![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 20 months ago
Closed 20 months ago
#14685 closed defect (duplicate)
Crash in garbage collection
| 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-14.3.1-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 0x0000000200f3c240 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/logger.py", line 508 in _log
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/logger.py", line 480 in warning
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/pdb/pdb.py", line 89 in open_pdb
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/pdb/__init__.py", line 45 in open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 513 in collated_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
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 1979 in _open_dropped_file
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 614 in dropEvent
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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, 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, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mlp._mlp, chimerax.coulombic._esp (total: 57)
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"version" : 2,
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"codeSigningMonitor" : 1,
"incident" : "E4F15E96-0A82-4161-B8A8-00B5B0F5E8AC",
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"procLaunch" : "2024-03-01 08:40:53.2496 -0500",
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"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"},
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"crashReporterKey" : "5122BE20-FC8B-A36E-6C2A-2FE6442C48DC",
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"codeSigningTeamID" : "LWV8X224YF",
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"wakeTime" : 2340,
"sleepWakeUUID" : "709E1BBC-FF7A-48CF-BCA7-9DD34D436FA6",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140722958827351\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc9df90000-7ffcc6d40000 [653.7M] r-x\/r-x SM=COW ...t_id=16684b57",
"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":78620},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140722958827351\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc9df90000-7ffcc6d40000 [653.7M] r-x\/r-x SM=COW ...t_id=16684b57",
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"faultingThread" : 0,
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[deleted to fit within ticket limits]
> hide #!8 models
> show #!9 models
> contacts /B restrict /A interModel false intraMol false ignoreHiddenModels
> true select true color #ff2600 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
142 contacts
atom1 atom2 overlap distance
A11_APL1_9.pdb #9/B LYS 10 OXT A11_APL1_9.pdb #9/A THR 80 1HG2 0.257 2.223
A11_APL1_9.pdb #9/B VAL 2 CG1 A11_APL1_9.pdb #9/A TYR 9 OH 0.204 2.996
A11_APL1_9.pdb #9/B VAL 2 CG1 A11_APL1_9.pdb #9/A TYR 7 CE2 0.194 3.206
A11_APL1_9.pdb #9/B SER 1 O A11_APL1_9.pdb #9/A TYR 159 HH 0.180 1.900
A11_APL1_9.pdb #9/B VAL 8 O A11_APL1_9.pdb #9/A TRP 147 HE1 0.179 1.901
A11_APL1_9.pdb #9/B SER 1 2H A11_APL1_9.pdb #9/A TYR 171 OH 0.168 1.932
A11_APL1_9.pdb #9/B LYS 10 O A11_APL1_9.pdb #9/A THR 143 HG1 0.165 1.915
A11_APL1_9.pdb #9/B LYS 10 1HZ A11_APL1_9.pdb #9/A ASP 116 OD2 0.156 1.924
A11_APL1_9.pdb #9/B VAL 2 3HG2 A11_APL1_9.pdb #9/A ASN 66 CB 0.140 2.560
A11_APL1_9.pdb #9/B VAL 2 CG2 A11_APL1_9.pdb #9/A ASN 66 1HB 0.137 2.563
A11_APL1_9.pdb #9/B VAL 2 3HG2 A11_APL1_9.pdb #9/A ASN 66 1HB 0.131 1.869
A11_APL1_9.pdb #9/B VAL 2 O A11_APL1_9.pdb #9/A ASN 66 2HD2 0.124 1.956
A11_APL1_9.pdb #9/B LYS 10 C A11_APL1_9.pdb #9/A TYR 84 HH 0.114 2.586
A11_APL1_9.pdb #9/B LYS 10 O A11_APL1_9.pdb #9/A TYR 84 HH 0.098 1.982
A11_APL1_9.pdb #9/B LYS 10 H A11_APL1_9.pdb #9/A ASP 77 OD1 0.082 1.998
A11_APL1_9.pdb #9/B VAL 2 2HG1 A11_APL1_9.pdb #9/A TYR 7 CE2 0.080 2.620
A11_APL1_9.pdb #9/B LYS 10 OXT A11_APL1_9.pdb #9/A LYS 146 2HZ 0.055 2.025
A11_APL1_9.pdb #9/B LYS 10 2HB A11_APL1_9.pdb #9/A THR 143 OG1 0.045 2.455
A11_APL1_9.pdb #9/B VAL 3 HB A11_APL1_9.pdb #9/A TYR 159 CD1 0.027 2.673
A11_APL1_9.pdb #9/B VAL 8 HB A11_APL1_9.pdb #9/A TRP 147 CD1 0.017 2.683
A11_APL1_9.pdb #9/B VAL 2 1HG1 A11_APL1_9.pdb #9/A TYR 9 OH 0.017 2.483
A11_APL1_9.pdb #9/B LYS 10 O A11_APL1_9.pdb #9/A TYR 84 HE2 0.015 2.465
A11_APL1_9.pdb #9/B VAL 8 O A11_APL1_9.pdb #9/A TRP 147 NE1 0.005 2.700
A11_APL1_9.pdb #9/B VAL 2 CG2 A11_APL1_9.pdb #9/A ASN 66 CB -0.012 3.412
A11_APL1_9.pdb #9/B LYS 10 3HZ A11_APL1_9.pdb #9/A TRP 147 CZ2 -0.013 2.713
A11_APL1_9.pdb #9/B VAL 8 C A11_APL1_9.pdb #9/A TRP 147 HE1 -0.014 2.714
A11_APL1_9.pdb #9/B VAL 2 CG1 A11_APL1_9.pdb #9/A TYR 7 CZ -0.024 3.424
A11_APL1_9.pdb #9/B VAL 8 HB A11_APL1_9.pdb #9/A TRP 147 NE1 -0.036 2.661
A11_APL1_9.pdb #9/B VAL 2 2HG1 A11_APL1_9.pdb #9/A TYR 99 OH -0.048 2.548
A11_APL1_9.pdb #9/B LYS 10 1HZ A11_APL1_9.pdb #9/A ASP 116 CG -0.050 2.750
A11_APL1_9.pdb #9/B LYS 10 C A11_APL1_9.pdb #9/A THR 143 HG1 -0.059 2.759
A11_APL1_9.pdb #9/B VAL 2 2HG1 A11_APL1_9.pdb #9/A TYR 7 CZ -0.064 2.764
A11_APL1_9.pdb #9/B SER 1 1HB A11_APL1_9.pdb #9/A GLU 63 2HG -0.067 2.067
A11_APL1_9.pdb #9/B LYS 10 2HD A11_APL1_9.pdb #9/A TYR 123 CE2 -0.069 2.769
A11_APL1_9.pdb #9/B GLY 4 1HA A11_APL1_9.pdb #9/A ASN 66 CG -0.074 2.774
A11_APL1_9.pdb #9/B LYS 10 C A11_APL1_9.pdb #9/A LYS 146 1HD -0.076 2.776
A11_APL1_9.pdb #9/B LYS 10 3HZ A11_APL1_9.pdb #9/A TRP 147 CH2 -0.086 2.786
A11_APL1_9.pdb #9/B VAL 2 2HG1 A11_APL1_9.pdb #9/A TYR 7 CD2 -0.091 2.791
A11_APL1_9.pdb #9/B LYS 10 2HG A11_APL1_9.pdb #9/A ASP 77 CG -0.091 2.791
A11_APL1_9.pdb #9/B LYS 10 CB A11_APL1_9.pdb #9/A THR 143 OG1 -0.111 3.311
A11_APL1_9.pdb #9/B LYS 10 O A11_APL1_9.pdb #9/A TYR 84 CE2 -0.118 3.298
A11_APL1_9.pdb #9/B VAL 3 HB A11_APL1_9.pdb #9/A TYR 159 CE1 -0.120 2.820
A11_APL1_9.pdb #9/B LYS 10 OXT A11_APL1_9.pdb #9/A THR 80 CG2 -0.124 3.304
A11_APL1_9.pdb #9/B VAL 2 CG1 A11_APL1_9.pdb #9/A TYR 99 OH -0.138 3.338
A11_APL1_9.pdb #9/B LYS 10 NZ A11_APL1_9.pdb #9/A ASP 116 OD2 -0.142 2.847
A11_APL1_9.pdb #9/B VAL 8 C A11_APL1_9.pdb #9/A TRP 147 NE1 -0.146 3.471
A11_APL1_9.pdb #9/B LYS 10 C A11_APL1_9.pdb #9/A THR 80 1HG2 -0.148 2.848
A11_APL1_9.pdb #9/B LYS 10 HA A11_APL1_9.pdb #9/A THR 143 3HG2 -0.151 2.151
A11_APL1_9.pdb #9/B LYS 10 O A11_APL1_9.pdb #9/A LYS 146 1HD -0.153 2.633
A11_APL1_9.pdb #9/B LYS 10 C A11_APL1_9.pdb #9/A LYS 146 2HZ -0.160 2.860
A11_APL1_9.pdb #9/B LYS 10 2HB A11_APL1_9.pdb #9/A THR 143 HG1 -0.162 2.162
A11_APL1_9.pdb #9/B LYS 10 O A11_APL1_9.pdb #9/A THR 143 HA -0.165 2.645
A11_APL1_9.pdb #9/B GLY 4 CA A11_APL1_9.pdb #9/A ASN 66 CG -0.172 3.572
A11_APL1_9.pdb #9/B VAL 3 O A11_APL1_9.pdb #9/A ASN 66 2HB -0.173 2.653
A11_APL1_9.pdb #9/B VAL 2 CG1 A11_APL1_9.pdb #9/A TYR 7 CD2 -0.179 3.579
A11_APL1_9.pdb #9/B SER 1 N A11_APL1_9.pdb #9/A TYR 171 OH -0.181 2.906
A11_APL1_9.pdb #9/B VAL 2 H A11_APL1_9.pdb #9/A GLU 63 2HG -0.181 2.181
A11_APL1_9.pdb #9/B VAL 8 O A11_APL1_9.pdb #9/A TRP 147 CE2 -0.186 3.366
A11_APL1_9.pdb #9/B LYS 10 CG A11_APL1_9.pdb #9/A ASP 77 CG -0.186 3.586
A11_APL1_9.pdb #9/B SER 1 C A11_APL1_9.pdb #9/A TYR 7 OH -0.189 3.389
A11_APL1_9.pdb #9/B VAL 2 O A11_APL1_9.pdb #9/A ASN 66 ND2 -0.193 2.898
A11_APL1_9.pdb #9/B SER 1 N A11_APL1_9.pdb #9/A TRP 167 CG -0.206 3.531
A11_APL1_9.pdb #9/B GLY 4 1HA A11_APL1_9.pdb #9/A ASN 66 OD1 -0.213 2.693
A11_APL1_9.pdb #9/B VAL 2 HA A11_APL1_9.pdb #9/A TYR 99 HH -0.215 2.215
A11_APL1_9.pdb #9/B VAL 3 CB A11_APL1_9.pdb #9/A TYR 159 CD1 -0.217 3.617
A11_APL1_9.pdb #9/B LYS 10 1HD A11_APL1_9.pdb #9/A ASP 77 2HB -0.221 2.221
A11_APL1_9.pdb #9/B VAL 8 CB A11_APL1_9.pdb #9/A TRP 147 CD1 -0.223 3.623
A11_APL1_9.pdb #9/B LYS 10 NZ A11_APL1_9.pdb #9/A TRP 147 CH2 -0.223 3.548
A11_APL1_9.pdb #9/B LYS 10 O A11_APL1_9.pdb #9/A THR 143 CA -0.224 3.404
A11_APL1_9.pdb #9/B LYS 10 CD A11_APL1_9.pdb #9/A LEU 81 1HD1 -0.224 2.924
A11_APL1_9.pdb #9/B LYS 10 CD A11_APL1_9.pdb #9/A LEU 81 1HD2 -0.227 2.927
A11_APL1_9.pdb #9/B VAL 2 CB A11_APL1_9.pdb #9/A TYR 9 OH -0.232 3.432
A11_APL1_9.pdb #9/B VAL 2 CB A11_APL1_9.pdb #9/A TYR 99 OH -0.232 3.432
A11_APL1_9.pdb #9/B LYS 10 C A11_APL1_9.pdb #9/A TYR 84 OH -0.233 3.433
A11_APL1_9.pdb #9/B VAL 8 CB A11_APL1_9.pdb #9/A TRP 147 NE1 -0.241 3.566
A11_APL1_9.pdb #9/B LYS 10 CD A11_APL1_9.pdb #9/A LEU 81 CD1 -0.247 3.647
A11_APL1_9.pdb #9/B GLY 4 N A11_APL1_9.pdb #9/A ASN 66 ND2 -0.249 3.499
A11_APL1_9.pdb #9/B LYS 10 CA A11_APL1_9.pdb #9/A THR 143 HG1 -0.249 2.949
A11_APL1_9.pdb #9/B SER 1 O A11_APL1_9.pdb #9/A TYR 159 OH -0.251 2.831
A11_APL1_9.pdb #9/B LYS 10 CD A11_APL1_9.pdb #9/A LEU 81 CD2 -0.253 3.653
A11_APL1_9.pdb #9/B LYS 10 OXT A11_APL1_9.pdb #9/A LYS 146 NZ -0.254 2.959
A11_APL1_9.pdb #9/B LYS 10 CB A11_APL1_9.pdb #9/A THR 143 HG1 -0.255 2.955
A11_APL1_9.pdb #9/B VAL 2 2HG1 A11_APL1_9.pdb #9/A TYR 99 HH -0.264 2.264
A11_APL1_9.pdb #9/B SER 1 N A11_APL1_9.pdb #9/A TRP 167 CD1 -0.267 3.592
A11_APL1_9.pdb #9/B SER 1 2HB A11_APL1_9.pdb #9/A TYR 59 CE1 -0.267 2.967
A11_APL1_9.pdb #9/B SER 1 1HB A11_APL1_9.pdb #9/A GLU 63 CG -0.268 2.968
A11_APL1_9.pdb #9/B LYS 10 H A11_APL1_9.pdb #9/A ASP 77 CG -0.272 2.972
A11_APL1_9.pdb #9/B SER 1 C A11_APL1_9.pdb #9/A TYR 159 HH -0.275 2.975
A11_APL1_9.pdb #9/B VAL 2 C A11_APL1_9.pdb #9/A ASN 66 2HD2 -0.276 2.976
A11_APL1_9.pdb #9/B SER 1 1H A11_APL1_9.pdb #9/A TRP 167 CD1 -0.280 2.980
A11_APL1_9.pdb #9/B GLY 4 N A11_APL1_9.pdb #9/A ASN 66 CG -0.288 3.613
A11_APL1_9.pdb #9/B LYS 10 1HG A11_APL1_9.pdb #9/A THR 143 CG2 -0.289 2.989
A11_APL1_9.pdb #9/B VAL 3 HB A11_APL1_9.pdb #9/A TYR 159 CG -0.292 2.992
A11_APL1_9.pdb #9/B VAL 2 3HG1 A11_APL1_9.pdb #9/A TYR 7 CE2 -0.294 2.994
A11_APL1_9.pdb #9/B LYS 10 O A11_APL1_9.pdb #9/A THR 143 OG1 -0.295 2.875
A11_APL1_9.pdb #9/B LYS 10 2HZ A11_APL1_9.pdb #9/A TYR 123 CD2 -0.299 2.999
A11_APL1_9.pdb #9/B LYS 10 N A11_APL1_9.pdb #9/A ASP 77 OD1 -0.299 3.004
A11_APL1_9.pdb #9/B VAL 2 2HG1 A11_APL1_9.pdb #9/A TYR 9 OH -0.303 2.803
A11_APL1_9.pdb #9/B SER 1 N A11_APL1_9.pdb #9/A TYR 59 HE1 -0.305 2.930
A11_APL1_9.pdb #9/B SER 1 2H A11_APL1_9.pdb #9/A TYR 171 HH -0.306 2.306
A11_APL1_9.pdb #9/B VAL 2 HB A11_APL1_9.pdb #9/A TYR 9 HH -0.306 2.306
A11_APL1_9.pdb #9/B VAL 8 CG2 A11_APL1_9.pdb #9/A ALA 152 2HB -0.313 3.013
A11_APL1_9.pdb #9/B VAL 8 1HG2 A11_APL1_9.pdb #9/A ALA 152 2HB -0.314 2.314
A11_APL1_9.pdb #9/B LYS 10 CB A11_APL1_9.pdb #9/A LEU 81 CD1 -0.318 3.718
A11_APL1_9.pdb #9/B VAL 2 CA A11_APL1_9.pdb #9/A TYR 99 HH -0.320 3.020
A11_APL1_9.pdb #9/B GLY 4 CA A11_APL1_9.pdb #9/A ASN 66 OD1 -0.321 3.501
A11_APL1_9.pdb #9/B LYS 10 2HD A11_APL1_9.pdb #9/A LEU 81 1HD1 -0.323 2.323
A11_APL1_9.pdb #9/B GLY 9 O A11_APL1_9.pdb #9/A LYS 146 CD -0.325 3.505
A11_APL1_9.pdb #9/B VAL 8 O A11_APL1_9.pdb #9/A TRP 147 CZ2 -0.327 3.507
A11_APL1_9.pdb #9/B GLY 4 1HA A11_APL1_9.pdb #9/A ASN 66 CB -0.327 3.027
A11_APL1_9.pdb #9/B LYS 10 2HG A11_APL1_9.pdb #9/A ASP 77 OD2 -0.340 2.820
A11_APL1_9.pdb #9/B LYS 10 C A11_APL1_9.pdb #9/A LYS 146 CD -0.342 3.742
A11_APL1_9.pdb #9/B LYS 10 O A11_APL1_9.pdb #9/A TYR 84 OH -0.344 2.924
A11_APL1_9.pdb #9/B LYS 10 3HZ A11_APL1_9.pdb #9/A TRP 147 HZ2 -0.345 2.345
A11_APL1_9.pdb #9/B VAL 2 HB A11_APL1_9.pdb #9/A TYR 9 OH -0.349 2.849
A11_APL1_9.pdb #9/B SER 1 1H A11_APL1_9.pdb #9/A TRP 167 CG -0.351 3.051
A11_APL1_9.pdb #9/B VAL 2 CB A11_APL1_9.pdb #9/A TYR 99 HH -0.358 3.058
A11_APL1_9.pdb #9/B VAL 2 2HG1 A11_APL1_9.pdb #9/A TYR 7 CE1 -0.359 3.059
A11_APL1_9.pdb #9/B LYS 10 NZ A11_APL1_9.pdb #9/A TRP 147 CZ2 -0.359 3.684
A11_APL1_9.pdb #9/B LYS 10 O A11_APL1_9.pdb #9/A TYR 84 CZ -0.365 3.545
A11_APL1_9.pdb #9/B VAL 2 CG1 A11_APL1_9.pdb #9/A TYR 99 HH -0.370 3.070
A11_APL1_9.pdb #9/B VAL 3 C A11_APL1_9.pdb #9/A ASN 66 ND2 -0.370 3.695
A11_APL1_9.pdb #9/B LYS 10 CB A11_APL1_9.pdb #9/A LEU 81 1HD1 -0.374 3.074
A11_APL1_9.pdb #9/B LYS 10 NZ A11_APL1_9.pdb #9/A TRP 147 HH2 -0.374 2.999
A11_APL1_9.pdb #9/B VAL 2 HA A11_APL1_9.pdb #9/A TYR 159 OH -0.376 2.876
A11_APL1_9.pdb #9/B LYS 10 NZ A11_APL1_9.pdb #9/A ASP 116 CG -0.377 3.702
A11_APL1_9.pdb #9/B VAL 2 HB A11_APL1_9.pdb #9/A TYR 99 OH -0.379 2.879
A11_APL1_9.pdb #9/B VAL 8 1HG1 A11_APL1_9.pdb #9/A ALA 150 CB -0.379 3.079
A11_APL1_9.pdb #9/B LYS 10 2HG A11_APL1_9.pdb #9/A ASP 77 OD1 -0.379 2.859
A11_APL1_9.pdb #9/B LYS 10 CA A11_APL1_9.pdb #9/A THR 143 OG1 -0.383 3.583
A11_APL1_9.pdb #9/B VAL 3 CB A11_APL1_9.pdb #9/A TYR 159 CE1 -0.384 3.784
A11_APL1_9.pdb #9/B LYS 10 1HZ A11_APL1_9.pdb #9/A ASP 116 CB -0.386 3.086
A11_APL1_9.pdb #9/B VAL 8 CG1 A11_APL1_9.pdb #9/A TRP 147 CD1 -0.387 3.787
A11_APL1_9.pdb #9/B VAL 2 2HG2 A11_APL1_9.pdb #9/A GLU 63 2HG -0.387 2.387
A11_APL1_9.pdb #9/B LYS 10 CD A11_APL1_9.pdb #9/A ASP 77 CG -0.391 3.791
A11_APL1_9.pdb #9/B LYS 10 OXT A11_APL1_9.pdb #9/A LYS 146 1HD -0.393 2.873
A11_APL1_9.pdb #9/B GLY 9 C A11_APL1_9.pdb #9/A TRP 147 HE1 -0.393 3.093
A11_APL1_9.pdb #9/B VAL 2 2HG1 A11_APL1_9.pdb #9/A TYR 7 CG -0.395 3.095
A11_APL1_9.pdb #9/B SER 1 3H A11_APL1_9.pdb #9/A TRP 167 CD1 -0.397 3.097
A11_APL1_9.pdb #9/B LYS 10 OXT A11_APL1_9.pdb #9/A LYS 146 CD -0.397 3.577
A11_APL1_9.pdb #9/B LYS 10 2HB A11_APL1_9.pdb #9/A LEU 81 1HD1 -0.397 2.397
A11_APL1_9.pdb #9/B SER 1 1H A11_APL1_9.pdb #9/A TRP 167 NE1 -0.399 3.024
142 contacts
> contacts /B:1 restrict /A interModel false intraMol false ignoreHiddenModels
> true select true color #ff2600 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
17 contacts
atom1 atom2 overlap distance
A11_APL1_9.pdb #9/B SER 1 O A11_APL1_9.pdb #9/A TYR 159 HH 0.180 1.900
A11_APL1_9.pdb #9/B SER 1 2H A11_APL1_9.pdb #9/A TYR 171 OH 0.168 1.932
A11_APL1_9.pdb #9/B SER 1 1HB A11_APL1_9.pdb #9/A GLU 63 2HG -0.067 2.067
A11_APL1_9.pdb #9/B SER 1 N A11_APL1_9.pdb #9/A TYR 171 OH -0.181 2.906
A11_APL1_9.pdb #9/B SER 1 C A11_APL1_9.pdb #9/A TYR 7 OH -0.189 3.389
A11_APL1_9.pdb #9/B SER 1 N A11_APL1_9.pdb #9/A TRP 167 CG -0.206 3.531
A11_APL1_9.pdb #9/B SER 1 O A11_APL1_9.pdb #9/A TYR 159 OH -0.251 2.831
A11_APL1_9.pdb #9/B SER 1 N A11_APL1_9.pdb #9/A TRP 167 CD1 -0.267 3.592
A11_APL1_9.pdb #9/B SER 1 2HB A11_APL1_9.pdb #9/A TYR 59 CE1 -0.267 2.967
A11_APL1_9.pdb #9/B SER 1 1HB A11_APL1_9.pdb #9/A GLU 63 CG -0.268 2.968
A11_APL1_9.pdb #9/B SER 1 C A11_APL1_9.pdb #9/A TYR 159 HH -0.275 2.975
A11_APL1_9.pdb #9/B SER 1 1H A11_APL1_9.pdb #9/A TRP 167 CD1 -0.280 2.980
A11_APL1_9.pdb #9/B SER 1 N A11_APL1_9.pdb #9/A TYR 59 HE1 -0.305 2.930
A11_APL1_9.pdb #9/B SER 1 2H A11_APL1_9.pdb #9/A TYR 171 HH -0.306 2.306
A11_APL1_9.pdb #9/B SER 1 1H A11_APL1_9.pdb #9/A TRP 167 CG -0.351 3.051
A11_APL1_9.pdb #9/B SER 1 3H A11_APL1_9.pdb #9/A TRP 167 CD1 -0.397 3.097
A11_APL1_9.pdb #9/B SER 1 1H A11_APL1_9.pdb #9/A TRP 167 NE1 -0.399 3.024
17 contacts
> hide #!9 models
> show #!10 models
> contacts /B:1 restrict /A interModel false intraMol false ignoreHiddenModels
> true select true color #ff2600 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
35 contacts
atom1 atom2 overlap distance
A11_APL1_10.pdb #10/B SER 1 O A11_APL1_10.pdb #10/A TYR 159 HH 0.241 1.839
A11_APL1_10.pdb #10/B SER 1 HA A11_APL1_10.pdb #10/A GLU 63 CD 0.163 2.537
A11_APL1_10.pdb #10/B SER 1 HG A11_APL1_10.pdb #10/A GLU 63 OE2 0.156 1.924
A11_APL1_10.pdb #10/B SER 1 C A11_APL1_10.pdb #10/A TYR 7 OH 0.088 3.112
A11_APL1_10.pdb #10/B SER 1 HA A11_APL1_10.pdb #10/A GLU 63 OE1 0.084 2.396
A11_APL1_10.pdb #10/B SER 1 N A11_APL1_10.pdb #10/A TYR 7 OH 0.021 2.704
A11_APL1_10.pdb #10/B SER 1 CA A11_APL1_10.pdb #10/A TYR 7 OH -0.008 3.208
A11_APL1_10.pdb #10/B SER 1 N A11_APL1_10.pdb #10/A TYR 171 OH -0.048 2.773
A11_APL1_10.pdb #10/B SER 1 CB A11_APL1_10.pdb #10/A TRP 167 CD1 -0.095 3.495
A11_APL1_10.pdb #10/B SER 1 2HB A11_APL1_10.pdb #10/A TRP 167 CD1 -0.106 2.806
A11_APL1_10.pdb #10/B SER 1 HA A11_APL1_10.pdb #10/A GLU 63 OE2 -0.109 2.589
A11_APL1_10.pdb #10/B SER 1 HG A11_APL1_10.pdb #10/A GLU 63 CD -0.147 2.847
A11_APL1_10.pdb #10/B SER 1 O A11_APL1_10.pdb #10/A TYR 159 HE1 -0.156 2.636
A11_APL1_10.pdb #10/B SER 1 CA A11_APL1_10.pdb #10/A GLU 63 OE1 -0.186 3.366
A11_APL1_10.pdb #10/B SER 1 CA A11_APL1_10.pdb #10/A GLU 63 CD -0.191 3.591
A11_APL1_10.pdb #10/B SER 1 1H A11_APL1_10.pdb #10/A TYR 171 OH -0.196 2.296
A11_APL1_10.pdb #10/B SER 1 3H A11_APL1_10.pdb #10/A TYR 7 OH -0.201 2.301
A11_APL1_10.pdb #10/B SER 1 2H A11_APL1_10.pdb #10/A TYR 171 OH -0.201 2.301
A11_APL1_10.pdb #10/B SER 1 O A11_APL1_10.pdb #10/A TYR 159 OH -0.219 2.799
A11_APL1_10.pdb #10/B SER 1 1H A11_APL1_10.pdb #10/A TYR 171 CZ -0.233 2.933
A11_APL1_10.pdb #10/B SER 1 C A11_APL1_10.pdb #10/A TYR 7 CZ -0.233 3.633
A11_APL1_10.pdb #10/B SER 1 C A11_APL1_10.pdb #10/A TYR 7 CE1 -0.239 3.639
A11_APL1_10.pdb #10/B SER 1 CB A11_APL1_10.pdb #10/A GLU 63 OE2 -0.244 3.424
A11_APL1_10.pdb #10/B SER 1 O A11_APL1_10.pdb #10/A TYR 159 CE1 -0.254 3.434
A11_APL1_10.pdb #10/B SER 1 C A11_APL1_10.pdb #10/A TYR 159 HH -0.260 2.960
A11_APL1_10.pdb #10/B SER 1 N A11_APL1_10.pdb #10/A TYR 171 CZ -0.271 3.596
A11_APL1_10.pdb #10/B SER 1 OG A11_APL1_10.pdb #10/A GLU 63 OE2 -0.287 2.867
A11_APL1_10.pdb #10/B SER 1 N A11_APL1_10.pdb #10/A TYR 171 CE2 -0.293 3.618
A11_APL1_10.pdb #10/B SER 1 CA A11_APL1_10.pdb #10/A GLU 63 OE2 -0.296 3.476
A11_APL1_10.pdb #10/B SER 1 CB A11_APL1_10.pdb #10/A TRP 167 CG -0.317 3.717
A11_APL1_10.pdb #10/B SER 1 1H A11_APL1_10.pdb #10/A TYR 171 CE2 -0.336 3.036
A11_APL1_10.pdb #10/B SER 1 N A11_APL1_10.pdb #10/A TYR 171 HE2 -0.339 2.964
A11_APL1_10.pdb #10/B SER 1 O A11_APL1_10.pdb #10/A TYR 159 CZ -0.382 3.562
A11_APL1_10.pdb #10/B SER 1 2H A11_APL1_10.pdb #10/A TYR 7 OH -0.395 2.495
A11_APL1_10.pdb #10/B SER 1 2HB A11_APL1_10.pdb #10/A TRP 167 CG -0.399 3.099
35 contacts
> contacts /B restrict /A interModel false intraMol false ignoreHiddenModels
> true select true color #ff2600 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
161 contacts
atom1 atom2 overlap distance
A11_APL1_10.pdb #10/B SER 1 O A11_APL1_10.pdb #10/A TYR 159 HH 0.241 1.839
A11_APL1_10.pdb #10/B LYS 10 CD A11_APL1_10.pdb #10/A THR 143 OG1 0.228 2.972
A11_APL1_10.pdb #10/B LYS 10 H A11_APL1_10.pdb #10/A ASP 77 OD1 0.218 1.862
A11_APL1_10.pdb #10/B VAL 2 H A11_APL1_10.pdb #10/A GLU 63 OE1 0.201 1.879
A11_APL1_10.pdb #10/B LYS 10 C A11_APL1_10.pdb #10/A THR 80 HG1 0.184 2.516
A11_APL1_10.pdb #10/B SER 1 HA A11_APL1_10.pdb #10/A GLU 63 CD 0.163 2.537
A11_APL1_10.pdb #10/B LYS 10 O A11_APL1_10.pdb #10/A THR 80 1HG2 0.163 2.317
A11_APL1_10.pdb #10/B VAL 8 O A11_APL1_10.pdb #10/A TRP 147 CH2 0.161 3.019
A11_APL1_10.pdb #10/B SER 1 HG A11_APL1_10.pdb #10/A GLU 63 OE2 0.156 1.924
A11_APL1_10.pdb #10/B VAL 2 2HG1 A11_APL1_10.pdb #10/A TYR 7 CE2 0.154 2.546
A11_APL1_10.pdb #10/B LYS 10 1HD A11_APL1_10.pdb #10/A THR 143 OG1 0.145 2.355
A11_APL1_10.pdb #10/B LYS 10 N A11_APL1_10.pdb #10/A TRP 147 HH2 0.139 2.486
A11_APL1_10.pdb #10/B LYS 10 NZ A11_APL1_10.pdb #10/A ASP 77 CG 0.131 3.194
A11_APL1_10.pdb #10/B LYS 10 O A11_APL1_10.pdb #10/A LYS 146 NZ 0.128 2.577
A11_APL1_10.pdb #10/B VAL 3 H A11_APL1_10.pdb #10/A TYR 99 OH 0.125 1.975
A11_APL1_10.pdb #10/B LYS 10 OXT A11_APL1_10.pdb #10/A THR 80 HG1 0.107 1.973
A11_APL1_10.pdb #10/B VAL 2 CG2 A11_APL1_10.pdb #10/A ASN 66 1HB 0.105 2.595
A11_APL1_10.pdb #10/B LYS 10 CG A11_APL1_10.pdb #10/A TRP 147 CH2 0.104 3.296
A11_APL1_10.pdb #10/B VAL 3 H A11_APL1_10.pdb #10/A TYR 99 CZ 0.102 2.598
A11_APL1_10.pdb #10/B VAL 2 2HG2 A11_APL1_10.pdb #10/A GLU 63 OE1 0.098 2.382
A11_APL1_10.pdb #10/B SER 1 C A11_APL1_10.pdb #10/A TYR 7 OH 0.088 3.112
A11_APL1_10.pdb #10/B SER 1 HA A11_APL1_10.pdb #10/A GLU 63 OE1 0.084 2.396
A11_APL1_10.pdb #10/B LYS 10 O A11_APL1_10.pdb #10/A LYS 146 3HZ 0.076 2.004
A11_APL1_10.pdb #10/B VAL 2 CG1 A11_APL1_10.pdb #10/A TYR 9 HH 0.069 2.631
A11_APL1_10.pdb #10/B LYS 10 CD A11_APL1_10.pdb #10/A THR 143 HG1 0.065 2.635
A11_APL1_10.pdb #10/B VAL 2 HA A11_APL1_10.pdb #10/A TYR 99 OH 0.031 2.469
A11_APL1_10.pdb #10/B VAL 2 CG2 A11_APL1_10.pdb #10/A ASN 66 CB 0.025 3.375
A11_APL1_10.pdb #10/B SER 1 N A11_APL1_10.pdb #10/A TYR 7 OH 0.021 2.704
A11_APL1_10.pdb #10/B LYS 10 1HD A11_APL1_10.pdb #10/A THR 143 HG1 0.005 1.995
A11_APL1_10.pdb #10/B LYS 10 2HD A11_APL1_10.pdb #10/A THR 143 CG2 -0.006 2.706
A11_APL1_10.pdb #10/B SER 1 CA A11_APL1_10.pdb #10/A TYR 7 OH -0.008 3.208
A11_APL1_10.pdb #10/B GLY 9 C A11_APL1_10.pdb #10/A TRP 147 HH2 -0.009 2.709
A11_APL1_10.pdb #10/B VAL 2 CG1 A11_APL1_10.pdb #10/A TYR 9 OH -0.010 3.210
A11_APL1_10.pdb #10/B VAL 2 2HG1 A11_APL1_10.pdb #10/A TYR 9 HH -0.013 2.013
A11_APL1_10.pdb #10/B VAL 2 3HG1 A11_APL1_10.pdb #10/A GLU 63 OE1 -0.020 2.500
A11_APL1_10.pdb #10/B LYS 10 1HE A11_APL1_10.pdb #10/A ASP 77 2HB -0.021 2.021
A11_APL1_10.pdb #10/B LYS 10 3HZ A11_APL1_10.pdb #10/A ASP 77 CG -0.027 2.727
A11_APL1_10.pdb #10/B VAL 2 CA A11_APL1_10.pdb #10/A TYR 99 OH -0.028 3.228
A11_APL1_10.pdb #10/B VAL 2 CG1 A11_APL1_10.pdb #10/A TYR 7 CE2 -0.036 3.436
A11_APL1_10.pdb #10/B LYS 10 C A11_APL1_10.pdb #10/A THR 80 1HG2 -0.043 2.743
A11_APL1_10.pdb #10/B VAL 2 HB A11_APL1_10.pdb #10/A TYR 9 OH -0.047 2.547
A11_APL1_10.pdb #10/B SER 1 N A11_APL1_10.pdb #10/A TYR 171 OH -0.048 2.773
A11_APL1_10.pdb #10/B LYS 10 1HG A11_APL1_10.pdb #10/A TRP 147 CH2 -0.056 2.756
A11_APL1_10.pdb #10/B VAL 3 HB A11_APL1_10.pdb #10/A TYR 99 CE1 -0.061 2.761
A11_APL1_10.pdb #10/B LYS 10 N A11_APL1_10.pdb #10/A ASP 77 OD1 -0.067 2.772
A11_APL1_10.pdb #10/B LYS 10 H A11_APL1_10.pdb #10/A ASP 77 CG -0.082 2.782
A11_APL1_10.pdb #10/B VAL 2 H A11_APL1_10.pdb #10/A GLU 63 CD -0.093 2.793
A11_APL1_10.pdb #10/B LYS 10 CE A11_APL1_10.pdb #10/A ASP 77 2HB -0.094 2.794
A11_APL1_10.pdb #10/B SER 1 CB A11_APL1_10.pdb #10/A TRP 167 CD1 -0.095 3.495
A11_APL1_10.pdb #10/B VAL 3 HA A11_APL1_10.pdb #10/A TYR 159 CE1 -0.098 2.798
A11_APL1_10.pdb #10/B LYS 10 O A11_APL1_10.pdb #10/A THR 80 CG2 -0.103 3.283
A11_APL1_10.pdb #10/B SER 1 2HB A11_APL1_10.pdb #10/A TRP 167 CD1 -0.106 2.806
A11_APL1_10.pdb #10/B SER 1 HA A11_APL1_10.pdb #10/A GLU 63 OE2 -0.109 2.589
A11_APL1_10.pdb #10/B LYS 10 1HE A11_APL1_10.pdb #10/A ASP 77 CB -0.110 2.810
A11_APL1_10.pdb #10/B VAL 3 3HG2 A11_APL1_10.pdb #10/A TYR 159 CD2 -0.111 2.811
A11_APL1_10.pdb #10/B VAL 3 3HG2 A11_APL1_10.pdb #10/A TYR 159 CG -0.112 2.812
A11_APL1_10.pdb #10/B VAL 3 2HG1 A11_APL1_10.pdb #10/A TYR 99 CZ -0.115 2.815
A11_APL1_10.pdb #10/B VAL 2 CB A11_APL1_10.pdb #10/A TYR 9 OH -0.118 3.318
A11_APL1_10.pdb #10/B LYS 10 CD A11_APL1_10.pdb #10/A THR 143 CG2 -0.121 3.521
A11_APL1_10.pdb #10/B GLY 9 CA A11_APL1_10.pdb #10/A THR 73 3HG2 -0.127 2.827
A11_APL1_10.pdb #10/B VAL 2 2HG1 A11_APL1_10.pdb #10/A TYR 7 CD2 -0.130 2.830
A11_APL1_10.pdb #10/B LYS 10 CE A11_APL1_10.pdb #10/A ASP 77 CG -0.132 3.532
A11_APL1_10.pdb #10/B VAL 3 HA A11_APL1_10.pdb #10/A TYR 159 CD1 -0.138 2.838
A11_APL1_10.pdb #10/B SER 1 HG A11_APL1_10.pdb #10/A GLU 63 CD -0.147 2.847
A11_APL1_10.pdb #10/B LYS 10 2HE A11_APL1_10.pdb #10/A LEU 81 1HD1 -0.154 2.154
A11_APL1_10.pdb #10/B SER 1 O A11_APL1_10.pdb #10/A TYR 159 HE1 -0.156 2.636
A11_APL1_10.pdb #10/B VAL 3 CG1 A11_APL1_10.pdb #10/A TYR 99 CZ -0.158 3.558
A11_APL1_10.pdb #10/B VAL 2 1HG2 A11_APL1_10.pdb #10/A ASN 66 1HB -0.161 2.161
A11_APL1_10.pdb #10/B LYS 10 2HD A11_APL1_10.pdb #10/A THR 143 1HG2 -0.164 2.164
A11_APL1_10.pdb #10/B LYS 10 NZ A11_APL1_10.pdb #10/A ASP 77 OD2 -0.170 2.875
A11_APL1_10.pdb #10/B VAL 2 CB A11_APL1_10.pdb #10/A TYR 99 OH -0.173 3.373
A11_APL1_10.pdb #10/B LYS 10 1HE A11_APL1_10.pdb #10/A ASP 77 CG -0.174 2.874
A11_APL1_10.pdb #10/B GLY 7 CA A11_APL1_10.pdb #10/A GLN 155 OE1 -0.175 3.355
A11_APL1_10.pdb #10/B VAL 2 N A11_APL1_10.pdb #10/A GLU 63 OE1 -0.182 2.887
A11_APL1_10.pdb #10/B VAL 2 CG2 A11_APL1_10.pdb #10/A GLU 63 OE1 -0.186 3.366
A11_APL1_10.pdb #10/B SER 1 CA A11_APL1_10.pdb #10/A GLU 63 OE1 -0.186 3.366
A11_APL1_10.pdb #10/B LYS 10 1HG A11_APL1_10.pdb #10/A THR 143 3HG2 -0.189 2.189
A11_APL1_10.pdb #10/B LYS 10 N A11_APL1_10.pdb #10/A TRP 147 CH2 -0.190 3.515
A11_APL1_10.pdb #10/B SER 1 CA A11_APL1_10.pdb #10/A GLU 63 CD -0.191 3.591
A11_APL1_10.pdb #10/B VAL 3 H A11_APL1_10.pdb #10/A TYR 99 CE1 -0.196 2.896
A11_APL1_10.pdb #10/B SER 1 1H A11_APL1_10.pdb #10/A TYR 171 OH -0.196 2.296
A11_APL1_10.pdb #10/B SER 1 3H A11_APL1_10.pdb #10/A TYR 7 OH -0.201 2.301
A11_APL1_10.pdb #10/B SER 1 2H A11_APL1_10.pdb #10/A TYR 171 OH -0.201 2.301
A11_APL1_10.pdb #10/B LYS 10 2HG A11_APL1_10.pdb #10/A TRP 147 CH2 -0.204 2.904
A11_APL1_10.pdb #10/B VAL 2 1HG2 A11_APL1_10.pdb #10/A ASN 66 CB -0.207 2.907
A11_APL1_10.pdb #10/B VAL 8 O A11_APL1_10.pdb #10/A TRP 147 HH2 -0.209 2.689
A11_APL1_10.pdb #10/B LYS 10 3HZ A11_APL1_10.pdb #10/A ASP 77 OD2 -0.214 2.294
A11_APL1_10.pdb #10/B LYS 10 CE A11_APL1_10.pdb #10/A ASP 77 CB -0.217 3.617
A11_APL1_10.pdb #10/B SER 1 O A11_APL1_10.pdb #10/A TYR 159 OH -0.219 2.799
A11_APL1_10.pdb #10/B GLY 9 1HA A11_APL1_10.pdb #10/A THR 73 3HG2 -0.220 2.220
A11_APL1_10.pdb #10/B VAL 2 HA A11_APL1_10.pdb #10/A TYR 7 CE1 -0.225 2.925
A11_APL1_10.pdb #10/B VAL 3 N A11_APL1_10.pdb #10/A TYR 99 CZ -0.228 3.553
A11_APL1_10.pdb #10/B LYS 10 2HD A11_APL1_10.pdb #10/A THR 143 OG1 -0.230 2.730
A11_APL1_10.pdb #10/B LYS 10 1HG A11_APL1_10.pdb #10/A TRP 147 CZ3 -0.232 2.932
A11_APL1_10.pdb #10/B SER 1 1H A11_APL1_10.pdb #10/A TYR 171 CZ -0.233 2.933
A11_APL1_10.pdb #10/B SER 1 C A11_APL1_10.pdb #10/A TYR 7 CZ -0.233 3.633
A11_APL1_10.pdb #10/B VAL 3 CA A11_APL1_10.pdb #10/A TYR 159 CE1 -0.235 3.635
A11_APL1_10.pdb #10/B VAL 3 H A11_APL1_10.pdb #10/A TYR 99 HH -0.237 2.237
A11_APL1_10.pdb #10/B LYS 10 C A11_APL1_10.pdb #10/A THR 80 OG1 -0.238 3.438
A11_APL1_10.pdb #10/B SER 1 C A11_APL1_10.pdb #10/A TYR 7 CE1 -0.239 3.639
A11_APL1_10.pdb #10/B LYS 10 1HB A11_APL1_10.pdb #10/A ASP 77 OD1 -0.240 2.720
A11_APL1_10.pdb #10/B SER 1 CB A11_APL1_10.pdb #10/A GLU 63 OE2 -0.244 3.424
A11_APL1_10.pdb #10/B LYS 10 O A11_APL1_10.pdb #10/A LYS 146 2HZ -0.245 2.325
A11_APL1_10.pdb #10/B VAL 3 N A11_APL1_10.pdb #10/A TYR 99 OH -0.248 2.973
A11_APL1_10.pdb #10/B LYS 10 NZ A11_APL1_10.pdb #10/A ASP 77 CB -0.249 3.574
A11_APL1_10.pdb #10/B VAL 3 2HG1 A11_APL1_10.pdb #10/A TYR 99 OH -0.251 2.751
A11_APL1_10.pdb #10/B SER 1 O A11_APL1_10.pdb #10/A TYR 159 CE1 -0.254 3.434
A11_APL1_10.pdb #10/B VAL 2 HB A11_APL1_10.pdb #10/A TYR 99 OH -0.254 2.754
A11_APL1_10.pdb #10/B SER 1 C A11_APL1_10.pdb #10/A TYR 159 HH -0.260 2.960
A11_APL1_10.pdb #10/B VAL 2 N A11_APL1_10.pdb #10/A TYR 7 CZ -0.262 3.587
A11_APL1_10.pdb #10/B LYS 10 CA A11_APL1_10.pdb #10/A TRP 147 HH2 -0.263 2.963
A11_APL1_10.pdb #10/B LYS 10 2HE A11_APL1_10.pdb #10/A LEU 81 1HD2 -0.267 2.267
A11_APL1_10.pdb #10/B VAL 2 CG1 A11_APL1_10.pdb #10/A GLU 63 OE1 -0.268 3.448
A11_APL1_10.pdb #10/B SER 1 N A11_APL1_10.pdb #10/A TYR 171 CZ -0.271 3.596
A11_APL1_10.pdb #10/B LYS 10 C A11_APL1_10.pdb #10/A THR 80 CG2 -0.282 3.682
A11_APL1_10.pdb #10/B VAL 2 CG1 A11_APL1_10.pdb #10/A MET 45 CE -0.286 3.686
A11_APL1_10.pdb #10/B VAL 3 CB A11_APL1_10.pdb #10/A TYR 99 CE1 -0.287 3.687
A11_APL1_10.pdb #10/B SER 1 OG A11_APL1_10.pdb #10/A GLU 63 OE2 -0.287 2.867
A11_APL1_10.pdb #10/B VAL 2 2HG1 A11_APL1_10.pdb #10/A TYR 9 OH -0.290 2.790
A11_APL1_10.pdb #10/B LYS 10 CE A11_APL1_10.pdb #10/A LEU 81 1HD2 -0.292 2.992
A11_APL1_10.pdb #10/B LYS 10 1HZ A11_APL1_10.pdb #10/A ASP 77 CG -0.293 2.993
A11_APL1_10.pdb #10/B SER 1 N A11_APL1_10.pdb #10/A TYR 171 CE2 -0.293 3.618
A11_APL1_10.pdb #10/B SER 1 CA A11_APL1_10.pdb #10/A GLU 63 OE2 -0.296 3.476
A11_APL1_10.pdb #10/B VAL 3 CG1 A11_APL1_10.pdb #10/A TYR 99 CE2 -0.300 3.700
A11_APL1_10.pdb #10/B VAL 8 O A11_APL1_10.pdb #10/A TRP 147 CZ3 -0.305 3.485
A11_APL1_10.pdb #10/B LYS 10 CG A11_APL1_10.pdb #10/A TRP 147 HH2 -0.308 3.008
A11_APL1_10.pdb #10/B SER 1 CB A11_APL1_10.pdb #10/A TRP 167 CG -0.317 3.717
A11_APL1_10.pdb #10/B VAL 3 N A11_APL1_10.pdb #10/A TYR 99 CE1 -0.318 3.643
A11_APL1_10.pdb #10/B GLY 9 C A11_APL1_10.pdb #10/A TRP 147 CH2 -0.318 3.718
A11_APL1_10.pdb #10/B LYS 10 CB A11_APL1_10.pdb #10/A ASP 77 OD1 -0.319 3.499
A11_APL1_10.pdb #10/B LYS 10 CA A11_APL1_10.pdb #10/A TRP 147 CH2 -0.319 3.719
A11_APL1_10.pdb #10/B VAL 3 CG2 A11_APL1_10.pdb #10/A TYR 159 CD2 -0.324 3.724
A11_APL1_10.pdb #10/B LYS 10 CG A11_APL1_10.pdb #10/A THR 143 3HG2 -0.331 3.031
A11_APL1_10.pdb #10/B LYS 10 CG A11_APL1_10.pdb #10/A THR 143 HG1 -0.331 3.031
A11_APL1_10.pdb #10/B LYS 10 OXT A11_APL1_10.pdb #10/A THR 80 OG1 -0.332 2.912
A11_APL1_10.pdb #10/B VAL 3 CA A11_APL1_10.pdb #10/A TYR 159 CZ -0.333 3.733
A11_APL1_10.pdb #10/B GLY 9 1HA A11_APL1_10.pdb #10/A THR 73 CG2 -0.334 3.034
A11_APL1_10.pdb #10/B VAL 3 2HG1 A11_APL1_10.pdb #10/A TYR 99 CE2 -0.335 3.035
A11_APL1_10.pdb #10/B SER 1 1H A11_APL1_10.pdb #10/A TYR 171 CE2 -0.336 3.036
A11_APL1_10.pdb #10/B SER 1 N A11_APL1_10.pdb #10/A TYR 171 HE2 -0.339 2.964
A11_APL1_10.pdb #10/B LYS 10 C A11_APL1_10.pdb #10/A LYS 146 3HZ -0.343 3.043
A11_APL1_10.pdb #10/B VAL 2 1HG1 A11_APL1_10.pdb #10/A MET 45 CE -0.344 3.044
A11_APL1_10.pdb #10/B VAL 3 CB A11_APL1_10.pdb #10/A TYR 99 CZ -0.344 3.744
A11_APL1_10.pdb #10/B VAL 3 N A11_APL1_10.pdb #10/A TYR 159 CZ -0.344 3.669
A11_APL1_10.pdb #10/B VAL 2 2HG1 A11_APL1_10.pdb #10/A TYR 7 CZ -0.352 3.052
A11_APL1_10.pdb #10/B VAL 2 CG1 A11_APL1_10.pdb #10/A TYR 7 CZ -0.353 3.753
A11_APL1_10.pdb #10/B VAL 2 CG1 A11_APL1_10.pdb #10/A MET 45 3HE -0.354 3.054
A11_APL1_10.pdb #10/B LYS 10 HA A11_APL1_10.pdb #10/A TRP 147 CZ3 -0.368 3.068
A11_APL1_10.pdb #10/B VAL 2 HB A11_APL1_10.pdb #10/A TYR 99 HH -0.377 2.377
A11_APL1_10.pdb #10/B LYS 10 2HE A11_APL1_10.pdb #10/A LEU 81 CD1 -0.378 3.078
A11_APL1_10.pdb #10/B VAL 3 2HG1 A11_APL1_10.pdb #10/A TYR 99 HH -0.382 2.382
A11_APL1_10.pdb #10/B SER 1 O A11_APL1_10.pdb #10/A TYR 159 CZ -0.382 3.562
A11_APL1_10.pdb #10/B VAL 2 CA A11_APL1_10.pdb #10/A TYR 7 CE1 -0.384 3.784
A11_APL1_10.pdb #10/B LYS 10 CG A11_APL1_10.pdb #10/A TRP 147 CZ3 -0.385 3.785
A11_APL1_10.pdb #10/B LYS 10 NZ A11_APL1_10.pdb #10/A ASP 77 2HB -0.385 3.010
A11_APL1_10.pdb #10/B VAL 2 3HG2 A11_APL1_10.pdb #10/A ASN 66 CB -0.385 3.085
A11_APL1_10.pdb #10/B LYS 10 1HZ A11_APL1_10.pdb #10/A ASP 77 CB -0.385 3.085
A11_APL1_10.pdb #10/B VAL 2 CA A11_APL1_10.pdb #10/A TYR 7 CZ -0.387 3.787
A11_APL1_10.pdb #10/B VAL 2 C A11_APL1_10.pdb #10/A TYR 159 CE1 -0.389 3.789
A11_APL1_10.pdb #10/B SER 1 2H A11_APL1_10.pdb #10/A TYR 7 OH -0.395 2.495
A11_APL1_10.pdb #10/B SER 1 2HB A11_APL1_10.pdb #10/A TRP 167 CG -0.399 3.099
161 contacts
> H-Bonds /B:1
Unknown command: H-Bonds /B:1
> hbonds /B:1
140 hydrogen bonds found
> hbonds #1/B:1
10 hydrogen bonds found
> hbonds #2/B:1
15 hydrogen bonds found
> hbonds #3/B:1
15 hydrogen bonds found
> hbonds #4/B:1
15 hydrogen bonds found
> hbonds #5/B:1
15 hydrogen bonds found
> hbonds #6/B:1
15 hydrogen bonds found
> hbonds #7/B:1
15 hydrogen bonds found
> hbonds #8/B:1
19 hydrogen bonds found
> hbonds #9/B:1
6 hydrogen bonds found
> hbonds #10/B:1
15 hydrogen bonds found
> mlp /B
Map values for surface "A11_APL1_4.pdb_B SES surface": minimum -20.66, mean
-3.55, maximum 16.65
Map values for surface "A11_APL1_8.pdb_B SES surface": minimum -20.82, mean
-3.784, maximum 16.1
Map values for surface "A11_APL1_1.pdb_B SES surface": minimum -19.11, mean
-3.834, maximum 16.78
Map values for surface "A11_APL1_5.pdb_B SES surface": minimum -20.03, mean
-3.684, maximum 16.31
Map values for surface "A11_APL1_7.pdb_B SES surface": minimum -21.43, mean
-3.668, maximum 17.69
Map values for surface "A11_APL1_2.pdb_B SES surface": minimum -20.1, mean
-3.764, maximum 17.27
Map values for surface "A11_APL1_6.pdb_B SES surface": minimum -19.44, mean
-3.73, maximum 17.07
Map values for surface "A11_APL1_9.pdb_B SES surface": minimum -20.01, mean
-3.594, maximum 16.81
Map values for surface "A11_APL1_10.pdb_B SES surface": minimum -19.46, mean
-3.809, maximum 17.35
Map values for surface "A11_APL1_3.pdb_B SES surface": minimum -19.85, mean
-3.667, maximum 15.95
> coloumbic /B
Unknown command: coloumbic /B
> coluombic /B
Unknown command: coluombic /B
> coulombic /B
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for A11_APL1_1.pdb_B SES surface #1.2: minimum, -9.76, mean
1.46, maximum 10.26
Coulombic values for A11_APL1_2.pdb_B SES surface #2.2: minimum, -9.82, mean
1.62, maximum 10.68
Coulombic values for A11_APL1_3.pdb_B SES surface #3.2: minimum, -9.46, mean
1.57, maximum 10.61
Coulombic values for A11_APL1_4.pdb_B SES surface #4.2: minimum, -9.34, mean
1.76, maximum 10.85
Coulombic values for A11_APL1_5.pdb_B SES surface #5.2: minimum, -9.71, mean
1.62, maximum 10.43
Coulombic values for A11_APL1_6.pdb_B SES surface #6.2: minimum, -10.44, mean
1.61, maximum 10.81
Coulombic values for A11_APL1_7.pdb_B SES surface #7.2: minimum, -10.04, mean
1.69, maximum 10.74
Coulombic values for A11_APL1_8.pdb_B SES surface #8.2: minimum, -9.26, mean
1.65, maximum 11.26
Coulombic values for A11_APL1_9.pdb_B SES surface #9.2: minimum, -9.84, mean
1.65, maximum 9.50
Coulombic values for A11_APL1_10.pdb_B SES surface #10.2: minimum, -9.73, mean
1.61, maximum 10.55
> show #11 models
> show #!9 models
> show #!8 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> rmsd #1/B to #2/B
RMSD between 105 atom pairs is 1.311
> rmsd #1/B to #3/B
RMSD between 105 atom pairs is 1.839
> rmsd #1/B to #4/B
RMSD between 105 atom pairs is 2.146
> rmsd #1/B to #5/B
RMSD between 105 atom pairs is 1.651
> rmsd #1/B to #6/B
RMSD between 105 atom pairs is 1.535
> rmsd #1/B to #7/B
RMSD between 105 atom pairs is 1.994
> rmsd #1/B to #8/B
RMSD between 105 atom pairs is 1.827
> rmsd #1/B to #9/B
RMSD between 105 atom pairs is 2.454
> rmsd #1/B to #10/B
RMSD between 105 atom pairs is 1.855
> rmsd #2/B to #3/B
RMSD between 105 atom pairs is 1.566
> rmsd #2/B to #4/B
RMSD between 105 atom pairs is 1.668
> rmsd #2/B to #5/B
RMSD between 105 atom pairs is 1.303
> rmsd #2/B to #6/B
RMSD between 105 atom pairs is 2.007
> rmsd #2/B to #7/B
RMSD between 105 atom pairs is 1.742
> rmsd #2/B to #8/B
RMSD between 105 atom pairs is 1.876
> rmsd #2/B to #9/B
RMSD between 105 atom pairs is 2.436
> rmsd #2/B to #10/B
RMSD between 105 atom pairs is 1.788
> rmsd #3/B to #4/B
RMSD between 105 atom pairs is 1.946
> rmsd #3/B to #5/B
RMSD between 105 atom pairs is 1.102
> rmsd #3/B to #6/B
RMSD between 105 atom pairs is 1.649
> rmsd #3/B to #7/B
RMSD between 105 atom pairs is 1.829
> rmsd #3/B to #8/B
RMSD between 105 atom pairs is 1.800
> rmsd #3/B to #9/B
RMSD between 105 atom pairs is 2.396
> rmsd #3/B to #10/B
RMSD between 105 atom pairs is 2.211
> rmsd #4/B to #5/B
RMSD between 105 atom pairs is 1.718
> rmsd #4/B to #6/B
RMSD between 105 atom pairs is 2.160
> rmsd #4/B to #7/B
RMSD between 105 atom pairs is 1.139
> rmsd #4/B to #8/B
RMSD between 105 atom pairs is 1.848
> rmsd #4/B to #9/B
RMSD between 105 atom pairs is 1.880
> rmsd #4/B to #10/B
RMSD between 105 atom pairs is 2.311
> rmsd #5/B to #6/B
RMSD between 105 atom pairs is 1.888
> rmsd #5/B to #7/B
RMSD between 105 atom pairs is 1.556
> rmsd #5/B to #8/B
RMSD between 105 atom pairs is 1.631
> rmsd #5/B to #9/B
RMSD between 105 atom pairs is 2.266
> rmsd #5/B to #10/B
RMSD between 105 atom pairs is 1.959
> rmsd #6/B to #7/B
RMSD between 105 atom pairs is 2.001
> rmsd #6/B to #7/B
RMSD between 105 atom pairs is 2.001
> rmsd #6/B to #8/B
RMSD between 105 atom pairs is 1.746
> rmsd #6/B to #9/B
RMSD between 105 atom pairs is 2.176
> rmsd #6/B to #10/B
RMSD between 105 atom pairs is 2.215
> rmsd #7/B to #8/B
RMSD between 105 atom pairs is 1.865
> rmsd #7/B to #9/B
RMSD between 105 atom pairs is 1.668
> rmsd #7/B to #10/B
RMSD between 105 atom pairs is 2.062
> rmsd #8/B to #9/B
RMSD between 105 atom pairs is 2.070
> rmsd #8/B to #10/B
RMSD between 105 atom pairs is 2.310
> rmsd #9/B to #10/B
RMSD between 105 atom pairs is 2.724
> select /A
43500 atoms, 44120 bonds, 2760 residues, 10 models selected
> hide sel atoms
> select clear
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> save "/Users/amandahuff/OneDrive - Johns
> Hopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11 NEW/7ow4_APL1/APL1
> electrostatic charge of anchor mod.png" width 663 height 635 supersample 3
> close all
> open "/Users/amandahuff/Library/CloudStorage/OneDrive-
> JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
> NEW/7ow4_parental/A11Parental_1.pdb"
Summary of feedback from opening
/Users/amandahuff/Library/CloudStorage/OneDrive-
JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
NEW/7ow4_parental/A11Parental_1.pdb
---
warnings | Ignored bad PDB record found on line 4462
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 4463
#BEGIN_POSE_ENERGIES_TABLE 65de52b14b55f_P4_0016.pdb
Ignored bad PDB record found on line 4464
label fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih
dslf_ca_dih rama omega fa_dun p_aa_pp ref total
Ignored bad PDB record found on line 4465
weights 0.8 0.44 0.65 0.004 1 0.49 0.585 1.17 1.17 1.1 1 1 1 1 0.2 0.5 0.56
0.32 1 NA
Ignored bad PDB record found on line 4466
pose -1056.43 100.034 532.197 2.12118 0.768788 -23.2915 -55.3316 -125.482
-30.4497 -27.5533 -7.16081 0.470131 0.567418 0.10012 -13.4304 62.2158 191.788
-26.3016 -60.28 -535.444
302 messages similar to the above omitted
Chain information for A11Parental_1.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open "/Users/amandahuff/Library/CloudStorage/OneDrive-
> JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
> NEW/7ow4_parental/A11Parental_2.pdb"
Summary of feedback from opening
/Users/amandahuff/Library/CloudStorage/OneDrive-
JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
NEW/7ow4_parental/A11Parental_2.pdb
---
warnings | Ignored bad PDB record found on line 4462
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 4463
#BEGIN_POSE_ENERGIES_TABLE 65de52b14b55f_P3_0030.pdb
Ignored bad PDB record found on line 4464
label fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih
dslf_ca_dih rama omega fa_dun p_aa_pp ref total
Ignored bad PDB record found on line 4465
weights 0.8 0.44 0.65 0.004 1 0.49 0.585 1.17 1.17 1.1 1 1 1 1 0.2 0.5 0.56
0.32 1 NA
Ignored bad PDB record found on line 4466
pose -1058.61 99.6619 535.441 2.1172 0.769511 -23.5686 -55.3316 -125.482
-30.4127 -27.5263 -7.1665 0.474333 0.575353 0.100124 -12.3879 62.5159 190.52
-24.9437 -60.28 -533.536
302 messages similar to the above omitted
Chain information for A11Parental_2.pdb #2
---
Chain | Description
A | No description available
B | No description available
> open "/Users/amandahuff/Library/CloudStorage/OneDrive-
> JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
> NEW/7ow4_parental/A11Parental_3.pdb"
Summary of feedback from opening
/Users/amandahuff/Library/CloudStorage/OneDrive-
JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
NEW/7ow4_parental/A11Parental_3.pdb
---
warnings | Ignored bad PDB record found on line 4462
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 4463
#BEGIN_POSE_ENERGIES_TABLE 65de52b14b55f_P3_0002.pdb
Ignored bad PDB record found on line 4464
label fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih
dslf_ca_dih rama omega fa_dun p_aa_pp ref total
Ignored bad PDB record found on line 4465
weights 0.8 0.44 0.65 0.004 1 0.49 0.585 1.17 1.17 1.1 1 1 1 1 0.2 0.5 0.56
0.32 1 NA
Ignored bad PDB record found on line 4466
pose -1062.46 103.437 536.258 2.13772 0.772106 -23.7008 -55.3316 -125.482
-28.3903 -26.5414 -7.16226 0.484369 0.554829 0.100115 -13.6575 62.2546 190.477
-26.0162 -60.28 -532.547
302 messages similar to the above omitted
Chain information for A11Parental_3.pdb #3
---
Chain | Description
A | No description available
B | No description available
> open "/Users/amandahuff/Library/CloudStorage/OneDrive-
> JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
> NEW/7ow4_parental/A11Parental_4.pdb"
Summary of feedback from opening
/Users/amandahuff/Library/CloudStorage/OneDrive-
JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
NEW/7ow4_parental/A11Parental_4.pdb
---
warnings | Ignored bad PDB record found on line 4462
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 4463
#BEGIN_POSE_ENERGIES_TABLE 65de52b14b55f_P4_0045.pdb
Ignored bad PDB record found on line 4464
label fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih
dslf_ca_dih rama omega fa_dun p_aa_pp ref total
Ignored bad PDB record found on line 4465
weights 0.8 0.44 0.65 0.004 1 0.49 0.585 1.17 1.17 1.1 1 1 1 1 0.2 0.5 0.56
0.32 1 NA
Ignored bad PDB record found on line 4466
pose -1055.06 99.8695 531.158 2.1606 0.769757 -23.2958 -55.3316 -125.482
-30.4361 -25.6974 -7.17506 0.479723 0.555341 0.100118 -13.7748 62.2325 192.781
-26.0363 -60.28 -532.463
302 messages similar to the above omitted
Chain information for A11Parental_4.pdb #4
---
Chain | Description
A | No description available
B | No description available
> open "/Users/amandahuff/Library/CloudStorage/OneDrive-
> JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
> NEW/7ow4_parental/A11Parental_5.pdb"
Summary of feedback from opening
/Users/amandahuff/Library/CloudStorage/OneDrive-
JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
NEW/7ow4_parental/A11Parental_5.pdb
---
warnings | Ignored bad PDB record found on line 4462
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 4463
#BEGIN_POSE_ENERGIES_TABLE 65de52b14b55f_P3_0021.pdb
Ignored bad PDB record found on line 4464
label fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih
dslf_ca_dih rama omega fa_dun p_aa_pp ref total
Ignored bad PDB record found on line 4465
weights 0.8 0.44 0.65 0.004 1 0.49 0.585 1.17 1.17 1.1 1 1 1 1 0.2 0.5 0.56
0.32 1 NA
Ignored bad PDB record found on line 4466
pose -1055.18 100.752 534.05 2.1259 0.769161 -23.5847 -55.3316 -125.482
-29.5717 -27.1518 -7.25526 0.450411 0.601285 0.100124 -13.7343 62.1444 190.125
-25.8772 -60.28 -532.331
302 messages similar to the above omitted
Chain information for A11Parental_5.pdb #5
---
Chain | Description
A | No description available
B | No description available
> open "/Users/amandahuff/Library/CloudStorage/OneDrive-
> JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
> NEW/7ow4_parental/A11Parental_6.pdb"
Summary of feedback from opening
/Users/amandahuff/Library/CloudStorage/OneDrive-
JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
NEW/7ow4_parental/A11Parental_6.pdb
---
warnings | Ignored bad PDB record found on line 4462
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 4463
#BEGIN_POSE_ENERGIES_TABLE 65de52b14b55f_P3_0012.pdb
Ignored bad PDB record found on line 4464
label fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih
dslf_ca_dih rama omega fa_dun p_aa_pp ref total
Ignored bad PDB record found on line 4465
weights 0.8 0.44 0.65 0.004 1 0.49 0.585 1.17 1.17 1.1 1 1 1 1 0.2 0.5 0.56
0.32 1 NA
Ignored bad PDB record found on line 4466
pose -1061.79 102.409 536.863 2.11486 0.769798 -23.1526 -55.3316 -125.482
-35.2917 -24.2608 -7.17361 0.470738 0.568717 0.100117 -12.1372 62.6794 192.655
-25.8527 -60.28 -532.125
302 messages similar to the above omitted
Chain information for A11Parental_6.pdb #6
---
Chain | Description
A | No description available
B | No description available
> open "/Users/amandahuff/Library/CloudStorage/OneDrive-
> JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
> NEW/7ow4_parental/A11Parental_7.pdb"
Summary of feedback from opening
/Users/amandahuff/Library/CloudStorage/OneDrive-
JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
NEW/7ow4_parental/A11Parental_7.pdb
---
warnings | Ignored bad PDB record found on line 4462
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 4463
#BEGIN_POSE_ENERGIES_TABLE 65de52b14b55f_P3_0026.pdb
Ignored bad PDB record found on line 4464
label fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih
dslf_ca_dih rama omega fa_dun p_aa_pp ref total
Ignored bad PDB record found on line 4465
weights 0.8 0.44 0.65 0.004 1 0.49 0.585 1.17 1.17 1.1 1 1 1 1 0.2 0.5 0.56
0.32 1 NA
Ignored bad PDB record found on line 4466
pose -1062.63 104.992 536.085 2.12978 0.766762 -23.5496 -55.3316 -125.482
-32.9465 -25.2512 -7.17277 0.474606 0.560914 0.100113 -12.3153 62.4889 190.974
-25.4827 -60.28 -531.866
302 messages similar to the above omitted
Chain information for A11Parental_7.pdb #7
---
Chain | Description
A | No description available
B | No description available
> open "/Users/amandahuff/Library/CloudStorage/OneDrive-
> JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
> NEW/7ow4_parental/A11Parental_8.pdb"
Summary of feedback from opening
/Users/amandahuff/Library/CloudStorage/OneDrive-
JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
NEW/7ow4_parental/A11Parental_8.pdb
---
warnings | Ignored bad PDB record found on line 4462
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 4463
#BEGIN_POSE_ENERGIES_TABLE 65de52b14b55f_P4_0001.pdb
Ignored bad PDB record found on line 4464
label fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih
dslf_ca_dih rama omega fa_dun p_aa_pp ref total
Ignored bad PDB record found on line 4465
weights 0.8 0.44 0.65 0.004 1 0.49 0.585 1.17 1.17 1.1 1 1 1 1 0.2 0.5 0.56
0.32 1 NA
Ignored bad PDB record found on line 4466
pose -1064.93 101.232 539.26 2.13185 0.770792 -23.5228 -55.3316 -125.482
-33.1658 -25.3525 -7.1595 0.47766 0.563003 0.100119 -9.83864 63.2235 190.387
-24.111 -60.28 -531.027
302 messages similar to the above omitted
Chain information for A11Parental_8.pdb #8
---
Chain | Description
A | No description available
B | No description available
> open "/Users/amandahuff/Library/CloudStorage/OneDrive-
> JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
> NEW/7ow4_parental/A11Parental_9.pdb"
Summary of feedback from opening
/Users/amandahuff/Library/CloudStorage/OneDrive-
JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
NEW/7ow4_parental/A11Parental_9.pdb
---
warnings | Ignored bad PDB record found on line 4462
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 4463
#BEGIN_POSE_ENERGIES_TABLE 65de52b14b55f_P3_0042.pdb
Ignored bad PDB record found on line 4464
label fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih
dslf_ca_dih rama omega fa_dun p_aa_pp ref total
Ignored bad PDB record found on line 4465
weights 0.8 0.44 0.65 0.004 1 0.49 0.585 1.17 1.17 1.1 1 1 1 1 0.2 0.5 0.56
0.32 1 NA
Ignored bad PDB record found on line 4466
pose -1066.52 103.861 539.874 2.14491 0.76745 -22.982 -55.3316 -125.482
-34.5666 -26.6943 -7.16661 0.471623 0.565113 0.100113 -9.16255 62.49 193.066
-25.1916 -60.28 -530.038
302 messages similar to the above omitted
Chain information for A11Parental_9.pdb #9
---
Chain | Description
A | No description available
B | No description available
> open "/Users/amandahuff/Library/CloudStorage/OneDrive-
> JohnsHopkins/Jaffee_Lab/APL_project/KRAS_APL_models/A11
> NEW/7ow4_parental/A11Parental_10.pdb"
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGQ3LL/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 10 days, 13 hours, 58 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
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 , 20 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 → Crash in garbage collection |
comment:2 by , 20 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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