id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18751 Crash moving window between screens sphulera@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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All rights reserved. How to cite UCSF ChimeraX > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G H | No description available I L | No description available > lighting soft > hide atoms > show cartoons > style stick Changed 18366 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 1 item > set bgColor #ffffff00 > color /A,C,E,F,B,D lightgray > color /L,I #b0e694 > color /H,G #9cecc7 > surface /A,C,E,B,D,F > interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0 17 contacting residues > color sel #b0e694 surfaces > name frozen li_contacts sel > interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0 110 contacting residues > color sel #9cecc7 surfaces > name frozen hg_contacts sel > select li_contacts & hg_contacts 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel darkgreen > hide surfaces > open 6V8X fromDatabase pdb format mmcif 6v8x title: VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...] Chain information for 6v8x #2 --- Chain | Description | UniProt A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505 B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664 C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216 D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216 Non-standard residues in 6v8x #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 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) > mmaker #2/A to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 6v8x, chain A (#2), sequence alignment score = 1782.7 RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs: 1.616) > color #2/C hotpink target c > color #2/D lightpink target c > color #2/A lightgray > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > select #1/A,H,L #2/A,C,D 12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected > select ~sel 30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected > hide sel cartoons > hide #2/A cartoons > lighting soft > hide atoms > show cartoons > style stick Changed 43191 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 2 items > set bgColor #ffffff00 > delete atoms #2/C:111-216 > delete atoms #2/D:107-216 > define centroid #1/A name centroid_ach_5fo4 Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935] > define centroid #2/A name centroid_ach_vrco1 Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473 205.15865745] > define centroid #2/C,D name centroid_fab_vrco1 Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441 202.42807093] > define centroid #1/H,L name centroid_5fo4 Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242] > select #1.8 #1.9 2 atoms, 2 residues, 2 models selected > define axis sel name axis_5f04 Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at [193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829 -0.31288049], radius 1, and length 32.1167 > select #2.2 #2.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_vrco1 Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153 149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1, and length 35.3008 > select #1/A,H,L #2/A,C,D 10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected > select ~sel 30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected > hide sel cartoons > open 9D7o fromDatabase pdb format mmcif 9d7o title: Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...] Chain information for 9d7o #3 --- Chain | Description | UniProt A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504 B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664 G | CH103 Fab light chain | H | CH103 Fab heavy chain | Non-standard residues in 9d7o #3 --- BMA — beta-D-mannopyranose (beta-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) > mmaker #3/E to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 9d7o, chain E (#3), sequence alignment score = 1832.3 RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs: 1.395) > lighting soft > hide atoms > show cartoons > style stick Changed 58739 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 3 items > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > define centroid #3/E name centroid_ech_9d7o Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702 156.64264453] > delete atoms #3/H:111-216 > delete atoms #3/G:107-216 > define centroid #3/G,H name centroid_ch103_9d7o Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981 180.26864021] > select #3.2 #3.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_ch103 Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254 ] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length 34.0007 > hide #1 & ~/A,H,L cartoons > hide #2 & ~/A,C,D cartoons > hide #3 & ~/E,H,G cartoons > select clear > hide #3.2 models > hide #3.3 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!1 models > show #!2 models > show #!1 models > hide #!1 models > hide #!2 models > show #!1 models > show #!2 models > hide #!1 models > hide #!2 models > info rescolor #3/H:20 #!3/H:20 color #9389c3 > info rescolor #3/G:20 #!3/G:20 color #e3f0ef > ui tool show ""Color Actions"" > color #3/G #cyan Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #3/G cyan > color #3/G e3f0ef Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #3/G #e3f0ef > show #!2 models > hide #!2 models > show #!2 models > show #!1 models > hide #!2 models > hide #!3 models > show #!2 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!2 models > hide #!3 models > show #!1 models > show #!3 models > select add #1.10 1 model selected No visible atoms selected No visible residues selected > select subtract #1.10 Nothing selected > select add #1.10 1 model selected > close session > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G H | No description available I L | No description available > lighting soft > hide atoms > show cartoons > style stick Changed 18366 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 1 item > set bgColor #ffffff00 > color /A,C,E,F,B,D lightgray > color /L,I #b0e694 > color /H,G #9cecc7 > surface /A,C,E,B,D,F > interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0 17 contacting residues > color sel #b0e694 surfaces > name frozen li_contacts sel > interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0 110 contacting residues > color sel #9cecc7 surfaces > name frozen hg_contacts sel > select li_contacts & hg_contacts 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel darkgreen > hide surfaces > open 6V8X fromDatabase pdb format mmcif 6v8x title: VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...] Chain information for 6v8x #2 --- Chain | Description | UniProt A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505 B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664 C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216 D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216 Non-standard residues in 6v8x #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 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) > mmaker #2/A to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 6v8x, chain A (#2), sequence alignment score = 1782.7 RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs: 1.616) > color #2/C hotpink target c > color #2/D lightpink target c > color #2/A lightgray > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > select #1/A,H,L #2/A,C,D 12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected > select ~sel 30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected > hide sel cartoons > hide #2/A cartoons > lighting soft > hide atoms > show cartoons > style stick Changed 43191 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 2 items > set bgColor #ffffff00 > delete atoms #2/C:111-216 > delete atoms #2/D:107-216 > define centroid #1/A name centroid_ach_5fo4 Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935] > define centroid #2/A name centroid_ach_vrco1 Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473 205.15865745] > define centroid #2/C,D name centroid_fab_vrco1 Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441 202.42807093] > define centroid #1/H,L name centroid_5fo4 Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242] > select #1.8 #1.9 2 atoms, 2 residues, 2 models selected > define axis sel name axis_5f04 Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at [193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829 -0.31288049], radius 1, and length 32.1167 > select #2.2 #2.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_vrco1 Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153 149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1, and length 35.3008 > select #1/A,H,L #2/A,C,D 10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected > select ~sel 30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected > hide sel cartoons > open 9D7o fromDatabase pdb format mmcif 9d7o title: Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...] Chain information for 9d7o #3 --- Chain | Description | UniProt A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504 B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664 G | CH103 Fab light chain | H | CH103 Fab heavy chain | Non-standard residues in 9d7o #3 --- BMA — beta-D-mannopyranose (beta-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) > mmaker #3/E to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 9d7o, chain E (#3), sequence alignment score = 1832.3 RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs: 1.395) > lighting soft > hide atoms > show cartoons > style stick Changed 58739 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 3 items > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > define centroid #3/E name centroid_ech_9d7o Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702 156.64264453] > delete atoms #3/H:111-216 > delete atoms #3/G:107-216 > define centroid #3/G,H name centroid_ch103_9d7o Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981 180.26864021] > select #3.2 #3.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_ch103 Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254 ] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length 34.0007 > hide #1 & ~/A,H,L cartoons > hide #2 & ~/A,C,D cartoons > hide #3 & ~/E,H,G cartoons > color #3/E lightgray > color #3/G #b0e694 > color #3/H #9389c3 > select clear > hide #!2 models > hide #!3 models > color /A,C,E,F,B,D lightgray > select :276 72 atoms, 63 bonds, 9 residues, 3 models selected > select ~sel & ##selected 57765 atoms, 59330 bonds, 43 pseudobonds, 7145 residues, 6 models selected > select clear > select :295 75 atoms, 66 bonds, 9 residues, 3 models selected > select :368 72 atoms, 63 bonds, 9 residues, 3 models selected > show #!2 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > hide #!1 models > show sel & #!3 atoms > show #!2 models > hide #!3 models > show sel & #!2 atoms > show #!1 models > hide #!2 models > show sel & #!1 atoms > show #!2 models > show #!3 models > ui tool show H-Bonds > hbonds sel color #000404 interModel false angleSlop 50.0 intraMol false > intraRes false select true reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 50 degrees Models used: 1 92-5F04_Q23_J473_real_space_refined_071.pdb 2 6v8x 3 9d7o 13 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 N 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H TYR 32 OH no hydrogen 3.361 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/G ARG 96 NE 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/C ASP 368 OD1 no hydrogen 3.015 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/G ARG 96 NH2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/C ASP 368 OD1 no hydrogen 2.904 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 96 NE 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD1 no hydrogen 3.193 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 96 NH2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD1 no hydrogen 2.917 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 100E NH1 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD2 no hydrogen 2.899 N/A 6v8x #!2/A ASP 368 N 6v8x #!2/C GLY 54 O no hydrogen 3.323 N/A 6v8x #!2/E ASP 368 N 6v8x #!2/G GLY 54 O no hydrogen 3.323 N/A 6v8x #!2/I ASP 368 N 6v8x #!2/K GLY 54 O no hydrogen 3.323 N/A 9d7o #!3/E ASP 368 N 9d7o #!3/H TYR 33 OH no hydrogen 3.265 N/A 9d7o #!3/H TYR 33 OH 9d7o #!3/E ASP 368 OD1 no hydrogen 2.720 N/A 9d7o #!3/H ARG 97 NE 9d7o #!3/E ASP 368 OD2 no hydrogen 2.784 N/A 9d7o #!3/H ARG 97 NH2 9d7o #!3/E ASP 368 OD2 no hydrogen 2.726 N/A 13 hydrogen bonds found > select clear > color #1.2-11#2.2-5#3.2-5#!1-3 byhetero > hide #!2 models > hide #!3 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > show #!1 models > hide #!3 models > hide #!1 models > hide #!2 models > show #!2 models > show #!3 models > show #!1 models > select :NAG,NAM,MAN,BMA 3746 atoms, 3861 bonds, 274 residues, 3 models selected > select :NAG,NAM,MAN,BMA 3746 atoms, 3861 bonds, 274 residues, 3 models selected > show sel atoms > select clear > select :276 72 atoms, 63 bonds, 9 residues, 3 models selected > hide #!2 models > hide #!3 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > show #!1 models > close session > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G H | No description available I L | No description available > lighting soft > hide atoms > show cartoons > style stick Changed 18366 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 1 item > set bgColor #ffffff00 > color /A,C,E,F,B,D lightgray > color /L,I #b0e694 > color /H,G #9cecc7 > surface /A,C,E,B,D,F > interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0 17 contacting residues > color sel #b0e694 surfaces > name frozen li_contacts sel > interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0 110 contacting residues > color sel #9cecc7 surfaces > name frozen hg_contacts sel > select li_contacts & hg_contacts 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel darkgreen > hide surfaces > open 6V8X fromDatabase pdb format mmcif 6v8x title: VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...] Chain information for 6v8x #2 --- Chain | Description | UniProt A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505 B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664 C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216 D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216 Non-standard residues in 6v8x #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 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) > mmaker #2/A to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 6v8x, chain A (#2), sequence alignment score = 1782.7 RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs: 1.616) > color #2/C hotpink target c > color #2/D lightpink target c > color #2/A lightgray > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > select #1/A,H,L #2/A,C,D 12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected > select ~sel 30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected > hide sel cartoons > hide #2/A cartoons > lighting soft > hide atoms > show cartoons > style stick Changed 43191 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 2 items > set bgColor #ffffff00 > delete atoms #2/C:111-216 > delete atoms #2/D:107-216 > define centroid #1/A name centroid_ach_5fo4 Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935] > define centroid #2/A name centroid_ach_vrco1 Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473 205.15865745] > define centroid #2/C,D name centroid_fab_vrco1 Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441 202.42807093] > define centroid #1/H,L name centroid_5fo4 Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242] > select #1.8 #1.9 2 atoms, 2 residues, 2 models selected > define axis sel name axis_5f04 Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at [193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829 -0.31288049], radius 1, and length 32.1167 > select #2.2 #2.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_vrco1 Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153 149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1, and length 35.3008 > select #1/A,H,L #2/A,C,D 10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected > select ~sel 30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected > hide sel cartoons > open 9D7o fromDatabase pdb format mmcif 9d7o title: Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...] Chain information for 9d7o #3 --- Chain | Description | UniProt A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504 B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664 G | CH103 Fab light chain | H | CH103 Fab heavy chain | Non-standard residues in 9d7o #3 --- BMA — beta-D-mannopyranose (beta-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) > mmaker #3/E to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 9d7o, chain E (#3), sequence alignment score = 1832.3 RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs: 1.395) > lighting soft > hide atoms > show cartoons > style stick Changed 58739 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 3 items > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > define centroid #3/E name centroid_ech_9d7o Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702 156.64264453] > delete atoms #3/H:111-216 > delete atoms #3/G:107-216 > define centroid #3/G,H name centroid_ch103_9d7o Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981 180.26864021] > select #3.2 #3.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_ch103 Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254 ] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length 34.0007 > hide #1 & ~/A,H,L cartoons > hide #2 & ~/A,C,D cartoons > hide #3 & ~/E,H,G cartoons > color #3/E lightgray > color #3/G #b0e694 > color #3/H #9389c3 > hide #3.3 models > hide #3.2 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > select add #2.3 3 atoms, 3 residues, 3 models selected > select subtract #2.3 2 atoms, 2 residues, 2 models selected > select add #2.4 2 atoms, 2 residues, 3 models selected > color #2.4 hot pink > select clear > select add #2.4 1 model selected > color #2.4 black > select clear > select add #1.10 1 model selected > show #!1 models > color #1.10 black > select clear > select add #3.4 1 model selected > color #1.2-10#2.2-4#!1-2 black > show #!3 models > close session > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G H | No description available I L | No description available > lighting soft > hide atoms > show cartoons > style stick Changed 18366 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 1 item > set bgColor #ffffff00 > color /A,C,E,F,B,D lightgray > color /L,I #b0e694 > color /H,G #9cecc7 > surface /A,C,E,B,D,F > interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0 17 contacting residues > color sel #b0e694 surfaces > name frozen li_contacts sel > interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0 110 contacting residues > color sel #9cecc7 surfaces > name frozen hg_contacts sel > select li_contacts & hg_contacts 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel darkgreen > hide surfaces > open 6V8X fromDatabase pdb format mmcif 6v8x title: VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...] Chain information for 6v8x #2 --- Chain | Description | UniProt A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505 B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664 C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216 D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216 Non-standard residues in 6v8x #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 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) > mmaker #2/A to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 6v8x, chain A (#2), sequence alignment score = 1782.7 RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs: 1.616) > color #2/C hotpink target c > color #2/D lightpink target c > color #2/A lightgray > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > select #1/A,H,L #2/A,C,D 12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected > select ~sel 30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected > hide sel cartoons > hide #2/A cartoons > lighting soft > hide atoms > show cartoons > style stick Changed 43191 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 2 items > set bgColor #ffffff00 > delete atoms #2/C:111-216 > delete atoms #2/D:107-216 > define centroid #1/A name centroid_ach_5fo4 Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935] > define centroid #2/A name centroid_ach_vrco1 Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473 205.15865745] > define centroid #2/C,D name centroid_fab_vrco1 Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441 202.42807093] > define centroid #1/H,L name centroid_5fo4 Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242] > select #1.8 #1.9 2 atoms, 2 residues, 2 models selected > define axis sel name axis_5f04 Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at [193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829 -0.31288049], radius 1, and length 32.1167 > select #2.2 #2.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_vrco1 Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153 149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1, and length 35.3008 > select #1/A,H,L #2/A,C,D 10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected > select ~sel 30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected > hide sel cartoons > open 9D7o fromDatabase pdb format mmcif 9d7o title: Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...] Chain information for 9d7o #3 --- Chain | Description | UniProt A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504 B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664 G | CH103 Fab light chain | H | CH103 Fab heavy chain | Non-standard residues in 9d7o #3 --- BMA — beta-D-mannopyranose (beta-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) > mmaker #3/E to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 9d7o, chain E (#3), sequence alignment score = 1832.3 RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs: 1.395) > lighting soft > hide atoms > show cartoons > style stick Changed 58739 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 3 items > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > define centroid #3/E name centroid_ech_9d7o Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702 156.64264453] > delete atoms #3/H:111-216 > delete atoms #3/G:107-216 > define centroid #3/G,H name centroid_ch103_9d7o Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981 180.26864021] > select #3.2 #3.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_ch103 Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254 ] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length 34.0007 > hide #1 & ~/A,H,L cartoons > hide #2 & ~/A,C,D cartoons > hide #3 & ~/E,H,G cartoons > color #3/E lightgray > color #3/G #b0e694 > color #3/H #9389c3 > color #1.10 #2.4 #3.4 black > hide #3.3 models > hide #3.2 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > hide #3.4 models > show #3.4 models > hide #3.4 models > show #3.4 models > color #3/G #e3f0ef > ui tool show ""Color Actions"" > color #3/G lightcyan > color #3/G skyblue > color #3/G lightskyblue > color #3/G lpaleturquoise Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #3/G paleturquoise > close session > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G H | No description available I L | No description available > lighting soft > hide atoms > show cartoons > style stick Changed 18366 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 1 item > set bgColor #ffffff00 > color /A,C,E,F,B,D lightgray > color /L,I #b0e694 > color /H,G #9cecc7 > surface /A,C,E,B,D,F > interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0 17 contacting residues > color sel #b0e694 surfaces > name frozen li_contacts sel > interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0 110 contacting residues > color sel #9cecc7 surfaces > name frozen hg_contacts sel > select li_contacts & hg_contacts 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel darkgreen > hide surfaces > open 6V8X fromDatabase pdb format mmcif 6v8x title: VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...] Chain information for 6v8x #2 --- Chain | Description | UniProt A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505 B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664 C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216 D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216 Non-standard residues in 6v8x #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 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) > mmaker #2/A to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 6v8x, chain A (#2), sequence alignment score = 1782.7 RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs: 1.616) > color #2/C hotpink target c > color #2/D lightpink target c > color #2/A lightgray > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > select #1/A,H,L #2/A,C,D 12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected > select ~sel 30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected > hide sel cartoons > hide #2/A cartoons > lighting soft > hide atoms > show cartoons > style stick Changed 43191 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 2 items > set bgColor #ffffff00 > delete atoms #2/C:111-216 > delete atoms #2/D:107-216 > define centroid #1/A name centroid_ach_5fo4 Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935] > define centroid #2/A name centroid_ach_vrco1 Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473 205.15865745] > define centroid #2/C,D name centroid_fab_vrco1 Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441 202.42807093] > define centroid #1/H,L name centroid_5fo4 Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242] > select #1.8 #1.9 2 atoms, 2 residues, 2 models selected > define axis sel name axis_5f04 Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at [193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829 -0.31288049], radius 1, and length 32.1167 > select #2.2 #2.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_vrco1 Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153 149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1, and length 35.3008 > select #1/A,H,L #2/A,C,D 10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected > select ~sel 30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected > hide sel cartoons > open 9D7o fromDatabase pdb format mmcif 9d7o title: Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...] Chain information for 9d7o #3 --- Chain | Description | UniProt A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504 B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664 G | CH103 Fab light chain | H | CH103 Fab heavy chain | Non-standard residues in 9d7o #3 --- BMA — beta-D-mannopyranose (beta-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) > mmaker #3/E to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 9d7o, chain E (#3), sequence alignment score = 1832.3 RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs: 1.395) > lighting soft > hide atoms > show cartoons > style stick Changed 58739 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 3 items > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > define centroid #3/E name centroid_ech_9d7o Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702 156.64264453] > delete atoms #3/H:111-216 > delete atoms #3/G:107-216 > define centroid #3/G,H name centroid_ch103_9d7o Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981 180.26864021] > select #3.2 #3.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_ch103 Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254 ] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length 34.0007 > hide #1 & ~/A,H,L cartoons > hide #2 & ~/A,C,D cartoons > hide #3 & ~/E,H,G cartoons > color #3/E lightgray > color #3/G #b0e694 > color #3/H #9389c3 > color #3/G paleturquoise > hide #3.2 #3.3 > color #1.10 #2.4 #3.4 black > hide #!3 models > hide #!2 models > show #!2 models > hide #!1 models > color #2/A lightgray > show #!1 models > color #1/A lightgray > hide #!2 models > select #1/A:276 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color (#!1 & sel) byelement > color (#!1 & sel) byhetero > color #1/A lightgray > color (#!1 & sel) byelement > color #1/A lightgray > color (#!1 & sel) byhetero > select clear > color #1/A :NAG,NAM,BMA,MAN > select #1/A :NAG,NAM,BMA,MAN 344 atoms, 352 bonds, 25 residues, 1 model selected > show sel atoms > select #1/A :978,990 28 atoms, 29 bonds, 2 residues, 1 model selected > select clear > select #1/A :NAG,NAM,BMA,MAN 344 atoms, 352 bonds, 25 residues, 1 model selected > hide sel atoms > select #1/A :978,990 28 atoms, 29 bonds, 2 residues, 1 model selected > show sel atoms > select clear > close session > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G H | No description available I L | No description available > lighting soft > hide atoms > show cartoons > style stick Changed 18366 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 1 item > set bgColor #ffffff00 > color /A,C,E,F,B,D lightgray > color /L,I #b0e694 > color /H,G #9cecc7 > surface /A,C,E,B,D,F > interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0 17 contacting residues > color sel #b0e694 surfaces > name frozen li_contacts sel > interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0 110 contacting residues > color sel #9cecc7 surfaces > name frozen hg_contacts sel > select li_contacts & hg_contacts 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel darkgreen > hide surfaces > open 6V8X fromDatabase pdb format mmcif 6v8x title: VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...] Chain information for 6v8x #2 --- Chain | Description | UniProt A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505 B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664 C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216 D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216 Non-standard residues in 6v8x #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 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) > mmaker #2/A to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 6v8x, chain A (#2), sequence alignment score = 1782.7 RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs: 1.616) > color #2/C hotpink target c > color #2/D lightpink target c > color #2/A lightgray > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > select #1/A,H,L #2/A,C,D 12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected > select ~sel 30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected > hide sel cartoons > hide #2/A cartoons > lighting soft > hide atoms > show cartoons > style stick Changed 43191 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 2 items > set bgColor #ffffff00 > delete atoms #2/C:111-216 > delete atoms #2/D:107-216 > define centroid #1/A name centroid_ach_5fo4 Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935] > define centroid #2/A name centroid_ach_vrco1 Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473 205.15865745] > define centroid #2/C,D name centroid_fab_vrco1 Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441 202.42807093] > define centroid #1/H,L name centroid_5fo4 Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242] > select #1.8 #1.9 2 atoms, 2 residues, 2 models selected > define axis sel name axis_5f04 Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at [193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829 -0.31288049], radius 1, and length 32.1167 > select #2.2 #2.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_vrco1 Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153 149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1, and length 35.3008 > select #1/A,H,L #2/A,C,D 10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected > select ~sel 30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected > hide sel cartoons > open 9D7o fromDatabase pdb format mmcif 9d7o title: Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...] Chain information for 9d7o #3 --- Chain | Description | UniProt A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504 B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664 G | CH103 Fab light chain | H | CH103 Fab heavy chain | Non-standard residues in 9d7o #3 --- BMA — beta-D-mannopyranose (beta-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) > mmaker #3/E to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 9d7o, chain E (#3), sequence alignment score = 1832.3 RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs: 1.395) > lighting soft > hide atoms > show cartoons > style stick Changed 58739 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 3 items > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > define centroid #3/E name centroid_ech_9d7o Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702 156.64264453] > delete atoms #3/H:111-216 > delete atoms #3/G:107-216 > define centroid #3/G,H name centroid_ch103_9d7o Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981 180.26864021] > select #3.2 #3.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_ch103 Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254 ] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length 34.0007 > hide #1 & ~/A,H,L cartoons > hide #2 & ~/A,C,D cartoons > hide #3 & ~/E,H,G cartoons > color #3/E lightgray > color #3/G #b0e694 > color #3/H #9389c3 > color #3/G paleturquoise > hide #3.2 #3.3 > color #1.10 #2.4 #3.4 black > color #1/A lightgray > color #1 byhetero > select #1/A :978,99028 atoms Expected a keyword > show sel atoms > hide #!2 models > hide #!3 models > color #1 byhetero > select #1/A :978,990,276 36 atoms, 37 bonds, 3 residues, 1 model selected > show sel atoms > select clear > show #!2 models > hide #!1 models > select #2/A :276 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A :NAG,NAM,BMA,MAN 56 atoms, 56 bonds, 4 residues, 1 model selected > show sel atoms > select #2 :NAG,NAM,BMA,MAN 1416 atoms, 1470 bonds, 105 residues, 1 model selected > show sel atoms > select clear > select #2 /Q 39 atoms, 41 bonds, 3 residues, 1 model selected > select #2/A :276 /Q 47 atoms, 49 bonds, 4 residues, 1 model selected > show #!3 models > hide #!2 models > select #3/A :276 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/E :276 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3 :NAG,NAM,BMA,MAN 1312 atoms, 1351 bonds, 95 residues, 1 model selected > show sel atoms > select clear > close session > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G H | No description available I L | No description available > lighting soft > hide atoms > show cartoons > style stick Changed 18366 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 1 item > set bgColor #ffffff00 > color /A,C,E,F,B,D lightgray > color /L,I #b0e694 > color /H,G #9cecc7 > surface /A,C,E,B,D,F > interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0 17 contacting residues > color sel #b0e694 surfaces > name frozen li_contacts sel > interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0 110 contacting residues > color sel #9cecc7 surfaces > name frozen hg_contacts sel > select li_contacts & hg_contacts 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel darkgreen > hide surfaces > open 6V8X fromDatabase pdb format mmcif 6v8x title: VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...] Chain information for 6v8x #2 --- Chain | Description | UniProt A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505 B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664 C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216 D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216 Non-standard residues in 6v8x #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 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) > mmaker #2/A to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 6v8x, chain A (#2), sequence alignment score = 1782.7 RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs: 1.616) > color #2/C hotpink target c > color #2/D lightpink target c > color #2/A lightgray > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > select #1/A,H,L #2/A,C,D 12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected > select ~sel 30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected > hide sel cartoons > hide #2/A cartoons > lighting soft > hide atoms > show cartoons > style stick Changed 43191 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 2 items > set bgColor #ffffff00 > delete atoms #2/C:111-216 > delete atoms #2/D:107-216 > define centroid #1/A name centroid_ach_5fo4 Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935] > define centroid #2/A name centroid_ach_vrco1 Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473 205.15865745] > define centroid #2/C,D name centroid_fab_vrco1 Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441 202.42807093] > define centroid #1/H,L name centroid_5fo4 Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242] > select #1.8 #1.9 2 atoms, 2 residues, 2 models selected > define axis sel name axis_5f04 Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at [193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829 -0.31288049], radius 1, and length 32.1167 > select #2.2 #2.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_vrco1 Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153 149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1, and length 35.3008 > select #1/A,H,L #2/A,C,D 10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected > select ~sel 30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected > hide sel cartoons > open 9D7o fromDatabase pdb format mmcif 9d7o title: Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...] Chain information for 9d7o #3 --- Chain | Description | UniProt A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504 B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664 G | CH103 Fab light chain | H | CH103 Fab heavy chain | Non-standard residues in 9d7o #3 --- BMA — beta-D-mannopyranose (beta-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) > mmaker #3/E to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 9d7o, chain E (#3), sequence alignment score = 1832.3 RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs: 1.395) > lighting soft > hide atoms > show cartoons > style stick Changed 58739 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 3 items > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > define centroid #3/E name centroid_ech_9d7o Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702 156.64264453] > delete atoms #3/H:111-216 > delete atoms #3/G:107-216 > define centroid #3/G,H name centroid_ch103_9d7o Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981 180.26864021] > select #3.2 #3.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_ch103 Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254 ] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length 34.0007 > hide #1 & ~/A,H,L cartoons > hide #2 & ~/A,C,D cartoons > hide #3 & ~/E,H,G cartoons > color #3/E lightgray > color #3/G #b0e694 > color #3/H #9389c3 > color #3/G paleturquoise > hide #3.2 #3.3 > color #1.10 #2.4 #3.4 black > color #1/A lightgray > color #1 byhetero > select #1/A :978,990,276 36 atoms, 37 bonds, 3 residues, 1 model selected > show sel atoms > color #2 byhetero > select #2/A :276 /Q 47 atoms, 49 bonds, 4 residues, 1 model selected > show sel atoms > color #3 byhetero > select #3/E :276 /j 36 atoms, 37 bonds, 3 residues, 1 model selected > show sel atoms > hide #!2 models > hide #!3 models > show #!2 models > hide #!2 models > close session > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G H | No description available I L | No description available > lighting soft > hide atoms > show cartoons > style stick Changed 18366 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 1 item > set bgColor #ffffff00 > color /A,C,E,F,B,D lightgray > color /L,I #b0e694 > color /H,G #9cecc7 > surface /A,C,E,B,D,F > interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0 17 contacting residues > color sel #b0e694 surfaces > name frozen li_contacts sel > interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0 110 contacting residues > color sel #9cecc7 surfaces > name frozen hg_contacts sel > select li_contacts & hg_contacts 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel darkgreen > hide surfaces > open 6V8X fromDatabase pdb format mmcif 6v8x title: VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...] Chain information for 6v8x #2 --- Chain | Description | UniProt A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505 B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664 C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216 D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216 Non-standard residues in 6v8x #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 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) > mmaker #2/A to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 6v8x, chain A (#2), sequence alignment score = 1782.7 RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs: 1.616) > color #2/C hotpink target c > color #2/D lightpink target c > color #2/A lightgray > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > select #1/A,H,L #2/A,C,D 12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected > select ~sel 30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected > hide sel cartoons > hide #2/A cartoons > lighting soft > hide atoms > show cartoons > style stick Changed 43191 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 2 items > set bgColor #ffffff00 > delete atoms #2/C:111-216 > delete atoms #2/D:107-216 > define centroid #1/A name centroid_ach_5fo4 Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935] > define centroid #2/A name centroid_ach_vrco1 Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473 205.15865745] > define centroid #2/C,D name centroid_fab_vrco1 Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441 202.42807093] > define centroid #1/H,L name centroid_5fo4 Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242] > select #1.8 #1.9 2 atoms, 2 residues, 2 models selected > define axis sel name axis_5f04 Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at [193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829 -0.31288049], radius 1, and length 32.1167 > select #2.2 #2.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_vrco1 Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153 149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1, and length 35.3008 > select #1/A,H,L #2/A,C,D 10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected > select ~sel 30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected > hide sel cartoons > open 9D7o fromDatabase pdb format mmcif 9d7o title: Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...] Chain information for 9d7o #3 --- Chain | Description | UniProt A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504 B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664 G | CH103 Fab light chain | H | CH103 Fab heavy chain | Non-standard residues in 9d7o #3 --- BMA — beta-D-mannopyranose (beta-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) > mmaker #3/E to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 9d7o, chain E (#3), sequence alignment score = 1832.3 RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs: 1.395) > lighting soft > hide atoms > show cartoons > style stick Changed 58739 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 3 items > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > define centroid #3/E name centroid_ech_9d7o Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702 156.64264453] > delete atoms #3/H:111-216 > delete atoms #3/G:107-216 > define centroid #3/G,H name centroid_ch103_9d7o Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981 180.26864021] > select #3.2 #3.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_ch103 Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254 ] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length 34.0007 > hide #1 & ~/A,H,L cartoons > hide #2 & ~/A,C,D cartoons > hide #3 & ~/E,H,G cartoons > color #3/E lightgray > color #3/G #b0e694 > color #3/H #9389c3 > color #3/G paleturquoise > hide #3.2 #3.3 > color #1.10 #2.4 #3.4 black > color #1/A lightgray > color #1 byhetero > select #1/A :978,990,276 36 atoms, 37 bonds, 3 residues, 1 model selected > show sel atoms > color #2 byhetero > select #2/A :276 /Q 47 atoms, 49 bonds, 4 residues, 1 model selected > color sel lightgray > show sel atoms > color #3 byhetero > select #3/E :276 /j 36 atoms, 37 bonds, 3 residues, 1 model selected > color set lightgray Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > show sel atoms > hide #!2 models > hide #!1 models > show #!2 models > hide #!3 models > show #!1 models > hide #!2 models > close session > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G H | No description available I L | No description available > lighting soft > hide atoms > show cartoons > style stick Changed 18366 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 1 item > set bgColor #ffffff00 > color /A,C,E,F,B,D lightgray > color /L,I #b0e694 > color /H,G #9cecc7 > surface /A,C,E,B,D,F > interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0 17 contacting residues > color sel #b0e694 surfaces > name frozen li_contacts sel > interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0 110 contacting residues > color sel #9cecc7 surfaces > name frozen hg_contacts sel > select li_contacts & hg_contacts 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel darkgreen > hide surfaces > open 6V8X fromDatabase pdb format mmcif 6v8x title: VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...] Chain information for 6v8x #2 --- Chain | Description | UniProt A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505 B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664 C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216 D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216 Non-standard residues in 6v8x #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 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) > mmaker #2/A to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 6v8x, chain A (#2), sequence alignment score = 1782.7 RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs: 1.616) > color #2/C hotpink target c > color #2/D lightpink target c > color #2/A lightgray > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > select #1/A,H,L #2/A,C,D 12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected > select ~sel 30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected > hide sel cartoons > hide #2/A cartoons > lighting soft > hide atoms > show cartoons > style stick Changed 43191 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 2 items > set bgColor #ffffff00 > delete atoms #2/C:111-216 > delete atoms #2/D:107-216 > define centroid #1/A name centroid_ach_5fo4 Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935] > define centroid #2/A name centroid_ach_vrco1 Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473 205.15865745] > define centroid #2/C,D name centroid_fab_vrco1 Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441 202.42807093] > define centroid #1/H,L name centroid_5fo4 Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242] > select #1.8 #1.9 2 atoms, 2 residues, 2 models selected > define axis sel name axis_5f04 Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at [193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829 -0.31288049], radius 1, and length 32.1167 > select #2.2 #2.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_vrco1 Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153 149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1, and length 35.3008 > select #1/A,H,L #2/A,C,D 10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected > select ~sel 30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected > hide sel cartoons > open 9D7o fromDatabase pdb format mmcif 9d7o title: Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...] Chain information for 9d7o #3 --- Chain | Description | UniProt A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504 B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664 G | CH103 Fab light chain | H | CH103 Fab heavy chain | Non-standard residues in 9d7o #3 --- BMA — beta-D-mannopyranose (beta-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) > mmaker #3/E to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 9d7o, chain E (#3), sequence alignment score = 1832.3 RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs: 1.395) > lighting soft > hide atoms > show cartoons > style stick Changed 58739 atom styles > graphics silhouettes true width 1.5 > camera ortho > setattr g display false Assigning display attribute to 3 items > cartoon style protein modeHelix default arrows false xsection oval width .6 > thickness .6 > define centroid #3/E name centroid_ech_9d7o Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702 156.64264453] > delete atoms #3/H:111-216 > delete atoms #3/G:107-216 > define centroid #3/G,H name centroid_ch103_9d7o Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981 180.26864021] > select #3.2 #3.3 2 atoms, 2 residues, 2 models selected > define axis sel name axis_ch103 Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254 ] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length 34.0007 > hide #1 & ~/A,H,L cartoons > hide #2 & ~/A,C,D cartoons > hide #3 & ~/E,H,G cartoons > color #3/E lightgray > color #3/G #b0e694 > color #3/H #9389c3 > color #3/G paleturquoise > hide #3.2 #3.3 > color #1.10 #2.4 #3.4 black > color #1/A lightgray > color #1 byhetero > select #1/A :978,990,276 36 atoms, 37 bonds, 3 residues, 1 model selected > show sel atoms > select #2/A :276 /Q 47 atoms, 49 bonds, 4 residues, 1 model selected > color sel lightgray > color #2 byhetero > show sel atoms > select #3/E :276 /j 36 atoms, 37 bonds, 3 residues, 1 model selected > color sel lightgray > color #3 byhetero > show sel atoms > hide #!3 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > select clear > show #!2 models > hide #!2 models > hide #!3 models > show #!1 models > show #!2 models > show #!3 models > hide #!3 models > hide #!2 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/session_090925.cxs"" > save view Cannot determine format for 'view' > view name front > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04_front.png"" > width 2000 height 1450 supersample 4 transparentBackground true > show #!2 models > hide #!1 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/6v8x_Vrc01_front.png"" > width 894 height 648 supersample 3 > show #!3 models > hide #!2 models > hide models > show #!1 models > show #!2 models > show #!3 models > close session > open ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/session_090925.cxs"" > format session opened ChimeraX session > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > hide #!2 models > hide #!3 models > show #!1 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04_front.png"" > width 2000 height 1450 supersample 4 transparentBackground true > show #!2 models > hide #!1 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/6v8x_vrc01_front.png"" > width 2000 height 1450 supersample 4 transparentBackground true > show #!3 models > hide #!2 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/9d7o_ch103_front.png"" > width 2000 height 1450 supersample 4 transparentBackground true > buried-area #1/H withAtoms2 #1/A Unknown command: measure buried-area #1/H withAtoms2 #1/A > measure buriedarea #2/H withAtoms2 #2/B & ~:NAG,NAM,MAN,BMA Buried area between #2/H and #2/B & ~:NAG,NAM,MAN,BMA = 0 area #2/H = 12380, area #2/B & ~:NAG,NAM,MAN,BMA = 10725, area both = 23104 > measure buriedarea #2/H withAtoms2 #2/A & ~:NAG,NAM,MAN,BMA Buried area between #2/H and #2/A & ~:NAG,NAM,MAN,BMA = 3.638e-12 area #2/H = 12380, area #2/A & ~:NAG,NAM,MAN,BMA = 23865, area both = 36244 > measure buriedarea #2/H withAtoms2 #2/A Buried area between #2/H and #2/A = 0 area #2/H = 12380, area #2/A = 24506, area both = 36886 > measure buriedarea #1/H withAtoms2 #1/A Buried area between #1/H and #1/A = 1306.8 area #1/H = 6633.3, area #1/A = 25476, area both = 29496 > measure buriedarea #1/H withAtoms2 #1/A Buried area between #1/H and #1/A = 1306.8 area #1/H = 6633.3, area #1/A = 25476, area both = 29496 > measure buriedarea #1/H withAtoms2 #1/A Buried area between #1/H and #1/A = 1306.8 area #1/H = 6633.3, area #1/A = 25476, area both = 29496 > show #!1 models > hide #!3 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > measure buriedarea #1/H withAtoms2 #1/A Buried area between #1/H and #1/A = 1306.8 area #1/H = 6633.3, area #1/A = 25476, area both = 29496 > measure buriedarea #1/L withAtoms2 #1/A Buried area between #1/L and #1/A = 183.36 area #1/L = 5984.2, area #1/A = 25476, area both = 31094 > measure buriedarea #2/C withAtoms2 #2/A Buried area between #2/C and #2/A = 876.62 area #2/C = 6814.1, area #2/A = 24506, area both = 29567 > measure buriedarea #2/D withAtoms2 #2/A Buried area between #2/D and #2/A = 202.75 area #2/D = 5617.7, area #2/A = 24506, area both = 29718 > measure buriedarea #3/H withAtoms2 #3/E Buried area between #3/H and #3/E = 838.66 area #3/H = 6548.2, area #3/E = 23696, area both = 28566 > measure buriedarea #3/G withAtoms2 #3/E Buried area between #3/G and #3/E = 284.47 area #3/G = 5811.3, area #3/E = 23696, area both = 28938 > show #!2 models > show #!1 models > hide #!2 models > hide #!3 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/session_090925.cxs"" > hide #1.10 models > measure buriedarea #1/H withAtoms2 #1/A Buried area between #1/H and #1/A = 1306.8 area #1/H = 6633.3, area #1/A = 25476, area both = 29496 > measure buriedarea #1/L withAtoms2 #1/A Buried area between #1/L and #1/A = 183.36 area #1/L = 5984.2, area #1/A = 25476, area both = 31094 > measure buriedarea #2/C withAtoms2 #2/A Buried area between #2/C and #2/A = 876.62 area #2/C = 6814.1, area #2/A = 24506, area both = 29567 > measure buriedarea #2/D withAtoms2 #2/A Buried area between #2/D and #2/A = 202.75 area #2/D = 5617.7, area #2/A = 24506, area both = 29718 > measure buriedarea #3/H withAtoms2 #3/E Buried area between #3/H and #3/E = 838.66 area #3/H = 6548.2, area #3/E = 23696, area both = 28566 > measure buriedarea #3/G withAtoms2 #3/E Buried area between #3/G and #3/E = 284.47 area #3/G = 5811.3, area #3/E = 23696, area both = 28938 > close session > open ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/session_090925.cxs"" > format session opened ChimeraX session > measure buriedarea #1/H withAtoms2 #1/A Buried area between #1/H and #1/A = 1306.8 area #1/H = 6633.3, area #1/A = 25476, area both = 29496 > measure buriedarea #1/L withAtoms2 #1/A Buried area between #1/L and #1/A = 183.36 area #1/L = 5984.2, area #1/A = 25476, area both = 31094 > measure buriedarea #2/C withAtoms2 #2/A Buried area between #2/C and #2/A = 876.62 area #2/C = 6814.1, area #2/A = 24506, area both = 29567 > measure buriedarea #2/D withAtoms2 #2/A Buried area between #2/D and #2/A = 202.75 area #2/D = 5617.7, area #2/A = 24506, area both = 29718 > measure buriedarea #3/H withAtoms2 #3/E Buried area between #3/H and #3/E = 838.66 area #3/H = 6548.2, area #3/E = 23696, area both = 28566 > measure buriedarea #3/G withAtoms2 #3/E Buried area between #3/G and #3/E = 284.47 area #3/G = 5811.3, area #3/E = 23696, area both = 28938 > select #1/A:368 8 atoms, 7 bonds, 1 residue, 1 model selected > show #!2 models > show #!3 models > hide #!2 models > hide #!1 models > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > select #1/A:368, #2/A:368, #3/E:368 Expected an objects specifier or a keyword > select #1/A:368 #2/A:368 #3/E:368 24 atoms, 21 bonds, 3 residues, 3 models selected > show #!2 models > show #!1 models > show sel atoms > hide #!3 models > hide #!2 models > hide #1.10 models > show #!2 models > show #!3 models > ui tool show H-Bonds > hbonds sel color #000404 interModel false angleSlop 50.0 intraMol false > intraRes false select true reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 50 degrees Models used: 1 92-5F04_Q23_J473_real_space_refined_071.pdb 2 6v8x 3 9d7o 9 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 N 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H TYR 32 OH no hydrogen 3.361 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 96 NE 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD1 no hydrogen 3.193 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 96 NH2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD1 no hydrogen 2.917 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 100E NH1 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD2 no hydrogen 2.899 N/A 6v8x #!2/A ASP 368 N 6v8x #!2/C GLY 54 O no hydrogen 3.323 N/A 9d7o #!3/E ASP 368 N 9d7o #!3/H TYR 33 OH no hydrogen 3.265 N/A 9d7o #!3/H TYR 33 OH 9d7o #!3/E ASP 368 OD1 no hydrogen 2.720 N/A 9d7o #!3/H ARG 97 NE 9d7o #!3/E ASP 368 OD2 no hydrogen 2.784 N/A 9d7o #!3/H ARG 97 NH2 9d7o #!3/E ASP 368 OD2 no hydrogen 2.726 N/A 9 hydrogen bonds found > select clear > hide #!2 models > hide #!3 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > hide #3.4 models > show #!1 models > hide #!3 models > show #!2 models > hide #!1 models > hide #2.4 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > select #1/C:59 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:59 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select clear > ui mousemode right select > select #!2/C:53 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #!2/C:55 4 atoms, 3 bonds, 1 residue, 1 model selected > select #!2/C:54 4 atoms, 3 bonds, 1 residue, 1 model selected > select #!2/C:53 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/C:71 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #!2/C:70 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 48 atoms, 47 bonds, 6 residues, 1 model selected > select up 948 atoms, 975 bonds, 118 residues, 1 model selected > hide sel atoms > select #2/C:71 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!3 models > show #!1 models > hide #!2 models > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > hide #!3 models > open 3Jwd fromDatabase pdb format mmcif Summary of feedback from opening 3Jwd fetched from pdb --- notes | Fetching compressed mmCIF 3jwd from http://files.rcsb.org/download/3jwd.cif Fetching CCD GOL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif Fetching CCD YCM from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/YCM/YCM.cif 3jwd title: Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Architecture and Basis of Conformational Mobility [more info...] Chain information for 3jwd #4 --- Chain | Description | UniProt A B | HIV-1 GP120 ENVELOPE GLYCOPROTEIN | C D | T-cell surface glycoprotein CD4 | CD4_HUMAN 1001-1183 H P | FAB 48D HEAVY CHAIN | L O | FAB 48D LIGHT CHAIN | Non-standard residues in 3jwd #4 --- GOL — glycerol (glycerin; propane-1,2,3-triol) 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) 3jwd mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > hide #!1 models > hide #!4 atoms > show #!4 cartoons > mmaker #4 to #1 Specify a single 'to' model only Drag select of 487 residues, 1 pseudobonds > select up 4574 atoms, 4657 bonds, 1 pseudobond, 587 residues, 2 models selected > select up 7574 atoms, 7757 bonds, 1 pseudobond, 977 residues, 2 models selected > delete atoms (#!4 & sel) > delete bonds (#!4 & sel) > mmaker #4/A to #1/A 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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with 3jwd, chain A (#4), sequence alignment score = 1293.4 RMSD between 260 pruned atom pairs is 0.898 angstroms; (across all 351 pairs: 5.931) > show #!1 models > hide #!1 models > show #!1 models > select #4/L:195 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 46 atoms, 46 bonds, 6 residues, 1 model selected > select up 1635 atoms, 1672 bonds, 213 residues, 1 model selected > delete atoms sel > delete bonds sel > select #4/H:142 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 79 atoms, 79 bonds, 11 residues, 1 model selected > select up 1654 atoms, 1697 bonds, 220 residues, 1 model selected > delete atoms sel > delete bonds sel > select #4/A:368 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > color sel byhetero > select clear > hide #!1 models > select #4/C:71 Nothing selected > select #4/C:1058 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > color sel byhetero > select clear > show #!3 models > hide #!3 models > ui tool show ""Side View"" > show #!3 models > hide #!4 models > show #!2 models > hide #!3 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > show #!4 models > hide #!3 models > show #!2 models > hide #!4 models > select #!2/C:71@NE 1 atom, 1 residue, 1 model selected > color sel byhetero > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel byhetero > color #2/C hotpink target a > color sel byhetero > select clear > show #!3 models > hide #!2 models > show #!4 models > hide #!3 models > show #!3 models > hide #!4 models > show #!2 models > hide #!3 models > show #!1 models > hide #!2 models > show #!4 models > hide #!1 models > show #!3 models > hide #!4 models > cartoon style #3.2-3,5#!3 xsection oval modeHelix default > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > show #!4 models > hide #!3 models > show #!3 models > hide #!4 models > show #!2 models > hide #!3 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > show #!4 models > hide #!3 models > show #!1 models > hide #!4 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > show #!4 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > show #!2 models > hide #!3 models > hide #!4 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #1 models > hide #!1 models > show #!1 models > hide #1.10 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > show #!1 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04__CD4BS.png"" > width 2000 height 1450 supersample 4 transparentBackground true > show #!2 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/6v8x_vrc01__CD4BS.png"" > width 2000 height 1450 supersample 4 transparentBackground true > show #!3 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/9d7o_ch103__CD4BS.png"" > width 2000 height 1450 supersample 4 transparentBackground true > show #!4 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/3jwd_cd4_GP120_CD4BS.png"" > width 2000 height 1450 supersample 4 transparentBackground true > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > show #!1 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04__CD4BS.png"" > width 2000 height 1450 supersample 4 transparentBackground true > hide #!1 models > show #!2 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/6v8x_vrc01__CD4BS.png"" > width 2000 height 1450 supersample 4 transparentBackground true > hide #!2 models > show #!3 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/9d7o_ch103__CD4BS.png"" > width 2000 height 1450 supersample 4 transparentBackground true > hide #!3 models > show #!4 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/3jwd_cd4_GP120_CD4BS.png"" > width 2000 height 1450 supersample 4 transparentBackground true > hide #!4 models > show #!4 models > color #4/A lightgray > color #4 byhetero > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > show #!1 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04__CD4BS.png"" > width 2000 height 1450 supersample 4 transparentBackground true > hide #!1 models > show #!2 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/6v8x_vrc01__CD4BS.png"" > width 2000 height 1450 supersample 4 transparentBackground true > hide #!2 models > show #!3 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/9d7o_ch103__CD4BS.png"" > width 2000 height 1450 supersample 4 transparentBackground true > hide #!3 models > show #!4 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/3jwd_cd4_GP120_CD4BS.png"" > width 2000 height 1450 supersample 4 transparentBackground true > hide #!4 models > show #!4 models > info rescolor #4/C:1058 #4/C:1058 color #e0f38d > show #!3 models > hide #!4 models > show #!2 models > show #!1 models > hide #!2 models > hide #!3 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/session_090925.cxs"" > hide #1.8-9#!1 atoms > show #1.8-9#!1 atoms > hide #1.8-9#!1 atoms > hide #!1 models > show #!1 models > ui tool show ""Side View"" > setattr g display false Assigning display attribute to 7 items > select add #1 18368 atoms, 18867 bonds, 17 pseudobonds, 2269 residues, 6 models selected > show sel cartoons > select clear > show #!4 models > hide #!4 models > select #1 ~/A Expected a keyword > select #1 & ~/A 14531 atoms, 14917 bonds, 10 pseudobonds, 1804 residues, 5 models selected > hide sel cartoons > show #!2 models > hide #!1 models > select #2 & ~/A 19699 atoms, 20229 bonds, 11 pseudobonds, 2445 residues, 5 models selected > hide sel cartoons > select clear > hide #2.2-3#!2 atoms > show #!3 models > hide #!2 models > select #3 & ~/E 12728 atoms, 13061 bonds, 12 pseudobonds, 1557 residues, 5 models selected > hide sel cartoons > hide sel atoms > select clear > hide #3.2-3#!3 atoms > show #!4 models > hide #!3 models > hide #!4 atoms > select #4 & ~/A 1759 atoms, 1464 bonds, 501 residues, 1 model selected > hide sel cartoons > show #!1 models > hide #!4 models > interfaces select /A, contacting /H,L bothSides true areaCutoff 0 Missing required ""contacting"" argument > interfaces select #1/A, contacting /H,L bothSides true areaCutoff 0 Missing required ""contacting"" argument > interfaces select #1/A, contacting #1/H,L bothSides true areaCutoff 0 Missing required ""contacting"" argument > interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0 1376 contacting residues > color sel #b0e694 surfaces > surface (#!1 & sel) > surface hidePatches (#!1 & sel) > select clear > interfaces select /A,C,E contacting /L,H bothSides true areaCutoff 0 1061 contacting residues > interfaces select /A contacting /L,H bothSides true areaCutoff 0 388 contacting residues > interfaces select /A contacting /L,H bothSides false areaCutoff 0 193 contacting residues > surface (#!1 & sel) > color sel #b0e694 surfaces > surface #1/A > color /A,C,E,F,B,D lightgray > color /L,I #b0e694 > color /H,G #9cecc7 > select up 3045 atoms, 3031 bonds, 397 residues, 5 models selected > select clear > interfaces select /A contacting /L,H bothSides false areaCutoff 0 193 contacting residues > color sel #b0e694 surfaces > select clear > show #!2 models > hide #!1 models > surface #2/A > interfaces select #2/A contacting #2/C,D bothSides false areaCutoff 0 25 contacting residues > show #!1 models > hide #!1 models > color sel hotpink > select clear > show #!3 models > hide #!2 models > surface #3/E > interfaces select #3/E contacting #3/H,G bothSides false areaCutoff 0 25 contacting residues > color sel #9389c3 > show #!4 models > hide #!3 models > select add #4 4992 atoms, 4486 bonds, 1 pseudobond, 1028 residues, 4 models selected > show sel & #!4 cartoons > interfaces select #4/A contacting #3/C bothSides false areaCutoff 0 4 contacting residues > interfaces select #4/A contacting #4/C bothSides false areaCutoff 0 26 contacting residues > select clear > select #4/C:1168 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 78 atoms, 78 bonds, 9 residues, 1 model selected > select up 1432 atoms, 1454 bonds, 184 residues, 1 model selected > hide sel cartoons > interfaces select #4/A contacting #4/C bothSides false areaCutoff 0 26 contacting residues > surface #4/A > interfaces select #4/A contacting #4/C bothSides false areaCutoff 0 26 contacting residues > color sel #e0f38d > hide #!4 models > show #!4 models > select add #4 4834 atoms, 4486 bonds, 1 pseudobond, 1006 residues, 3 models selected > select clear > show #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!3 models > show #!2 models > hide #!4 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > show #!4 models > hide #!3 models > hide #!4 models > show #!4 models > view name footprint > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > show #!1 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04_footprint.png"" > width 2000 height 1450 supersample 4 transparentBackground true > hide #!1 models > show #!2 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/6v8x_vrc01_footprint.png"" > width 2000 height 1450 supersample 4 transparentBackground true > hide #!2 models > show #!3 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/9d7o_ch103_footprint.png"" > width 2000 height 1450 supersample 4 transparentBackground true > hide #!3 models > show #!4 models > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/3jwd_cd4_GP120_footprint.png"" > width 2000 height 1450 supersample 4 transparentBackground true > hide #!4 models > show #!1 models > surface hidePatches #1.2-9,12-13#!1 > select #1/H,L 1807 atoms, 1856 bonds, 234 residues, 1 model selected > show sel cartoons > select clear > select #!1/H:96 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #!1/H:100C 19 atoms, 17 bonds, 2 residues, 1 model selected > select add #!1/H:100B 31 atoms, 29 bonds, 3 residues, 1 model selected > select add #!1/H:100 37 atoms, 34 bonds, 4 residues, 1 model selected > select add #!1/H:99 43 atoms, 39 bonds, 5 residues, 1 model selected > select add #!1/H:98 49 atoms, 44 bonds, 6 residues, 1 model selected > select add #!1/H:97 53 atoms, 47 bonds, 7 residues, 1 model selected > select add #!1/H:100A 67 atoms, 62 bonds, 8 residues, 1 model selected > show sel atoms > color sel byhetero > select add #!1/H:100E 78 atoms, 72 bonds, 9 residues, 1 model selected > select add #!1/H:100D 82 atoms, 75 bonds, 10 residues, 1 model selected > show sel atoms > color sel byhetero > ui tool show H-Bonds > hbonds sel color #000404 interModel false angleSlop 50.0 intraMol false > intraRes false select true reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 50 degrees Models used: 1 92-5F04_Q23_J473_real_space_refined_071.pdb 8 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASN 195 ND2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H SER 100 O no hydrogen 3.395 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASN 195 ND2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H TRP 100A O no hydrogen 2.913 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASN 425 ND2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H LEU 100C O no hydrogen 2.872 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 96 NE 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD1 no hydrogen 3.193 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 96 NH2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD1 no hydrogen 2.917 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 100E NE 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A GLN 428 OE1 no hydrogen 2.930 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 100E NH1 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD2 no hydrogen 2.899 N/A 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 100E NH2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A GLN 428 OE1 no hydrogen 2.894 N/A 8 hydrogen bonds found > color (#!1 & sel) byhetero > select clear > show #1.11 models > select #1/L 815 atoms, 835 bonds, 108 residues, 1 model selected > hide sel cartoons > select #!1/H:98@CB 1 atom, 1 residue, 1 model selected > select add #!1/H:100@OG 2 atoms, 1 bond, 2 residues, 1 model selected > hide sel atoms > select up 5 atoms, 2 bonds, 3 residues, 1 model selected > hide sel atoms > select #!1/H:98@OG 1 atom, 1 residue, 1 model selected > hide sel atoms > select #!1/H:100@CB 1 atom, 1 residue, 1 model selected > hide sel atoms > select #!1/H:100B@CG 1 atom, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > hide sel atoms > select clear > ui tool show ""Side View"" > save ""/Users/sphulera/OneDrive - The Scripps Research > Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04_alpha_helix.png"" > width 2000 height 1450 supersample 4 transparentBackground true ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: Z1B600163LL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 5 days, 4 hours, 10 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG HDR 4K: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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 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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 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 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX