![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15689 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1-x86_64-i386-64bit
ChimeraX Version: 1.8rc202405282004 (2024-05-28 20:04:22 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 0x00007ff85474bb40 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 157 in asArray
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2828 in set_matrix
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 817 in set_projection_matrix
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 725 in _use_shader
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 801 in _opengl_shader
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 698 in shader
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 818 in _draw_geometry
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 787 in draw_self
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1554 in draw_opaque
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 258 in _draw_scene
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 307 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 53)
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{
"uptime" : 900000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
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"coalitionID" : 98869,
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"releaseType" : "User"
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"captureTime" : "2024-07-26 16:31:18.9729 -0400",
"codeSigningMonitor" : 0,
"incident" : "898E7521-13AB-4A72-9C0C-BA0E985AE630",
"pid" : 59344,
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"bug_type" : "309",
"procLaunch" : "2024-07-22 12:06:37.2136 -0400",
"procStartAbsTime" : 748316834145824,
"procExitAbsTime" : 906791666636185,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8-rc2024.05.28.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"crashReporterKey" : "FDC29741-6154-3BE4-FA2A-E996A55D5BE5",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
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"sleepWakeUUID" : "0ABB6D2E-E7D8-40CD-A0E0-DD7603D0C2E0",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487294295\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffefd000-7fffffefe000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":59344},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737487294295\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffefd000-7fffffefe000 [ 4K] r-x\/r-x SM=SHM ",
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"faultingThread" : 0,
"threads" : 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"deploymentId" : 400000007
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8rc202405282004 (2024-05-28)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20242905_epac2_sur1_whole_dock/Shibisaki Pared Down
> Models/Electrostatic Models/model002.03.pdb" format pdb
No such file/path: /Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
Rotations/Klein Lab Rotation/Epac2-SUR1
project/20242905_epac2_sur1_whole_dock/Shibisaki Pared Down
Models/Electrostatic Models/model002.03.pdb
> open "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.00.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.01.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.02.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.03.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.04.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.05.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.06.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.07.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.08.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.09.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.10.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.11.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.12.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.13.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.14.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.15.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.16.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.17.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.18.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.19.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.20.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.21.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.22.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.23.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.24.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.25.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.26.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.27.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.28.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.29.pdb"
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.00.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.01.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.02.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.03.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.04.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.05.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.06.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.07.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.08.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.09.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.10.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.11.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.12.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.13.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.14.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.15.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.16.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.17.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.18.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.19.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.20.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.21.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.22.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.23.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.24.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.25.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.26.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.27.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.28.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.29.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Chain information for model.000.00.pdb
---
Chain | Description
1.2/A | No description available
1.1/E | No description available
Chain information for model.000.01.pdb
---
Chain | Description
2.2/A | No description available
2.1/E | No description available
Chain information for model.000.02.pdb
---
Chain | Description
3.2/A | No description available
3.1/E | No description available
Chain information for model.000.03.pdb
---
Chain | Description
4.2/A | No description available
4.1/E | No description available
Chain information for model.000.04.pdb
---
Chain | Description
5.2/A | No description available
5.1/E | No description available
Chain information for model.000.05.pdb
---
Chain | Description
6.2/A | No description available
6.1/E | No description available
Chain information for model.000.06.pdb
---
Chain | Description
7.2/A | No description available
7.1/E | No description available
Chain information for model.000.07.pdb
---
Chain | Description
8.2/A | No description available
8.1/E | No description available
Chain information for model.000.08.pdb
---
Chain | Description
9.2/A | No description available
9.1/E | No description available
Chain information for model.000.09.pdb
---
Chain | Description
10.2/A | No description available
10.1/E | No description available
Chain information for model.000.10.pdb
---
Chain | Description
11.2/A | No description available
11.1/E | No description available
Chain information for model.000.11.pdb
---
Chain | Description
12.2/A | No description available
12.1/E | No description available
Chain information for model.000.12.pdb
---
Chain | Description
13.2/A | No description available
13.1/E | No description available
Chain information for model.000.13.pdb
---
Chain | Description
14.2/A | No description available
14.1/E | No description available
Chain information for model.000.14.pdb
---
Chain | Description
15.2/A | No description available
15.1/E | No description available
Chain information for model.000.15.pdb
---
Chain | Description
16.2/A | No description available
16.1/E | No description available
Chain information for model.000.16.pdb
---
Chain | Description
17.2/A | No description available
17.1/E | No description available
Chain information for model.000.17.pdb
---
Chain | Description
18.2/A | No description available
18.1/E | No description available
Chain information for model.000.18.pdb
---
Chain | Description
19.2/A | No description available
19.1/E | No description available
Chain information for model.000.19.pdb
---
Chain | Description
20.2/A | No description available
20.1/E | No description available
Chain information for model.000.20.pdb
---
Chain | Description
21.2/A | No description available
21.1/E | No description available
Chain information for model.000.21.pdb
---
Chain | Description
22.2/A | No description available
22.1/E | No description available
Chain information for model.000.22.pdb
---
Chain | Description
23.2/A | No description available
23.1/E | No description available
Chain information for model.000.23.pdb
---
Chain | Description
24.2/A | No description available
24.1/E | No description available
Chain information for model.000.24.pdb
---
Chain | Description
25.2/A | No description available
25.1/E | No description available
Chain information for model.000.25.pdb
---
Chain | Description
26.2/A | No description available
26.1/E | No description available
Chain information for model.000.26.pdb
---
Chain | Description
27.2/A | No description available
27.1/E | No description available
Chain information for model.000.27.pdb
---
Chain | Description
28.2/A | No description available
28.1/E | No description available
Chain information for model.000.28.pdb
---
Chain | Description
29.2/A | No description available
29.1/E | No description available
Chain information for model.000.29.pdb
---
Chain | Description
30.2/A | No description available
30.1/E | No description available
> set bgColor white
> hide #1.2 models
> hide #2.2 models
> hide #3.2 models
> hide #4.2 models
> hide #5.2 models
> hide #6.2 models
> hide #7.2 models
> hide #8.2 models
> hide #!9.1 models
> show #!9.1 models
> hide #9.2 models
> hide #10.2 models
> hide #11.2 models
> hide #12.2 models
> hide #13.2 models
> hide #14.2 models
> hide #15.2 models
> hide #16.2 models
> hide #17.2 models
> hide #18.2 models
> hide #19.2 models
> hide #20.2 models
> hide #21.2 models
> hide #22.2 models
> hide #23.2 models
> hide #24.2 models
> hide #25.2 models
> hide #26.2 models
> hide #27.2 models
> hide #28.2 models
> hide #29.2 models
> hide #30.2 models
> color
> #1.1#2.1#3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1#15.1#16.1#17.1#18.1#19.1#20.1#21.1#22.1#23.1#24.1#25.1#26.1#27.1#28.1#29.1#30.1#!1-30
> red
> surface
> #1.1#2.1#3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1#15.1#16.1#17.1#18.1#19.1#20.1#21.1#22.1#23.1#24.1#25.1#26.1#27.1#28.1#29.1#30.1#!1-30
> hide
> #1.2#2.2#3.2#4.2#5.2#6.2#7.2#8.2#9.2#10.2#11.2#12.2#13.2#14.2#15.2#16.2#17.2#18.2#19.2#20.2#21.2#22.2#23.2#24.2#25.2#26.2#27.2#28.2#29.2#30.2#!1-30#!1.1#!2.1#!3.1#!4.1#!5.1#!6.1#!7.1#!8.1#!9.1#!10.1#!11.1#!12.1#!13.1#!14.1#!15.1#!16.1#!17.1#!18.1#!19.1#!20.1#!21.1#!22.1#!23.1#!24.1#!25.1#!26.1#!27.1#!28.1#!29.1#!30.1
> target m
> show #1.2 models
> show #2.2 models
> show #3.2 models
> show #4.2 models
> show #5.2 models
> show #6.2 models
> show #7.2 models
> show #8.2 models
> show #9.2 models
> show #10.2 models
> show #11.2 models
> show #12.2 models
> show #13.2 models
> show #14.2 models
> show #15.2 models
> show #16.2 models
> show #!17.1 models
> hide #!17.1 models
> show #17.2 models
> show #18.2 models
> show #19.2 models
> show #20.2 models
> show #21.2 models
> show #22.2 models
> show #23.2 models
> show #24.2 models
> show #25.2 models
> show #26.2 models
> show #27.2 models
> show #28.2 models
> show #29.2 models
> show #30.2 models
> surface
> #1.2#2.2#3.2#4.2#5.2#6.2#7.2#8.2#9.2#10.2#11.2#12.2#13.2#14.2#15.2#16.2#17.2#18.2#19.2#20.2#21.2#22.2#23.2#24.2#25.2#26.2#27.2#28.2#29.2#30.2#!1-30
> color
> #1.2#2.2#3.2#4.2#5.2#6.2#7.2#8.2#9.2#10.2#11.2#12.2#13.2#14.2#15.2#16.2#17.2#18.2#19.2#20.2#21.2#22.2#23.2#24.2#25.2#26.2#27.2#28.2#29.2#30.2#!1-30
> red
> select ~sel & ##selected
Nothing selected
> hide
> #!1-30#!1.1-2#!2.1-2#!3.1-2#!4.1-2#!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2
> target m
> show #!1.1 models
> show #!2.1 models
> show #!3.1 models
> show #!4.1 models
> show #!5.1 models
> show #!6.1 models
> show #!7.1 models
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> show #!25.1 models
> show #!26.1 models
> show #!27.1 models
> show #!28.1 models
> show #!29.1 models
> show #!30.1 models
> color
> #1.1#2.1#3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1#15.1#16.1#17.1#18.1#19.1#20.1#21.1#22.1#23.1#24.1#25.1#26.1#27.1#28.1#29.1#30.1#!1-30
> cyan
> hide
> #!2-30#!1.1-2#!2.1-2#!3.1-2#!4.1-2#!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2
> target m
> show #!1.1 models
> show #!1.2 models
> save /Users/AmyDeLury/Desktop/image1.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model000.00.pdb" models #1
> close #1
> show #!2 models
> show #!2.1 models
> show #!2.2 models
> save /Users/AmyDeLury/Desktop/image1.png supersample 3
> close #2
> show #!3 models
> show #!3.1 models
> show #!3.2 models
> save /Users/AmyDeLury/Desktop/image2.png supersample 3
> close #3
> open "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.01.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Balanced
> Models/model.000.02.pdb"
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.01.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.02.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Chain information for model.000.01.pdb
---
Chain | Description
1.2/A | No description available
1.1/E | No description available
Chain information for model.000.02.pdb
---
Chain | Description
2.2/A | No description available
2.1/E | No description available
> hide #1.2 models
> hide #2.2 models
> color #1.1#2.1#!1-2 cyan
> surface #1.1#2.1#!1-2
> hide #!2.1 models
> show #2.2 models
> show #1.2 models
> hide #!2 models
> show #!2 models
> hide #!1.1 models
> color #1.2#2.2#!1-2 red
> surface #1.2#2.2#!1-2
> hide #!2.2 models
> hide #!1.2 models
> hide #!2 models
> show #!1.1 models
> show #!1.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.01.pdb" models #1
> close #1
> show #!2 models
> show #!2.1 models
> show #!2.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.02.pdb" models #2
> close #2.1
> close #2
> show #!4 models
> show #!4.1 models
> show #!4.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.03.pdb" models #4
> save /Users/AmyDeLury/Desktop/image3.png supersample 3
> close #4
> show #!5 models
> show #!5.1 models
> show #!5.2 models
> save /Users/AmyDeLury/Desktop/image4.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.04.pdb" models #5
> close #5
> show #!6 models
> show #!6.1 models
> show #!6.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.05.pdb" models #6
> save /Users/AmyDeLury/Desktop/image5.png supersample 3
> close #6
> show #!7 models
> show #!7.1 models
> show #!7.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.06.pdb" models #7
> save /Users/AmyDeLury/Desktop/image6.png supersample 3
> close #7
> show #!8 models
> show #!8.1 models
> show #!8.2 models
> hide #!8.2 models
> show #!8.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.07.pdb" models #8
> save /Users/AmyDeLury/Desktop/image7.png supersample 3
> close #8
> show #!9 models
> show #!9.1 models
> hide #!9.1 models
> show #!9.1 models
> show #!9.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.08.pdb" models #9
> save /Users/AmyDeLury/Desktop/image8.png supersample 3
> close #9
> show #!10 models
> show #!10.1 models
> show #!10.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.09.pdb" models #10
> save /Users/AmyDeLury/Desktop/image9.png supersample 3
> close #10
> show #!11 models
> show #!11.1 models
> show #!11.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.10.pdb" models #11
> save /Users/AmyDeLury/Desktop/image10.png supersample 3
> close #11
> show #!12 models
> show #!12.1 models
> show #!12.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.11.pdb" models #12
> save /Users/AmyDeLury/Desktop/image11.png supersample 3
> close #12
> show #!13.1 models
> show #!13.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.12.pdb" models #13
> save /Users/AmyDeLury/Desktop/image12.png supersample 3
> close #13
> show #!14 models
> show #!14.1 models
> show #!14.2 models
> hide #!14.2 models
> show #!14.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.13.pdb" models #14
> close #14
> show #!15 models
> show #!15.1 models
> show #!15.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.14.pdb" models #15
> save /Users/AmyDeLury/Desktop/image13.png supersample 3
> close #15
> show #!16 models
> show #!16.1 models
> show #!16.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.15.pdb" models #16
> save /Users/AmyDeLury/Desktop/image14.png supersample 3
> close #16
> show #!17 models
> show #!17.1 models
> show #!17.2 models
> save /Users/AmyDeLury/Desktop/image15.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.16.pdb" models #17
> open "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.13.pdb"
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/Modified
Models/model000.13.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Start residue of secondary structure not found: HELIX 1 1 VAL E 606 LEU E 615
1 10
Start residue of secondary structure not found: HELIX 2 2 LYS E 720 ALA E 727
1 8
Start residue of secondary structure not found: HELIX 3 3 VAL E 784 ILE E 789
1 6
Start residue of secondary structure not found: HELIX 4 4 LYS E 796 ALA E 805
1 10
Start residue of secondary structure not found: HELIX 5 5 GLN E 809 ASP E 813
1 5
13 messages similar to the above omitted
Chain information for model000.13.pdb
---
Chain | Description
1.2/A | No description available
1.1/E | No description available
> hide #!17 models
> hide #!17.1 models
> close #17
> surface #1
> color #1 cyan
> hide #!1.2 models
> hide #!1.1 models
> show #!1.2 models
> color #1.2#!1 red
> show #!1.1 models
> save /Users/AmyDeLury/Desktop/image16.png supersample 3
> close #1
> show #!18 models
> show #!18.1 models
> show #!18.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.17.pdb" models #18
> save /Users/AmyDeLury/Desktop/image17.png supersample 3
> close #18
> show #!19 models
> show #!19.1 models
> show #!19.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.18.pdb" models #19
> save /Users/AmyDeLury/Desktop/image18.png supersample 3
> close #19
> show #!20 models
> show #!20.1 models
> show #!20.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.19.pdb" models #20
> save /Users/AmyDeLury/Desktop/image19.png supersample 3
> close #20
> show #!21 models
> show #!21.1 models
> show #!21.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.20.pdb" models #21
> save /Users/AmyDeLury/Desktop/image20.png supersample 3
> close #21
> show #!22 models
> show #!22.1 models
> show #!22.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.21.pdb" models #22
> save /Users/AmyDeLury/Desktop/image21.png supersample 3
> close #22
> show #!23 models
> show #!23.1 models
> show #!23.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.22.pdb" models #23
> save /Users/AmyDeLury/Desktop/image22.png supersample 3
> close #23
> show #!24 models
> show #!24.1 models
> show #!24.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.23.pdb" models #24
> save /Users/AmyDeLury/Desktop/image23.png supersample 3
> close #24
> show #!25.1 models
> show #!25.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.24.pdb" models #25
> save /Users/AmyDeLury/Desktop/image24.png supersample 3
> close #25
> show #!26.1 models
> show #!26.2 models
> save /Users/AmyDeLury/Desktop/image25.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.25.pdb" models #26
> close #26
> show #!27 models
> show #!27.1 models
> show #!27.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.26.pdb" models #27
> save /Users/AmyDeLury/Desktop/image26.png supersample 3
> close #27#27.1-2
> show #!28.1 models
> show #!28.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.27.pdb" models #28
> save /Users/AmyDeLury/Desktop/image27.png supersample 3
> close #28
> show #!29.1 models
> show #!29.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.28.pdb" models #29
> save /Users/AmyDeLury/Desktop/image28.png supersample 3
> close #29
> show #!30 models
> show #!30.1 models
> show #!30.2 models
> save /Users/AmyDeLury/Desktop/image29.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.29.pdb"
> close #30
> open "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/Modified
> Models/model000.13.pdb" format pdb
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/Modified
Models/model000.13.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Start residue of secondary structure not found: HELIX 1 1 VAL E 606 LEU E 615
1 10
Start residue of secondary structure not found: HELIX 2 2 LYS E 720 ALA E 727
1 8
Start residue of secondary structure not found: HELIX 3 3 VAL E 784 ILE E 789
1 6
Start residue of secondary structure not found: HELIX 4 4 LYS E 796 ALA E 805
1 10
Start residue of secondary structure not found: HELIX 5 5 GLN E 809 ASP E 813
1 5
13 messages similar to the above omitted
Chain information for model000.13.pdb
---
Chain | Description
1.2/A | No description available
1.1/E | No description available
> close
> open "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.00.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.01.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.02.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.03.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.04.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.05.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.06.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.07.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.08.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.09.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.10.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.11.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.12.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.13.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.14.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.15.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.16.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.17.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.18.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.19.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.20.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.21.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.22.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.23.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.24.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.25.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.26.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.27.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/model.002.28.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Electrostatic
> Models/model.002.29.pdb"
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Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
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> surface
> hide
> #!1-30#!1.1-2#!2.1-2#!3.1-2#!4.1-2#!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2
> target m
> show
> #!1.1#!2.1#!3.1#!4.1#!5.1#!6.1#!7.1#!8.1#!9.1#!10.1#!11.1#!12.1#!13.1#!14.1#!15.1#!16.1#!17.1#!18.1#!19.1#!20.1#!21.1#!22.1#!23.1#!24.1#!25.1#!26.1#!27.1#!28.1#!29.1#!30.1
> target m
> color
> #1.1#2.1#3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1#15.1#16.1#17.1#18.1#19.1#20.1#21.1#22.1#23.1#24.1#25.1#26.1#27.1#28.1#29.1#30.1#!1-30
> red
> hide
> #!1.1#!2.1#!3.1#!4.1#!5.1#!6.1#!7.1#!8.1#!9.1#!10.1#!11.1#!12.1#!13.1#!14.1#!15.1#!16.1#!17.1#!18.1#!19.1#!20.1#!21.1#!22.1#!23.1#!24.1#!25.1#!26.1#!27.1#!28.1#!29.1#!30.1
> target m
> show #!30.2 models
> show #!29.2 models
> hide #!29.2 models
> hide #!30.2 models
> color #!1-30 cyan
> show
> #!1.1#!2.1#!3.1#!4.1#!5.1#!6.1#!7.1#!8.1#!9.1#!10.1#!11.1#!12.1#!13.1#!14.1#!15.1#!16.1#!17.1#!18.1#!19.1#!20.1#!21.1#!22.1#!23.1#!24.1#!25.1#!26.1#!27.1#!28.1#!29.1#!30.1
> target m
> color
> #1.1#2.1#3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1#15.1#16.1#17.1#18.1#19.1#20.1#21.1#22.1#23.1#24.1#25.1#26.1#27.1#28.1#29.1#30.1#!1-30
> cyan
> hide
> #!1.1#!2.1#!3.1#!4.1#!5.1#!6.1#!7.1#!8.1#!9.1#!10.1#!11.1#!12.1#!13.1#!14.1#!15.1#!16.1#!17.1#!18.1#!19.1#!20.1#!21.1#!22.1#!23.1#!24.1#!25.1#!26.1#!27.1#!28.1#!29.1#!30.1
> target m
> show #!1.2 models
> hide #!1.2 models
> show
> #!1.2#!2.2#!3.2#!4.2#!5.2#!6.2#!7.2#!8.2#!9.2#!10.2#!11.2#!12.2#!13.2#!14.2#!15.2#!16.2#!17.2#!18.2#!19.2#!20.2#!21.2#!22.2#!23.2#!24.2#!25.2#!26.2#!27.2#!28.2#!29.2#!30.2
> target m
> color
> #1.2#2.2#3.2#4.2#5.2#6.2#7.2#8.2#9.2#10.2#11.2#12.2#13.2#14.2#15.2#16.2#17.2#18.2#19.2#20.2#21.2#22.2#23.2#24.2#25.2#26.2#27.2#28.2#29.2#30.2#!1-30
> red
> hide
> #!1.2#!2.2#!3.2#!4.2#!5.2#!6.2#!7.2#!8.2#!9.2#!10.2#!11.2#!12.2#!13.2#!14.2#!15.2#!16.2#!17.2#!18.2#!19.2#!20.2#!21.2#!22.2#!23.2#!24.2#!25.2#!26.2#!27.2#!28.2#!29.2#!30.2
> target m
> show #!1.1 models
> show #!1.2 models
> save /Users/AmyDeLury/Desktop/image1.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.00.pdb" models #1
> close #1
> show #!2.1 models
> show #!2.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.01.pdb"
> save /Users/AmyDeLury/Desktop/image1.png supersample 3
> close #2
> show #!3.1 models
> show #!3.2 models
> save /Users/AmyDeLury/Desktop/image2.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.02.pdb" models #3
> close #3
> show #!4.1 models
> show #!4.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.03.pdb" models #4
> save /Users/AmyDeLury/Desktop/image3.png supersample 3
> close #4
> show #!5.1 models
> show #!5.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.04.pdb" models #5
> save /Users/AmyDeLury/Desktop/image4.png supersample 3
> close #5
> show #!6.1 models
> hide #!6.1 models
> show #!6.2 models
> show #!6.1 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.05.pdb" models #6
> save /Users/AmyDeLury/Desktop/image5.png supersample 3
> close #6
> show #!7.1 models
> show #!7.2 models
> save /Users/AmyDeLury/Desktop/image6.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.06.pdb" models #7
> close #7
> show #!8.1 models
> show #!8.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.07.pdb" models #8
> save /Users/AmyDeLury/Desktop/image7.png supersample 3
> close #8
> show #!9.1 models
> show #!9.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.08.pdb" models #9
> save /Users/AmyDeLury/Desktop/image8.png supersample 3
> close #9
> show #!10.1 models
> show #!10.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.09.pdb" models #10
> save /Users/AmyDeLury/Desktop/image9.png supersample 3
> close #10
> show #!11.2 models
> show #!11.1 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.10.pdb" models #11
> save /Users/AmyDeLury/Desktop/image10.png supersample 3
> close #11
> show #!12.1 models
> hide #!13 models
> show #!13 models
> show #!12.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.11.pdb" models #12
> save /Users/AmyDeLury/Desktop/image11.png supersample 3
> close #12
> show #!13.1 models
> show #!13.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.12.pdb" models #13
> save /Users/AmyDeLury/Desktop/image12.png supersample 3
> close #13
> show #!14.1 models
> show #!14.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.13.pdb" models #14
> save /Users/AmyDeLury/Desktop/image13.png supersample 3
> close #14
> show #!15.1 models
> show #!15.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.14.pdb" models #15
> save /Users/AmyDeLury/Desktop/image14.png supersample 3
> close #15
> show #!16.1 models
> show #!16.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.15.pdb" models #16
> save /Users/AmyDeLury/Desktop/image15.png supersample 3
> close #16
> show #!17.1 models
> show #!17.2 models
> save /Users/AmyDeLury/Desktop/image16.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.16.pdb" models #17
> close #17
> show #!18.1 models
> show #!18.2 models
> save /Users/AmyDeLury/Desktop/image17.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.17.pdb" models #18
> close #18
> show #!19.1 models
> show #!19.2 models
> hide #!19.2 models
> show #!19.2 models
> save /Users/AmyDeLury/Desktop/image18.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.18.pdb" models #19
> close #19
> show #!20.1 models
> show #!20.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.19.pdb" models #20
> save /Users/AmyDeLury/Desktop/image19.png supersample 3
> close #20
> show #!21.1 models
> show #!21.2 models
> save /Users/AmyDeLury/Desktop/image20.png supersample 3
No model chosen to save relative to
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.20.pdb" models #21
> close #21
> show #!22.1 models
> show #!22.2 models
> save /Users/AmyDeLury/Desktop/image21.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.21.pdb" models #22
> close #22.1
> close #22
> show #!23.1 models
> show #!23.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.22.pdb" models #23
> save /Users/AmyDeLury/Desktop/image22.png supersample 3
> close #23
> show #!24.1 models
> show #!24.2 models
> hide #!24.2 models
> show #!24.2 models
> save /Users/AmyDeLury/Desktop/image23.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.23.pdb" models #24
> close #24
> show #!25.1 models
> show #!25.2 models
> save /Users/AmyDeLury/Desktop/image24.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.24.pdb" models #25
> close #25
> show #!26.1 models
> show #!26.2 models
> save /Users/AmyDeLury/Desktop/image25.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.25.pdb" models #26
> close #26
> show #!27.1 models
> show #!27.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.26.pdb" models #27
> save /Users/AmyDeLury/Desktop/image26.png supersample 3
> close #27
> show #!28.1 models
> show #!28.2 models
> save /Users/AmyDeLury/Desktop/image27.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.27.pdb" models #28
> close #28
> show #!29.1 models
> show #!29.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.28.pdb" models #29
> save /Users/AmyDeLury/Desktop/image28.png supersample 3
> close #29
> show #!30.1 models
> hide #!30.1 models
> show #!30.2 models
> show #!30.1 models
> save /Users/AmyDeLury/Desktop/image29.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Electrostatic Models/Modified
> Models/model002.29.pdb"
> close #30
> open "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.00.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.01.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.02.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.03.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.04.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.05.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.06.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.07.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.08.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.09.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.10.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.11.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.12.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.13.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.14.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.15.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.16.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.17.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.18.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.19.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.20.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.21.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.22.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.23.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.24.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.25.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.26.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.27.pdb" "/Users/AmyDeLury/Downloads/UB (University at
> Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model.004.28.pdb"
> "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab Rotations/Klein
> Lab Rotation/Epac2-SUR1 project/20240719_Shibisaki_model/Hydrophobic
> Models/model.004.29.pdb"
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Chain | Description
18.2/A | No description available
18.1/E | No description available
Chain information for model.004.18.pdb
---
Chain | Description
19.2/A | No description available
19.1/E | No description available
Chain information for model.004.19.pdb
---
Chain | Description
20.2/A | No description available
20.1/E | No description available
Chain information for model.004.20.pdb
---
Chain | Description
21.2/A | No description available
21.1/E | No description available
Chain information for model.004.21.pdb
---
Chain | Description
22.2/A | No description available
22.1/E | No description available
Chain information for model.004.22.pdb
---
Chain | Description
23.2/A | No description available
23.1/E | No description available
Chain information for model.004.23.pdb
---
Chain | Description
24.2/A | No description available
24.1/E | No description available
Chain information for model.004.24.pdb
---
Chain | Description
25.2/A | No description available
25.1/E | No description available
Chain information for model.004.25.pdb
---
Chain | Description
26.2/A | No description available
26.1/E | No description available
Chain information for model.004.26.pdb
---
Chain | Description
27.2/A | No description available
27.1/E | No description available
Chain information for model.004.27.pdb
---
Chain | Description
28.2/A | No description available
28.1/E | No description available
Chain information for model.004.28.pdb
---
Chain | Description
29.2/A | No description available
29.1/E | No description available
Chain information for model.004.29.pdb
---
Chain | Description
30.2/A | No description available
30.1/E | No description available
> surface
> ui windowfill toggle
> hide
> #!1-30#!1.1-2#!2.1-2#!3.1-2#!4.1-2#!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2
> target m
> show #!1.1 models
> show #!2.1 models
> show #!3.1 models
> show #!4.1 models
> show #!5.1 models
> show #!6.1 models
> show #!7.1 models
> show #!8.1 models
> show #!9.1 models
> show #!10.1 models
> show #!11.1 models
> show #!12.1 models
> show #!13.1 models
> show #!14.1 models
> show #!15.2 models
> hide #!15.2 models
> show #!15.1 models
> show #!16.1 models
> show #!17.1 models
> show #!18.1 models
> show #!19 models
> hide #!19 models
> show #!19.1 models
> show #!20.1 models
> show #!21.1 models
> show #!22 models
> show #!22.1 models
> hide #!22 models
> show #!23.1 models
> show #!24.1 models
> show #!25.1 models
> show #!26.1 models
> show #!27.1 models
> show #!28.1 models
> show #!29.1 models
> show #!30.1 models
> color
> #1.1#2.1#3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1#15.1#16.1#17.1#18.1#19.1#20.1#21.1#23.1#24.1#25.1#26.1#27.1#28.1#29.1#30.1#!1-21,23-30
> red
> hide
> #!1-30#!1.1-2#!2.1-2#!3.1-2#!4.1-2#!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2
> target m
> show #!1.2 models
> show #!2.2 models
> show #!3.2 models
> show #!4.2 models
> show #!5.2 models
> show #!6.2 models
> show #!7.2 models
> show #!8.2 models
> show #!9.2 models
> show #!10.2 models
> show #!11.2 models
> show #!12.2 models
> show #!13.2 models
> show #!14.2 models
> show #!15.2 models
> show #!16.2 models
> show #!17.2 models
> show #!18.2 models
> show #!19.2 models
> show #!20.2 models
> show #!21.2 models
> show #!22.2 models
> show #!23.2 models
> show #!24.2 models
> hide
> #!1-30#!1.1-2#!2.1-2#!3.1-2#!4.1-2#!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2
> target m
> show #!1.1 models
> show #!2.1 models
> show #!3.1 models
> show #!4.1 models
> show #!5.1 models
> show #!6.1 models
> show #!7.1 models
> show #!8.1 models
> show #!9.1 models
> show #!10.1 models
> show #!11.1 models
> show #!12.1 models
> show #!13.1 models
> show #!14.1 models
> show #!15.1 models
> show #!16.1 models
> show #!17.1 models
> show #!18.1 models
> show #!19.1 models
> show #!20.1 models
> show #!21.1 models
> show #!23.1 models
> show #!22.1 models
> show #!24.1 models
> show #!25.1 models
> show #!26.1 models
> show #!27.1 models
> show #!28.1 models
> show #!29.1 models
> show #!30.1 models
> color
> #1.1#2.1#3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1#15.1#16.1#17.1#18.1#19.1#20.1#21.1#22.1#23.1#24.1#25.1#26.1#27.1#28.1#29.1#30.1#!1-30
> cyan
> hide
> #!1-30#!1.1-2#!2.1-2#!3.1-2#!4.1-2#!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2
> target m
> show #!1.2 models
> show #!2.2 models
> show #!3.2 models
> show #!4.2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1.2/A #2.2/A #3.2/A #4.2/A #5.2/A #6.2/A #7.2/A #8.2/A
> #9.2/A #10.2/A #11.2/A #12.2/A #13.2/A #14.2/A #15.2/A #16.2/A #17.2/A
> #18.2/A #19.2/A #20.2/A #21.2/A #22.2/A #23.2/A #24.2/A #25.2/A #26.2/A
> #27.2/A #28.2/A #29.2/A #30.2/A
Alignment identifier is 1
> show #!5.2 models
> show #!6.2 models
> show #!7.2 models
> show #!8.2 models
> show #!9.2 models
> show #!10.2 models
> show #!11.2 models
> show #!12.2 models
> show #!13.2 models
> show #!14.2 models
> show #!15.2 models
> show #!16.2 models
> show #!17.2 models
> show #!18.2 models
> show #!19.2 models
> show #!20.2 models
> show #!21.2 models
> show #!22.2 models
> show #!23.2 models
> show #!24.2 models
> show #!25.2 models
> show #!26.2 models
> show #!27.2 models
> show #!28.2 models
> show #!29.2 models
> show #!30.2 models
> color
> #1.2#2.2#3.2#4.2#5.2#6.2#7.2#8.2#9.2#10.2#11.2#12.2#13.2#14.2#15.2#16.2#17.2#18.2#19.2#20.2#21.2#22.2#23.2#24.2#25.2#26.2#27.2#28.2#29.2#30.2#!1-30
> red
> hide
> #!1-30#!1.1-2#!2.1-2#!3.1-2#!4.1-2#!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2
> target m
> show #!1.2 models
> show #!1.1 models
> save /Users/AmyDeLury/Desktop/image1.png supersample 3
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/Refined
> Models/model004.01.pdb" models #1
> close #1
> show #!2.1 models
> show #!2.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model004.01.pdb" models
> #2
> save /Users/AmyDeLury/Desktop/image1.png supersample 3
> close #2
> show #!4 models
> hide #!4 models
> show #!3.2 models
> show #!3.1 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model004.02.pdb" models
> #3
> save /Users/AmyDeLury/Desktop/image2.png supersample 3
> close #3
> show #!4.1 models
> show #!4.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model004.03.pdb" models
> #4
> save /Users/AmyDeLury/Desktop/image3.png supersample 3
> close #4
> show #!5.1 models
> show #!5.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model004.04.pdb" models
> #5
> save /Users/AmyDeLury/Desktop/image4.png supersample 3
> close #5
> show #!6.1 models
> show #!6.2 models
> save "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model004.05.pdb" models
> #6
> close #6
> open "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Hydrophobic Models/model004.05.pdb"
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Hydrophobic Models/model004.05.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Start residue of secondary structure not found: HELIX 1 1 VAL E 606 LEU E 615
1 10
Start residue of secondary structure not found: HELIX 2 2 LYS E 720 ALA E 727
1 8
Start residue of secondary structure not found: HELIX 3 3 VAL E 784 ILE E 789
1 6
Start residue of secondary structure not found: HELIX 4 4 LYS E 796 ALA E 805
1 10
Start residue of secondary structure not found: HELIX 5 5 GLN E 809 ASP E 813
1 5
13 messages similar to the above omitted
Chain information for model004.05.pdb
---
Chain | Description
1.2/A | No description available
1.1/E | No description available
> surface #1
> hide #!1 models
> hide #!1.2 models
> show #!1 models
> color #1.1#!1 cyan
> show #!1.2 models
> hide #!1.1 models
> color #1.2#!1 red
> show #!1.1 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8rc202405282004 (2024-05-28)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.1.35
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 64 GB
System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0)
OS Loader Version: 580~743
Software:
System Software Overview:
System Version: macOS 14.1 (23B74)
Kernel Version: Darwin 23.1.0
Time since boot: 25 days, 7 hours, 2 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202405282004
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.0.13
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.2
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.52.4
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.45
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.12.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 15 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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