id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8359 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description Last time you used ChimeraX it crashed. 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All rights reserved. > open ""/Users/amberms/Desktop/NEC Paper/figures/012023.cxs"" Opened cryosparc_P183_J130_locfilter_flip.mrc as #5, grid size 220,220,220, pixel 1.67, shown at level 0.0152, step 1, values float32 Log from Fri Jan 20 15:36:51 2023UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open ""/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"" Opened cryosparc_P183_J130_locfilter_flip.mrc as #5, grid size 220,220,220, pixel 1.67, shown at level 0.0152, step 1, values float32 Log from Mon Jan 16 15:41:27 2023 > lighting soft > set bgColor white UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/amberms/Desktop/group/Modeling/122122/RealSpaceRefine_19/NEC_011123_2_RSR_015_Arg474_real_space_refined_019.pdb Chain information for NEC_011123_2_RSR_015_Arg474_real_space_refined_019.pdb #1 --- Chain | Description A C | No description available B | No description available D H | No description available E | No description available G | No description available > open > /Users/amberms/Desktop/group/Modeling/122122/RealSpaceRefine_21/01123_real_space_refined_021.pdb Chain information for 01123_real_space_refined_021.pdb #2 --- Chain | Description A C | No description available B | No description available D H | No description available E | No description available G | No description available > open > /Users/amberms/Desktop/group/Modeling/122122/RealSpaceRefine_22/01123_real_space_refined_022.pdb Chain information for 01123_real_space_refined_022.pdb #3 --- Chain | Description A C | No description available B | No description available D H | No description available E | No description available G | No description available > open /Users/amberms/Desktop/group/Modeling/122122/01123.pdb Summary of feedback from opening /Users/amberms/Desktop/group/Modeling/122122/01123.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 23743 messages similar to the above omitted Chain information for 01123.pdb #4 --- Chain | Description A C | No description available B | No description available D H | No description available E | No description available G | No description available > hide atoms > show cartoons > select #1:A:402,411,412,414,471,474,478,481 517 atoms, 525 bonds, 24 residues, 1 model selected > hide #!1 models > show #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > select #1/A:402,411,412,414,471,474,478,481 124 atoms, 120 bonds, 8 residues, 1 model selected > show sel atoms > style sel ball Changed 124 atom styles > color sel yellow > select #1/C:402,411,412,414,471,474,478,481 135 atoms, 131 bonds, 8 residues, 1 model selected > show sel atoms > style sel stick Changed 135 atom styles > style sel ball Changed 135 atom styles > color sel yellow > select #A/C:402,411,412,414,471,474,478,481 Expected an objects specifier or a keyword > show #!2 models > show #!3 models > show #!4 models > select #2/C:402,411,412,414,471,474,478,481 135 atoms, 131 bonds, 8 residues, 1 model selected > show sel atoms > style sel ball Changed 135 atom styles > color sel cyan > select #2/A:402,411,412,414,471,474,478,481 135 atoms, 131 bonds, 8 residues, 1 model selected > show sel atoms > style sel ball Changed 135 atom styles > color sel cyan > select #3/A:402,411,412,414,471,474,478,481 135 atoms, 131 bonds, 8 residues, 1 model selected > show sel atoms > style sel ball Changed 135 atom styles > color sel #ff9300ff > select #3/C:402,411,412,414,471,474,478,481 135 atoms, 131 bonds, 8 residues, 1 model selected > show sel atoms > style sel ball Changed 135 atom styles > color sel #ff2600ff > color sel #ff9300ff > select #4/A:402,411,412,414,471,474,478,481 135 atoms, 131 bonds, 8 residues, 1 model selected > show sel atoms > style sel ball Changed 135 atom styles > color sel #ff2f92ff > select #4/C:402,411,412,414,471,474,478,481 135 atoms, 131 bonds, 8 residues, 1 model selected > show sel atoms > style sel ball Changed 135 atom styles > color sel #ff40ffff > color sel #ff2f92ff > select clear > select H 75541 atoms, 9172 residues, 4 models selected > hide sel target a > hide sel cartoons > hide #!2 models > hide #!3 models > hide #!4 models > hide #!1 models > show #!2 models > show #!3 models > show #!4 models > show #!1 models > color sel byhetero > color sel byhetero > color sel byhetero > select #1,2,3,4/A,C:402,411,412,414,471,474,478,481 1069 atoms, 1037 bonds, 64 residues, 4 models selected > color sel byhetero > select clear > hide #!2 models > hide #!4 models > show #!4 models > hide #!3 models > hide #!4 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!4 models > show #!2 cartoons > show #!4 models > show #!2,4 cartoons > hide #!4 models > show #!4 models > open > /Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc Opened cryosparc_P183_J130_locfilter_flip.mrc as #5, grid size 220,220,220, pixel 1.67, shown at level 0.00879, step 1, values float32 > volume #5 level 0.01524 > lighting soft > transparency 50 > hide #!2 models > show #!2 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!5 models > hide #!2 cartoons > graphics silhouettes true > ui tool show Distances > select add #2/A:474@NH1 1 atom, 1 residue, 1 model selected > select add #2/A:478@OE1 2 atoms, 2 residues, 1 model selected > distance #2/A:474@NH1 #2/A:478@OE1 Distance between 01123_real_space_refined_021.pdb #2/A ARG 474 NH1 and GLU 478 OE1: 2.424Å > select clear > select add #2/A:474@NE 1 atom, 1 residue, 1 model selected > select add #2/A:471@OD1 2 atoms, 2 residues, 1 model selected > distance #2/A:474@NE #2/A:471@OD1 Distance between 01123_real_space_refined_021.pdb #2/A ARG 474 NE and ASP 471 OD1: 3.466Å > select clear > select add #2/A:471@OD1 1 atom, 1 residue, 1 model selected > select add #2/A:474@NH2 2 atoms, 2 residues, 1 model selected > distance #2/A:471@OD1 #2/A:474@NH2 Distance between 01123_real_space_refined_021.pdb #2/A ASP 471 OD1 and ARG 474 NH2: 3.419Å > select clear > select add #2/C:474@NH2 1 atom, 1 residue, 1 model selected > select add #2/C:478@OE2 2 atoms, 2 residues, 1 model selected > distance #2/C:474@NH2 #2/C:478@OE2 Distance between 01123_real_space_refined_021.pdb #2/C ARG 474 NH2 and GLU 478 OE2: 3.263Å > select clear > select add #2/C:474@NH1 1 atom, 1 residue, 1 model selected > select add #2/C:478@OE2 2 atoms, 2 residues, 1 model selected > distance #2/C:474@NH1 #2/C:478@OE2 Distance between 01123_real_space_refined_021.pdb #2/C ARG 474 NH1 and GLU 478 OE2: 4.710Å > select clear > select add #2/C:471@OD1 1 atom, 1 residue, 1 model selected > select add #2/C:474@NH1 2 atoms, 2 residues, 1 model selected > distance #2/C:471@OD1 #2/C:474@NH1 Distance between 01123_real_space_refined_021.pdb #2/C ASP 471 OD1 and ARG 474 NH1: 5.085Å > show #!1 models > hide #!1 models > select clear > select add #2/C:471@OD1 1 atom, 1 residue, 1 model selected > select add #2/A:474@NE 2 atoms, 2 residues, 1 model selected > distance #2/C:471@OD1 #2/A:474@NE Distance between 01123_real_space_refined_021.pdb #2/C ASP 471 OD1 and /A ARG 474 NE: 5.557Å > distance style symbol false > distance style symbol true > show sel cartoons > hide #!6 models > show sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain #2/B Alignment identifier is 2/B > sequence chain #2/E Alignment identifier is 2/E > hide #!2 models > show #!2 models > select #2 40815 atoms, 41357 bonds, 7 pseudobonds, 2637 residues, 2 models selected > show sel cartoons > select clear > show #!5 models > show #!3 models > show #!2-3 cartoons > hide #!5 models > show #!4 models > hide #6.1 models > hide #!4 models > show #!4 models > hide #!2 models > show #!2 models > hide #!2-4 cartoons > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!6 models > hide #!4 models > select add #2/C:471@CG 1 atom, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ASP rotLib Dunbrack 01123_real_space_refined_021.pdb #2/C ASP 471: phi -62.9, psi -41.8 trans Changed 90 bond radii > show #!5 models > hide #!5 models > show #!4 models > hide #!4 models > hide #!6 models > hide sel atoms > select clear > hide #!2 atoms > show #!2 cartoons > select #2/A,C 34134 atoms, 34486 bonds, 7 pseudobonds, 2100 residues, 2 models selected > select #2/D,H 2796 atoms, 2864 bonds, 344 residues, 1 model selected > color sel #ff9300ff > select #2/G 1246 atoms, 1344 bonds, 39 residues, 1 model selected > color sel #ff2f92ff > select #2/B 1304 atoms, 1316 bonds, 76 residues, 1 model selected > color sel #531b93ff > select #2/E 1335 atoms, 1347 bonds, 78 residues, 1 model selected > color sel #009193ff > select clear > show #!5 models > color zone #5 near #2 distance 5 > select #2/E 1335 atoms, 1347 bonds, 78 residues, 1 model selected > color sel #531b93ff > hide #!5 models > select #2/B 1304 atoms, 1316 bonds, 76 residues, 1 model selected > color sel #ff2f92ff > select #2/G 1246 atoms, 1344 bonds, 39 residues, 1 model selected > color sel #00fdffff > select clear > show #!5 models > color zone #5 near #2 distance 5 > save ""/Users/amberms/Desktop/NEC Paper/figures/figure1A.png"" width 1704 > height 1146 supersample 4 transparentBackground true > hide #!5 models > save ""/Users/amberms/Desktop/NEC Paper/figures/figure1B.png"" width 1704 > height 1146 supersample 4 transparentBackground true > view name figure_1 > view list Named views: figure_1 > view figure_1 > select #2/G 1246 atoms, 1344 bonds, 39 residues, 1 model selected > color sel #00fdff33 > select #2/B 1304 atoms, 1316 bonds, 76 residues, 1 model selected > color sel #00fdff05 > color sel #00fdff33 > color sel #ff2f92ff > color sel #ff2f9233 > select #2/E 1335 atoms, 1347 bonds, 78 residues, 1 model selected > color sel #531b93ff > color sel #531b9333 > select #2/D,H 2796 atoms, 2864 bonds, 344 residues, 1 model selected > color sel #ff9300ff > color sel #ff930033 > select clear > select #2/A,C:402,411,412,414,474,478,481 246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected > show sel atoms > style sel ball Changed 246 atom styles > color (#!2 & sel) #fffb00ff > color (#!2 & sel) #011993ff > color (#!2 & sel) #00fdffff > color (#!2 & sel) #0096ffff > color (#!2 & sel) #0433ffff > color (#!2 & sel) #0096ffff > color (#!2 & sel) #00f900ff > color (#!2 & sel) #8efa00ff > color (#!2 & sel) #00f900ff > color sel byhetero > select H 75541 atoms, 9172 residues, 4 models selected > hide (#!2 & sel) target a > select #2/A,C 34134 atoms, 34486 bonds, 7 pseudobonds, 2100 residues, 2 models selected > color (#!2 & sel) #a9a9a9ff > color (#!2 & sel) #a9a9a933 > color (#!2 & sel) #a9a9a900 > color (#!2 & sel) #a9a9a980 > color (#!2 & sel) #a9a9a9b3 > select clear > select #2/A,C:402,411,412,414,474,478,481 246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected > color (#!2 & sel) #00f900ff > color sel byhetero > select clear > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure2A.png"" width 1704 > height 1146 supersample 4 transparentBackground true > select #2/A,C:402,411,412,414,474,478,481 246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected > color (#!2 & sel) #009193ff > color (#!2 & sel) #011993ff > color (#!2 & sel) #005493ff > color (#!2 & sel) #fffb00ff > select #2/B,E,D,H, G 6681 atoms, 6871 bonds, 537 residues, 1 model selected > hide sel cartoons > select #2/A,C:402,411,412,414,474,478,481 246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected > color sel byhetero > select clear > select #2/A,C:402,411,412,414,474,478,481 246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected > color (#!2 & sel) #fffc79ff > color (#!2 & sel) #fffb00ff > color (#!2 & sel) #0096ffff > color (#!2 & sel) #fffb00ff > color sel byhetero > select #2/A,C:471 24 atoms, 22 bonds, 2 residues, 1 model selected > show sel atoms > style sel ball Changed 24 atom styles > select H 75541 atoms, 9172 residues, 4 models selected > hide (#!2 & sel) target a > select #2/A,C:471 24 atoms, 22 bonds, 2 residues, 1 model selected > color sel #00fa92ff > color sel #00fdffff > color sel byhetero > select clear > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > select #2/A,C:402,411,412,414,474,478,481,471 270 atoms, 262 bonds, 7 pseudobonds, 16 residues, 2 models selected > graphics silhouettes true > select clear > view name figure_2a > view list Named views: figure_1, figure_2a > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure2A.png"" width 1704 > height 1146 supersample 3 > show #!5 models > transparency 50 > hide #!5 models > show #!5 models > transparency 90 > select #2/A,C 34134 atoms, 34486 bonds, 7 pseudobonds, 2100 residues, 2 models selected > color (#!2 & sel) #929292ff > color (#!2 & sel) #a9a9a9ff > select clear > select #2/A,C:402,411,412,414,474,478,481 246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected > color (#!2 & sel) #fffb00ff > color sel byhetero > select #2/A,C:471 24 atoms, 22 bonds, 2 residues, 1 model selected > color sel #0096ffff > color sel #00fdffff > color sel byhetero > select clear > view name figure_2b > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure2A_2.png"" width 1704 > height 1146 supersample 4 transparentBackground true > view name figure_2c > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure2B.png"" width 1704 > height 1146 supersample 4 transparentBackground true > transparency 70 > transparency 80 > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure2B.png"" width 1704 > height 1146 supersample 4 transparentBackground true > hide #!5 models > save ""/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"" > show #!2 cartoons > hide #!2 atoms > select #2/A,C 34134 atoms, 34486 bonds, 7 pseudobonds, 2100 residues, 2 models selected > color (#!2 & sel) #a9a9a9ff > select #2/D,H 2796 atoms, 2864 bonds, 344 residues, 1 model selected > color sel #ff9300ff > select #2/B 1304 atoms, 1316 bonds, 76 residues, 1 model selected > color sel #ff2f92ff > select #2/E 1335 atoms, 1347 bonds, 78 residues, 1 model selected > color sel #531b93ff > select #2/G 1246 atoms, 1344 bonds, 39 residues, 1 model selected > color sel #0096ffff > color sel #00fdffff > select clear > select #2/D,H,E,B,G 6681 atoms, 6871 bonds, 537 residues, 1 model selected > hide sel cartoons > open 5DIS Summary of feedback from opening 5DIS fetched from pdb --- warnings | Unknown polymer entity '6' near line 18113 Atom OXT is not in the residue template for PRO /C:301 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 5dis title: Crystal structure of a CRM1-RanGTP-SPN1 export complex bound to a 113 amino acid FG-repeat containing fragment of Nup214 [more info...] Chain information for 5dis #7 --- Chain | Description A | Exportin-1 B | GTP-binding nuclear protein Ran C | Snurportin-1 D | Maltose-binding periplasmic protein,Nuclear pore complex protein Nup214 Non-standard residues in 5dis #7 --- GLC — alpha-D-glucopyranose GTP — guanosine-5'-triphosphate MG — magnesium ion > mmaker #7/A to #2/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01123_real_space_refined_021.pdb, chain A (#2) with 5dis, chain A (#7), sequence alignment score = 5346.9 RMSD between 980 pruned atom pairs is 0.691 angstroms; (across all 1030 pairs: 1.266) > select #7/B,D,C 6591 atoms, 6740 bonds, 20 pseudobonds, 843 residues, 3 models selected > hide sel cartoons > hide sel atoms > hide #!2 models > hide sel atoms > select #7/E 23 atoms, 24 bonds, 2 residues, 1 model selected > hide sel atoms > select #7/A:1101,499,491 36 atoms, 38 bonds, 3 residues, 1 model selected > hide sel atoms > select clear > open > /Users/amberms/Desktop/group/Modeling/122122/RealSpaceRefine_21/01123_real_space_refined_021.pdb Chain information for 01123_real_space_refined_021.pdb #8 --- Chain | Description A C | No description available B | No description available D H | No description available E | No description available G | No description available > hide #!7-8 atoms > show #!7-8 cartoons > select #7/B,D,C 6591 atoms, 6740 bonds, 20 pseudobonds, 843 residues, 3 models selected > hide sel cartoons > hide #!8 models > show #!8 models > hide #!8 models > show #!2 models > show #!8 models > hide #!2 models > mmaker #8/C to #2/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01123_real_space_refined_021.pdb, chain A (#2) with 01123_real_space_refined_021.pdb, chain C (#8), sequence alignment score = 5413.4 RMSD between 1025 pruned atom pairs is 0.435 angstroms; (across all 1050 pairs: 1.023) > hide #!8 models > show #!8 models > show #!2 models > hide #!8 models > show #!8 models > select #8/A,B,D,E,H,G 23748 atoms, 24114 bonds, 1587 residues, 1 model selected > hide sel cartoons > hide #!2 models > show #!2 models > select #2/C,B,D,E,H,G 23748 atoms, 24114 bonds, 3 pseudobonds, 1587 residues, 2 models selected > hide sel cartoons > hide #!8 models > hide #!2 models > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_5DIS.png"" width 1704 > height 1146 supersample 4 transparentBackground true > hide #!7 models > show #!2 models > hide #!2 models > show #!3 models > show #!3 cartoons > hide #!3 models > show #!7 models > view name figure_3_1 > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_5DIS.png"" width 1704 > height 1146 supersample 4 transparentBackground true > hide #!7 models > show #!2 models > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1A.png"" width 1704 > height 1146 supersample 4 transparentBackground true > hide #!2 models > show #!8 models > show #!2 models > hide #!2 models > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1C.png"" width 1704 > height 1146 supersample 4 transparentBackground true > show #!2 models > hide #!2 models > show #!5 models > hide #!5 models > hide #!8 models > show #!2 models > show #!8 models > hide #!2 models > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1C.png"" width 1704 > height 1146 supersample 4 transparentBackground true > save ""/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"" > show #!7 models > hide #!8 models > show #!8 models > hide #!7 models > select #8/C:389-400 167 atoms, 169 bonds, 12 residues, 1 model selected > color sel yellow > select clear > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1C.png"" width 1704 > height 1146 supersample 4 transparentBackground true > hide #!8 models > show #!1 models > hide #!1 models > show #!2 models > select #2/A:389-400 167 atoms, 169 bonds, 12 residues, 1 model selected > color sel yellow > select clear > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1A.png"" width 1704 > height 1146 supersample 4 transparentBackground true > show #!8 models > hide #!8 models > show #!2 cartoons > select #2/B,E,D,H,G 6681 atoms, 6871 bonds, 537 residues, 1 model selected > hide sel cartoons > select #2/C 17067 atoms, 17243 bonds, 3 pseudobonds, 1050 residues, 2 models selected > color (#!2 & sel) #797979ff > select clear > select #2/C:389-400 167 atoms, 169 bonds, 12 residues, 1 model selected > color sel yellow > select clear > view name figure_3_2 > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_dimerloops.png"" width > 1704 height 1146 supersample 4 transparentBackground true > view name figure_3_2 > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_dimerloops.png"" width > 1704 height 1146 supersample 4 transparentBackground true > show #!2 surfaces > select #2/D,H 2796 atoms, 2864 bonds, 344 residues, 1 model selected > select #2/B,E,G 3885 atoms, 4007 bonds, 193 residues, 1 model selected > hide sel surfaces > coulombic sel The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: 01123_real_space_refined_021.pdb #2/G A 119 O5' 01123_real_space_refined_021.pdb #2/G G 171 OP1 01123_real_space_refined_021.pdb #2/G G 171 P 01123_real_space_refined_021.pdb #2/G G 171 O5' 01123_real_space_refined_021.pdb #2/G G 171 OP2 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 01123_real_space_refined_021.pdb_B SES surface #2.3: minimum, -12.25, mean 5.44, maximum 22.90 Coulombic values for 01123_real_space_refined_021.pdb_E SES surface #2.6: minimum, -8.00, mean 3.96, maximum 20.57 Coulombic values for 01123_real_space_refined_021.pdb_G SES surface #2.7: minimum, -28.79, mean -14.78, maximum -1.19 To also show corresponding color key, enter the above coulombic command and add key true > hide sel surfaces > select clear > coulombic #!2 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 01123_real_space_refined_021.pdb_A SES surface #2.2: minimum, -29.56, mean -1.13, maximum 19.93 Coulombic values for 01123_real_space_refined_021.pdb_B SES surface #2.3: minimum, -12.25, mean 5.44, maximum 22.90 Coulombic values for 01123_real_space_refined_021.pdb_C SES surface #2.4: minimum, -19.04, mean -1.19, maximum 18.78 Coulombic values for 01123_real_space_refined_021.pdb_D SES surface #2.5: minimum, -11.36, mean 2.56, maximum 16.39 Coulombic values for 01123_real_space_refined_021.pdb_E SES surface #2.6: minimum, -8.00, mean 3.96, maximum 20.57 Coulombic values for 01123_real_space_refined_021.pdb_G SES surface #2.7: minimum, -28.79, mean -14.78, maximum -1.19 Coulombic values for 01123_real_space_refined_021.pdb_H SES surface #2.8: minimum, -10.42, mean 2.57, maximum 18.49 To also show corresponding color key, enter the above coulombic command and add key true > select #2/B,E,G 3885 atoms, 4007 bonds, 193 residues, 1 model selected > hide sel surfaces > view name figure_3_3 > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES.png"" width 1704 > height 1146 supersample 4 transparentBackground true > show sel atoms > hide sel atoms > show sel cartoons > select clear > view name figure_3_4 > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES_2.png"" width 1704 > height 1146 supersample 3 > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES_2.png"" width 1704 > height 1146 supersample 4 transparentBackground true > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES_3.png"" width 1704 > height 1146 supersample 4 transparentBackground true > view name figure_3_5 > save ""/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"" > hide #!2 surfaces > select #2/G 1246 atoms, 1344 bonds, 39 residues, 1 model selected > color (#!2 & sel) #00fdffff > color (#!2 & sel) #00fdff80 > color (#!2 & sel) #00fdff00 > color (#!2 & sel) #00fdff4d > select #2/B 1304 atoms, 1316 bonds, 76 residues, 1 model selected > color (#!2 & sel) #ff2f92ff > color (#!2 & sel) #ff2f924d > select clear > view name figure_3_6 > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_RevBS.png"" width 1704 > height 1146 supersample 4 transparentBackground true > save ""/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"" ——— End of log from Mon Jan 16 15:41:27 2023 ——— opened ChimeraX session > open ""/Users/amberms/Desktop/NEC Paper/figures/NEC_011923.pdb"" Chain information for NEC_011923.pdb #9 --- Chain | Description A C | No description available B | No description available D H | No description available E | No description available G | No description available > open ""/Users/amberms/Desktop/NEC Paper/figures/NEC_011923.pdb"" Chain information for NEC_011923.pdb #10 --- Chain | Description A C | No description available B | No description available D H | No description available E | No description available G | No description available > save ""/Users/amberms/Desktop/NEC Paper/figures/012023.cxs"" > hide #9-10#!2 atoms > show #9-10#!2 cartoons > mmaker #10/C to #9/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker NEC_011923.pdb, chain A (#9) with NEC_011923.pdb, chain C (#10), sequence alignment score = 5399.6 RMSD between 1025 pruned atom pairs is 0.429 angstroms; (across all 1050 pairs: 1.010) > hide #10 models > hide #9 models > hide #!2 models > show #!7 models > view list Named views: figure_1, figure_2a, figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3, figure_3_4, figure_3_5, figure_3_6 > view figure_3_2 > coulombic #!7 The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: 5dis #7/A GLU 1048 OXT 5dis #7/D GLY 2027 OXT 5dis #7/C GLY 287 OXT 5dis #7/B MET 179 O Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of 5dis #/B MET 179 H bonded to atom that should not have hydrogens (copy of 5dis #/B MET 179 C) > select H 132205 atoms, 16051 residues, 7 models selected > select #7/B 1440 atoms, 1466 bonds, 6 pseudobonds, 183 residues, 2 models selected > delete atoms (#!7 & sel) > delete bonds (#!7 & sel) > coulombic #!7 The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: 5dis #7/A GLU 1048 OXT 5dis #7/D GLY 2027 OXT 5dis #7/C GLY 287 OXT Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 5dis_A SES surface #7.3: minimum, -25.78, mean -2.95, maximum 10.90 Coulombic values for 5dis_C SES surface #7.4: minimum, -32.04, mean -0.55, maximum 10.32 Coulombic values for 5dis_D SES surface #7.5: minimum, -18.89, mean -2.55, maximum 13.38 To also show corresponding color key, enter the above coulombic command and add key true > select #7/C,D 5151 atoms, 5274 bonds, 14 pseudobonds, 660 residues, 2 models selected > hide sel surfaces > view figure_3_2 > hide #!7 models > select #7 13551 atoms, 13843 bonds, 15 pseudobonds, 1698 residues, 2 models selected > select clear > select #7 13551 atoms, 13843 bonds, 15 pseudobonds, 1698 residues, 2 models selected > view figure_3_3 > show #!2 models > view list Named views: figure_1, figure_2a, figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3, figure_3_4, figure_3_5, figure_3_6 > view figure_3_4 > view figure_3_3 > view figure_3_4 > view figure_3_5 > view figure_3_6 > show #9 models > show #10 models > hide #10 models > ~select #7 3 models selected > hide #!2 models > select #9/A 17067 atoms, 17243 bonds, 1050 residues, 1 model selected > color sel #a9a9a9ff > select #9/C 17067 atoms, 17243 bonds, 1050 residues, 1 model selected > color sel #797979ff > select #9/D,H 2796 atoms, 2864 bonds, 344 residues, 1 model selected > color sel #ff9300ff > select #9/B 1326 atoms, 1338 bonds, 79 residues, 1 model selected > color sel #531b93ff > select #9/E 1349 atoms, 1361 bonds, 80 residues, 1 model selected > color sel #ff2f92ff > select #9/G 1246 atoms, 1344 bonds, 39 residues, 1 model selected > color sel #00fdffff > select clear > save ""/Users/amberms/Desktop/NEC Paper/figures/012023.cxs"" > select #9/B 1326 atoms, 1338 bonds, 79 residues, 1 model selected > color sel #ff2f92ff > select #9/E 1349 atoms, 1361 bonds, 80 residues, 1 model selected > color sel #531b93ff > select clear > select #9/C:389-400 167 atoms, 169 bonds, 12 residues, 1 model selected > color sel #8efa00ff > select #9/A:389-400 167 atoms, 169 bonds, 12 residues, 1 model selected > color sel #fffb00ff > select clear > select #9/E 1349 atoms, 1361 bonds, 80 residues, 1 model selected > select #9/E:13-26 253 atoms, 254 bonds, 14 residues, 1 model selected > color sel #9437ffff > color sel #7a81ffff > color sel #531b93ff > color sel #875093ff > color sel #875093ff > color sel #8f5f93ff > color sel #8f5f93ff > color sel #937392ff > color sel #937392ff > color sel #835b93ff > color sel #835b93ff > color sel #935b90ff > color sel #935b90ff > color sel #934f81ff > color sel #934f81ff > color sel #936791ff > color sel #936791ff > select #9/E:51-60 171 atoms, 171 bonds, 10 residues, 1 model selected > color sel #011993ff > color sel #936791ff > select clear > view list Named views: figure_1, figure_2a, figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3, figure_3_4, figure_3_5, figure_3_6 > view figure_3_2 > view figure_3_3 > view figure_3_3 > view figure_3_4 > view figure_3_5 > view figure_3_5 > select #9/E:13-26,51-60 424 atoms, 425 bonds, 24 residues, 1 model selected > color sel #ff85ffff > color sel #ff8ad8ff > color sel #d783ffff > select clear > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_C.png"" width 1704 > height 1146 supersample 4 transparentBackground true > view name figure3_c > view name figure3_C_2 > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_2.png"" width 1704 > height 1146 supersample 4 transparentBackground true > view list Named views: figure3_C_2, figure3_c, figure_1, figure_2a, figure_2b, figure_2c, figure_3_1, figure_3_2, figure_3_3, figure_3_4, figure_3_5, figure_3_6 > view figure3_C_2 > select #9/E:51-60 171 atoms, 171 bonds, 10 residues, 1 model selected > color sel #531b93ff > select clear > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_3.png"" width 1704 > height 1146 supersample 4 transparentBackground true > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_zoomout.png"" width > 1704 height 1146 supersample 4 transparentBackground true > select #9/G,B 2572 atoms, 2682 bonds, 118 residues, 1 model selected > color sel #c0c0c0ff > color sel #d6d6d6ff > color sel #c0c0c0ff > select #9/A,C,D,H 36930 atoms, 37350 bonds, 2444 residues, 1 model selected > color sel #a9a9a9ff > color sel #c0c0c0ff > select #9/A:389-400 167 atoms, 169 bonds, 12 residues, 1 model selected > color sel #fffb00ff > select #9/C:389-400 167 atoms, 169 bonds, 12 residues, 1 model selected > color sel #8efa00ff > select clear > view figure3_C_2 > view figure_3_1 > select #9/B,C,D,E,G,H 23784 atoms, 24150 bonds, 1592 residues, 1 model selected > hide sel cartoons > select #9/A 17067 atoms, 17243 bonds, 1050 residues, 1 model selected > color sel #d6d6d6ff > color sel #ebebebff > select clear > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3A.png"" width 1704 > height 1146 supersample 4 transparentBackground true > select #9/A 17067 atoms, 17243 bonds, 1050 residues, 1 model selected > color sel #a9a9a9ff > select #9/A:389-400 167 atoms, 169 bonds, 12 residues, 1 model selected > color sel #fffb00ff > select clear > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3A_3.png"" width 1704 > height 1146 supersample 4 transparentBackground true > hide #9 models > show #10 models > select #10/B,A,D,E,G,H 23784 atoms, 24150 bonds, 1592 residues, 1 model selected > hide sel cartoons > select #10/C 17067 atoms, 17243 bonds, 1050 residues, 1 model selected > color sel #797979ff > select #10/C:389-400 167 atoms, 169 bonds, 12 residues, 1 model selected > color sel #8efa00ff > select clear > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3A_4.png"" width 1704 > height 1146 supersample 4 transparentBackground true > show #9 models > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3A_5.png"" width 1704 > height 1146 supersample 4 transparentBackground true > hide #9 models > hide #10 models > show #!7 models > hide #!7 surfaces > save ""/Users/amberms/Desktop/NEC Paper/figures/Figure3A_2.png"" width 1704 > height 1146 supersample 4 transparentBackground true > view name loopcloseup > save ""/Users/amberms/Desktop/NEC Paper/figures/012023.cxs"" ——— End of log from Fri Jan 20 15:36:51 2023 ——— opened ChimeraX session OpenGL version: 4.1 INTEL-18.8.4 OpenGL renderer: Intel(R) Iris(TM) Graphics 6100 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro12,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2.9 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 430.140.3.0.0 OS Loader Version: 540.120.3~19 SMC Version (system): 2.28f7 Software: System Software Overview: System Version: macOS 12.5.1 (21G83) Kernel Version: Darwin 21.6.0 Time since boot: 5 days 47 minutes Graphics/Displays: Intel Iris Graphics 6100: Chipset Model: Intel Iris Graphics 6100 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x162b Revision ID: 0x0009 Metal Family: Supported, Metal GPUFamily macOS 1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2416D: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 59.00Hz Framebuffer Depth: 24-Bit Color (ARGB8888) Display Serial Number: TN5PP6CO174S Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-Clipper: 0.16.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.2.2 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 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tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 }}} " defect closed normal Core duplicate all ChimeraX