id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20528 ChimeraX bug report submission nicolejohnson@… "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.26200 ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description intermolecular h bonds will not display. command ""hbonds sel intramol false"" leads to log saying there are hbonds detected, that they are visible in the model panel, but no bonds are visible. It will show intramolecular hbonds when tried, but even ""hbonds reveal true"" does not make intermolecular h bonds visible. Log: UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open ""C:\Users\nvirg\Box\McLellan > Lab\Share\R2P2\P1-Respiroviruses\PIV3F_Antibodies\JB1 cryo- > EM\20260603_PIV3F-JB1.cxs"" format session Opened cryosparc_P355_J108_006_volume_map_sharp_EMReady_v2.2.2.mrc as #2, grid size 384,384,384, pixel 0.933, shown at level 4.96, step 1, values float32 Opened cryosparc_P355_J108_006_volume_map_sharp_EMReady_v2.2.2.mrc copy as #5, grid size 384,384,384, pixel 0.933, shown at level 4.96, step 1, values float32 Opened cryosparc_P363_J86_006_volume_map_sharp-EMReady.mrc as #7, grid size 384,384,384, pixel 0.833, shown at level 4.22, step 1, values float32 Log from Thu Jun 4 17:13:35 2026UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open ""C:/Users/nvirg/Box/McLellan > Lab/Share/R2P2/P1-Respiroviruses/PIV3F_Antibodies/JB1 cryo- > EM/20260603_PIV3F-JB1.cxs"" Opened cryosparc_P355_J108_006_volume_map_sharp_EMReady_v2.2.2.mrc as #2, grid size 384,384,384, pixel 0.933, shown at level 4.96, step 1, values float32 Opened cryosparc_P355_J108_006_volume_map_sharp_EMReady_v2.2.2.mrc copy as #5, grid size 384,384,384, pixel 0.933, shown at level 4.96, step 1, values float32 Opened cryosparc_P363_J86_006_volume_map_sharp-EMReady.mrc as #7, grid size 384,384,384, pixel 0.833, shown at level 4.22, step 1, values float32 Log from Wed Jun 3 14:56:59 2026UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open ""C:/Users/nvirg/Box/McLellan > Lab/Share/R2P2/P1-Respiroviruses/PIV3F_Antibodies/JB3 cryo- > EM/Figures/PIV3F-JB3.cxs"" Opened cryosparc_P363_J86_006_volume_map_sharp-EMReady.mrc as #2, grid size 384,384,384, pixel 0.833, shown at level 5.57, step 1, values float32 Log from Thu May 7 11:49:50 2026 > mousemode middleMode center > cofr centerOfView > alias cofron cofr centerofview showpivot true > alias cofroff cofr centerofview showpivot false > alias symclip cofr centerofview; clip near -$1 far $1 position cofr > alias cootmode set bgColor black; surface cap false; surface style solid; > lighting flat; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style > solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70; > cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues > cornflower blue > alias cootmode_mesh set bgColor black; surface cap false; surface style > mesh; lighting flat; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball; > style ions ball; size ballscale 0.2; size stickradius 0.07; cofr > centerofview; clip near -10 far 10 position cofr; color ##~num_residues > #3d60ffff; transparency 50 > alias cootmode_off surface style solid; lighting soft; graphics silhouettes > false; hide atoms; default_mol_display; transparency 0; symclip 40; color > ##~num_residues grey; size stickradius 0.2; > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000; > marker #10000 position cofr; sel ~sel; surface zone ##~num_residues > nearAtoms sel distance 15; close #10000 > alias map_unsphere surface unzone ##~num_residues > alias default_mol_display ~disp; rib; rainbow chain palette Pastel1-5; > lighting soft; > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ##~num_residues > alias licorice car style protein modeh default arrows f xsect oval width 1 > thick 1; style stick; size stickRadius 0.5; ~disp @H*; color byhet > alias caps_off surface cap false > alias caps_on surface cap true > alias rock_movie cofr showpivot false; movie record supersample 3; rock y > 40; wait 136; movie encode ~/Desktop/rock_movie.mp4 quality high; stop > alias publication_figure save Figure.png format png supersample 3 > transparentBackground true width 3000 height 3000 > buttonpanel Shortcuts rows 3 columns 5 > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add Hide_H command ""~disp @H*"" > buttonpanel Shortcuts add Licorice command licorice > buttonpanel Shortcuts add Ribbons command ""preset ribbons"" > buttonpanel Shortcuts add RockMovie command rock_movie > buttonpanel Shortcuts add SymClip10 command ""symclip 10"" > buttonpanel Shortcuts add SymClip20 command ""symclip 20"" > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add PubFigure command publication_figure > buttonpanel Shortcuts add coot_mode command cootmode > buttonpanel Shortcuts add coot_mesh command cootmode_mesh > buttonpanel Shortcuts add coot_off command cootmode_off > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/jm88942/Box/McLellan > Lab/Share/R2P2/P1-Respiroviruses/PIV3F_Antibodies/JB3 cryo- > EM/Phenix/PIV3F-JB3_rsr_465.pdb"" Chain information for PIV3F-JB3_rsr_465.pdb #1 --- Chain | Description A B C | No description available D F H | No description available E G L | No description available > open ""C:/Users/jm88942/Box/McLellan > Lab/Share/R2P2/P1-Respiroviruses/PIV3F_Antibodies/JB3 cryo- > EM/Maps/cryosparc_P363_J86_006_volume_map_sharp-EMReady.mrc"" Opened cryosparc_P363_J86_006_volume_map_sharp-EMReady.mrc as #2, grid size 384,384,384, pixel 0.833, shown at level 0.441, step 2, values float32 > volume #2 level 5.573 > hide atoms > show cartoons Computing secondary structure > volume #2 step 1 > set bgColor white > lighting soft > hide #!2 models > select #1/A 3237 atoms, 3287 bonds, 3 pseudobonds, 419 residues, 2 models selected > color sel cornflowerblue > select add #1 14823 atoms, 15096 bonds, 9 pseudobonds, 1938 residues, 2 models selected > select subtract #1 Nothing selected > color sel blue > select #1/A 3237 atoms, 3287 bonds, 3 pseudobonds, 419 residues, 2 models selected > color sel blue > color sel mediumblue > select add #2 3237 atoms, 3287 bonds, 3 pseudobonds, 419 residues, 4 models selected > select subtract #2 3237 atoms, 3287 bonds, 3 pseudobonds, 419 residues, 2 models selected > show #!2 models > color sel dodgerblue > hide #!2 models > color sel cornflowerblue > select #1/B 3237 atoms, 3287 bonds, 3 pseudobonds, 419 residues, 2 models selected > color sel springgreen > select #1/C 3237 atoms, 3287 bonds, 3 pseudobonds, 419 residues, 2 models selected > color sel aqua > color sel darkseagreen > select #1/B 3237 atoms, 3287 bonds, 3 pseudobonds, 419 residues, 2 models selected > color sel skyblue > select #1/A 3237 atoms, 3287 bonds, 3 pseudobonds, 419 residues, 2 models selected > color sel royalblue > select #1/B 3237 atoms, 3287 bonds, 3 pseudobonds, 419 residues, 2 models selected > color sel darkseagreen > select #1/C 3237 atoms, 3287 bonds, 3 pseudobonds, 419 residues, 2 models selected > color sel skyblue > select #1/D,F,H 2790 atoms, 2865 bonds, 357 residues, 1 model selected > color sel salmon > hide #!1 models > show #!1 models > select add #1 14823 atoms, 15096 bonds, 9 pseudobonds, 1938 residues, 2 models selected > select subtract #1 Nothing selected > select #1/E,G,L 2322 atoms, 2370 bonds, 324 residues, 1 model selected > color sel white > select add #1 14823 atoms, 15096 bonds, 9 pseudobonds, 1938 residues, 2 models selected > select subtract #1 Nothing selected > select #1/E,G,L 2322 atoms, 2370 bonds, 324 residues, 1 model selected > color sel azure > color sel linen > select add #1 14823 atoms, 15096 bonds, 9 pseudobonds, 1938 residues, 2 models selected > select subtract #1 Nothing selected > graphics silhouettes true > show #!2 models > surface dust #2 size 8.33 > color zone #2 near #1 distance 5 > save C:/Users/jm88942/Desktop/PIV3F-JB3.cxs includeMaps true > hide #1.1 models > hide #!1 models > publication_figure > save Figure.png format png supersample 3 transparentBackground true width > 3000 height 3000 > publication_figure > save Figure.png format png supersample 3 transparentBackground true width > 3000 height 3000 > save C:/Users/jm88942/Desktop/PIV3F-JB3.cxs includeMaps true > hide #!2 models > show #!1 models > select #1/A,B,C 9711 atoms, 9861 bonds, 9 pseudobonds, 1257 residues, 2 models selected > show sel surfaces > transparency (#!1 & sel) 50 > transparency (#!1 & sel) 80 > hide #!1 models > show #!1 models > select add #1 14823 atoms, 15096 bonds, 9 pseudobonds, 1938 residues, 5 models selected > select subtract #1 3 models selected > select #1/A,B,C/173,328,122,369 9711 atoms, 9861 bonds, 9 pseudobonds, 1257 residues, 2 models selected > select #1/A,B,C:173,328,122,369 90 atoms, 78 bonds, 12 residues, 1 model selected > style sel sphere Changed 90 atom styles > show sel atoms > color sel magenta > select add #1 14823 atoms, 15096 bonds, 9 pseudobonds, 1938 residues, 5 models selected > select subtract #1 3 models selected > publication_figure > save Figure.png format png supersample 3 transparentBackground true width > 3000 height 3000 > select #1/A,B,C: Expected an objects specifier or a keyword > select #1/A,B,C 9711 atoms, 9861 bonds, 9 pseudobonds, 1257 residues, 2 models selected > transparency (#!1 & sel) 50 > select add #1 14823 atoms, 15096 bonds, 9 pseudobonds, 1938 residues, 5 models selected > select subtract #1 3 models selected > publication_figure > save Figure.png format png supersample 3 transparentBackground true width > 3000 height 3000 > lighting simple [Repeated 1 time(s)] > lighting soft > lighting full > lighting soft > select #1/A,B,C 9711 atoms, 9861 bonds, 9 pseudobonds, 1257 residues, 2 models selected > transparency (#!1 & sel) 70 > select add #1 14823 atoms, 15096 bonds, 9 pseudobonds, 1938 residues, 5 models selected > select subtract #1 3 models selected > publication_figure > save Figure.png format png supersample 3 transparentBackground true width > 3000 height 3000 > save C:/Users/jm88942/Desktop/PIV3F-JB3.cxs includeMaps true ——— End of log from Thu May 7 11:49:50 2026 ——— > view name session-start opened ChimeraX session > close session > open ""C:/Users/nvirg/Box/McLellan > Lab/Share/R2P2/P1-Respiroviruses/PIV3F_Antibodies/JB1 cryo- > EM/COOT/PIV3F-JB1-3-30_rsr_456.pdb"" Chain information for PIV3F-JB1-3-30_rsr_456.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available H | No description available L | No description available > open ""C:/Users/nvirg/Box/McLellan > Lab/Share/R2P2/P1-Respiroviruses/PIV3F_Antibodies/JB1 cryo- > EM/COOT/cryosparc_P355_J108_006_volume_map_sharp_EMReady_v2.2.2.mrc"" Opened cryosparc_P355_J108_006_volume_map_sharp_EMReady_v2.2.2.mrc as #2, grid size 384,384,384, pixel 0.933, shown at level -0.0298, step 2, values float32 > volume #2 level 5.616 > hide atoms > show cartoons > volume #2 step 1 > volume #2 level 4.959 > lighting soft > hide #!2 models > color #1/A royalblue > color #1/B darkseagreen > color #1/C skyblue > color #1/H gold > color #1/L lemonchiffon > open 6mjz Summary of feedback from opening 6mjz fetched from pdb --- note | Fetching compressed mmCIF 6mjz from http://files.rcsb.org/download/6mjz.cif 6mjz title: Cryo-EM structure of Human Parainfluenza Virus Type 3 (hPIV3) in complex with antibody PIA174 [more info...] Chain information for 6mjz #3 --- Chain | Description | UniProt A B C | Fusion glycoprotein F0 | A0A059QA82_9MONO 19-481 H | PIA174 Fab Heavy chain | L | PIA174 Fab Light chain | > hide atoms > show cartoons > mmaker #3 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 PIV3F-JB1-3-30_rsr_456.pdb, chain B (#1) with 6mjz, chain A (#3), sequence alignment score = 1876.2 RMSD between 261 pruned atom pairs is 1.281 angstroms; (across all 415 pairs: 2.592) > show #!2 models > hide #!3 models > ui mousemode right ""map eraser"" > volume erase #2 center 179.39,178.73,266.43 radius 20.659 Opened cryosparc_P355_J108_006_volume_map_sharp_EMReady_v2.2.2.mrc copy as #5, grid size 384,384,384, pixel 0.933, shown at step 1, values float32 > volume erase #5 center 179.77,193.33,262.5 radius 20.601 > volume erase #5 center 170.59,166.98,261.23 radius 20.601 > volume erase #5 center 192.66,164.86,264.92 radius 20.601 > surface dust #5 size 9.33 > ui mousemode right select > color zone #2 near #1 distance 15 > color zone #5 near #1 distance 15 > save ""C:/Users/nvirg/Box/McLellan > Lab/Share/R2P2/P1-Respiroviruses/PIV3F_Antibodies/JB1 cryo- > EM/20260603_PIV3F-JB3.cxs"" includeMaps true > show #!3 models > hide #!1 models > show #!1 models > hide #!5 models > hide #!3 models > show #!5 models > hide #!5 models > show #!3 models > select #3/H 928 atoms, 955 bonds, 120 residues, 1 model selected > color sel red > select #3/L 837 atoms, 859 bonds, 108 residues, 1 model selected > color sel white > select clear > select #1/A:188-190, 194 29 atoms, 27 bonds, 4 residues, 1 model selected > color sel gold > select #3/C:190,191,194 17 atoms, 15 bonds, 3 residues, 1 model selected > select #3/C:190,191,194 17 atoms, 15 bonds, 3 residues, 1 model selected > color sel red > select #1/B:59-61, 187-194,197 86 atoms, 83 bonds, 12 residues, 1 model selected > select #1/B:59-61, 187-194,197 86 atoms, 83 bonds, 12 residues, 1 model selected > color sel gold > select #3/A: 187,188,190-194, 61,62 59 atoms, 56 bonds, 9 residues, 1 model selected > color sel red > select #3/B:190,191,194 17 atoms, 15 bonds, 3 residues, 1 model selected > color sel red > select clear > select #1/C: 189,190,193,194,197,198 50 atoms, 47 bonds, 6 residues, 1 model selected > select #1/C: 189,190,193,194,197,198 50 atoms, 47 bonds, 6 residues, 1 model selected > color sel gold > select up 236 atoms, 239 bonds, 32 residues, 1 model selected > select up 1379 atoms, 1392 bonds, 182 residues, 1 model selected > select clear > select #3/B:188-191,193,194,197 50 atoms, 47 bonds, 7 residues, 1 model selected > color sel red > select clear > select #1/B:185,188,189 23 atoms, 22 bonds, 3 residues, 1 model selected > select #1/B:185 7 atoms, 7 bonds, 1 residue, 1 model selected > color sel lemonchiffon > color sel #FFEA70 > undo > select up 52 atoms, 52 bonds, 7 residues, 1 model selected > select clear > select #1/B:188,189 16 atoms, 15 bonds, 2 residues, 1 model selected > color sel #FFF099 > select clear > select #1/C:59,61,62,66,69 40 atoms, 36 bonds, 5 residues, 1 model selected > color sel lemonchiffon > select #1/C:59,61,62,66,69, 187,188,190-193 80 atoms, 74 bonds, 11 residues, 1 model selected > color sel lemonchiffon > select #3/A:188-191 28 atoms, 27 bonds, 4 residues, 1 model selected > color sel mistyrose > color #3/L mistyrose > undo [Repeated 1 time(s)] > select #3/A:189 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 24 atoms, 23 bonds, 3 residues, 1 model selected > select down 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel mistyrose > select #3/A:188,190,191 17 atoms, 15 bonds, 3 residues, 1 model selected > select #3/A:188,190,191 17 atoms, 15 bonds, 3 residues, 1 model selected > color sel #FFB6AD > select #3/C:59, 186-188,190-193 54 atoms, 51 bonds, 8 residues, 1 model selected > ui mousemode right select > select subtract #3/C:191 50 atoms, 46 bonds, 7 residues, 1 model selected > select subtract #3/C:190 42 atoms, 39 bonds, 6 residues, 1 model selected > color sel mistyrose > select clear > select #3/C:190 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #3/C:191 12 atoms, 10 bonds, 2 residues, 1 model selected > color sel #FFB6AD > select clear > hide #3/H,L cartoons > hide #1/H,L cartoons > dssp > color #3/L mistyrose > open 8tqk Summary of feedback from opening 8tqk fetched from pdb --- note | Fetching compressed mmCIF 8tqk from http://files.rcsb.org/download/8tqk.cif 8tqk title: Human parainfluenza virus type 3 prefusion F trimer in complex with rPIV3-18 Fab [more info...] Chain information for 8tqk #4 --- Chain | Description | UniProt A B C | Fusion glycoprotein F0 | A0A059QA82_9MONO 19-481 D F H | Heavy chain Fab rPIV3-18 | E G L | Light chain Fab rPIV3-28 | > hide atoms > show cartoons > open ""C:/Users/nvirg/Box/McLellan > Lab/Share/R2P2/P1-Respiroviruses/PIV3F_Antibodies/JB3 cryo- > EM/COOT/PIV3F-Trimer-coot-1-Isolde-Apr1.pdb"" Chain information for PIV3F-Trimer-coot-1-Isolde-Apr1.pdb #6 --- Chain | Description A | No description available B C | No description available H | No description available L | No description available > hide atoms > show cartoons > mmaker #6 to #4 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 8tqk, chain C (#4) with PIV3F-Trimer-coot-1-Isolde-Apr1.pdb, chain C (#6), sequence alignment score = 1975.1 RMSD between 240 pruned atom pairs is 1.008 angstroms; (across all 414 pairs: 3.003) > hide #!1 models > hide #!3 models > open ""C:/Users/nvirg/Box/McLellan > Lab/Share/R2P2/P1-Respiroviruses/PIV3F_Antibodies/JB3 cryo- > EM/Maps/cryosparc_P363_J86_006_volume_map_sharp-EMReady.mrc"" Opened cryosparc_P363_J86_006_volume_map_sharp-EMReady.mrc as #7, grid size 384,384,384, pixel 0.833, shown at level 0.441, step 2, values float32 > close #6 > open ""C:/Users/nvirg/Box/McLellan > Lab/Share/R2P2/P1-Respiroviruses/PIV3F_Antibodies/JB3 cryo- > EM/COOT/PIV3F-JB3-CryoAtomChimera.pdb"" Chain information for PIV3F-JB3-CryoAtomChimera.pdb #6 --- Chain | Description H | No description available L | No description available N | No description available P | No description available g | No description available h | No description available > volume #7 level 4.218 > volume #7 step 1 > select ~sel & ##selected Nothing selected > mmaker #4 to #6 Computing secondary structure 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 PIV3F-JB3-CryoAtomChimera.pdb, chain N (#6) with 8tqk, chain C (#4), sequence alignment score = 704 RMSD between 139 pruned atom pairs is 0.939 angstroms; (across all 146 pairs: 1.099) > hide #6 models > save ""C:/Users/nvirg/Box/McLellan > Lab/Share/R2P2/P1-Respiroviruses/PIV3F_Antibodies/JB1 cryo- > EM/20260603_PIV3F-JB3.cxs"" includeMaps true ——— End of log from Wed Jun 3 14:56:59 2026 ——— > view name session-start opened ChimeraX session > hide #!4 models > show #!1 models > hide #1/H,L cartoons > select clear > color #1/B royalblue > color #1/C darkseagreen > color #1/A skyblue > show #1 cartoons > show #!5 models > hide cartoons > color zone #5 near #1 distance 12 > hide #!1 models > show #!1 models > hide #!5 models > show #1/A,B,C cartoons > turn y 1 > turn y -1 [Repeated 1 time(s)] > turn x 1 > turn x -1 [Repeated 1 time(s)] > turn x 0.5 > turn y 0.5 > turn x -0.5 > turn x 0.5 > turn x 90 [Repeated 2 time(s)] > show #!5 models > hide #!1 models > save C:\Users\nvirg/Desktop\image20.png supersample 3 > turn y 180 > turn y 10 > turn y -10 [Repeated 2 time(s)] > save C:\Users\nvirg/Desktop\image21.png supersample 3 > save ""C:/Users/nvirg/Box/McLellan > Lab/Share/R2P2/P1-Respiroviruses/PIV3F_Antibodies/JB1 cryo- > EM/20260603_PIV3F-JB1.cxs"" includeMaps true ——— End of log from Thu Jun 4 17:13:35 2026 ——— > view name session-start opened ChimeraX session > show #!1 models > hide #!5 models > show #1 cartoons > select #1:198 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1:193,194,198 69 atoms, 63 bonds, 9 residues, 1 model selected > show sel atoms > style sel stick Changed 69 atom styles > ui mousemode right select > select clear > select #1/H:102 4 atoms, 3 bonds, 1 residue, 1 model selected > select clear > open ""C:/Users/nvirg/Box/NicoleJohnson/Lab Files/PIV3 VHH/VHH > Manuscript/Data/CryoEM/PIV3_1D10_4C06/PIV191530_trimer_only.pdb"" Chain information for PIV191530_trimer_only.pdb #8 --- Chain | Description A B C | No description available D G H I | No description available > mmaker #8 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 PIV3F-JB1-3-30_rsr_456.pdb, chain B (#1) with PIV191530_trimer_only.pdb, chain A (#8), sequence alignment score = 1875.3 RMSD between 215 pruned atom pairs is 1.049 angstroms; (across all 403 pairs: 4.112) > hide #8 atoms > show #8 cartoons > hide #!1 models > select #8:193,194,198 66 atoms, 60 bonds, 9 residues, 1 model selected > show sel atoms > style sel stick Changed 66 atom styles > select #8:195 18 atoms, 15 bonds, 3 residues, 1 model selected > select #8:195,340 36 atoms, 30 bonds, 6 residues, 1 model selected > select #8/B:186 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/B:195 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/B:186 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > open ""C:/Users/nvirg/Box/NicoleJohnson/Lab Files/PIV3 VHH/PIV3 > F201114_04C06/Finalized_Structure/20230928_PIV3F201114_4C06_trimer_ISOLDE_noH_real_space_refined.pdb"" Chain information for 20230928_PIV3F201114_4C06_trimer_ISOLDE_noH_real_space_refined.pdb #9 --- Chain | Description A B C | No description available U W Y | No description available > mmaker #9 to #8 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 PIV191530_trimer_only.pdb, chain A (#8) with 20230928_PIV3F201114_4C06_trimer_ISOLDE_noH_real_space_refined.pdb, chain A (#9), sequence alignment score = 1927.7 RMSD between 395 pruned atom pairs is 0.921 angstroms; (across all 419 pairs: 1.545) > hide #9 atoms > show #9 cartoons > select #9:193,194,198 69 atoms, 63 bonds, 9 residues, 1 model selected > show sel atoms > style sel stick Changed 69 atom styles > select clear > color #8,9 byhetero > color #!8-9 bychain > color #8/A indian red > color #9/A light pink > color #8/B cornflower blue > color #8/A light steel blue > color #8/C light steel blue > color #9/C light steel blue > color #8/C gold > color #9/B lemon chiffon > color #8,9 byhetero > select zone #9/A: 193 6 Selected 239 atoms, 1 surfaces > show sel atoms > select clear > style #8-9 stick Changed 26419 atom styles > select #8/C:182 9 atoms, 8 bonds, 1 residue, 1 model selected > select zone #9/A: 198 10 Selected 1485 atoms, 1 surfaces > show sel atoms > select clear > select #9/A:198 9 atoms, 8 bonds, 1 residue, 1 model selected > hide #!8 models > swappa #9:198 arg Unknown command: swappa #9:198 arg > swapaa #9:198 arg Using Dunbrack library 20230928_PIV3F201114_4C06_trimer_ISOLDE_noH_real_space_refined.pdb #9/A GLN 198: phi -59.8, psi -43.8 trans 20230928_PIV3F201114_4C06_trimer_ISOLDE_noH_real_space_refined.pdb #9/B GLN 198: phi -59.8, psi -43.9 trans 20230928_PIV3F201114_4C06_trimer_ISOLDE_noH_real_space_refined.pdb #9/C GLN 198: phi -59.8, psi -44.0 trans Density criteria with multiple volume models open; Need to specify one to use via 'density' keyword. > close #2 > close #5 > close #7 > swapaa #9:198 arg Using Dunbrack library 20230928_PIV3F201114_4C06_trimer_ISOLDE_noH_real_space_refined.pdb #9/A GLN 198: phi -59.8, psi -43.8 trans 20230928_PIV3F201114_4C06_trimer_ISOLDE_noH_real_space_refined.pdb #9/B GLN 198: phi -59.8, psi -43.9 trans 20230928_PIV3F201114_4C06_trimer_ISOLDE_noH_real_space_refined.pdb #9/C GLN 198: phi -59.8, psi -44.0 trans Applying ARG rotamer (chi angles: -70.7 177.7 -180.0 172.6) to 20230928_PIV3F201114_4C06_trimer_ISOLDE_noH_real_space_refined.pdb #9/A ARG 198 Applying ARG rotamer (chi angles: -70.7 177.7 -180.0 172.6) to 20230928_PIV3F201114_4C06_trimer_ISOLDE_noH_real_space_refined.pdb #9/B ARG 198 Applying ARG rotamer (chi angles: -70.7 177.7 -180.0 172.6) to 20230928_PIV3F201114_4C06_trimer_ISOLDE_noH_real_space_refined.pdb #9/C ARG 198 > select #9/C:202 5 atoms, 4 bonds, 1 residue, 1 model selected > hide #!9 models > show #!1 models > hide #1 atoms > select #1:198 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1:193 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/C:182 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > show #!9 models > hide #9 atoms > select #9:193 27 atoms, 24 bonds, 3 residues, 1 model selected > show sel atoms > hide #!1 models > select #9/B:181 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > show #!1 models > hide #!9 models > select #1:193 27 atoms, 24 bonds, 3 residues, 1 model selected > show sel atoms > select #1/H:110 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/C:185 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:186 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > select #1/C:194 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > show #!3 models > show #3 cartoons > hide #3 atoms > select #3:194 15 atoms, 12 bonds, 3 residues, 1 model selected > show sel atoms > hide #!1 models > show #!1 models > hide #!3 models > hide #!1 models > show #!9 models > select #9/A:193 9 atoms, 8 bonds, 1 residue, 1 model selected > hbonds sel intraMol false 2 hydrogen bonds found > select #9/B:181 9 atoms, 8 bonds, 1 residue, 1 model selected > select #9/B:180 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/B:182 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > show #9 atoms > select add #9 13062 atoms, 13272 bonds, 6 pseudobonds, 1701 residues, 2 models selected > select subtract #9 Nothing selected > select add #2 2 pseudobonds, 1 model selected > select subtract #2 Nothing selected > select #9/A:193 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 176 atoms, 178 bonds, 23 residues, 1 model selected > select up 1645 atoms, 1664 bonds, 214 residues, 1 model selected > select down 176 atoms, 178 bonds, 23 residues, 1 model selected > select down 9 atoms, 8 bonds, 1 residue, 1 model selected > select down 9 atoms, 8 bonds, 1 residue, 1 model selected > select down 9 atoms, 8 bonds, 1 residue, 1 model selected > select down 9 atoms, 8 bonds, 1 residue, 1 model selected > hbonds sel intraMol false showDist true 2 hydrogen bonds found > show hbonds > select add #2 9 atoms, 8 bonds, 2 pseudobonds, 1 residue, 3 models selected > hbonds reveal true 13598 hydrogen bonds found > hbonds reveal true intraMol false 7840 hydrogen bonds found > ui tool show H-Bonds QWindowsWindow::setGeometry: Unable to set geometry 662x780+1590+737 (frame: 684x836+1579+692) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY2"". Resulting geometry: 656x763+1593+751 (frame: 678x819+1582+706) margins: 11, 45, 11, 11 minimum size: 441x520 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=684, y=836))) > hbonds reveal true 13598 hydrogen bonds found > select #9/A:202 5 atoms, 4 bonds, 1 residue, 1 model selected > hbonds reveal true intraMol false intermol true Expected a keyword > hbonds reveal true 13598 hydrogen bonds found QWindowsWindow::setGeometry: Unable to set geometry 900x731+1470+762 (frame: 922x787+1459+717) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY2"". Resulting geometry: 894x714+1473+776 (frame: 916x770+1462+731) margins: 11, 45, 11, 11 minimum size: 600x333 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=922, y=556))) OpenGL version: 3.3.0 NVIDIA 577.02 OpenGL renderer: NVIDIA GeForce RTX 4070 Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_US.cp1252 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: windows Manufacturer: LENOVO Model: 83FD OS: Microsoft Windows 11 Home (Build 26200) Memory: 16,944,848,896 MaxProcessMemory: 137,438,953,344 CPU: 32 Intel(R) Core(TM) i9-14900HX OSLanguage: en-US Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 build: 1.2.2.post1 certifi: 2025.6.15 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.18 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.25.2 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.10.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 comtypes: 1.4.10 contourpy: 1.3.2 coverage: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.4 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 nvidia-cuda-cupti-cu12: 12.9.79 nvidia-cuda-nvcc-cu12: 12.9.86 nvidia-cuda-nvrtc-cu12: 12.9.86 nvidia-cuda-runtime-cu12: 12.9.79 nvidia-cufft-cu12: 11.4.1.4 nvidia-nvjitlink-cu12: 12.9.86 OpenMM: 8.2.0 OpenMM-CUDA-12: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pywin32: 310 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.0 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 WMI: 1.5.1 }}} " defect new normal Unassigned