295.44
> surface dust #11 size 13.8
> fitmap #11 inMap #4
Fit map cryosparc_P30_J280_class_08_00027_volume.mrc z flip in map
cryosparc_P30_J279_map.mrc using 102298 points
correlation = 0.8925, correlation about mean = 0.5767, overlap = 958.6
steps = 172, shift = 10.7, angle = 16.9 degrees
Position of cryosparc_P30_J280_class_08_00027_volume.mrc z flip (#11) relative
to cryosparc_P30_J279_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.99999904 -0.00116328 0.00074464 249.06176278
0.00116310 -0.99999929 -0.00024302 248.90777913
0.00074493 -0.00024215 0.99999969 1.24883054
Axis 0.00037212 -0.00012116 0.99999992
Axis point 124.45826735 124.52639149 0.00000000
Rotation angle (degrees) 179.93335425
Shift along axis 1.31135186
> volume #11 level 0.05725
> volume #11 level 0.06342
> volume #11 level 0.07083
> select subtract #11
Nothing selected
> hide #!4 models
> save /Users/ruchigautamsharma/Desktop/image7.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4
> show #!4 models
> show #!3 models
> show #!2 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!2 models
> hide #!3 models
> open /Users/ruchigautamsharma/Desktop/25HepE525K/8qyq.pdb
8qyq.pdb title:
Beta-cardiac myosin S1 fragment In the pre-powerstroke state complexed to
mavacamten [more info...]
Chain information for 8qyq.pdb #5
---
Chain | Description | UniProt
A B | myosin-7 | MYH7_BOVIN 1-807
C | myosin light chain 3 | MYL3_BOVIN 1-199
D | myosin light chain 3 | MYL3_BOVIN 1-199
Non-standard residues in 8qyq.pdb #5
---
ADP — adenosine-5'-diphosphate
BEF — beryllium trifluoride ion
FMT — formic acid
GOL — glycerol (glycerin; propane-1,2,3-triol)
MG — magnesium ion
XB2 —
6-[[(1~{S})-1-phenylethyl]amino]-3-propan-2-yl-1~{H}-pyrimidine-2,4-dione
> select #5/B
6497 atoms, 6383 bonds, 8 pseudobonds, 1018 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select #5/D
602 atoms, 605 bonds, 3 pseudobonds, 86 residues, 2 models selected
> hide sel cartoons
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.99553,0.05401,0.077471,-2.8146,-0.030633,0.96065,-0.27608,6.0307,-0.089333,0.27247,0.95801,-6.3562
> view matrix models
> #5,0.99476,0.059463,0.083204,-3.0609,-0.032039,0.95383,-0.29862,6.6171,-0.097119,0.29439,0.95074,-6.797
> view matrix models
> #5,0.84862,0.26572,-0.45743,1.348,0.52607,-0.33296,0.78255,20.637,0.05564,-0.90473,-0.42234,49.406
> view matrix models
> #5,-0.20948,0.94179,-0.26296,-32.356,0.63406,0.33555,0.69669,9.3355,0.74437,-0.020792,-0.66744,44.88
> view matrix models
> #5,-0.26135,0.93427,-0.24258,-33.342,0.74088,0.35525,0.57,12.994,0.61871,-0.030752,-0.78502,45.702
> view matrix models
> #5,-0.27941,0.93151,-0.23283,-33.736,0.77438,0.36199,0.51894,14.36,0.56769,-0.035305,-0.82249,45.838
> view matrix models
> #5,-0.37124,0.91598,-0.15218,-36.338,0.9014,0.39485,0.17771,22.376,0.22287,-0.071201,-0.97224,44.77
> view matrix models
> #5,-0.41927,0.90453,-0.077722,-38.282,0.90689,0.41333,-0.08192,27.324,-0.041974,-0.10483,-0.9936,42.18
> view matrix models
> #5,-0.44992,0.89092,0.061874,-41.255,0.77059,0.4223,-0.47733,33.225,-0.4514,-0.16708,-0.87654,35.351
> view matrix models
> #5,-0.31556,0.89055,0.32762,-44.738,0.035597,0.35613,-0.93376,33.51,-0.94824,-0.28299,-0.14408,15.954
> view matrix models
> #5,-0.16915,0.90579,0.3885,-44.23,-0.41809,0.29101,-0.86053,27.006,-0.89252,-0.30799,0.32948,7.6715
> view matrix models
> #5,-0.31793,0.89036,0.32585,-44.732,0.044144,0.35721,-0.93298,33.592,-0.94709,-0.28224,-0.15287,16.132
> view matrix models
> #5,-0.16449,0.90636,0.38916,-44.19,-0.4306,0.28897,-0.85503,26.761,-0.88742,-0.30822,0.34275,7.4794
> view matrix models
> #5,0.9568,-0.19924,0.21174,-0.56848,0.28104,0.4472,-0.84914,33.288,0.074496,0.87196,0.48387,-7.475
> view matrix models
> #5,0.93545,-0.26582,0.23296,0.14939,0.35203,0.64149,-0.68159,26.655,0.031741,0.71961,0.69366,-9.0199
> view matrix models
> #5,0.91741,-0.3204,0.23603,1.0211,0.39769,0.75969,-0.51451,21.332,-0.014464,0.56588,0.82436,-8.9778
> view matrix models
> #5,0.95721,-0.19796,0.21112,-0.57814,0.27948,0.44284,-0.85193,33.417,0.075155,0.87447,0.47922,-7.4258
> view matrix models
> #5,0.97238,-0.14881,0.17983,-0.79935,0.21341,0.25467,-0.94319,38.437,0.094555,0.95551,0.27939,-4.8593
> view matrix models
> #5,0.98941,-0.090123,0.11382,-0.49676,0.10944,-0.052142,-0.99262,44.656,0.095393,0.99456,-0.041726,0.82277
> view matrix models
> #5,-0.35779,-0.60534,0.71102,-20.504,0.19127,-0.79279,-0.57871,53.561,0.914,-0.07106,0.39943,26.714
> view matrix models
> #5,-0.60867,0.67803,0.41206,-45.977,-0.79266,-0.54248,-0.27823,28.041,0.034888,-0.49597,0.86764,13.998
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.60867,0.67803,0.41206,-23.555,-0.79266,-0.54248,-0.27823,128.79,0.034888,-0.49597,0.86764,182.06
> view matrix models
> #5,-0.60867,0.67803,0.41206,37.381,-0.79266,-0.54248,-0.27823,174.2,0.034888,-0.49597,0.86764,205.17
> view matrix models
> #5,-0.60867,0.67803,0.41206,99.031,-0.79266,-0.54248,-0.27823,162.54,0.034888,-0.49597,0.86764,155.36
> view matrix models
> #5,-0.60867,0.67803,0.41206,98.801,-0.79266,-0.54248,-0.27823,159.71,0.034888,-0.49597,0.86764,149.89
> view matrix models
> #5,-0.60867,0.67803,0.41206,105.09,-0.79266,-0.54248,-0.27823,156.53,0.034888,-0.49597,0.86764,147.11
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.23298,0.92288,0.30662,107.22,-0.95501,-0.15762,-0.25124,145.28,-0.18353,-0.35136,0.91808,139.83
> view matrix models
> #5,-0.098877,0.94921,0.29871,108.71,-0.97369,-0.030362,-0.22583,141.73,-0.20529,-0.31318,0.92724,138.51
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.098877,0.94921,0.29871,108.51,-0.97369,-0.030362,-0.22583,147.51,-0.20529,-0.31318,0.92724,141.89
> fitmap #5 inMap #4
Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943
atoms
average map value = 0.04173, steps = 400
shifted from previous position = 15.1
rotated from previous position = 20 degrees
atoms outside contour = 9505, contour level = 0.04236
Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.58239663 0.81290458 -0.00055383 102.85355786
0.70719581 0.50699846 0.49277443 96.93889710
0.40085939 0.28659850 -0.87015691 105.31002093
Axis -0.44484143 -0.86608184 -0.22807532
Axis point 21.76765973 0.00000000 42.22852380
Rotation angle (degrees) 166.60041068
Shift along axis -153.72915848
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.37977,0.92425,0.039174,104.73,-0.87919,-0.37378,0.29547,144.57,0.28774,0.077772,0.95455,140.89
> view matrix models
> #5,0.32827,-0.92374,-0.19734,159.88,0.44949,0.33651,-0.82748,170.74,0.83078,0.18294,0.52568,155.01
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.32827,-0.92374,-0.19734,161.33,0.44949,0.33651,-0.82748,156.99,0.83078,0.18294,0.52568,143.67
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.52982,-0.80788,-0.25811,162.9,0.69083,0.58764,-0.42123,146.68,0.49198,0.044868,0.86945,134.89
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.52982,-0.80788,-0.25811,162.52,0.69083,0.58764,-0.42123,163.45,0.49198,0.044868,0.86945,142.3
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.72386,-0.68979,0.014695,136.61,0.19093,-0.22074,-0.95646,184.86,0.66301,-0.68954,0.29149,172.48
> view matrix models
> #5,0.50281,-0.86437,-0.0066101,158.26,0.47814,0.28449,-0.83093,175.36,0.72011,0.41464,0.55634,143.83
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.50281,-0.86437,-0.0066101,160.27,0.47814,0.28449,-0.83093,157.85,0.72011,0.41464,0.55634,140.82
> view matrix models
> #5,0.50281,-0.86437,-0.0066101,169.69,0.47814,0.28449,-0.83093,74.983,0.72011,0.41464,0.55634,59.074
> view matrix models
> #5,0.50281,-0.86437,-0.0066101,164.23,0.47814,0.28449,-0.83093,100.24,0.72011,0.41464,0.55634,83.15
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.35446,-0.92893,-0.10696,165.58,0.84213,0.36685,-0.39528,94.756,0.40642,0.050033,0.91231,79.421
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.35446,-0.92893,-0.10696,172.36,0.84213,0.36685,-0.39528,136.98,0.40642,0.050033,0.91231,91.143
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.56298,-0.74543,0.35692,145.92,0.33568,-0.60087,-0.72544,157.6,0.75523,-0.2886,0.58851,110.05
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.56298,-0.74543,0.35692,130.04,0.33568,-0.60087,-0.72544,145.96,0.75523,-0.2886,0.58851,88.151
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.082785,-0.99082,0.10686,147.28,0.60357,-0.13517,-0.78577,140.83,0.793,-0.00055352,0.60922,81.985
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.082785,-0.99082,0.10686,146.82,0.60357,-0.13517,-0.78577,138.38,0.793,-0.00055352,0.60922,93.162
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.3921,-0.86583,0.3108,135.56,0.71686,-0.49931,-0.48661,141.85,0.57651,0.032004,0.81646,85.171
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.3921,-0.86583,0.3108,138.82,0.71686,-0.49931,-0.48661,142.44,0.57651,0.032004,0.81646,82.838
> fitmap #5 inMap #4
Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943
atoms
average map value = 0.07346, steps = 220
shifted from previous position = 13.1
rotated from previous position = 20.7 degrees
atoms outside contour = 3995, contour level = 0.04236
Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.48628488 -0.87349851 -0.02296421 131.98115481
-0.50944434 0.26206455 0.81962712 104.75313384
-0.70992497 0.41027126 -0.57243691 157.52284441
Axis -0.46589276 0.78183820 0.41433437
Axis point 115.26114932 0.00000000 25.56332067
Rotation angle (degrees) 153.93923432
Shift along axis 85.67806483
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 40 atom styles
> rainbow sel
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> show #!5 models
> select #5/A
6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select #5/C
1260 atoms, 1265 bonds, 172 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> hide sel atoms
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> select #5/A
6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> style sel ball
Changed 40 atom styles
> show sel cartoons
> select #5/A
6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected
> show sel cartoons
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> style sel ball
Changed 40 atom styles
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> style sel ball
Changed 40 atom styles
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> show sel atoms
> show sel cartoons
> hide sel atoms
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> style sel ball
Changed 40 atom styles
> select ::name="ADP"
108 atoms, 116 bonds, 4 residues, 2 models selected
> style sel & #!5 ball
Changed 54 atom styles
> rainbow sel & #!5
> select add #5
14997 atoms, 14795 bonds, 20 pseudobonds, 2294 residues, 4 models selected
> select add #3
33777 atoms, 33932 bonds, 39 pseudobonds, 4620 residues, 6 models selected
> select subtract #3
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> select ::name="ADP"
108 atoms, 116 bonds, 4 residues, 2 models selected
> select add #5
14997 atoms, 14795 bonds, 20 pseudobonds, 2294 residues, 4 models selected
> select subtract #5
54 atoms, 58 bonds, 2 residues, 1 model selected
> select ::name="ADP"
108 atoms, 116 bonds, 4 residues, 2 models selected
> style sel & #!5 ball
Changed 54 atom styles
> rainbow sel & #!5
> select #5/A
6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> color sel byhetero
> show #!3 models
> show #!2 models
> hide #!5 models
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> select subtract #5
Nothing selected
> hide #!3 models
> fitmap #2 inMap #4
Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840
atoms
average map value = 0.03324, steps = 212
shifted from previous position = 0.00596
rotated from previous position = 0.00292 degrees
atoms outside contour = 78983, contour level = 0.04236
Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.89771304 0.39493434 0.19528995 171.43072531
-0.43439308 -0.71937790 -0.54203144 713.12426462
-0.07357955 -0.57142130 0.81735167 187.01292814
Axis -0.03369168 0.30822422 -0.95071694
Axis point 167.15376056 366.03172418 0.00000000
Rotation angle (degrees) 154.14093715
Shift along axis 36.23002059
> hide #!2 models
> show #!3 models
> fitmap #3 inMap #4
Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834
atoms
average map value = 0.06921, steps = 64
shifted from previous position = 0.0125
rotated from previous position = 0.00171 degrees
atoms outside contour = 5339, contour level = 0.04236
Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99529777 -0.04988324 0.08303014 -93.89145014
-0.05712784 -0.99454304 0.08729576 330.45021647
0.07822245 -0.09162861 -0.99271620 332.90769160
Axis -0.99882138 0.02683827 -0.04044199
Axis point 0.00000000 171.52297541 160.98536353
Rotation angle (degrees) 174.86125937
Shift along axis 89.18605104
> show #!2 models
> show #!5 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> hide #!2 models
> fitmap #5 inMap #4
Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943
atoms
average map value = 0.07346, steps = 28
shifted from previous position = 0.026
rotated from previous position = 0.0648 degrees
atoms outside contour = 4000, contour level = 0.04236
Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.48597381 -0.87364307 -0.02402555 131.99331828
-0.50982761 0.26105496 0.81971099 104.73346858
-0.70986284 0.41060696 -0.57227324 157.51977670
Axis -0.46618686 0.78153309 0.41457912
Axis point 115.27505316 0.00000000 25.56334997
Rotation angle (degrees) 153.97413268
Shift along axis 85.62353087
> show #!3 models
> show #!2 models
> hide #!5 models
> hide #!2 models
> select add #3
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 3 models selected
> view matrix models
> #3,0.95172,-0.29911,0.069057,-20.803,0.28197,0.94071,0.18854,-169,-0.12136,-0.15997,0.97963,-13.019
> fitmap #3 inMap #4
Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834
atoms
average map value = 0.06921, steps = 76
shifted from previous position = 3.09
rotated from previous position = 0.00809 degrees
atoms outside contour = 5343, contour level = 0.04236
Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99529429 -0.04999011 0.08300768 -93.86164081
-0.05722488 -0.99454601 0.08719835 330.49357732
0.07819590 -0.09153812 -0.99272664 332.89632413
Axis -0.99882051 0.02688932 -0.04042956
Axis point 0.00000000 171.53441271 160.98537615
Rotation angle (degrees) 174.86666587
Shift along axis 89.17882775
> select subtract #3
Nothing selected
> show #!2 models
> select add #2
99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 3 models selected
> hide #!3 models
> view matrix models
> #2,-0.97957,0.18401,0.081197,326.1,0.20088,0.91487,0.35022,-426.82,-0.0098435,0.35937,-0.93314,214.54,#1,1,0,0,0,0,1,0,0,0,0,1,0
> fitmap #2 inMap #4
Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840
atoms
average map value = 0.03324, steps = 224
shifted from previous position = 2.05
rotated from previous position = 0.0135 degrees
atoms outside contour = 78989, contour level = 0.04236
Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.89780391 0.39481948 0.19510437 171.55908545
-0.43419345 -0.71946808 -0.54207170 713.11615692
-0.07364910 -0.57138713 0.81736929 187.01348437
Axis -0.03361936 0.30821036 -0.95072399
Axis point 167.18733995 366.02013285 0.00000000
Rotation angle (degrees) 154.15167345
Shift along axis 36.22387450
> show #!3 models
> select subtract #2
Nothing selected
> volume #4 level 0.03302
> hide #!3 models
> hide #!2 models
> show #!5 models
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> color sel byhetero
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> show sel atoms
> hide #!5 models
> show #!5 models
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> hide sel cartoons
> ui mousemode right translate
> volume #4 level 0.04236
> volume #4 level 0.08254
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> fitmap #5 inMap #4
Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943
atoms
average map value = 0.07346, steps = 28
shifted from previous position = 0.0249
rotated from previous position = 0.0574 degrees
atoms outside contour = 9432, contour level = 0.082538
Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.48625976 -0.87350889 -0.02310098 131.98359794
-0.50952602 0.26196441 0.81960836 104.75385886
-0.70988356 0.41031312 -0.57245827 157.52305140
Axis -0.46592829 0.78181077 0.41434616
Axis point 115.26244630 0.00000000 25.56654333
Rotation angle (degrees) 153.94551965
Shift along axis 85.67187553
> volume #4 level 0.06852
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.68456,-0.70867,0.17078,136.17,0.45982,-0.60159,-0.65319,142.81,0.56564,-0.36862,0.73768,90.628
> view matrix models
> #5,-0.67257,-0.72389,0.15376,136.39,0.47921,-0.58434,-0.6549,142.55,0.56392,-0.36678,0.7399,90.602
> fitmap #5 inMap #4
Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943
atoms
average map value = 0.07346, steps = 84
shifted from previous position = 0.173
rotated from previous position = 4.64 degrees
atoms outside contour = 7674, contour level = 0.068522
Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.48604532 -0.87361366 -0.02364530 131.98433118
-0.50971212 0.26139904 0.81967316 104.73161110
-0.70989682 0.41045061 -0.57234325 157.51876880
Axis -0.46610167 0.78163575 0.41448135
Axis point 115.26785562 0.00000000 25.56530335
Rotation angle (degrees) 153.96091166
Shift along axis 85.63244638
> ui mousemode right translate
> volume #4 level 0.05824
> hide sel cartoons
> show #!3 models
> show #!2 models
> volume #4 level 0.03582
> select subtract #5
Nothing selected
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> save /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_3.cxs
> volume #4 level 0.04703
> volume #4 level 0.03302
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> save
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_20240903.cxs
> includeMaps true
——— End of log from Tue Sep 3 19:15:56 2024 ———
opened ChimeraX session
> volume #4 level 0.04423
> select
> #2/B:12-16,20-28,99-111,136-142,154-166,184-199,216-222,224-231,271-274,284-291,295-301,311-315,326-337,343-360,378-388,393-400,417-447,473-503,518-525,530-538,545-555,593-597,604-611,615-619,647-664,686-696,698-707,715-722,727-729,738-748,753-755,767-824,828-832,837-965,968-995,998-1165,1168-1171
11706 atoms, 11732 bonds, 715 residues, 1 model selected
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> volume #4 level 0.06198
> volume #4 level 0.05357
> volume #4 level 0.04703
> show #!3 models
> show #!2 models
> hide #!3 models
> select add #2
99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 3 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!10 models
> transparency #4.1#10.1 0
> hide #!4 models
> transparency #10.1 50
> ui mousemode right select
> hide #!10 models
Drag select of 18 residues
Drag select of 24 residues
> style sel ball
Changed 309 atom styles
> show sel atoms
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue M3L (net charge +1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/tmpytfstoqe/ante.in.mol2 -fi
mol2 -o
/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/tmpytfstoqe/ante.out.mol2 -fo
mol2 -c bcc -nc 1 -j 5 -s 2 -dr n
(M3L) ``
(M3L) `Welcome to antechamber 20.0: molecular input file processor.`
(M3L) ``
(M3L) `Info: Finished reading file
(/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/tmpytfstoqe/ante.in.mol2);
atoms read (43), bonds read (42).`
(M3L) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(M3L) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(M3L) ``
(M3L) ``
(M3L) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(M3L) `Info: Total number of electrons: 134; net charge: 1`
(M3L) ``
(M3L) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(M3L) ``
(M3L) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(M3L) ``
(M3L) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(M3L) ``
Charges for residue M3L determined
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 8g4l.pdb_A SES surface #2.2: minimum, -21.91, mean -0.65,
maximum 19.75
Coulombic values for 8g4l.pdb_B SES surface #2.3: minimum, -23.19, mean -0.75,
maximum 24.96
Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16,
maximum 15.27
Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34,
maximum 15.00
To also show corresponding color key, enter the above coulombic command and
add key true
> ui mousemode right translate
Drag select of 8g4l.pdb_B SES surface, 200 of 1516366 triangles, 8act.pdb_A
SES surface, 14 of 807322 triangles, 1 atoms, 12 residues
> select add #3
18867 atoms, 19195 bonds, 19 pseudobonds, 2331 residues, 7 models selected
> select add #2
118674 atoms, 119507 bonds, 24 pseudobonds, 8474 residues, 10 models selected
> select subtract #3
99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 7 models selected
> select subtract #2
2 models selected
> save /Users/ruchigautamsharma/Desktop/image1.png supersample 3
> show #!10 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> show #!10 models
> hide #!10 models
Drag select of 42 residues
> select add #3
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected
> select subtract #3
2 models selected
Drag select of 25 residues
> style sel ball
Changed 204 atom styles
> show sel atoms
> coulombic sel
Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16,
maximum 15.27
Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34,
maximum 15.00
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of 8act.pdb_B SES surface, 36 of 774284 triangles, 13 residues
Drag select of 8act.pdb_B SES surface, 335 of 774284 triangles, 1 atoms, 32
residues, 1 bonds
> style sel ball
Changed 263 atom styles
> show sel atoms
> coulombic sel
Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16,
maximum 15.27
Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34,
maximum 15.00
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of 20 atoms, 46 residues, 17 bonds
Drag select of 8act.pdb_A SES surface, 1775 of 807322 triangles, 8act.pdb_B
SES surface, 1980 of 774284 triangles, 44 atoms, 78 residues, 37 bonds
Drag select of 8act.pdb_B SES surface, 1283 of 774284 triangles, 62 atoms, 33
residues, 49 bonds
> coulombic sel
Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16,
maximum 15.27
Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34,
maximum 15.00
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!10 models
> select add #3
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected
> select subtract #3
2 models selected
> hide #!3 models
> show #!3 models
> hide #!10 models
> save /Users/ruchigautamsharma/Desktop/image2.png supersample 3
> hide #!3 models
> show #!2 models
> show #!10 models
> hide #!5 models
> ui mousemode right translate
> hide #!10 models
> ui mousemode right select
Drag select of 40 atoms, 31 residues, 37 bonds, 1 pseudobonds
> style sel ball
Changed 477 atom styles
> show sel atoms
> coulombic sel
Coulombic values for 8g4l.pdb_A SES surface #2.2: minimum, -21.91, mean -0.65,
maximum 19.75
Coulombic values for 8g4l.pdb_B SES surface #2.3: minimum, -23.19, mean -0.75,
maximum 24.96
To also show corresponding color key, enter the above coulombic command and
add key true
> ui mousemode right translate
> show #!10 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!10 models
> save /Users/ruchigautamsharma/Desktop/image3.png supersample 3
> save "/Users/ruchigautamsharma/Desktop/25HepE525K/interaction
> 25HepE525K.cxs" includeMaps true
——— End of log from Wed Sep 25 04:14:14 2024 ———
opened ChimeraX session
> select add #2
99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 3 models selected
> select subtract #2
2 models selected
> hide #!2 models
> ui mousemode right select
Drag select of 50 atoms, 26 residues, 42 bonds
Drag select of 8act.pdb_A SES surface, 9674 of 807322 triangles, 8act.pdb_B
SES surface, 2496 of 774284 triangles, 48 atoms, 91 residues, 38 bonds
Drag select of 8act.pdb_A SES surface, 5160 of 807322 triangles, 8act.pdb_B
SES surface, 2203 of 774284 triangles, 69 atoms, 95 residues, 57 bonds
> coulombic sel
Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16,
maximum 15.27
Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34,
maximum 15.00
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of 8act.pdb_A SES surface, 1211 of 807322 triangles, 8act.pdb_B
SES surface, 784 of 774284 triangles, 4 atoms, 22 residues, 4 bonds
> ui mousemode right translate
> ui mousemode right select
Drag select of 8act.pdb_A SES surface, 9181 of 807322 triangles, 8act.pdb_B
SES surface, 7593 of 774284 triangles, 46 atoms, 34 residues, 39 bonds
> select add #3
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected
> select subtract #3
2 models selected
Drag select of 8act.pdb_A SES surface, 45732 of 807322 triangles, 8act.pdb_B
SES surface, 16784 of 774284 triangles, 242 atoms, 415 residues, 1
pseudobonds, 201 bonds
> select add #3
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected
> select subtract #3
2 models selected
Drag select of 8act.pdb_A SES surface, 170 of 807322 triangles, 8act.pdb_B SES
surface, 459 of 774284 triangles
> ui mousemode right translate
> ui mousemode right select
Drag select of 8act.pdb_A SES surface, 40121 of 807322 triangles, 8act.pdb_B
SES surface, 13087 of 774284 triangles, 153 atoms, 281 residues, 127 bonds
> select add #3
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
8act.pdb #3/D SER 195 OXT
8act.pdb #3/C SER 195 OXT
8act.pdb #3/E GLU 163 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16,
maximum 15.27
Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34,
maximum 15.00
Coulombic values for 8act.pdb_C SES surface #3.5: minimum, -22.56, mean -3.87,
maximum 14.68
Coulombic values for 8act.pdb_D SES surface #3.6: minimum, -19.82, mean -3.44,
maximum 15.48
Coulombic values for 8act.pdb_E SES surface #3.7: minimum, -20.97, mean -5.04,
maximum 8.16
Coulombic values for 8act.pdb_F SES surface #3.8: minimum, -22.95, mean -4.14,
maximum 7.43
To also show corresponding color key, enter the above coulombic command and
add key true
> ui mousemode right translate
> show #!10 models
> show #!4 models
> hide #!10 models
> select subtract #3
6 models selected
> hide #!3 models
> show #!10 models
> hide #!4 models
> show #!3 models
> save
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs
——— End of log from Thu Sep 26 13:06:28 2024 ———
opened ChimeraX session
> show #!2 models
> close #6
> close #7
> close #8
> close #9
> close #11
> save
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs
——— End of log from Thu Sep 26 13:21:30 2024 ———
opened ChimeraX session
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #10 level 0.07481
> show #!3 models
> show #!2 models
> hide #!2 models
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J276_map_sharp.mrc
Opened cryosparc_P30_J276_map_sharp.mrc as #6, grid size 300,300,300, pixel
0.83, shown at level 0.0289, step 2, values float32
> hide #!3 models
> select add #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-13.259,0,1,0,-59.644,0,0,1,-60.922
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.97989,-0.19467,-0.043828,17.497,0.19799,0.97586,0.092126,-93.748,0.024836,-0.09895,0.99478,-51.92
> undo
[Repeated 1 time(s)]
> volumeflip #6
Unknown command: volumeflip #6
> volume flip #6
Opened cryosparc_P30_J276_map_sharp.mrc z flip as #7, grid size 300,300,300,
pixel 0.83, shown at step 1, values float32
> select subtract #6
Nothing selected
> select add #7
2 models selected
> view matrix models
> #7,0.96691,0.024547,-0.25392,32.662,0.2299,0.34752,0.90905,-65.44,0.11056,-0.93735,0.33038,177.52
> view matrix models
> #7,-0.99755,-0.034454,-0.060947,267.99,-0.00070731,0.87544,-0.48332,74.136,0.070008,-0.48209,-0.87332,277.93
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.99755,-0.034454,-0.060947,269.51,-0.00070731,0.87544,-0.48332,81.793,0.070008,-0.48209,-0.87332,283.92
> fitmap #7 inMap #10
Fit map cryosparc_P30_J276_map_sharp.mrc z flip in map
cryosparc_P30_J280_class_05_00027_volume.mrc z flip using 270132 points
correlation = 0.765, correlation about mean = 0.4371, overlap = 1.18e+04
steps = 156, shift = 3.04, angle = 18.9 degrees
Position of cryosparc_P30_J276_map_sharp.mrc z flip (#7) relative to
cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) coordinates:
Matrix rotation and translation
0.99868521 -0.01194978 0.04985040 -4.14668671
0.01153380 0.99989629 0.00862389 -2.79643992
-0.04994828 -0.00803759 0.99871946 7.43685902
Axis -0.16040788 0.96080890 0.22608753
Axis point 148.17070643 0.00000000 88.18561170
Rotation angle (degrees) 2.97697945
Shift along axis -0.34030206
> ui mousemode right translate
> hide #!10 models
> volume #7 level 0.009114
> transparency sel 50
> show #!2 models
> volume #7 level 0.00811
> volume #7 level 0.00611
> volume #7 level 0.00111
> surface dust #7 size 8.3
> fitmap #2 inMap #7
Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J276_map_sharp.mrc z flip (#7)
using 99840 atoms
average map value = 0.07007, steps = 304
shifted from previous position = 0.129
rotated from previous position = 0.285 degrees
atoms outside contour = 75934, contour level = 0.00111
Position of 8g4l.pdb (#2) relative to cryosparc_P30_J276_map_sharp.mrc z flip
(#7) coordinates:
Matrix rotation and translation
0.90356614 -0.36251243 -0.22837025 69.94133890
0.42750669 0.72750591 0.53663133 -463.88516185
-0.02839482 -0.58251171 0.81232619 178.12186061
Axis -0.80838767 -0.14444773 0.57065245
Axis point 0.00000000 -62.59090162 802.47834953
Rotation angle (degrees) 43.80505846
Shift along axis 112.11311861
> show #!3 models
> select subtract #7
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J366_003_volume_map_sharp.mrc
Opened cryosparc_P30_J366_003_volume_map_sharp.mrc as #8, grid size
300,300,300, pixel 0.83, shown at level 0.0628, step 2, values float32
> volume flip #8
Opened cryosparc_P30_J366_003_volume_map_sharp.mrc z flip as #9, grid size
300,300,300, pixel 0.83, shown at step 1, values float32
> close #8
> close #6
> select add #9
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.72491,0.12345,-0.6777,107.22,-0.31498,0.93434,-0.16672,71.607,0.61261,0.33432,0.71619,-88.209
> view matrix models
> #9,-0.78393,-0.37061,0.49809,227.29,-0.46679,0.88081,-0.079276,87.942,-0.40935,-0.29465,-0.86349,320.77
> view matrix models
> #9,-0.9341,-0.13426,0.33081,241.15,-0.20068,0.96381,-0.17551,53.522,-0.29528,-0.23033,-0.92723,305.45
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.9341,-0.13426,0.33081,237.7,-0.20068,0.96381,-0.17551,58.891,-0.29528,-0.23033,-0.92723,312.4
> select subtract #9
Nothing selected
> hide #!9 models
> hide #!7 models
> show #!10 models
> show #!9 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!2 models
> fitmap #10 inMap #9
Fit map cryosparc_P30_J280_class_05_00027_volume.mrc z flip in map
cryosparc_P30_J366_003_volume_map_sharp.mrc z flip using 110989 points
correlation = 0.8661, correlation about mean = 0.6378, overlap = 1281
steps = 248, shift = 14.1, angle = 17.3 degrees
Position of cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) relative
to cryosparc_P30_J366_003_volume_map_sharp.mrc z flip (#9) coordinates:
Matrix rotation and translation
0.99912867 0.03701040 0.01929050 -6.45856044
-0.03695133 0.99931125 -0.00340957 4.82258956
-0.01940341 0.00269379 0.99980811 2.58781556
Axis 0.07292398 0.46232197 -0.88370838
Axis point 133.82942588 176.61647977 0.00000000
Rotation angle (degrees) 2.39837754
Shift along axis -0.52826911
> show #!2 models
> hide #!9 models
> fitmap #2 inMap #10
Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J280_class_05_00027_volume.mrc
z flip (#10) using 99840 atoms
average map value = 0.0705, steps = 2000
shifted from previous position = 42.4
rotated from previous position = 17.7 degrees
atoms outside contour = 75484, contour level = 0.074814
Position of 8g4l.pdb (#2) relative to
cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) coordinates:
Matrix rotation and translation
0.89869523 -0.39132784 -0.19801364 76.37796838
0.43305938 0.72042893 0.54170263 -464.23480660
-0.06932856 -0.57257723 0.81691423 184.96627548
Axis -0.80046161 -0.09244309 0.59221237
Axis point 0.00000000 -34.72317143 823.48795667
Rotation angle (degrees) 44.10881728
Shift along axis 91.31698418
> show #!9 models
> hide #!10 models
> surface dust #9 size 8.3
> volume #9 level 0.04335
> transparency #2.2-3#9.1 50
> volume #9 level 0.04552
> show #!3 models
> hide #!2 models
> fitmap #3 inMap #9
Fit molecule 8act.pdb (#3) to map cryosparc_P30_J366_003_volume_map_sharp.mrc
z flip (#9) using 18834 atoms
average map value = 0.07945, steps = 224
shifted from previous position = 13.7
rotated from previous position = 17.3 degrees
atoms outside contour = 5855, contour level = 0.045517
Position of 8act.pdb (#3) relative to
cryosparc_P30_J366_003_volume_map_sharp.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.99082281 0.08342546 -0.10635013 340.09974533
0.09230379 0.99239110 -0.08148569 -89.94149170
0.09874294 -0.09055440 -0.99098422 327.06025206
Axis -0.04413312 -0.99809091 0.04320662
Axis point 163.69830978 0.00000000 170.46022157
Rotation angle (degrees) 174.10287196
Shift along axis 88.89128906
> hide #!3 models
> show #!3 models
> save /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_4.cxs
——— End of log from Fri Sep 27 17:28:16 2024 ———
opened ChimeraX session
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color #9 #78c1fe80 models
> select
> #2/A:10-16,20-27,82-84,90-92,98-111,136-142,154-168,184-199,216-231,271-273,284-291,295-301,307-309,311-314,325-338,343-359,379-388,393-400,417-447,473-504,518-524,530-539,545-555,604-611,615-618,647-662,686-696,698-707,715-723,738-748,753-755,769-826,829-836,842-919,922-1171
11821 atoms, 11850 bonds, 720 residues, 1 model selected
> select add #2
99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 4 models selected
> select subtract #2
2 models selected
> select #2/A:483-484
37 atoms, 36 bonds, 2 residues, 1 model selected
> select #2/A:483-485
56 atoms, 55 bonds, 3 residues, 1 model selected
> style sel ball
Changed 56 atom styles
> show sel atoms
> rainbow sel
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> coulombic sel
Coulombic values for 8g4l.pdb_A SES surface #2.2: minimum, -21.91, mean -0.65,
maximum 19.75
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!9 models
> show #!9 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_4.cxs
Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83,
shown at level 0.047, step 1, values float32
Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.38, shown at level 0.0748, step 1, values float32
Opened cryosparc_P30_J276_map_sharp.mrc z flip as #7, grid size 300,300,300,
pixel 0.83, shown at level 0.00111, step 1, values float32
Opened cryosparc_P30_J366_003_volume_map_sharp.mrc z flip as #9, grid size
300,300,300, pixel 0.83, shown at level 0.0455, step 1, values float32
Log from Fri Sep 27 17:28:16 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs
Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83,
shown at level 0.047, step 1, values float32
Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32
Log from Thu Sep 26 13:21:30 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs
Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83,
shown at level 0.047, step 1, values float32
Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid
size 180,180,180, pixel 1.38, shown at level 0.0903, step 1, values float32
Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size
180,180,180, pixel 1.38, shown at level 0.0709, step 1, values float32
Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size
180,180,180, pixel 1.38, shown at level 0.0781, step 1, values float32
Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size
180,180,180, pixel 1.38, shown at level 0.0892, step 1, values float32
Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32
Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size
180,180,180, pixel 1.38, shown at level 0.0708, step 1, values float32
Log from Thu Sep 26 13:06:28 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/ruchigautamsharma/Desktop/25HepE525K/interaction
> 25HepE525K.cxs"
Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83,
shown at level 0.047, step 1, values float32
Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid
size 180,180,180, pixel 1.38, shown at level 0.0903, step 1, values float32
Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size
180,180,180, pixel 1.38, shown at level 0.0709, step 1, values float32
Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size
180,180,180, pixel 1.38, shown at level 0.0781, step 1, values float32
Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size
180,180,180, pixel 1.38, shown at level 0.0892, step 1, values float32
Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32
Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size
180,180,180, pixel 1.38, shown at level 0.0708, step 1, values float32
Log from Wed Sep 25 04:14:14 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_20240903.cxs
Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83,
shown at level 0.033, step 1, values float32
Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid
size 180,180,180, pixel 1.38, shown at level 0.0903, step 1, values float32
Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size
180,180,180, pixel 1.38, shown at level 0.0709, step 1, values float32
Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size
180,180,180, pixel 1.38, shown at level 0.0781, step 1, values float32
Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size
180,180,180, pixel 1.38, shown at level 0.0892, step 1, values float32
Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32
Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size
180,180,180, pixel 1.38, shown at level 0.0708, step 1, values float32
Log from Tue Sep 3 19:15:56 2024 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: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ruchigautamsharma/Downloads/cryosparc_P30_J277_005_volume_map_sharp.mrc
Opened cryosparc_P30_J277_005_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.83, shown at level 0.061, step 2, values float32
> set bgColor white
> color #1 #699dbfff models
> color #1 #6b98bfff models
> surface dust #1 size 8.3
> transparency 50
> volume #1 level 0.04162
> volume #1 step 1
> volume #1 level 0.04802
> open /Users/ruchigautamsharma/Desktop/pdbs/8g4l.pdb
Summary of feedback from opening
/Users/ruchigautamsharma/Desktop/pdbs/8g4l.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER CONTRACTILE PROTEIN 2023-02-10 XXXX
Chain information for 8g4l.pdb #2
---
Chain | Description
A B | No description available
C D | No description available
E F | No description available
G H | No description available
I J | No description available
K L | No description available
M N | No description available
> ui mousemode right select
Drag select of 62714 atoms, 4 pseudobonds
> ui mousemode right translate
> select /E
5809 atoms, 5816 bonds, 355 residues, 1 model selected
> hide sel atoms
> select /F
5809 atoms, 5816 bonds, 355 residues, 1 model selected
> hide sel atoms
> select /G
5820 atoms, 5829 bonds, 357 residues, 1 model selected
> hide sel atoms
> select /H
5820 atoms, 5829 bonds, 357 residues, 1 model selected
> hide sel atoms
> select /I
5683 atoms, 5699 bonds, 350 residues, 1 model selected
> hide sel atoms
> select /J
5683 atoms, 5699 bonds, 350 residues, 1 model selected
> hide sel atoms
> select /K
5823 atoms, 5842 bonds, 359 residues, 1 model selected
> hide sel atoms
> select /L
5823 atoms, 5842 bonds, 359 residues, 1 model selected
> hide sel atoms
> select /L
5823 atoms, 5842 bonds, 359 residues, 1 model selected
> select /M
5809 atoms, 5829 bonds, 358 residues, 1 model selected
> hide sel atoms
> select /M
5809 atoms, 5829 bonds, 358 residues, 1 model selected
> select /N
5809 atoms, 5829 bonds, 358 residues, 1 model selected
> hide sel atoms
> ui mousemode right select
Drag select of 39683 atoms, 4 pseudobonds
> select clear
Drag select of 31714 atoms, 4 pseudobonds
> select clear
Drag select of 41883 atoms, 4 pseudobonds
> show sel cartoons
> hide sel atoms
> ui mousemode right "translate selected models"
> select add #2
99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 2 models selected
> view matrix models #2,1,0,0,-145.97,0,1,0,-273.41,0,0,1,-71.128
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.33201,0.77488,0.53789,-305.02,0.61793,-0.25218,0.7447,-219.31,0.7127,0.57962,-0.39509,36.051
> view matrix models
> #2,0.68978,-0.71496,0.11413,226.44,-0.050952,0.10931,0.9927,-277.33,-0.72222,-0.69057,0.038968,877.43
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.68978,-0.71496,0.11413,251.77,-0.050952,0.10931,0.9927,-152.19,-0.72222,-0.69057,0.038968,779.18
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.78513,-0.60169,0.14676,156.66,0.1682,0.43522,0.88447,-322.45,-0.59606,-0.66974,0.44291,558.11
> view matrix models
> #2,-0.50413,0.63042,0.59027,-182.3,0.83794,0.19158,0.51104,-264.56,0.20909,0.75224,-0.62484,116.61
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.50413,0.63042,0.59027,-238.07,0.83794,0.19158,0.51104,-324.86,0.20909,0.75224,-0.62484,-90.886
> view matrix models
> #2,-0.50413,0.63042,0.59027,-157.14,0.83794,0.19158,0.51104,-349.51,0.20909,0.75224,-0.62484,-89.187
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.64055,0.44273,0.62745,-45.163,0.76397,0.28458,0.57911,-397.18,0.077832,0.8503,-0.52052,-136.51
> view matrix models
> #2,-0.53777,0.61178,0.58011,-133.79,0.81962,0.21814,0.52975,-363.7,0.19755,0.76035,-0.61874,-91.81
> ui mousemode right select
Drag select of 57 atoms, 260 residues
> hide sel cartoons
> hide sel atoms
Drag select of 68 residues
Drag select of 120 residues
> hide sel cartoons
> select add #2
99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.53777,0.61178,0.58011,-133.74,0.81962,0.21814,0.52975,-360.37,0.19755,0.76035,-0.61874,-108
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.82313,0.40245,0.40062,100.33,0.56745,0.60968,0.55344,-466.49,-0.021518,0.68288,-0.73021,26.515
> open /Users/ruchigautamsharma/Desktop/pdbs/8act.pdb
8act.pdb title:
Structure of the human β-cardiac myosin folded-back off state [more info...]
Chain information for 8act.pdb #3
---
Chain | Description | UniProt
A B | myosin-7 | MYH7_HUMAN 3-906
C D | myosin light chain 3 | MYL3_HUMAN 39-195
E F | myosin regulatory light chain 2, ventricular/cardiac muscle isoform |
MLRV_HUMAN 20-163
Non-standard residues in 8act.pdb #3
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
PO4 — phosphate ion
> select add #3
118674 atoms, 119507 bonds, 23 pseudobonds, 8474 residues, 5 models selected
> select subtract #2
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,4.2373,0,1,0,-97.37,0,0,1,-63.243
> view matrix models #3,1,0,0,2.676,0,1,0,-7.5822,0,0,1,-6.9289
> view matrix models #3,1,0,0,-28.537,0,1,0,-116.48,0,0,1,-73.257
> view matrix models #3,1,0,0,-74.431,0,1,0,-86.716,0,0,1,-91.941
> view matrix models #3,1,0,0,-77.549,0,1,0,-89.295,0,0,1,-82.343
> hide #!1 models
> open /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J279_map.mrc
Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83,
shown at level 0.0557, step 2, values float32
> select subtract #3
Nothing selected
> select add #4
2 models selected
> view matrix models #4,1,0,0,-3.5551,0,1,0,1.2444,0,0,1,9.7098
> view matrix models #4,1,0,0,-29.5,0,1,0,31.846,0,0,1,74.225
> volume #4 level 0.03328
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.91868,-0.12918,-0.37327,255.55,-0.23246,-0.5872,0.77534,174.17,-0.31934,0.79907,0.50942,65.389
> view matrix models
> #4,-0.91602,-0.1276,-0.38031,255.91,-0.21581,-0.6424,0.73535,184.54,-0.33814,0.75567,0.56091,66.973
> view matrix models
> #4,-0.8978,-0.097493,-0.42947,255.87,-0.045054,-0.94974,0.30978,258.35,-0.43809,0.29747,0.84829,104
> view matrix models
> #4,0.93714,0.02002,0.34839,-67.977,0.070672,-0.98855,-0.1333,304.93,0.34173,0.14954,-0.92782,253.19
> transparency sel 50
> view matrix models
> #4,0.98946,0.13009,0.063575,-53.463,0.13724,-0.98257,-0.1254,295.46,0.046154,0.13281,-0.99007,297.27
> surface dust #4 size 8.3
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.98946,0.13009,0.063575,-55.693,0.13724,-0.98257,-0.1254,243.61,0.046154,0.13281,-0.99007,230.84
> select subtract #4
Nothing selected
> select add #4
2 models selected
> hide #!2 models
> view matrix models
> #4,0.98946,0.13009,0.063575,-17.14,0.13724,-0.98257,-0.1254,238.58,0.046154,0.13281,-0.99007,218.87
> view matrix models
> #4,0.98946,0.13009,0.063575,-14.137,0.13724,-0.98257,-0.1254,247.93,0.046154,0.13281,-0.99007,226.91
> fitmap #3 inMap #4
Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834
atoms
average map value = 0.06921, steps = 132
shifted from previous position = 3.77
rotated from previous position = 11.1 degrees
atoms outside contour = 3445, contour level = 0.033285
Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99530642 -0.04985030 0.08294620 -93.88397645
-0.05708112 -0.99455248 0.08721873 330.44446938
0.07814647 -0.09154402 -0.99272998 332.89917405
Axis -0.99882356 0.02681814 -0.04040165
Axis point 0.00000000 171.51399022 160.98585768
Rotation angle (degrees) 174.86592494
Shift along axis 89.18575633
> color #4 #a1d7ff80 models
> color #4 #76ffcf80 models
> view matrix models
> #4,0.98946,0.13009,0.063575,-14.422,0.13724,-0.98257,-0.1254,247.38,0.046154,0.13281,-0.99007,228.5
> fitmap #3 inMap #4
Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834
atoms
average map value = 0.06921, steps = 72
shifted from previous position = 1.7
rotated from previous position = 0.0115 degrees
atoms outside contour = 3448, contour level = 0.033285
Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99528837 -0.04999379 0.08307632 -93.87652160
-0.05723957 -0.99453995 0.08725781 330.47220450
0.07826037 -0.09160194 -0.99271567 332.89509969
Axis -0.99881903 0.02689404 -0.04046312
Axis point 0.00000000 171.52859786 160.98201658
Rotation angle (degrees) 174.86310814
Shift along axis 89.18341503
> ui mousemode right translate
> show #!2 models
> hide #!3 models
> select add #2
99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 4 models selected
> select subtract #2
2 models selected
> select add #2
99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 4 models selected
> select subtract #4
99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.82313,0.40245,0.40062,100.26,0.56745,0.60968,0.55344,-467.99,-0.021518,0.68288,-0.73021,28.334
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.98302,0.15318,0.10103,348.35,0.18276,0.76793,0.61391,-438.53,0.016457,0.62195,-0.78289,59.345
> view matrix models
> #2,-0.8026,0.36897,0.46871,89.465,0.5558,0.74787,0.36301,-472.01,-0.2166,0.55187,-0.80531,169.18
> fitmap #2 inMap #4
Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840
atoms
average map value = 0.03324, steps = 1916
shifted from previous position = 40
rotated from previous position = 19.9 degrees
atoms outside contour = 75314, contour level = 0.033285
Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.89768062 0.39496708 0.19537273 171.38448995
-0.43446605 -0.71933681 -0.54202750 713.12497930
-0.07354423 -0.57145040 0.81733450 187.01973679
Axis -0.03372507 0.30823754 -0.95071144
Axis point 167.14028490 366.03689970 0.00000000
Rotation angle (degrees) 154.13723635
Shift along axis 36.23013114
> volume #4 step 1
> select subtract #2
Nothing selected
> color #4 #7cc1f980 models
> show #!3 models
> save /Users/ruchigautamsharma/Desktop/image5.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie4.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie4.mp4
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:524-525
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #2/A:524-526
56 atoms, 55 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 56 atom styles
> rainbow sel
> select #2/A:940
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/A:939-940
44 atoms, 43 bonds, 2 residues, 1 model selected
> select
> #2/A:10-16,20-27,82-84,90-92,98-111,136-142,154-168,184-199,216-231,271-273,284-291,295-301,307-309,311-314,325-338,343-359,379-388,393-400,417-447,473-504,518-524,530-539,545-555,604-611,615-618,647-662,686-696,698-707,715-723,738-748,753-755,769-826,829-836,842-919,922-1171
11821 atoms, 11850 bonds, 720 residues, 1 model selected
> ui mousemode right translate
> select #2/A:903
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:903-904
39 atoms, 38 bonds, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> select #2/B:903
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/B:903-904
39 atoms, 38 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 39 atom styles
> rainbow sel
> close #1
> volume #4 level 0.04236
> ui mousemode right distance
> distance #2/B:903@OE2 #2/A:525@CD
Distance between 8g4l.pdb #2/B GLU 903 OE2 and /A GLU 525 CD: 7.678Å
> save /Users/ruchigautamsharma/Desktop/image6.png supersample 3
> open
> "/Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_00_00027_volume
> (1).mrc"
Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc as #5, grid size
180,180,180, pixel 1.38, shown at level 0.123, step 1, values float32
> flip volume #5
Unknown command: flip volume #5
> volume flip #5
Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid
size 180,180,180, pixel 1.38, shown at step 1, values float32
> select add #6
39 atoms, 38 bonds, 2 residues, 3 models selected
> select add #2
99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 5 models selected
> select subtract #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-12.543,0,1,0,-4.9141,0,0,1,-59.886
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.97719,-0.1898,-0.095255,24.452,0.21213,0.85157,0.47941,-74.838,-0.0098755,-0.48869,0.8724,14.37
> view matrix models
> #6,0.9436,-0.26902,-0.193,50.243,0.32425,0.63294,0.70303,-91.715,-0.066973,-0.72595,0.68448,72.907
> view matrix models
> #6,0.94098,-0.27295,-0.20014,51.932,0.33074,0.6159,0.71504,-92.063,-0.071902,-0.73903,0.66983,76.899
> view matrix models
> #6,-0.96802,-0.2488,0.032094,272.71,-0.24873,0.93529,-0.25172,66.645,0.032612,-0.25166,-0.96727,208.41
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.96802,-0.2488,0.032094,298.35,-0.24873,0.93529,-0.25172,67.863,0.032612,-0.25166,-0.96727,270.44
> view matrix models
> #6,-0.96802,-0.2488,0.032094,280.09,-0.24873,0.93529,-0.25172,73.622,0.032612,-0.25166,-0.96727,274.5
> view matrix models
> #6,-0.96802,-0.2488,0.032094,279.77,-0.24873,0.93529,-0.25172,74.716,0.032612,-0.25166,-0.96727,273.45
> close #5
> hide #!2 models
> hide #!3 models
> hide #!4 models
> volume #6 level 0.09029
> surface dust #6 size 13.8
> ui mousemode right translate
> select subtract #6
Nothing selected
> save /Users/ruchigautamsharma/Desktop/image7.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!3 models
> fitmap #4 inMap #6
Fit map cryosparc_P30_J279_map.mrc in map
cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip using 398148 points
correlation = 0.9513, correlation about mean = 0.6514, overlap = 4478
steps = 120, shift = 2.21, angle = 10.5 degrees
Position of cryosparc_P30_J279_map.mrc (#4) relative to
cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.99999913 -0.00034252 -0.00127077 249.21336620
0.00034239 -0.99999993 0.00010594 248.98589046
-0.00127081 0.00010551 0.99999919 -1.22511845
Axis -0.00063596 0.00005334 0.99999980
Axis point 124.58497705 124.51431379 0.00000000
Rotation angle (degrees) 179.98037890
Shift along axis -1.37032688
> show #!2 models
> show #!3 models
> undo
[Repeated 3 time(s)]
> select add #6
2 models selected
> hide #!3 models
> hide #!2 models
> ui mousemode right "translate selected models"
> fitmap #6 inMap #4
Fit map cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip in map
cryosparc_P30_J279_map.mrc using 102014 points
correlation = 0.9277, correlation about mean = 0.6892, overlap = 1011
steps = 48, shift = 0.0317, angle = 0.033 degrees
Position of cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip (#6)
relative to cryosparc_P30_J279_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.99999934 -0.00020646 -0.00113078 249.17086350
0.00020623 -0.99999996 0.00020732 248.95988727
-0.00113082 0.00020709 0.99999934 1.49527864
Axis -0.00056633 0.00010440 0.99999983
Axis point 124.57301229 124.49271938 0.00000000
Rotation angle (degrees) 179.98817733
Shift along axis 1.38015468
> select subtract #6
Nothing selected
> show #!2 models
> hide #!6 models
> fitmap #2 inMap #4
Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840
atoms
average map value = 0.03324, steps = 796
shifted from previous position = 21.2
rotated from previous position = 10.5 degrees
atoms outside contour = 78980, contour level = 0.04236
Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.89772325 0.39491741 0.19527728 171.44427967
-0.43436867 -0.71936134 -0.54207299 713.11865308
-0.07359913 -0.57145385 0.81732715 187.04031769
Axis -0.03368282 0.30824538 -0.95071039
Axis point 167.15705533 366.03494475 0.00000000
Rotation angle (degrees) 154.14213016
Shift along axis 36.21962762
> show #!3 models
> hide #!2 models
> fitmap #3 inMap #4
Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834
atoms
average map value = 0.06921, steps = 156
shifted from previous position = 2.77
rotated from previous position = 10.5 degrees
atoms outside contour = 5343, contour level = 0.04236
Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99530058 -0.04986346 0.08300844 -93.89354486
-0.05710589 -0.99454449 0.08729358 330.43411156
0.07820282 -0.09162362 -0.99271820 332.90953349
Axis -0.99882208 0.02682778 -0.04043159
Axis point 0.00000000 171.51509590 160.98648532
Rotation angle (degrees) 174.86146946
Shift along axis 89.18769933
> show #!2 models
> show #!6 models
> hide #!6 models
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_01_00027_volume.mrc
Opened cryosparc_P30_J280_class_01_00027_volume.mrc as #5, grid size
180,180,180, pixel 1.38, shown at level 0.12, step 1, values float32
> volume flip #6
Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip z flip as #7,
grid size 180,180,180, pixel 1.38, shown at step 1, values float32
> undo
> hide #!6 models
> show #!6 models
> hide #!7 models
> close #7
> volume flip #5
Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size
180,180,180, pixel 1.38, shown at step 1, values float32
> hide #!6 models
> close #5
> select add #7
2 models selected
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.84223,-0.48294,-0.23962,106.87,0.48671,0.48999,0.7232,-95.43,-0.23185,-0.72572,0.64774,158.93
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.84223,-0.48294,-0.23962,105.38,0.48671,0.48999,0.7232,-78.575,-0.23185,-0.72572,0.64774,170.33
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.95159,-0.22068,-0.21396,309.08,-0.18623,0.96771,-0.16985,66.446,0.24453,-0.12179,-0.96196,238.05
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.95159,-0.22068,-0.21396,310.5,-0.18623,0.96771,-0.16985,52.678,0.24453,-0.12179,-0.96196,229.62
> volume #7 level 0.07479
> surface dust #7 size 13.8
> fitmap #7 inMap #4
Fit map cryosparc_P30_J280_class_01_00027_volume.mrc z flip in map
cryosparc_P30_J279_map.mrc using 113502 points
correlation = 0.9643, correlation about mean = 0.8414, overlap = 1130
steps = 208, shift = 5.04, angle = 14.9 degrees
Position of cryosparc_P30_J280_class_01_00027_volume.mrc z flip (#7) relative
to cryosparc_P30_J279_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.99999966 -0.00026364 -0.00078820 249.12543022
0.00026376 -0.99999995 -0.00015099 248.98160004
-0.00078816 -0.00015120 0.99999968 1.49763888
Axis -0.00039360 -0.00007449 0.99999992
Axis point 124.54659569 124.50727948 0.00000000
Rotation angle (degrees) 179.98489106
Shift along axis 1.38103566
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> select subtract #7
Nothing selected
> volume #7 level 0.0619
> volume #7 level 0.07092
> save /Users/ruchigautamsharma/Desktop/image7.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4
> show #!6 models
> show #!4 models
> show #!3 models
> show #!2 models
> save
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_classes.cxs
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_02_00027_volume.mrc
Opened cryosparc_P30_J280_class_02_00027_volume.mrc as #5, grid size
180,180,180, pixel 1.38, shown at level 0.119, step 1, values float32
> volume flip #5
Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size
180,180,180, pixel 1.38, shown at step 1, values float32
> close #5
> select add #8
2 models selected
> hide #!3 models
> hide #!2 models
> hide #!6 models
> hide #!7 models
> view matrix models #8,1,0,0,2.8324,0,1,0,-4.8659,0,0,1,8.6713
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.96696,-0.17515,-0.18521,304.59,-0.10484,0.93554,-0.33731,57.912,0.23235,-0.30675,-0.92299,250.36
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.96696,-0.17515,-0.18521,302.83,-0.10484,0.93554,-0.33731,66.738,0.23235,-0.30675,-0.92299,248.15
> surface dust #8 size 13.8
> fitmap #8 inMap #4
Fit map cryosparc_P30_J280_class_02_00027_volume.mrc z flip in map
cryosparc_P30_J279_map.mrc using 58302 points
correlation = 0.9609, correlation about mean = 0.7291, overlap = 874.3
steps = 144, shift = 5.03, angle = 14.4 degrees
Position of cryosparc_P30_J280_class_02_00027_volume.mrc z flip (#8) relative
to cryosparc_P30_J279_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.99999916 0.00002492 -0.00129399 249.16805302
-0.00002528 -0.99999996 0.00027762 248.99198953
-0.00129399 0.00027765 0.99999912 1.50291671
Axis 0.00064340 -0.00013133 -0.99999978
Axis point 124.58607228 124.49433268 0.00000000
Rotation angle (degrees) 179.99856201
Shift along axis -1.37530370
> show #!7 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> select subtract #8
Nothing selected
> hide #!4 models
> volume #8 level 0.07811
> surface dust #8 size 13.8
> save /Users/ruchigautamsharma/Desktop/image7.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4
> show #!4 models
> show #!3 models
> show #!2 models
> hide #!8 models
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_04_00027_volume.mrc
Opened cryosparc_P30_J280_class_04_00027_volume.mrc as #5, grid size
180,180,180, pixel 1.38, shown at level 0.122, step 1, values float32
> volume flip #5
Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size
180,180,180, pixel 1.38, shown at step 1, values float32
> close #5
> select add #9
2 models selected
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.94987,-0.3125,-0.0095436,296.08,-0.29326,0.90112,-0.31935,89.841,0.1084,-0.30054,-0.94759,261.2
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.94987,-0.3125,-0.0095436,296.29,-0.29326,0.90112,-0.31935,94.465,0.1084,-0.30054,-0.94759,265.66
> surface dust #9 size 13.8
> fitmap #9 inMap #4
Fit map cryosparc_P30_J280_class_04_00027_volume.mrc z flip in map
cryosparc_P30_J279_map.mrc using 58281 points
correlation = 0.9434, correlation about mean = 0.6496, overlap = 833.5
steps = 116, shift = 5.59, angle = 6.08 degrees
Position of cryosparc_P30_J280_class_04_00027_volume.mrc z flip (#9) relative
to cryosparc_P30_J279_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.99999961 -0.00086803 -0.00014872 249.12096554
0.00086814 -0.99999934 -0.00074800 249.01468160
-0.00014807 -0.00074812 0.99999971 1.52412702
Axis -0.00007408 -0.00037371 0.99999993
Axis point 124.50649781 124.56168997 0.00000000
Rotation angle (degrees) 179.95026257
Shift along axis 1.41261188
> hide #!4 models
> select subtract #9
Nothing selected
> volume #9 level 0.07975
> show #!4 models
> hide #!4 models
> volume #9 level 0.08919
> save /Users/ruchigautamsharma/Desktop/image7.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4
> show #!4 models
> show #!3 models
> show #!2 models
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_05_00027_volume.mrc
Opened cryosparc_P30_J280_class_05_00027_volume.mrc as #5, grid size
180,180,180, pixel 1.38, shown at level 0.125, step 1, values float32
> volume flip #5
Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.38, shown at step 1, values float32
> close #5
> color #10 #4ab7ffff models
> color #10 #fbd6ffff models
> color #10 #ffb5b1ff models
> color #10 #f7b45cff models
> color #10 #30bdf7ff models
> hide #!9 models
> hide #!2 models
> hide #!3 models
> volume #10 level 0.09708
> select add #10
2 models selected
> view matrix models #10,1,0,0,3.1115,0,1,0,-2.0096,0,0,1,8.118
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.79927,-0.55558,-0.2291,334.52,-0.51624,0.8299,-0.21156,112.19,0.30768,-0.050826,-0.95013,212.13
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.79927,-0.55558,-0.2291,333.19,-0.51624,0.8299,-0.21156,115.1,0.30768,-0.050826,-0.95013,210.7
> surface dust #10 size 13.8
> fitmap #10 inMap #4
Fit map cryosparc_P30_J280_class_05_00027_volume.mrc z flip in map
cryosparc_P30_J279_map.mrc using 84424 points
correlation = 0.9741, correlation about mean = 0.8468, overlap = 1111
steps = 276, shift = 5.07, angle = 25.6 degrees
Position of cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) relative
to cryosparc_P30_J279_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.99999922 0.00035517 0.00119687 248.79666503
-0.00035522 -0.99999994 -0.00003695 249.05630070
0.00119686 -0.00003738 0.99999928 1.23988110
Axis -0.00059829 0.00001925 -0.99999982
Axis point 124.42007755 124.50606948 0.00000000
Rotation angle (degrees) 179.97964879
Shift along axis -1.38393827
> hide #!4 models
> save /Users/ruchigautamsharma/Desktop/image7.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4
> show #!4 models
> show #!2 models
> show #!3 models
> select subtract #10
Nothing selected
> hide #!10 models
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_08_00027_volume.mrc
Opened cryosparc_P30_J280_class_08_00027_volume.mrc as #5, grid size
180,180,180, pixel 1.38, shown at level 0.121, step 1, values float32
> volume flip #5
Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size
180,180,180, pixel 1.38, shown at step 1, values float32
> close #5
> volume #11 level 0.08441
> hide #!3 models
> hide #!2 models
> select add #11
2 models selected
> view matrix models #11,1,0,0,1.1155,0,1,0,-3.8677,0,0,1,5.8448
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.99209,-0.0053981,-0.12542,17.552,0.081093,0.7902,0.60746,-62.634,0.095827,-0.61282,0.78439,87.413
> view matrix models
> #11,0.99729,-0.013338,-0.072294,11.493,0.039229,0.92824,0.36991,-44.599,0.062172,-0.37174,0.92625,48.066
> view matrix models
> #11,0.96616,0.092495,-0.24077,23.583,0.23126,0.10267,0.96746,-47.711,0.1142,-0.99041,0.077802,210.68
> view matrix models
> #11,-0.87555,-0.41067,0.25448,270.56,-0.45727,0.87442,-0.16216,91.081,-0.15593,-0.25834,-0.95338,285.91
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.87555,-0.41067,0.25448,270.16,-0.45727,0.87442,-0.16216,97.04,-0.15593,-0.25834,-0.95338,295.44
> surface dust #11 size 13.8
> fitmap #11 inMap #4
Fit map cryosparc_P30_J280_class_08_00027_volume.mrc z flip in map
cryosparc_P30_J279_map.mrc using 102298 points
correlation = 0.8925, correlation about mean = 0.5767, overlap = 958.6
steps = 172, shift = 10.7, angle = 16.9 degrees
Position of cryosparc_P30_J280_class_08_00027_volume.mrc z flip (#11) relative
to cryosparc_P30_J279_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.99999904 -0.00116328 0.00074464 249.06176278
0.00116310 -0.99999929 -0.00024302 248.90777913
0.00074493 -0.00024215 0.99999969 1.24883054
Axis 0.00037212 -0.00012116 0.99999992
Axis point 124.45826735 124.52639149 0.00000000
Rotation angle (degrees) 179.93335425
Shift along axis 1.31135186
> volume #11 level 0.05725
> volume #11 level 0.06342
> volume #11 level 0.07083
> select subtract #11
Nothing selected
> hide #!4 models
> save /Users/ruchigautamsharma/Desktop/image7.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4
> show #!4 models
> show #!3 models
> show #!2 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!2 models
> hide #!3 models
> open /Users/ruchigautamsharma/Desktop/25HepE525K/8qyq.pdb
8qyq.pdb title:
Beta-cardiac myosin S1 fragment In the pre-powerstroke state complexed to
mavacamten [more info...]
Chain information for 8qyq.pdb #5
---
Chain | Description | UniProt
A B | myosin-7 | MYH7_BOVIN 1-807
C | myosin light chain 3 | MYL3_BOVIN 1-199
D | myosin light chain 3 | MYL3_BOVIN 1-199
Non-standard residues in 8qyq.pdb #5
---
ADP — adenosine-5'-diphosphate
BEF — beryllium trifluoride ion
FMT — formic acid
GOL — glycerol (glycerin; propane-1,2,3-triol)
MG — magnesium ion
XB2 —
6-[[(1~{S})-1-phenylethyl]amino]-3-propan-2-yl-1~{H}-pyrimidine-2,4-dione
> select #5/B
6497 atoms, 6383 bonds, 8 pseudobonds, 1018 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select #5/D
602 atoms, 605 bonds, 3 pseudobonds, 86 residues, 2 models selected
> hide sel cartoons
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.99553,0.05401,0.077471,-2.8146,-0.030633,0.96065,-0.27608,6.0307,-0.089333,0.27247,0.95801,-6.3562
> view matrix models
> #5,0.99476,0.059463,0.083204,-3.0609,-0.032039,0.95383,-0.29862,6.6171,-0.097119,0.29439,0.95074,-6.797
> view matrix models
> #5,0.84862,0.26572,-0.45743,1.348,0.52607,-0.33296,0.78255,20.637,0.05564,-0.90473,-0.42234,49.406
> view matrix models
> #5,-0.20948,0.94179,-0.26296,-32.356,0.63406,0.33555,0.69669,9.3355,0.74437,-0.020792,-0.66744,44.88
> view matrix models
> #5,-0.26135,0.93427,-0.24258,-33.342,0.74088,0.35525,0.57,12.994,0.61871,-0.030752,-0.78502,45.702
> view matrix models
> #5,-0.27941,0.93151,-0.23283,-33.736,0.77438,0.36199,0.51894,14.36,0.56769,-0.035305,-0.82249,45.838
> view matrix models
> #5,-0.37124,0.91598,-0.15218,-36.338,0.9014,0.39485,0.17771,22.376,0.22287,-0.071201,-0.97224,44.77
> view matrix models
> #5,-0.41927,0.90453,-0.077722,-38.282,0.90689,0.41333,-0.08192,27.324,-0.041974,-0.10483,-0.9936,42.18
> view matrix models
> #5,-0.44992,0.89092,0.061874,-41.255,0.77059,0.4223,-0.47733,33.225,-0.4514,-0.16708,-0.87654,35.351
> view matrix models
> #5,-0.31556,0.89055,0.32762,-44.738,0.035597,0.35613,-0.93376,33.51,-0.94824,-0.28299,-0.14408,15.954
> view matrix models
> #5,-0.16915,0.90579,0.3885,-44.23,-0.41809,0.29101,-0.86053,27.006,-0.89252,-0.30799,0.32948,7.6715
> view matrix models
> #5,-0.31793,0.89036,0.32585,-44.732,0.044144,0.35721,-0.93298,33.592,-0.94709,-0.28224,-0.15287,16.132
> view matrix models
> #5,-0.16449,0.90636,0.38916,-44.19,-0.4306,0.28897,-0.85503,26.761,-0.88742,-0.30822,0.34275,7.4794
> view matrix models
> #5,0.9568,-0.19924,0.21174,-0.56848,0.28104,0.4472,-0.84914,33.288,0.074496,0.87196,0.48387,-7.475
> view matrix models
> #5,0.93545,-0.26582,0.23296,0.14939,0.35203,0.64149,-0.68159,26.655,0.031741,0.71961,0.69366,-9.0199
> view matrix models
> #5,0.91741,-0.3204,0.23603,1.0211,0.39769,0.75969,-0.51451,21.332,-0.014464,0.56588,0.82436,-8.9778
> view matrix models
> #5,0.95721,-0.19796,0.21112,-0.57814,0.27948,0.44284,-0.85193,33.417,0.075155,0.87447,0.47922,-7.4258
> view matrix models
> #5,0.97238,-0.14881,0.17983,-0.79935,0.21341,0.25467,-0.94319,38.437,0.094555,0.95551,0.27939,-4.8593
> view matrix models
> #5,0.98941,-0.090123,0.11382,-0.49676,0.10944,-0.052142,-0.99262,44.656,0.095393,0.99456,-0.041726,0.82277
> view matrix models
> #5,-0.35779,-0.60534,0.71102,-20.504,0.19127,-0.79279,-0.57871,53.561,0.914,-0.07106,0.39943,26.714
> view matrix models
> #5,-0.60867,0.67803,0.41206,-45.977,-0.79266,-0.54248,-0.27823,28.041,0.034888,-0.49597,0.86764,13.998
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.60867,0.67803,0.41206,-23.555,-0.79266,-0.54248,-0.27823,128.79,0.034888,-0.49597,0.86764,182.06
> view matrix models
> #5,-0.60867,0.67803,0.41206,37.381,-0.79266,-0.54248,-0.27823,174.2,0.034888,-0.49597,0.86764,205.17
> view matrix models
> #5,-0.60867,0.67803,0.41206,99.031,-0.79266,-0.54248,-0.27823,162.54,0.034888,-0.49597,0.86764,155.36
> view matrix models
> #5,-0.60867,0.67803,0.41206,98.801,-0.79266,-0.54248,-0.27823,159.71,0.034888,-0.49597,0.86764,149.89
> view matrix models
> #5,-0.60867,0.67803,0.41206,105.09,-0.79266,-0.54248,-0.27823,156.53,0.034888,-0.49597,0.86764,147.11
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.23298,0.92288,0.30662,107.22,-0.95501,-0.15762,-0.25124,145.28,-0.18353,-0.35136,0.91808,139.83
> view matrix models
> #5,-0.098877,0.94921,0.29871,108.71,-0.97369,-0.030362,-0.22583,141.73,-0.20529,-0.31318,0.92724,138.51
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.098877,0.94921,0.29871,108.51,-0.97369,-0.030362,-0.22583,147.51,-0.20529,-0.31318,0.92724,141.89
> fitmap #5 inMap #4
Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943
atoms
average map value = 0.04173, steps = 400
shifted from previous position = 15.1
rotated from previous position = 20 degrees
atoms outside contour = 9505, contour level = 0.04236
Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.58239663 0.81290458 -0.00055383 102.85355786
0.70719581 0.50699846 0.49277443 96.93889710
0.40085939 0.28659850 -0.87015691 105.31002093
Axis -0.44484143 -0.86608184 -0.22807532
Axis point 21.76765973 0.00000000 42.22852380
Rotation angle (degrees) 166.60041068
Shift along axis -153.72915848
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.37977,0.92425,0.039174,104.73,-0.87919,-0.37378,0.29547,144.57,0.28774,0.077772,0.95455,140.89
> view matrix models
> #5,0.32827,-0.92374,-0.19734,159.88,0.44949,0.33651,-0.82748,170.74,0.83078,0.18294,0.52568,155.01
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.32827,-0.92374,-0.19734,161.33,0.44949,0.33651,-0.82748,156.99,0.83078,0.18294,0.52568,143.67
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.52982,-0.80788,-0.25811,162.9,0.69083,0.58764,-0.42123,146.68,0.49198,0.044868,0.86945,134.89
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.52982,-0.80788,-0.25811,162.52,0.69083,0.58764,-0.42123,163.45,0.49198,0.044868,0.86945,142.3
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.72386,-0.68979,0.014695,136.61,0.19093,-0.22074,-0.95646,184.86,0.66301,-0.68954,0.29149,172.48
> view matrix models
> #5,0.50281,-0.86437,-0.0066101,158.26,0.47814,0.28449,-0.83093,175.36,0.72011,0.41464,0.55634,143.83
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.50281,-0.86437,-0.0066101,160.27,0.47814,0.28449,-0.83093,157.85,0.72011,0.41464,0.55634,140.82
> view matrix models
> #5,0.50281,-0.86437,-0.0066101,169.69,0.47814,0.28449,-0.83093,74.983,0.72011,0.41464,0.55634,59.074
> view matrix models
> #5,0.50281,-0.86437,-0.0066101,164.23,0.47814,0.28449,-0.83093,100.24,0.72011,0.41464,0.55634,83.15
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.35446,-0.92893,-0.10696,165.58,0.84213,0.36685,-0.39528,94.756,0.40642,0.050033,0.91231,79.421
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.35446,-0.92893,-0.10696,172.36,0.84213,0.36685,-0.39528,136.98,0.40642,0.050033,0.91231,91.143
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.56298,-0.74543,0.35692,145.92,0.33568,-0.60087,-0.72544,157.6,0.75523,-0.2886,0.58851,110.05
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.56298,-0.74543,0.35692,130.04,0.33568,-0.60087,-0.72544,145.96,0.75523,-0.2886,0.58851,88.151
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.082785,-0.99082,0.10686,147.28,0.60357,-0.13517,-0.78577,140.83,0.793,-0.00055352,0.60922,81.985
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.082785,-0.99082,0.10686,146.82,0.60357,-0.13517,-0.78577,138.38,0.793,-0.00055352,0.60922,93.162
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.3921,-0.86583,0.3108,135.56,0.71686,-0.49931,-0.48661,141.85,0.57651,0.032004,0.81646,85.171
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.3921,-0.86583,0.3108,138.82,0.71686,-0.49931,-0.48661,142.44,0.57651,0.032004,0.81646,82.838
> fitmap #5 inMap #4
Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943
atoms
average map value = 0.07346, steps = 220
shifted from previous position = 13.1
rotated from previous position = 20.7 degrees
atoms outside contour = 3995, contour level = 0.04236
Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.48628488 -0.87349851 -0.02296421 131.98115481
-0.50944434 0.26206455 0.81962712 104.75313384
-0.70992497 0.41027126 -0.57243691 157.52284441
Axis -0.46589276 0.78183820 0.41433437
Axis point 115.26114932 0.00000000 25.56332067
Rotation angle (degrees) 153.93923432
Shift along axis 85.67806483
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 40 atom styles
> rainbow sel
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> show #!5 models
> select #5/A
6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select #5/C
1260 atoms, 1265 bonds, 172 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> hide sel atoms
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> select #5/A
6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> style sel ball
Changed 40 atom styles
> show sel cartoons
> select #5/A
6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected
> show sel cartoons
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> style sel ball
Changed 40 atom styles
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> style sel ball
Changed 40 atom styles
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> show sel atoms
> show sel cartoons
> hide sel atoms
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> style sel ball
Changed 40 atom styles
> select ::name="ADP"
108 atoms, 116 bonds, 4 residues, 2 models selected
> style sel & #!5 ball
Changed 54 atom styles
> rainbow sel & #!5
> select add #5
14997 atoms, 14795 bonds, 20 pseudobonds, 2294 residues, 4 models selected
> select add #3
33777 atoms, 33932 bonds, 39 pseudobonds, 4620 residues, 6 models selected
> select subtract #3
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> select ::name="ADP"
108 atoms, 116 bonds, 4 residues, 2 models selected
> select add #5
14997 atoms, 14795 bonds, 20 pseudobonds, 2294 residues, 4 models selected
> select subtract #5
54 atoms, 58 bonds, 2 residues, 1 model selected
> select ::name="ADP"
108 atoms, 116 bonds, 4 residues, 2 models selected
> style sel & #!5 ball
Changed 54 atom styles
> rainbow sel & #!5
> select #5/A
6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> color sel byhetero
> show #!3 models
> show #!2 models
> hide #!5 models
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> select subtract #5
Nothing selected
> hide #!3 models
> fitmap #2 inMap #4
Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840
atoms
average map value = 0.03324, steps = 212
shifted from previous position = 0.00596
rotated from previous position = 0.00292 degrees
atoms outside contour = 78983, contour level = 0.04236
Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.89771304 0.39493434 0.19528995 171.43072531
-0.43439308 -0.71937790 -0.54203144 713.12426462
-0.07357955 -0.57142130 0.81735167 187.01292814
Axis -0.03369168 0.30822422 -0.95071694
Axis point 167.15376056 366.03172418 0.00000000
Rotation angle (degrees) 154.14093715
Shift along axis 36.23002059
> hide #!2 models
> show #!3 models
> fitmap #3 inMap #4
Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834
atoms
average map value = 0.06921, steps = 64
shifted from previous position = 0.0125
rotated from previous position = 0.00171 degrees
atoms outside contour = 5339, contour level = 0.04236
Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99529777 -0.04988324 0.08303014 -93.89145014
-0.05712784 -0.99454304 0.08729576 330.45021647
0.07822245 -0.09162861 -0.99271620 332.90769160
Axis -0.99882138 0.02683827 -0.04044199
Axis point 0.00000000 171.52297541 160.98536353
Rotation angle (degrees) 174.86125937
Shift along axis 89.18605104
> show #!2 models
> show #!5 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> hide #!2 models
> fitmap #5 inMap #4
Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943
atoms
average map value = 0.07346, steps = 28
shifted from previous position = 0.026
rotated from previous position = 0.0648 degrees
atoms outside contour = 4000, contour level = 0.04236
Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.48597381 -0.87364307 -0.02402555 131.99331828
-0.50982761 0.26105496 0.81971099 104.73346858
-0.70986284 0.41060696 -0.57227324 157.51977670
Axis -0.46618686 0.78153309 0.41457912
Axis point 115.27505316 0.00000000 25.56334997
Rotation angle (degrees) 153.97413268
Shift along axis 85.62353087
> show #!3 models
> show #!2 models
> hide #!5 models
> hide #!2 models
> select add #3
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 3 models selected
> view matrix models
> #3,0.95172,-0.29911,0.069057,-20.803,0.28197,0.94071,0.18854,-169,-0.12136,-0.15997,0.97963,-13.019
> fitmap #3 inMap #4
Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834
atoms
average map value = 0.06921, steps = 76
shifted from previous position = 3.09
rotated from previous position = 0.00809 degrees
atoms outside contour = 5343, contour level = 0.04236
Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99529429 -0.04999011 0.08300768 -93.86164081
-0.05722488 -0.99454601 0.08719835 330.49357732
0.07819590 -0.09153812 -0.99272664 332.89632413
Axis -0.99882051 0.02688932 -0.04042956
Axis point 0.00000000 171.53441271 160.98537615
Rotation angle (degrees) 174.86666587
Shift along axis 89.17882775
> select subtract #3
Nothing selected
> show #!2 models
> select add #2
99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 3 models selected
> hide #!3 models
> view matrix models
> #2,-0.97957,0.18401,0.081197,326.1,0.20088,0.91487,0.35022,-426.82,-0.0098435,0.35937,-0.93314,214.54,#1,1,0,0,0,0,1,0,0,0,0,1,0
> fitmap #2 inMap #4
Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840
atoms
average map value = 0.03324, steps = 224
shifted from previous position = 2.05
rotated from previous position = 0.0135 degrees
atoms outside contour = 78989, contour level = 0.04236
Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.89780391 0.39481948 0.19510437 171.55908545
-0.43419345 -0.71946808 -0.54207170 713.11615692
-0.07364910 -0.57138713 0.81736929 187.01348437
Axis -0.03361936 0.30821036 -0.95072399
Axis point 167.18733995 366.02013285 0.00000000
Rotation angle (degrees) 154.15167345
Shift along axis 36.22387450
> show #!3 models
> select subtract #2
Nothing selected
> volume #4 level 0.03302
> hide #!3 models
> hide #!2 models
> show #!5 models
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> color sel byhetero
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> show sel atoms
> hide #!5 models
> show #!5 models
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> hide sel cartoons
> ui mousemode right translate
> volume #4 level 0.04236
> volume #4 level 0.08254
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> fitmap #5 inMap #4
Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943
atoms
average map value = 0.07346, steps = 28
shifted from previous position = 0.0249
rotated from previous position = 0.0574 degrees
atoms outside contour = 9432, contour level = 0.082538
Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.48625976 -0.87350889 -0.02310098 131.98359794
-0.50952602 0.26196441 0.81960836 104.75385886
-0.70988356 0.41031312 -0.57245827 157.52305140
Axis -0.46592829 0.78181077 0.41434616
Axis point 115.26244630 0.00000000 25.56654333
Rotation angle (degrees) 153.94551965
Shift along axis 85.67187553
> volume #4 level 0.06852
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.68456,-0.70867,0.17078,136.17,0.45982,-0.60159,-0.65319,142.81,0.56564,-0.36862,0.73768,90.628
> view matrix models
> #5,-0.67257,-0.72389,0.15376,136.39,0.47921,-0.58434,-0.6549,142.55,0.56392,-0.36678,0.7399,90.602
> fitmap #5 inMap #4
Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943
atoms
average map value = 0.07346, steps = 84
shifted from previous position = 0.173
rotated from previous position = 4.64 degrees
atoms outside contour = 7674, contour level = 0.068522
Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.48604532 -0.87361366 -0.02364530 131.98433118
-0.50971212 0.26139904 0.81967316 104.73161110
-0.70989682 0.41045061 -0.57234325 157.51876880
Axis -0.46610167 0.78163575 0.41448135
Axis point 115.26785562 0.00000000 25.56530335
Rotation angle (degrees) 153.96091166
Shift along axis 85.63244638
> ui mousemode right translate
> volume #4 level 0.05824
> hide sel cartoons
> show #!3 models
> show #!2 models
> volume #4 level 0.03582
> select subtract #5
Nothing selected
> select add #5
14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected
> save /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_3.cxs
> volume #4 level 0.04703
> volume #4 level 0.03302
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> save
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_20240903.cxs
> includeMaps true
——— End of log from Tue Sep 3 19:15:56 2024 ———
opened ChimeraX session
> volume #4 level 0.04423
> select
> #2/B:12-16,20-28,99-111,136-142,154-166,184-199,216-222,224-231,271-274,284-291,295-301,311-315,326-337,343-360,378-388,393-400,417-447,473-503,518-525,530-538,545-555,593-597,604-611,615-619,647-664,686-696,698-707,715-722,727-729,738-748,753-755,767-824,828-832,837-965,968-995,998-1165,1168-1171
11706 atoms, 11732 bonds, 715 residues, 1 model selected
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> volume #4 level 0.06198
> volume #4 level 0.05357
> volume #4 level 0.04703
> show #!3 models
> show #!2 models
> hide #!3 models
> select add #2
99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 3 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!10 models
> transparency #4.1#10.1 0
> hide #!4 models
> transparency #10.1 50
> ui mousemode right select
> hide #!10 models
Drag select of 18 residues
Drag select of 24 residues
> style sel ball
Changed 309 atom styles
> show sel atoms
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue M3L (net charge +1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/tmpytfstoqe/ante.in.mol2 -fi
mol2 -o
/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/tmpytfstoqe/ante.out.mol2 -fo
mol2 -c bcc -nc 1 -j 5 -s 2 -dr n
(M3L) ``
(M3L) `Welcome to antechamber 20.0: molecular input file processor.`
(M3L) ``
(M3L) `Info: Finished reading file
(/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/tmpytfstoqe/ante.in.mol2);
atoms read (43), bonds read (42).`
(M3L) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(M3L) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(M3L) ``
(M3L) ``
(M3L) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(M3L) `Info: Total number of electrons: 134; net charge: 1`
(M3L) ``
(M3L) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(M3L) ``
(M3L) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(M3L) ``
(M3L) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(M3L) ``
Charges for residue M3L determined
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 8g4l.pdb_A SES surface #2.2: minimum, -21.91, mean -0.65,
maximum 19.75
Coulombic values for 8g4l.pdb_B SES surface #2.3: minimum, -23.19, mean -0.75,
maximum 24.96
Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16,
maximum 15.27
Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34,
maximum 15.00
To also show corresponding color key, enter the above coulombic command and
add key true
> ui mousemode right translate
Drag select of 8g4l.pdb_B SES surface, 200 of 1516366 triangles, 8act.pdb_A
SES surface, 14 of 807322 triangles, 1 atoms, 12 residues
> select add #3
18867 atoms, 19195 bonds, 19 pseudobonds, 2331 residues, 7 models selected
> select add #2
118674 atoms, 119507 bonds, 24 pseudobonds, 8474 residues, 10 models selected
> select subtract #3
99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 7 models selected
> select subtract #2
2 models selected
> save /Users/ruchigautamsharma/Desktop/image1.png supersample 3
> show #!10 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> show #!10 models
> hide #!10 models
Drag select of 42 residues
> select add #3
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected
> select subtract #3
2 models selected
Drag select of 25 residues
> style sel ball
Changed 204 atom styles
> show sel atoms
> coulombic sel
Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16,
maximum 15.27
Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34,
maximum 15.00
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of 8act.pdb_B SES surface, 36 of 774284 triangles, 13 residues
Drag select of 8act.pdb_B SES surface, 335 of 774284 triangles, 1 atoms, 32
residues, 1 bonds
> style sel ball
Changed 263 atom styles
> show sel atoms
> coulombic sel
Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16,
maximum 15.27
Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34,
maximum 15.00
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of 20 atoms, 46 residues, 17 bonds
Drag select of 8act.pdb_A SES surface, 1775 of 807322 triangles, 8act.pdb_B
SES surface, 1980 of 774284 triangles, 44 atoms, 78 residues, 37 bonds
Drag select of 8act.pdb_B SES surface, 1283 of 774284 triangles, 62 atoms, 33
residues, 49 bonds
> coulombic sel
Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16,
maximum 15.27
Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34,
maximum 15.00
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!10 models
> select add #3
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected
> select subtract #3
2 models selected
> hide #!3 models
> show #!3 models
> hide #!10 models
> save /Users/ruchigautamsharma/Desktop/image2.png supersample 3
> hide #!3 models
> show #!2 models
> show #!10 models
> hide #!5 models
> ui mousemode right translate
> hide #!10 models
> ui mousemode right select
Drag select of 40 atoms, 31 residues, 37 bonds, 1 pseudobonds
> style sel ball
Changed 477 atom styles
> show sel atoms
> coulombic sel
Coulombic values for 8g4l.pdb_A SES surface #2.2: minimum, -21.91, mean -0.65,
maximum 19.75
Coulombic values for 8g4l.pdb_B SES surface #2.3: minimum, -23.19, mean -0.75,
maximum 24.96
To also show corresponding color key, enter the above coulombic command and
add key true
> ui mousemode right translate
> show #!10 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!10 models
> save /Users/ruchigautamsharma/Desktop/image3.png supersample 3
> save "/Users/ruchigautamsharma/Desktop/25HepE525K/interaction
> 25HepE525K.cxs" includeMaps true
——— End of log from Wed Sep 25 04:14:14 2024 ———
opened ChimeraX session
> select add #2
99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 3 models selected
> select subtract #2
2 models selected
> hide #!2 models
> ui mousemode right select
Drag select of 50 atoms, 26 residues, 42 bonds
Drag select of 8act.pdb_A SES surface, 9674 of 807322 triangles, 8act.pdb_B
SES surface, 2496 of 774284 triangles, 48 atoms, 91 residues, 38 bonds
Drag select of 8act.pdb_A SES surface, 5160 of 807322 triangles, 8act.pdb_B
SES surface, 2203 of 774284 triangles, 69 atoms, 95 residues, 57 bonds
> coulombic sel
Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16,
maximum 15.27
Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34,
maximum 15.00
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of 8act.pdb_A SES surface, 1211 of 807322 triangles, 8act.pdb_B
SES surface, 784 of 774284 triangles, 4 atoms, 22 residues, 4 bonds
> ui mousemode right translate
> ui mousemode right select
Drag select of 8act.pdb_A SES surface, 9181 of 807322 triangles, 8act.pdb_B
SES surface, 7593 of 774284 triangles, 46 atoms, 34 residues, 39 bonds
> select add #3
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected
> select subtract #3
2 models selected
Drag select of 8act.pdb_A SES surface, 45732 of 807322 triangles, 8act.pdb_B
SES surface, 16784 of 774284 triangles, 242 atoms, 415 residues, 1
pseudobonds, 201 bonds
> select add #3
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected
> select subtract #3
2 models selected
Drag select of 8act.pdb_A SES surface, 170 of 807322 triangles, 8act.pdb_B SES
surface, 459 of 774284 triangles
> ui mousemode right translate
> ui mousemode right select
Drag select of 8act.pdb_A SES surface, 40121 of 807322 triangles, 8act.pdb_B
SES surface, 13087 of 774284 triangles, 153 atoms, 281 residues, 127 bonds
> select add #3
18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
8act.pdb #3/D SER 195 OXT
8act.pdb #3/C SER 195 OXT
8act.pdb #3/E GLU 163 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16,
maximum 15.27
Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34,
maximum 15.00
Coulombic values for 8act.pdb_C SES surface #3.5: minimum, -22.56, mean -3.87,
maximum 14.68
Coulombic values for 8act.pdb_D SES surface #3.6: minimum, -19.82, mean -3.44,
maximum 15.48
Coulombic values for 8act.pdb_E SES surface #3.7: minimum, -20.97, mean -5.04,
maximum 8.16
Coulombic values for 8act.pdb_F SES surface #3.8: minimum, -22.95, mean -4.14,
maximum 7.43
To also show corresponding color key, enter the above coulombic command and
add key true
> ui mousemode right translate
> show #!10 models
> show #!4 models
> hide #!10 models
> select subtract #3
6 models selected
> hide #!3 models
> show #!10 models
> hide #!4 models
> show #!3 models
> save
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs
——— End of log from Thu Sep 26 13:06:28 2024 ———
opened ChimeraX session
> show #!2 models
> close #6
> close #7
> close #8
> close #9
> close #11
> save
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs
——— End of log from Thu Sep 26 13:21:30 2024 ———
opened ChimeraX session
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #10 level 0.07481
> show #!3 models
> show #!2 models
> hide #!2 models
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J276_map_sharp.mrc
Opened cryosparc_P30_J276_map_sharp.mrc as #6, grid size 300,300,300, pixel
0.83, shown at level 0.0289, step 2, values float32
> hide #!3 models
> select add #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-13.259,0,1,0,-59.644,0,0,1,-60.922
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.97989,-0.19467,-0.043828,17.497,0.19799,0.97586,0.092126,-93.748,0.024836,-0.09895,0.99478,-51.92
> undo
[Repeated 1 time(s)]
> volumeflip #6
Unknown command: volumeflip #6
> volume flip #6
Opened cryosparc_P30_J276_map_sharp.mrc z flip as #7, grid size 300,300,300,
pixel 0.83, shown at step 1, values float32
> select subtract #6
Nothing selected
> select add #7
2 models selected
> view matrix models
> #7,0.96691,0.024547,-0.25392,32.662,0.2299,0.34752,0.90905,-65.44,0.11056,-0.93735,0.33038,177.52
> view matrix models
> #7,-0.99755,-0.034454,-0.060947,267.99,-0.00070731,0.87544,-0.48332,74.136,0.070008,-0.48209,-0.87332,277.93
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.99755,-0.034454,-0.060947,269.51,-0.00070731,0.87544,-0.48332,81.793,0.070008,-0.48209,-0.87332,283.92
> fitmap #7 inMap #10
Fit map cryosparc_P30_J276_map_sharp.mrc z flip in map
cryosparc_P30_J280_class_05_00027_volume.mrc z flip using 270132 points
correlation = 0.765, correlation about mean = 0.4371, overlap = 1.18e+04
steps = 156, shift = 3.04, angle = 18.9 degrees
Position of cryosparc_P30_J276_map_sharp.mrc z flip (#7) relative to
cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) coordinates:
Matrix rotation and translation
0.99868521 -0.01194978 0.04985040 -4.14668671
0.01153380 0.99989629 0.00862389 -2.79643992
-0.04994828 -0.00803759 0.99871946 7.43685902
Axis -0.16040788 0.96080890 0.22608753
Axis point 148.17070643 0.00000000 88.18561170
Rotation angle (degrees) 2.97697945
Shift along axis -0.34030206
> ui mousemode right translate
> hide #!10 models
> volume #7 level 0.009114
> transparency sel 50
> show #!2 models
> volume #7 level 0.00811
> volume #7 level 0.00611
> volume #7 level 0.00111
> surface dust #7 size 8.3
> fitmap #2 inMap #7
Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J276_map_sharp.mrc z flip (#7)
using 99840 atoms
average map value = 0.07007, steps = 304
shifted from previous position = 0.129
rotated from previous position = 0.285 degrees
atoms outside contour = 75934, contour level = 0.00111
Position of 8g4l.pdb (#2) relative to cryosparc_P30_J276_map_sharp.mrc z flip
(#7) coordinates:
Matrix rotation and translation
0.90356614 -0.36251243 -0.22837025 69.94133890
0.42750669 0.72750591 0.53663133 -463.88516185
-0.02839482 -0.58251171 0.81232619 178.12186061
Axis -0.80838767 -0.14444773 0.57065245
Axis point 0.00000000 -62.59090162 802.47834953
Rotation angle (degrees) 43.80505846
Shift along axis 112.11311861
> show #!3 models
> select subtract #7
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J366_003_volume_map_sharp.mrc
Opened cryosparc_P30_J366_003_volume_map_sharp.mrc as #8, grid size
300,300,300, pixel 0.83, shown at level 0.0628, step 2, values float32
> volume flip #8
Opened cryosparc_P30_J366_003_volume_map_sharp.mrc z flip as #9, grid size
300,300,300, pixel 0.83, shown at step 1, values float32
> close #8
> close #6
> select add #9
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.72491,0.12345,-0.6777,107.22,-0.31498,0.93434,-0.16672,71.607,0.61261,0.33432,0.71619,-88.209
> view matrix models
> #9,-0.78393,-0.37061,0.49809,227.29,-0.46679,0.88081,-0.079276,87.942,-0.40935,-0.29465,-0.86349,320.77
> view matrix models
> #9,-0.9341,-0.13426,0.33081,241.15,-0.20068,0.96381,-0.17551,53.522,-0.29528,-0.23033,-0.92723,305.45
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.9341,-0.13426,0.33081,237.7,-0.20068,0.96381,-0.17551,58.891,-0.29528,-0.23033,-0.92723,312.4
> select subtract #9
Nothing selected
> hide #!9 models
> hide #!7 models
> show #!10 models
> show #!9 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!2 models
> fitmap #10 inMap #9
Fit map cryosparc_P30_J280_class_05_00027_volume.mrc z flip in map
cryosparc_P30_J366_003_volume_map_sharp.mrc z flip using 110989 points
correlation = 0.8661, correlation about mean = 0.6378, overlap = 1281
steps = 248, shift = 14.1, angle = 17.3 degrees
Position of cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) relative
to cryosparc_P30_J366_003_volume_map_sharp.mrc z flip (#9) coordinates:
Matrix rotation and translation
0.99912867 0.03701040 0.01929050 -6.45856044
-0.03695133 0.99931125 -0.00340957 4.82258956
-0.01940341 0.00269379 0.99980811 2.58781556
Axis 0.07292398 0.46232197 -0.88370838
Axis point 133.82942588 176.61647977 0.00000000
Rotation angle (degrees) 2.39837754
Shift along axis -0.52826911
> show #!2 models
> hide #!9 models
> fitmap #2 inMap #10
Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J280_class_05_00027_volume.mrc
z flip (#10) using 99840 atoms
average map value = 0.0705, steps = 2000
shifted from previous position = 42.4
rotated from previous position = 17.7 degrees
atoms outside contour = 75484, contour level = 0.074814
Position of 8g4l.pdb (#2) relative to
cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) coordinates:
Matrix rotation and translation
0.89869523 -0.39132784 -0.19801364 76.37796838
0.43305938 0.72042893 0.54170263 -464.23480660
-0.06932856 -0.57257723 0.81691423 184.96627548
Axis -0.80046161 -0.09244309 0.59221237
Axis point 0.00000000 -34.72317143 823.48795667
Rotation angle (degrees) 44.10881728
Shift along axis 91.31698418
> show #!9 models
> hide #!10 models
> surface dust #9 size 8.3
> volume #9 level 0.04335
> transparency #2.2-3#9.1 50
> volume #9 level 0.04552
> show #!3 models
> hide #!2 models
> fitmap #3 inMap #9
Fit molecule 8act.pdb (#3) to map cryosparc_P30_J366_003_volume_map_sharp.mrc
z flip (#9) using 18834 atoms
average map value = 0.07945, steps = 224
shifted from previous position = 13.7
rotated from previous position = 17.3 degrees
atoms outside contour = 5855, contour level = 0.045517
Position of 8act.pdb (#3) relative to
cryosparc_P30_J366_003_volume_map_sharp.mrc z flip (#9) coordinates:
Matrix rotation and translation
-0.99082281 0.08342546 -0.10635013 340.09974533
0.09230379 0.99239110 -0.08148569 -89.94149170
0.09874294 -0.09055440 -0.99098422 327.06025206
Axis -0.04413312 -0.99809091 0.04320662
Axis point 163.69830978 0.00000000 170.46022157
Rotation angle (degrees) 174.10287196
Shift along axis 88.89128906
> hide #!3 models
> show #!3 models
> save /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_4.cxs
——— End of log from Fri Sep 27 17:28:16 2024 ———
opened ChimeraX session
OpenGL version: 4.1 INTEL-22.5.11
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel 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: MacBookPro15,4
Processor Name: Quad-Core Intel Core i7
Processor Speed: 1.7 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
OS Loader Version: 580.140.1~8
Software:
System Software Overview:
System Version: macOS 14.6 (23G80)
Kernel Version: Darwin 23.6.0
Time since boot: 11 hours, 48 minutes
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
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: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
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: 1.5.14
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: 1.0.4
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: 1.12.4
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: 1.33.3
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: 0.2.1
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: 4.47.2
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: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
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: 10.2.0
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: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
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: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 13 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Unknown crash |
comment:2 by , 13 months ago
| Status: | accepted → feedback |
|---|
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Hi Ruchi,
--Eric