id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16941 ArrayMemoryError saving session with maps chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type3/job175/postprocess_masked.mrc Opened postprocess_masked.mrc as #1, grid size 288,288,288, pixel 0.83, shown at level 0.0169, step 2, values float32 > open > D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type3/postprocess_masked.mrc Opened postprocess_masked.mrc as #2, grid size 288,288,288, pixel 0.83, shown at level 0.00335, step 2, values float32 > close #1 > rename #2 5fad_Type3 > volume #2 step 1 > volume #2 level 0.1 > volume #2 level 0.001 > volume #2 level 0.01401 > ui tool show ""Color Actions"" > set bgColor white > graphics silhouettes true > color white target acs > open D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type3/Type3_3layer_R2.pdb Chain information for Type3_3layer_R2.pdb #1 --- Chain | Description A B C D E F | No description available > style stick Changed 2982 atom styles > transparency 80 > transparency 90 > transparency 80 > hide #!2 models Drag select of 50 atoms, 52 bonds > select up 59 atoms, 53 bonds, 11 residues, 1 model selected > select up 150 atoms, 147 bonds, 11 residues, 1 model selected > select up 208 atoms, 206 bonds, 16 residues, 1 model selected > select up 994 atoms, 1002 bonds, 66 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 43 atoms, 44 bonds > select up 54 atoms, 47 bonds, 8 residues, 1 model selected > select up 108 atoms, 104 bonds, 8 residues, 1 model selected > select up 181 atoms, 179 bonds, 14 residues, 1 model selected > select up 994 atoms, 1002 bonds, 66 residues, 1 model selected > delete atoms sel > delete bonds sel > show #!2 models > hide #1 models > show #1 models > hide #!2 models > select add #1 994 atoms, 1002 bonds, 66 residues, 1 model selected > hide H > select clear Drag select of 485 atoms, 494 bonds > color sel royal blue target acs > select clear > select add #1 994 atoms, 1002 bonds, 66 residues, 1 model selected > color sel royal blue target acs > color sel dodger blue target acs > color sel byhetero target acs > select clear > show #!2 models > volume zone #2 nearAtoms #1 range 4.98 > volume zone #2 nearAtoms #1 range 2 > volume #2 level 0.02153 [Repeated 1 time(s)] > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > volume #2 level 0.01668 > select add #1 994 atoms, 1002 bonds, 66 residues, 1 model selected > volume zone #2 nearAtoms sel & #1 range 4.98 > volume zone #2 nearAtoms sel & #1 range 2 > volume #2 level 0.01903 > select add #2 994 atoms, 1002 bonds, 66 residues, 3 models selected > select subtract #2 994 atoms, 1002 bonds, 66 residues, 1 model selected > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > volume #2 level 0.01683 > volume #2 region 0,0,0,287,287,287 > select clear > volume zone #2 nearAtoms #1 range 4.98 > volume zone #2 nearAtoms #1 range 2 > select clear > volume #2 level 0.01856 > select add #1 994 atoms, 1002 bonds, 66 residues, 1 model selected > set sel stickRadius 2 Expected keyword ""selectionColor"" or ""selectionWidth"" > set stickRadius 2set sel stickRadius 2 Expected a keyword > set stickRadius 2 Expected a keyword > set size stickRadius 2 Expected a keyword > size stickRadius 2 Changed 1002 bond radii > size stickRadius 0.5 Changed 1002 bond radii > size stickRadius 0.3 Changed 1002 bond radii > select clear > volume #2 level 0.01997 > volume #2 level 0.01887 > select add #2 2 models selected > select subtract #2 Nothing selected > select add #2 2 models selected > select subtract #2 Nothing selected > select add #1 994 atoms, 1002 bonds, 66 residues, 1 model selected > select subtract #1 Nothing selected > select add #2 2 models selected > select subtract #2 Nothing selected > select add #2 2 models selected > select subtract #2 Nothing selected > select add #2 2 models selected > select subtract #2 Nothing selected > combine #2 No structures specified > select add #2 2 models selected > combine #2 No structures specified > combine #2 bring to #3 Expected a keyword > combine #2 to #3 Expected a keyword > combine sel No structures specified > select subtract #2 Nothing selected > select add #2 2 models selected > select subtract #2 Nothing selected > select add #2 2 models selected > select subtract #2 Nothing selected > select add #1 994 atoms, 1002 bonds, 66 residues, 1 model selected > select add #2 994 atoms, 1002 bonds, 66 residues, 3 models selected > volume sel region all imageMode ""full region"" > volume unzone sel > mousemode rightMode ""crop volume"" > volume #2 level 0.01589 > select clear > volume #2 level 0.01636 > open D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type3/Type3_3layer_R2.pdb Chain information for Type3_3layer_R2.pdb #3 --- Chain | Description A B C D E F | No description available > style stick Changed 3976 atom styles > hide #1 models > select add #3 2982 atoms, 3006 bonds, 198 residues, 1 model selected > color sel cornflower blue > color sel byhetero > hide H > select clear > size sel stickRadius 0.3 Changed 0 bond radii > select add #3 2982 atoms, 3006 bonds, 198 residues, 1 model selected > size sel stickRadius 0.3 Changed 3006 bond radii > select clear > size sel stickRadius 0.2 Changed 0 bond radii > select add #3 2982 atoms, 3006 bonds, 198 residues, 1 model selected > size sel stickRadius 0.2 Changed 3006 bond radii > select clear > select add #3 2982 atoms, 3006 bonds, 198 residues, 1 model selected > size sel stickRadius 0.25 Changed 3006 bond radii > select clear > open > D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type2/job195/postprocess_masked.mrc Opened postprocess_masked.mrc as #4, grid size 288,288,288, pixel 0.83, shown at level 0.0009, step 2, values float32 > volume #4 level 0.01037 > hide #3 models > hide #!2 models > volume #4 step 1 > select add #4 2 models selected > surface dust #4 size 8.3 > surface dust #4 size 3 > surface dust #4 size 5 > select clear > rename #4 5fad_Type2 > select add #4 2 models selected > color sel white target acs > transparency #4.1 80 > select clear > open > D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type2/PHENIX/RealSpaceRefine_2/5FAD_Type2_3layer_R2_real_space_refined.pdb Chain information for 5FAD_Type2_3layer_R2_real_space_refined.pdb #5 --- Chain | Description A B C D E F | No description available > style #5 stick Changed 1356 atom styles > select add #5 1356 atoms, 1374 bonds, 186 residues, 1 model selected > size sel stickRadius 0.25 Changed 1374 bond radii > color sel orange red target acs > color sel orange target acs > color sel byhetero target acs > select clear > hide #5 models > hide #!4 models > open D:/YYX/data/Mice_amyloid/Model/ApoE4/job135/postprocess_masked.mrc Opened postprocess_masked.mrc as #6, grid size 288,288,288, pixel 0.83, shown at level 0.0013, step 2, values float32 > rename #6 5Fad_ApoE4 > volume #6 step 1 > volume #6 level 0.01002 > volume #6 level 0.01227 > select add #6 2 models selected > color sel white target acs > transparency #6.1 80 > select clear > open > D:/YYX/data/Mice_amyloid/Model/ApoE4/PHENIX/RealSpaceRefine_2/ApoE4_Type2_3layer_R1_real_space_refined.pdb Chain information for ApoE4_Type2_3layer_R1_real_space_refined.pdb #7 --- Chain | Description A B C D E F | No description available > select add #7 1356 atoms, 1374 bonds, 186 residues, 1 model selected > style sel stick Changed 1356 atom styles > size sel stickRadius 0.25 Changed 1374 bond radii > color sel green target acs > color sel forest green target acs > color sel byhetero target acs > select clear > select add #7 1356 atoms, 1374 bonds, 186 residues, 1 model selected > color sel sea green target acs > color sel byhetero target acs > color sel green target acs > color sel byhetero target acs > color sel forest green target acs > color sel byhetero target acs > select clear > select add #7 1356 atoms, 1374 bonds, 186 residues, 1 model selected > color sel green target acs > color sel byhetero target acs > select clear > volume #6 level 0.00915 > show #5 models > show #!4 models > hide #7 models > hide #!6 models > select add #4 2 models selected > select subtract #4 Nothing selected > volume #4 level 0.009144 > volume #4 level 0.009602 > hide #5 models > hide #!4 models > show #!6 models > show #5 models > show #!4 models > hide #!6 models > hide #!4 models > hide #5 models > show #7 models > show #!6 models > save ""D:/YYX/data/Mice_amyloid/Model/Mouse model.cxs"" includeMaps true > hide #!6 models > hide #7 models > show #5 models > show #!4 models > hide #!4 models > show #!4 models > open > D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type2/job195/postprocess_masked.mrc Opened 5fad_Type2 as #8, grid size 288,288,288, pixel 0.83, shown at level 0.0009, step 2, values float32 > select add #8 2 models selected > volume #8 level 0.01051 > volume #8 step 1 > volume #8 level 0.01271 > hide #!4 models > show #!6 models > hide #!6 models > show #1 models > hide #1 models > show #!4 models > hide #!4 models > show #!4 models > hide #5 models > hide #!4 models > close #8 > show #1 models > hide #1 models > show #!2 models > show #3 models > select add #3 2982 atoms, 3006 bonds, 198 residues, 1 model selected > select subtract #3 Nothing selected > select add #1 994 atoms, 1002 bonds, 66 residues, 1 model selected > select subtract #1 Nothing selected > show #1 models > hide #1 models > hide #!2 models > show #!2 models > volume #2 level 0.01448 > hide #!2 models > hide #3 models > show #!4 models > show #5 models > volume #4 level 0.009144 > surface dust #4 size 8.3 > surface dust #4 size 0 > volume #4 level 0.01342 > volume #4 level 0.01418 > volume #4 region 0,0,0,287,287,287 > show #!6 models > hide #5 models > show #7 models > hide #!4 models Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\history.py"", line 109, in save json.dump(obj, f, ensure_ascii=False) File ""C:\Program Files\ChimeraX\bin\lib\json\\__init__.py"", line 180, in dump fp.write(chunk) OSError: [Errno 28] No space left on device During handling of the above exception, another exception occurred: OSError: [Errno 28] No space left on device During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 350, in _command_started_cb self.history_dialog.add(self._just_typed_command or cmd_text, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 452, in add self._history.enqueue((item, typed)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\history.py"", line 171, in enqueue self.save() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\history.py"", line 201, in save self._history.save(self._queue) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\history.py"", line 109, in save json.dump(obj, f, ensure_ascii=False) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\safesave.py"", line 85, in __exit__ self._f.close() OSError: [Errno 28] No space left on device Error processing trigger ""command started"": OSError: [Errno 28] No space left on device File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\safesave.py"", line 85, in __exit__ self._f.close() See log for complete Python traceback. > hide #!6 models > show #!6 models > hide #7 models > show #7 models > select add #7 1356 atoms, 1374 bonds, 186 residues, 1 model selected > select subtract #7 Nothing selected > volume #6 level 0.009524 > hide #7 models > show #7 models > hide #!6 models > show #!6 models > show #!4 models > hide #!4 models > show #3 models > hide #3 models > rename #4 5fad_Type2_P21 > open > D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type2/job153/postprocess_masked.mrc Opened postprocess_masked.mrc as #8, grid size 288,288,288, pixel 0.83, shown at level 0.000903, step 2, values float32 > rename #8 5fad_Type2_C1 > volume #8 step 1 > hide #!6 models > hide #7 models > volume #8 level 0.008596 > open D:/YYX/data/Mice_amyloid/Model/emd_13809.map.mrc MRC header value nsymbt (-816136225) is invalid > open D:/YYX/data/Mice_amyloid/Model/emd_13809.mrc Opened emd_13809.mrc as #9, grid size 256,256,256, pixel 0.73, shown at level 0.00605, step 1, values float32 > close #9 > save ""D:/YYX/data/Mice_amyloid/Model/Mouse model.cxs"" includeMaps true > open > D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type2/PHENIX/RealSpaceRefine_5/5FAD_Type2_3layer_C1_R2_real_space_refined.pdb Chain information for 5FAD_Type2_3layer_C1_R2_real_space_refined.pdb #9 --- Chain | Description A B C D E F | No description available > select add #8 2 models selected > volume #8 color white > transparency #8.1 80 > style #9 stick Changed 1356 atom styles > hide #!8 models > select add #9 1356 atoms, 1374 bonds, 186 residues, 3 models selected > ui tool show ""Color Actions"" > color sel orange red target acs > color sel orange target acs > show #!8 models > color #8 #ffffff33 models > select subtract #9 2 models selected > select subtract #8 Nothing selected > select add #9 1356 atoms, 1374 bonds, 186 residues, 1 model selected > color sel byhetero target acs > select subtract #9 Nothing selected > select add #9 1356 atoms, 1374 bonds, 186 residues, 1 model selected > size sel stickRadius 2.5 Changed 1374 bond radii > size sel stickRadius 0.25 Changed 1374 bond radii > select clear > volume #8 level 0.01005 > volume #8 level 0.009524 > volume #8 region 0,0,24,287,287,287 > volume #8 level 0.009922 > volume #8 level 0.01085 > show #7 models > hide #!8 models > hide #9 models > show #!6 models > volume #6 level 0.00901 > hide #7 models > hide #!6 models > show #9 models > show #!8 models > volume #8 level 0.009392 > volume #8 level 0.01005 > volume #8 level 0.01019 > show #1 models > show #!2 models > hide #!8 models > hide #9 models > volume #2 level 0.01432 > hide #1 models > show #3 models > volume #2 level 0.01464 > volume #2 region 0,0,10,287,287,287 > hide #3 models > hide #!2 models > show #3 models > show #!2 models > show #1 models > hide #1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > show #5 models > show #!8 models > hide #!8 models > show #7 models > hide #7 models > hide #5 models > hide #!2 models > show #!2 models > hide #3 models > show #3 models > hide #!2 models > hide #3 models > show #!4 models > hide #!4 models > show #!8 models > show #9 models > hide #9 models > show #9 models > hide #9 models > hide #!8 models > show #5 models > show #!4 models > hide #!4 models > hide #5 models > show #9 models > show #!8 models > hide #!8 models > hide #9 models > show #!6 models > show #7 models > hide #7 models > show #7 models > hide #!6 models > show #!6 models > volume #2 level 0.01626 > volume #2 level 0.01497 > hide #!2 models > volume #6 level 0.01132 > hide #!6 models > hide #7 models > show #9 models > show #!8 models > hide #!8 models > ui tool show ""Color Actions"" > hide #9 models > show #9 models > select add #9 1356 atoms, 1374 bonds, 186 residues, 1 model selected > ui tool show ""Color Actions"" > color sel slate blue target acs > show #1 models > hide #1 models > color sel purple target acs > color sel orchid target acs > color sel medium orchid target acs > show #1 models > hide #1 models > show #7 models > hide #7 models > color sel magenta target acs > color sel hot pink target acs > color sel blue violet target acs > color sel medium orchid target acs > color sel orchid target acs > color sel medium orchid target acs > color sel medium violet red target acs > color sel medium orchid target acs > color sel indigo target acs > color sel medium slate blue target acs > color sel slate blue target acs [Repeated 1 time(s)] > show #1 models > hide #1 models > color sel dark slate blue target acs > color sel rebecca purple target acs > color sel dark violet target acs > color sel hot pink target acs > color sel blue violet target acs > color sel medium orchid target acs > select clear > show #!8 models > hide #!8 models > show #7 models > hide #7 models > show #1 models > hide #1 models > select add #9 1356 atoms, 1374 bonds, 186 residues, 1 model selected > color sel blue violet target acs > color sel orchid target acs > color sel medium orchid target acs > color sel medium violet red target acs > color sel medium orchid target acs > color sel orchid target acs > color sel dark magenta target acs > color sel purple target acs > color sel plum target acs > color sel violet target acs [Repeated 1 time(s)] > color sel indigo target acs > color sel deep sky blue target acs > color sel orchid target acs > color sel medium orchid target acs > color sel medium violet red target acs > color sel medium orchid target acs > color sel dark orchid target acs > color sel medium violet red target acs > color sel medium purple target acs > color sel byhetero target acs > select clear > show #7 models > hide #7 models > hide #9 models > show #9 models > show #!8 models > hide #!8 models > show #7 models > hide #7 models > show #1 models > hide #1 models > show #1 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #!2 models > show #3 models > hide #9 models > hide #!2 models > hide #1 models > hide #3 models > show #1 models > hide #1 models > show #!2 models > show #3 models > hide #3 models > show #1 models > close #1 > show #3 models > show #9 models > hide #!2 models > select add #3 2982 atoms, 3006 bonds, 198 residues, 1 model selected > hide #9 models > color sel cornflower blue target acs > color sel byhetero target acs > select clear > hide #3 models > show #7 models > select add #7 1356 atoms, 1374 bonds, 186 residues, 1 model selected > color sel dark sea green target acs > color sel light green target acs > color sel dark green target acs > color sel green target acs > color sel lime green target acs > color sel spring green target acs > color sel lawn green target acs > color sel chartreuse target acs > color sel forest green target acs > color sel medium sea green target acs > color sel sea green target acs > color sel olive drab target acs > color sel byhetero target acs > color sel yellow green target acs > color sel byhetero target acs > color sel olive drab target acs > color sel sea green target acs > color sel byhetero target acs > color sel dark olive green target acs > color sel yellow green target acs > color sel dark khaki target acs > color sel olive target acs > color sel lime target acs > color sel green target acs > color sel chartreuse target acs > color sel lawn green target acs > color sel spring green target acs > color sel lime green target acs > color sel forest green target acs > color sel medium sea green target acs > color sel teal target acs > color sel medium spring green target acs > color sel olive drab target acs > color sel green yellow target acs > color sel green target acs [Repeated 3 time(s)] > color sel lime target acs > color sel chartreuse target acs > color sel lawn green target acs > color sel spring green target acs > color sel lime green target acs > color sel forest green target acs > color sel medium sea green target acs > color sel sea green target acs > color sel medium sea green target acs > color sel byhetero target acs > select clear > show #3 models > hide #3 models > show #9 models > hide #9 models > color #7 #00aa00ff > select add #7 1356 atoms, 1374 bonds, 186 residues, 1 model selected > color sel byhetero target acs > select clear > show #3 models > hide #3 models > show #9 models > hide #9 models > select add #7 1356 atoms, 1374 bonds, 186 residues, 1 model selected > color sel green target acs > color sel byhetero target acs > select clear > show #9 models > hide #9 models > select add #7 1356 atoms, 1374 bonds, 186 residues, 1 model selected > color sel forest green target acs > color sel byhetero target acs > select clear > show #9 models > hide #9 models > show #3 models > hide #3 models > show #!8 models > hide #!8 models > show #!6 models > hide #!6 models > select add #7 1356 atoms, 1374 bonds, 186 residues, 1 model selected > color sel lime green target acs > color sel medium sea green target acs > color sel sea green target acs > color #7 #00aa7fff > color #7 #55aa00ff > color #7 #55ff00ff > color #7 springgreen > color #7 lime > color #7 #55aa00ff > color #7 #55aa7fff > color #7 #55aa00ff > color #7 #00aa7fff > color #7 #00aa00ff > color #7 #265c4aff > color #7 #28543eff > color #7 #ccccccff > color #7 #00aaffff > color #7 #00aa7fff > color #7 #00aa00ff > color sel byhetero target acs > select clear > show #!8 models > hide #!8 models > show #!6 models > hide #!6 models > show #5 models > hide #5 models > show #5 models > hide #5 models > close #4 > show #5 models > hide #5 models > close #5 > show #3 models > hide #3 models > show #!2 models > show #3 models > hide #3 models > show #!8 models > show #9 models > hide #9 models > show #9 models > hide #!8 models > hide #9 models > hide #!2 models > hide #7 models > show #!2 models > save ""D:/YYX/data/Mice_amyloid/Model/Mouse model.cxs"" includeMaps true > show #3 models > show #!6 models > hide #!6 models > show #7 models > hide #7 models > show #!8 models > show #9 models > hide #!8 models > hide #9 models > hide #3 models > hide #!2 models > show #!2 models > show #3 models > hide #3 models > hide #!2 models > show #!6 models > hide #!6 models > show #!8 models > show #9 models > hide #!8 models > show #!8 models > hide #9 models > show #9 models > hide #9 models > show #9 models > hide #9 models > hide #!8 models > show #!8 models > select add #8 2 models selected > select subtract #8 Nothing selected > select add #3 2982 atoms, 3006 bonds, 198 residues, 1 model selected > select subtract #3 Nothing selected > select add #2 2 models selected > hide #!8 models > show #!2 models > hide #!2 models > show #!2 models > color sel cornflower blue target acs > transparency #2.1 0 > select clear > graphics silhouettes false > graphics silhouettes true > graphics silhouettes true width 2 > select clear > hide #!2 models > show #!2 models > show #!6 models > hide #!2 models > show #!2 models > hide #!6 models > volume #2 level 0.01685 > volume #!2 region all imageMode ""full region"" > volume unzone #!2 > mousemode rightMode ""crop volume"" > surface dust #2 size 8.3 > surface dust #2 size 0 [Repeated 1 time(s)] > volume #2 level 0.01403 > volume #2 level 0.01308 > volume #2 level 0.0145 > volume #2 level 0.01544 > volume #2 level 0.0145 > volume #2 level 0.01434 > volume #2 level 0.014 > volume #2 level 0.0143 > volume #2 level 0.0142 > volume #2 level 0.014 > volume #2 level 0.0142 > show #3 models > hide #3 models > save D:/YYX/WorkReport/202412/5FAD_6M_Type3.png width 1341 height 820 > supersample 3 transparentBackground true > save D:/YYX/WorkReport/202412/5FAD_6M_Type3_top.png width 1341 height 820 > supersample 3 transparentBackground true > color #2 white models > select add #2 2 models selected > transparency #2.1 80 > select clear > show #3 models > volume zone #2 nearAtoms #3 range 4.98 > volume zone #2 nearAtoms #3 range 2 > volume #2 level 0.02047 > volume #2 level 0.01922 > volume #!2 region all imageMode ""full region"" > volume unzone #!2 > mousemode rightMode ""crop volume"" > volume #2 level 0.01436 > volume #2 level 0.01608 > volume #2 level 0.0142 > volume #2 level 0.02063 > volume #2 level 0.142 > volume #2 level 0.0142 > combine #3 > hide #!2 models > hide #3 models > hide #1 models > show #1 models > rename #1 ""copy of Type3_1layer_R2.pdb"" > select add #1/D:28@CE 1 atom, 4 bonds, 1 residue, 1 model selected > select up 8 atoms, 4 bonds, 4 residues, 1 model selected > select up 52 atoms, 48 bonds, 4 residues, 1 model selected > select up 152 atoms, 148 bonds, 12 residues, 1 model selected > select up 1988 atoms, 2004 bonds, 132 residues, 1 model selected > delete atoms sel > delete bonds sel > show #!2 models > select clear > volume zone #2 nearAtoms #1 range 4.98 > volume zone #2 nearAtoms #1 range 2 > volume #2 level 0.01922 > volume #2 level 0.0142 > hide #1 models > show #1 models > hide #!2 models > show #!2 models > show #3 models > hide #3 models > show #3 models > hide #3 models > select add #1 994 atoms, 1002 bonds, 66 residues, 1 model selected > volume #!2 region all imageMode ""full region"" > volume unzone #!2 > mousemode rightMode ""crop volume"" > select clear > select add #2 2 models selected > ui tool show ""Segment Map"" Segmenting 5fad_Type3, density threshold 0.014200 Showing 44 region surfaces 392 watershed regions, grouped to 44 regions Showing 5fad_Type3.seg - 44 regions, 44 surfaces > select #4.42 1 model selected > select add #4.29 2 models selected Grouped 2 regions > select add #4.41 2 models selected > select add #4.30 3 models selected > select subtract #4.29 2 models selected > select add #4.29 3 models selected Grouped 3 regions Grouped 40 regions > select clear > select #4.29 1 model selected > select #4.1 1 model selected Opened 5fad_Type3_imasked as #5, grid size 288,288,288, pixel 0.83, shown at step 1, values float32 > hide #!4 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!5 models > show #!5 models > rename #5 5fad_Type3_ED > show #!2 models > select add #2 3 models selected Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 2 maps. > hide #!5 models > select add #1 994 atoms, 1002 bonds, 66 residues, 4 models selected > select subtract #1 3 models selected > select add #1 994 atoms, 1002 bonds, 66 residues, 4 models selected > select add #4 994 atoms, 1002 bonds, 66 residues, 6 models selected > select subtract #4 994 atoms, 1002 bonds, 66 residues, 3 models selected > hide #1 models > show #1 models > hide #!2 models > show #!2 models > volume zone #2 nearAtoms sel & #1 range 4.98 > volume zone #2 nearAtoms sel & #1 range 2 > select clear > show #!5 models > select clear > save ""D:/YYX/WorkReport/202412/5FAD_6M_Type3_model in map.png"" width 1318 > height 820 supersample 3 transparentBackground true > hide #1 models > hide #!2 models > hide #!5 models > show #9 models > show #!8 models > volume #8 level 0.01121 > volume #8 level 0.01159 > volume #8 level 0.01337 > volume #8 level 0.01273 > volume #8 level 0.01082 > select add #8 2 models selected > surface dust #8 size 8.3 > surface dust #8 size 3 > surface dust #8 size 2 > surface dust #8 size 0 > surface dust #8 size 1 > surface dust #8 size 2 > surface dust #8 size 2.5 > surface dust #8 size 2 > volume #8 level 0.009679 > volume #8 region 0,0,26,287,287,287 > surface dust #8 size 0 > select #8 2 models selected > select clear > volume #8 level 0.01 > volume #8 level 0.015 > volume #8 level 0.013 > volume #8 level 0.01084 > volume #8 level 0.011 > select add #9 1356 atoms, 1374 bonds, 186 residues, 1 model selected > select add #8 1356 atoms, 1374 bonds, 186 residues, 3 models selected > select subtract #8 1356 atoms, 1374 bonds, 186 residues, 1 model selected > volume zone #8 nearAtoms sel & #9 range 4.98 > volume zone #8 nearAtoms sel & #9 range 2 > volume #!8 region all imageMode ""full region"" > volume unzone #!8 > mousemode rightMode ""crop volume"" > select clear > combine #9 > rename #10 ""copy of 5FAD_Type2_1layer_C1_R2_real_space_refined.pdb"" > hide #9 models > hide #!8 models > select #10/D:41@CA 1 atom, 1 residue, 1 model selected > select up 7 atoms, 3 bonds, 5 residues, 1 model selected > select up 32 atoms, 28 bonds, 5 residues, 1 model selected > select up 75 atoms, 71 bonds, 11 residues, 1 model selected > select up 904 atoms, 916 bonds, 124 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear Drag select of 7 atoms, 7 bonds > select clear > show #!8 models > volume zone #8 nearAtoms #10 range 4.98 > volume zone #8 nearAtoms #10 range 2 > select clear > save ""D:/YYX/WorkReport/202412/5FAD_6M_Type2_model in map.png"" width 1318 > height 820 supersample 3 transparentBackground true > hide #!8 models > show #!8 models > show #9 models > hide #10 models > show #10 models > hide #!8 models > hide #9 models > show #!8 models > show #9 models > hide #9 models > hide #10 models > volume #!8 region all imageMode ""full region"" > volume unzone #!8 > mousemode rightMode ""crop volume"" > select add #8 2 models selected > color sel medium purple target acs > select clear > transparency #8 0 > select clear > save D:/YYX/WorkReport/202412/5FAD_6M_Type2_top.png width 1318 height 820 > supersample 3 transparentBackground true > save D:/YYX/WorkReport/202412/5FAD_6M_Type2.png width 1318 height 820 > supersample 3 transparentBackground true > hide #!8 models > show #!8 models > hide #!8 models > show #!6 models > show #7 models > combine #7 > rename #11 ""copy of ApoE4_Type2_1layer_R1_real_space_refined.pdb"" > hide #7 models > hide #!6 models > select add #11/C:28@NZ 1 atom, 2 bonds, 1 residue, 1 model selected > select add #11/E:28@CD 2 atoms, 2 bonds, 2 residues, 1 model selected > select up 6 atoms, 2 bonds, 4 residues, 1 model selected > select up 33 atoms, 29 bonds, 4 residues, 1 model selected > select up 45 atoms, 41 bonds, 7 residues, 1 model selected > select up 904 atoms, 916 bonds, 124 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > show #!6 models > volume #6 level 0.009351 > volume #6 level 0.009474 > select add #11 452 atoms, 458 bonds, 62 residues, 1 model selected > volume zone #6 nearAtoms sel & #11 range 4.98 > volume zone #6 nearAtoms sel & #11 range 2 > select clear > volume #6 level 0.01058 > show #!5 models > hide #!5 models > volume #!6 region all imageMode ""full region"" > volume unzone #!6 > mousemode rightMode ""crop volume"" > volume #6 level 0.009597 > volume #6 level 0.01 > volume #6 level 0.008 > volume #6 level 0.009 > volume #6 level 0.0095 > volume #6 level 0.009 > volume #6 level 0.0092 > volume zone #6 nearAtoms #11 range 4.98 > volume zone #6 nearAtoms #11 range 2 > volume #6 region 0,0,0,287,287,287 > volume #6 level 0.0095 > volume #!6 region all imageMode ""full region"" > volume unzone #!6 > mousemode rightMode ""crop volume"" > volume zone #6 nearAtoms #11 range 4.98 > volume zone #6 nearAtoms #11 range 2 > volume #6 level 0.01184 > volume #6 level 0.0095 > volume #6 level 0.00987 > volume #!6 region all imageMode ""full region"" > volume unzone #!6 > mousemode rightMode ""crop volume"" > volume #6 level 0.01 > volume #6 level 0.098 > volume #6 level 0.0098 > volume #6 level 0.0095 > volume #6 level 0.0098 > volume zone #6 nearAtoms #11 range 4.98 > volume zone #6 nearAtoms #11 range 2 > save D:/YYX/WorkReport/202412/ApoE4_5FAD_Type2.png width 1318 height 820 > supersample 3 transparentBackground true > hide #!6 models > hide #11 models > show #11 models > show #!8 models > hide #!8 models > show #1 models > hide #1 models > show #3 models > hide #3 models > show #9 models > hide #9 models > show #10 models > hide #11 models > show #9 models > hide #9 models > show #!8 models > hide #!8 models > show #9 models > hide #9 models > show #!8 models > color #8 white models > transparency #8,10 80 > hide #!8 models > show #!8 models > volume zone #8 nearAtoms #10 range 4.98 > volume zone #8 nearAtoms #10 range 2 > volume #!8 region all imageMode ""full region"" > volume unzone #!8 > mousemode rightMode ""crop volume"" > hide #!8 models > hide #10 models > show #11 models > hide #11 models > show #1 models > show #!2 models > show #3 models > hide #1 models > hide #!2 models > show #!2 models > hide #3 models > show #1 models > hide #1 models > hide #!2 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #11 models > hide #11 models > show #7 models > show #!6 models > volume #!6 region all imageMode ""full region"" > volume unzone #!6 > mousemode rightMode ""crop volume"" > hide #7 models > show #11 models > volume #6 region 0,0,0,287,287,287 [Repeated 1 time(s)] > hide #!6 models > hide #11 models > show #3 models > hide #3 models > show #!5 models > hide #!5 models > show #7 models > hide #7 models > show #!8 models > show #9 models > volume #8 region 0,0,0,286,287,287 > volume #8 region 0,0,0,285,287,287 > volume #8 region 0,0,0,284,287,287 [Repeated 2 time(s)] > hide #!8 models > hide #9 models > show #11 models > show #7 models > hide #7 models > show #!8 models > hide #!8 models > show #!6 models > hide #11 models > color #6 #00aa0033 models > transparency #6 0 > volume #6 level 0.01264 > volume #6 level 0.012 > volume #6 level 0.01225 > volume #6 level 0.01 > volume #6 level 0.011 > volume #6 level 0.012 > volume #6 level 0.01286 > volume #6 level 0.012 > save D:/YYX/WorkReport/202412/ApoE4_5FAD_Type2_top.png width 1318 height 820 > supersample 3 transparentBackground true > save D:/YYX/WorkReport/202412/ApoE4_5FAD_Type2_side.png width 1318 height > 820 supersample 3 transparentBackground true > color #6 #ffffff33 models > transparency #6 80 > show #11 models > volume zone #6 nearAtoms #11 range 4.98 > volume zone #6 nearAtoms #11 range 2 > save ""D:/YYX/WorkReport/202412/ApoE4_5FAD_Type2_model in map.png"" width 1318 > height 820 supersample 3 transparentBackground true > hide #!6 models > hide #11 models > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!8 models > open > D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type2/5FAD_Type2_3layer_C1_R6.pdb Chain information for 5FAD_Type2_3layer_C1_R6.pdb #12 --- Chain | Description A B C D E F | No description available > style #12 stick Changed 1356 atom styles > show #10 models > hide #12 models > hide #10 models > show #10 models > close #10 > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #9 models > hide #9 models > show #9 models > hide #9 models > show #9 models > close #9 > show #12 models > hide #!8 models > select add #12 1356 atoms, 1374 bonds, 186 residues, 1 model selected > ui tool show ""Color Actions"" > color sel medium purple target acs > color sel byhetero target acs > select clear > combine #12 > hide #9 models > hide #12 models > show #12 models > show #9 models > hide #12 models > hide #9 models > show #9 models > show #!8 models > hide #!8 models > select add #9/D:26@CA 1 atom, 2 bonds, 1 residue, 1 model selected > select up 7 atoms, 3 bonds, 4 residues, 1 model selected > select up 31 atoms, 27 bonds, 4 residues, 1 model selected > select up 85 atoms, 81 bonds, 13 residues, 1 model selected > select up 904 atoms, 916 bonds, 124 residues, 1 model selected > delete atoms sel > delete bonds sel > show #!8 models > show #12 models > hide #12 models > volume zone #8 nearAtoms #9 range 4.98 > volume zone #8 nearAtoms #9 range 2 > save ""D:/YYX/WorkReport/202412/5FAD_6M_Type2_model in map.png"" width 1318 > height 820 supersample 3 transparentBackground true > hide #!8 models > show #12 models > hide #9 models > show #9 models > show #!8 models > hide #9 models > hide #!8 models > open D:/YYX/data/Mice_amyloid/Model/7q4m.pdb 7q4m.pdb title: Type II β-amyloid 42 filaments from human brain [more info...] Chain information for 7q4m.pdb #10 --- Chain | Description | UniProt A B C D E F G H I J | amyloid-β precursor protein | A4_HUMAN Non-standard residues in 7q4m.pdb #10 --- UNX — unknown atom or ion > select add #10 2270 atoms, 2290 bonds, 320 residues, 1 model selected > style sel stick Changed 2270 atom styles > color sel gray > color sel dark gray > ui tool show ""Color Actions"" > color sel byhetero target acs > select clear > hide #10 models > show #10 models > hide #12 models > show #9 models > hide #9 models > show #12 models > hide #10 models > hide #12 models > show #3 models > hide #3 models > show #10 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 226 atoms, 229 bonds, 31 residues, 1 model selected > select clear > hide #10 models > show #!8 models > hide #!8 models > show #9 models > hide #9 models > show #12 models > hide #12 models > show #10 models > hide #10 models > show #12 models > hide #12 models > show #12 models > hide #12 models > show #9 models > hide #9 models > show #9 models > select add #9 452 atoms, 458 bonds, 62 residues, 1 model selected > hide sel atoms > show sel cartoons > show sel surfaces [Repeated 1 time(s)] > hide sel surfaces > show sel surfaces > hide sel surfaces > select clear > show #12 models > hide #!9 models > show #12 cartoons > hide #12 atoms > hide #12 models > show #!9 models > hide #!9 models > show #12 models > show #10 models > ui tool show Distances > select #10/J:28@NZ 1 atom, 1 residue, 1 model selected > select add #10/I:28@O 2 atoms, 2 residues, 1 model selected > distance #10/J:28@NZ #10/I:28@O Distance between 7q4m.pdb #10/J LYS 28 NZ and /I LYS 28 O: 3.126Å > select #10/J:28@NZ 1 atom, 1 residue, 1 model selected > select add #10/I:42@OXT 2 atoms, 2 residues, 1 model selected > distance #10/J:28@NZ #10/I:42@OXT Distance between 7q4m.pdb #10/J LYS 28 NZ and /I ALA 42 OXT: 3.439Å > select #10/J:28@NZ 1 atom, 1 residue, 1 model selected > select #10/G:42@OXT 1 atom, 1 residue, 1 model selected > select add #10/J:28@NZ 2 atoms, 2 residues, 1 model selected > distance #10/G:42@OXT #10/J:28@NZ Distance between 7q4m.pdb #10/G ALA 42 OXT and /J LYS 28 NZ: 2.931Å > select #10/J:28@NZ 1 atom, 1 residue, 1 model selected > select add #10/G:28@O 2 atoms, 2 residues, 1 model selected > distance #10/J:28@NZ #10/G:28@O Distance between 7q4m.pdb #10/J LYS 28 NZ and /G LYS 28 O: 4.564Å > select clear > hide #12 models > show #12 models > hide #10 models > hide #!13 models > hide #13.1 models > select add #12 1356 atoms, 1374 bonds, 186 residues, 1 model selected > select subtract #12 Nothing selected > select add #12 1356 atoms, 1374 bonds, 186 residues, 1 model selected > style sel stick Changed 1356 atom styles > show sel atoms > hide sel cartoons > select clear > select #12/A:28@NZ 1 atom, 1 residue, 1 model selected > select add #12/E:28@O 2 atoms, 2 residues, 1 model selected > distance #12/A:28@NZ #12/E:28@O Distance between 5FAD_Type2_3layer_C1_R6.pdb #12/A LYS 28 NZ and /E LYS 28 O: 5.598Å > distance #12/A:28@NZ #12/E:28@O Distance already exists; modify distance properties with 'distance style' > select clear [Repeated 1 time(s)] > select #12/A:28@NZ 1 atom, 1 residue, 1 model selected > select add #12/E:28@O 2 atoms, 2 residues, 1 model selected > distance #12/A:28@NZ #12/E:28@O Distance already exists; modify distance properties with 'distance style' > show #!13 models > show #13.1 models > select #12/A:28@NZ 1 atom, 1 residue, 1 model selected > select #12/D:28@O 1 atom, 1 residue, 1 model selected > select add #12/A:28@NZ 2 atoms, 2 residues, 1 model selected > distance #12/D:28@O #12/A:28@NZ Distance between 5FAD_Type2_3layer_C1_R6.pdb #12/D LYS 28 O and /A LYS 28 NZ: 3.306Å > select #12/A:28@NZ 1 atom, 1 residue, 1 model selected > select add #12/D:42@OXT 2 atoms, 2 residues, 1 model selected > distance #12/A:28@NZ #12/D:42@OXT Distance between 5FAD_Type2_3layer_C1_R6.pdb #12/A LYS 28 NZ and /D ALA 42 OXT: 3.997Å > hide #12 models > show #10 models > hide #10 models > show #!9 models > hide #!9 models > show #12 models > select #12/A:28@NZ 1 atom, 1 residue, 1 model selected > select add #12/E:42@OXT 2 atoms, 2 residues, 1 model selected > distance #12/A:28@NZ #12/E:42@OXT Distance between 5FAD_Type2_3layer_C1_R6.pdb #12/A LYS 28 NZ and /E ALA 42 OXT: 7.688Å > select clear > show #!8 models > hide #!8 models > show #!8 models > select add #8 2 models selected > volume sel region all imageMode ""full region"" > volume unzone sel > mousemode rightMode ""crop volume"" > select clear > ~distance #10/J:28@NZ #10/I:28@O > ~distance #12/A:28@NZ #12/E:42@OXT > ~distance #10/G:42@OXT #10/J:28@NZ > ~distance #12/A:28@NZ #12/D:42@OXT > ~distance #12/A:28@NZ #12/E:28@O > ~distance #10/J:28@NZ #10/I:42@OXT > ~distance #12/D:28@O #12/A:28@NZ > ~distance #10/J:28@NZ #10/G:28@O > hide #!8 models > hide #12 cartoons > hide #12 atoms > show #12 cartoons > style #12 stick Changed 1356 atom styles > select add #12 1356 atoms, 1374 bonds, 186 residues, 1 model selected > style sel stick Changed 1356 atom styles > hide sel cartoons > show sel atoms > select clear > select #12/F:28@NZ 1 atom, 1 residue, 1 model selected > select clear > show #!8 models > volume #8 level 0.003876 > hide #!2 models > volume #6 level 0.011 > volume #8 level 0.011 > hide #!8 models > show #7 models > hide #12 models > show #!6 models > hide #7 models > show #!8 models > show #!9 models > hide #!6 models > hide #!9 models > show #12 models > volume #8 region 0,0,10,287,287,287 > volume #8 region 0,0,14,287,287,287 > save ""D:/YYX/data/Mice_amyloid/Model/Mouse model.cxs"" includeMaps true Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 299, in process return copy_state(data, convert=convert) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 219, in copy_state return _copy(data) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 207, in _copy return data.copy() numpy.core._exceptions._ArrayMemoryError: Unable to allocate 91.1 MiB for an array with shape (288, 288, 288) and data type uint32 During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> 'segment map' -> '5fad_Type3.seg': Unable to allocate 91.1 MiB for an array with shape (288, 288, 288) and data type uint32 ValueError: error processing: 'tools' -> -> 'segment map' -> '5fad_Type3.seg': Unable to allocate 91.1 MiB for an array with shape (288, 288, 288) and data type uint32 File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 299, in process return copy_state(data, convert=convert) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 219, in copy_state return _copy(data) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 207, in _copy return data.copy() numpy.core._exceptions._ArrayMemoryError: Unable to allocate 91.1 MiB for an array with shape (288, 288, 288) and data type uint32 During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> 'segment map' -> '5fad_Type3.seg': Unable to allocate 91.1 MiB for an array with shape (288, 288, 288) and data type uint32 ValueError: error processing: 'tools' -> -> 'segment map' -> '5fad_Type3.seg': Unable to allocate 91.1 MiB for an array with shape (288, 288, 288) and data type uint32 File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 475.14 OpenGL renderer: NVIDIA GeForce GT 730/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: zh_CN.cp936 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: LENOVO Model: 90L0CTO1WW OS: Microsoft Windows 10 企业版 (Build 19045) Memory: 17,110,429,696 MaxProcessMemory: 137,438,953,344 CPU: 12 AMD Ryzen 5 3600 6-Core Processor OSLanguage: zh-CN Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 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: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 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: 2022.6 pywin32: 303 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 WMI: 1.5.1 zipp: 3.11.0 }}} " defect closed normal Sessions limitation all ChimeraX