id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15095 Crash in garbage collection r.machne@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-6.5.0-26-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description crashed during saving chimera x session file, an empty (!) file named 6kwy.cxs.1658553.tmp was on the hard drive, but the session was lost. Fatal Python error: Segmentation fault Thread 0x00007e85637fe640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 975 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007e8563fff640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 975 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007e8580ff9640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.11/selectors.py"", line 415 in select File ""/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 975 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007e85817fa640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 975 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007e8581ffb640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 975 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007e85827fc640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 975 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007e8582ffd640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 975 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007e85837fe640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 975 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007e8583fff640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 975 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007e85a4ff9640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 975 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007e85a57fa640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 975 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007e8684a83b80 (most recent call first): Garbage-collecting File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 2000 in save_state File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 219 in take_snapshot File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 1417 in take_snapshot File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py"", line 296 in process File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py"", line 273 in discovery File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py"", line 636 in save File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py"", line 912 in save File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 95 in save File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 101 in provider_save File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 86 in cmd_save File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 62 in display File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 138 in show_save_file_dialog File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 127 in File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/usr/lib/ucsf-chimerax/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.pdb_lib._load_libs, 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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 61) ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/raim/AF-P25786-F1-model_v4.pdb AF-P25786-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for proteasome subunit α type-1 (P25786) [more info...] Chain information for AF-P25786-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | proteasome subunit α type-1 | PSA1_HUMAN 1-263 > lighting soft > lighting full > lighting simple > set bgColor white > style sphere Changed 2074 atom styles > style ball Changed 2074 atom styles > select add #1 2074 atoms, 2115 bonds, 263 residues, 1 model selected > select subtract #1 Nothing selected > save /home/raim/test.cxs > select ::name=""LEU"" 192 atoms, 170 bonds, 24 residues, 1 model selected > save /home/raim/test.cxs > open /home/raim/test.pdb test.pdb title: Alphafold monomer V2.0 prediction for proteasome subunit α type-1 (P25786) [more info...] Chain information for test.pdb #2 --- Chain | Description | UniProt A | proteasome subunit α type-1 | PSA1_HUMAN 1-263 > hide #1 models > select add #1 2074 atoms, 2115 bonds, 263 residues, 1 model selected > select subtract #1 Nothing selected > select add #2 1052 atoms, 1051 bonds, 263 residues, 1 model selected > select subtract #2 Nothing selected > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" ""space-filling (chain colors)"" Using preset: Initial Styles / Space-Filling (Chain Colors) Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. Alignment identifier is 1 > select #1/A:93 #2/A:93 12 atoms, 10 bonds, 2 residues, 2 models selected > select #1/A:93-99 #2/A:93-99 90 atoms, 90 bonds, 14 residues, 2 models selected Proteasome Subunit Α Type-1 [ID: 1] region 2 chains [93-99] RMSD: 0.000 > select #1/A:158 #2/A:158 9 atoms, 7 bonds, 2 residues, 2 models selected > select #1/A:158-164 #2/A:158-164 75 atoms, 73 bonds, 14 residues, 2 models selected Proteasome Subunit Α Type-1 [ID: 1] region 2 chains [158-164] RMSD: 0.000 > select add #1 2102 atoms, 2142 bonds, 270 residues, 2 models selected > select subtract #1 28 atoms, 27 bonds, 7 residues, 1 model selected > select #1/A:188 #2/A:188 11 atoms, 9 bonds, 2 residues, 2 models selected > select #1/A:188-194 #2/A:188-194 82 atoms, 81 bonds, 14 residues, 2 models selected Proteasome Subunit Α Type-1 [ID: 1] region 2 chains [188-194] RMSD: 0.000 > style sel & #2 sphere Changed 28 atom styles > style sel & #2 ball Changed 28 atom styles > rainbow sel & #2 > coulombic sel & #2 The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: test.pdb #2/A MET 1 test.pdb #2/A PHE 2 test.pdb #2/A ARG 3 test.pdb #2/A ASN 4 test.pdb #2/A GLN 5 test.pdb #2/A TYR 6 test.pdb #2/A ASP 7 test.pdb #2/A ASN 8 test.pdb #2/A ASP 9 test.pdb #2/A VAL 10 test.pdb #2/A THR 11 test.pdb #2/A VAL 12 test.pdb #2/A TRP 13 test.pdb #2/A SER 14 test.pdb #2/A PRO 15 test.pdb #2/A GLN 16 test.pdb #2/A ARG 18 test.pdb #2/A ILE 19 test.pdb #2/A HIS 20 test.pdb #2/A GLN 21 test.pdb #2/A ILE 22 test.pdb #2/A GLU 23 test.pdb #2/A TYR 24 test.pdb #2/A ALA 25 test.pdb #2/A MET 26 test.pdb #2/A GLU 27 test.pdb #2/A ALA 28 test.pdb #2/A VAL 29 test.pdb #2/A LYS 30 test.pdb #2/A GLN 31 test.pdb #2/A SER 33 test.pdb #2/A ALA 34 test.pdb #2/A THR 35 test.pdb #2/A VAL 36 test.pdb #2/A LEU 38 test.pdb #2/A LYS 39 test.pdb #2/A SER 40 test.pdb #2/A LYS 41 test.pdb #2/A THR 42 test.pdb #2/A HIS 43 test.pdb #2/A ALA 44 test.pdb #2/A VAL 45 test.pdb #2/A LEU 46 test.pdb #2/A VAL 47 test.pdb #2/A ALA 48 test.pdb #2/A LEU 49 test.pdb #2/A LYS 50 test.pdb #2/A ARG 51 test.pdb #2/A ALA 52 test.pdb #2/A GLN 53 test.pdb #2/A SER 54 test.pdb #2/A GLU 55 test.pdb #2/A LEU 56 test.pdb #2/A ALA 57 test.pdb #2/A ALA 58 test.pdb #2/A HIS 59 test.pdb #2/A GLN 60 test.pdb #2/A LYS 61 test.pdb #2/A LYS 62 test.pdb #2/A ILE 63 test.pdb #2/A LEU 64 test.pdb #2/A HIS 65 test.pdb #2/A VAL 66 test.pdb #2/A ASP 67 test.pdb #2/A ASN 68 test.pdb #2/A HIS 69 test.pdb #2/A ILE 70 test.pdb #2/A ILE 72 test.pdb #2/A SER 73 test.pdb #2/A ILE 74 test.pdb #2/A ALA 75 test.pdb #2/A LEU 77 test.pdb #2/A THR 78 test.pdb #2/A ALA 79 test.pdb #2/A ASP 80 test.pdb #2/A ALA 81 test.pdb #2/A ARG 82 test.pdb #2/A LEU 83 test.pdb #2/A LEU 84 test.pdb #2/A CYS 85 test.pdb #2/A ASN 86 test.pdb #2/A PHE 87 test.pdb #2/A MET 88 test.pdb #2/A ARG 89 test.pdb #2/A GLN 90 test.pdb #2/A GLU 91 test.pdb #2/A CYS 92 test.pdb #2/A LEU 93 test.pdb #2/A ASP 94 test.pdb #2/A SER 95 test.pdb #2/A ARG 96 test.pdb #2/A PHE 97 test.pdb #2/A VAL 98 test.pdb #2/A PHE 99 test.pdb #2/A ASP 100 test.pdb #2/A ARG 101 test.pdb #2/A PRO 102 test.pdb #2/A LEU 103 test.pdb #2/A PRO 104 test.pdb #2/A VAL 105 test.pdb #2/A SER 106 test.pdb #2/A ARG 107 test.pdb #2/A LEU 108 test.pdb #2/A VAL 109 test.pdb #2/A SER 110 test.pdb #2/A LEU 111 test.pdb #2/A ILE 112 test.pdb #2/A SER 114 test.pdb #2/A LYS 115 test.pdb #2/A THR 116 test.pdb #2/A GLN 117 test.pdb #2/A ILE 118 test.pdb #2/A PRO 119 test.pdb #2/A THR 120 test.pdb #2/A GLN 121 test.pdb #2/A ARG 122 test.pdb #2/A TYR 123 test.pdb #2/A ARG 125 test.pdb #2/A ARG 126 test.pdb #2/A PRO 127 test.pdb #2/A TYR 128 test.pdb #2/A VAL 130 test.pdb #2/A LEU 132 test.pdb #2/A LEU 133 test.pdb #2/A ILE 134 test.pdb #2/A ALA 135 test.pdb #2/A TYR 137 test.pdb #2/A ASP 138 test.pdb #2/A ASP 139 test.pdb #2/A MET 140 test.pdb #2/A PRO 142 test.pdb #2/A HIS 143 test.pdb #2/A ILE 144 test.pdb #2/A PHE 145 test.pdb #2/A GLN 146 test.pdb #2/A THR 147 test.pdb #2/A CYS 148 test.pdb #2/A PRO 149 test.pdb #2/A SER 150 test.pdb #2/A ALA 151 test.pdb #2/A ASN 152 test.pdb #2/A TYR 153 test.pdb #2/A PHE 154 test.pdb #2/A ASP 155 test.pdb #2/A CYS 156 test.pdb #2/A ARG 157 test.pdb #2/A ALA 158 test.pdb #2/A MET 159 test.pdb #2/A SER 160 test.pdb #2/A ILE 161 test.pdb #2/A ALA 163 test.pdb #2/A ARG 164 test.pdb #2/A SER 165 test.pdb #2/A GLN 166 test.pdb #2/A SER 167 test.pdb #2/A ALA 168 test.pdb #2/A ARG 169 test.pdb #2/A THR 170 test.pdb #2/A TYR 171 test.pdb #2/A LEU 172 test.pdb #2/A GLU 173 test.pdb #2/A ARG 174 test.pdb #2/A HIS 175 test.pdb #2/A MET 176 test.pdb #2/A SER 177 test.pdb #2/A GLU 178 test.pdb #2/A PHE 179 test.pdb #2/A MET 180 test.pdb #2/A GLU 181 test.pdb #2/A CYS 182 test.pdb #2/A ASN 183 test.pdb #2/A LEU 184 test.pdb #2/A ASN 185 test.pdb #2/A GLU 186 test.pdb #2/A LEU 187 test.pdb #2/A VAL 188 test.pdb #2/A LYS 189 test.pdb #2/A HIS 190 test.pdb #2/A LEU 192 test.pdb #2/A ARG 193 test.pdb #2/A ALA 194 test.pdb #2/A LEU 195 test.pdb #2/A ARG 196 test.pdb #2/A GLU 197 test.pdb #2/A THR 198 test.pdb #2/A LEU 199 test.pdb #2/A PRO 200 test.pdb #2/A ALA 201 test.pdb #2/A GLU 202 test.pdb #2/A GLN 203 test.pdb #2/A ASP 204 test.pdb #2/A LEU 205 test.pdb #2/A THR 206 test.pdb #2/A THR 207 test.pdb #2/A LYS 208 test.pdb #2/A ASN 209 test.pdb #2/A VAL 210 test.pdb #2/A SER 211 test.pdb #2/A ILE 212 test.pdb #2/A ILE 214 test.pdb #2/A VAL 215 test.pdb #2/A LYS 217 test.pdb #2/A ASP 218 test.pdb #2/A LEU 219 test.pdb #2/A GLU 220 test.pdb #2/A PHE 221 test.pdb #2/A THR 222 test.pdb #2/A ILE 223 test.pdb #2/A TYR 224 test.pdb #2/A ASP 225 test.pdb #2/A ASP 226 test.pdb #2/A ASP 227 test.pdb #2/A ASP 228 test.pdb #2/A VAL 229 test.pdb #2/A SER 230 test.pdb #2/A PRO 231 test.pdb #2/A PHE 232 test.pdb #2/A LEU 233 test.pdb #2/A GLU 234 test.pdb #2/A LEU 236 test.pdb #2/A GLU 237 test.pdb #2/A GLU 238 test.pdb #2/A ARG 239 test.pdb #2/A PRO 240 test.pdb #2/A GLN 241 test.pdb #2/A ARG 242 test.pdb #2/A LYS 243 test.pdb #2/A ALA 244 test.pdb #2/A GLN 245 test.pdb #2/A PRO 246 test.pdb #2/A ALA 247 test.pdb #2/A GLN 248 test.pdb #2/A PRO 249 test.pdb #2/A ALA 250 test.pdb #2/A ASP 251 test.pdb #2/A GLU 252 test.pdb #2/A PRO 253 test.pdb #2/A ALA 254 test.pdb #2/A GLU 255 test.pdb #2/A LYS 256 test.pdb #2/A ALA 257 test.pdb #2/A ASP 258 test.pdb #2/A GLU 259 test.pdb #2/A PRO 260 test.pdb #2/A MET 261 test.pdb #2/A GLU 262 test.pdb #2/A HIS 263 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for test.pdb_A SES surface #2.1: minimum, -36.03, mean -12.72, maximum 4.89 To also show corresponding color key, enter the above coulombic command and add key true > style sel & #!2 sphere Changed 28 atom styles > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 28 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > select subtract #2.1 54 atoms, 54 bonds, 7 residues, 2 models selected > select add #2.1 1106 atoms, 54 bonds, 270 residues, 2 models selected > hide #2.1 models > show #2.1 models > select subtract #2.1 54 atoms, 54 bonds, 7 residues, 2 models selected > select ::name=""SER"" 160 atoms, 128 bonds, 32 residues, 2 models selected > coulombic sel & #!2 Coulombic values for test.pdb_A SES surface #2.1: minimum, -36.03, mean -12.72, maximum 4.89 To also show corresponding color key, enter the above coulombic command and add key true > select #1/A#2/A 3126 atoms, 3166 bonds, 526 residues, 2 models selected > coulombic sel & #!2 Coulombic values for test.pdb_A SES surface #2.1: minimum, -36.03, mean -12.72, maximum 4.89 To also show corresponding color key, enter the above coulombic command and add key true Alignment identifier is 2 > select #1/A:97-98 #2/A:97-98 26 atoms, 25 bonds, 4 residues, 2 models selected > select #1/A:97-104 #2/A:97-104 102 atoms, 104 bonds, 16 residues, 2 models selected Proteasome Subunit Α Type-1 [ID: 2] region 2 chains [97-104] RMSD: 0.000 > rainbow sel & #!2 > hbonds sel & #!2 reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: test.pdb #2/A PRO 253 N; test.pdb #2/A PRO 260 N; test.pdb #2/A PRO 249 N; test.pdb #2/A PRO 15 N; test.pdb #2/A PRO 104 N; test.pdb #2/A PRO 142 N; test.pdb #2/A PRO 102 N; test.pdb #2/A PRO 200 N; test.pdb #2/A PRO 149 N; test.pdb #2/A PRO 119 N; test.pdb #2/A PRO 240 N; test.pdb #2/A PRO 231 N; test.pdb #2/A PRO 246 N; test.pdb #2/A PRO 127 N 14 hydrogen bonds found > color sel & #!2 bypolymer > color sel & #!2 bychain > style sel & #!2 sphere Changed 32 atom styles > style sel & #!2 ball Changed 32 atom styles > nucleotides sel & #!2 atoms > style nucleic & sel & #!2 stick Changed 0 atom styles > nucleotides sel & #!2 fill > style nucleic & sel & #!2 stick Changed 0 atom styles > hide #3 models > hide #3 target m > lighting simple > lighting full > lighting soft > lighting simple > lighting shadows true > graphics silhouettes true > set bgColor black > set bgColor gray > ui tool show ""Side View"" > ui mousemode right distance > distance #2/A:173@CA #2/A:248@O Distance between test.pdb #2/A GLU 173 CA and GLN 248 O: 33.403Å > save /home/raim/test.cxs QXcbConnection: XCB error: 3 (BadWindow), sequence: 30577, resource id: 23134165, major code: 40 (TranslateCoords), minor code: 0 > show sel & #!2 surfaces > hide sel & #!2 surfaces > show sel & #!2 surfaces > hide sel & #!2 surfaces > style sel & #!2 ball Changed 32 atom styles > style sel & #!2 sphere Changed 32 atom styles > style sel & #!2 sphere Changed 32 atom styles > style sel & #!2 ball Changed 32 atom styles > style sel & #!2 sphere Changed 32 atom styles > style sel & #!2 ball Changed 32 atom styles > nucleotides sel & #!2 fill > style nucleic & sel & #!2 stick Changed 0 atom styles > mlp sel & #!2 Map values for surface ""test.pdb_A SES surface"": minimum -27.35, mean -15.1, maximum -2.702 To also show corresponding color key, enter the above mlp command and add key true > style sel & #!2 ball Changed 32 atom styles > hide sel & #!2 surfaces > hide sel & #!2 atoms > show sel & #!2 atoms > show sel & #!2 cartoons > nucleotides sel & #!2 atoms > style nucleic & sel & #!2 stick Changed 0 atom styles > color sel & #!2 byhetero > color sel & #!2 bychain > ui tool show ""AlphaFold Error Plot"" > open /home/raim/test2.pdb test2.pdb title: Alphafold monomer V2.0 prediction for proteasome subunit α type-1 (P25786) [more info...] Chain information for test2.pdb #5 --- Chain | Description | UniProt A | proteasome subunit α type-1 | PSA1_HUMAN 1-263 > hide #4.1 models > hide #!4 models > hide #2.1 models > hide #!2 models > help help:devel > open 2zcp Summary of feedback from opening 2zcp fetched from pdb --- warning | PDB entry 2ZCP has been replaced by 3W7F notes | Fetching compressed mmCIF 2zcp from http://files.rcsb.org/download/2zcp.cif Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif Fetching CCD FPS from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/FPS/FPS.cif 2zcp title: Crystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with farnesyl thiopyrophosphate [more info...] Chain information for 2zcp #6 --- Chain | Description | UniProt A B | Dehydrosqualene synthase | A9JQL9_STAAU 1-287 Non-standard residues in 2zcp #6 --- FPS — S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate (farnesyl thiopyrophosphate) MG — magnesium ion 2zcp mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly Drag select of 13 residues > delete /b > surface :fps sharpBoundaries false > surface :fps sharpBoundaries falsesurface protein sharp false Invalid ""sharpBoundaries"" argument: Expected true or false (or 1 or 0) > surface :fps sharpBoundaries false > contactArea #1.3 with #1.2 distance 3 slab -.1,0 color tan Unknown command: measure contactArea #1.3 with #1.2 distance 3 slab -.1,0 color tan Downloading file set_radius_to_bfactor.py > open /home/raim/Downloads/set_radius_to_bfactor.py executed set_radius_to_bfactor.py > select #2-36 4721 atoms, 4596 bonds, 33 pseudobonds, 989 residues, 8 models selected > select #2-36 4721 atoms, 4596 bonds, 33 pseudobonds, 989 residues, 8 models selected > open /home/raim/Downloads/set_radius_to_bfactor.py executed set_radius_to_bfactor.py > save /home/raim/Downloads/test.png width 1014 height 717 supersample 3 > close session > open 121p Summary of feedback from opening 121p fetched from pdb --- note | Fetching compressed mmCIF 121p from http://files.rcsb.org/download/121p.cif 121p title: Struktur und guanosintriphosphat-hydrolysemechanismus des C-terminal verkuerzten menschlichen krebsproteins P21-H-ras [more info...] Chain information for 121p #1 --- Chain | Description | UniProt A | H-RAS P21 PROTEIN | RASH_HUMAN 1-166 Non-standard residues in 121p #1 --- GCP — phosphomethylphosphonic acid guanylate ester MG — magnesium ion 121p mmCIF Assemblies --- 1| author_defined_assembly > hide solvent > style ligand ball Changed 32 atom styles > style ligand ball Changed 32 atom styles > open https://www.rbvi.ucsf.edu/chimerax/data/conservation- > coloring/121p-consurf.aln Summary of feedback from opening //www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln fetched from https --- notes | Fetching 121p-consurf.aln from https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln Downloaded 121p-consurf.aln to /home/raim/Downloads/121p-consurf.aln Alignment identifier is 121p-consurf.aln Associated 121p chain A to Input_pdb_SEQRES_A with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment 121p-consurf.aln Opened 150 sequences from 121p-consurf.aln > color byattribute seq_conservation 1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83 > open 1avo Summary of feedback from opening 1avo fetched from pdb --- note | Fetching compressed mmCIF 1avo from http://files.rcsb.org/download/1avo.cif 1avo title: Proteasome activator reg(α) [more info...] Chain information for 1avo #2 --- Chain | Description | UniProt A C E G I K M | 11S REGULATOR | PSME1_HUMAN 4-63 B D F H J L N | 11S REGULATOR | PSME1_HUMAN 104-242 > open 1avo 1avo title: Proteasome activator reg(α) [more info...] Chain information for 1avo #3 --- Chain | Description | UniProt A C E G I K M | 11S REGULATOR | PSME1_HUMAN 4-63 B D F H J L N | 11S REGULATOR | PSME1_HUMAN 104-242 > close session > open 1avo 1avo title: Proteasome activator reg(α) [more info...] Chain information for 1avo #1 --- Chain | Description | UniProt A C E G I K M | 11S REGULATOR | PSME1_HUMAN 4-63 B D F H J L N | 11S REGULATOR | PSME1_HUMAN 104-242 Alignment identifier is 1 Alignment identifier is 2 > close session > open 6kwy Summary of feedback from opening 6kwy fetched from pdb --- note | Fetching compressed mmCIF 6kwy from http://files.rcsb.org/download/6kwy.cif 6kwy title: human PA200-20S complex [more info...] Chain information for 6kwy #1 --- Chain | Description | UniProt A O | Proteasome subunit alpha type-2 | PSA2_HUMAN 0-233 B P | Proteasome subunit alpha type-4 | PSA4_HUMAN 1-261 C Q | Proteasome subunit alpha type-7 | PSA7_HUMAN 1-248 D R | Proteasome subunit alpha type-5 | PSA5_HUMAN 1-241 E S | Proteasome subunit alpha type-1 | PSA1_HUMAN 1-263 F T | Proteasome subunit alpha type-3 | PSA3_HUMAN 0-254 G U | Proteasome subunit alpha type-6 | PSA6_HUMAN 1-246 H V | Proteasome subunit beta type-7 | PSB7_HUMAN -42-234 I W | Proteasome subunit beta type-3 | PSB3_HUMAN 0-204 J X | Proteasome subunit beta type-2 | PSB2_HUMAN 1-201 K Y | Proteasome subunit beta type-5 | PSB5_HUMAN -58-204 L Z | Proteasome subunit beta type-1 | PSB1_HUMAN -27-213 M a | Proteasome subunit beta type-4 | PSB4_HUMAN -44-219 N b | Proteasome subunit beta type-6 | PSB6_HUMAN -33-205 c | Proteasome activator complex subunit 4 | PSME4_HUMAN 1-1843 Non-standard residues in 6kwy #1 --- IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol 1,2,3,4,5,6-hexakisphosphate) K0W — [(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[oxidanyl(phosphonooxy)phosphoryl]oxy-3,4,5,6-tetraphosphonooxy- cyclohexyl] phosphono hydrogen phosphate > hide cartoons > show cartoons > hide surfaces > color byhetero > color bychain > color bypolymer > hide surfaces > select /E/S 3737 atoms, 3807 bonds, 478 residues, 1 model selected > show sel cartoons > show sel atoms > show sel surfaces > hide sel surfaces > show sel cartoons > rainbow sel > coulombic sel The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /E GLN 53 /E SER 54 /E GLU 55 /E LYS 208 /S PHE 2 /S ARG 3 /S GLN 53 /S ASP 218 /S GLU 238 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 6kwy_E SES surface #1.2: minimum, -15.15, mean -0.41, maximum 12.39 Coulombic values for 6kwy_S SES surface #1.3: minimum, -12.87, mean -0.28, maximum 11.57 To also show corresponding color key, enter the above coulombic command and add key true > hide sel surfaces > color sel bychain > mlp sel Map values for surface ""6kwy_E SES surface"": minimum -29.14, mean -4.827, maximum 22.49 Map values for surface ""6kwy_S SES surface"": minimum -28.74, mean -4.883, maximum 22.05 To also show corresponding color key, enter the above mlp command and add key true > select 62346 atoms, 63535 bonds, 5 pseudobonds, 7970 residues, 2 models selected > show sel cartoons > hide sel surfaces > show sel cartoons > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel ball Changed 62346 atom styles > hide sel surfaces > hide sel atoms > select clear > select /E/S 3737 atoms, 3807 bonds, 478 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" Alignment identifier is 1 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > select /E,S:166 18 atoms, 16 bonds, 2 residues, 1 model selected > select /E,S:166-171 100 atoms, 100 bonds, 12 residues, 1 model selected > show sel surfaces > select clear > select /E,S:52 10 atoms, 8 bonds, 2 residues, 1 model selected > select /E,S:52-69 273 atoms, 277 bonds, 36 residues, 1 model selected > select /E,S:160-161 28 atoms, 26 bonds, 4 residues, 1 model selected > select /E,S:156-161 88 atoms, 86 bonds, 12 residues, 1 model selected > select /E,S:204 16 atoms, 14 bonds, 2 residues, 1 model selected > select /E,S:204-213 140 atoms, 138 bonds, 20 residues, 1 model selected > select /E,S:222 14 atoms, 12 bonds, 2 residues, 1 model selected > select /E,S:222-224 54 atoms, 54 bonds, 6 residues, 1 model selected > select /E,S:69 20 atoms, 20 bonds, 2 residues, 1 model selected > select /E,S:69-79 146 atoms, 146 bonds, 22 residues, 1 model selected > coulombic sel Coulombic values for 6kwy_E SES surface #1.2: minimum, -15.15, mean -0.41, maximum 12.39 Coulombic values for 6kwy_S SES surface #1.3: minimum, -12.87, mean -0.28, maximum 11.57 To also show corresponding color key, enter the above coulombic command and add key true > select /E:1-2/S:2 24 atoms, 23 bonds, 3 residues, 1 model selected > select /E:1-17/S:2-17 268 atoms, 275 bonds, 33 residues, 1 model selected Alignment identifier is 2 > select /E,S:11 14 atoms, 12 bonds, 2 residues, 1 model selected > select /E,S:11-13 56 atoms, 58 bonds, 6 residues, 1 model selected > select 62346 atoms, 63535 bonds, 5 pseudobonds, 7970 residues, 2 models selected > color sel bypolymer > color sel bychain > color (#!1 & sel) hot pink > color (#!1 & sel) light gray > select clear > select /E,S:11 14 atoms, 12 bonds, 2 residues, 1 model selected > select /E,S:11-13 56 atoms, 58 bonds, 6 residues, 1 model selected > color (#!1 & sel) red > show sel surfaces > select /E,S:52 10 atoms, 8 bonds, 2 residues, 1 model selected > select /E,S:52-54 31 atoms, 29 bonds, 6 residues, 1 model selected > color (#!1 & sel) yellow > show sel surfaces > style sel ball Changed 31 atom styles > style sel sphere Changed 31 atom styles > style sel sphere Changed 31 atom styles > style sel stick Changed 31 atom styles > style sel ball Changed 31 atom styles > style sel sphere Changed 31 atom styles > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 31 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > undo > select 62346 atoms, 63535 bonds, 5 pseudobonds, 7970 residues, 2 models selected > hide sel surfaces > select /E,S:11 14 atoms, 12 bonds, 2 residues, 1 model selected > select /E,S:11-13 56 atoms, 58 bonds, 6 residues, 1 model selected > color (#!1 & sel) purple > show sel surfaces > select /E,S:52 10 atoms, 8 bonds, 2 residues, 1 model selected > select /E,S:52-54 31 atoms, 29 bonds, 6 residues, 1 model selected > show sel surfaces > select /E,S:141 8 atoms, 6 bonds, 2 residues, 1 model selected > select /E,S:141-143 42 atoms, 44 bonds, 6 residues, 1 model selected > color (#!1 & sel) blue > show sel surfaces > save /home/raim/data/mistrans/figures/saap_3d/test.png width 987 height 1035 > supersample 3 > save /home/raim/data/mistrans/figures/saap_3d/6kwy_psma1.png width 987 > height 1035 supersample 3 > close session > open /home/raim/test.pdb format pdb test.pdb title: Alphafold monomer V2.0 prediction for proteasome subunit α type-1 (P25786) [more info...] Chain information for test.pdb #1 --- Chain | Description | UniProt A | proteasome subunit α type-1 | PSA1_HUMAN 1-263 Alignment identifier is 1/A > select /A:11-12 8 atoms, 7 bonds, 2 residues, 1 model selected > select /A:11-13 12 atoms, 11 bonds, 3 residues, 1 model selected > select /A:52 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:52-54 12 atoms, 11 bonds, 3 residues, 1 model selected > select /A:11 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:11-13 12 atoms, 11 bonds, 3 residues, 1 model selected > select /A:50-51 8 atoms, 7 bonds, 2 residues, 1 model selected > select /A:50-53 16 atoms, 15 bonds, 4 residues, 1 model selected > close session > open /home/raim/AF-P25786-F1-model_v4.pdb format pdb AF-P25786-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for proteasome subunit α type-1 (P25786) [more info...] Chain information for AF-P25786-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | proteasome subunit α type-1 | PSA1_HUMAN 1-263 > close session > open 6kwy format mmcif fromDatabase pdb 6kwy title: human PA200-20S complex [more info...] Chain information for 6kwy #1 --- Chain | Description | UniProt A O | Proteasome subunit alpha type-2 | PSA2_HUMAN 0-233 B P | Proteasome subunit alpha type-4 | PSA4_HUMAN 1-261 C Q | Proteasome subunit alpha type-7 | PSA7_HUMAN 1-248 D R | Proteasome subunit alpha type-5 | PSA5_HUMAN 1-241 E S | Proteasome subunit alpha type-1 | PSA1_HUMAN 1-263 F T | Proteasome subunit alpha type-3 | PSA3_HUMAN 0-254 G U | Proteasome subunit alpha type-6 | PSA6_HUMAN 1-246 H V | Proteasome subunit beta type-7 | PSB7_HUMAN -42-234 I W | Proteasome subunit beta type-3 | PSB3_HUMAN 0-204 J X | Proteasome subunit beta type-2 | PSB2_HUMAN 1-201 K Y | Proteasome subunit beta type-5 | PSB5_HUMAN -58-204 L Z | Proteasome subunit beta type-1 | PSB1_HUMAN -27-213 M a | Proteasome subunit beta type-4 | PSB4_HUMAN -44-219 N b | Proteasome subunit beta type-6 | PSB6_HUMAN -33-205 c | Proteasome activator complex subunit 4 | PSME4_HUMAN 1-1843 Non-standard residues in 6kwy #1 --- IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol 1,2,3,4,5,6-hexakisphosphate) K0W — [(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[oxidanyl(phosphonooxy)phosphoryl]oxy-3,4,5,6-tetraphosphonooxy- cyclohexyl] phosphono hydrogen phosphate > save /home/raim/data/mistrans/figures/saap_3d/6kwy.cxs ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2 OpenGL renderer: Mesa Intel(R) HD Graphics 530 (SKL GT2) OpenGL vendor: Intel Python: 3.11.2 Locale: en_US.UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=xubuntu XDG_SESSION_DESKTOP=xubuntu XDG_CURRENT_DESKTOP=XFCE DISPLAY=:0.0 Manufacturer: Dell Inc. Model: OptiPlex 7040 OS: Ubuntu 22.04 Jammy Jellyfish Architecture: 64bit ELF Virtual Machine: none CPU: 8 Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz Cache Size: 8192 KB Memory: total used free shared buff/cache available Mem: 62Gi 19Gi 2.1Gi 3.9Gi 40Gi 38Gi Swap: 2.0Gi 632Mi 1.4Gi Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 530 [8086:1912] (rev 06) DeviceName: Intel HD Graphics Subsystem: Dell HD Graphics 530 [1028:06b9] Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 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: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 23.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX