id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8703 MemoryError saving session chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 1.5rc202211120143 (2022-11-12 01:43:47 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.5rc202211120143 (2022-11-12) © 2016-2022 Regents of the University of California. All rights reserved. > open C:\\\Users\\\yangx\\\Desktop\\\PhK_figures\\\Extended_fugure\\\beta- > ADP.cxs Opened 1254_global_2.9.mrc as #2, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Log from Mon Mar 13 22:44:38 2023UCSF ChimeraX version: 1.5rc202211120143 (2022-11-12) © 2016-2022 Regents of the University of California. All rights reserved. > open C:\\\Users\\\yangx\\\Desktop\\\PhK_figures\\\Extended_fugure\\\beta- > ADP.cxs Opened 1254_global_2.9.mrc as #2, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Log from Tue Feb 7 16:56:44 2023UCSF ChimeraX version: 1.5rc202211120143 (2022-11-12) © 2016-2022 Regents of the University of California. All rights reserved. > open C:\\\Users\\\yangx\\\Desktop\\\PhK_figures\\\Figure2\\\beta_D1-D5.cxs Opened 1254_global_2.9.mrc as #2, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 0 as #3.1, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 1 as #3.2, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 2 as #3.3, grid size 450,450,450, pixel 1.07, shown at level 0.006, step 1, values float32 Opened 1254_global_2.9.mrc 3 as #3.4, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 4 as #3.5, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 5 as #3.6, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 6 as #3.7, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 7 as #3.8, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 8 as #3.9, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 9 as #3.10, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 10 as #3.11, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Log from Fri Feb 3 18:52:14 2023UCSF ChimeraX version: 1.5rc202211120143 (2022-11-12) © 2016-2022 Regents of the University of California. All rights reserved. > open C:\\\Users\\\yangx\\\Desktop\\\PhK_figures\\\Figure2\\\beta_D1-D5.cxs Opened 1254_global_2.9.mrc as #2, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 0 as #3.1, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 1 as #3.2, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 2 as #3.3, grid size 450,450,450, pixel 1.07, shown at level 0.006, step 1, values float32 Opened 1254_global_2.9.mrc 3 as #3.4, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 4 as #3.5, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 5 as #3.6, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 6 as #3.7, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 7 as #3.8, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 8 as #3.9, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 9 as #3.10, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 10 as #3.11, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Log from Wed Feb 1 10:44:09 2023UCSF ChimeraX version: 1.5rc202211120143 (2022-11-12) © 2016-2022 Regents of the University of California. All rights reserved. > open > C:\\\Users\\\yangx\\\Desktop\\\PhK_figures\\\Figure2\\\beta_far_split.cxs Opened 1254_global_2.9.mrc as #2, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 0 as #3.1, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 1 as #3.2, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 2 as #3.3, grid size 450,450,450, pixel 1.07, shown at level 0.006, step 1, values float32 Opened 1254_global_2.9.mrc 3 as #3.4, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 4 as #3.5, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 5 as #3.6, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 6 as #3.7, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 7 as #3.8, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 8 as #3.9, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 9 as #3.10, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 10 as #3.11, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Log from Tue Jan 31 14:40:14 2023UCSF ChimeraX version: 1.5rc202211120143 (2022-11-12) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > C:\\\ShareCache\\\肖俊宇_1406180305\\\Lab\\\杨晓珂_1801110533\\\5.20220614_hPhK_active_CALM\\\1254_active_Holo_tetramer_23_AGC- > coot-14.pdb Summary of feedback from opening C:\\\ShareCache\\\肖俊宇_1406180305\\\Lab\\\杨晓珂_1801110533\\\5.20220614_hPhK_active_CALM\\\1254_active_Holo_tetramer_23_AGC- coot-14.pdb --- warnings | Start residue of secondary structure not found: HELIX 212 212 VAL A 767 LEU A 770 1 4 Start residue of secondary structure not found: HELIX 233 233 GLY D 8 THR D 21 1 14 Start residue of secondary structure not found: HELIX 234 234 LEU D 23 HIS D 25 1 3 Start residue of secondary structure not found: HELIX 235 235 VAL D 44 SER D 50 1 7 Start residue of secondary structure not found: HELIX 236 236 LEU D 52 ASN D 64 1 13 118 messages similar to the above omitted Chain information for 1254_active_Holo_tetramer_23_AGC-coot-14.pdb #1 --- Chain | Description A | No description available B | No description available C G K O | No description available E I M | No description available F J N | No description available > show cartoons > show atoms > hide atoms > dssp > select /A:6-1221 7587 atoms, 7745 bonds, 3 pseudobonds, 959 residues, 2 models selected > select /A /F /H /J 24364 atoms, 24904 bonds, 7 pseudobonds, 3030 residues, 2 models selected > select clear > select /B:43-1093 8264 atoms, 8450 bonds, 2 pseudobonds, 1023 residues, 2 models selected > select /B:43-1093 8264 atoms, 8450 bonds, 2 pseudobonds, 1023 residues, 2 models selected > select /G:327-380 411 atoms, 420 bonds, 1 pseudobond, 49 residues, 2 models selected > select /G:327-380 411 atoms, 420 bonds, 1 pseudobond, 49 residues, 2 models selected > select /K:327-380 411 atoms, 420 bonds, 1 pseudobond, 49 residues, 2 models selected > select /O:327-380 411 atoms, 420 bonds, 1 pseudobond, 49 residues, 2 models selected > select /E:3-1221 7674 atoms, 7827 bonds, 6 pseudobonds, 970 residues, 2 models selected > select /I:3-1221 7674 atoms, 7827 bonds, 6 pseudobonds, 970 residues, 2 models selected > select /M:3-1221 7674 atoms, 7827 bonds, 6 pseudobonds, 970 residues, 2 models selected > select /F:6-1093 8366 atoms, 8556 bonds, 2 pseudobonds, 1034 residues, 2 models selected > select /J:6-1093 8366 atoms, 8556 bonds, 2 pseudobonds, 1034 residues, 2 models selected > select /N:6-1093 8366 atoms, 8556 bonds, 2 pseudobonds, 1034 residues, 2 models selected > select /b /F /N /J 33449 atoms, 34207 bonds, 8 pseudobonds, 4130 residues, 2 models selected > select /a /c /g /k /o /e /i /m 32313 atoms, 32974 bonds, 25 pseudobonds, 4069 residues, 2 models selected > hide sel cartoons > set bgColor white > lighting soft > select /b 8306 atoms, 8494 bonds, 2 pseudobonds, 1025 residues, 2 models selected > ui tool show ""Color Actions"" > color sel dark green > select /e 7689 atoms, 7844 bonds, 6 pseudobonds, 971 residues, 2 models selected > select /n 8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected > color sel dark sea green > select /f 8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected > color sel lime green > select /j 8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected > color sel medium sea green > select clear > select /j 8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected > color sel lime green > select /n 8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected > select /f 8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected > color sel medium sea green > select clear > select 1101 Expected an objects specifier or a keyword > show atoms > undo > select /b:1101 15 atoms, 14 bonds, 1 residue, 1 model selected > show sel atoms > select /b:1090,1101 21 atoms, 20 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 21 atom styles > color sel byhetero > select /b:1090,1101 /f:1090,1101 /n:1090,1101 /j:1090,1101 84 atoms, 80 bonds, 8 residues, 1 model selected > show sel atoms > style sel stick Changed 84 atom styles > color sel byhetero > select clear > select /a /c /g /k /o /e /i /m 32313 atoms, 32974 bonds, 25 pseudobonds, 4069 residues, 2 models selected > show sel cartoons > select /a /e /i /m 30669 atoms, 31294 bonds, 21 pseudobonds, 3873 residues, 2 models selected > ui tool show ""Color Actions"" > color sel goldenrod > select /c /g /k /o 1644 atoms, 1680 bonds, 4 pseudobonds, 196 residues, 2 models selected > color sel medium turquoise > select /a:1220,1301 /e:1220,1301 /i:1220,1301 /m:1220,1301 84 atoms, 88 bonds, 8 residues, 1 model selected > show sel atoms > style sel stick Changed 84 atom styles > color sel byhetero > select clear > select /a /c /g /k /o /e /i /m 32313 atoms, 32974 bonds, 25 pseudobonds, 4069 residues, 2 models selected > hide sel cartoons > show sel cartoons > select clear > show surfaces > hide surfaces > select /a /c /g /k /o /e /i /m 32313 atoms, 32974 bonds, 25 pseudobonds, 4069 residues, 2 models selected > hide sel cartoons > hide sel atoms > select up 65762 atoms, 67181 bonds, 33 pseudobonds, 8199 residues, 10 models selected > select down 32313 atoms, 32974 bonds, 25 pseudobonds, 4069 residues, 14 models selected > select /b:1090,1101 /f:1090,1101 /n:1090,1101 /j:1090,1101 84 atoms, 80 bonds, 8 residues, 1 model selected > show sel surfaces > hide sel surfaces > open C:/Users/yangx/Desktop/5.20220614_hPhK_active_CALM/1254_global_2.9.mrc Opened 1254_global_2.9.mrc as #2, grid size 450,450,450, pixel 1.07, shown at level 0.000934, step 2, values float32 > volume #2 step 1 > volume #2 level 0.05581 > color (#!1 & sel) light gray > ui tool show ""Color Zone"" > color zone #2 near #1 distance 6.42 > volume #2 level 0.09913 > volume #2 level 0.2074 > volume #2 level 0.06935 > volume #2 level 0.07205 > color zone #2 near #1 distance 5 > volume splitbyzone #2 Opened 1254_global_2.9.mrc 0 as #3.1, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 1 as #3.2, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 2 as #3.3, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 3 as #3.4, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 4 as #3.5, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 5 as #3.6, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 6 as #3.7, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 7 as #3.8, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 8 as #3.9, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 9 as #3.10, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 Opened 1254_global_2.9.mrc 10 as #3.11, grid size 450,450,450, pixel 1.07, shown at level 0.0721, step 1, values float32 > hide #!3 models > show #!3 models > hide #!3.2 models > hide #!3.4 models > hide #!3.5 models > hide #!3.8 models > hide #!3.9 models > hide #!3.10 models > hide #!3.11 models > hide #!3.7 models > hide #!3.6 models > hide #!3 models > hide #!3.1 models > show #!3.1 models > hide #!3 models > show #!3 models > hide #!3.1 models > hide #!3 models > show #!3 models > volume #3.3 level 0.01407 > select clear > volume #3.3 level 0.009991 > volume #3.3 level 0.008 > volume #3.3 level 0.005 > volume #3.3 level 0.002 > ui tool show ""Hide Dust"" > surface dust #3.3 size 6.42 > surface dust #3.3 size 4.73 > surface dust #3.3 size 3.06 > surface dust #3.3 size 2.76 > surface dust #3.3 size 2.78 > surface dust #3.3 size 2.8 > surface dust #3.3 size 2.82 > surface dust #3.3 size 2.43 > surface dust #3.3 size 2.73 [Repeated 1 time(s)] > volume #3.3 level 0.006 > save C:/Users/yangx/Desktop/PhK_figures/Figure2/beta_far_split.cxs > includeMaps true ——— End of log from Tue Jan 31 14:40:14 2023 ——— opened ChimeraX session > ui mousemode right ""pick blobs"" > select /N:1045 8 atoms, 7 bonds, 1 residue, 1 model selected > select /N:1046 9 atoms, 8 bonds, 1 residue, 1 model selected > ui mousemode right ""pick blobs"" [Repeated 1 time(s)] > ui mousemode right ""translate selected atoms"" > ui mousemode right pivot [Repeated 1 time(s)] > ui mousemode right ""translate selected atoms"" > ui mousemode right pivot > ui mousemode right ""pick blobs"" [Repeated 1 time(s)] > undo [Repeated 2 time(s)] > select clear > interfaces ~solvent 16 buried areas: N B 1845, M O 1775, E G 1775, I K 1775, F J 1768, A C 1720, B A 1642, J I 1502, N M 1492, F E 1481, F A 1117, N I 961, J M 941, B E 921, J N 828, F B 822 > ui dockable true ""Chain Contacts"" > hide sel cartoons > hide #!3 models > hide sel atoms > hide sel cartoons > hide sel atoms > show sel surfaces > ui tool show ""Color Actions"" > color sel dark green > select clear > lighting soft > lighting full > lighting simple > lighting soft > ui windowfill toggle > undo > show sel cartoons > save C:/Users/yangx/Desktop/PhK_figures/Figure2/beta4.cxs > hide sel cartoons > hide sel atoms > hide sel surfaces > select /f:1090 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel cartoons > select clear > select /f:1090 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel cartoons > show sel atoms > select clear [Repeated 2 time(s)] > select /F:1090 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > ui tool show ""Color Actions"" > color sel medium sea green > select clear > select /f:43-480 3546 atoms, 3636 bonds, 438 residues, 1 model selected > color sel teal > select /f:481-690 1694 atoms, 1728 bonds, 210 residues, 1 model selected > color sel steel blue > select /f:709-778 553 atoms, 561 bonds, 70 residues, 1 model selected > select /f:481-690 1694 atoms, 1728 bonds, 210 residues, 1 model selected > color sel steel blue > select /f:709-778 553 atoms, 561 bonds, 70 residues, 1 model selected > color sel cadet blue > select /f:779-917 1117 atoms, 1145 bonds, 139 residues, 1 model selected > color sel light slate gray > select /f:924-1080 1283 atoms, 1306 bonds, 157 residues, 1 model selected > color sel slate gray > select clear > select /f:924-1080 1283 atoms, 1306 bonds, 157 residues, 1 model selected > color sel slate gray > color sel light slate gray > color sel slate gray > color sel medium aquamarine > color sel cornflower blue > color sel dark cyan > color sel medium aquamarine > color sel royal blue > color sel indigo > color sel slate gray > color sel medium blue > color sel dark blue > color sel cadet blue > color sel medium aquamarine > select clear > save C:/Users/yangx/Desktop/PhK_figures/Figure2/beta_D1-D5.cxs ——— End of log from Wed Feb 1 10:44:09 2023 ——— opened ChimeraX session > select /b:43-480 /f:43-480 /n:43-480 /j:43-480 14184 atoms, 14544 bonds, 1752 residues, 1 model selected > ui tool show ""Color Actions"" > color sel teal > select /b:481-690 /f:481-690 /n:481-690 /j:481-690 6714 atoms, 6848 bonds, 1 pseudobond, 832 residues, 2 models selected > select /b:709-778 /f:709-778 /n:709-778 /j:709-778 2199 atoms, 2231 bonds, 278 residues, 1 model selected > color sel cadet blue > select /a:748-822 /e:748-822 /m:748-822 /i:748-822 1689 atoms, 1712 bonds, 7 pseudobonds, 207 residues, 2 models selected > select /b:779-917 /f:779-917 /n:779-917 /j:779-917 4468 atoms, 4580 bonds, 556 residues, 1 model selected > color sel sea green > select /b:924-1080 /f:924-1080 /n:924-1080 /j:924-1080 5132 atoms, 5224 bonds, 628 residues, 1 model selected > color sel cornflower blue > select /b:918-923,1081-1093 /f:918-923,1081-1093 /n:918-923,1081-1093 > /j:918-923,1081-1093 584 atoms, 584 bonds, 76 residues, 1 model selected > color sel cornflower blue > select /b:1090,1101 /f:1090,1101 /n:1090,1101 /j:1090,1101 84 atoms, 80 bonds, 8 residues, 1 model selected > show sel atoms > hide sel atoms > select /f:1090,1101 21 atoms, 20 bonds, 2 residues, 1 model selected > show sel atoms > color sel cornflower blue > color (#!1 & sel) byhetero > select clear > select /f 8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected > view sel > select clear > save C:/Users/yangx/Desktop/PhK_figures/Figure2/beta_D1-D5.cxs ——— End of log from Fri Feb 3 18:52:14 2023 ——— opened ChimeraX session > show #!3 models > hide #!3 models > ui tool show ""Color Zone"" > color zone #2 near #1 distance 1.07 > close #3 > show #!2 models > color zone #2 near #1 distance 1.07 [Repeated 1 time(s)] > color zone #2 near #1 distance 6 > select /b:6 27 atoms, 29 bonds, 1 residue, 1 model selected > show sel atoms > select /f：6 Expected an objects specifier or a keyword > show sel atoms > hide #!2 models > select /f:6 27 atoms, 29 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 27 atom styles > select /b:6 27 atoms, 29 bonds, 1 residue, 1 model selected > hide sel atoms > select /f:6 27 atoms, 29 bonds, 1 residue, 1 model selected > color (#!1 & sel) gray > show #!2 models > color zone #2 near #1 distance 6 > transparency (#!1 & sel) 70 > select clear > transparency 70 > hide cartoons > select /b: 556,578,579,795,798,799,859,211,213,214,274 105 atoms, 103 bonds, 11 residues, 1 model selected > show sel atoms > hide sel atoms > select /f: 556,578,579,795,798,799,859,211,213,214,274 105 atoms, 103 bonds, 11 residues, 1 model selected > show sel atoms > style sel stick Changed 105 atom styles > color (#!1 & sel) byhetero > lighting full > lighting shadows false > select /f:6 27 atoms, 29 bonds, 1 residue, 1 model selected > color (#!1 & sel) byhetero > select clear > show cartoons > transparency 30 cartoons > select #2 4 models selected > select #2 4 models selected > select up 65762 atoms, 67181 bonds, 8199 residues, 5 models selected > select up 65762 atoms, 67181 bonds, 33 pseudobonds, 8199 residues, 18 models selected > select #2 4 models selected > select /f:43-100 453 atoms, 464 bonds, 58 residues, 1 model selected > hide sel cartoons > select #2 4 models selected > select #2 4 models selected > select clear > save C:/Users/yangx/Desktop/PhK_figures/Extended_fugure/beta-ADP.tif width > 1857 height 1168 supersample 3 > save C:/Users/yangx/Desktop/PhK_figures/Extended_fugure/beta-ADP.cxs ——— End of log from Tue Feb 7 16:56:44 2023 ——— opened ChimeraX session > ui tool show ""Hide Dust"" > surface dust #2 size 6.42 > surface dust #2 size 4.05 > save C:/Users/yangx/Desktop/PhK_figures/Extended_fugure/beta-ADP.tif width > 1965 height 1152 supersample 3 > save C:/Users/yangx/Desktop/PhK_figures/Extended_fugure/beta-ADP.cxs ——— End of log from Mon Mar 13 22:44:38 2023 ——— opened ChimeraX session > close #2 > open C:/Users/yangx/Desktop/1254_global_2.9_bin_.mrc Opened 1254_global_2.9_bin_.mrc as #2, grid size 900,900,900, pixel 0.535, shown at step 1, values float32 > volume #2 region 0,0,0,899,899,899 step 4 [Repeated 1 time(s)] > volume #2 change image level -0.0004992,0 level 0.004475,0.8 level 1.271,1 > volume #2 level 0.06899 > volume #2 step 1 > ui tool show ""Hide Dust"" > surface dust #2 size 13.57 > surface dust #2 size 5.62 > volume #2 level 0.05 > volume #2 level 0.06 > volume #2 level 0.07 > ui tool show ""Color Zone"" > color zone #2 near #1 distance 5 > color single #2 > hide atoms > color zone #2 near #1 distance 5 > color single #2 > undo [Repeated 2 time(s)] > color single #2 > hide #!1 models > show #!1 models > hide #!2 models > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 2 models selected > color (#!1 & sel) light gray > color (#!1 & sel) gray > select clear > select /f:1-480 3573 atoms, 3665 bonds, 1 pseudobond, 439 residues, 2 models selected > ui tool show ""Color Actions"" > color sel teal > select /f:481-690 1694 atoms, 1728 bonds, 210 residues, 1 model selected > color sel steel blue > select /f:709-778 553 atoms, 561 bonds, 70 residues, 1 model selected > color sel cadet blue > select /f:779-917 1117 atoms, 1145 bonds, 139 residues, 1 model selected > color sel cadet blue > select /f:709-778 553 atoms, 561 bonds, 70 residues, 1 model selected > color sel medium sea green > select /F:6@C2' 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 2 models selected > color sel gray > show #!2 models > color zone #2 near #1 distance 5 > select clear > transparency #1#2.2#!2 40 > transparency #1#2.2#!2 60 > transparency #1#2.2#!2 50 > transparency 0 cartoons > transparency 10 cartoons > select clear > color #1#2.2#!2 byhetero > select clear > volume #2 level 0.08 > undo > color zone #2 near #1 distance 5 > color single #2 > volume #2 level 0.09 > surface dust #2 size 9 > surface dust #2 size 1 > surface dust #2 size 10 > surface dust #2 size 1 > surface dust #2 size 15 > surface dust #2 size 1 > surface dust #2 size 10 > hide #!2 models > select /f:709-778 553 atoms, 561 bonds, 70 residues, 1 model selected > ui tool show ""Color Actions"" > color sel medium sea green > select /f:779-917 1117 atoms, 1145 bonds, 139 residues, 1 model selected > color sel cadet blue > select /f:481-690 1694 atoms, 1728 bonds, 210 residues, 1 model selected > color sel steel blue > select /f:30-480 3546 atoms, 3636 bonds, 438 residues, 1 model selected > color sel teal > select /F:6@C2' 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 2 models selected > color sel gray > show #!2 models > color zone #2 near #1 distance 5 > select clear > color #1#2.2#!2 byhetero > transparency #1#2.2#!2 50 > select /f 8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected > select ~sel 57381 atoms, 58610 bonds, 31 pseudobonds, 7164 residues, 6 models selected > color (#!1 & sel) light gray > color zone #2 near #1 distance 5 > undo [Repeated 4 time(s)] > select /f 8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected > select ~sel 57381 atoms, 58610 bonds, 31 pseudobonds, 7164 residues, 6 models selected > color (#!1 & sel) light gray > color zone #2 near #1 distance 5 > select /f:918-1101 1444 atoms, 1469 bonds, 177 residues, 1 model selected > ui tool show ""Color Actions"" > color sel sea green > color zone #2 near #1 distance 5 > volume splitbyzone #2 Opened 1254_global_2.9_bin_.mrc 0 as #3.1, grid size 900,900,900, pixel 0.535, shown at level 0.09, step 1, values float32 Opened 1254_global_2.9_bin_.mrc 1 as #3.2, grid size 900,900,900, pixel 0.535, shown at level 0.09, step 1, values float32 Opened 1254_global_2.9_bin_.mrc 2 as #3.3, grid size 900,900,900, pixel 0.535, shown at level 0.09, step 1, values float32 Opened 1254_global_2.9_bin_.mrc 3 as #3.4, grid size 900,900,900, pixel 0.535, shown at level 0.09, step 1, values float32 Opened 1254_global_2.9_bin_.mrc 4 as #3.5, grid size 900,900,900, pixel 0.535, shown at level 0.09, step 1, values float32 Opened 1254_global_2.9_bin_.mrc 5 as #3.6, grid size 900,900,900, pixel 0.535, shown at level 0.09, step 1, values float32 Opened 1254_global_2.9_bin_.mrc 6 as #3.7, grid size 900,900,900, pixel 0.535, shown at level 0.09, step 1, values float32 Opened 1254_global_2.9_bin_.mrc 7 as #3.8, grid size 900,900,900, pixel 0.535, shown at level 0.09, step 1, values float32 > hide #!3.1 models > hide #!3.2 models > hide #!3.3 models > show #!3.3 models > hide #!3.4 models > show #!3.4 models > hide #!3.5 models > show #!3.5 models > hide #!3.7 models > show #!3.7 models > hide #!3.5 models > show #!3.5 models > hide #!3.6 models > hide #!3.8 models > hide sel cartoons [Repeated 1 time(s)] > select clear > hide cartoons > surface dust #3.8 size 7.77 > surface dust #3.7 size 5.84 > surface dust #3.6 size 3.21 > surface dust #3.6 size 3.19 > surface dust #3.6 size 3.17 > surface dust #3.6 size 3.15 > surface dust #3.6 size 3.13 > surface dust #3.6 size 3.11 > surface dust #3.6 size 3.09 > surface dust #3.6 size 3.07 > surface dust #3.6 size 3.05 > surface dust #3.6 size 3.03 > surface dust #3.6 size 3.01 > surface dust #3.6 size 2.96 > surface dust #3.6 size 7.49 > surface dust #3.5 size 6.9 > surface dust #3.4 size 3.21 > surface dust #3.4 size 7.41 > transparency #1#3.3-5,7#!3 50 > select clear > select /f 8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected > show sel cartoons > select clear > size stickRadius +.1 Changed 67181 bond radii > setattr p radius 0 Assigning radius attribute to 33 items > surface dust #3.3 size 3.21 > color #1#3.3-5,7#!3 byhetero > select clear > save C:/Users/yangx/Desktop/PhK_figures/2-Extended_Figure/beta-ADP.tif width > 1823 height 1168 supersample 3 > save C:/Users/yangx/Desktop/PhK_figures/2-Extended_Figure/beta-ADP.cxs Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: 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 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 0' -> 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: 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 0' -> : Error while saving session data for 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 0' -> ValueError: error processing: 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 0' -> : Error while saving session data for 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 0' -> 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 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: 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 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 0' -> 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: 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 0' -> : Error while saving session data for 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 0' -> ValueError: error processing: 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 0' -> : Error while saving session data for 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 0' -> 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. > save C:/Users/yangx/Desktop/PhK_figures/2-Extended_Figure/beta-ADP.cxs > includeMaps true Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: 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 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 1' -> 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: 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 1' -> : Error while saving session data for 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 1' -> ValueError: error processing: 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 1' -> : Error while saving session data for 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 1' -> 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 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: 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 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 1' -> 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: 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 1' -> : Error while saving session data for 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 1' -> ValueError: error processing: 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 1' -> : Error while saving session data for 'models' -> -> 'surface' -> '1254_global_2.9_bin_.mrc 1' -> 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 496.13 OpenGL renderer: NVIDIA GeForce RTX 3060 Ti/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: ASUS Model: System Product Name OS: Microsoft Windows 11 专业版 (Build 22621) Memory: 17,061,335,040 MaxProcessMemory: 137,438,953,344 CPU: 12 AMD Ryzen 5 5600X 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: 1.5rc202211120143 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: 1.6.3 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: 5.0.0 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: 5.0.0 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: 3.0.32 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: 0.6.1 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.12 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 WMI: 1.5.1 zipp: 3.10.0 }}} " defect closed normal Sessions limitation all ChimeraX