id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15998 Cannot update file history chjorth@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22631 ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Hello, I'm having issues saving a .cxs session. After saving, the log says I have permissions denied. I've tried un-installing and re-installing several versiosn of ChimeraX over the past few months and nothing has resolved this saving issue. This is the pop-up window notifying failure to save: ""Error processing trigger ""file history changed"": PermissionError: [Errno 13] Permission denied: 'C:\\Users\\chris\\AppData\\Local\\Temp\\chbp8qmgij_1.html' File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\widgets\htmlview.py"", line 244, in setHtml tf = open(self._tf_name, ""wb"") ^^^^^^^^^^^^^^^^^^^^^^^^^"" I attached a note file of the log text. Thanks for the help. Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > surface cap true Log from Wed Sep 4 19:17:24 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Supplemental Figure #_modes of neut/9-4-2024_Gc with all 4 > Sites models.cxs"" Opened cryosparc_P409_J122_004_volume_map_sharp.mrc as #1, grid size 220,220,220, pixel 1.88, shown at level 0.2, step 1, values float32 Log from Thu Aug 15 18:02:26 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site 6/8-15-2024_Site 6 models and J122 map for > figure.cxs"" Opened cryosparc_P409_J122_004_volume_map_sharp.mrc as #1, grid size 220,220,220, pixel 1.88, shown at level 0.2, step 1, values float32 Log from Thu Aug 15 11:55:54 2024 Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Structure Files/Gc-4Ffabs/Finalizing Site 6 cryo > map/cryosparc_P409_J122_004_volume_map_sharp.mrc"" Opened cryosparc_P409_J122_004_volume_map_sharp.mrc as #1, grid size 220,220,220, pixel 1.88, shown at level 0.0904, step 1, values float32 > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Structure Files/Gc-4Ffabs/Finalizing Site 6 cryo > map/cryosparc_P409_J125_003_volume_map_sharp.mrc"" Opened cryosparc_P409_J125_003_volume_map_sharp.mrc as #2, grid size 220,220,220, pixel 1.88, shown at level 0.0551, step 1, values float32 > open > C:/Users/ckh755/Downloads/cryosparc_P409_J120_class_01_00062_volume_sharp.mrc Opened cryosparc_P409_J120_class_01_00062_volume_sharp.mrc as #3, grid size 128,128,128, pixel 3.23, shown at level 0.0946, step 1, values float32 > open > C:/Users/ckh755/Downloads/cryosparc_P409_J120_class_01_00062_volume_sharp.mrc Opened cryosparc_P409_J120_class_01_00062_volume_sharp.mrc as #4, grid size 128,128,128, pixel 3.23, shown at level 0.0946, step 1, values float32 > open C:/Users/ckh755/Downloads/cryosparc_P409_J119_class_01_final_volume.mrc Opened cryosparc_P409_J119_class_01_final_volume.mrc as #5, grid size 192,192,192, pixel 2.15, shown at level 0.0663, step 1, values float32 > open C:/Users/ckh755/Downloads/cryosparc_P409_J111_003_volume_map_sharp.mrc Opened cryosparc_P409_J111_003_volume_map_sharp.mrc as #6, grid size 220,220,220, pixel 1.88, shown at level 0.05, step 1, values float32 > close #4 > open C:/Users/ckh755/Downloads/cryosparc_P409_J105_004_volume_map_sharp.mrc Opened cryosparc_P409_J105_004_volume_map_sharp.mrc as #4, grid size 220,220,220, pixel 1.88, shown at level 0.0941, step 1, values float32 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > vop step 1 > vop level 0.2 > surface dust #1 size 18.8 > surface dust #2 size 18.8 > surface dust #3 size 32.3 > surface dust #5 size 21.5 > surface dust #6 size 18.8 > surface dust #4 size 18.8 > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!2 models > show #!1 models > show #!3 models > hide #!2 models > hide #!1 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > show #!6 models > hide #!5 models > close #2-6 > show #!1 models > volume #1 level 0.21 > volume #1 level 0.2 > surface dust #1 size 18.8 > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site > 6/Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH.pdb"" Chain information for Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH.pdb #2 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site > 6/Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH.pdb"" Chain information for Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH.pdb #3 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site > 6/Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH.pdb"" Chain information for Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH.pdb #4 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > rename #2 Gc-42437-36124_37847refined_350-noH.pdb > hide #!3 models > hide #!1 models > hide #!4 models > close #2-4 > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site > 6/Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for > 37847 Fv model.pdb"" Chain information for Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 37847 Fv model.pdb #2 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site > 6/Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for > 42437 Fv model.pdb"" Chain information for Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 42437 Fv model.pdb #3 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site > 6/Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc > domain I-II model.pdb"" Chain information for Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb #4 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site 6/Gc-42437-36124_refine_035_for 36124 Fab > model.pdb"" Chain information for Gc-42437-36124_refine_035_for 36124 Fab model.pdb #5 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > mmaker #5 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 37847 Fv model.pdb, chain G (#2) with Gc-42437-36124_refine_035_for 36124 Fab model.pdb, chain G (#5), sequence alignment score = 1511.8 RMSD between 235 pruned atom pairs is 0.897 angstroms; (across all 321 pairs: 2.280) > hide #2-5 target a > cartoon #2-5 > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!4 models > hide #!3 models Drag select of 150 residues > select up 2125 atoms, 2171 bonds, 271 residues, 1 model selected > select up 4240 atoms, 4343 bonds, 547 residues, 1 model selected > cartoon hide sel > hide #!2 models > show #!3 models Drag select of 227 residues, 1 pseudobonds > select up 2634 atoms, 2700 bonds, 1 pseudobond, 331 residues, 2 models selected > select up 4264 atoms, 4371 bonds, 1 pseudobond, 546 residues, 2 models selected > cartoon hide (#!3 & sel) > hide #!3 models > show #!4 models > select clear Drag select of 61 residues > select up 834 atoms, 850 bonds, 110 residues, 1 model selected > select up 1714 atoms, 1756 bonds, 226 residues, 1 model selected > cartoon hide sel Drag select of 143 residues > select up 1440 atoms, 1472 bonds, 186 residues, 1 model selected > select up 1738 atoms, 1784 bonds, 225 residues, 1 model selected > cartoon hide sel > show #!5 models > hide #!4 models Drag select of 92 residues > select up 1185 atoms, 1206 bonds, 156 residues, 1 model selected > select up 1714 atoms, 1754 bonds, 226 residues, 1 model selected > cartoon hide sel > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > show #!1 models > select add #1 1714 atoms, 1754 bonds, 226 residues, 3 models selected > select add #5 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 4 models selected > select subtract #5 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.98262,-0.1739,-0.064914,446.81,-0.063593,0.64393,-0.76244,239.77,0.17439,-0.74506,-0.6438,449.76 > view matrix models > #1,0.99758,-0.031402,-0.061997,19.397,-0.025974,-0.99591,0.086502,359.5,-0.06446,-0.084682,-0.99432,448.57 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.99758,-0.031402,-0.061997,19.753,-0.025974,-0.99591,0.086502,394.2,-0.06446,-0.084682,-0.99432,442.7 > view matrix models > #1,0.99758,-0.031402,-0.061997,21.992,-0.025974,-0.99591,0.086502,395.32,-0.06446,-0.084682,-0.99432,437.53 > select subtract #1 Nothing selected > transparency #1,4-5 50 > ui tool show ""Fit in Map"" > fitmap #4 inMap #1 Fit molecule Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb (#4) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 5978 atoms average map value = 0.3436, steps = 88 shifted from previous position = 8.78 rotated from previous position = 7.03 degrees atoms outside contour = 1389, contour level = 0.2 Position of Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb (#4) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99414132 0.07879143 -0.07399286 0.45674897 0.07681640 -0.99661836 -0.02917344 400.23012853 -0.07604126 0.02331866 -0.99683196 426.55477183 Axis 0.99853400 0.03896580 -0.03757008 Axis point 0.00000000 197.29859251 215.92025858 Rotation angle (degrees) 178.49383096 Shift along axis 0.02566740 > fitmap #5 inMap #1 Fit molecule Gc-42437-36124_refine_035_for 36124 Fab model.pdb (#5) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 8882 atoms average map value = 0.2656, steps = 80 shifted from previous position = 4.74 rotated from previous position = 9.22 degrees atoms outside contour = 3338, contour level = 0.2 Position of Gc-42437-36124_refine_035_for 36124 Fab model.pdb (#5) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.08397317 -0.06990450 0.99401301 188.88436047 -0.45519181 0.89006610 0.02414025 143.00806885 -0.88642480 -0.45043945 -0.10656163 111.56904090 Axis -0.24001391 0.95101250 -0.19485518 Axis point 168.97538130 0.00000000 -22.39729916 Rotation angle (degrees) 98.64050778 Shift along axis 68.92778219 > hide #!1 models > show #!1 models > hide #!5 models > hide #!4 models > show #!5 models > show #!4 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!4 models > hide #!1 models Drag select of 61 residues > select up 1021 atoms, 1034 bonds, 129 residues, 1 model selected > select up 3756 atoms, 3845 bonds, 481 residues, 1 model selected > cartoon hide sel > show #!4 models > select add #5 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 2 models selected > show #!3 models > show #!2 models > show #!1 models > select subtract #5 Nothing selected > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Structure Files/Gc-4Ffabs/Map for Gc245 med res map with Site 6 and > domain III/fold_gc_diii_36145_fv_model_4.cif"" Chain information for fold_gc_diii_36145_fv_model_4.cif #6 --- Chain | Description A | . B | . C | . > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Structure Files/Gc+Site2+Site5/Pymol/Gc-42437-36124_refine_035.pdb"" Chain information for Gc-42437-36124_refine_035.pdb #7 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > mmaker #6 to #7 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 Gc-42437-36124_refine_035.pdb, chain G (#7) with fold_gc_diii_36145_fv_model_4.cif, chain A (#6), sequence alignment score = 520.8 RMSD between 105 pruned atom pairs is 0.570 angstroms; (across all 105 pairs: 0.570) > hide #6-7 target a > select add #7 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 2 models selected > show #7 cartoons > select subtract #7 Nothing selected > show #!4 models > hide #!4 models > close #6#7 > show #!5 models > show #!4 models > show #!3 models > show #!2 models > show #!1 models > vop step 1 > vop level 0.2 > hide dust Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > close #2-5 > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site 6/Models for > Figure/Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for > Gc domain I-II model.pdb"" Chain information for Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb #2 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site 6/Models for > Figure/fold_gc_diii_36145_fv_model_4.cif"" Chain information for fold_gc_diii_36145_fv_model_4.cif #3 --- Chain | Description A | . B | . C | . > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site 6/Models for > Figure/Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for > 42437 Fv model.pdb"" Chain information for Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 42437 Fv model.pdb #4 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site 6/Models for > Figure/Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for > 37847 Fv model.pdb"" Chain information for Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 37847 Fv model.pdb #5 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site 6/Models for > Figure/Gc-42437-36124_refine_035_for 36124 Fab model.pdb"" Chain information for Gc-42437-36124_refine_035_for 36124 Fab model.pdb #6 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site 6/Models for > Figure/fold_gc_diii_36145_fv_model_4.cif"" Chain information for fold_gc_diii_36145_fv_model_4.cif #7 --- Chain | Description A | . B | . C | . > mmaker #3-7 too #2 > matchmaker #3-7 too #2 Expected a keyword > mmaker #3-7 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb, chain L (#2) with fold_gc_diii_36145_fv_model_4.cif, chain C (#3), sequence alignment score = 509 RMSD between 106 pruned atom pairs is 0.629 angstroms; (across all 108 pairs: 0.736) Matchmaker Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb, chain G (#2) with Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 42437 Fv model.pdb, chain G (#4), sequence alignment score = 1686.8 RMSD between 321 pruned atom pairs is 0.000 angstroms; (across all 321 pairs: 0.000) Matchmaker Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb, chain G (#2) with Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 37847 Fv model.pdb, chain G (#5), sequence alignment score = 1686.8 RMSD between 321 pruned atom pairs is 0.000 angstroms; (across all 321 pairs: 0.000) Matchmaker Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb, chain G (#2) with Gc-42437-36124_refine_035_for 36124 Fab model.pdb, chain G (#6), sequence alignment score = 1511.8 RMSD between 235 pruned atom pairs is 0.897 angstroms; (across all 321 pairs: 2.280) Matchmaker Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb, chain L (#2) with fold_gc_diii_36145_fv_model_4.cif, chain C (#7), sequence alignment score = 509 RMSD between 106 pruned atom pairs is 0.629 angstroms; (across all 108 pairs: 0.736) > hide #3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #7 models > hide #!2 models > show #3 models > show #!6 models > hide #3 models > show #!5 models > show #7 models > show #!4 models > show #3 models > show #!2 models > mmaker #3,7 to #6 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 Gc-42437-36124_refine_035_for 36124 Fab model.pdb, chain G (#6) with fold_gc_diii_36145_fv_model_4.cif, chain A (#3), sequence alignment score = 520.8 RMSD between 105 pruned atom pairs is 0.570 angstroms; (across all 105 pairs: 0.570) Matchmaker Gc-42437-36124_refine_035_for 36124 Fab model.pdb, chain G (#6) with fold_gc_diii_36145_fv_model_4.cif, chain A (#7), sequence alignment score = 520.8 RMSD between 105 pruned atom pairs is 0.570 angstroms; (across all 105 pairs: 0.570) > hide atoms > show cartoons > hide #7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #3 models > hide #!1 models > hide #2/H,L,A,B > hide cartoons #2/H,L,A,B Expected ',' or a keyword > hide cartoons #2/H,L,A,B Expected ',' or a keyword > hide #2/H,L,A,B cartoons [Repeated 1 time(s)] > show #3 models > hide #!2 models > show #!4 models > hide #3 models > show #!5 models > show #!2 models > hide #4/G,A,B cartoons > hide #5/G,H,L cartoons > hide #!5 models > hide #!4 models > hide #!2 models > show #!2 models > show #!6 models > hide #!2 models > hide #6/G,H,L cartoons > show #!5 models > show #!4 models > show #3 models > hide #3 models > show #!2 models > hide #!4 models > hide #!2 models > hide #!6 models > show #!4 models > hide #!5 models > show #!6 models > hide #!4 models > hide #!6 models > show #7 models > show #3 models > show #!2 models > hide #7 models > hide #3 models > hide #!2 models > show #7 models > show #!6 models > show #!5 models > show #!4 models > show #3 models > show #!2 models > color #3/B,C #DD833E > color #7/B,C #DD833E > color #6/A,B #78C14D > color #5/A,B #CC66A7 > color #4/H,L #9142AE > dssp > color #2/G:1041-1140,1232-1268,1419-1430 #FF7F7F [Repeated 1 time(s)] > color > #2/G:1141-1186,1205-1231,1269-1282,1296-1320,1347-1403,1410-1418,1187-1204 > #FFFF7F > color #2/G:1283-1295,1321-1346,1404-1409 #c18c7f > color #2/G:1442-1556, #7F7FFF Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #2/G:1431-1441, #7FFFFF Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #2/G:1431-1441, #7FFFFF Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #2/G:1442-1556 #7F7FFF > color #2/G:1431-1441 #7FFFFF > color #3/A:1442-1556 #7F7FFF > color #7/A:1442-1556 #7F7FFF > hide #!2 models > hide #!4 models > hide #!5 models > hide #!6 models > show #!2 models > hide #!2 models > color #3/A:1442-1556 #7F7FFF > color #7/A:1442-1556 #7F7FFF Drag select of 74 residues > select up 922 atoms, 934 bonds, 124 residues, 2 models selected > select up 1592 atoms, 1616 bonds, 210 residues, 2 models selected > color sel #7F7FFF > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A > color sel green > color #3/A:1-105 #7F7FFF > color #7/A:1-105 #7F7FFF > show #!6 models > show #!5 models > show #!4 models > show #!2 models > show #!1 models > select clear > hide #!1 models > show > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 > sticks Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > color > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 > #33FF33 > undo > color > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 > #33FF33 > select > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 72 atoms, 67 bonds, 12 residues, 1 model selected > show sel atoms > show sel atoms sticks Expected ',' or a keyword > show sel atoms as sticks Expected ',' or a keyword > style sel stick Changed 72 atom styles > color > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 > #33FF33 > save ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site 6/8-15-2024_Site 6 models and J122 map for > figure.cxs"" includeMaps true ——— End of log from Thu Aug 15 11:55:54 2024 ——— opened ChimeraX session > select > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 > sidechain only Expected a keyword > select sidechain only > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 Expected a keyword > select sidechain > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 Expected a keyword > color > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 > sideonly Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 > sideonly #33FF33 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select clear > select > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 > sideonly Expected a keyword > select > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 > sidechainonly Expected a keyword > select > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 > sidechain Expected a keyword > select sidechain > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 Expected a keyword > select side > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 Expected an objects specifier or a keyword > select sideonly > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 Expected a keyword > select > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 > sideonly Expected a keyword > select > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 72 atoms, 67 bonds, 12 residues, 1 model selected > show sel atoms as sticks Expected ',' or a keyword > show (sel-residues & sidechain) target ab > select clear > select > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 72 atoms, 67 bonds, 12 residues, 1 model selected > select #3/A:Cys 48 atoms, 40 bonds, 8 residues, 1 model selected > select #3,7/A:Cys 96 atoms, 80 bonds, 16 residues, 2 models selected > select #3/A:Cys 48 atoms, 40 bonds, 8 residues, 1 model selected > select #3,7/A:Cys 96 atoms, 80 bonds, 16 residues, 2 models selected > show (sel-residues & sidechain) target ab > show sel target ab > dssp > select up 572 atoms, 574 bonds, 78 residues, 2 models selected > select up 1592 atoms, 1616 bonds, 210 residues, 2 models selected > select up 5098 atoms, 5204 bonds, 662 residues, 2 models selected > select clear > select #3,7/A:Cys 96 atoms, 80 bonds, 16 residues, 2 models selected > bond sel Created 8 bonds > select > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 72 atoms, 67 bonds, 12 residues, 1 model selected > select #3,7/A:Cys@ca 16 atoms, 16 residues, 2 models selected > select #3,7/A:Cys@c 16 atoms, 16 residues, 2 models selected > select #3,7/A:Cys@sc Nothing selected > select #3,7/A:Cys@S Nothing selected > select #3,7/A:Cys target a Expected a keyword > color #3,7/A:Cys orange target a > color #3,7/A:Cys #33FF33 target a > color > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 > #33FF33 target a > select clear > show #2-7 target ab > cartoon #2-7 > hide #2-7 target a > color #2 #dadadaff > color #3 #dadadaff > color #4 #dadadaff > color #5 #dadadaff > color #6 #dadadaff > color #7 #dadadaff > dssp > mmaker #3-7 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb, chain L (#2) with fold_gc_diii_36145_fv_model_4.cif, chain C (#3), sequence alignment score = 509 RMSD between 106 pruned atom pairs is 0.629 angstroms; (across all 108 pairs: 0.736) Matchmaker Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb, chain G (#2) with Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 42437 Fv model.pdb, chain G (#4), sequence alignment score = 1686.8 RMSD between 321 pruned atom pairs is 0.000 angstroms; (across all 321 pairs: 0.000) Matchmaker Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb, chain G (#2) with Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 37847 Fv model.pdb, chain G (#5), sequence alignment score = 1686.8 RMSD between 321 pruned atom pairs is 0.000 angstroms; (across all 321 pairs: 0.000) Matchmaker Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb, chain G (#2) with Gc-42437-36124_refine_035_for 36124 Fab model.pdb, chain G (#6), sequence alignment score = 1511.8 RMSD between 235 pruned atom pairs is 0.897 angstroms; (across all 321 pairs: 2.280) Matchmaker Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb, chain L (#2) with fold_gc_diii_36145_fv_model_4.cif, chain C (#7), sequence alignment score = 509 RMSD between 106 pruned atom pairs is 0.629 angstroms; (across all 108 pairs: 0.736) > mmaker #3,7 to #6 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 Gc-42437-36124_refine_035_for 36124 Fab model.pdb, chain G (#6) with fold_gc_diii_36145_fv_model_4.cif, chain A (#3), sequence alignment score = 520.8 RMSD between 105 pruned atom pairs is 0.570 angstroms; (across all 105 pairs: 0.570) Matchmaker Gc-42437-36124_refine_035_for 36124 Fab model.pdb, chain G (#6) with fold_gc_diii_36145_fv_model_4.cif, chain A (#7), sequence alignment score = 520.8 RMSD between 105 pruned atom pairs is 0.570 angstroms; (across all 105 pairs: 0.570) > hide atoms > show cartoons > hide #2/H,L,A,B cartoons > hide #4/G,A,B cartoons > hide #5/G,H,L cartoons > hide #6/G,H,L cartoons > color #4/H,L #9142AE > color #5/A,B #CC66A7 > color #6/A,B #78C14D > color #3/B,C #DD833E > color #7/B,C #DD833E > color #2/G:1041-1140,1232-1268,1419-1430 #FF7F7F > color > #2/G:1141-1186,1205-1231,1269-1282,1296-1320,1347-1403,1410-1418,1187-1204 > #FFFF7F > color #2/G:1283-1295,1321-1346,1404-1409 #c18c7f > color #2/G:1442-1556 #7F7FFF > color #2/G:1431-1441 #7FFFFF > color #3/A:1-105 #7F7FFF > color #7/A:1-105 #7F7FFF > select > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 72 atoms, 67 bonds, 12 residues, 1 model selected > show (sel-residues & sidechain) target ab > color > #2/G:1165,1198,1169,1205,1173,1207,1175,1180,1193,1360,1208,1368,1236,1246,1305,1310,1452,1464,1455,1458,1519,1539,1528,1531 > #33FF33 target a > select #3,7/A:Cys 96 atoms, 88 bonds, 16 residues, 2 models selected > show (sel-residues & sidechain) target ab > bond sel Created 0 bonds > color #3,7/A:Cys #33FF33 target a > select clear > show #!1 models > color #1 #ffffff80 models > color #1 #ffffff > transparency #1 0.5 > transparency #1 0.1 > transparency #1 0.9 > hide #!1 models > show #!1 models > set trans #1 0.1 Expected a keyword > set transparent #1 0.1 Expected a keyword > set transparent #1 0.1 Expected a keyword > transparency #1 80 > transparency #1 60 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb (#2) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 5978 atoms average map value = 0.3436, steps = 88 shifted from previous position = 8.78 rotated from previous position = 7.03 degrees atoms outside contour = 1389, contour level = 0.2 Position of Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for Gc domain I-II model.pdb (#2) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99414132 0.07879143 -0.07399286 0.45674897 0.07681640 -0.99661836 -0.02917344 400.23012854 -0.07604126 0.02331866 -0.99683196 426.55477183 Axis 0.99853400 0.03896580 -0.03757008 Axis point 0.00000000 197.29859251 215.92025858 Rotation angle (degrees) 178.49383096 Shift along axis 0.02566740 > fitmap #3 inMap #1 Fit molecule fold_gc_diii_36145_fv_model_4.cif (#3) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 2549 atoms average map value = 0.2661, steps = 236 shifted from previous position = 39.5 rotated from previous position = 85 degrees atoms outside contour = 977, contour level = 0.2 Position of fold_gc_diii_36145_fv_model_4.cif (#3) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.43327688 -0.58616308 0.68460498 201.78701269 -0.66399689 -0.30601667 -0.68224770 181.73470487 0.60940895 -0.75017774 -0.25662052 177.31430354 Axis -0.53162842 0.58849294 -0.60913650 Axis point 29.96085983 172.73517154 0.00000000 Rotation angle (degrees) 176.33695573 Shift along axis -108.33473362 > fitmap #4 inMap #1 Fit molecule Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 42437 Fv model.pdb (#4) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 5978 atoms average map value = 0.3436, steps = 88 shifted from previous position = 8.78 rotated from previous position = 7.03 degrees atoms outside contour = 1389, contour level = 0.2 Position of Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 42437 Fv model.pdb (#4) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99414132 0.07879143 -0.07399286 0.45674897 0.07681640 -0.99661836 -0.02917344 400.23012854 -0.07604126 0.02331866 -0.99683196 426.55477183 Axis 0.99853400 0.03896580 -0.03757008 Axis point 0.00000000 197.29859251 215.92025858 Rotation angle (degrees) 178.49383096 Shift along axis 0.02566740 > fitmap #5 inMap #1 Fit molecule Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 37847 Fv model.pdb (#5) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 5978 atoms average map value = 0.3436, steps = 88 shifted from previous position = 8.78 rotated from previous position = 7.03 degrees atoms outside contour = 1389, contour level = 0.2 Position of Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 37847 Fv model.pdb (#5) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99414132 0.07879143 -0.07399286 0.45674897 0.07681640 -0.99661836 -0.02917344 400.23012854 -0.07604126 0.02331866 -0.99683196 426.55477183 Axis 0.99853400 0.03896580 -0.03757008 Axis point 0.00000000 197.29859251 215.92025858 Rotation angle (degrees) 178.49383096 Shift along axis 0.02566740 > fitmap #6 inMap #1 Fit molecule Gc-42437-36124_refine_035_for 36124 Fab model.pdb (#6) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 8882 atoms average map value = 0.2656, steps = 80 shifted from previous position = 4.74 rotated from previous position = 9.22 degrees atoms outside contour = 3338, contour level = 0.2 Position of Gc-42437-36124_refine_035_for 36124 Fab model.pdb (#6) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.08397309 -0.06990458 0.99401301 188.88436973 -0.45519258 0.89006571 0.02414027 143.00789182 -0.88642441 -0.45044021 -0.10656162 111.56919155 Axis -0.24001431 0.95101233 -0.19485553 Axis point 168.97544778 0.00000000 -22.39719531 Rotation angle (degrees) 98.64051649 Shift along axis 68.92744241 > select add #7 2549 atoms, 2606 bonds, 331 residues, 1 model selected > select add #3 5098 atoms, 5212 bonds, 662 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.8449,-0.50304,0.18194,221.78,0.18775,-0.03963,-0.98142,242.71,0.5009,0.86336,0.060961,268.04,#7,0.8449,-0.50304,0.18194,221.78,0.18775,-0.03963,-0.98142,242.71,0.5009,0.86336,0.060961,268.04 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.8449,-0.50304,0.18194,218.37,0.18775,-0.03963,-0.98142,204.84,0.5009,0.86336,0.060961,263.71,#7,0.8449,-0.50304,0.18194,218.37,0.18775,-0.03963,-0.98142,204.84,0.5009,0.86336,0.060961,263.71 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.83026,-0.52445,0.18873,218.31,0.038689,-0.28356,-0.95817,204.19,0.55603,0.80284,-0.21514,264.09,#7,0.83026,-0.52445,0.18873,218.31,0.038689,-0.28356,-0.95817,204.19,0.55603,0.80284,-0.21514,264.09 > fitmap #7 inMap #1 Fit molecule fold_gc_diii_36145_fv_model_4.cif (#7) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 2549 atoms average map value = 0.3309, steps = 92 shifted from previous position = 2.38 rotated from previous position = 23.3 degrees atoms outside contour = 797, contour level = 0.2 Position of fold_gc_diii_36145_fv_model_4.cif (#7) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.94449936 -0.21395042 0.24929136 212.07520004 -0.15522514 0.37814154 0.91264129 198.95293941 -0.28952741 -0.90068540 0.32394396 145.72302377 Axis -0.95811497 0.28469792 0.03102892 Axis point 0.00000000 240.54371130 -98.40037650 Rotation angle (degrees) 71.13784566 Shift along axis -142.02930880 > fitmap #3 inMap #1 Fit molecule fold_gc_diii_36145_fv_model_4.cif (#3) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 2549 atoms average map value = 0.3309, steps = 92 shifted from previous position = 2.38 rotated from previous position = 23.3 degrees atoms outside contour = 797, contour level = 0.2 Position of fold_gc_diii_36145_fv_model_4.cif (#3) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.94449936 -0.21395042 0.24929136 212.07520004 -0.15522514 0.37814154 0.91264129 198.95293941 -0.28952741 -0.90068540 0.32394396 145.72302377 Axis -0.95811497 0.28469792 0.03102892 Axis point 0.00000000 240.54371130 -98.40037650 Rotation angle (degrees) 71.13784566 Shift along axis -142.02930880 > select clear > undo [Repeated 7 time(s)] > show #!1 models > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site 6/Models for > Figure/Gc-42437-36124_refine_035_for domain III.pdb"" Chain information for Gc-42437-36124_refine_035_for domain III.pdb #8 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > select add #8 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 2 models selected > hide (#!8 & sel) target a > cartoon (#!8 & sel) > select clear Drag select of 132 residues > select up 1350 atoms, 1379 bonds, 177 residues, 1 model selected > select up 1714 atoms, 1754 bonds, 226 residues, 1 model selected > cartoon hide sel Drag select of 128 residues > select up 1296 atoms, 1322 bonds, 170 residues, 1 model selected > select up 3361 atoms, 3442 bonds, 443 residues, 1 model selected > select up 8882 atoms, 9094 bonds, 1154 residues, 1 model selected > select down 3361 atoms, 3442 bonds, 443 residues, 1 model selected > cartoon hide sel Drag select of 353 residues, 1 pseudobonds > cartoon hide (#!8 & sel) Drag select of 4 residues > cartoon hide sel Drag select of 13 residues > select clear Drag select of 10 residues > select #8/G:1436 10 atoms, 10 bonds, 1 residue, 1 model selected Drag select of 7 residues > select up 81 atoms, 80 bonds, 10 residues, 1 model selected > select up 2155 atoms, 2206 bonds, 276 residues, 1 model selected > cartoon hide sel > mmaker #8 to #7 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 fold_gc_diii_36145_fv_model_4.cif, chain A (#7) with Gc-42437-36124_refine_035_for domain III.pdb, chain G (#8), sequence alignment score = 520.8 RMSD between 105 pruned atom pairs is 0.570 angstroms; (across all 105 pairs: 0.570) > select add #8 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 2 models selected > select subtract #8 Nothing selected > select add #8 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 2 models selected > view matrix models > #8,0.13946,-0.060749,0.98836,211.93,0.54495,-0.82867,-0.12783,275.16,0.82679,0.55644,-0.08246,298.26 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.13946,-0.060749,0.98836,214.69,0.54495,-0.82867,-0.12783,269.87,0.82679,0.55644,-0.08246,298.5 > view matrix models > #8,0.13946,-0.060749,0.98836,215.21,0.54495,-0.82867,-0.12783,270.32,0.82679,0.55644,-0.08246,295.92 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.83928,-0.52768,-0.131,264.13,-0.2418,-0.14645,-0.95921,212.98,0.48697,0.83672,-0.25051,271.37 > view matrix models > #8,0.66366,-0.6478,-0.37404,255.57,-0.31356,0.21306,-0.92536,203.12,0.67914,0.73141,-0.061726,284.42 > view matrix models > #8,0.51522,-0.709,-0.48151,247.7,-0.082793,0.51802,-0.85135,212.09,0.85305,0.4785,0.2082,298.68 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.51522,-0.709,-0.48151,251.88,-0.082793,0.51802,-0.85135,208.26,0.85305,0.4785,0.2082,289.68 > view matrix models > #8,0.51522,-0.709,-0.48151,255.82,-0.082793,0.51802,-0.85135,212.59,0.85305,0.4785,0.2082,293.1 > hide #7 models > hide #3 models > fitmap #8 inMap #1 Fit molecule Gc-42437-36124_refine_035_for domain III.pdb (#8) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 8882 atoms average map value = 0.176, steps = 272 shifted from previous position = 34 rotated from previous position = 45.5 degrees atoms outside contour = 5087, contour level = 0.2 Position of Gc-42437-36124_refine_035_for domain III.pdb (#8) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.02816358 -0.35713950 -0.93362637 214.16585742 -0.05358637 -0.93319326 0.35535734 192.23128185 -0.99816598 0.04002151 -0.04541987 73.40749618 Axis -0.71273201 0.14587446 0.68610037 Axis point 0.00000000 127.80144058 123.83145931 Rotation angle (degrees) 167.21951974 Shift along axis -74.23631722 > view matrix models > #8,0.51522,-0.709,-0.48151,279.05,-0.082793,0.51802,-0.85135,231.88,0.85305,0.4785,0.2082,328.9 > select clear Drag select of 5 residues > cartoon hide sel > select add #8 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 2 models selected > view matrix models > #8,0.51522,-0.709,-0.48151,259.92,-0.082793,0.51802,-0.85135,213.39,0.85305,0.4785,0.2082,290.21 > fitmap #8 inMap #1 Fit molecule Gc-42437-36124_refine_035_for domain III.pdb (#8) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 8882 atoms average map value = 0.2656, steps = 536 shifted from previous position = 18.6 rotated from previous position = 117 degrees atoms outside contour = 3344, contour level = 0.2 Position of Gc-42437-36124_refine_035_for domain III.pdb (#8) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.08407712 -0.07018635 0.99398436 188.87403525 -0.45545392 0.88992728 0.02431375 142.98079709 -0.88628030 -0.45066984 -0.10678917 111.57911991 Axis -0.24022687 0.95095933 -0.19485225 Axis point 168.97140736 0.00000000 -22.37136483 Rotation angle (degrees) 98.65413594 Shift along axis 68.85486376 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.7769,-0.60798,0.16368,272.92,0.069998,-0.17495,-0.98209,232.7,0.62572,0.77444,-0.09336,272.94 > fitmap #8 inMap #1 Fit molecule Gc-42437-36124_refine_035_for domain III.pdb (#8) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 8882 atoms average map value = 0.07648, steps = 516 shifted from previous position = 27.5 rotated from previous position = 46.4 degrees atoms outside contour = 7383, contour level = 0.2 Position of Gc-42437-36124_refine_035_for domain III.pdb (#8) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.77327299 -0.61398100 0.15835473 249.23314880 -0.53262981 -0.49347488 0.68759583 127.20425412 -0.34402669 -0.61604373 -0.70861538 155.16983898 Axis -0.93153210 0.35898298 0.05813051 Axis point 0.00000000 147.87905583 43.53650009 Rotation angle (degrees) 135.59475538 Shift along axis -177.48441401 > view matrix models > #8,0.012136,-0.65811,-0.75282,231.06,0.21151,0.73753,-0.64133,226.39,0.9773,-0.15145,0.14815,306.95 > fitmap #8 inMap #1 Fit molecule Gc-42437-36124_refine_035_for domain III.pdb (#8) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 8882 atoms average map value = 0.176, steps = 156 shifted from previous position = 29.9 rotated from previous position = 25.8 degrees atoms outside contour = 5086, contour level = 0.2 Position of Gc-42437-36124_refine_035_for domain III.pdb (#8) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.02822536 -0.35707983 -0.93364732 214.17425912 -0.05317950 -0.93323314 0.35531374 192.26785250 -0.99818599 0.03962204 -0.04533017 73.40133493 Axis -0.71274420 0.14571039 0.68612257 Axis point 0.00000000 127.80819014 123.81373793 Rotation angle (degrees) 167.20507474 Shift along axis -74.27372517 > view matrix models > #8,0.54929,-0.7777,0.30571,262.85,0.60848,0.1215,-0.78421,258.13,0.57274,0.61678,0.53996,272.4 > view matrix models > #8,0.98478,0.084306,-0.15198,273.76,-0.16812,0.68367,-0.71016,206.04,0.04403,0.72491,0.68744,241.21 > view matrix models > #8,0.33928,-0.93695,0.083763,253.62,-0.273,-0.18328,-0.94439,213.69,0.9002,0.29754,-0.31797,295.68 > view matrix models > #8,0.39462,-0.77374,-0.49557,254.19,0.37213,0.62772,-0.68373,237.06,0.84011,0.085399,0.53565,295.59 > view matrix models > #8,0.50628,-0.68449,-0.52455,259.04,0.43851,0.7281,-0.52687,239.2,0.74256,0.036726,0.66877,290.9 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.50628,-0.68449,-0.52455,260.85,0.43851,0.7281,-0.52687,232.82,0.74256,0.036726,0.66877,294.4 > view matrix models > #8,0.50628,-0.68449,-0.52455,259.15,0.43851,0.7281,-0.52687,234.86,0.74256,0.036726,0.66877,292.62 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.71046,-0.63639,-0.30042,269.79,-0.055177,0.37521,-0.9253,212.82,0.70157,0.67397,0.23146,280.44 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.71046,-0.63639,-0.30042,269.95,-0.055177,0.37521,-0.9253,216.35,0.70157,0.67397,0.23146,280.33 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.47034,-0.6186,-0.62938,256.28,-0.036628,0.69889,-0.71429,212.34,0.88173,0.35901,0.30606,295.28 > fitmap #8 inMap #1 Fit molecule Gc-42437-36124_refine_035_for domain III.pdb (#8) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 8882 atoms average map value = 0.176, steps = 200 shifted from previous position = 30.5 rotated from previous position = 33.9 degrees atoms outside contour = 5084, contour level = 0.2 Position of Gc-42437-36124_refine_035_for domain III.pdb (#8) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.02846579 -0.35716487 -0.93360749 214.22136234 -0.05361459 -0.93318708 0.35536932 192.20666655 -0.99815589 0.03993912 -0.04571316 73.41212765 Axis -0.71283802 0.14587236 0.68599068 Axis point 0.00000000 127.79484990 123.82971619 Rotation angle (degrees) 167.21756364 Shift along axis -74.30745662 > select subtract #8 Nothing selected > hide #!8 models > show #7 models > show #3 models > hide #3 models > select add #7 2549 atoms, 2606 bonds, 331 residues, 1 model selected > view matrix models > #7,0.53763,-0.63696,0.55249,220.57,0.58343,-0.19204,-0.78913,242.82,0.60874,0.7466,0.26837,267.73 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.53763,-0.63696,0.55249,220.96,0.58343,-0.19204,-0.78913,206.82,0.60874,0.7466,0.26837,265.4 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.51686,-0.54473,0.66039,220.92,0.38052,-0.54484,-0.74723,205.9,0.76685,0.63751,-0.074325,265.97 > fitmap #7 inMap #1 Fit molecule fold_gc_diii_36145_fv_model_4.cif (#7) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 2549 atoms average map value = 0.3309, steps = 108 shifted from previous position = 6.67 rotated from previous position = 43.7 degrees atoms outside contour = 798, contour level = 0.2 Position of fold_gc_diii_36145_fv_model_4.cif (#7) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.94450415 -0.21421941 0.24904209 212.07200056 -0.15528555 0.37691342 0.91313891 198.93860506 -0.28947938 -0.90113612 0.32273111 145.69066637 Axis -0.95819556 0.28441602 0.03112547 Axis point 0.00000000 240.33195986 -98.12722032 Rotation angle (degrees) 71.21158121 Shift along axis -142.09043289 > view matrix models > #7,-0.97139,-0.14226,0.19015,215.31,-0.0019754,-0.79585,-0.60549,203.18,0.23747,-0.58854,0.7728,258.19 > view matrix models > #7,-0.89834,0.43844,-0.027539,216.64,-0.32528,-0.706,-0.62909,202.85,-0.29526,-0.55618,0.77684,257.4 > fitmap #7 inMap #1 Fit molecule fold_gc_diii_36145_fv_model_4.cif (#7) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 2549 atoms average map value = 0.3013, steps = 84 shifted from previous position = 3.13 rotated from previous position = 30.9 degrees atoms outside contour = 885, contour level = 0.2 Position of fold_gc_diii_36145_fv_model_4.cif (#7) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.83487440 0.22876868 -0.50064921 210.74752356 0.06868658 0.94573180 0.31760591 199.58572652 0.54613816 0.23077316 -0.80528061 152.65225563 Axis -0.08172408 -0.98520128 -0.15066392 Axis point 80.02337574 0.00000000 89.00037741 Rotation angle (degrees) 147.90967095 Shift along axis -236.85444724 > view matrix models > #7,0.48493,0.48601,-0.72707,219.45,-0.13988,-0.77756,-0.61305,204.64,-0.86329,0.399,-0.30908,257.39 > fitmap #7 inMap #1 Fit molecule fold_gc_diii_36145_fv_model_4.cif (#7) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 2549 atoms average map value = 0.3309, steps = 168 shifted from previous position = 3.89 rotated from previous position = 78.8 degrees atoms outside contour = 798, contour level = 0.2 Position of fold_gc_diii_36145_fv_model_4.cif (#7) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.94451810 -0.21410467 0.24908787 212.07272100 -0.15522013 0.37737858 0.91295790 198.93861830 -0.28946897 -0.90096870 0.32320755 145.69455183 Axis -0.95817618 0.28448358 0.03110477 Axis point 0.00000000 240.40110891 -98.22814510 Rotation angle (degrees) 71.18266373 Shift along axis -142.07646398 > select subtract #7 Nothing selected > show #3 models > hide #3 models > show #!8 models > select add #8 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 2 models selected > view matrix models > #8,0.7059,-0.56105,-0.43235,268.53,-0.30091,0.31504,-0.90011,203.57,0.64122,0.76549,0.053564,275.55 > view matrix models > #8,0.7488,-0.47118,-0.46615,269.52,-0.30705,0.37668,-0.87397,202.27,0.58739,0.79756,0.13739,272.04 > fitmap #8 inMap #1 Fit molecule Gc-42437-36124_refine_035_for domain III.pdb (#8) to map cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) using 8882 atoms average map value = 0.116, steps = 216 shifted from previous position = 25.8 rotated from previous position = 44.7 degrees atoms outside contour = 6444, contour level = 0.2 Position of Gc-42437-36124_refine_035_for domain III.pdb (#8) relative to cryosparc_P409_J122_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.62236525 0.14584208 -0.76901989 252.45418862 0.72587766 -0.47513329 0.49734292 230.82561825 -0.29285342 -0.86774330 -0.40156996 157.09268783 Axis -0.87630997 -0.30567257 0.37235080 Axis point 0.00000000 138.01238368 88.61468366 Rotation angle (degrees) 128.84156430 Shift along axis -233.29159342 > view matrix models > #8,0.68087,-0.3793,-0.62654,264.31,-0.43381,0.48039,-0.76225,193.57,0.59011,0.79079,0.16254,272.3 > select subtract #8 Nothing selected > hide #!8 models > volume #1 level 0.25 > volume #1 level 0.22 > volume #1 level 0.2 > volume #1 level 0.22 > volume #1 level 0.2 > hide #!1 models > hide #!4 models > hide #!5 models > show #!4 models > hide #!4 models > hide #7 models > show #7 models > hide #7 models > turn y 90 [Repeated 3 time(s)] > view matrix view matrix camera 0.36402,0.091799,-0.92685,-110.64,0.85547,-0.42649,0.29374,308.03,-0.36833,-0.89982,-0.23378,121.91 view matrix models #1,0.99758,-0.031402,-0.061997,21.992,-0.025974,-0.99591,0.086502,395.32,-0.06446,-0.084682,-0.99432,437.53,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,-0.51773,0.73064,0.4451,221.21,0.54891,-0.11538,0.82788,240.6,0.65624,0.67294,-0.34132,268.55,#4,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#8,0.68087,-0.3793,-0.62654,264.31,-0.43381,0.48039,-0.76225,193.57,0.59011,0.79079,0.16254,272.3,#8.1,1,0,0,0,0,1,0,0,0,0,1,0 > save C:\Users\ckh755\Desktop\image1.png supersample 3 > dssp > turn y 90 [Repeated 3 time(s)] > view matrix view matrix camera 0.39622,0.05884,-0.91627,-108.65,0.84363,-0.41716,0.33802,323.39,-0.36234,-0.90693,-0.21493,127.92 view matrix models #1,0.99758,-0.031402,-0.061997,21.992,-0.025974,-0.99591,0.086502,395.32,-0.06446,-0.084682,-0.99432,437.53,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,-0.51773,0.73064,0.4451,221.21,0.54891,-0.11538,0.82788,240.6,0.65624,0.67294,-0.34132,268.55,#4,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#8,0.68087,-0.3793,-0.62654,264.31,-0.43381,0.48039,-0.76225,193.57,0.59011,0.79079,0.16254,272.3,#8.1,1,0,0,0,0,1,0,0,0,0,1,0 > save C:\Users\ckh755\Desktop\image2.png supersample 3 > show #!1 models > show #3 models > hide #3 models > show #!4 models > show #!5 models > show #7 models > show #!8 models > hide #!8 models > show #3 models > mmaker #3 to #7 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 fold_gc_diii_36145_fv_model_4.cif, chain B (#7) with fold_gc_diii_36145_fv_model_4.cif, chain B (#3), sequence alignment score = 618.1 RMSD between 118 pruned atom pairs is 0.000 angstroms; (across all 118 pairs: 0.000) > hide #7 models > hide #3 models > show #3 models > close #7#8 > hide #!5 models > hide #!4 models > hide #3 models > hide #!2 models > hide #!1 models > select #6/A:108-214 826 atoms, 842 bonds, 107 residues, 1 model selected > hide sel > select #6/B:114-220 771 atoms, 789 bonds, 107 residues, 1 model selected > hide sel > select #6/A:108-214 826 atoms, 842 bonds, 107 residues, 1 model selected > hide cartoons sel Expected ',' or a keyword > select #6/B:114-220 771 atoms, 789 bonds, 107 residues, 1 model selected > hide cartoons sel Expected ',' or a keyword > hide sel cartoons > undo > select #6/A:108-214 826 atoms, 842 bonds, 107 residues, 1 model selected > hide sel cartoons > select #6/B:114-220 771 atoms, 789 bonds, 107 residues, 1 model selected > hide sel cartoons > show #!5 models > show #!4 models > show #3 models > show #!2 models > show #!1 models > ui tool show ""Map Eraser"" > volume erase #1 center 167.41,169.4,228.53 radius 16.921 > hide #7 models > close #7 > select add #6 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 2 models selected > select subtract #6 Nothing selected > save ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Figure #_Site 6/8-15-2024_Site 6 models and J122 map for > figure.cxs"" includeMaps true ——— End of log from Thu Aug 15 18:02:26 2024 ——— opened ChimeraX session > hide #!1 models > hide #!2 models > show #!2 models > hide #3 models > show #3 models > select add #4 5978 atoms, 6127 bonds, 4 pseudobonds, 772 residues, 2 models selected > select add #5 11956 atoms, 12254 bonds, 8 pseudobonds, 1544 residues, 4 models selected > select add #6 20838 atoms, 21348 bonds, 9 pseudobonds, 2698 residues, 6 models selected > lighting soft > dssp > graphics selection color black > select add #3 23387 atoms, 23954 bonds, 9 pseudobonds, 3029 residues, 7 models selected > select add #2 29365 atoms, 30081 bonds, 13 pseudobonds, 3801 residues, 9 models selected > graphics selection color black > select #2-6 29365 atoms, 30081 bonds, 13 pseudobonds, 3801 residues, 9 models selected > select subtract #6 20483 atoms, 20987 bonds, 12 pseudobonds, 2647 residues, 7 models selected > select add #6 29365 atoms, 30081 bonds, 13 pseudobonds, 3801 residues, 9 models selected > select subtract #5 23387 atoms, 23954 bonds, 9 pseudobonds, 3029 residues, 7 models selected > select clear Drag select of 43 residues > select clear > select add #6 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 2 models selected > select add #5 14860 atoms, 15221 bonds, 5 pseudobonds, 1926 residues, 4 models selected > select add #4 20838 atoms, 21348 bonds, 9 pseudobonds, 2698 residues, 6 models selected > select add #2 26816 atoms, 27475 bonds, 13 pseudobonds, 3470 residues, 8 models selected > select subtract #2 20838 atoms, 21348 bonds, 9 pseudobonds, 2698 residues, 6 models selected > select add #2 26816 atoms, 27475 bonds, 13 pseudobonds, 3470 residues, 8 models selected > select subtract #2 20838 atoms, 21348 bonds, 9 pseudobonds, 2698 residues, 6 models selected > select subtract #4 14860 atoms, 15221 bonds, 5 pseudobonds, 1926 residues, 4 models selected > select subtract #5 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 2 models selected > select subtract #6 Nothing selected Drag select of 48 residues > select up 978 atoms, 998 bonds, 125 residues, 1 model selected > select up 1714 atoms, 1756 bonds, 226 residues, 1 model selected > select up 5978 atoms, 6127 bonds, 772 residues, 1 model selected > select up 29365 atoms, 30081 bonds, 3801 residues, 7 models selected > select down 5978 atoms, 6127 bonds, 772 residues, 1 model selected > graphics selection color green > graphics selection color limegreen > select clear Drag select of 43 residues > select up 503 atoms, 512 bonds, 68 residues, 1 model selected > select up 1714 atoms, 1756 bonds, 226 residues, 1 model selected > surface sel Drag select of 25 residues > select up 699 atoms, 708 bonds, 86 residues, 1 model selected > select up 3361 atoms, 3442 bonds, 443 residues, 1 model selected > surface sel Drag select of 54 residues > select up 747 atoms, 758 bonds, 98 residues, 1 model selected > select up 1738 atoms, 1784 bonds, 225 residues, 1 model selected > select up 5978 atoms, 6127 bonds, 772 residues, 1 model selected > select up 29365 atoms, 30081 bonds, 3801 residues, 7 models selected > select down 5978 atoms, 6127 bonds, 772 residues, 5 models selected > surface sel > undo [Repeated 1 time(s)] > surface hidePatches (#!5 & sel) > select down 1738 atoms, 1784 bonds, 225 residues, 6 models selected > select down 747 atoms, 758 bonds, 98 residues, 3 models selected > select up 1738 atoms, 1784 bonds, 225 residues, 3 models selected > surface (#!5 & sel) Drag select of 57 residues > select up 922 atoms, 943 bonds, 119 residues, 1 model selected > select up 1753 atoms, 1794 bonds, 226 residues, 1 model selected > surface sel > select clear Drag select of Gc-42437-36124_refine_035_for 36124 Fab model.pdb_A SES surface, 29026 of 192580 triangles, Gc-42437-36124_refine_035_for 36124 Fab model.pdb_B SES surface, 16942 of 200702 triangles, 2 residues > select up 80 atoms, 80 bonds, 12 residues, 3 models selected > select up 3361 atoms, 3442 bonds, 443 residues, 3 models selected > surface hidePatches (#!6 & sel) > select clear Drag select of 97 residues > select up 1156 atoms, 1179 bonds, 145 residues, 3 models selected > select up 3361 atoms, 3442 bonds, 443 residues, 3 models selected > surface (#!6 & sel) > hide #!6 models > show #!6 models > select add #6 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 4 models selected > select subtract #6 2 models selected > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Structure Files/Gc-4Ffabs/Map for Gc245 med res map with Site 6 and > domain III/fold_gc_diii_36145_fv_model_4.cif"" Chain information for fold_gc_diii_36145_fv_model_4.cif #7 --- Chain | Description A | . B | . C | . > mm#7 to #3 Unknown command: mm#7 to #3 > mmaker #7 to #3 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 fold_gc_diii_36145_fv_model_4.cif, chain B (#3) with fold_gc_diii_36145_fv_model_4.cif, chain B (#7), sequence alignment score = 618.1 RMSD between 118 pruned atom pairs is 0.000 angstroms; (across all 118 pairs: 0.000) > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #7 models > show #7 models Drag select of 34 residues > select up 366 atoms, 371 bonds, 47 residues, 1 model selected > select up 796 atoms, 808 bonds, 105 residues, 1 model selected > delete atoms sel > delete bonds sel > close #7 > show #!6 models > show #!5 models > show #!4 models > show #!3 models > show #!2 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Structure Files/Gc-4Ffabs/Building for Gc-2-4-5 str/Combined > Models/AF2_37847_e61a7.result/37847_e61a7/37847_e61a7_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb"" Chain information for 37847_e61a7_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #7 --- Chain | Description A | No description available B | No description available > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Structure Files/Gc-4Ffabs/Building for Gc-2-4-5 str/Combined > Models/AF2_36145_203f6.result/36145_203f6/36145_203f6_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"" Chain information for 36145_203f6_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #8 --- Chain | Description A | No description available B | No description available > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Structure Files/Gc-4Ffabs/Building for Gc-2-4-5 str/Combined > Models/Gc-dI-dII_42437_37847_36124.pdb"" Chain information for Gc-dI-dII_42437_37847_36124.pdb #9 --- Chain | Description A | No description available B | No description available C | No description available D | No description available G | No description available H | No description available L | No description available > hide #7 models > hide #8 models > hide #!6 models Drag select of 7 atoms > delete atoms sel > delete bonds sel > hide #!9 models > show #7 models > mmaker #7 to #5 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 Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 37847 Fv model.pdb, chain A (#5) with 37847_e61a7_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain A (#7), sequence alignment score = 562.8 RMSD between 116 pruned atom pairs is 0.513 angstroms; (across all 116 pairs: 0.513) > show #!5 models > hide #!5 models > show #8 models > hide #7 models > show #!3 models > mmaker #8 to #3 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 fold_gc_diii_36145_fv_model_4.cif, chain B (#3) with 36145_203f6_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb, chain A (#8), sequence alignment score = 614.5 RMSD between 118 pruned atom pairs is 0.257 angstroms; (across all 118 pairs: 0.257) > show #!9 models > hide #!3 models > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Structure Files/Gc-4Ffabs/Building for Gc-2-4-5 str/Combined > Models/Gc-dI-dII_42437_37847_36124.pdb"" Chain information for Gc-dI-dII_42437_37847_36124.pdb #10 --- Chain | Description A | No description available B | No description available C | No description available D | No description available G | No description available H | No description available L | No description available Drag select of 7 atoms > delete atoms sel > delete bonds sel > hide #8 models Drag select of 13564 atoms, 4 pseudobonds, 84 bonds > select up 13864 atoms, 14186 bonds, 4 pseudobonds, 1786 residues, 4 models selected > select up 15188 atoms, 15556 bonds, 4 pseudobonds, 1964 residues, 4 models selected > delete atoms (#!9-10 & sel) > delete bonds (#!9-10 & sel) Drag select of 290 atoms, 2 pseudobonds > select clear Drag select of 394 atoms, 6 pseudobonds > delete atoms (#!9-10 & sel) > delete bonds (#!9-10 & sel) Drag select of 190 atoms, 4 pseudobonds > select up 206 atoms, 200 bonds, 4 pseudobonds, 24 residues, 4 models selected > select up 350 atoms, 342 bonds, 4 pseudobonds, 46 residues, 4 models selected > select up 458 atoms, 456 bonds, 4 pseudobonds, 60 residues, 4 models selected > select up 586 atoms, 584 bonds, 4 pseudobonds, 76 residues, 4 models selected > select up 7328 atoms, 7486 bonds, 8 pseudobonds, 964 residues, 4 models selected > select down 586 atoms, 584 bonds, 4 pseudobonds, 76 residues, 4 models selected > delete atoms (#!9-10 & sel) > delete bonds (#!9-10 & sel) > hide #!9 models > hide #!10 models > show #!2 models > show #!3 models > show #8 models > color #8/B,C #DD833E > color #8 #DD833E > hide #!3 models > hide #8 models > show #!3 models Drag select of fold_gc_diii_36145_fv_model_4.cif_B SES surface, 37504 of 104344 triangles, fold_gc_diii_36145_fv_model_4.cif_C SES surface, 30389 of 92906 triangles, 107 residues > select up 1216 atoms, 1241 bonds, 157 residues, 3 models selected > select up 1753 atoms, 1794 bonds, 226 residues, 3 models selected > surface hidePatches (#!3 & sel) > cartoon hide (#!3 & sel) > select add #3 2549 atoms, 2606 bonds, 331 residues, 3 models selected > select subtract #3 2 models selected > show #8 models > select add #8 3340 atoms, 3417 bonds, 439 residues, 1 model selected > surface sel > select subtract #8 2 models selected > hide #!8 models > hide #!3 models > hide #!2 models > show #!4 models > hide #!4 models > show #!4 models > show #!9 models > mmaker #9 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 42437 Fv model.pdb, chain B (#4) with Gc-dI-dII_42437_37847_36124.pdb, chain C (#9), sequence alignment score = 478.5 RMSD between 99 pruned atom pairs is 0.674 angstroms; (across all 108 pairs: 1.655) > mmaker #9 to #4/H 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 Gc-42437-36124_37847_refined_041-Isolde_real_space_refined_350-noH_for 42437 Fv model.pdb, chain H (#4) with Gc-dI-dII_42437_37847_36124.pdb, chain D (#9), sequence alignment score = 334.5 RMSD between 106 pruned atom pairs is 0.765 angstroms; (across all 117 pairs: 1.510) > hide #!4 models > show #!4 models > hide #!4 models > select add #9 3371 atoms, 3451 bonds, 444 residues, 1 model selected > hide sel target a > surface sel > cartoon (#!9 & sel) > color #9 #9142AE > select subtract #9 2 models selected > hide #!9 models > show #!10 models > color #10 #CC66A7 > hide #10 target a > cartoon #10 > surface #10 > show #!6 models > hide #!10 models > hide #!6 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #7 models > hide #!5 models > select add #7 3403 atoms, 3484 bonds, 448 residues, 1 model selected > surface sel > select subtract #7 2 models selected > hide #!7 models > show #!7 models > show #!5 models > hide #!5 models > show #!8 models > show #!9 models > hide #!4 models > show #!10 models > close #10 > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > rename #9 ""42437 xstal model"" > rename #9 ""42437 Fab xstal model"" > hide #!8 models > show #!8 models > rename #8 ""AF2 36145 Fab"" > hide #!7 models > show #!7 models > rename #7 ""AF2 37847 Fab"" > hide #!6 models > show #!6 models > rename #6 ""36124 Fab crystal"" > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > close #4-5 > hide #!3 models > show #!3 models > rename #3 ""AF3_domain III from bound w36145Fv"" > rename #2 ""Gc DI-DII from Gc/2/5xstal"" > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > hide #!8 models > show #!8 models > hide #!9 models > show #!9 models > transparency #2-3,6-9 50 > transparency #2-3,6-9 20 > transparency #2-3,6-9 30 > select add #6 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 2 models selected > cartoon (#!6 & sel) > undo > hide #!3 models > hide #!2 models > hide #!7 models > hide #!8 models > hide #!9 models > select #6/A:202@CB 1 atom, 1 residue, 1 model selected Drag select of Gc-42437-36124_refine_035_for 36124 Fab model.pdb_A SES surface, 137335 of 192580 triangles, Gc-42437-36124_refine_035_for 36124 Fab model.pdb_B SES surface, 147969 of 200702 triangles, 160 residues > select up 1502 atoms, 1534 bonds, 193 residues, 3 models selected > select up 3361 atoms, 3442 bonds, 443 residues, 3 models selected > cartoon (#!6 & sel) > show #!3 models > show #!2 models > show #!7 models > show #!8 models > show #!9 models > select add #6 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 4 models selected > select subtract #6 2 models selected > select clear > transparency #2-3,6-9 80 > transparency #2-3,6-9 90 > transparency #2-3,6-9 60 > select clear > view matrix camera > -0.056974,-0.13241,-0.98956,-198.4,0.90561,-0.42408,0.0045992,209.03,-0.42025,-0.8959,0.14407,268.38 > view matrix models > #1,0.99758,-0.031402,-0.061997,21.992,-0.025974,-0.99591,0.086502,395.32,-0.06446,-0.084682,-0.99432,437.53,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#4,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 Invalid ""models"" argument: No models specified by ""#4"" > view matrix camera > 0.39622,0.05884,-0.91627,-108.65,0.84363,-0.41716,0.33802,323.39,-0.36234,-0.90693,-0.21493,127.92 > view matrix models > #1,0.99758,-0.031402,-0.061997,21.992,-0.025974,-0.99591,0.086502,395.32,-0.06446,-0.084682,-0.99432,437.53,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,-0.51773,0.73064,0.4451,221.21,0.54891,-0.11538,0.82788,240.6,0.65624,0.67294,-0.34132,268.55,#4,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#8,0.68087,-0.3793,-0.62654,264.31,-0.43381,0.48039,-0.76225,193.57,0.59011,0.79079,0.16254,272.3,#8.1,1,0,0,0,0,1,0,0,0,0,1,0 Invalid ""models"" argument: No models specified by ""#4"" > view matrix camera > -0.056974,-0.13241,-0.98956,-198.4,0.90561,-0.42408,0.0045992,209.03,-0.42025,-0.8959,0.14407,268.38 > view matrix models > #1,0.99758,-0.031402,-0.061997,21.992,-0.025974,-0.99591,0.086502,395.32,-0.06446,-0.084682,-0.99432,437.53,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#4,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 Invalid ""models"" argument: No models specified by ""#4"" > view matrix camera > -0.056974,-0.13241,-0.98956,-198.4,0.90561,-0.42408,0.0045992,209.03,-0.42025,-0.8959,0.14407,268.38 > view matrix models > #1,0.99758,-0.031402,-0.061997,21.992,-0.025974,-0.99591,0.086502,395.32,-0.06446,-0.084682,-0.99432,437.53,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#4,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 Invalid ""models"" argument: No models specified by ""#4"" > color #7 #CC66A7 > transparency #2-3,6-9 60 > save 9-4-2024-Gc4Fabs-modes_1.png transparentBackground true > transparency #2-3,6-9 50 > transparency #2-3,6-9 40 > save 9-4-2024-Gc4Fabs-modes_2.png transparentBackground true > open 7a59 7a59 title: Crimean-Congo Hemorrhagic Fever Virus Envelope Glycoprotein Gc W1191H/W1197A/W1199A Mutant in Postfusion Conformation (Orthorhombic Crystal Form) [more info...] Chain information for 7a59 #4 --- Chain | Description | UniProt A B C | Envelopment polyprotein | GP_CCHFI 1041-1561 Non-standard residues in 7a59 #4 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CL — chloride ion FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PO4 — phosphate ion > close #4 > close #1 > open 7a59 7a59 title: Crimean-Congo Hemorrhagic Fever Virus Envelope Glycoprotein Gc W1191H/W1197A/W1199A Mutant in Postfusion Conformation (Orthorhombic Crystal Form) [more info...] Chain information for 7a59 #1 --- Chain | Description | UniProt A B C | Envelopment polyprotein | GP_CCHFI 1041-1561 Non-standard residues in 7a59 #1 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CL — chloride ion FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PO4 — phosphate ion > select #1/A: 1041-1140, 1232-1268, 1419-1430 954 atoms, 965 bonds, 1 pseudobond, 126 residues, 2 models selected > color sel #FF7F7F > select #1/A: 1141-1186, 1205-1231, 1269-1282, 1296-1320, 1347-1403, > 1410-1418, 1187-1204 1548 atoms, 1595 bonds, 196 residues, 1 model selected > color sel #FFFF7F > select #1/A: 1283-1295, 1321-1346, 1404-1409 364 atoms, 374 bonds, 45 residues, 1 model selected > color sel #c18c7f > select #1/A: 1431-1441 90 atoms, 90 bonds, 11 residues, 1 model selected > color sel #7FFFFF > select #1/A: 1442-1546 795 atoms, 811 bonds, 105 residues, 1 model selected > color sel #7F7FFF > select #1/A: 1547-1572 123 atoms, 124 bonds, 16 residues, 1 model selected > color sel #FF7FFF > cartoon hide #1/B > surface #1/B > color #1/B dark gray > transparency #1/B 30 > cartoon hide #1/C > surface #1/C > color #1/C white > transparency #1/C 30 > save ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Supplemental Figure #_modes of neut/9-4-2024_Gc with all 4 > Sites models.cxs"" > mmaker #1/A to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Gc DI-DII from Gc/2/5xstal, chain G (#2) with 7a59, chain A (#1), sequence alignment score = 1456.8 RMSD between 260 pruned atom pairs is 0.937 angstroms; (across all 321 pairs: 3.709) > hide #!2 models > hide #!3 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models Drag select of 7a59_B SES surface, 206050 of 450426 triangles, 7a59_C SES surface, 189804 of 434220 triangles, 216 atoms, 231 residues, 208 bonds > hide (#!1 & sel) target a > show #1/B cartoons > color #1/B dark gray > show #1/C cartoons > color #1/C white > surface hidePatches (#!1 & sel) [Repeated 1 time(s)] > select #1 12589 atoms, 12161 bonds, 3 pseudobonds, 2256 residues, 2 models selected > surface hidePatches (#!1 & sel) > select clear > show #!2 models > hide #!2 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > view matrix camera > -0.056974,-0.13241,-0.98956,-198.4,0.90561,-0.42408,0.0045992,209.03,-0.42025,-0.8959,0.14407,268.38 > view matrix models > #1,0.99758,-0.031402,-0.061997,21.992,-0.025974,-0.99591,0.086502,395.32,-0.06446,-0.084682,-0.99432,437.53,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#4,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 Invalid ""models"" argument: No models specified by ""#4"" > turn y 180 > view matrix view matrix camera 0.056975,-0.13241,0.98956,646.51,-0.90561,-0.42408,-0.0046034,248.75,0.42026,-0.8959,-0.14408,124.7 view matrix models #2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#6.3,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.8169,-0.21413,0.53556,204.47,0.42791,-0.39761,-0.81167,168.64,0.38675,0.89222,-0.23318,214.6,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.99431,0.074735,-0.075973,218.33,-0.026887,0.86575,0.49976,177.43,0.10312,-0.49487,0.86283,264.22,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.296,-0.067032,0.95283,-8.4654,0.64478,-0.72195,-0.25109,250.56,0.70473,0.68869,-0.17048,-85.496,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#1,-0.9757,0.21626,0.035289,201.77,-0.14806,-0.76939,0.62138,181.78,0.16153,0.60106,0.78271,185.59,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0 > show #!2 models > show #!3 models > view matrix view matrix camera 0.056975,-0.13241,0.98956,646.95,-0.90561,-0.42408,-0.0046034,204.41,0.42026,-0.8959,-0.14408,129.14 view matrix models #2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#6.3,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.8169,-0.21413,0.53556,204.47,0.42791,-0.39761,-0.81167,168.64,0.38675,0.89222,-0.23318,214.6,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.99431,0.074735,-0.075973,218.33,-0.026887,0.86575,0.49976,177.43,0.10312,-0.49487,0.86283,264.22,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.296,-0.067032,0.95283,-8.4654,0.64478,-0.72195,-0.25109,250.56,0.70473,0.68869,-0.17048,-85.496,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#1,-0.9757,0.21626,0.035289,201.77,-0.14806,-0.76939,0.62138,181.78,0.16153,0.60106,0.78271,185.59,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0 > turn y 90 [Repeated 7 time(s)] > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > select add #9 3371 atoms, 3451 bonds, 444 residues, 1 model selected > select add #8 6711 atoms, 6868 bonds, 883 residues, 4 models selected > select add #7 10114 atoms, 10352 bonds, 1331 residues, 7 models selected > select add #6 18996 atoms, 19446 bonds, 1 pseudobond, 2485 residues, 11 models selected > select add #3 21545 atoms, 22052 bonds, 1 pseudobond, 2816 residues, 14 models selected > surface style #3,6-9 mesh > transparency (#!3,6-9 & sel) 30 > transparency (#!3,6-9 & sel) 0 > select clear > view matrix view matrix camera 0.056974,0.036338,0.99772,652.72,-0.90561,-0.41878,0.066966,227.85,0.42026,-0.90737,0.009043,200.21 view matrix models #2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#6.3,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.8169,-0.21413,0.53556,204.47,0.42791,-0.39761,-0.81167,168.64,0.38675,0.89222,-0.23318,214.6,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.99431,0.074735,-0.075973,218.33,-0.026887,0.86575,0.49976,177.43,0.10312,-0.49487,0.86283,264.22,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.296,-0.067032,0.95283,-8.4654,0.64478,-0.72195,-0.25109,250.56,0.70473,0.68869,-0.17048,-85.496,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#1,-0.9757,0.21626,0.035289,201.77,-0.14806,-0.76939,0.62138,181.78,0.16153,0.60106,0.78271,185.59,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0 > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!2 models > save 9-4-2024-MODES-Site2-1.png transparentBackground true > turn y 90 [Repeated 3 time(s)] > turn x 90 > save 9-4-2024-MODES-Site2-1top.png transparentBackground true > hide #!9 models > show #!8 models > hide #!8 models > show #!7 models > turn x 90 [Repeated 2 time(s)] > turn y 90 [Repeated 2 time(s)] > show #!3 models > hide #!3 models > open ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Structure Files/Gc+Site2+Site5/Pymol/Gc-42437-36124_refine_035.pdb"" Chain information for Gc-42437-36124_refine_035.pdb #4 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > mmaker #4 t o #6 > matchmaker #4 to o #6 Invalid ""to"" argument: invalid atoms specifier > show #!6 models > hide #!7 models > hide #!4 models > show #!4 models > mmaker #6 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Gc-42437-36124_refine_035.pdb, chain G (#4) with 36124 Fab crystal, chain G (#6), sequence alignment score = 2561.7 RMSD between 481 pruned atom pairs is 0.000 angstroms; (across all 481 pairs: 0.000) > hide #!4 models > hide #!6 models > hide #!7 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > mmaker #4 to #6 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 36124 Fab crystal, chain G (#6) with Gc-42437-36124_refine_035.pdb, chain G (#4), sequence alignment score = 2561.7 RMSD between 481 pruned atom pairs is 0.000 angstroms; (across all 481 pairs: 0.000) > hide #!2 models > show #!4 models > show #!6 models > hide #!6 models > hide #!4 models > mmaker #4 to #2 bring #6 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 Gc DI-DII from Gc/2/5xstal, chain G (#2) with Gc-42437-36124_refine_035.pdb, chain G (#4), sequence alignment score = 1511.8 RMSD between 235 pruned atom pairs is 0.897 angstroms; (across all 321 pairs: 2.280) > show #!2 models > show #!4 models > show #!6 models > hide #!6 models > hide #!2 models Drag select of 521 atoms > select up 705 atoms, 712 bonds, 94 residues, 1 model selected > select up 1121 atoms, 1137 bonds, 152 residues, 1 model selected > select up 3361 atoms, 3442 bonds, 443 residues, 1 model selected > hide sel target a Drag select of 440 atoms > select up 606 atoms, 602 bonds, 78 residues, 1 model selected > select up 1080 atoms, 1101 bonds, 139 residues, 1 model selected > select up 1714 atoms, 1754 bonds, 226 residues, 1 model selected > select up 8882 atoms, 9094 bonds, 1154 residues, 1 model selected > select down 1714 atoms, 1754 bonds, 226 residues, 1 model selected > hide sel target a Drag select of 3807 atoms, 1 pseudobonds, 53 bonds > hide (#!4 & sel) target a > cartoon (#!4 & sel) > select clear > select #4/G: 1041-1140, 1232-1268, 1419-1430 963 atoms, 974 bonds, 127 residues, 1 model selected > color sel #FF7F7F > select #4/G: 1141-1186, 1205-1231, 1269-1282, 1296-1320, 1347-1403, > 1410-1418, 1187-1204 1570 atoms, 1615 bonds, 196 residues, 1 model selected > color sel #FFFF7F > select #4/G: 1283-1295, 1321-1346, 1404-1409 331 atoms, 339 bonds, 1 pseudobond, 41 residues, 2 models selected > color sel #c18c7f > select #4/G: 1431-1441 90 atoms, 90 bonds, 11 residues, 1 model selected > color sel #7FFFFF > select #4/G: 1442-1546 795 atoms, 807 bonds, 105 residues, 1 model selected > color sel #7F7FFF > select #4/G: 1547-1572 46 atoms, 48 bonds, 4 residues, 1 model selected > color sel #FF7FFF > select add #4 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 2 models selected > select subtract #4 Nothing selected > show #!2 models > show #!3 models > hide #!3 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > show #!6 models > hide #!8 models > show #!1 models > view matrix camera > 0.056974,0.036338,0.99772,652.72,-0.90561,-0.41878,0.066966,227.85,0.42026,-0.90737,0.009043,200.21 > view matrix models > #2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#6.3,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.8169,-0.21413,0.53556,204.47,0.42791,-0.39761,-0.81167,168.64,0.38675,0.89222,-0.23318,214.6,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.99431,0.074735,-0.075973,218.33,-0.026887,0.86575,0.49976,177.43,0.10312,-0.49487,0.86283,264.22,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.296,-0.067032,0.95283,-8.4654,0.64478,-0.72195,-0.25109,250.56,0.70473,0.68869,-0.17048,-85.496,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#1,-0.9757,0.21626,0.035289,201.77,-0.14806,-0.76939,0.62138,181.78,0.16153,0.60106,0.78271,185.59,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0 > save 9-4-2024-MODES-Site5-1.png transparentBackground true > turn y 90 [Repeated 2 time(s)] > select add #6 8882 atoms, 9094 bonds, 1 pseudobond, 1154 residues, 2 models selected > surface style #6 solid > select subtract #6 2 models selected > turn y 90 > view matrix camera > 0.056974,0.036338,0.99772,652.72,-0.90561,-0.41878,0.066966,227.85,0.42026,-0.90737,0.009043,200.21 > view matrix models > #2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#6.3,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.8169,-0.21413,0.53556,204.47,0.42791,-0.39761,-0.81167,168.64,0.38675,0.89222,-0.23318,214.6,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.99431,0.074735,-0.075973,218.33,-0.026887,0.86575,0.49976,177.43,0.10312,-0.49487,0.86283,264.22,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.296,-0.067032,0.95283,-8.4654,0.64478,-0.72195,-0.25109,250.56,0.70473,0.68869,-0.17048,-85.496,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#1,-0.9757,0.21626,0.035289,201.77,-0.14806,-0.76939,0.62138,181.78,0.16153,0.60106,0.78271,185.59,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0 > show #!7 models > show #!8 models > show #!9 models > show #!3 models > surface style solid > select clear > hide #!8 models > hide #!7 models > hide #!6 models > hide #!4 models > hide #!3 models > save 9-4-2024-MODES-Site2-front2.png transparentBackground true > turn x 90 > save 9-4-2024-MODES-Site2-top2.png transparentBackground true > turn x 90 [Repeated 2 time(s)] > hide #!9 models > show #!8 models > hide #!8 models > show #!6 models > hide #!6 models > show #!7 models > turn y 90 [Repeated 1 time(s)] > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > view matrix camera > 0.056974,0.036338,0.99772,652.72,-0.90561,-0.41878,0.066966,227.85,0.42026,-0.90737,0.009043,200.21 > view matrix models > #2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#6.3,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.8169,-0.21413,0.53556,204.47,0.42791,-0.39761,-0.81167,168.64,0.38675,0.89222,-0.23318,214.6,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.99431,0.074735,-0.075973,218.33,-0.026887,0.86575,0.49976,177.43,0.10312,-0.49487,0.86283,264.22,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.296,-0.067032,0.95283,-8.4654,0.64478,-0.72195,-0.25109,250.56,0.70473,0.68869,-0.17048,-85.496,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#1,-0.9757,0.21626,0.035289,201.77,-0.14806,-0.76939,0.62138,181.78,0.16153,0.60106,0.78271,185.59,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0 > turn y 90 [Repeated 1 time(s)] > save 9-4-2024-MODES-Site4-front1.png transparentBackground true > show #!4 models > hide #!1 models > save 9-4-2024-MODES-Site4-front2.png transparentBackground true > hide #!7 models > show #!6 models > save 9-4-2024-MODES-Site5-pre1.png transparentBackground true > show #!1 models > save 9-4-2024-MODES-Site5-post1.png transparentBackground true > hide #!6 models > show #!8 models > hide #!1 models > show #!3 models > hide #!8 models > show #!2 models > hide #!4 models > show #!8 models > save 9-4-2024-MODES-Site6-pre1.png transparentBackground true > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > turn y 90 [Repeated 1 time(s)] > show #!2 models > hide #!2 models > save 9-4-2024-MODES-Site6-both1.png transparentBackground true > hide #!1 models > show #!2 models > hide #!3 models > hide #!2 models > show #!4 models > show #!6 models > show #!7 models > show #!9 models > view matrix camera > 0.056974,0.036338,0.99772,652.72,-0.90561,-0.41878,0.066966,227.85,0.42026,-0.90737,0.009043,200.21 > view matrix models > #2,0.99404,0.10845,-0.011097,-16.565,-0.1089,0.99252,-0.055252,33.615,0.0050223,0.056131,0.99841,-20.521,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,0.96505,-0.16958,0.19978,218.27,0.10501,-0.44821,-0.88774,204.29,0.24009,0.8777,-0.41474,262.15,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,-0.014521,-0.06976,0.99746,199.01,0.37884,-0.92358,-0.059077,257.64,0.92535,0.37702,0.039838,302.31,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#6.3,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.8169,-0.21413,0.53556,204.47,0.42791,-0.39761,-0.81167,168.64,0.38675,0.89222,-0.23318,214.6,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.99431,0.074735,-0.075973,218.33,-0.026887,0.86575,0.49976,177.43,0.10312,-0.49487,0.86283,264.22,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.296,-0.067032,0.95283,-8.4654,0.64478,-0.72195,-0.25109,250.56,0.70473,0.68869,-0.17048,-85.496,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#1,-0.9757,0.21626,0.035289,201.77,-0.14806,-0.76939,0.62138,181.78,0.16153,0.60106,0.78271,185.59,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0' Invalid ""models"" argument: Require numeric values > save ""C:/Users/ckh755/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Figures/Supplemental Figure #_modes of neut/9-4-2024_Gc with all 4 > Sites models.cxs"" ——— End of log from Wed Sep 4 19:17:24 2024 ——— opened ChimeraX session > turn y 90 [Repeated 1 time(s)] > show #!1 models > hide #!6 models > hide #!7 models > hide #!9 models > show #!3 models > mmaker #3 to #4 bring #8 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Gc-42437-36124_refine_035.pdb, chain G (#4) with AF3_domain III from bound w36145Fv, chain A (#3), sequence alignment score = 520.8 RMSD between 105 pruned atom pairs is 0.570 angstroms; (across all 105 pairs: 0.570) > open ""C:/Users/chris/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Structure Files/Gc-4Ffabs/Map for Gc245 med res map with Site 6 and > domain III/fold_gc_diii_36145_fv_model_4_Coot-updatednumbering.pdb"" Chain information for fold_gc_diii_36145_fv_model_4_Coot-updatednumbering.pdb #5 --- Chain | Description A | No description available B | No description available C | No description available > mmaker #5 to #8 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF2 36145 Fab, chain A (#8) with fold_gc_diii_36145_fv_model_4_Coot-updatednumbering.pdb, chain B (#5), sequence alignment score = 614.5 RMSD between 118 pruned atom pairs is 0.257 angstroms; (across all 118 pairs: 0.257) > mmaker #5 to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7a59, chain A (#1) with fold_gc_diii_36145_fv_model_4_Coot- updatednumbering.pdb, chain A (#5), sequence alignment score = 500.4 RMSD between 100 pruned atom pairs is 0.595 angstroms; (across all 105 pairs: 1.273) > hide #!4 models > hide #!3 models > hide #!1 models > hide #!8 models Drag select of 130 residues > select up 1357 atoms, 1384 bonds, 175 residues, 1 model selected > select up 1753 atoms, 1794 bonds, 226 residues, 1 model selected > color sel #DD833E > cartoon hide sel > surface sel > select clear Drag select of 41 residues > select up 475 atoms, 482 bonds, 63 residues, 1 model selected > select up 796 atoms, 808 bonds, 105 residues, 1 model selected > color sel #7F7FFF > select clear > show #!4 models > hide #!4 models > show #!1 models > show #!2 models > hide #!2 models > show #!8 models > show #!3 models > hide #!5 models > save C:\Users\chris/Desktop\image1.png supersample 3 > show #!5 models > save C:\Users\chris/Desktop\image2.png supersample 3 > turn y 90 > save C:\Users\chris/Desktop\image3.png supersample 3 > save C:\Users\chris/Desktop\image4.png supersample 3 > show #!7 models > hide #!7 models > hide #!3 models > show #!3 models > save ""C:/Users/chris/Box/Christy Hjorth/CCHFV/Manuscripts/Gc Ab > Paper/Structure Files/Gc-4Ffabs/Map for Gc245 med res map with Site 6 and > domain III/9-23-2024_36145 and domain III.cxs"" Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\file_history.py"", line 93, in file_history_changed_cb self.update_html() File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\file_history.py"", line 88, in update_html fhw.setHtml(html) File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py"", line 244, in setHtml tf = open(self._tf_name, ""wb"") ^^^^^^^^^^^^^^^^^^^^^^^^^ PermissionError: [Errno 13] Permission denied: 'C:\\\Users\\\chris\\\AppData\\\Local\\\Temp\\\chbp8qmgij_1.html' Error processing trigger ""file history changed"": PermissionError: [Errno 13] Permission denied: 'C:\\\Users\\\chris\\\AppData\\\Local\\\Temp\\\chbp8qmgij_1.html' File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py"", line 244, in setHtml tf = open(self._tf_name, ""wb"") ^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\file_history.py"", line 93, in file_history_changed_cb self.update_html() File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\file_history.py"", line 88, in update_html fhw.setHtml(html) File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py"", line 244, in setHtml tf = open(self._tf_name, ""wb"") ^^^^^^^^^^^^^^^^^^^^^^^^^ PermissionError: [Errno 13] Permission denied: 'C:\\\Users\\\chris\\\AppData\\\Local\\\Temp\\\chbp8qmgij_1.html' Error processing trigger ""file history changed"": PermissionError: [Errno 13] Permission denied: 'C:\\\Users\\\chris\\\AppData\\\Local\\\Temp\\\chbp8qmgij_1.html' File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py"", line 244, in setHtml tf = open(self._tf_name, ""wb"") ^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > info path user unversioned data user unversioned data directory: C:\Users\chris\AppData\Local\UCSF\ChimeraX > cd C:/Apps/ChimeraX Current working directory is: C:\Apps\ChimeraX > save C:/Apps/ChimeraX/test.cxs Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\file_history.py"", line 93, in file_history_changed_cb self.update_html() File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\file_history.py"", line 88, in update_html fhw.setHtml(html) File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py"", line 244, in setHtml tf = open(self._tf_name, ""wb"") ^^^^^^^^^^^^^^^^^^^^^^^^^ PermissionError: [Errno 13] Permission denied: 'C:\\\Users\\\chris\\\AppData\\\Local\\\Temp\\\chbp8qmgij_1.html' Error processing trigger ""file history changed"": PermissionError: [Errno 13] Permission denied: 'C:\\\Users\\\chris\\\AppData\\\Local\\\Temp\\\chbp8qmgij_1.html' File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py"", line 244, in setHtml tf = open(self._tf_name, ""wb"") ^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\file_history.py"", line 93, in file_history_changed_cb self.update_html() File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\file_history.py"", line 88, in update_html fhw.setHtml(html) File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py"", line 244, in setHtml tf = open(self._tf_name, ""wb"") ^^^^^^^^^^^^^^^^^^^^^^^^^ PermissionError: [Errno 13] Permission denied: 'C:\\\Users\\\chris\\\AppData\\\Local\\\Temp\\\chbp8qmgij_1.html' Error processing trigger ""file history changed"": PermissionError: [Errno 13] Permission denied: 'C:\\\Users\\\chris\\\AppData\\\Local\\\Temp\\\chbp8qmgij_1.html' File ""C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py"", line 244, in setHtml tf = open(self._tf_name, ""wb"") ^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 512.72 OpenGL renderer: NVIDIA GeForce GTX 1650 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_US.cp1252 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: windows Manufacturer: Dell Inc. Model: G3 3500 OS: Microsoft Windows 11 Home (Build 22631) Memory: 16,963,534,848 MaxProcessMemory: 137,438,953,344 CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2024.6.2 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 ChimeraX-Clipper: 0.23.1 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.8 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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 comtypes: 1.4.1 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pywin32: 306 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 WMI: 1.5.1 File attachment: ChimeraX Save Issue.txt }}} [attachment:""ChimeraX Save Issue.txt""] " defect feedback normal UI chimera-programmers all ChimeraX