id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14958 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ 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, 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""_queue.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4806049792, ""size"" : 16384, ""uuid"" : ""dc7e074f-ad98-3934-aa21-85389e14162e"", ""path"" : ""\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_heapq.cpython-311-darwin.so"", ""name"" : ""_heapq.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4813545472, ""size"" : 49152, ""uuid"" : ""434ffdf5-a119-33d1-8f61-ae50457a3d17"", ""path"" : ""\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/array.cpython-311-darwin.so"", ""name"" : ""array.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4788555776, ""size"" : 65536, ""uuid"" : ""f5077020-095f-37b5-9841-9db3e15f3401"", ""path"" : ""\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_socket.cpython-311-darwin.so"", ""name"" : ""_socket.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4813266944, ""size"" : 180224, ""uuid"" : ""6f66f2fb-3370-3449-8c56-f3e0001309af"", ""path"" : ""\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/pyexpat.cpython-311-darwin.so"", ""name"" : ""pyexpat.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4813799424, ""size"" : 163840, ""uuid"" : ""a600179c-3d08-331c-ba58-5134eada0b7e"", ""path"" : ""\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/styles\/libqmacstyle.dylib"", ""name"" : ""libqmacstyle.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4806787072, ""size"" : 655360, ""uuid"" : ""4bf756eb-ff87-3f7f-8c98-b1eda6463b81"", ""path"" : ""\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib"", ""name"" : ""libqcocoa.dylib"" }, [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) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-22.5.10 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir9,1 Processor Name: Quad-Core Intel Core i5 Processor Speed: 1.1 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0) OS Loader Version: 580~1678 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 20 hours, 50 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a51 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-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 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX