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Opened 19 months ago
Closed 19 months ago
#14958 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-14.4.1-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff8571bb100 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py", line 806 in _find_acceptors
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py", line 498 in find_hbonds
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/cmd.py", line 94 in cmd_hbonds
File "/Applications/ChimeraX-1.7.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.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.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, lxml._elementpath, lxml.etree, chimerax.coulombic._esp (total: 62)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
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"modelCode" : "MacBookAir9,1",
"coalitionID" : 3343,
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"captureTime" : "2024-04-11 13:02:31.4486 -0400",
"codeSigningMonitor" : 0,
"incident" : "68D812FA-BCED-4BB7-9AD7-9AF67F2407AE",
"pid" : 6077,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-04-11 10:39:04.1251 -0400",
"procStartAbsTime" : 37295021994578,
"procExitAbsTime" : 44854849435630,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
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"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":6077},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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[deleted to fit within ticket limits]
/I ADP 501 C3' /I GLN 205 CB -0.297 4.057
/A ADP 501 O3' /A GLN 205 CB -0.299 3.639
/A ADP 501 N1 /A TRP 130 CB -0.300 3.820
/C ADP 501 N6 /C SER 257 CB -0.300 3.820
/G ADP 501 O3' /G GLY 132 CA -0.302 3.642
/B ADP 501 N6 /B TYR 336 CD2 -0.302 3.702
/E ADP 501 O2' /E GLY 207 C -0.302 3.372
/F ADP 501 O3B /F P3S 601 PA -0.303 3.823
/D ADP 501 O4' /D ASN 255 CG -0.307 3.377
/C ADP 501 O1A /C HOH 709 O -0.308 2.788
/D ADP 501 O1A /C HOH 707 O -0.310 2.790
/D ADP 501 O3B /D GLU 134 CD -0.310 3.610
/A ADP 501 N6 /A SER 257 CB -0.310 3.830
/I ADP 501 PA /I GLN 205 CD -0.312 4.022
/B ADP 501 PB /B ARG 319 NH1 -0.313 4.053
/B ADP 501 C2 /B TRP 130 O -0.314 3.494
/J ADP 501 PA /J GLU 134 OE2 -0.314 3.834
/B ADP 501 C3' /B GLN 205 CB -0.314 4.074
/J ADP 501 N3 /J GLY 132 CA -0.315 3.835
/A ADP 501 PB /A ARG 324 NH2 -0.315 4.055
/G ADP 501 N6 /G SER 257 CB -0.315 3.835
/A ADP 501 O3A /A GLU 134 CD -0.316 3.656
/A ADP 501 C4 /A PRO 208 CG -0.316 3.806
/F ADP 501 N6 /F TYR 336 CD2 -0.316 3.716
/G ADP 501 O2' /G GLY 207 C -0.316 3.386
/B ADP 501 N6 /B TYR 336 CB -0.316 3.836
/I ADP 501 O3' /I GLN 205 CB -0.317 3.657
/J ADP 501 O2' /J GLY 207 C -0.318 3.388
/E ADP 501 O2' /E PRO 208 N -0.319 3.419
/A ADP 501 C5' /A ASN 255 ND2 -0.320 3.840
/J ADP 501 O2A /J GLN 205 CD -0.321 3.351
/I ADP 501 PB /I ARG 324 NH2 -0.321 4.061
/G ADP 501 O4' /G ASN 255 CG -0.323 3.393
/J ADP 501 C5' /J ASN 255 ND2 -0.323 3.843
/F ADP 501 O3' /F GLN 205 CB -0.324 3.664
/E ADP 501 N9 /E PRO 208 CG -0.324 3.844
/H ADP 501 N6 /H ARG 262 CD -0.324 3.844
/B ADP 501 O2B /B GLU 338 CD -0.325 3.625
/I ADP 501 C4' /I ASN 255 CG -0.325 3.815
/H ADP 501 C3' /H GLN 205 CB -0.325 4.085
/B ADP 501 O5' /B GLU 134 CD -0.326 3.666
/I ADP 501 O1B /I ARG 324 NH2 -0.326 2.986
/D ADP 501 C5 /D TYR 336 CE2 -0.327 3.697
/B ADP 501 O2B /B ARG 324 NH1 -0.328 2.988
/H ADP 501 PA /H HOH 608 O -0.330 3.890
/F ADP 501 O2A /F GLU 203 OE2 -0.330 3.170
/F ADP 501 C5 /F PRO 208 CG -0.330 3.820
/J ADP 501 O3' /J GLN 205 CB -0.331 3.671
/B ADP 501 O2B /B GLU 134 OE1 -0.331 3.171
/E ADP 501 C5' /E ASN 255 ND2 -0.331 3.851
/E ADP 501 O2A /E GLN 205 CD -0.332 3.362
/E ADP 501 O2B /E GLU 338 OE2 -0.332 3.172
/G ADP 501 O5' /G GLU 134 CG -0.333 3.673
/A ADP 501 O5' /A GLU 134 CD -0.333 3.673
/G ADP 501 C4' /G ASN 255 CG -0.335 3.825
/J ADP 501 O3B /J ARG 324 NH1 -0.335 2.995
/E ADP 501 O1B /E ARG 324 NH2 -0.336 2.996
/B ADP 501 N6 /B SER 257 CB -0.336 3.856
/B ADP 501 C6 /B SER 257 OG -0.337 3.407
/F ADP 501 N6 /F ARG 262 CD -0.337 3.857
/J ADP 501 O2A /J GLU 203 OE2 -0.337 3.177
/J ADP 501 C2 /J PHE 131 CA -0.337 3.977
/C ADP 501 C2 /C TRP 130 O -0.338 3.518
/B ADP 501 N1 /B TRP 130 CB -0.339 3.859
/D ADP 501 PA /D HOH 747 O -0.339 3.899
/E ADP 501 C3' /E GLN 205 CB -0.340 4.100
/A ADP 501 O3B /A GLU 338 CD -0.340 3.640
/A ADP 501 N9 /A PRO 208 CG -0.340 3.860
/E ADP 501 O1A /D HOH 749 O -0.341 2.821
/F ADP 501 PA /F GLU 134 OE2 -0.342 3.862
/G ADP 501 PB /G GLU 134 OE2 -0.343 3.863
/D ADP 501 PB /D ARG 324 NH2 -0.343 4.083
/E ADP 501 C2 /E TRP 130 CB -0.343 3.983
/A ADP 501 C8 /A PRO 208 CG -0.344 3.984
/D ADP 501 O2B /D ARG 324 NH1 -0.345 3.005
/I ADP 501 O2B /I ARG 324 NH1 -0.346 3.006
/C ADP 501 N3 /C GLY 132 CA -0.347 3.867
/I ADP 501 PB /I ARG 319 NH1 -0.347 4.087
/G ADP 501 C2 /G TRP 130 O -0.349 3.529
/D ADP 501 O2' /D GLY 207 C -0.349 3.419
/A ADP 501 N3 /A GLY 132 CA -0.351 3.871
/H ADP 501 C1' /H GLY 132 CA -0.351 4.111
/B ADP 501 C1' /B GLY 132 CA -0.353 4.113
/F ADP 501 C3' /F GLN 205 CB -0.354 4.114
/A ADP 501 PB /A ARG 319 NH1 -0.354 4.094
/F ADP 501 C2 /F PHE 256 CA -0.354 3.994
/D ADP 501 C4' /D ASN 255 CG -0.355 3.845
/J ADP 501 O2' /J PRO 208 CG -0.355 3.695
/A ADP 501 C6 /A TYR 336 CD2 -0.356 3.726
/C ADP 501 C3' /C GLN 205 CB -0.358 4.118
/A ADP 501 C2 /A ASN 255 O -0.359 3.539
/F ADP 501 O2B /F GLU 134 OE1 -0.359 3.199
/G ADP 501 N3 /G ASN 255 CB -0.360 3.880
/H ADP 501 O2A /H GLN 205 CD -0.360 3.390
/F ADP 501 O3' /F GLY 132 CA -0.360 3.700
/E ADP 501 N6 /E SER 257 CB -0.361 3.881
/H ADP 501 O2B /H GLU 338 OE2 -0.361 3.201
/H ADP 501 N9 /H PRO 208 CG -0.363 3.883
/E ADP 501 C2 /E TRP 130 C -0.364 3.734
/J ADP 501 C5 /J PRO 208 CG -0.364 3.854
/A ADP 501 C6 /A SER 257 OG -0.366 3.436
/B ADP 501 N6 /B SER 257 OG -0.366 3.066
/E ADP 501 PA /E GLU 134 OE1 -0.368 3.888
/C ADP 501 N6 /C TRP 130 CE3 -0.368 3.768
/A ADP 501 N6 /A TRP 130 CE3 -0.369 3.769
/D ADP 501 N3 /D GLY 132 CA -0.370 3.890
/A ADP 501 PA /A GLN 205 CD -0.370 4.080
/D ADP 501 O5' /D GLN 205 CG -0.370 3.710
/I ADP 501 O2A /I GLN 205 NE2 -0.371 3.031
/G ADP 501 C5' /G ASN 255 ND2 -0.371 3.891
/D ADP 501 O2' /D PRO 208 N -0.371 3.471
/C ADP 501 C4' /C ASN 255 CG -0.371 3.861
/I ADP 501 O2' /I PRO 208 N -0.373 3.473
/F ADP 501 N7 /F PRO 208 CG -0.373 3.893
/E ADP 501 O4' /E ASN 255 CG -0.373 3.443
/A ADP 501 O2' /A GLY 207 C -0.374 3.444
/A ADP 501 PB /A P3S 601 O3A -0.375 3.895
/B ADP 501 N9 /B PRO 208 CG -0.375 3.895
/J ADP 501 N6 /J ARG 262 CD -0.376 3.896
/H ADP 501 O2A /H HOH 608 O -0.377 2.857
/G ADP 501 O3B /G GLU 134 OE1 -0.377 3.217
/D ADP 501 O2' /D ALA 191 CB -0.377 3.717
/J ADP 501 N1 /J TRP 130 CB -0.377 3.897
/E ADP 501 O3B /E HOH 627 O -0.378 2.858
/E ADP 501 C8 /E PRO 208 CG -0.379 4.019
/B ADP 501 O2' /B PRO 208 N -0.379 3.479
/I ADP 501 C8 /I PRO 208 CG -0.379 4.019
/H ADP 501 O2B /H ARG 324 NH1 -0.381 3.041
/B ADP 501 O2' /B PRO 208 CG -0.381 3.721
/I ADP 501 C6 /I TYR 336 CG -0.382 3.602
/C ADP 501 O2' /C ALA 191 CB -0.382 3.722
/H ADP 501 O3' /H GLN 205 CB -0.382 3.722
/C ADP 501 C5 /C TYR 336 CE2 -0.382 3.752
/G ADP 501 O2B /G GLU 134 OE1 -0.383 3.223
/F ADP 501 C8 /F TYR 336 CE2 -0.383 3.903
/B ADP 501 C5 /B TYR 336 CE2 -0.386 3.756
/J ADP 501 C2 /J GLY 132 N -0.386 3.786
/A ADP 501 C3' /A GLN 205 CB -0.386 4.146
/A ADP 501 O2' /A PRO 208 CG -0.389 3.729
/G ADP 501 PB /G P3S 601 O2A -0.389 3.909
/J ADP 501 C6 /J TYR 336 CG -0.389 3.609
/A ADP 501 O4' /A ASN 255 CG -0.389 3.459
/E ADP 501 N1 /E SER 257 OG -0.390 3.090
/D ADP 501 N6 /D SER 257 CB -0.390 3.910
/B ADP 501 O1A /A HOH 732 O -0.392 2.872
/E ADP 501 O3' /E GLN 205 CB -0.394 3.734
/A ADP 501 O2' /A ALA 191 CB -0.395 3.735
/C ADP 501 C5' /C HOH 739 O -0.396 3.736
/C ADP 501 N1 /C TRP 130 CB -0.398 3.918
/D ADP 501 O1B /D ARG 324 NH2 -0.398 3.058
/B ADP 501 N3 /B GLY 132 CA -0.399 3.919
/A ADP 501 N6 /A ARG 262 CG -0.399 3.919
647 contacts
> label @@display
> label height 1.3
> select clear
> close
> open 2qc8
2qc8 title:
Crystal structure of human glutamine synthetase in complex with ADP and
methionine sulfoximine phosphate [more info...]
Chain information for 2qc8 #1
---
Chain | Description | UniProt
A B C D E F G H I J | Glutamine synthetase | GLNA_HUMAN 5-365
Non-standard residues in 2qc8 #1
---
ADP — adenosine-5'-diphosphate
CL — chloride ion
MN — manganese (II) ion
P3S — L-methionine-S-sulfoximine phosphate
> hide solvent
> style stick
Changed 28837 atom styles
> select :P3S
150 atoms, 140 bonds, 10 residues, 1 model selected
> hide ~sel
> hbonds :P3S reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2qc8
121 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A HIS 253 NE2 /A P3S 601 O no hydrogen 2.681 N/A
/A ARG 299 NH1 /A P3S 601 OT no hydrogen 3.167 N/A
/A ARG 319 NE /A P3S 601 O1A no hydrogen 2.982 N/A
/A ARG 319 NE /A P3S 601 OE no hydrogen 3.242 N/A
/A ARG 319 NH1 /A P3S 601 O1A no hydrogen 2.967 N/A
/A ARG 340 NH1 /A P3S 601 O2A no hydrogen 2.969 N/A
/A ARG 340 NH2 /A P3S 601 OE no hydrogen 2.965 N/A
/A P3S 601 N /A GLU 136 OE1 no hydrogen 2.707 N/A
/A P3S 601 N /A GLU 136 OE2 no hydrogen 3.395 N/A
/A P3S 601 N /A GLY 249 O no hydrogen 2.664 N/A
/A P3S 601 N /A HOH 733 O no hydrogen 2.655 N/A
/B HIS 253 NE2 /B P3S 601 O no hydrogen 2.621 N/A
/B ARG 299 NH1 /B P3S 601 OT no hydrogen 3.037 N/A
/B ARG 319 NE /B P3S 601 O1A no hydrogen 2.927 N/A
/B ARG 319 NE /B P3S 601 OE no hydrogen 3.059 N/A
/B ARG 319 NH1 /B P3S 601 O1A no hydrogen 2.787 N/A
/B ARG 340 NH1 /B P3S 601 O2A no hydrogen 3.220 N/A
/B ARG 340 NH2 /B P3S 601 OE no hydrogen 3.192 N/A
/B P3S 601 N /B GLU 136 OE1 no hydrogen 2.685 N/A
/B P3S 601 N /B GLU 136 OE2 no hydrogen 3.568 N/A
/B P3S 601 N /B GLY 249 O no hydrogen 2.500 N/A
/B HOH 718 O /B P3S 601 OT no hydrogen 2.603 N/A
/B HOH 741 O /B P3S 601 O3A no hydrogen 3.311 N/A
/B HOH 744 O /B P3S 601 O3A no hydrogen 2.918 N/A
/C HIS 253 NE2 /C P3S 601 O no hydrogen 2.561 N/A
/C ARG 299 NH1 /C P3S 601 OT no hydrogen 2.934 N/A
/C ARG 319 NE /C P3S 601 O1A no hydrogen 3.258 N/A
/C ARG 319 NE /C P3S 601 OE no hydrogen 3.250 N/A
/C ARG 319 NH1 /C P3S 601 O1A no hydrogen 3.015 N/A
/C ARG 340 NH1 /C P3S 601 O2A no hydrogen 3.313 N/A
/C ARG 340 NH2 /C P3S 601 OE no hydrogen 3.060 N/A
/C P3S 601 N /C GLU 136 OE1 no hydrogen 2.671 N/A
/C P3S 601 N /C GLU 136 OE2 no hydrogen 3.184 N/A
/C P3S 601 N /C GLY 249 O no hydrogen 2.862 N/A
/C P3S 601 N /C HOH 730 O no hydrogen 2.710 N/A
/C HOH 704 O /C P3S 601 OT no hydrogen 2.778 N/A
/C HOH 740 O /C P3S 601 O3A no hydrogen 2.731 N/A
/D HIS 253 NE2 /D P3S 601 O no hydrogen 2.787 N/A
/D ARG 299 NH1 /D P3S 601 OT no hydrogen 3.081 N/A
/D ARG 319 NE /D P3S 601 O1A no hydrogen 3.015 N/A
/D ARG 319 NE /D P3S 601 OE no hydrogen 3.228 N/A
/D ARG 319 NH1 /D P3S 601 O1A no hydrogen 3.052 N/A
/D ARG 340 NH1 /D P3S 601 O2A no hydrogen 3.204 N/A
/D ARG 340 NH2 /D P3S 601 OE no hydrogen 3.172 N/A
/D P3S 601 N /D GLU 136 OE1 no hydrogen 2.769 N/A
/D P3S 601 N /D GLU 136 OE2 no hydrogen 3.291 N/A
/D P3S 601 N /D GLY 249 O no hydrogen 2.821 N/A
/D P3S 601 N /D HOH 711 O no hydrogen 2.672 N/A
/E HIS 253 NE2 /E P3S 601 O no hydrogen 2.761 N/A
/E ARG 299 NH1 /E P3S 601 OT no hydrogen 3.174 N/A
/E ARG 319 NE /E P3S 601 O1A no hydrogen 2.979 N/A
/E ARG 319 NE /E P3S 601 OE no hydrogen 3.237 N/A
/E ARG 319 NH1 /E P3S 601 O1A no hydrogen 3.014 N/A
/E ARG 340 NH1 /E P3S 601 O2A no hydrogen 3.258 N/A
/E ARG 340 NH2 /E P3S 601 OE no hydrogen 3.174 N/A
/E P3S 601 N /E GLU 136 OE1 no hydrogen 2.644 N/A
/E P3S 601 N /E GLU 136 OE2 no hydrogen 3.463 N/A
/E P3S 601 N /E GLY 249 O no hydrogen 2.745 N/A
/E P3S 601 NE /E HOH 629 O no hydrogen 3.237 N/A
/E P3S 601 O3A /E GLU 134 OE1 no hydrogen 2.958 N/A
/E P3S 601 O3A /E ADP 501 O3B no hydrogen 2.929 N/A
/E HOH 629 O /E P3S 601 O3A no hydrogen 2.602 N/A
/F HIS 253 NE2 /F P3S 601 O no hydrogen 2.805 N/A
/F ARG 299 NH1 /F P3S 601 OT no hydrogen 2.873 N/A
/F ARG 319 NE /F P3S 601 O1A no hydrogen 3.349 N/A
/F ARG 319 NE /F P3S 601 O2A no hydrogen 3.486 N/A
/F ARG 319 NE /F P3S 601 OE no hydrogen 3.321 N/A
/F ARG 319 NH1 /F P3S 601 O1A no hydrogen 3.177 N/A
/F ARG 340 NH1 /F P3S 601 O2A no hydrogen 2.797 N/A
/F ARG 340 NH2 /F P3S 601 OE no hydrogen 3.034 N/A
/F P3S 601 N /F GLU 136 OE1 no hydrogen 2.618 N/A
/F P3S 601 N /F GLU 136 OE2 no hydrogen 3.283 N/A
/F P3S 601 N /F GLY 249 O no hydrogen 2.573 N/A
/F P3S 601 N /F HOH 712 O no hydrogen 2.773 N/A
/F P3S 601 NE /F GLU 136 OE2 no hydrogen 3.229 N/A
/G HIS 253 NE2 /G P3S 601 O no hydrogen 2.785 N/A
/G ARG 299 NH1 /G P3S 601 OT no hydrogen 2.907 N/A
/G ARG 319 NE /G P3S 601 O1A no hydrogen 2.695 N/A
/G ARG 319 NE /G P3S 601 OE no hydrogen 3.178 N/A
/G ARG 319 NH1 /G P3S 601 O1A no hydrogen 2.829 N/A
/G ARG 340 NH1 /G P3S 601 O2A no hydrogen 3.137 N/A
/G ARG 340 NH2 /G P3S 601 OE no hydrogen 3.276 N/A
/G P3S 601 N /G GLU 136 OE1 no hydrogen 2.587 N/A
/G P3S 601 N /G GLU 136 OE2 no hydrogen 3.306 N/A
/G P3S 601 N /G GLY 249 O no hydrogen 2.509 N/A
/H HIS 253 NE2 /H P3S 601 O no hydrogen 2.707 N/A
/H ARG 299 NH1 /H P3S 601 OT no hydrogen 2.708 N/A
/H ARG 319 NE /H P3S 601 O1A no hydrogen 2.885 N/A
/H ARG 319 NE /H P3S 601 OE no hydrogen 3.235 N/A
/H ARG 319 NH1 /H P3S 601 O1A no hydrogen 2.947 N/A
/H ARG 340 NH1 /H P3S 601 O2A no hydrogen 3.511 N/A
/H ARG 340 NH2 /H P3S 601 OE no hydrogen 3.080 N/A
/H P3S 601 N /H GLU 136 OE1 no hydrogen 2.695 N/A
/H P3S 601 N /H GLU 136 OE2 no hydrogen 3.467 N/A
/H P3S 601 N /H GLY 249 O no hydrogen 2.568 N/A
/I HIS 253 NE2 /I P3S 601 O no hydrogen 3.058 N/A
/I ARG 299 NH1 /I P3S 601 OT no hydrogen 3.074 N/A
/I ARG 319 NE /I P3S 601 O1A no hydrogen 3.358 N/A
/I ARG 319 NE /I P3S 601 O2A no hydrogen 3.474 N/A
/I ARG 319 NE /I P3S 601 OE no hydrogen 3.425 N/A
/I ARG 319 NH1 /I P3S 601 O1A no hydrogen 2.998 N/A
/I ARG 319 NH1 /I P3S 601 O2A no hydrogen 3.373 N/A
/I ARG 340 NH1 /I P3S 601 O2A no hydrogen 3.004 N/A
/I ARG 340 NH2 /I P3S 601 OE no hydrogen 3.127 N/A
/I P3S 601 N /I GLU 136 OE1 no hydrogen 2.663 N/A
/I P3S 601 N /I GLU 136 OE2 no hydrogen 3.274 N/A
/I P3S 601 N /I GLY 249 O no hydrogen 2.753 N/A
/J HIS 253 NE2 /J P3S 601 O no hydrogen 2.812 N/A
/J ARG 299 NH1 /J P3S 601 OT no hydrogen 3.037 N/A
/J ARG 319 NE /J P3S 601 O1A no hydrogen 3.045 N/A
/J ARG 319 NE /J P3S 601 OE no hydrogen 3.164 N/A
/J ARG 319 NH1 /J P3S 601 O1A no hydrogen 2.967 N/A
/J ARG 340 NH1 /J P3S 601 O2A no hydrogen 3.191 N/A
/J ARG 340 NH2 /J P3S 601 OE no hydrogen 3.297 N/A
/J P3S 601 N /J GLU 136 OE1 no hydrogen 2.620 N/A
/J P3S 601 N /J GLU 136 OE2 no hydrogen 3.429 N/A
/J P3S 601 N /J GLY 249 O no hydrogen 2.591 N/A
/J P3S 601 N /J HOH 714 O no hydrogen 2.752 N/A
/J P3S 601 NE /J HOH 718 O no hydrogen 3.291 N/A
/J P3S 601 O1A /J P3S 601 OE no hydrogen 3.303 N/A
/J HOH 718 O /J P3S 601 O3A no hydrogen 2.759 N/A
121 hydrogen bonds found
> label @@display
> show sel
> hbonds :ADP reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2qc8
68 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A SER 257 OG /A ADP 501 N1 no hydrogen 2.922 N/A
/A ARG 324 NH1 /A ADP 501 O3B no hydrogen 3.143 N/A
/A ARG 324 NH2 /A ADP 501 O2B no hydrogen 2.951 N/A
/A ADP 501 N6 /A SER 257 OG no hydrogen 3.101 N/A
/A HOH 730 O /A ADP 501 O3B no hydrogen 2.554 N/A
/A HOH 731 O /A ADP 501 O1A no hydrogen 2.763 N/A
/A HOH 732 O /B ADP 501 O1A no hydrogen 2.872 N/A
/B SER 257 OG /B ADP 501 N1 no hydrogen 2.917 N/A
/B ARG 324 NH1 /B ADP 501 O2B no hydrogen 2.988 N/A
/B ARG 324 NH2 /B ADP 501 O1B no hydrogen 2.892 N/A
/B ADP 501 N6 /B SER 257 OG no hydrogen 3.066 N/A
/B HOH 741 O /B ADP 501 O2A no hydrogen 3.223 N/A
/B HOH 741 O /B ADP 501 O3B no hydrogen 3.216 N/A
/B HOH 742 O /B ADP 501 O2B no hydrogen 2.735 N/A
/B HOH 742 O /B ADP 501 O3A no hydrogen 3.334 N/A
/C SER 257 OG /C ADP 501 N1 no hydrogen 2.843 N/A
/C ARG 324 NH1 /C ADP 501 O2B no hydrogen 3.215 N/A
/C ARG 324 NH2 /C ADP 501 O1B no hydrogen 3.241 N/A
/C ADP 501 N6 /C SER 257 OG no hydrogen 2.916 N/A
/C HOH 707 O /D ADP 501 O1A no hydrogen 2.790 N/A
/C HOH 709 O /C ADP 501 O1A no hydrogen 2.788 N/A
/C HOH 736 O /C ADP 501 O2B no hydrogen 2.455 N/A
/C HOH 738 O /C ADP 501 O2A no hydrogen 3.030 N/A
/C HOH 739 O /C ADP 501 O1A no hydrogen 2.305 N/A
/D SER 257 OG /D ADP 501 N1 no hydrogen 2.918 N/A
/D ARG 324 NH1 /D ADP 501 O2B no hydrogen 3.005 N/A
/D ARG 324 NH2 /D ADP 501 O1B no hydrogen 3.058 N/A
/D ADP 501 N6 /D SER 257 OG no hydrogen 3.262 N/A
/D HOH 747 O /D ADP 501 O2A no hydrogen 2.899 N/A
/D HOH 747 O /D ADP 501 O3B no hydrogen 3.367 N/A
/D HOH 749 O /E ADP 501 O1A no hydrogen 2.821 N/A
/E SER 257 OG /E ADP 501 N1 no hydrogen 3.090 N/A
/E ARG 324 NH1 /E ADP 501 O2B no hydrogen 3.406 N/A
/E ARG 324 NH2 /E ADP 501 O1B no hydrogen 2.996 N/A
/E ADP 501 N6 /E SER 257 OG no hydrogen 3.295 N/A
/E P3S 601 O3A /E ADP 501 O3B no hydrogen 2.929 N/A
/E HOH 624 O /E ADP 501 O1A no hydrogen 2.441 N/A
/E HOH 624 O /E ADP 501 O3A no hydrogen 3.426 N/A
/E HOH 627 O /E ADP 501 O3B no hydrogen 2.858 N/A
/E HOH 628 O /E ADP 501 O2B no hydrogen 2.753 N/A
/F SER 257 OG /F ADP 501 N1 no hydrogen 2.693 N/A
/F ARG 324 NH1 /F ADP 501 O2B no hydrogen 3.296 N/A
/F ARG 324 NH2 /F ADP 501 O1B no hydrogen 3.380 N/A
/F ADP 501 N6 /F SER 257 OG no hydrogen 3.130 N/A
/F HOH 717 O /F ADP 501 O3B no hydrogen 2.595 N/A
/F HOH 718 O /F ADP 501 O2B no hydrogen 2.910 N/A
/G SER 257 OG /G ADP 501 N1 no hydrogen 2.634 N/A
/G ARG 324 NH1 /G ADP 501 O1B no hydrogen 3.383 N/A
/G ARG 324 NH1 /G ADP 501 O2B no hydrogen 3.441 N/A
/G ARG 324 NH2 /G ADP 501 O1B no hydrogen 3.130 N/A
/G ADP 501 N6 /G SER 257 OG no hydrogen 3.164 N/A
/H SER 257 OG /H ADP 501 N1 no hydrogen 2.906 N/A
/H ARG 324 NH1 /H ADP 501 O2B no hydrogen 3.041 N/A
/H ARG 324 NH2 /H ADP 501 O1B no hydrogen 3.209 N/A
/H ADP 501 N6 /H SER 257 OG no hydrogen 3.228 N/A
/I SER 257 OG /I ADP 501 N1 no hydrogen 2.906 N/A
/I ARG 324 NH1 /I ADP 501 O2B no hydrogen 3.006 N/A
/I ARG 324 NH2 /I ADP 501 O1B no hydrogen 2.986 N/A
/I ADP 501 N6 /I SER 257 OG no hydrogen 3.204 N/A
/I HOH 718 O /I ADP 501 O2A no hydrogen 2.751 N/A
/I HOH 718 O /I ADP 501 O3B no hydrogen 3.050 N/A
/I HOH 719 O /I ADP 501 O2B no hydrogen 2.492 N/A
/J SER 257 OG /J ADP 501 N1 no hydrogen 2.924 N/A
/J ARG 324 NH1 /J ADP 501 O2B no hydrogen 3.382 N/A
/J ARG 324 NH1 /J ADP 501 O3B no hydrogen 2.995 N/A
/J ARG 324 NH2 /J ADP 501 O2B no hydrogen 2.844 N/A
/J ADP 501 N6 /J SER 257 OG no hydrogen 3.207 N/A
/J HOH 717 O /J ADP 501 O1B no hydrogen 2.707 N/A
68 hydrogen bonds found
> label @@display
> select clear
> save /Users/isabelladibiasio/Desktop/image2.png supersample 3
> close
> open 2qc8
2qc8 title:
Crystal structure of human glutamine synthetase in complex with ADP and
methionine sulfoximine phosphate [more info...]
Chain information for 2qc8 #1
---
Chain | Description | UniProt
A B C D E F G H I J | Glutamine synthetase | GLNA_HUMAN 5-365
Non-standard residues in 2qc8 #1
---
ADP — adenosine-5'-diphosphate
CL — chloride ion
MN — manganese (II) ion
P3S — L-methionine-S-sulfoximine phosphate
> hide solvent
> style stick
Changed 28837 atom styles
> select :P3S
150 atoms, 140 bonds, 10 residues, 1 model selected
> hide ~sel
> hbonds :P3S reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2qc8
121 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A HIS 253 NE2 /A P3S 601 O no hydrogen 2.681 N/A
/A ARG 299 NH1 /A P3S 601 OT no hydrogen 3.167 N/A
/A ARG 319 NE /A P3S 601 O1A no hydrogen 2.982 N/A
/A ARG 319 NE /A P3S 601 OE no hydrogen 3.242 N/A
/A ARG 319 NH1 /A P3S 601 O1A no hydrogen 2.967 N/A
/A ARG 340 NH1 /A P3S 601 O2A no hydrogen 2.969 N/A
/A ARG 340 NH2 /A P3S 601 OE no hydrogen 2.965 N/A
/A P3S 601 N /A GLU 136 OE1 no hydrogen 2.707 N/A
/A P3S 601 N /A GLU 136 OE2 no hydrogen 3.395 N/A
/A P3S 601 N /A GLY 249 O no hydrogen 2.664 N/A
/A P3S 601 N /A HOH 733 O no hydrogen 2.655 N/A
/B HIS 253 NE2 /B P3S 601 O no hydrogen 2.621 N/A
/B ARG 299 NH1 /B P3S 601 OT no hydrogen 3.037 N/A
/B ARG 319 NE /B P3S 601 O1A no hydrogen 2.927 N/A
/B ARG 319 NE /B P3S 601 OE no hydrogen 3.059 N/A
/B ARG 319 NH1 /B P3S 601 O1A no hydrogen 2.787 N/A
/B ARG 340 NH1 /B P3S 601 O2A no hydrogen 3.220 N/A
/B ARG 340 NH2 /B P3S 601 OE no hydrogen 3.192 N/A
/B P3S 601 N /B GLU 136 OE1 no hydrogen 2.685 N/A
/B P3S 601 N /B GLU 136 OE2 no hydrogen 3.568 N/A
/B P3S 601 N /B GLY 249 O no hydrogen 2.500 N/A
/B HOH 718 O /B P3S 601 OT no hydrogen 2.603 N/A
/B HOH 741 O /B P3S 601 O3A no hydrogen 3.311 N/A
/B HOH 744 O /B P3S 601 O3A no hydrogen 2.918 N/A
/C HIS 253 NE2 /C P3S 601 O no hydrogen 2.561 N/A
/C ARG 299 NH1 /C P3S 601 OT no hydrogen 2.934 N/A
/C ARG 319 NE /C P3S 601 O1A no hydrogen 3.258 N/A
/C ARG 319 NE /C P3S 601 OE no hydrogen 3.250 N/A
/C ARG 319 NH1 /C P3S 601 O1A no hydrogen 3.015 N/A
/C ARG 340 NH1 /C P3S 601 O2A no hydrogen 3.313 N/A
/C ARG 340 NH2 /C P3S 601 OE no hydrogen 3.060 N/A
/C P3S 601 N /C GLU 136 OE1 no hydrogen 2.671 N/A
/C P3S 601 N /C GLU 136 OE2 no hydrogen 3.184 N/A
/C P3S 601 N /C GLY 249 O no hydrogen 2.862 N/A
/C P3S 601 N /C HOH 730 O no hydrogen 2.710 N/A
/C HOH 704 O /C P3S 601 OT no hydrogen 2.778 N/A
/C HOH 740 O /C P3S 601 O3A no hydrogen 2.731 N/A
/D HIS 253 NE2 /D P3S 601 O no hydrogen 2.787 N/A
/D ARG 299 NH1 /D P3S 601 OT no hydrogen 3.081 N/A
/D ARG 319 NE /D P3S 601 O1A no hydrogen 3.015 N/A
/D ARG 319 NE /D P3S 601 OE no hydrogen 3.228 N/A
/D ARG 319 NH1 /D P3S 601 O1A no hydrogen 3.052 N/A
/D ARG 340 NH1 /D P3S 601 O2A no hydrogen 3.204 N/A
/D ARG 340 NH2 /D P3S 601 OE no hydrogen 3.172 N/A
/D P3S 601 N /D GLU 136 OE1 no hydrogen 2.769 N/A
/D P3S 601 N /D GLU 136 OE2 no hydrogen 3.291 N/A
/D P3S 601 N /D GLY 249 O no hydrogen 2.821 N/A
/D P3S 601 N /D HOH 711 O no hydrogen 2.672 N/A
/E HIS 253 NE2 /E P3S 601 O no hydrogen 2.761 N/A
/E ARG 299 NH1 /E P3S 601 OT no hydrogen 3.174 N/A
/E ARG 319 NE /E P3S 601 O1A no hydrogen 2.979 N/A
/E ARG 319 NE /E P3S 601 OE no hydrogen 3.237 N/A
/E ARG 319 NH1 /E P3S 601 O1A no hydrogen 3.014 N/A
/E ARG 340 NH1 /E P3S 601 O2A no hydrogen 3.258 N/A
/E ARG 340 NH2 /E P3S 601 OE no hydrogen 3.174 N/A
/E P3S 601 N /E GLU 136 OE1 no hydrogen 2.644 N/A
/E P3S 601 N /E GLU 136 OE2 no hydrogen 3.463 N/A
/E P3S 601 N /E GLY 249 O no hydrogen 2.745 N/A
/E P3S 601 NE /E HOH 629 O no hydrogen 3.237 N/A
/E P3S 601 O3A /E GLU 134 OE1 no hydrogen 2.958 N/A
/E P3S 601 O3A /E ADP 501 O3B no hydrogen 2.929 N/A
/E HOH 629 O /E P3S 601 O3A no hydrogen 2.602 N/A
/F HIS 253 NE2 /F P3S 601 O no hydrogen 2.805 N/A
/F ARG 299 NH1 /F P3S 601 OT no hydrogen 2.873 N/A
/F ARG 319 NE /F P3S 601 O1A no hydrogen 3.349 N/A
/F ARG 319 NE /F P3S 601 O2A no hydrogen 3.486 N/A
/F ARG 319 NE /F P3S 601 OE no hydrogen 3.321 N/A
/F ARG 319 NH1 /F P3S 601 O1A no hydrogen 3.177 N/A
/F ARG 340 NH1 /F P3S 601 O2A no hydrogen 2.797 N/A
/F ARG 340 NH2 /F P3S 601 OE no hydrogen 3.034 N/A
/F P3S 601 N /F GLU 136 OE1 no hydrogen 2.618 N/A
/F P3S 601 N /F GLU 136 OE2 no hydrogen 3.283 N/A
/F P3S 601 N /F GLY 249 O no hydrogen 2.573 N/A
/F P3S 601 N /F HOH 712 O no hydrogen 2.773 N/A
/F P3S 601 NE /F GLU 136 OE2 no hydrogen 3.229 N/A
/G HIS 253 NE2 /G P3S 601 O no hydrogen 2.785 N/A
/G ARG 299 NH1 /G P3S 601 OT no hydrogen 2.907 N/A
/G ARG 319 NE /G P3S 601 O1A no hydrogen 2.695 N/A
/G ARG 319 NE /G P3S 601 OE no hydrogen 3.178 N/A
/G ARG 319 NH1 /G P3S 601 O1A no hydrogen 2.829 N/A
/G ARG 340 NH1 /G P3S 601 O2A no hydrogen 3.137 N/A
/G ARG 340 NH2 /G P3S 601 OE no hydrogen 3.276 N/A
/G P3S 601 N /G GLU 136 OE1 no hydrogen 2.587 N/A
/G P3S 601 N /G GLU 136 OE2 no hydrogen 3.306 N/A
/G P3S 601 N /G GLY 249 O no hydrogen 2.509 N/A
/H HIS 253 NE2 /H P3S 601 O no hydrogen 2.707 N/A
/H ARG 299 NH1 /H P3S 601 OT no hydrogen 2.708 N/A
/H ARG 319 NE /H P3S 601 O1A no hydrogen 2.885 N/A
/H ARG 319 NE /H P3S 601 OE no hydrogen 3.235 N/A
/H ARG 319 NH1 /H P3S 601 O1A no hydrogen 2.947 N/A
/H ARG 340 NH1 /H P3S 601 O2A no hydrogen 3.511 N/A
/H ARG 340 NH2 /H P3S 601 OE no hydrogen 3.080 N/A
/H P3S 601 N /H GLU 136 OE1 no hydrogen 2.695 N/A
/H P3S 601 N /H GLU 136 OE2 no hydrogen 3.467 N/A
/H P3S 601 N /H GLY 249 O no hydrogen 2.568 N/A
/I HIS 253 NE2 /I P3S 601 O no hydrogen 3.058 N/A
/I ARG 299 NH1 /I P3S 601 OT no hydrogen 3.074 N/A
/I ARG 319 NE /I P3S 601 O1A no hydrogen 3.358 N/A
/I ARG 319 NE /I P3S 601 O2A no hydrogen 3.474 N/A
/I ARG 319 NE /I P3S 601 OE no hydrogen 3.425 N/A
/I ARG 319 NH1 /I P3S 601 O1A no hydrogen 2.998 N/A
/I ARG 319 NH1 /I P3S 601 O2A no hydrogen 3.373 N/A
/I ARG 340 NH1 /I P3S 601 O2A no hydrogen 3.004 N/A
/I ARG 340 NH2 /I P3S 601 OE no hydrogen 3.127 N/A
/I P3S 601 N /I GLU 136 OE1 no hydrogen 2.663 N/A
/I P3S 601 N /I GLU 136 OE2 no hydrogen 3.274 N/A
/I P3S 601 N /I GLY 249 O no hydrogen 2.753 N/A
/J HIS 253 NE2 /J P3S 601 O no hydrogen 2.812 N/A
/J ARG 299 NH1 /J P3S 601 OT no hydrogen 3.037 N/A
/J ARG 319 NE /J P3S 601 O1A no hydrogen 3.045 N/A
/J ARG 319 NE /J P3S 601 OE no hydrogen 3.164 N/A
/J ARG 319 NH1 /J P3S 601 O1A no hydrogen 2.967 N/A
/J ARG 340 NH1 /J P3S 601 O2A no hydrogen 3.191 N/A
/J ARG 340 NH2 /J P3S 601 OE no hydrogen 3.297 N/A
/J P3S 601 N /J GLU 136 OE1 no hydrogen 2.620 N/A
/J P3S 601 N /J GLU 136 OE2 no hydrogen 3.429 N/A
/J P3S 601 N /J GLY 249 O no hydrogen 2.591 N/A
/J P3S 601 N /J HOH 714 O no hydrogen 2.752 N/A
/J P3S 601 NE /J HOH 718 O no hydrogen 3.291 N/A
/J P3S 601 O1A /J P3S 601 OE no hydrogen 3.303 N/A
/J HOH 718 O /J P3S 601 O3A no hydrogen 2.759 N/A
121 hydrogen bonds found
> label @@display
> select :ADP
270 atoms, 290 bonds, 10 residues, 1 model selected
> show sel
> hbonds :ADP, P3S reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2qc8
188 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A HIS 253 NE2 /A P3S 601 O no hydrogen 2.681 N/A
/A SER 257 OG /A ADP 501 N1 no hydrogen 2.922 N/A
/A ARG 299 NH1 /A P3S 601 OT no hydrogen 3.167 N/A
/A ARG 319 NE /A P3S 601 O1A no hydrogen 2.982 N/A
/A ARG 319 NE /A P3S 601 OE no hydrogen 3.242 N/A
/A ARG 319 NH1 /A P3S 601 O1A no hydrogen 2.967 N/A
/A ARG 324 NH1 /A ADP 501 O3B no hydrogen 3.143 N/A
/A ARG 324 NH2 /A ADP 501 O2B no hydrogen 2.951 N/A
/A ARG 340 NH1 /A P3S 601 O2A no hydrogen 2.969 N/A
/A ARG 340 NH2 /A P3S 601 OE no hydrogen 2.965 N/A
/A ADP 501 N6 /A SER 257 OG no hydrogen 3.101 N/A
/A P3S 601 N /A GLU 136 OE1 no hydrogen 2.707 N/A
/A P3S 601 N /A GLU 136 OE2 no hydrogen 3.395 N/A
/A P3S 601 N /A GLY 249 O no hydrogen 2.664 N/A
/A P3S 601 N /A HOH 733 O no hydrogen 2.655 N/A
/A HOH 730 O /A ADP 501 O3B no hydrogen 2.554 N/A
/A HOH 731 O /A ADP 501 O1A no hydrogen 2.763 N/A
/A HOH 732 O /B ADP 501 O1A no hydrogen 2.872 N/A
/B HIS 253 NE2 /B P3S 601 O no hydrogen 2.621 N/A
/B SER 257 OG /B ADP 501 N1 no hydrogen 2.917 N/A
/B ARG 299 NH1 /B P3S 601 OT no hydrogen 3.037 N/A
/B ARG 319 NE /B P3S 601 O1A no hydrogen 2.927 N/A
/B ARG 319 NE /B P3S 601 OE no hydrogen 3.059 N/A
/B ARG 319 NH1 /B P3S 601 O1A no hydrogen 2.787 N/A
/B ARG 324 NH1 /B ADP 501 O2B no hydrogen 2.988 N/A
/B ARG 324 NH2 /B ADP 501 O1B no hydrogen 2.892 N/A
/B ARG 340 NH1 /B P3S 601 O2A no hydrogen 3.220 N/A
/B ARG 340 NH2 /B P3S 601 OE no hydrogen 3.192 N/A
/B ADP 501 N6 /B SER 257 OG no hydrogen 3.066 N/A
/B P3S 601 N /B GLU 136 OE1 no hydrogen 2.685 N/A
/B P3S 601 N /B GLU 136 OE2 no hydrogen 3.568 N/A
/B P3S 601 N /B GLY 249 O no hydrogen 2.500 N/A
/B HOH 718 O /B P3S 601 OT no hydrogen 2.603 N/A
/B HOH 741 O /B ADP 501 O2A no hydrogen 3.223 N/A
/B HOH 741 O /B ADP 501 O3B no hydrogen 3.216 N/A
/B HOH 741 O /B P3S 601 O3A no hydrogen 3.311 N/A
/B HOH 742 O /B ADP 501 O2B no hydrogen 2.735 N/A
/B HOH 742 O /B ADP 501 O3A no hydrogen 3.334 N/A
/B HOH 744 O /B P3S 601 O3A no hydrogen 2.918 N/A
/C HIS 253 NE2 /C P3S 601 O no hydrogen 2.561 N/A
/C SER 257 OG /C ADP 501 N1 no hydrogen 2.843 N/A
/C ARG 299 NH1 /C P3S 601 OT no hydrogen 2.934 N/A
/C ARG 319 NE /C P3S 601 O1A no hydrogen 3.258 N/A
/C ARG 319 NE /C P3S 601 OE no hydrogen 3.250 N/A
/C ARG 319 NH1 /C P3S 601 O1A no hydrogen 3.015 N/A
/C ARG 324 NH1 /C ADP 501 O2B no hydrogen 3.215 N/A
/C ARG 324 NH2 /C ADP 501 O1B no hydrogen 3.241 N/A
/C ARG 340 NH1 /C P3S 601 O2A no hydrogen 3.313 N/A
/C ARG 340 NH2 /C P3S 601 OE no hydrogen 3.060 N/A
/C ADP 501 N6 /C SER 257 OG no hydrogen 2.916 N/A
/C P3S 601 N /C GLU 136 OE1 no hydrogen 2.671 N/A
/C P3S 601 N /C GLU 136 OE2 no hydrogen 3.184 N/A
/C P3S 601 N /C GLY 249 O no hydrogen 2.862 N/A
/C P3S 601 N /C HOH 730 O no hydrogen 2.710 N/A
/C HOH 704 O /C P3S 601 OT no hydrogen 2.778 N/A
/C HOH 707 O /D ADP 501 O1A no hydrogen 2.790 N/A
/C HOH 709 O /C ADP 501 O1A no hydrogen 2.788 N/A
/C HOH 736 O /C ADP 501 O2B no hydrogen 2.455 N/A
/C HOH 738 O /C ADP 501 O2A no hydrogen 3.030 N/A
/C HOH 739 O /C ADP 501 O1A no hydrogen 2.305 N/A
/C HOH 740 O /C P3S 601 O3A no hydrogen 2.731 N/A
/D HIS 253 NE2 /D P3S 601 O no hydrogen 2.787 N/A
/D SER 257 OG /D ADP 501 N1 no hydrogen 2.918 N/A
/D ARG 299 NH1 /D P3S 601 OT no hydrogen 3.081 N/A
/D ARG 319 NE /D P3S 601 O1A no hydrogen 3.015 N/A
/D ARG 319 NE /D P3S 601 OE no hydrogen 3.228 N/A
/D ARG 319 NH1 /D P3S 601 O1A no hydrogen 3.052 N/A
/D ARG 324 NH1 /D ADP 501 O2B no hydrogen 3.005 N/A
/D ARG 324 NH2 /D ADP 501 O1B no hydrogen 3.058 N/A
/D ARG 340 NH1 /D P3S 601 O2A no hydrogen 3.204 N/A
/D ARG 340 NH2 /D P3S 601 OE no hydrogen 3.172 N/A
/D ADP 501 N6 /D SER 257 OG no hydrogen 3.262 N/A
/D P3S 601 N /D GLU 136 OE1 no hydrogen 2.769 N/A
/D P3S 601 N /D GLU 136 OE2 no hydrogen 3.291 N/A
/D P3S 601 N /D GLY 249 O no hydrogen 2.821 N/A
/D P3S 601 N /D HOH 711 O no hydrogen 2.672 N/A
/D HOH 747 O /D ADP 501 O2A no hydrogen 2.899 N/A
/D HOH 747 O /D ADP 501 O3B no hydrogen 3.367 N/A
/D HOH 749 O /E ADP 501 O1A no hydrogen 2.821 N/A
/E HIS 253 NE2 /E P3S 601 O no hydrogen 2.761 N/A
/E SER 257 OG /E ADP 501 N1 no hydrogen 3.090 N/A
/E ARG 299 NH1 /E P3S 601 OT no hydrogen 3.174 N/A
/E ARG 319 NE /E P3S 601 O1A no hydrogen 2.979 N/A
/E ARG 319 NE /E P3S 601 OE no hydrogen 3.237 N/A
/E ARG 319 NH1 /E P3S 601 O1A no hydrogen 3.014 N/A
/E ARG 324 NH1 /E ADP 501 O2B no hydrogen 3.406 N/A
/E ARG 324 NH2 /E ADP 501 O1B no hydrogen 2.996 N/A
/E ARG 340 NH1 /E P3S 601 O2A no hydrogen 3.258 N/A
/E ARG 340 NH2 /E P3S 601 OE no hydrogen 3.174 N/A
/E ADP 501 N6 /E SER 257 OG no hydrogen 3.295 N/A
/E P3S 601 N /E GLU 136 OE1 no hydrogen 2.644 N/A
/E P3S 601 N /E GLU 136 OE2 no hydrogen 3.463 N/A
/E P3S 601 N /E GLY 249 O no hydrogen 2.745 N/A
/E P3S 601 NE /E HOH 629 O no hydrogen 3.237 N/A
/E P3S 601 O3A /E GLU 134 OE1 no hydrogen 2.958 N/A
/E P3S 601 O3A /E ADP 501 O3B no hydrogen 2.929 N/A
/E HOH 624 O /E ADP 501 O1A no hydrogen 2.441 N/A
/E HOH 624 O /E ADP 501 O3A no hydrogen 3.426 N/A
/E HOH 627 O /E ADP 501 O3B no hydrogen 2.858 N/A
/E HOH 628 O /E ADP 501 O2B no hydrogen 2.753 N/A
/E HOH 629 O /E P3S 601 O3A no hydrogen 2.602 N/A
/F HIS 253 NE2 /F P3S 601 O no hydrogen 2.805 N/A
/F SER 257 OG /F ADP 501 N1 no hydrogen 2.693 N/A
/F ARG 299 NH1 /F P3S 601 OT no hydrogen 2.873 N/A
/F ARG 319 NE /F P3S 601 O1A no hydrogen 3.349 N/A
/F ARG 319 NE /F P3S 601 O2A no hydrogen 3.486 N/A
/F ARG 319 NE /F P3S 601 OE no hydrogen 3.321 N/A
/F ARG 319 NH1 /F P3S 601 O1A no hydrogen 3.177 N/A
/F ARG 324 NH1 /F ADP 501 O2B no hydrogen 3.296 N/A
/F ARG 324 NH2 /F ADP 501 O1B no hydrogen 3.380 N/A
/F ARG 340 NH1 /F P3S 601 O2A no hydrogen 2.797 N/A
/F ARG 340 NH2 /F P3S 601 OE no hydrogen 3.034 N/A
/F ADP 501 N6 /F SER 257 OG no hydrogen 3.130 N/A
/F P3S 601 N /F GLU 136 OE1 no hydrogen 2.618 N/A
/F P3S 601 N /F GLU 136 OE2 no hydrogen 3.283 N/A
/F P3S 601 N /F GLY 249 O no hydrogen 2.573 N/A
/F P3S 601 N /F HOH 712 O no hydrogen 2.773 N/A
/F P3S 601 NE /F GLU 136 OE2 no hydrogen 3.229 N/A
/F HOH 717 O /F ADP 501 O3B no hydrogen 2.595 N/A
/F HOH 718 O /F ADP 501 O2B no hydrogen 2.910 N/A
/G HIS 253 NE2 /G P3S 601 O no hydrogen 2.785 N/A
/G SER 257 OG /G ADP 501 N1 no hydrogen 2.634 N/A
/G ARG 299 NH1 /G P3S 601 OT no hydrogen 2.907 N/A
/G ARG 319 NE /G P3S 601 O1A no hydrogen 2.695 N/A
/G ARG 319 NE /G P3S 601 OE no hydrogen 3.178 N/A
/G ARG 319 NH1 /G P3S 601 O1A no hydrogen 2.829 N/A
/G ARG 324 NH1 /G ADP 501 O1B no hydrogen 3.383 N/A
/G ARG 324 NH1 /G ADP 501 O2B no hydrogen 3.441 N/A
/G ARG 324 NH2 /G ADP 501 O1B no hydrogen 3.130 N/A
/G ARG 340 NH1 /G P3S 601 O2A no hydrogen 3.137 N/A
/G ARG 340 NH2 /G P3S 601 OE no hydrogen 3.276 N/A
/G ADP 501 N6 /G SER 257 OG no hydrogen 3.164 N/A
/G P3S 601 N /G GLU 136 OE1 no hydrogen 2.587 N/A
/G P3S 601 N /G GLU 136 OE2 no hydrogen 3.306 N/A
/G P3S 601 N /G GLY 249 O no hydrogen 2.509 N/A
/H HIS 253 NE2 /H P3S 601 O no hydrogen 2.707 N/A
/H SER 257 OG /H ADP 501 N1 no hydrogen 2.906 N/A
/H ARG 299 NH1 /H P3S 601 OT no hydrogen 2.708 N/A
/H ARG 319 NE /H P3S 601 O1A no hydrogen 2.885 N/A
/H ARG 319 NE /H P3S 601 OE no hydrogen 3.235 N/A
/H ARG 319 NH1 /H P3S 601 O1A no hydrogen 2.947 N/A
/H ARG 324 NH1 /H ADP 501 O2B no hydrogen 3.041 N/A
/H ARG 324 NH2 /H ADP 501 O1B no hydrogen 3.209 N/A
/H ARG 340 NH1 /H P3S 601 O2A no hydrogen 3.511 N/A
/H ARG 340 NH2 /H P3S 601 OE no hydrogen 3.080 N/A
/H ADP 501 N6 /H SER 257 OG no hydrogen 3.228 N/A
/H P3S 601 N /H GLU 136 OE1 no hydrogen 2.695 N/A
/H P3S 601 N /H GLU 136 OE2 no hydrogen 3.467 N/A
/H P3S 601 N /H GLY 249 O no hydrogen 2.568 N/A
/I HIS 253 NE2 /I P3S 601 O no hydrogen 3.058 N/A
/I SER 257 OG /I ADP 501 N1 no hydrogen 2.906 N/A
/I ARG 299 NH1 /I P3S 601 OT no hydrogen 3.074 N/A
/I ARG 319 NE /I P3S 601 O1A no hydrogen 3.358 N/A
/I ARG 319 NE /I P3S 601 O2A no hydrogen 3.474 N/A
/I ARG 319 NE /I P3S 601 OE no hydrogen 3.425 N/A
/I ARG 319 NH1 /I P3S 601 O1A no hydrogen 2.998 N/A
/I ARG 319 NH1 /I P3S 601 O2A no hydrogen 3.373 N/A
/I ARG 324 NH1 /I ADP 501 O2B no hydrogen 3.006 N/A
/I ARG 324 NH2 /I ADP 501 O1B no hydrogen 2.986 N/A
/I ARG 340 NH1 /I P3S 601 O2A no hydrogen 3.004 N/A
/I ARG 340 NH2 /I P3S 601 OE no hydrogen 3.127 N/A
/I ADP 501 N6 /I SER 257 OG no hydrogen 3.204 N/A
/I P3S 601 N /I GLU 136 OE1 no hydrogen 2.663 N/A
/I P3S 601 N /I GLU 136 OE2 no hydrogen 3.274 N/A
/I P3S 601 N /I GLY 249 O no hydrogen 2.753 N/A
/I HOH 718 O /I ADP 501 O2A no hydrogen 2.751 N/A
/I HOH 718 O /I ADP 501 O3B no hydrogen 3.050 N/A
/I HOH 719 O /I ADP 501 O2B no hydrogen 2.492 N/A
/J HIS 253 NE2 /J P3S 601 O no hydrogen 2.812 N/A
/J SER 257 OG /J ADP 501 N1 no hydrogen 2.924 N/A
/J ARG 299 NH1 /J P3S 601 OT no hydrogen 3.037 N/A
/J ARG 319 NE /J P3S 601 O1A no hydrogen 3.045 N/A
/J ARG 319 NE /J P3S 601 OE no hydrogen 3.164 N/A
/J ARG 319 NH1 /J P3S 601 O1A no hydrogen 2.967 N/A
/J ARG 324 NH1 /J ADP 501 O2B no hydrogen 3.382 N/A
/J ARG 324 NH1 /J ADP 501 O3B no hydrogen 2.995 N/A
/J ARG 324 NH2 /J ADP 501 O2B no hydrogen 2.844 N/A
/J ARG 340 NH1 /J P3S 601 O2A no hydrogen 3.191 N/A
/J ARG 340 NH2 /J P3S 601 OE no hydrogen 3.297 N/A
/J ADP 501 N6 /J SER 257 OG no hydrogen 3.207 N/A
/J P3S 601 N /J GLU 136 OE1 no hydrogen 2.620 N/A
/J P3S 601 N /J GLU 136 OE2 no hydrogen 3.429 N/A
/J P3S 601 N /J GLY 249 O no hydrogen 2.591 N/A
/J P3S 601 N /J HOH 714 O no hydrogen 2.752 N/A
/J P3S 601 NE /J HOH 718 O no hydrogen 3.291 N/A
/J P3S 601 O1A /J P3S 601 OE no hydrogen 3.303 N/A
/J HOH 717 O /J ADP 501 O1B no hydrogen 2.707 N/A
/J HOH 718 O /J P3S 601 O3A no hydrogen 2.759 N/A
188 hydrogen bonds found
> label @@display
> label height 1.4
> label height 1.25
> label height 1.2
> select clear
> select :P3S
150 atoms, 140 bonds, 1 pseudobond, 10 residues, 2 models selected
> hide label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> clear label
Unknown command: clear label
> save /Users/isabelladibiasio/Desktop/image3.png supersample 3
> select clear
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A GLU 24
/A GLY 365
/B GLU 24
/B GLY 365
/C GLU 24
/C GLY 365
/D GLU 24
/D GLY 365
/E GLU 24
/F GLU 24
/F GLY 365
/G GLU 24
/G GLY 365
/H GLU 24
/H GLY 365
/I GLU 24
/I GLY 365
/J GLU 24
/J GLY 365
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 2qc8_A SES surface #1.4: minimum, -25.33, mean -1.22,
maximum 12.45
Coulombic values for 2qc8_B SES surface #1.5: minimum, -25.37, mean -1.39,
maximum 13.66
Coulombic values for 2qc8_C SES surface #1.6: minimum, -24.81, mean -1.40,
maximum 12.60
Coulombic values for 2qc8_D SES surface #1.7: minimum, -25.31, mean -1.47,
maximum 11.67
Coulombic values for 2qc8_E SES surface #1.8: minimum, -24.90, mean -1.00,
maximum 24.49
Coulombic values for 2qc8_F SES surface #1.9: minimum, -26.55, mean -1.18,
maximum 28.25
Coulombic values for 2qc8_G SES surface #1.10: minimum, -25.62, mean -1.45,
maximum 18.46
Coulombic values for 2qc8_H SES surface #1.11: minimum, -25.18, mean -1.39,
maximum 16.49
Coulombic values for 2qc8_I SES surface #1.12: minimum, -24.97, mean -1.37,
maximum 19.34
Coulombic values for 2qc8_J SES surface #1.13: minimum, -25.19, mean -1.39,
maximum 17.12
To also show corresponding color key, enter the above coulombic command and
add key true
> select :P3S
150 atoms, 140 bonds, 1 pseudobond, 10 residues, 2 models selected
> undo
> close
> open 2qc8
2qc8 title:
Crystal structure of human glutamine synthetase in complex with ADP and
methionine sulfoximine phosphate [more info...]
Chain information for 2qc8 #1
---
Chain | Description | UniProt
A B C D E F G H I J | Glutamine synthetase | GLNA_HUMAN 5-365
Non-standard residues in 2qc8 #1
---
ADP — adenosine-5'-diphosphate
CL — chloride ion
MN — manganese (II) ion
P3S — L-methionine-S-sulfoximine phosphate
> hide solvent
> select :P3S
150 atoms, 140 bonds, 10 residues, 1 model selected
> hide ~sel
> select :ADP
270 atoms, 290 bonds, 10 residues, 1 model selected
> show sel
> hbonds :ADP, P3S reveal true log true
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
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How to cite UCSF ChimeraX
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Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
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Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 19 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 , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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