id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9924 Unable to restore objects of NewerVersionQuery class dzyla@… Zach Pearson "{{{ The following bug report has been submitted: Platform: Linux-5.10.0-1050-oem-x86_64-with-glibc2.35 ChimeraX Version: 1.7.dev202309300109 (2023-09-30 01:09:06 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.7.dev202309300109 (2023-09-30) © 2016-2023 Regents of the University of California. All rights reserved. > open > /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_updated.cxs Log from Fri Oct 6 18:25:59 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open > C:\\\Users\\\didny\\\OneDrive\\\Code\\\work\\\FectoFab_paper\\\figure_notebooks\\\F_mabs_session_comparison.cxs Log from Fri Oct 6 16:48:39 2023 > lighting soft > camera ortho > ui mousemode right ""translate selected models"" > lighting soft > hide atoms > set bgColor #ffffff00 > camera ortho > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 UCSF ChimeraX version: 1.7.dev202309300109 (2023-09-30) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > pen > /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/RealSpaceRefine_7/Fecto2M_post_J772-coot-113_real_space_refined_007.pdb Unknown command: pen /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/RealSpaceRefine_7/Fecto2M_post_J772-coot-113_real_space_refined_007.pdb > lighting soft > hide atoms > set bgColor #ffffff00 > graphics silhouettes true width 5 > camera ortho > open > /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/J783__localfilterZ.mrc Opened J783__localfilterZ.mrc as #1, grid size 400,400,400, pixel 0.99, shown at level 4.98e-05, step 2, values float32 > volume #2 step 1 No volumes specified > volume #2 level 0.1124 No volumes specified > transparency 90 > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > show cartoons > style stick Changed 0 atom styles > view matrix camera > -0.74823,0.042535,-0.66207,7.8769,0.66342,0.053621,-0.74632,-20.179,0.0037562,-0.99766,-0.06834,147.61 > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0 Invalid ""models"" argument: No models specified by ""#2"" > zoom 0.45 > cartoon suppressBackboneDisplay false > color #1/a #2e7fbd > color #1/b #60a4d8 > color #1/c #9dc7e7 > color #1/A #c57e9e > color #1/B #bc8ba7 > color #1/C #b094ab > close #2 > open > /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab- > coot-124_water_merged_F.pdb Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #2 --- Chain | Description A C E | No description available B D F | No description available G I K | No description available H J L | No description available > hide atoms > lighting model #1,2 depthCue false > hide #1/B,b,C,c cartoons > show #2/A,B cartoons > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > matchmaker #2/B to #1/a:290-373 No 'to' model specified > color #2/A #8a8a8a > color #2/C #a3a3a3 > color #2/E #6d6d6d > color #2/B #7ab497 > color #2/F #72a27e > color #2/D #728f83 > view matrix camera > -0.84574,0.026011,-0.53296,40.496,0.53352,0.025995,-0.84538,-47.511,-0.008135,-0.99933,-0.035864,165.23 > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.039804,-0.96395,-0.2631,417.2,0.97181,0.023887,-0.23454,73.398,0.23237,-0.26502,0.93583,78.447 > zoom 0.9 > matchmaker #2/B to #1/a:290-373 No 'to' model specified > show #1/A,a cartoons > show #2/A,B cartoons > hide ~:24-48,290-373 cartoons > view matrix camera > -0.76786,-0.36016,-0.52979,31.136,0.63944,-0.48073,-0.6,17.901,-0.038586,-0.7995,0.59944,405.36 > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.039803,-0.96395,-0.2631,417.2,0.97181,0.023888,-0.23454,73.398,0.23237,-0.26502,0.93583,78.447 > zoom 2 [Repeated 1 time(s)] > close session > open > /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/RealSpaceRefine_7/Fecto2M_post_J772-coot-113_real_space_refined_007.pdb Chain information for Fecto2M_post_J772-coot-113_real_space_refined_007.pdb #1 --- Chain | Description A B C | No description available a b | No description available c | No description available > lighting soft > hide atoms > set bgColor #ffffff00 > graphics silhouettes true width 5 > camera ortho > open > /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/J783__localfilterZ.mrc Opened J783__localfilterZ.mrc as #2, grid size 400,400,400, pixel 0.99, shown at level 4.98e-05, step 2, values float32 > volume #2 step 1 > volume #2 level 0.1124 > transparency 90 > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > show cartoons > style stick Changed 9894 atom styles > view matrix camera > -0.74823,0.042535,-0.66207,7.8769,0.66342,0.053621,-0.74632,-20.179,0.0037562,-0.99766,-0.06834,147.61 > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0 > zoom 0.45 > cartoon suppressBackboneDisplay false > color #1/a #2e7fbd > color #1/b #60a4d8 > color #1/c #9dc7e7 > color #1/A #c57e9e > color #1/B #bc8ba7 > color #1/C #b094ab > close #2 > open > /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab- > coot-124_water_merged_F.pdb Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #2 --- Chain | Description A C E | No description available B D F | No description available G I K | No description available H J L | No description available > hide atoms > lighting model #1,2 depthCue false > hide #1/B,b,C,c cartoons > show #2/A,B cartoons > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > matchmaker #2/B to #1/a:290-373 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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence alignment score = 372.7 RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs: 1.831) > color #2/A #8a8a8a > color #2/C #a3a3a3 > color #2/E #6d6d6d > color #2/B #7ab497 > color #2/F #72a27e > color #2/D #728f83 > view matrix camera > -0.84574,0.026011,-0.53296,40.496,0.53352,0.025995,-0.84538,-47.511,-0.008135,-0.99933,-0.035864,165.23 > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.039804,-0.96395,-0.2631,417.2,0.97181,0.023887,-0.23454,73.398,0.23237,-0.26502,0.93583,78.447 > zoom 0.9 > matchmaker #2/B to #1/a:290-373 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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence alignment score = 372.7 RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs: 1.831) > color #2/C #9e0142 > color #2/D:110-137 #e95c47 > color #2/D:138-166 #fdbf6f > color #2/D:167-288 #ffffbe > color #2/D:229-377 #bfe5a0 > color #2/D:378-461 #54aead > color #2/D:462-487 #5e4fa2 > color #1/B #9e0142 > color #1/b:110-137 #e95c47 > color #1/b:138-166 #fdbf6f > color #1/b:167-288 #ffffbe > color #1/b:229-377 #bfe5a0 > color #1/b:378-461 #54aead > color #1/b:462-487 #5e4fa2 > close session > open > /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/RealSpaceRefine_7/Fecto2M_post_J772-coot-113_real_space_refined_007.pdb Chain information for Fecto2M_post_J772-coot-113_real_space_refined_007.pdb #1 --- Chain | Description A B C | No description available a b | No description available c | No description available > lighting soft > hide atoms > set bgColor #ffffff00 > graphics silhouettes true width 5 > camera ortho > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > show cartoons > style stick Changed 9894 atom styles > view matrix camera > -0.74823,0.042535,-0.66207,7.8769,0.66342,0.053621,-0.74632,-20.179,0.0037562,-0.99766,-0.06834,147.61 > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0 Invalid ""models"" argument: No models specified by ""#2"" > zoom 0.45 > cartoon suppressBackboneDisplay false > color #1/a #2e7fbd > color #1/b #60a4d8 > color #1/c #9dc7e7 > color #1/A #c57e9e > color #1/B #bc8ba7 > color #1/C #b094ab > open > /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab- > coot-124_water_merged_F.pdb Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #2 --- Chain | Description A C E | No description available B D F | No description available G I K | No description available H J L | No description available > hide atoms > lighting model #1,2 depthCue false > hide #1/B,b,C,c cartoons > show #2/A,B cartoons > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > matchmaker #2/B to #1/a:290-373 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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence alignment score = 372.7 RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs: 1.831) > color #2/A #8a8a8a > color #2/C #a3a3a3 > color #2/E #6d6d6d > color #2/B #7ab497 > color #2/F #72a27e > color #2/D #728f83 > view matrix camera > -0.84574,0.026011,-0.53296,40.496,0.53352,0.025995,-0.84538,-47.511,-0.008135,-0.99933,-0.035864,165.23 > zoom 0.9 > matchmaker #2/B to #1/a:290-373 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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence alignment score = 372.7 RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs: 1.831) > transparency #2/C-W 100 cartoons > transparency #2 100 cartoons > color #1/A #9e0142 > color #1/a:110-137 #e95c47 > color #1/a:138-166 #fdbf6f > color #1/a:167-288 #ffffbe > color #1/a:229-377 #bfe5a0 > color #1/a:378-461 #54aead > color #1/a:462-487 #5e4fa2 > matchmaker #1/a:374-426 to #2/B:374-426 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 FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2) with Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1), sequence alignment score = 261.2 RMSD between 48 pruned atom pairs is 1.045 angstroms; (across all 53 pairs: 1.286) > hide :24-48,290-373 cartoons > hide :49-290 cartoons > view matrix camera > -0.98693,-0.058747,0.14997,233.46,-0.15529,0.099693,-0.98282,-136.45,0.042785,-0.99328,-0.10751,192.2 > matchmaker #2/B to #1/a:290-373 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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence alignment score = 372.7 RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs: 1.831) > color #1/A #9e0142 > color #1/a:110-137 #e95c47 > color #1/a:138-166 #fdbf6f > color #1/a:167-288 #ffffbe > color #1/a:229-377 #bfe5a0 > color #1/a:374-461 #54aead > color #1/a:462-487 #5e4fa2 > view matrix view matrix camera -0.90459,-0.41928,0.076824,206.19,0.006944,-0.19472,-0.98083,-135.96,0.4262,-0.88673,0.17907,288.7 view matrix models #1,0.89496,0.093382,0.43626,-102.81,-0.22871,0.93562,0.26891,-9.4126,-0.38306,-0.34044,0.8587,169.45,#2,0.1565,-0.97608,0.1509,311.64,0.98083,0.17155,0.092386,-15.061,-0.11606,0.13355,0.98422,52.011 > close session > open > /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/RealSpaceRefine_7/Fecto2M_post_J772-coot-113_real_space_refined_007.pdb Chain information for Fecto2M_post_J772-coot-113_real_space_refined_007.pdb #1 --- Chain | Description A B C | No description available a b | No description available c | No description available > lighting soft > hide atoms > set bgColor #ffffff00 > graphics silhouettes true width 5 > camera ortho > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > show cartoons > style stick Changed 9894 atom styles > view matrix camera > -0.74823,0.042535,-0.66207,7.8769,0.66342,0.053621,-0.74632,-20.179,0.0037562,-0.99766,-0.06834,147.61 > zoom 0.45 > cartoon suppressBackboneDisplay false > color #1/a #2e7fbd > color #1/b #60a4d8 > color #1/c #9dc7e7 > color #1/A #c57e9e > color #1/B #bc8ba7 > color #1/C #b094ab > open > /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab- > coot-124_water_merged_F.pdb Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #2 --- Chain | Description A C E | No description available B D F | No description available G I K | No description available H J L | No description available > hide atoms > lighting model #1,2 depthCue false > hide #1/B,b,C,c cartoons > show #2/A,B cartoons > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > matchmaker #2/B to #1/a:290-373 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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence alignment score = 372.7 RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs: 1.831) > color #2/A #8a8a8a > color #2/C #a3a3a3 > color #2/E #6d6d6d > color #2/B #7ab497 > color #2/F #72a27e > color #2/D #728f83 > view matrix camera > -0.84574,0.026011,-0.53296,40.496,0.53352,0.025995,-0.84538,-47.511,-0.008135,-0.99933,-0.035864,165.23 > transparency #2 100 cartoons > color #1/A #9e0142 > color #1/a:110-137 #e95c47 > color #1/a:138-166 #fdbf6f > color #1/a:167-288 #ffffbe > color #1/a:229-377 #bfe5a0 > color #1/a:374-461 #54aead > color #1/a:462-487 #5e4fa2 > hide :24-48,290-373 cartoons > hide :49-290 cartoons > view matrix camera > -0.90459,-0.41928,0.076824,206.19,0.006944,-0.19472,-0.98083,-135.96,0.4262,-0.88673,0.17907,288.7 > view matrix view matrix camera -0.99653,-0.031509,0.076824,202.17,-0.069875,-0.18189,-0.98083,-136.26,0.044881,-0.98281,0.17907,288.8 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.039804,-0.96395,-0.2631,417.2,0.97181,0.023887,-0.23454,73.398,0.23237,-0.26502,0.93583,78.447 > view matrix camera > -0.99653,-0.031509,0.076824,202.17,-0.069875,-0.18189,-0.98083,-136.26,0.044881,-0.98281,0.17907,288.8 > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto2M_post_pre_trans_DII.png > supersample 8 transparentBackground true height 2500 > matchmaker #1/a:374-426 to #2/B:374-426 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 FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2) with Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1), sequence alignment score = 261.2 RMSD between 48 pruned atom pairs is 1.045 angstroms; (across all 53 pairs: 1.286) > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto2M_post_pre_trans_DII_local.png > supersample 8 transparentBackground true height 2500 > show #1/A,a cartoons > show #2/A,B > show #2/A,B cartoons > hide atoms > matchmaker #2/B to #1/a:290-373 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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence alignment score = 372.7 RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs: 1.831) > hide :24-48 cartoons > hide :288-5000 cartoons > view matrix camera > -0.89502,-0.33808,0.29088,275.58,-0.3106,0.004444,-0.95052,-108.34,0.32006,-0.9411,-0.10898,160.67 [Repeated 1 time(s)] > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto2M_post_pre_trans_DIII.png > supersample 8 transparentBackground true height 2500 > matchmaker #2/B to #1/a:290-373 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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence alignment score = 372.7 RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs: 1.831) > matchmaker #2/A to #1/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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain A (#1) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain A (#2), sequence alignment score = 348.8 RMSD between 41 pruned atom pairs is 0.980 angstroms; (across all 72 pairs: 3.967) > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto2M_post_pre_trans_DIII_aln.png > supersample 8 transparentBackground true height 2500 > close session > open > /media/dzyla/Data/Data_exchange/pycharm/structures/structure_comparison/Fecto2M_post_super.pdb Chain information for Fecto2M_post_super.pdb #1 --- Chain | Description A B C | No description available a b | No description available c | No description available > lighting soft > hide atoms > set bgColor #ffffff00 > graphics silhouettes true width 5 > camera ortho > open > /media/dzyla/Data/Data_exchange/pycharm/structures/structure_comparison/Fecto2M_fab_super.pdb Chain information for Fecto2M_fab_super.pdb #2 --- Chain | Description A C E | No description available B D F | No description available G I K | No description available H J L | No description available > hide atoms > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > show cartoons > style stick Changed 26083 atom styles > zoom 0.45 > cartoon suppressBackboneDisplay false > lighting model #1,2 depthCue false > hide #2/G-L cartoons > turn z -35 models #1-2 > move x 100 models #1 > color #1 #9dc7e7 > color #2 #7ab497 > select #2/ C:27,C:28,C:31,C:36,C:37,C:38,C:39,C:40,C:41 58 atoms, 57 bonds, 9 residues, 1 model selected > select add #2/ > D:295,D:297,D:339,D:382,D:383,D:384,D:434,D:435,D:436,D:437,D:438,D:439 159 atoms, 156 bonds, 21 residues, 1 model selected > select add #2/ F:121,F:122,F:123,F:124,F:125 188 atoms, 184 bonds, 26 residues, 1 model selected > show sel atoms > style sel sphere Changed 188 atom styles > select clear > select #2/ D:418,D:434,D:435 25 atoms, 23 bonds, 3 residues, 1 model selected > show sel atoms > style sel sphere Changed 25 atom styles > select clear > select add #1/ B:27,B:28,B:31,B:36,B:37,B:38,B:39,B:40,B:41 58 atoms, 57 bonds, 9 residues, 1 model selected > select add #1/ > b:295,b:297,b:339,b:382,b:383,b:384,b:434,b:435,b:436,b:437,b:438,b:439 159 atoms, 156 bonds, 21 residues, 1 model selected > select add #1/ c:121,c:122,c:123,c:124,c:125 159 atoms, 156 bonds, 21 residues, 1 model selected > select add #1/ b:418,b:434,b:435 167 atoms, 163 bonds, 22 residues, 1 model selected > color #2/ C:27,C:28,C:31,C:36,C:37,C:38,C:39,C:40,C:41 #6a64a5 > color #2/ > D:295,D:297,D:339,D:382,D:383,D:384,D:434,D:435,D:436,D:437,D:438,D:439 > #6a64a5 > color #2/ F:121,F:122,F:123,F:124,F:125 #6a64a5 > color #2/ D:418,D:434,D:435 #b188a7 > color #1/ B:27,B:28,B:31,B:36,B:37,B:38,B:39,B:40,B:41 #6a64a5 > color #1/ > b:295,b:297,b:339,b:382,b:383,b:384,b:434,b:435,b:436,b:437,b:438,b:439 > #6a64a5 > color #1/ c:121,c:122,c:123,c:124,c:125 #6a64a5 > color #1/ b:418,b:434,b:435 #b188a7 > show sel atoms > style sel sphere Changed 167 atom styles > select clear > view matrix camera > 0.99309,-0.023442,0.115,291.87,-0.11595,-0.043809,0.99229,479.85,-0.018223,-0.99876,-0.046225,163.54 > transparancy 100 c Unknown command: transparancy 100 c > transparancy #1,2 100 c Unknown command: transparancy #1,2 100 c > transparency #1-2 100 cartoons > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/pre_post_epitope_trans.png > supersample 8 transparentBackground true height 2500 > close session > open 8DMJ Summary of feedback from opening 8DMJ fetched from pdb --- note | Fetching compressed mmCIF 8dmj from http://files.rcsb.org/download/8dmj.cif 8dmj title: Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...] Chain information for 8dmj #1 --- Chain | Description | UniProt A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113 117-488 D H | antibody 1H1 heavy chain | E L | antibody 1H1 light chain | > open 8DMJ 8dmj title: Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...] Chain information for 8dmj #2 --- Chain | Description | UniProt A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113 117-488 D H | antibody 1H1 heavy chain | E L | antibody 1H1 light chain | > open 7UOP Summary of feedback from opening 7UOP fetched from pdb --- note | Fetching compressed mmCIF 7uop from http://files.rcsb.org/download/7uop.cif 7uop title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more info...] Chain information for 7uop #3 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 4H3 heavy chain | E F L | Fab 4H3 light chain | Non-standard residues in 7uop #3 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPA Summary of feedback from opening 7UPA fetched from pdb --- note | Fetching compressed mmCIF 7upa from http://files.rcsb.org/download/7upa.cif 7upa title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more info...] Chain information for 7upa #4 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480 B C H | Fab 1H8 heavy chain | E F L | Fab 1H8 light chain | Non-standard residues in 7upa #4 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPD Summary of feedback from opening 7UPD fetched from pdb --- note | Fetching compressed mmCIF 7upd from http://files.rcsb.org/download/7upd.cif 7upd title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more info...] Chain information for 7upd #5 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474 B C H | Fab 2B12 heavy chain | E F L | Fab 2B12 light chain | Non-standard residues in 7upd #5 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPK Summary of feedback from opening 7UPK fetched from pdb --- note | Fetching compressed mmCIF 7upk from http://files.rcsb.org/download/7upk.cif 7upk title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more info...] Chain information for 7upk #6 --- Chain | Description | UniProt A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480 C E H | Fab 1A9 heavy chain | F G L | Fab 1A9 light chain | > open 7UP9 Summary of feedback from opening 7UP9 fetched from pdb --- note | Fetching compressed mmCIF 7up9 from http://files.rcsb.org/download/7up9.cif 7up9 title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more info...] Chain information for 7up9 #7 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 H | Fab 2D3 heavy chain | L | Fab 2D3 light chain | Non-standard residues in 7up9 #7 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPB Summary of feedback from opening 7UPB fetched from pdb --- note | Fetching compressed mmCIF 7upb from http://files.rcsb.org/download/7upb.cif 7upb title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more info...] Chain information for 7upb #8 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 1H1 heavy chain | E F L | Fab 1H1 light chain | Non-standard residues in 7upb #8 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 8DG8 Summary of feedback from opening 8DG8 fetched from pdb --- note | Fetching compressed mmCIF 8dg8 from http://files.rcsb.org/download/8dg8.cif 8dg8 title: Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more info...] Chain information for 8dg8 #9 --- Chain | Description A B C | Fusion glycoprotein F0 H | 3x1 monoclonal antibody, VH region L | 3x1 monoclonal antibody, VL region Non-standard residues in 8dg8 #9 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 6T3F Summary of feedback from opening 6T3F fetched from pdb --- note | Fetching compressed mmCIF 6t3f from http://files.rcsb.org/download/6t3f.cif 6t3f title: Crystal structure Nipah virus fusion glycoprotein in complex with a neutralising Fab fragment [more info...] Chain information for 6t3f #10 --- Chain | Description | UniProt F | Fusion glycoprotein F0 | FUS_NIPAV 26-482 H | Fab66 heavy chain | L | Fab66 light chain | Non-standard residues in 6t3f #10 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose 6t3f mmCIF Assemblies --- 1| author_and_software_defined_assembly > lighting soft [Repeated 1 time(s)] > hide atoms > show cartoons > close session > open > /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab- > coot-124_water_merged_F.pdb Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1 --- Chain | Description A C E | No description available B D F | No description available G I K | No description available H J L | No description available > open 8DMJ 8dmj title: Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...] Chain information for 8dmj #2 --- Chain | Description | UniProt A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113 117-488 D H | antibody 1H1 heavy chain | E L | antibody 1H1 light chain | > open 8DMJ 8dmj title: Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...] Chain information for 8dmj #3 --- Chain | Description | UniProt A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113 117-488 D H | antibody 1H1 heavy chain | E L | antibody 1H1 light chain | > open 7UOP 7uop title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more info...] Chain information for 7uop #4 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 4H3 heavy chain | E F L | Fab 4H3 light chain | Non-standard residues in 7uop #4 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPA 7upa title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more info...] Chain information for 7upa #5 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480 B C H | Fab 1H8 heavy chain | E F L | Fab 1H8 light chain | Non-standard residues in 7upa #5 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPD 7upd title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more info...] Chain information for 7upd #6 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474 B C H | Fab 2B12 heavy chain | E F L | Fab 2B12 light chain | Non-standard residues in 7upd #6 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPK 7upk title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more info...] Chain information for 7upk #7 --- Chain | Description | UniProt A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480 C E H | Fab 1A9 heavy chain | F G L | Fab 1A9 light chain | > open 7UP9 7up9 title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more info...] Chain information for 7up9 #8 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 H | Fab 2D3 heavy chain | L | Fab 2D3 light chain | Non-standard residues in 7up9 #8 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPB 7upb title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more info...] Chain information for 7upb #9 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 1H1 heavy chain | E F L | Fab 1H1 light chain | Non-standard residues in 7upb #9 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 8DG8 8dg8 title: Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more info...] Chain information for 8dg8 #10 --- Chain | Description A B C | Fusion glycoprotein F0 H | 3x1 monoclonal antibody, VH region L | 3x1 monoclonal antibody, VL region Non-standard residues in 8dg8 #10 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 6T3F 6t3f title: Crystal structure Nipah virus fusion glycoprotein in complex with a neutralising Fab fragment [more info...] Chain information for 6t3f #11 --- Chain | Description | UniProt F | Fusion glycoprotein F0 | FUS_NIPAV 26-482 H | Fab66 heavy chain | L | Fab66 light chain | Non-standard residues in 6t3f #11 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose 6t3f mmCIF Assemblies --- 1| author_and_software_defined_assembly > close session > print('open > /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab- > coot-124_water_merged_F.pdb') Unknown command: print('open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab- coot-124_water_merged_F.pdb') > print('open > /home/dzyla/OneDrive/Code/F_fab/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009(1).pdb') Unknown command: print('open /home/dzyla/OneDrive/Code/F_fab/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009(1).pdb') > force pdb_name in ['8DMJ', '8DMJ', '7UOP', '7UPA', '7UPD', '7UPK', '7UP9', > '7UPB', '8DG8', '6T3F']: force is provided by the uninstalled bundle SEQCROW versions 1.6.6 – 1.8.2 > print(f'open {pdb_name}') Unknown command: print(f'open {pdb_name}') > open > /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab- > coot-124_water_merged_F.pdb Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1 --- Chain | Description A C E | No description available B D F | No description available G I K | No description available H J L | No description available > open > /home/dzyla/OneDrive/Code/F_fab/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009(1).pdb No such file/path: /home/dzyla/OneDrive/Code/F_fab/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009(1).pdb > open 8DMJ 8dmj title: Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...] Chain information for 8dmj #2 --- Chain | Description | UniProt A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113 117-488 D H | antibody 1H1 heavy chain | E L | antibody 1H1 light chain | > open 8DMJ 8dmj title: Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...] Chain information for 8dmj #3 --- Chain | Description | UniProt A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113 117-488 D H | antibody 1H1 heavy chain | E L | antibody 1H1 light chain | > open 7UOP 7uop title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more info...] Chain information for 7uop #4 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 4H3 heavy chain | E F L | Fab 4H3 light chain | Non-standard residues in 7uop #4 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPA 7upa title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more info...] Chain information for 7upa #5 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480 B C H | Fab 1H8 heavy chain | E F L | Fab 1H8 light chain | Non-standard residues in 7upa #5 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPD 7upd title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more info...] Chain information for 7upd #6 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474 B C H | Fab 2B12 heavy chain | E F L | Fab 2B12 light chain | Non-standard residues in 7upd #6 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPK 7upk title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more info...] Chain information for 7upk #7 --- Chain | Description | UniProt A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480 C E H | Fab 1A9 heavy chain | F G L | Fab 1A9 light chain | > open 7UP9 7up9 title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more info...] Chain information for 7up9 #8 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 H | Fab 2D3 heavy chain | L | Fab 2D3 light chain | Non-standard residues in 7up9 #8 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPB 7upb title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more info...] Chain information for 7upb #9 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 1H1 heavy chain | E F L | Fab 1H1 light chain | Non-standard residues in 7upb #9 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 8DG8 8dg8 title: Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more info...] Chain information for 8dg8 #10 --- Chain | Description A B C | Fusion glycoprotein F0 H | 3x1 monoclonal antibody, VH region L | 3x1 monoclonal antibody, VL region Non-standard residues in 8dg8 #10 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 6T3F 6t3f title: Crystal structure Nipah virus fusion glycoprotein in complex with a neutralising Fab fragment [more info...] Chain information for 6t3f #11 --- Chain | Description | UniProt F | Fusion glycoprotein F0 | FUS_NIPAV 26-482 H | Fab66 heavy chain | L | Fab66 light chain | Non-standard residues in 6t3f #11 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose 6t3f mmCIF Assemblies --- 1| author_and_software_defined_assembly > close session > open > /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab- > coot-124_water_merged_F.pdb Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1 --- Chain | Description A C E | No description available B D F | No description available G I K | No description available H J L | No description available > open > /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/structures_PDBs/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb Chain information for Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb #2 --- Chain | Description A | No description available C E G | No description available D F | No description available > open 8DMJ 8dmj title: Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...] Chain information for 8dmj #3 --- Chain | Description | UniProt A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113 117-488 D H | antibody 1H1 heavy chain | E L | antibody 1H1 light chain | > open 8DMJ 8dmj title: Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...] Chain information for 8dmj #4 --- Chain | Description | UniProt A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113 117-488 D H | antibody 1H1 heavy chain | E L | antibody 1H1 light chain | > open 7UOP 7uop title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more info...] Chain information for 7uop #5 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 4H3 heavy chain | E F L | Fab 4H3 light chain | Non-standard residues in 7uop #5 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPA 7upa title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more info...] Chain information for 7upa #6 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480 B C H | Fab 1H8 heavy chain | E F L | Fab 1H8 light chain | Non-standard residues in 7upa #6 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPD 7upd title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more info...] Chain information for 7upd #7 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474 B C H | Fab 2B12 heavy chain | E F L | Fab 2B12 light chain | Non-standard residues in 7upd #7 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPK 7upk title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more info...] Chain information for 7upk #8 --- Chain | Description | UniProt A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480 C E H | Fab 1A9 heavy chain | F G L | Fab 1A9 light chain | > open 7UP9 7up9 title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more info...] Chain information for 7up9 #9 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 H | Fab 2D3 heavy chain | L | Fab 2D3 light chain | Non-standard residues in 7up9 #9 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPB 7upb title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more info...] Chain information for 7upb #10 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 1H1 heavy chain | E F L | Fab 1H1 light chain | Non-standard residues in 7upb #10 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 8DG8 8dg8 title: Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more info...] Chain information for 8dg8 #11 --- Chain | Description A B C | Fusion glycoprotein F0 H | 3x1 monoclonal antibody, VH region L | 3x1 monoclonal antibody, VL region Non-standard residues in 8dg8 #11 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 6T3F 6t3f title: Crystal structure Nipah virus fusion glycoprotein in complex with a neutralising Fab fragment [more info...] Chain information for 6t3f #12 --- Chain | Description | UniProt F | Fusion glycoprotein F0 | FUS_NIPAV 26-482 H | Fab66 heavy chain | L | Fab66 light chain | Non-standard residues in 6t3f #12 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose 6t3f mmCIF Assemblies --- 1| author_and_software_defined_assembly > lighting soft > hide atoms > set bgColor #ffffff00 > graphics silhouettes true width 5 > camera ortho > close session > lighting soft > hide atoms > set bgColor #ffffff00 > graphics silhouettes true width 5 > camera ortho > open > /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab- > coot-124_water_merged_F.pdb Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1 --- Chain | Description A C E | No description available B D F | No description available G I K | No description available H J L | No description available > open > /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/structures_PDBs/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb Chain information for Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb #2 --- Chain | Description A | No description available C E G | No description available D F | No description available > open 8DMJ 8dmj title: Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...] Chain information for 8dmj #3 --- Chain | Description | UniProt A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113 117-488 D H | antibody 1H1 heavy chain | E L | antibody 1H1 light chain | > open 8DMJ 8dmj title: Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...] Chain information for 8dmj #4 --- Chain | Description | UniProt A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113 117-488 D H | antibody 1H1 heavy chain | E L | antibody 1H1 light chain | > open 7UOP 7uop title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more info...] Chain information for 7uop #5 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 4H3 heavy chain | E F L | Fab 4H3 light chain | Non-standard residues in 7uop #5 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPA 7upa title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more info...] Chain information for 7upa #6 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480 B C H | Fab 1H8 heavy chain | E F L | Fab 1H8 light chain | Non-standard residues in 7upa #6 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPD 7upd title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more info...] Chain information for 7upd #7 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474 B C H | Fab 2B12 heavy chain | E F L | Fab 2B12 light chain | Non-standard residues in 7upd #7 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPK 7upk title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more info...] Chain information for 7upk #8 --- Chain | Description | UniProt A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480 C E H | Fab 1A9 heavy chain | F G L | Fab 1A9 light chain | > open 7UP9 7up9 title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more info...] Chain information for 7up9 #9 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 H | Fab 2D3 heavy chain | L | Fab 2D3 light chain | Non-standard residues in 7up9 #9 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPB 7upb title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more info...] Chain information for 7upb #10 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 1H1 heavy chain | E F L | Fab 1H1 light chain | Non-standard residues in 7upb #10 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 8DG8 8dg8 title: Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more info...] Chain information for 8dg8 #11 --- Chain | Description A B C | Fusion glycoprotein F0 H | 3x1 monoclonal antibody, VH region L | 3x1 monoclonal antibody, VL region Non-standard residues in 8dg8 #11 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 6T3F 6t3f title: Crystal structure Nipah virus fusion glycoprotein in complex with a neutralising Fab fragment [more info...] Chain information for 6t3f #12 --- Chain | Description | UniProt F | Fusion glycoprotein F0 | FUS_NIPAV 26-482 H | Fab66 heavy chain | L | Fab66 light chain | Non-standard residues in 6t3f #12 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose 6t3f mmCIF Assemblies --- 1| author_and_software_defined_assembly > hide atoms > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > show cartoons > style stick Changed 157624 atom styles > zoom 0.45 > cartoon suppressBackboneDisplay false > lighting model #1-100 depthCue false > lighting soft > mmaker #1 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain F (#1), sequence alignment score = 1790.1 RMSD between 363 pruned atom pairs is 0.706 angstroms; (across all 372 pairs: 0.837) > mmaker #2 to #2 Must use different reference and match structures > mmaker #3 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain E (#2) with 8dmj, chain A (#3), sequence alignment score = 723.5 RMSD between 39 pruned atom pairs is 0.733 angstroms; (across all 252 pairs: 19.926) > mmaker #4 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain E (#2) with 8dmj, chain A (#4), sequence alignment score = 723.5 RMSD between 39 pruned atom pairs is 0.733 angstroms; (across all 252 pairs: 19.926) > mmaker #5 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7uop, chain G (#5), sequence alignment score = 900.1 RMSD between 213 pruned atom pairs is 1.353 angstroms; (across all 362 pairs: 2.794) > mmaker #6 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7upa, chain D (#6), sequence alignment score = 902.3 RMSD between 227 pruned atom pairs is 1.351 angstroms; (across all 367 pairs: 3.175) > mmaker #7 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7upd, chain A (#7), sequence alignment score = 885.6 RMSD between 262 pruned atom pairs is 1.274 angstroms; (across all 361 pairs: 2.567) > mmaker #8 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7upk, chain B (#8), sequence alignment score = 912.5 RMSD between 227 pruned atom pairs is 1.243 angstroms; (across all 358 pairs: 2.604) > mmaker #9 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7up9, chain G (#9), sequence alignment score = 902.5 RMSD between 269 pruned atom pairs is 1.254 angstroms; (across all 362 pairs: 2.596) > mmaker #10 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7upb, chain G (#10), sequence alignment score = 888.7 RMSD between 270 pruned atom pairs is 1.267 angstroms; (across all 362 pairs: 2.541) > mmaker #11 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 8dg8, chain C (#11), sequence alignment score = 578.5 RMSD between 93 pruned atom pairs is 0.983 angstroms; (across all 340 pairs: 5.826) > mmaker #12 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 6t3f, chain F (#12), sequence alignment score = 911.4 RMSD between 263 pruned atom pairs is 1.279 angstroms; (across all 364 pairs: 2.713) > hide #2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!8 models > hide #!9 models > hide #!11 models > hide #!12 models > hide #10 models > hide #!7 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!9 models > show #10 models > hide #10 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!12 models > hide #!9 models > show #!9 models > show #2 models > hide #1 models > mmaker #9/G to #2/C 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7up9, chain G (#9), sequence alignment score = 898.3 RMSD between 265 pruned atom pairs is 1.251 angstroms; (across all 362 pairs: 2.613) > hide #!12 models > hide #!9 models > color #1/G,I,K #b188a7 > color #1/H,J,L #6a64a5 > color #1/B,D,F #72a27e > color #1/A,C,E #a7a7a7 > color #2/A,C,E #a7a7a7 > show #!9 models > show #!11 models > hide #!11 models > show #10 models > hide #10 models > show #!12 models > hide #!12 models > hide #!9 models > show #1 models > hide #1 models > color #2/A,B,C #a7a7a7 > color #2 bychain > color #2/F,A,E #a7a7a7 > color #2/F,A,E #72a27e > color #2 bychain > color #2/F,A,E #72a27e > color #2/G,D,C #a7a7a7 > color #2/F,A,E #72a27e > color #2 bychain > print('color #2/G,E,C #72a27e') Unknown command: print('color #2/G,E,C #72a27e') > color #2/G,E,C #72a27e > color #2/F,D,A #a7a7a7 > color #2/G,E,C #72a27e > show #1 models > hide #1/A-F > hide #1/A-F cartoons > show #!3 models > hide #2 models > show #2 models > hide #1/A-F,G,H,L,K cartoons > hide #!3 models > show #!4 models > hide #!4 models > show #!4 models > show #!3 models > hide #2 models > hide #1 models > hide #!3 models > show #!3 models > close session > lighting soft > hide atoms > set bgColor #ffffff00 > graphics silhouettes true width 5 > camera ortho > open > /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab- > coot-124_water_merged_F.pdb Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1 --- Chain | Description A C E | No description available B D F | No description available G I K | No description available H J L | No description available > open > /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/structures_PDBs/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb Chain information for Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb #2 --- Chain | Description A | No description available C E G | No description available D F | No description available > open 7UOP 7uop title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more info...] Chain information for 7uop #3 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 4H3 heavy chain | E F L | Fab 4H3 light chain | Non-standard residues in 7uop #3 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPA 7upa title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more info...] Chain information for 7upa #4 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480 B C H | Fab 1H8 heavy chain | E F L | Fab 1H8 light chain | Non-standard residues in 7upa #4 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPD 7upd title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more info...] Chain information for 7upd #5 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474 B C H | Fab 2B12 heavy chain | E F L | Fab 2B12 light chain | Non-standard residues in 7upd #5 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPK 7upk title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more info...] Chain information for 7upk #6 --- Chain | Description | UniProt A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480 C E H | Fab 1A9 heavy chain | F G L | Fab 1A9 light chain | > open 7UP9 7up9 title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more info...] Chain information for 7up9 #7 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 H | Fab 2D3 heavy chain | L | Fab 2D3 light chain | Non-standard residues in 7up9 #7 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPB 7upb title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more info...] Chain information for 7upb #8 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 1H1 heavy chain | E F L | Fab 1H1 light chain | Non-standard residues in 7upb #8 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 8DG8 8dg8 title: Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more info...] Chain information for 8dg8 #9 --- Chain | Description A B C | Fusion glycoprotein F0 H | 3x1 monoclonal antibody, VH region L | 3x1 monoclonal antibody, VL region Non-standard residues in 8dg8 #9 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 6T3F 6t3f title: Crystal structure Nipah virus fusion glycoprotein in complex with a neutralising Fab fragment [more info...] Chain information for 6t3f #10 --- Chain | Description | UniProt F | Fusion glycoprotein F0 | FUS_NIPAV 26-482 H | Fab66 heavy chain | L | Fab66 light chain | Non-standard residues in 6t3f #10 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose 6t3f mmCIF Assemblies --- 1| author_and_software_defined_assembly > hide atoms > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > show cartoons > style stick Changed 135564 atom styles > zoom 0.45 > cartoon suppressBackboneDisplay false > lighting model #1-100 depthCue false > lighting soft > mmaker #1 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain F (#1), sequence alignment score = 1790.1 RMSD between 363 pruned atom pairs is 0.706 angstroms; (across all 372 pairs: 0.837) > mmaker #2 to #2 Must use different reference and match structures > mmaker #3 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7uop, chain G (#3), sequence alignment score = 900.1 RMSD between 213 pruned atom pairs is 1.353 angstroms; (across all 362 pairs: 2.794) > mmaker #4 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7upa, chain D (#4), sequence alignment score = 902.3 RMSD between 227 pruned atom pairs is 1.351 angstroms; (across all 367 pairs: 3.175) > mmaker #5 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7upd, chain A (#5), sequence alignment score = 885.6 RMSD between 262 pruned atom pairs is 1.274 angstroms; (across all 361 pairs: 2.567) > mmaker #6 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7upk, chain B (#6), sequence alignment score = 912.5 RMSD between 227 pruned atom pairs is 1.243 angstroms; (across all 358 pairs: 2.604) > mmaker #7 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7up9, chain G (#7), sequence alignment score = 902.5 RMSD between 269 pruned atom pairs is 1.254 angstroms; (across all 362 pairs: 2.596) > mmaker #8 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7upb, chain G (#8), sequence alignment score = 888.7 RMSD between 270 pruned atom pairs is 1.267 angstroms; (across all 362 pairs: 2.541) > mmaker #9/G to #2/C No molecules/chains to match specified > color #2/F,D,A #a7a7a7 > color #2/G,E,C #72a27e > hide #1/A-F,G,H,L,K cartoons > hide #2,8#!3-7,9-10 target m > hide #1 models > show #1 models > show #2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #8 models > show #!9 models > show #!10 models > mmaker #1 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain F (#1), sequence alignment score = 1790.1 RMSD between 363 pruned atom pairs is 0.706 angstroms; (across all 372 pairs: 0.837) > mmaker #2 to #2 Must use different reference and match structures > mmaker #3 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7uop, chain G (#3), sequence alignment score = 900.1 RMSD between 213 pruned atom pairs is 1.353 angstroms; (across all 362 pairs: 2.794) > mmaker #4 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7upa, chain D (#4), sequence alignment score = 902.3 RMSD between 227 pruned atom pairs is 1.351 angstroms; (across all 367 pairs: 3.175) > mmaker #5 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7upd, chain A (#5), sequence alignment score = 885.6 RMSD between 262 pruned atom pairs is 1.274 angstroms; (across all 361 pairs: 2.567) > mmaker #6 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7upk, chain B (#6), sequence alignment score = 912.5 RMSD between 227 pruned atom pairs is 1.243 angstroms; (across all 358 pairs: 2.604) > mmaker #7 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7up9, chain G (#7), sequence alignment score = 902.5 RMSD between 269 pruned atom pairs is 1.254 angstroms; (across all 362 pairs: 2.596) > mmaker #8 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7upb, chain G (#8), sequence alignment score = 888.7 RMSD between 270 pruned atom pairs is 1.267 angstroms; (across all 362 pairs: 2.541) > mmaker #9 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 8dg8, chain C (#9), sequence alignment score = 578.5 RMSD between 93 pruned atom pairs is 0.983 angstroms; (across all 340 pairs: 5.826) > color #2/F,D,A #a7a7a7 > color #2/G,E,C #72a27e > hide #1/A-F,G,H,L,K cartoons > hide #8#!3-7,9-10 target m > show #!10 models > mmaker #10 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 6t3f, chain F (#10), sequence alignment score = 911.4 RMSD between 263 pruned atom pairs is 1.279 angstroms; (across all 364 pairs: 2.713) > show #!9 models > mmaker #1 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain F (#1), sequence alignment score = 1790.1 RMSD between 363 pruned atom pairs is 0.706 angstroms; (across all 372 pairs: 0.837) > mmaker #2 to #2 Must use different reference and match structures > mmaker #3 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7uop, chain G (#3), sequence alignment score = 900.1 RMSD between 213 pruned atom pairs is 1.353 angstroms; (across all 362 pairs: 2.794) > mmaker #4 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7upa, chain D (#4), sequence alignment score = 902.3 RMSD between 227 pruned atom pairs is 1.351 angstroms; (across all 367 pairs: 3.175) > mmaker #5 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7upd, chain A (#5), sequence alignment score = 885.6 RMSD between 262 pruned atom pairs is 1.274 angstroms; (across all 361 pairs: 2.567) > mmaker #6 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7upk, chain B (#6), sequence alignment score = 912.5 RMSD between 227 pruned atom pairs is 1.243 angstroms; (across all 358 pairs: 2.604) > mmaker #7 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7up9, chain G (#7), sequence alignment score = 902.5 RMSD between 269 pruned atom pairs is 1.254 angstroms; (across all 362 pairs: 2.596) > mmaker #8 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7upb, chain G (#8), sequence alignment score = 888.7 RMSD between 270 pruned atom pairs is 1.267 angstroms; (across all 362 pairs: 2.541) > mmaker #9 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 8dg8, chain C (#9), sequence alignment score = 578.5 RMSD between 93 pruned atom pairs is 0.983 angstroms; (across all 340 pairs: 5.826) > mmaker #9/G to #2/C No molecules/chains to match specified > color #2/F,D,A #a7a7a7 > color #2/G,E,C #72a27e > hide #1/A-F,G,H,L,K cartoons > hide #!9 models > show #!9 models > hide #!10 models > mmaker #9/B to #2/C 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 8dg8, chain B (#9), sequence alignment score = 549.2 RMSD between 103 pruned atom pairs is 1.081 angstroms; (across all 335 pairs: 6.197) > hide #2 models > show #2 models > hide #1 models > show #1 models > show #!3 models > color #1/G,I,K #b188a7 > color #1/H,J,L #6a64a5 > hide #1 models > hide #!3 models > hide #!9 models > show #!3 models > hide #2 models > color #!3 bychain > hide #3/G,A,D,C,F,B,E cartoons > show #2 models > show #1 models > show #!4 models > hide #!3 models > hide #1 models > hide #2 models > show #1 models > show #!5 models > hide #!4 models > show #!4 models > hide #!5 models > hide ~#4/C,F cartoons > show #!3 models > show #2 models > hide ~#4/A,B,D,E,G,H,I,J,K cartoons > hide #4/A,B,D,E,G,H,I,J,K cartoons > show #1-2#!3-4 cartoons > hide #4/A,B,D,E,G,H,I,J,K cartoons > hide #!3 models > hide #2 models > hide #1 models > hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons > show #1 models > color #1/G,I,K #b188a7 > color #1/H,J,L #6a64a5 > color #2/F,D,A #a7a7a7 > color #2/G,E,C #72a27e > hide #1/A-F,G,H,L,K cartoons > hide #3/G,A,D,C,F,B,E cartoons > hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons [Repeated 1 time(s)] > show #2 models > show #!3 models > show #!5 models > show #1-2#!3-5 cartoons > hide #!4 models > hide #!3 models > hide #2 models > hide #1 models > hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons > show #2 models > show #1 models > color #1/G,I,K #b188a7 > color #1/H,J,L #6a64a5 > color #2/F,D,A #a7a7a7 > color #2/G,E,C #72a27e > hide #1/A,C,D,F,G,H,K,L,M,N,O,P cartoons > hide #3/G,A,D,C,F,B,E cartoons > hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons [Repeated 1 time(s)] > hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons > show #!3 models > show #!4 models > show #!6 models > show #5-10 cartoons > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #1 models > show #!5 models > hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons > show #!6 models > hide #1/A,B,C,D,F,H,I,J,K,L,M,N,O,P cartoons > hide #6/A,B,C,D,F,H,I,J,K,L,M,N,O,P cartoons > hide #!5 models > hide #!6 models > show #!7 models > show #1 models > hide #1 models > show #!3 models > show #!4 models > hide #!3 models > mmaker #7/G to #2/C 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7up9, chain G (#7), sequence alignment score = 898.3 RMSD between 265 pruned atom pairs is 1.251 angstroms; (across all 362 pairs: 2.613) > hide #7/A,B,C,D,F,I,J,K,M,N,O,P cartoons > hide #7/A,B,C,D,F,G,I,J,K,M,N,O,P cartoons > hide #!4 models > hide #!7 models > show #8 models > hide #8/A,B,C,D,E,F,G,I,J,K,M,N,O,P cartoons > hide #8 models > show #!9 models > hide #9/A,B,C,D,F,I,J,K,M,N,O,P cartoons > hide #!9 models > show #!10 models > color #2#!10 bychain > hide #2 models > hide #10/A,B,C,D,F,I,J,K,M,N,O,P cartoons > show #1 models > hide #1 models > show #2 models > show #!3 models > close session > lighting soft > hide atoms > set bgColor #ffffff00 > graphics silhouettes true width 5 > camera ortho > open > /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab- > coot-124_water_merged_F.pdb Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1 --- Chain | Description A C E | No description available B D F | No description available G I K | No description available H J L | No description available > open > /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/structures_PDBs/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb Chain information for Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb #2 --- Chain | Description A | No description available C E G | No description available D F | No description available > open 7UOP 7uop title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more info...] Chain information for 7uop #3 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 4H3 heavy chain | E F L | Fab 4H3 light chain | Non-standard residues in 7uop #3 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPA 7upa title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more info...] Chain information for 7upa #4 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480 B C H | Fab 1H8 heavy chain | E F L | Fab 1H8 light chain | Non-standard residues in 7upa #4 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPD 7upd title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more info...] Chain information for 7upd #5 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474 B C H | Fab 2B12 heavy chain | E F L | Fab 2B12 light chain | Non-standard residues in 7upd #5 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPK 7upk title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more info...] Chain information for 7upk #6 --- Chain | Description | UniProt A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480 C E H | Fab 1A9 heavy chain | F G L | Fab 1A9 light chain | > open 7UP9 7up9 title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more info...] Chain information for 7up9 #7 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 H | Fab 2D3 heavy chain | L | Fab 2D3 light chain | Non-standard residues in 7up9 #7 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPB 7upb title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more info...] Chain information for 7upb #8 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 1H1 heavy chain | E F L | Fab 1H1 light chain | Non-standard residues in 7upb #8 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 8DG8 8dg8 title: Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more info...] Chain information for 8dg8 #9 --- Chain | Description A B C | Fusion glycoprotein F0 H | 3x1 monoclonal antibody, VH region L | 3x1 monoclonal antibody, VL region Non-standard residues in 8dg8 #9 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 6T3F 6t3f title: Crystal structure Nipah virus fusion glycoprotein in complex with a neutralising Fab fragment [more info...] Chain information for 6t3f #10 --- Chain | Description | UniProt F | Fusion glycoprotein F0 | FUS_NIPAV 26-482 H | Fab66 heavy chain | L | Fab66 light chain | Non-standard residues in 6t3f #10 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose 6t3f mmCIF Assemblies --- 1| author_and_software_defined_assembly > hide atoms > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > show cartoons > style stick Changed 135564 atom styles > zoom 0.45 > cartoon suppressBackboneDisplay false > lighting model #1-100 depthCue false > lighting soft > mmaker #1 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain F (#1), sequence alignment score = 1790.1 RMSD between 363 pruned atom pairs is 0.706 angstroms; (across all 372 pairs: 0.837) > mmaker #2 to #2 Must use different reference and match structures > mmaker #3 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7uop, chain G (#3), sequence alignment score = 900.1 RMSD between 213 pruned atom pairs is 1.353 angstroms; (across all 362 pairs: 2.794) > mmaker #4 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7upa, chain D (#4), sequence alignment score = 902.3 RMSD between 227 pruned atom pairs is 1.351 angstroms; (across all 367 pairs: 3.175) > mmaker #5 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7upd, chain A (#5), sequence alignment score = 885.6 RMSD between 262 pruned atom pairs is 1.274 angstroms; (across all 361 pairs: 2.567) > mmaker #6 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7upk, chain B (#6), sequence alignment score = 912.5 RMSD between 227 pruned atom pairs is 1.243 angstroms; (across all 358 pairs: 2.604) > mmaker #7/G to #2/C 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7up9, chain G (#7), sequence alignment score = 898.3 RMSD between 265 pruned atom pairs is 1.251 angstroms; (across all 362 pairs: 2.613) > mmaker #8 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7upb, chain G (#8), sequence alignment score = 888.7 RMSD between 270 pruned atom pairs is 1.267 angstroms; (across all 362 pairs: 2.541) > mmaker #9 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 8dg8, chain C (#9), sequence alignment score = 578.5 RMSD between 93 pruned atom pairs is 0.983 angstroms; (across all 340 pairs: 5.826) > mmaker #9/B to #2/C 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 8dg8, chain B (#9), sequence alignment score = 549.2 RMSD between 103 pruned atom pairs is 1.081 angstroms; (across all 335 pairs: 6.197) > color #1/G,I,K #b188a7 > color #1/H,J,L #6a64a5 > color #2/F,D,A #a7a7a7 > color #2/G,E,C #72a27e > hide #1/A,C,D,F,G,H,K,L,M,N,O,P cartoons > hide #3/G,A,D,C,F,B,E cartoons > hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons [Repeated 1 time(s)] > hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons > hide #6/A,B,C,D,F,H,I,J,K,L,M,N,O,P cartoons > hide #7/A,B,C,D,F,G,I,J,K,M,N,O,P cartoons > hide #8/A,B,C,D,E,F,G,I,J,K,M,N,O,P cartoons > hide #9/A,B,C,D,F,I,J,K,M,N,O,P cartoons > hide #10/A,B,C,D,F,I,J,K,M,N,O,P cartoons > close session > lighting soft > hide atoms > set bgColor #ffffff00 > graphics silhouettes true width 5 > camera ortho > open > /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab- > coot-124_water_merged_F.pdb Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1 --- Chain | Description A C E | No description available B D F | No description available G I K | No description available H J L | No description available > open > /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/structures_PDBs/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb Chain information for Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb #2 --- Chain | Description A | No description available C E G | No description available D F | No description available > open 7UOP 7uop title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more info...] Chain information for 7uop #3 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 4H3 heavy chain | E F L | Fab 4H3 light chain | Non-standard residues in 7uop #3 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPA 7upa title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more info...] Chain information for 7upa #4 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480 B C H | Fab 1H8 heavy chain | E F L | Fab 1H8 light chain | Non-standard residues in 7upa #4 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPD 7upd title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more info...] Chain information for 7upd #5 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474 B C H | Fab 2B12 heavy chain | E F L | Fab 2B12 light chain | Non-standard residues in 7upd #5 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPK 7upk title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more info...] Chain information for 7upk #6 --- Chain | Description | UniProt A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480 C E H | Fab 1A9 heavy chain | F G L | Fab 1A9 light chain | > open 7UP9 7up9 title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more info...] Chain information for 7up9 #7 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 H | Fab 2D3 heavy chain | L | Fab 2D3 light chain | Non-standard residues in 7up9 #7 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7UPB 7upb title: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more info...] Chain information for 7upb #8 --- Chain | Description | UniProt A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475 B C H | Fab 1H1 heavy chain | E F L | Fab 1H1 light chain | Non-standard residues in 7upb #8 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 8DG8 8dg8 title: Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more info...] Chain information for 8dg8 #9 --- Chain | Description A B C | Fusion glycoprotein F0 H | 3x1 monoclonal antibody, VH region L | 3x1 monoclonal antibody, VL region Non-standard residues in 8dg8 #9 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 6T3F 6t3f title: Crystal structure Nipah virus fusion glycoprotein in complex with a neutralising Fab fragment [more info...] Chain information for 6t3f #10 --- Chain | Description | UniProt F | Fusion glycoprotein F0 | FUS_NIPAV 26-482 H | Fab66 heavy chain | L | Fab66 light chain | Non-standard residues in 6t3f #10 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose 6t3f mmCIF Assemblies --- 1| author_and_software_defined_assembly > hide atoms > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > show cartoons > style stick Changed 135564 atom styles > zoom 0.45 > cartoon suppressBackboneDisplay false > lighting model #1-100 depthCue false > lighting soft > mmaker #1 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain F (#1), sequence alignment score = 1790.1 RMSD between 363 pruned atom pairs is 0.706 angstroms; (across all 372 pairs: 0.837) > mmaker #2 to #2 Must use different reference and match structures > mmaker #3 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7uop, chain G (#3), sequence alignment score = 900.1 RMSD between 213 pruned atom pairs is 1.353 angstroms; (across all 362 pairs: 2.794) > mmaker #4 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7upa, chain D (#4), sequence alignment score = 902.3 RMSD between 227 pruned atom pairs is 1.351 angstroms; (across all 367 pairs: 3.175) > mmaker #5 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7upd, chain A (#5), sequence alignment score = 885.6 RMSD between 262 pruned atom pairs is 1.274 angstroms; (across all 361 pairs: 2.567) > mmaker #6 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7upk, chain B (#6), sequence alignment score = 912.5 RMSD between 227 pruned atom pairs is 1.243 angstroms; (across all 358 pairs: 2.604) > mmaker #7/G to #2/C 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 7up9, chain G (#7), sequence alignment score = 898.3 RMSD between 265 pruned atom pairs is 1.251 angstroms; (across all 362 pairs: 2.613) > mmaker #8 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain G (#2) with 7upb, chain G (#8), sequence alignment score = 888.7 RMSD between 270 pruned atom pairs is 1.267 angstroms; (across all 362 pairs: 2.541) > mmaker #9/B to #2/C 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 8dg8, chain B (#9), sequence alignment score = 549.2 RMSD between 103 pruned atom pairs is 1.081 angstroms; (across all 335 pairs: 6.197) > mmaker #10 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 6t3f, chain F (#10), sequence alignment score = 911.4 RMSD between 263 pruned atom pairs is 1.279 angstroms; (across all 364 pairs: 2.713) > color #1/G,I,K #b188a7 > color #1/H,J,L #6a64a5 > color #2/F,D,A #a7a7a7 > color #2/G,E,C #72a27e > hide #1/A,C,D,F,G,H,K,L,M,N,O,P cartoons > hide #3/G,A,D,C,F,B,E cartoons > hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons [Repeated 1 time(s)] > hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons > hide #6/A,B,C,D,F,H,I,J,K,L,M,N,O,P cartoons > hide #7/A,B,C,D,F,G,I,J,K,M,N,O,P cartoons > hide #8/A,B,C,D,E,F,G,I,J,K,M,N,O,P cartoons > hide #9/A,B,C,D,F,I,J,K,M,N,O,P cartoons > hide #10/A,B,C,D,F,I,J,K,M,N,O,P cartoons > hide #1 models > show #1 models > hide #1/A,B,C,D,E,F,G,H,K,L cartoons > color #3 #d95847 > color #4 #3b4cc0 > color #5 #f18d6f > color #6 #aac7fd > color #7 #f7b89c > color #8 #b40426 > color #9 #5d7ce6 > color #10 #82a6fb > hide #!10 models > hide #!9 models > hide #8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #1 models > show #!3 models > show #!4 models > define axis #2 Axis 'Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb #2/axis' centered at [132.07156997 131.9736923 125.48036225] with direction [-0.00317055 -0.00116313 0.9999943 ], radius 23.6761, and length 107.201 > hide #!4 models > hide #!3 models > show #!3 models > define axis #2 radius 5 Axis 'Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb #2/axis' centered at [132.07156997 131.9736923 125.48036225] with direction [-0.00317055 -0.00116313 0.9999943 ], radius 5, and length 107.201 > close #2.1 > define axis #3 @@display radius 5 Must specify a set of atoms or a plane > define axis #3@@display radius 5 Must specify a set of atoms or a plane > define axis #3 and @@display r 5 Expected a keyword > define axis #3 radius 5 Axis '7uop #3/axis' centered at [132.58980133 132.06261726 141.02272846] with direction [0.02033736 0.03261893 0.99926093], radius 5, and length 129.889 > close #3.2 > define axis #3/L,H radius 5 Axis '7uop #3/axis' centered at [134.19998443 171.79838611 174.79014516] with direction [-0.54656499 0.54821979 -0.63302589], radius 5, and length 53.0916 > close #3.2 > define axis #3/H radius 5 Axis '7uop #3/axis' centered at [140.01239955 164.12249353 183.10141926] with direction [0.6329338 0.59571875 0.49448354], radius 5, and length 52.3638 > show #!4 models > define axis #4/C radius 5 Axis '7upa #4/axis' centered at [ 85.97369891 142.01804641 125.37514389] with direction [-0.8230718 -0.56721815 -0.02857245], radius 5, and length 47.3939 > show #!5 models > define axis #5/B radius 5 Axis '7upd #5/axis' centered at [ 95.87753356 155.20302377 87.46728033] with direction [0.67325938 0.35084133 0.65087032], radius 5, and length 43.5673 > show #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > show #!2 models > define axis #6/E radius 5 Axis '7upk #6/axis' centered at [ 88.49402984 115.34643043 136.2780465 ] with direction [-0.75084234 -0.30557612 0.58554164], radius 5, and length 46.005 > close #3.2#4.2#5.2#6.2 axis to axis: distance: 21.887Å; angle: 81.6° > open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb Chain information for fab_af2.pdb #11 --- Chain | Description A | No description available B | No description available > color #11 #dedddaff > hide #!6 models > show #1 models > mmaker #11 to #1 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 FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain H (#1) with fab_af2.pdb, chain A (#11), sequence alignment score = 608.4 RMSD between 117 pruned atom pairs is 0.513 angstroms; (across all 119 pairs: 0.605) > mmaker #11 to #1/I 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 FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain I (#1) with fab_af2.pdb, chain B (#11), sequence alignment score = 549.7 RMSD between 107 pruned atom pairs is 0.487 angstroms; (across all 107 pairs: 0.487) > define axis #11 radius 5 Axis 'fab_af2.pdb #11/axis' centered at [134.92205552 199.21482183 116.20704463] with direction [0.29937749 0.93410689 0.19446706], radius 5, and length 76.5755 > hide #1 models > show #!3 models > mmaker #11 to #3/L 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 7uop, chain L (#3) with fab_af2.pdb, chain B (#11), sequence alignment score = 315.7 RMSD between 96 pruned atom pairs is 0.931 angstroms; (across all 106 pairs: 1.462) > mmaker #11 to #1/I 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 FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain I (#1) with fab_af2.pdb, chain B (#11), sequence alignment score = 549.7 RMSD between 107 pruned atom pairs is 0.487 angstroms; (across all 107 pairs: 0.487) > open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb Chain information for fab_af2.pdb #12 --- Chain | Description A | No description available B | No description available > mmaker #12 to #3/L 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 7uop, chain L (#3) with fab_af2.pdb, chain B (#12), sequence alignment score = 315.7 RMSD between 96 pruned atom pairs is 0.931 angstroms; (across all 106 pairs: 1.462) > define axis #12 radius 5 Axis 'fab_af2.pdb #12/axis' centered at [136.1808451 185.14787868 185.38873437] with direction [0.05507823 0.80887232 0.58539897], radius 5, and length 76.5755 > open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb Chain information for fab_af2.pdb #13 --- Chain | Description A | No description available B | No description available > hide #!3 models > show #!4 models > mmaker #13 to #4/F 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 7upa, chain F (#4) with fab_af2.pdb, chain B (#13), sequence alignment score = 367.3 RMSD between 104 pruned atom pairs is 0.737 angstroms; (across all 106 pairs: 0.883) > define axis #13 radius 5 Axis 'fab_af2.pdb #13/axis' centered at [ 68.29352293 146.2888834 135.58720417] with direction [-0.99988945 -0.01085239 0.01016461], radius 5, and length 76.5755 > hide #!4 models > show #!5 models > open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb Chain information for fab_af2.pdb #14 --- Chain | Description A | No description available B | No description available > mmaker #14 to #5/B 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 7upd, chain B (#5) with fab_af2.pdb, chain A (#14), sequence alignment score = 330.8 RMSD between 102 pruned atom pairs is 0.943 angstroms; (across all 115 pairs: 1.567) > define axis #14 radius 5 Axis 'fab_af2.pdb #14/axis' centered at [ 75.50786032 156.83255137 89.48139637] with direction [-0.8997972 0.17395918 -0.40012898], radius 5, and length 76.5755 > open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb Chain information for fab_af2.pdb #15 --- Chain | Description A | No description available B | No description available > hide #!5 models > show #!6 models > mmaker #15 to #6/E 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 7upk, chain E (#6) with fab_af2.pdb, chain A (#15), sequence alignment score = 334.2 RMSD between 105 pruned atom pairs is 0.880 angstroms; (across all 115 pairs: 1.604) > define axis #15 radius 5 Axis 'fab_af2.pdb #15/axis' centered at [ 70.8730715 123.10044819 135.20212854] with direction [-0.98934821 -0.14290781 0.02770338], radius 5, and length 76.5755 > hide #!6 models > show #!7 models > open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb Chain information for fab_af2.pdb #16 --- Chain | Description A | No description available B | No description available > mmaker #16 to #7/L 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 7up9, chain L (#7) with fab_af2.pdb, chain B (#16), sequence alignment score = 351.5 RMSD between 104 pruned atom pairs is 0.765 angstroms; (across all 107 pairs: 1.035) > define axis #16 radius 5 Axis 'fab_af2.pdb #16/axis' centered at [ 84.64639356 153.38938629 188.11426666] with direction [-0.61152451 0.06837696 0.78826542], radius 5, and length 76.5755 > open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb Chain information for fab_af2.pdb #17 --- Chain | Description A | No description available B | No description available > hide #!7 models > show #8 models > mmaker #17 to #8/L 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 7upb, chain L (#8) with fab_af2.pdb, chain B (#17), sequence alignment score = 379.7 RMSD between 102 pruned atom pairs is 0.747 angstroms; (across all 106 pairs: 1.014) > define axis #17 radius 5 Axis 'fab_af2.pdb #17/axis' centered at [ 80.39113677 192.08979514 106.53048684] with direction [-0.57880148 0.81196359 -0.07552475], radius 5, and length 76.5755 > open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb Chain information for fab_af2.pdb #18 --- Chain | Description A | No description available B | No description available > hide #8 models > show #!9 models > mmaker #18 to #9/L 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 8dg8, chain L (#9) with fab_af2.pdb, chain B (#18), sequence alignment score = 199.7 RMSD between 72 pruned atom pairs is 1.058 angstroms; (across all 101 pairs: 2.403) > define axis #18 radius 5 Axis 'fab_af2.pdb #18/axis' centered at [ 81.23556488 180.66688792 157.90592962] with direction [-0.6455834 0.76169205 0.05520224], radius 5, and length 76.5755 > open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb Chain information for fab_af2.pdb #19 --- Chain | Description A | No description available B | No description available > hide #!9 models > show #!10 models > mmaker #19 to #10/L 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 6t3f, chain L (#10) with fab_af2.pdb, chain B (#19), sequence alignment score = 637.6 RMSD between 89 pruned atom pairs is 0.827 angstroms; (across all 211 pairs: 7.541) > define axis #19 radius 5 Axis 'fab_af2.pdb #19/axis' centered at [132.02301441 173.04240741 193.91243283] with direction [-0.34119941 -0.33010458 -0.88012154], radius 5, and length 76.5755 > hide #!10 models > hide #!11 models > show #!11 models > show #!10 models > hide #!10 models > hide #11-19 cartoons axis #2.2 to axis #11.1: distance: 357.072Å; angle: 78.9° axis #2.2 to axis #12.1: distance: 261.535Å; angle: 54.2° axis #2.2 to axis #13.1: distance: 100.174Å; angle: 89.2° axis #2.2 to axis #14.1: distance: 319.900Å; angle: 66.6° axis #2.2 to axis #15.1: distance: 208.294Å; angle: 88.2° axis #2.2 to axis #16.1: distance: 453.097Å; angle: 37.8° axis #2.2 to axis #17.1: distance: 91.194Å; angle: 85.7° axis #2.2 to axis #18.1: distance: 447.749Å; angle: 86.8° axis #2.2 to axis #19.1: distance: 389.458Å; angle: 28.5° > save > /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_comaprison.pdb > save > /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison.cxs > show #11-19 cartoons > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > hide #11-19 cartoons > color #19.1 #dc8add > color #11.1 #dc8add > color #11.1 #c061cb > color #11.1 #9141ac > color #11.1 #813d9c > color #19.1 #f66151 > color #12.1 #ffa348 > color #16.1 #f6d32d > color #18.1 #f9f06b > color #18.1 #e5a50a > color #18.1 #c64600 > color #18.1 #a51d2d > color #13.1 #99c1f1 > color #15.1 #1a5fb4 > color #14.1 #8ff0a4 > color #17.1 #26a269 > color #14.1 #bf5c40 > color #14.1 #4081bf > color #14.1 #ab40bf > color #14.1 #bf408d > color #14.1 #bf4067 > color #19.1 #b340bf > color #19.1 #b140bf > color #19.1 #8a40bf > color #19.1 #6d40bf > color #19.1 #7040bf > color #19.1 #b840bf > color #19.1 #bf40aa > color #19.1 #bf40a5 > color #19.1 #bf40a7 > color #19.1 #b640bf > undo [Repeated 3 time(s)] > color #19.1 #f66151 > color #14.1 #8540bf > color #14.1 #8745bf > color #14.1 #773da9 > color #14.1 #8254a9 > color #14.1 #7d51a3 > color #14.1 #7e53a3 > color #14.1 #6f4990 > color #14.1 #704a90 > color #14.1 #4d3363 > color #14.1 #4d3263 > color #14.1 #4e3364 > color #14.1 #401564 > color #14.1 #541c84 > color #14.1 #551c85 > color #14.1 #572185 > color #14.1 #7c2fbe > color #14.1 #8440be > color #14.1 #974ad9 > color #14.1 #a262d9 > color #14.1 #ad69e7 > color #14.1 #b77ee7 > color #14.1 #c387f7 > color #14.1 #c488f7 > color #14.1 #c689f9 > color #14.1 #c68af9 > color #14.1 #cd9af9 > color #14.1 #d09cfc > color #14.1 #d6a8fc > color #14.1 #d8aaff > color #14.1 #d7a9fe > color #14.1 #cea2f4 > color #14.1 #cfa3f4 > color #14.1 #ca9fef > color #17.1 #5640bf > color #17.1 #8f40bf > color #17.1 #a940bf > color #17.1 #a640bf > color #17.1 #7540bf > color #17.1 #7340bf > color #17.1 #7040bf > color #17.1 #6d40bf > color #17.1 #4140bf > color #17.1 #4440bf > color #17.1 #7840bf > color #17.1 #9940bf > color #17.1 #9f40bf > color #17.1 #a440bf > color #17.1 #ab40bf > color #17.1 #b640bf > color #17.1 #be40bf > color #17.1 #bf40be > color #17.1 #bf40bc > color #17.1 #bf40b9 > color #17.1 #bf40af > color #17.1 #bf40ac > color #17.1 #bf409f > color #17.1 #bf409a > color #17.1 #bf4098 > color #17.1 #bf409a > color #17.1 #bf499d > color #17.1 #b24492 > color #17.1 #b22689 > color #17.1 #d02ca1 > color #17.1 #d0219d > color #17.1 #d822a3 > color #17.1 #d81ba1 > color #17.1 #dd1ca5 > color #17.1 #dc1ca4 > color #17.1 #dc2aa8 > color #17.1 #d529a3 > color #17.1 #d52ba4 > color #17.1 #d32aa2 > save > /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison.cxs > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_top.png > supersample 8 transparentBackground true height 2500 > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_side.png > supersample 8 transparentBackground true height 2500 > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_top_angle.png > supersample 8 transparentBackground true height 2500 > show #!3 models > show #8 models > show #!7 models > hide #!11 models > hide #!12 models > hide #!13 models > hide #!14 models > hide #!15 models > hide #!16 models > hide #!17 models > hide #!18 models > hide #!19 models > hide #8 models > hide #!7 models > hide #!3 models > show #!11 models > show #!12 models > show #!13 models > show #!14 models > show #!15 models > show #!17 models > show #!16 models > show #!18 models > show #!19 models > show #!3 models > hide #!3 models > color #3 #ffbe6fff > show #!3 models > show #!10 models > color #10 #d95847ff > color #9 #c01c28ff > show #!9 models > show #!7 models > color #7 #f8e45cff > color #7 #f6d32dff > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_top_noodle.png > supersample 8 transparentBackground true height 2500 > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_side_noodle.png > supersample 8 transparentBackground true height 2500 > hide #!7 models > hide #!9 models > hide #!10 models > hide #!11 models > show #!11 models > show #!10 models > show #!9 models > hide #!9 models > hide #!3 models > hide #!10 models > color #5 #99c1f1ff > show #!5 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > hide #!5 models > show #!4 models > color #4 #99c1f1ff > show #!6 models > color #6 #1a5fb4ff > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_top_face_noodle.png > supersample 8 transparentBackground true height 2500 > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_side_face_noodle.png > supersample 8 transparentBackground true height 2500 > hide #!6 models > hide #!4 models > show #1 models > color #1 #813d9cff > color #1 #613583ff > color #1 #813d9cff > color #1 #9141acff > color #1 #6a64a5ff > show #8 models > color #8 #d32aa2ff > show #!5 models > color #5 #ca9fefff > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_top_bottom_noodle.png > supersample 8 transparentBackground true height 2500 > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_side_bottom_noodle.png > supersample 8 transparentBackground true height 2500 > save > /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison.cxs ——— End of log from Fri Oct 6 16:48:39 2023 ——— opened ChimeraX session > show #!10 models > show #!9 models > show #!7 models > show #!6 models > show #!4 models > show #!3 models > open 7KI6 Summary of feedback from opening 7KI6 fetched from pdb --- note | Fetching compressed mmCIF 7ki6 from http://files.rcsb.org/download/7ki6.cif 7ki6 title: Structure of the HeV F glycoprotein in complex with the 1F5 neutralizing antibody [more info...] Chain information for 7ki6 #20 --- Chain | Description | UniProt A B E | Fusion glycoprotein F0 | F4YH70_9MONO C F L | 1F5 Fab light chain | D G H | 1F5 heavy chain | Non-standard residues in 7ki6 #20 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > mmaker #20 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain E (#2) with 7ki6, chain A (#20), sequence alignment score = 869.1 RMSD between 267 pruned atom pairs is 1.325 angstroms; (across all 357 pairs: 2.520) > hide atoms > show cartoons > hide #1/A,B,C,D,E,F,G,H,K,L cartoons > hide #3/G,A,D,C,F,B,E cartoons > hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons [Repeated 1 time(s)] > hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons > hide #6/A,B,C,D,F,H,I,J,K,L,M,N,O,P cartoons > hide #7/A,B,C,D,F,G,I,J,K,M,N,O,P cartoons > hide #8/A,B,C,D,E,F,G,I,J,K,M,N,O,P cartoons > hide #9/A,B,C,D,F,I,J,K,M,N,O,P cartoons > hide #10/A,B,C,D,F,I,J,K,M,N,O,P c\ Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #8#!3-7,9-19 target m > hide #1 target m > show #1 models > show #!6 models > hide #!6 models > hide #1/A,B,E,F,G,H,I,J,K,L,M,N,O,P cartoons > hide #20/A,B,E,F,G,H,I,J,K,L,M,N,O,P cartoons > open 7KI4 Summary of feedback from opening 7KI4 fetched from pdb --- note | Fetching compressed mmCIF 7ki4 from http://files.rcsb.org/download/7ki4.cif 7ki4 title: Structure of the NiV F glycoprotein in complex with the 12B2 neutralizing antibody [more info...] Chain information for 7ki4 #21 --- Chain | Description | UniProt A B E | Fusion glycoprotein F0 | FUS_NIPAV C F L | 12B2 Fab light chain | D G H | 12B2 heavy chain | Non-standard residues in 7ki4 #21 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > hide #1#!2,20-21 atoms > show #1#!2,20-21 cartoons > mmaker #21 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain E (#2) with 7ki4, chain A (#21), sequence alignment score = 888.3 RMSD between 267 pruned atom pairs is 1.313 angstroms; (across all 368 pairs: 2.911) > hide #1/A,B,C,D,E,F,G,H,K,L cartoons > hide #3/G,A,D,C,F,B,E cartoons > hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons [Repeated 1 time(s)] > hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons > hide #6/A,B,C,D,F,H,I,J,K,L,M,N,O,P cartoons > hide #7/A,B,C,D,F,G,I,J,K,M,N,O,P cartoons > hide #8/A,B,C,D,E,F,G,I,J,K,M,N,O,P cartoons > hide #9/A,B,C,D,F,I,J,K,M,N,O,P cartoons > hide #10/A,B,C,D,F,I,J,K,M,N,O,P cartoons > hide #20/A,B,E,F,G,H,I,J,K,L,M,N,O,P cartoons > show #!3 models > hide #!3 models > show #!4 models > hide #!20 models > show #!20 models > hide #!20 models > show #!15 models > hide #!15 models > show #!13 models > hide #!13 models > show #!12 models > hide #!12 models > show #8 models > hide #8 models > show #!9 models > hide #!9 models > show #!6 models > hide #!6 models > show #!5 models > hide #!5 models > show #!3 models > show #8 models > hide #8 models > show #!15 models > hide #!15 models > show #!10 models > hide #21/A,B,E,F,G,H,I,J,K,L,M,N,O,P cartoons > show #!9 models > show #!7 models > show #!15 models > hide #!4 models > hide #1 models > hide #!15 models > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > color #21 #ff007fff > color #21 #ff5500ff > color #21 #d04500ff > color #21 #c84300ff > save > C:/Users/didny/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_updated.cxs > save > C:/Users/didny/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_top_noodle.png > supersample 8 transparentBackground true height 2500 > save > C:/Users/didny/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_side_noodle.png > supersample 8 transparentBackground true height 2500 > hide #!10 models > hide #!9 models > hide #!7 models > hide #!3 models > hide #!21 models > show #!20 models > show #!6 models > hide #!6 models > show #!6 models > show #!4 models > color #20 #55ffffff > color #20 #aaffffff > color #20 #5555ffff > color #20 #5500ffff > color #20 #55007fff > color #20 blue > color #20 #00007fff > color #20 #aaffffff > color #20 cyan > color #20 #aaffffff > color #20 #8dd3d3ff > save > C:/Users/didny/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_face_top_noodle.png > supersample 8 transparentBackground true height 2500 > save > C:/Users/didny/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_face_side1_noodle.png > supersample 8 transparentBackground true height 2500 > save > C:/Users/didny/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_face_side2_noodle.png > supersample 8 transparentBackground true height 2500 > save > C:/Users/didny/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_face_top_noodle.png > supersample 8 transparentBackground true height 2500 > hide #!6 models > hide #!4 models > open > C:/Users/didny/OneDrive/Code/work/FectoFab_paper/figure_notebooks/structures_PDBs/fab_af2.pdb Chain information for fab_af2.pdb #22 --- Chain | Description A | No description available B | No description available > mmaker #22 to #20 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 7ki6, chain H (#20) with fab_af2.pdb, chain A (#22), sequence alignment score = 800.3 RMSD between 113 pruned atom pairs is 0.602 angstroms; (across all 117 pairs: 1.363) > mmaker #22 to #20/D 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 7ki6, chain D (#20) with fab_af2.pdb, chain A (#22), sequence alignment score = 809.3 RMSD between 113 pruned atom pairs is 0.602 angstroms; (across all 117 pairs: 1.363) > define axis #22 radius 5 Axis 'fab_af2.pdb #22/axis' centered at [ 73.44504807 134.30578164 152.24514275] with direction [-0.93683251 -0.18283826 0.29818623], radius 5, and length 76.5755 > hide #!22 models > show #!22 models > close #22.1 > define axis #22/A-B radius 5 Axis 'fab_af2.pdb #22/axis' centered at [ 73.44504807 134.30578164 152.24514275] with direction [-0.93683251 -0.18283826 0.29818623], radius 5, and length 76.5755 > close #22.1 > show #!21 models > open E:/Downloads/fab_af2.pdb Chain information for fab_af2.pdb #23 --- Chain | Description A | No description available B | No description available > mmaker #23 to #21/D 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 7ki4, chain D (#21) with fab_af2.pdb, chain A (#23), sequence alignment score = 682.2 RMSD between 112 pruned atom pairs is 0.745 angstroms; (across all 117 pairs: 1.608) > define axis #23 radius 5 Axis 'fab_af2.pdb #23/axis' centered at [164.30463436 152.96821533 194.08491756] with direction [-0.57893742 -0.47128773 -0.66537158], radius 5, and length 76.5755 > close #23.1 > save > C:/Users/didny/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_updated.cxs ——— End of log from Fri Oct 6 18:25:59 2023 ——— opened ChimeraX session > define axis #23 radius 5 Axis 'fab_af2.pdb #23/axis' centered at [164.30463499 152.96821592 194.08491844] with direction [-0.57893742 -0.47128773 -0.66537158], radius 5, and length 76.5755 > color #23.1 #c84300 > hide #!21 models > show #!21 models > hide #!21 models > hide #22 models > show #22 models > hide #!23 models > show #!23 models > hide #22 cartoons > hide #21 cartoons > hide #23 cartoons > define axis #22 radius 5 Axis 'fab_af2.pdb #22/axis' centered at [ 73.44504695 134.30578133 152.24514318] with direction [-0.93683251 -0.18283825 0.29818622], radius 5, and length 76.5755 > color #22.1 #8dd3d3 > hide #22 cartoons > hide #20 cartoons > show #!21 models > show #!19 models > show #!18 models > show #!17 models > show #!16 models > show #!15 models > show #!14 models > show #!13 models > show #!12 models > show #!11 models > show #!10 models > hide #!10 models > hide #11-23 cartoons > save > /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_updated_linux.cxs Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 299, in process return copy_state(data, convert=convert) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 219, in copy_state return _copy(data) ^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 217, in _copy return convert(data) ^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 298, in convert return add_obj(obj, parents) ^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 270, in _add_obj uid = _UniqueName.from_obj(self.session, obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 143, in from_obj raise RuntimeError( RuntimeError: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 901, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/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 ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 299, in process return copy_state(data, convert=convert) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 219, in copy_state return _copy(data) ^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 217, in _copy return convert(data) ^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 298, in convert return add_obj(obj, parents) ^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 270, in _add_obj uid = _UniqueName.from_obj(self.session, obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 143, in from_obj raise RuntimeError( RuntimeError: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/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 ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 901, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/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 > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_sticks_top.png > supersample 8 transparentBackground true height 2500 > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_sticks_side1.png > supersample 8 transparentBackground true height 2500 > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_sticks_side2.png > supersample 8 transparentBackground true height 2500 > open 6TYS 6tys title: A potent cross-neutralizing antibody targeting the fusion glycoprotein inhibits Nipah virus and Hendra virus infection [more info...] Chain information for 6tys #24 --- Chain | Description | UniProt A B E | Fusion glycoprotein F0 | FUS_NIPAV 1-494 C F H | 5B3 antibody heavy chain | D G L | 5B3 antibody light chain | Non-standard residues in 6tys #24 --- BMA — beta-D-mannopyranose MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose > mmaker #24 to #2 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 Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb, chain C (#2) with 6tys, chain A (#24), sequence alignment score = 875.7 RMSD between 274 pruned atom pairs is 1.273 angstroms; (across all 367 pairs: 2.961) > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > hide #!2,11-24 atoms > show #24 cartoons > hide #24/A,B,C,D,E,F,G,I,J,K cartoons > color #24 #3584e4ff > color #24 #404ebfff > color #24 #4050bfff > color #24 #303763ff > color #24 #313449ff > color #24 #363a55ff > open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb Chain information for fab_af2.pdb #25 --- Chain | Description A | No description available B | No description available > mmaker #25 to #24/L 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 6tys, chain L (#24) with fab_af2.pdb, chain B (#25), sequence alignment score = 399 RMSD between 106 pruned atom pairs is 0.651 angstroms; (across all 107 pairs: 0.679) > define axis #25 radius 5 Axis 'fab_af2.pdb #25/axis' centered at [ 70.29107461 138.97084878 150.75967364] with direction [-0.92877463 0.13498417 0.3451912 ], radius 5, and length 76.5755 > color #25.1 #363a55 > hide #25 cartoons > hide #!11-23,25 target m > show #!6 models > show #!4 models > show #!21 models > show #!20 models > hide #!20 models > hide #!21 models > show #!20-21 target m > hide #!21 models > hide #!20 models > show #!20 models > show #!21 models > show #21/C,D cartoons > show #20/C,D cartoons > hide #!21 models > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_face_top1.png > supersample 8 transparentBackground true height 2500 > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_face_side1.png > supersample 8 transparentBackground true height 2500 > save > /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_updated_linux.cxs Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 299, in process return copy_state(data, convert=convert) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 219, in copy_state return _copy(data) ^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 217, in _copy return convert(data) ^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 298, in convert return add_obj(obj, parents) ^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 270, in _add_obj uid = _UniqueName.from_obj(self.session, obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 143, in from_obj raise RuntimeError( RuntimeError: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 901, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/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 ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 299, in process return copy_state(data, convert=convert) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 219, in copy_state return _copy(data) ^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 217, in _copy return convert(data) ^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 298, in convert return add_obj(obj, parents) ^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 270, in _add_obj uid = _UniqueName.from_obj(self.session, obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 143, in from_obj raise RuntimeError( RuntimeError: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/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 ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 901, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/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. > hide #!24 models > hide #!20 models > hide #!6 models > hide #!4 models > show #!11-19 target m > show #!22-23 target m > show #!25 target m > show #!22-23 target m > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_sticks_top.png > supersample 8 transparentBackground true height 2500 > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_sticks_side1.png > supersample 8 transparentBackground true height 2500 > save > /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_sticks_side2.png > supersample 8 transparentBackground true height 2500 > save > /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_linux.cxs Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 299, in process return copy_state(data, convert=convert) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 219, in copy_state return _copy(data) ^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 217, in _copy return convert(data) ^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 298, in convert return add_obj(obj, parents) ^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 270, in _add_obj uid = _UniqueName.from_obj(self.session, obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 143, in from_obj raise RuntimeError( RuntimeError: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 901, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/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 ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 299, in process return copy_state(data, convert=convert) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 219, in copy_state return _copy(data) ^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/state.py"", line 217, in _copy return convert(data) ^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 298, in convert return add_obj(obj, parents) ^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 270, in _add_obj uid = _UniqueName.from_obj(self.session, obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 143, in from_obj raise RuntimeError( RuntimeError: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/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 ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 901, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/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 535.104.12 OpenGL renderer: Quadro T2000 with Max-Q Design/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: en_US.UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:1 Manufacturer: LENOVO Model: 20TJS07400 OS: Ubuntu 22.04 Jammy Jellyfish Architecture: 64bit ELF Virtual Machine: none CPU: 12 Intel(R) Xeon(R) W-10855M CPU @ 2.80GHz Cache Size: 12288 KB Memory: total used free shared buff/cache available Mem: 62Gi 27Gi 1.0Gi 603Mi 33Gi 33Gi Swap: 2.0Gi 1.3Gi 741Mi Graphics: 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU117GLM [Quadro T2000 Mobile / Max-Q] [10de:1fb8] (rev a1) Subsystem: Lenovo TU117GLM [Quadro T2000 Mobile / Max-Q] [17aa:22c0] Kernel driver in use: nvidia Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.4.0 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.7.22 cftime: 1.6.2 charset-normalizer: 3.3.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.11.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.48 ChimeraX-AtomicLibrary: 10.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.3 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.4 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202309300109 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.2 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.2.1 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.12 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.11 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 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: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.10 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.2 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.32.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.4 contourpy: 1.1.1 cxservices: 1.2.2 cycler: 0.12.0 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 executing: 2.0.0 filelock: 3.9.0 fonttools: 4.43.0 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.2 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.7 numpy: 1.25.1 openvr: 1.23.701 packaging: 23.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.10.0 prompt-toolkit: 3.0.39 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.0 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.0.5 wcwidth: 0.2.8 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed high 1.7 Sessions fixed Greg Couch all ChimeraX