id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2936 MemoryError saving session chimerax-bug-report@… Greg Couch "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.91 (2019-12-23) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:\\\Users\\\Anthony Bochler\\\Desktop\\\Thèse\\\Images\\\ribo-TC- > yeast-coli.cxs"" opened ChimeraX session > open ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/PDB/43s+ddx- > noATP+GMP-1704.pdb"" Summary of feedback from opening C:/Users/Anthony Bochler/Desktop/Thèse/Images/PDB/43s+ddx-noATP+GMP-1704.pdb --- warnings | Ignored bad PDB record found on line 635 TER ***** ZN e 301 Duplicate atom serial number found: 26426 Ignored bad PDB record found on line 136188 TER ***** U 02323 Chain information for 43s+ddx-noATP+GMP-1704.pdb #5 --- Chain | Description 0 | No description available 1 | No description available 5 | No description available 8 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available f | No description available g | No description available h | No description available i | No description available j | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available y | No description available > hide #!2 models > hide #5.1 models > show #5.1 models > select #5.1 10 pseudobonds, 1 model selected > select #5/W:56@CG2 1 atom, 1 model selected > ui mousemode rightMode pivot > select #5/W:51@O 1 atom, 1 model selected > select #5/0:1326@C5' 1 atom, 1 model selected > select up 23 atoms, 25 bonds, 1 model selected > select up 45795 atoms, 51207 bonds, 1 model selected > color #5/0 white > select #5/C:107@N 1 atom, 1 model selected > select up 66 atoms, 62 bonds, 1 model selected > select up 694 atoms, 704 bonds, 1 model selected > select up 22489 atoms, 22898 bonds, 1 model selected > color #5/0 #eb0026 > color #5/0 white > color sel #eb0026 > select #5/A:8@CG2 1 atom, 1 model selected > select up 8 atoms, 7 bonds, 1 model selected > select up 330 atoms, 341 bonds, 1 model selected > select up 3894 atoms, 3974 bonds, 1 model selected > color sel #ffa100 > select #5/Y:312@NH2 1 atom, 1 model selected > select up 11 atoms, 10 bonds, 1 model selected > select up 193 atoms, 192 bonds, 1 model selected > select #5/5:339@CG1 1 atom, 1 model selected > select up 7 atoms, 6 bonds, 1 model selected > select up 48 atoms, 49 bonds, 1 model selected > select up 3246 atoms, 3304 bonds, 1 model selected > color sel orange > select #5/1:62@O2' 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > select up 1606 atoms, 1798 bonds, 1 model selected > color sel #c70066 > select #5/V:70@CG2 1 atom, 1 model selected > select up 7 atoms, 6 bonds, 1 model selected > select up 110 atoms, 112 bonds, 1 model selected > select up 790 atoms, 800 bonds, 1 model selected > select #5/n:161@N 1 atom, 1 model selected > select up 9 atoms, 8 bonds, 1 model selected > select up 39 atoms, 38 bonds, 1 model selected > select up 1798 atoms, 1820 bonds, 1 model selected > color sel red > select #5/V:51@CE2 1 atom, 1 model selected > select up 11 atoms, 11 bonds, 1 model selected > select up 70 atoms, 70 bonds, 1 model selected > select up 790 atoms, 800 bonds, 1 model selected > color sel #30ffc7 > select #5/C:106@O 1 atom, 1 model selected > select up 13404 atoms, 13560 bonds, 1 model selected > select up 16831 atoms, 17131 bonds, 1 model selected > select up 26383 atoms, 26872 bonds, 1 model selected > color sel #ff0d0d > select #5/n:239@N 1 atom, 1 model selected > select up 8 atoms, 7 bonds, 1 model selected > select up 45 atoms, 46 bonds, 1 model selected > select up 1798 atoms, 1820 bonds, 1 model selected > color sel #a62929 > select #5/0:48@N2 1 atom, 1 model selected > select up 23 atoms, 25 bonds, 1 model selected > select up 45795 atoms, 51207 bonds, 1 model selected > select #5/Y:253@CG1 1 atom, 1 model selected > select up 8 atoms, 7 bonds, 1 model selected > select up 77 atoms, 76 bonds, 1 model selected > select up 1388 atoms, 1407 bonds, 1 model selected > color sel #00ab24 > select #5/w:150@CA 1 atom, 1 model selected > select up 9 atoms, 8 bonds, 1 model selected > select up 469 atoms, 475 bonds, 1 model selected > select up 1162 atoms, 1177 bonds, 1 model selected > color sel #3050f8 > select clear > save session ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/ribo-TC-yeast- > coli.cxs"" > select #5/a:50@CD 1 atom, 1 model selected > select up 115 atoms, 104 bonds, 1 model selected > select up 1950 atoms, 1969 bonds, 1 model selected > select up 14750 atoms, 15004 bonds, 1 model selected > select up 14769 atoms, 15021 bonds, 1 model selected > select up 14949 atoms, 15205 bonds, 1 model selected > select up 18149 atoms, 18472 bonds, 1 model selected > color sel #575961 > select #5/f:254@C 1 atom, 1 model selected > select up 9 atoms, 8 bonds, 1 model selected > select up 58 atoms, 60 bonds, 1 model selected > select up 12259 atoms, 12512 bonds, 1 model selected > hide #5/f > select #5/y:101@CB 1 atom, 1 model selected > select up 25 atoms, 22 bonds, 1 model selected > select up 287 atoms, 288 bonds, 1 model selected > select up 2768 atoms, 2817 bonds, 1 model selected > select up 2777 atoms, 2825 bonds, 1 model selected > select up 3089 atoms, 3144 bonds, 1 model selected > select up 3884 atoms, 3954 bonds, 1 model selected > select up 3893 atoms, 3962 bonds, 1 model selected > select up 4089 atoms, 4160 bonds, 1 model selected > select up 4514 atoms, 4595 bonds, 1 model selected > select up 4525 atoms, 4605 bonds, 1 model selected > select up 4540 atoms, 4620 bonds, 1 model selected > select up 6296 atoms, 6405 bonds, 1 model selected > color sel #575961 > select #5/c:21@CG2 1 atom, 1 model selected > select up 7 atoms, 6 bonds, 1 model selected > select up 125 atoms, 126 bonds, 1 model selected > select up 480 atoms, 488 bonds, 1 model selected > select up 530 atoms, 534 bonds, 1 model selected > select up 813 atoms, 821 bonds, 1 model selected > select up 8036 atoms, 8175 bonds, 1 model selected > color sel #575961 > select #5/b:44@CE1 1 atom, 1 model selected > select up 10 atoms, 10 bonds, 1 model selected > select up 94 atoms, 95 bonds, 1 model selected > select up 1019 atoms, 1037 bonds, 1 model selected > select up 136895 atoms, 144093 bonds, 1 model selected > select down 1019 atoms, 1037 bonds, 1 model selected > color sel #575961 > select #5/Q:13@CA 1 atom, 1 model selected > select up 56 atoms, 51 bonds, 1 model selected > select up 678 atoms, 685 bonds, 1 model selected > color sel #575961 > select up 2587 atoms, 2626 bonds, 1 model selected > color sel #575961 > select clear > save session ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/ribo-TC-yeast- > coli.cxs"" > lighting full > lighting soft > select #5/U:102@CG 1 atom, 1 model selected > select up 8 atoms, 7 bonds, 1 model selected > select up 100 atoms, 99 bonds, 1 model selected > select up 526 atoms, 527 bonds, 1 model selected > color sel #575961 > select clear Expected a keyword > save image eIFs-colored.tiff format tiff transparentBackground true [Errno 13] Permission denied: 'eIFs-colored.tiff' > style #!5 ball Changed 136895 atom styles > style #!5 stick Changed 136895 atom styles > style #!5 sphere Changed 136895 atom styles > save image eIFs-colored.tiff transparentBackground true [Errno 13] Permission denied: 'eIFs-colored.tiff' > save image ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/eIFs-colored- > parasite.tif"" width 1341 height 825 > set bgColor white > set bgColor gray > set bgColor white > set bgColor transparent > save image ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/eIFs-colored- > parasite.tif"" width 1341 height 825 > set bgColor white > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting soft > lighting full > lighting simple > lighting soft > lighting full > lighting soft > lighting full > lighting soft > lighting full > lighting soft > lighting full > lighting soft > lighting full > lighting soft > lighting full > lighting shadows false > lighting full > lighting shadows false > lighting shadows true > save image ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/eIFs-colored- > parasite.tif"" width 1341 height 825 > save image ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/eIFs-colored- > parasite-90°.tif"" width 1341 height 825 > select #5 136895 atoms, 144093 bonds, 10 pseudobonds, 2 models selected > show sel surfaces > select #5/f:1296@CA 1 atom, 1 model selected > hide #5/f Expected ',' or a keyword > select #5/f:1302@ND2 1 atom, 1 model selected > select up 8 atoms, 7 bonds, 2 models selected > select up 134 atoms, 136 bonds, 2 models selected > select up 12259 atoms, 12512 bonds, 2 models selected Expected ',' or a keyword Expected ',' or a keyword Expected ',' or a keyword > hide sel > surface hide #5/f > hide #!5 models > show #!4 models > select #4/C1:540@C3' 1 atom, 1 model selected > select up 23 atoms, 25 bonds, 1 model selected > select up 38107 atoms, 42619 bonds, 1 model selected > select up 38814 atoms, 42619 bonds, 1 model selected > color sel #ffd123 > show sel surfaces > show sel surfaces > view > hide #4/C1 > select clear > select #4/C1:528@C6 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 2 models selected > select up 38107 atoms, 42619 bonds, 2 models selected > select up 38814 atoms, 42619 bonds, 2 models selected > color sel #ffd123 > select clear > select #4/D1:3028@C5' 1 atom, 1 model selected > select up 23 atoms, 25 bonds, 2 models selected > hide #4/D1 > select up 68577 atoms, 76764 bonds, 2 models selected > select up 70152 atoms, 76764 bonds, 2 models selected > color sel #006bff > color sel #2194D6 > select clear > select #4/DC:340@CB 1 atom, 1 model selected > select up 5 atoms, 4 bonds, 2 models selected > select up 641 atoms, 639 bonds, 2 models selected > select up 1798 atoms, 1789 bonds, 2 models selected > select up 1888 atoms, 1867 bonds, 17 models selected > select up 6042 atoms, 6322 bonds, 17 models selected > select up 15177 atoms, 15372 bonds, 17 models selected > select up 15244 atoms, 15425 bonds, 26 models selected > select up 19117 atoms, 19690 bonds, 26 models selected > select up 23147 atoms, 23641 bonds, 26 models selected > color sel #d9ffff > select up 23157 atoms, 23649 bonds, 28 models selected > select up 23256 atoms, 23748 bonds, 28 models selected > select up 24556 atoms, 25048 bonds, 28 models selected > select up 24582 atoms, 25063 bonds, 32 models selected > select up 25174 atoms, 25655 bonds, 32 models selected > select up 28843 atoms, 29315 bonds, 32 models selected > color sel #d9ffff > select up 28853 atoms, 29323 bonds, 35 models selected > select up 28888 atoms, 29358 bonds, 35 models selected > select up 29188 atoms, 29658 bonds, 35 models selected > color sel #d9ffff > select #4/B2,B3 6086 atoms, 6629 bonds, 305 pseudobonds, 3 models selected > select #4/B2 2649 atoms, 2883 bonds, 158 pseudobonds, 3 models selected > select #4/D2 2642 atoms, 2883 bonds, 150 pseudobonds, 3 models selected > color sel #2194D6 > select #4/D3 3437 atoms, 3746 bonds, 148 pseudobonds, 3 models selected > color sel #2194D6 > select #4/Cd:91@CB 1 atom, 1 model selected > select up 70 atoms, 56 bonds, 15 models selected > select up 1375 atoms, 1359 bonds, 15 models selected > select up 10214 atoms, 10181 bonds, 15 models selected > select up 10233 atoms, 10196 bonds, 19 models selected > select up 10730 atoms, 10693 bonds, 19 models selected > select up 11848 atoms, 11811 bonds, 19 models selected > color sel #ffff30 > color sel #ffd98f > select #4/Dg:85@CA 1 atom, 1 model selected > select up 35 atoms, 28 bonds, 8 models selected > select up 717 atoms, 709 bonds, 8 models selected > select up 2961 atoms, 2932 bonds, 8 models selected > color sel #ffd98f > select up 309610 atoms, 331239 bonds, 8 models selected > select down 2961 atoms, 2932 bonds, 67 models selected > select #4/CJ:24@CB 1 atom, 1 model selected > select up 5 atoms, 4 bonds, 2 models selected > select up 142 atoms, 141 bonds, 2 models selected > select up 658 atoms, 657 bonds, 2 models selected > color sel #ffd98f > select #4/CF:69@CA 1 atom, 1 model selected > select up 5 atoms, 4 bonds, 2 models selected > select up 24 atoms, 23 bonds, 2 models selected > select up 382 atoms, 381 bonds, 2 models selected > color sel #ffd98f > select clear > select #4/Di:12@CA 1 atom, 1 model selected > select up 5 atoms, 4 bonds, 2 models selected > select up 25 atoms, 24 bonds, 2 models selected > select up 60 atoms, 59 bonds, 2 models selected > color sel #ffff30 > color sel #d9ffff > select clear > select #4/C1:440@N3 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 2 models selected > select up 38107 atoms, 42619 bonds, 2 models selected > select clear > graphics silhouettes false > graphics silhouettes true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting full > lighting soft > lighting full > lighting simple > lighting soft > lighting full > lighting soft > show #!2 models > hide #!2 models > lighting full > lighting soft > lighting full > lighting soft > lighting full > lighting soft > lighting full > lighting soft > save image 80S-yeast.tiff format tiff transparentBackground true [Errno 13] Permission denied: '80S-yeast.tiff' > save image 80S-yeast.tiff format tiff transparentBackground true [Errno 13] Permission denied: '80S-yeast.tiff' > save image 80S-yeast.tif format tiff transparentBackground true [Errno 13] Permission denied: '80S-yeast.tif' > save image ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/80S-yeast.tif"" > width 1341 height 825 Expected an axis vector or a keyword > turn x 180 > turn y 180 > save image ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/80S-yeast-180.tif"" > width 1341 height 802 > toolshed show ""Side View"" > lighting full > lighting soft > save image ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/80S-yeast-EPA- > sites.tif"" width 1341 height 802 > save session ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/80S-yeast-EPA- > sites.cxs"" > save session ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/80S-yeast-SSU- > side.cxs"" > save image ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/80S-yeast-SSU- > side.tif"" width 1341 height 802 > hide #!4 models > show #!3 models Unknown command: load 5LI0 > open 5LI0 Summary of feedback from opening 5LI0 fetched from pdb --- notes | Fetching compressed mmCIF 5li0 from http://files.rcsb.org/download/5li0.cif Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif Fetching CCD O from http://ligand-expo.rcsb.org/reports/O/O/O.cif Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif 5li0 title: 70S ribosome from Staphylococcus aureus [more info...] Chain information for 5li0 #6 --- Chain | Description 0 | 50S ribosomal protein L28 1 | 50S ribosomal protein L29 2 | 50S ribosomal protein L30 3 | 50S ribosomal protein L31 type B 4 | 50S ribosomal protein L32 5 | 50S ribosomal protein L33 2 6 | 50S ribosomal protein L34 7 | 50S ribosomal protein L35 8 | 50S ribosomal protein L36 A | 23S ribosomal RNA B | 5S ribosomal RNA D | 50S ribosomal protein L2 E | 50S ribosomal protein L3 F | 50S ribosomal protein L4 G | 50S ribosomal protein L5 H | 50S ribosomal protein L6 M | 50S ribosomal protein L13 N | 50S ribosomal protein L14 O | 50S ribosomal protein L15 P | 50S ribosomal protein L16 Q | 50S ribosomal protein L17 R | 50S ribosomal protein L18 S | 50S ribosomal protein L19 T | 50S ribosomal protein L20 U | 50S ribosomal protein L21 V | 50S ribosomal protein L22 W | 50S ribosomal protein L23 X | 50S ribosomal protein L24 Y | 50S ribosomal protein L25 Z | 50S ribosomal protein L27 a | 16S ribosomal RNA b | 30S ribosomal protein S2 c | 30S ribosomal protein S3 d | 30S ribosomal protein S4 e | 30S ribosomal protein S5 f | 30S ribosomal protein S6 g | 30S ribosomal protein S7 h | 30S ribosomal protein S8 i | 30S ribosomal protein S9 j | 30S ribosomal protein S10 k | 30S ribosomal protein S11 l | 30S ribosomal protein S12 m | 30S ribosomal protein S13 n | 30S ribosomal protein S14 type Z o | 30S ribosomal protein S15 p | 30S ribosomal protein S16 q | 30S ribosomal protein S17 r | 30S ribosomal protein S18 s | 30S ribosomal protein S19 t | 30S ribosomal protein S20 Non-standard residues in 5li0 #6 --- MG — magnesium ion O — oxygen atom ZN — zinc ion > hide #!3 models > select #6 140825 atoms, 152930 bonds, 4526 pseudobonds, 4 models selected > show sel surfaces > hide #6/a > select #6/a:425@O2' 1 atom, 1 model selected > select up 23 atoms, 25 bonds, 2 models selected > select up 33126 atoms, 37086 bonds, 2 models selected > select up 33140 atoms, 37086 bonds, 2 models selected > color sel #ffd123 > color sel #ffd98f > color sel #ffd123 > select #6/s:21@CB 1 atom, 1 model selected > select up 72 atoms, 62 bonds, 11 models selected > select up 1133 atoms, 1133 bonds, 11 models selected > select up 11098 atoms, 11256 bonds, 11 models selected > select up 11179 atoms, 11329 bonds, 19 models selected > select up 11865 atoms, 12024 bonds, 19 models selected > select up 18051 atoms, 18307 bonds, 19 models selected > color sel #ffd98f > select #6/n:22@CG2 1 atom, 1 model selected > select up 15 atoms, 13 bonds, 3 models selected > select up 389 atoms, 395 bonds, 3 models selected > select up 1179 atoms, 1206 bonds, 3 models selected > color sel #ffd98f > select #6/A:1142@C1' 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 2 models selected > select up 62475 atoms, 69965 bonds, 2 models selected > color sel #2194D6 > select #6/B:62@O2' 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 2 models selected > select up 2427 atoms, 2714 bonds, 2 models selected > color sel #2194D6 > select #6/S:42@CG2 1 atom, 1 model selected > select up 153 atoms, 135 bonds, 20 models selected > select up 2254 atoms, 2263 bonds, 20 models selected > select up 18239 atoms, 18463 bonds, 20 models selected > select up 18248 atoms, 18471 bonds, 21 models selected > select up 18288 atoms, 18511 bonds, 21 models selected > select up 18468 atoms, 18693 bonds, 21 models selected > select up 18500 atoms, 18721 bonds, 24 models selected > select up 18679 atoms, 18902 bonds, 24 models selected > select up 20105 atoms, 20344 bonds, 24 models selected > color sel #b3e3f5 > select clear > save image ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/70S-staph.tif"" > width 1341 height 802 > turn y 180 > lighting full > lighting soft > save image ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/70S-staph-180.tif"" > width 1341 height 802 > save session ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/70S-staph.cxs"" > hide #!6 models > show #!2 models > select #2 239041 atoms, 257813 bonds, 5 pseudobonds, 2 models selected > show sel surfaces > select #2/E:521@C5' 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 2 models selected > select up 53434 atoms, 59734 bonds, 2 models selected > select up 239041 atoms, 257813 bonds, 2 models selected > select down 53434 atoms, 59734 bonds, 50 models selected > select #2/E:704@O2P 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 2 models selected > select up 53434 atoms, 59734 bonds, 2 models selected > color sel #ffd98f > color sel #ffd123 > select #2/M:140@O 1 atom, 1 model selected > select up 118 atoms, 109 bonds, 14 models selected > select up 3880 atoms, 3954 bonds, 14 models selected > select up 31993 atoms, 32600 bonds, 14 models selected > color sel #ffd98f > select #2/Y:103@CE 1 atom, 1 model selected > select up 61 atoms, 53 bonds, 9 models selected > select up 4612 atoms, 4689 bonds, 9 models selected > select up 4692 atoms, 4762 bonds, 16 models selected > select up 9579 atoms, 9730 bonds, 16 models selected > select up 35224 atoms, 35819 bonds, 16 models selected > color sel #ffd98f > select #2/O:19@OG1 1 atom, 1 model selected > select up 18 atoms, 16 bonds, 3 models selected > select up 923 atoms, 939 bonds, 3 models selected > select up 5072 atoms, 5156 bonds, 3 models selected > select up 239041 atoms, 257813 bonds, 3 models selected > color sel #ffd98f > hide #!2 models > show #!4 models > hide #!4 models > show #!2 models > select up 108670 atoms, 117066 bonds, 2 pseudobonds, 47 models selected > select up 193780 atoms, 211756 bonds, 2 pseudobonds, 47 models selected > select down 108670 atoms, 117066 bonds, 2 pseudobonds, 47 models selected > select clear > color sel #b3e3f5 > color sel #b3e3f5 > color sel #b3e3f5 > color sel #b3e3f5 > color sel #b3e3f5 > color sel #b3e3f5 > select #2/B:329@P 1 atom, 1 model selected > select #2/E 53434 atoms, 59734 bonds, 1 pseudobond, 2 models selected > color sel #ffd123 > color sel #b3e3f5 > select #2/A:1909@O2 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 2 models selected > select up 42172 atoms, 47209 bonds, 2 models selected > color sel #2196D6 > select #2/B:232@P 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 2 models selected > select up 34483 atoms, 38561 bonds, 2 models selected > color sel #2196D6 > color sel #b3e3f5 > color sel #b3e3f5 > select #2/G:40@O2' 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 2 models selected > select up 1543 atoms, 1722 bonds, 2 models selected > color sel #2196D6 > select up 239041 atoms, 257813 bonds, 2 models selected > select down 1543 atoms, 1722 bonds, 50 models selected > select clear > select #2/H:62@O2' 1 atom, 1 model selected > select up 23 atoms, 25 bonds, 2 models selected > select up 2836 atoms, 3169 bonds, 2 models selected > select up 239041 atoms, 257813 bonds, 2 models selected > select up 239041 atoms, 257813 bonds, 5 pseudobonds, 51 models selected > select down 239041 atoms, 257813 bonds, 50 models selected > select down 2836 atoms, 3169 bonds, 50 models selected > color sel #2196D6 > select #2/F:129@O2' 1 atom, 1 model selected > select up 23 atoms, 25 bonds, 2 models selected > select up 3806 atoms, 4256 bonds, 2 models selected > color sel #2196D6 > select clear > save image ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/90S-kineto.tif"" > width 1341 height 802 > color sel #ffd123 > color sel #ffd98f > select clear > save image ""C:/Users/Anthony > Bochler/Desktop/Thèse/Images/90S-kineto-180.tif"" width 1341 height 802 > save session ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/ribo-kineto- > blueyellow.cxs"" Traceback (most recent call last): File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 561, in save fserialize(stream, data) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\serialize.py"", line 63, in msgpack_serialize stream.write(packer.pack(obj)) File ""msgpack\\_packer.pyx"", line 284, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 290, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 287, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 234, in msgpack._cmsgpack.Packer._pack File ""msgpack\\_packer.pyx"", line 234, in msgpack._cmsgpack.Packer._pack File ""msgpack\\_packer.pyx"", line 277, in msgpack._cmsgpack.Packer._pack File ""stringsource"", line 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap File ""_serialize.pyx"", line 242, in core._serialize._encode_ext File ""msgpack\\_packer.pyx"", line 284, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 290, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 287, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 234, in msgpack._cmsgpack.Packer._pack File ""msgpack\\_packer.pyx"", line 263, in msgpack._cmsgpack.Packer._pack File ""msgpack\\_packer.pyx"", line 277, in msgpack._cmsgpack.Packer._pack File ""stringsource"", line 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap File ""_serialize.pyx"", line 215, in core._serialize._encode_ext File ""msgpack\\_packer.pyx"", line 284, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 290, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 287, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 234, in msgpack._cmsgpack.Packer._pack MemoryError MemoryError File ""msgpack\\_packer.pyx"", line 234, in msgpack._cmsgpack.Packer._pack See log for complete Python traceback. Traceback (most recent call last): File ""C:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 911, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 641, in file_save_cb self.save_dialog.display(self, session) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\ui\save_dialog.py"", line 139, in display fmt.save(session, filename) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 1100, in save run(session, cmd) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 992, in save_session save(session, filename, **kw) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 229, in export result = self.export_func(session, path, **kw) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 561, in save fserialize(stream, data) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\serialize.py"", line 63, in msgpack_serialize stream.write(packer.pack(obj)) File ""msgpack\\_packer.pyx"", line 284, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 290, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 287, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 234, in msgpack._cmsgpack.Packer._pack File ""msgpack\\_packer.pyx"", line 234, in msgpack._cmsgpack.Packer._pack File ""msgpack\\_packer.pyx"", line 277, in msgpack._cmsgpack.Packer._pack File ""stringsource"", line 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap File ""_serialize.pyx"", line 242, in core._serialize._encode_ext File ""msgpack\\_packer.pyx"", line 284, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 290, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 287, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 234, in msgpack._cmsgpack.Packer._pack File ""msgpack\\_packer.pyx"", line 263, in msgpack._cmsgpack.Packer._pack File ""msgpack\\_packer.pyx"", line 277, in msgpack._cmsgpack.Packer._pack File ""stringsource"", line 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap File ""_serialize.pyx"", line 215, in core._serialize._encode_ext File ""msgpack\\_packer.pyx"", line 284, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 290, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 287, in msgpack._cmsgpack.Packer.pack File ""msgpack\\_packer.pyx"", line 234, in msgpack._cmsgpack.Packer._pack MemoryError MemoryError File ""msgpack\\_packer.pyx"", line 234, in msgpack._cmsgpack.Packer._pack See log for complete Python traceback. > save session ""C:/Users/Anthony Bochler/Desktop/Thèse/Images/ribo-kineto- > blueyellow.cxs"" Traceback (most recent call last): File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 556, in save mgr.discovery(self._state_containers) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 288, in process return copy_state(data, convert=convert) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 210, in copy_state return _copy(data) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 198, in _copy return data.copy() MemoryError: Unable to allocate array with shape (191951, 3) and data type float32 MemoryError: Unable to allocate array with shape (191951, 3) and data type float32 File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 198, in _copy return data.copy() See log for complete Python traceback. Traceback (most recent call last): File ""C:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 911, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 641, in file_save_cb self.save_dialog.display(self, session) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\ui\save_dialog.py"", line 139, in display fmt.save(session, filename) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 1100, in save run(session, cmd) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 992, in save_session save(session, filename, **kw) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 229, in export result = self.export_func(session, path, **kw) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 556, in save mgr.discovery(self._state_containers) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 288, in process return copy_state(data, convert=convert) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 210, in copy_state return _copy(data) File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 198, in _copy return data.copy() MemoryError: Unable to allocate array with shape (191951, 3) and data type float32 MemoryError: Unable to allocate array with shape (191951, 3) and data type float32 File ""C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 198, in _copy return data.copy() See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 432.00 OpenGL renderer: GeForce GTX 1080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Sessions fixed all ChimeraX