id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8850 Problem creating pseudobond group during session restore jitued@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.3.1-arm64-arm-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_gp17-gp18 Interaction2.cxs"" Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level 0.5, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Log from Mon Apr 17 17:14:38 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp13d-gp17-Interaction.cxs"" Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level 0.5, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Log from Mon Apr 17 15:22:23 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp13d-gp17-Interaction2.cxs"" Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level 0.5, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Log from Mon Apr 17 14:56:24 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp13d-gp17-Interaction.cxs"" Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level 0.5, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Log from Mon Apr 17 14:45:58 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp13d-gp17-Interaction.cxs"" Opened cryosparc_P2_J765_009_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level 0.5, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Log from Mon Apr 17 13:40:26 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/13d-17-Interaction.cxs"" Opened cryosparc_P2_J765_009_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level 0.5, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size 512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32 Log from Mon Apr 17 13:31:58 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/01_tail_tip_colored.cxs"" Opened cryosparc_P2_J765_009_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32 Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level 0.5, step 1, values float32 Log from Mon Apr 17 13:03:15 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/cryosparc_P2_J765_009_volume_map_sharp.mrc Opened cryosparc_P2_J765_009_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.06, shown at level 0.287, step 2, values float32 > open > /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/06_tail_tip_refined_real_space_refined_012_VV_SS.pdb Chain information for 06_tail_tip_refined_real_space_refined_012_VV_SS.pdb #2 --- Chain | Description A B C D E F G H I J K L M N O P Q R | No description available a b c d e f g h i j k l | No description available m n o p q r | No description available s t u | No description available v w x | No description available > open > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/02_Tail_tip > | Structures/03_Small Map | alphafold/00_Small_.mrc"" Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level 0.000118, step 2, values float32 > color #3 #941100ff models > color #1 #d6d6d6ff models > select /A-L 27168 atoms, 27768 bonds, 3600 residues, 1 model selected No map chosen to save > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/06_gp13_12mer_ring_SS.pdb"" selectedOnly true > relModel #1 > select /M-R 13584 atoms, 13884 bonds, 1800 residues, 1 model selected > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/06_gp13d_6mer_ring_SS.pdb"" selectedOnly true > relModel #1 > select /m-r 14124 atoms, 14574 bonds, 1746 residues, 1 model selected > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/06_gp17_17mer_ring_SS.pdb"" selectedOnly true > relModel #1 > select /a-l 28464 atoms, 29268 bonds, 3732 residues, 1 model selected > select /a,c,e,g,i,k 14232 atoms, 14634 bonds, 1866 residues, 1 model selected > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/06_gp23_ring_a_SS.pdb"" selectedOnly true > relModel #1 > select /b,d,f,h,j,l 14232 atoms, 14634 bonds, 1866 residues, 1 model selected > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/06_gp23_ring_b_SS.pdb"" selectedOnly true > relModel #1 > select clear > select /s-u 13746 atoms, 14100 bonds, 1758 residues, 1 model selected > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/06_gp18_3mer_ring_SS.pdb"" selectedOnly true > relModel #1 > select /v-x 2592 atoms, 2649 bonds, 345 residues, 1 model selected > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/06_gp20_3mer_ring_SS.pdb"" selectedOnly true > relModel #1 > select add #2 99678 atoms, 102243 bonds, 12981 residues, 1 model selected > select subtract #2 Nothing selected > hide cartoons > hide atoms > volume #3 step 1 > volume #1 step 1 > set bgColor white > set bgColor #ffffff00 > surface dust #1 size 10.6 > surface dust #3 size 10.6 > hide #2 models > hide #!1 models > volume #3 level 0.5 > volume #3 level 0.4 > volume #3 level 0.5 > show #2 models > lighting depthCue false > camera ortho > show #!1 models > lighting soft > lighting shadows true intensity 0.5 > lighting soft > graphics silhouettes true > hide #!1 models > hide #!3 models > hide #2 models > show #2 models > select add #2 99678 atoms, 102243 bonds, 12981 residues, 1 model selected > hide #2 models > select subtract #2 Nothing selected > show #2 models > show atoms > show cartoons > style ball Changed 99678 atom styles > style stick Changed 99678 atom styles > hide cartoons > show cartoons > hide atoms > open > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/05_gp13_12mer_ring_SS.pdb"" > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/05_gp13d_6mer_ring_SS.pdb"" > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/05_gp17_6mer_ring_SS.pdb"" > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/05_gp18_3mer_ring_SS.pdb"" > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/05_gp20_3mer_ring_SS.pdb"" > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/05_gp23_ring_a_SS.pdb"" > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/05_gp23_ring_b_SS.pdb"" Summary of feedback from opening /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip | Interaction/03_TT | rings/05_gp13_12mer_ring_SS.pdb --- warnings | Start residue of secondary structure not found: HELIX 56 56 PHE M 4 LYS M 8 1 5 Start residue of secondary structure not found: HELIX 57 57 ALA M 12 LEU M 14 1 3 Start residue of secondary structure not found: HELIX 58 58 ARG M 102 TRP M 109 1 8 Start residue of secondary structure not found: HELIX 59 59 PRO M 202 ARG M 205 1 4 Start residue of secondary structure not found: HELIX 60 60 VAL M 208 ALA M 211 1 4 709 messages similar to the above omitted Summary of feedback from opening /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip | Interaction/03_TT | rings/05_gp13d_6mer_ring_SS.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4 LYS A 8 1 5 Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109 1 8 Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211 1 10 Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5 846 messages similar to the above omitted Summary of feedback from opening /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip | Interaction/03_TT | rings/05_gp17_6mer_ring_SS.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4 LYS A 8 1 5 Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109 1 8 Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211 1 10 Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5 840 messages similar to the above omitted Summary of feedback from opening /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip | Interaction/03_TT | rings/05_gp18_3mer_ring_SS.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4 LYS A 8 1 5 Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109 1 8 Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211 1 10 Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5 861 messages similar to the above omitted Summary of feedback from opening /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip | Interaction/03_TT | rings/05_gp20_3mer_ring_SS.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4 LYS A 8 1 5 Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109 1 8 Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211 1 10 Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5 953 messages similar to the above omitted Summary of feedback from opening /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip | Interaction/03_TT | rings/05_gp23_ring_a_SS.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4 LYS A 8 1 5 Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109 1 8 Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211 1 10 Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5 840 messages similar to the above omitted Summary of feedback from opening /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip | Interaction/03_TT | rings/05_gp23_ring_b_SS.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4 LYS A 8 1 5 Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109 1 8 Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211 1 10 Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5 838 messages similar to the above omitted Chain information for 05_gp13_12mer_ring_SS.pdb #4 --- Chain | Description A B C D E F G H I J K L | No description available Chain information for 05_gp13d_6mer_ring_SS.pdb #5 --- Chain | Description M N O P Q R | No description available Chain information for 05_gp17_6mer_ring_SS.pdb #6 --- Chain | Description m n o p q r | No description available Chain information for 05_gp18_3mer_ring_SS.pdb #7 --- Chain | Description s t u | No description available Chain information for 05_gp20_3mer_ring_SS.pdb #8 --- Chain | Description v w x | No description available Chain information for 05_gp23_ring_a_SS.pdb #9 --- Chain | Description a c e g i k | No description available Chain information for 05_gp23_ring_b_SS.pdb #10 --- Chain | Description b d f h j l | No description available > open > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/06_gp13d-gp17_model_SS.pdb"" > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/06_gp13d-gp23_model_SS.pdb"" > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/06_gp17-gp18_model_SS.pdb"" > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/06_gp17-gp23_model_SS.pdb"" > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/06_gp18-gp20_model_SS.pdb"" > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_TT | rings/06_gp18-gp23_model_SS.pdb"" Summary of feedback from opening /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip | Interaction/03_TT | rings/06_gp13d-gp17_model_SS.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4 LYS A 8 1 5 Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109 1 8 Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211 1 10 Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5 704 messages similar to the above omitted Summary of feedback from opening /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip | Interaction/03_TT | rings/06_gp13d-gp23_model_SS.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4 LYS A 8 1 5 Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109 1 8 Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211 1 10 Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5 560 messages similar to the above omitted Summary of feedback from opening /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip | Interaction/03_TT | rings/06_gp17-gp18_model_SS.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4 LYS A 8 1 5 Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109 1 8 Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211 1 10 Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5 719 messages similar to the above omitted Summary of feedback from opening /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip | Interaction/03_TT | rings/06_gp17-gp23_model_SS.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4 LYS A 8 1 5 Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109 1 8 Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211 1 10 Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5 554 messages similar to the above omitted Summary of feedback from opening /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip | Interaction/03_TT | rings/06_gp18-gp20_model_SS.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4 LYS A 8 1 5 Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109 1 8 Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211 1 10 Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5 832 messages similar to the above omitted Summary of feedback from opening /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip | Interaction/03_TT | rings/06_gp18-gp23_model_SS.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4 LYS A 8 1 5 Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109 1 8 Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211 1 10 Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5 575 messages similar to the above omitted Chain information for 06_gp13d-gp17_model_SS.pdb #11 --- Chain | Description M N O P Q R | No description available m n o p q r | No description available Chain information for 06_gp13d-gp23_model_SS.pdb #12 --- Chain | Description M N O P Q R | No description available a b c d e f g h i j k l | No description available Chain information for 06_gp17-gp18_model_SS.pdb #13 --- Chain | Description m n o p q r | No description available s t u | No description available Chain information for 06_gp17-gp23_model_SS.pdb #14 --- Chain | Description a b c d e f g h i j k l | No description available m n o p q r | No description available Chain information for 06_gp18-gp20_model_SS.pdb #15 --- Chain | Description s t u | No description available v w x | No description available Chain information for 06_gp18-gp23_model_SS.pdb #16 --- Chain | Description a b c d e f g h i j k l | No description available s t u | No description available > ui tool show ""Color Actions"" > color dark gray > color light gray > color #2,4-16 #d6d6d6ff > color #2,4-16 #ebebebff > style ball Changed 398118 atom styles > show surfaces > show #!3 models > show #!1 models > ui tool show ""Color Actions"" > color #ffffffff > color #ebebebff > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting flat > lighting soft > lighting simple > lighting soft > hide #!1 models > hide #!3 models > select /A-L 54336 atoms, 55536 bonds, 7200 residues, 2 models selected > color (#!2,4 & sel) light gray > select /M-R 54336 atoms, 55536 bonds, 7200 residues, 4 models selected > ui tool show ""Color Actions"" > color sel gold > select /v-x 7776 atoms, 7947 bonds, 1035 residues, 3 models selected > color sel orange red > select /s-u 68730 atoms, 70500 bonds, 8790 residues, 5 models selected > color sel deep sky blue > color sel cornflower blue > select /m-r 84204 atoms, 86754 bonds, 10530 residues, 6 models selected > select /m, o, q 42102 atoms, 43377 bonds, 5265 residues, 6 models selected > color sel deep pink > color sel hot pink > select /n, p, r 42102 atoms, 43377 bonds, 5265 residues, 6 models selected > color sel blue violet > select /s-u 68730 atoms, 70500 bonds, 8790 residues, 5 models selected > color sel deep sky blue > select /a,c,e,g,i,k 84744 atoms, 87054 bonds, 11130 residues, 6 models selected > select /a 14124 atoms, 14509 bonds, 1855 residues, 6 models selected > select add #2 111430 atoms, 114313 bonds, 14525 residues, 12 models selected > select subtract #2 11752 atoms, 12070 bonds, 1544 residues, 52 models selected > select add #12 51428 atoms, 52783 bonds, 6765 residues, 10 models selected > select subtract #12 9380 atoms, 9631 bonds, 1233 residues, 26 models selected > select add #4 34284 atoms, 35085 bonds, 4533 residues, 8 models selected > select subtract #4 7116 atoms, 7317 bonds, 933 residues, 18 models selected > select add #9 18976 atoms, 19512 bonds, 2488 residues, 6 models selected > select subtract #9 4744 atoms, 4878 bonds, 622 residues, 10 models selected > select add #9 18976 atoms, 19512 bonds, 2488 residues, 5 models selected > select /a 14124 atoms, 14509 bonds, 1855 residues, 6 models selected > select add #4 39028 atoms, 39963 bonds, 5155 residues, 12 models selected > select subtract #4 11860 atoms, 12195 bonds, 1555 residues, 22 models selected > select add #2 109166 atoms, 111999 bonds, 14225 residues, 10 models selected > select subtract #2 9488 atoms, 9756 bonds, 1244 residues, 50 models selected > select /a,c,e,g,i,k 84744 atoms, 87054 bonds, 11130 residues, 6 models selected > select add #4 98328 atoms, 100938 bonds, 12930 residues, 42 models selected > select subtract #4 71160 atoms, 73170 bonds, 9330 residues, 47 models selected > select add #2 156606 atoms, 160779 bonds, 20445 residues, 35 models selected > select subtract #2 56928 atoms, 58536 bonds, 7464 residues, 70 models selected > color sel chartreuse > select /b,d,f,h,j,l 84744 atoms, 87054 bonds, 11130 residues, 6 models selected > select add #4 98328 atoms, 100938 bonds, 12930 residues, 42 models selected > select subtract #4 71160 atoms, 73170 bonds, 9330 residues, 47 models selected > select add #2 156606 atoms, 160779 bonds, 20445 residues, 35 models selected > select subtract #2 56928 atoms, 58536 bonds, 7464 residues, 70 models selected > color sel tomato > color sel dark orange > color sel orange > color sel light salmon > color sel green yellow > color sel gold > color sel yellow > color sel coral > color sel azure > color sel cyan > color sel orange > show #!1 models > show #!3 models > view orient > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/01_tail_tip_colored.cxs"" includeMaps true ——— End of log from Mon Apr 17 13:03:15 2023 ——— opened ChimeraX session > turn x -90 > view > hide #!16 models > select add #16 84906 atoms, 87270 bonds, 11088 residues, 4 models selected > select add #14 113262 atoms, 116478 bonds, 14700 residues, 19 models selected > select subtract #16 71052 atoms, 73110 bonds, 9210 residues, 36 models selected > select subtract #14 28464 atoms, 29268 bonds, 3732 residues, 20 models selected > select add #12 56280 atoms, 57786 bonds, 7398 residues, 2 models selected > select subtract #12 14232 atoms, 14634 bonds, 1866 residues, 19 models selected > select add #10 14232 atoms, 14634 bonds, 1866 residues, 1 model selected > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > hide #!10 models > select add #10 14232 atoms, 14634 bonds, 1866 residues, 1 model selected > select subtract #10 Nothing selected > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!1 models > select #2/a,c,e,g,i,k 14232 atoms, 14634 bonds, 1866 residues, 1 model selected > show #!9 models > hide #!9 models > ui tool show ""Color Actions"" > color sel lime > color sel lawn green > show #!9 models > hide #!2 models > show #!2 models > select #2/b,d,f,h,j,l 14232 atoms, 14634 bonds, 1866 residues, 1 model selected > ui tool show ""Color Actions"" > color sel orange > select clear > show #!1 models > hide #!9 models > select add #2 99678 atoms, 102243 bonds, 12981 residues, 1 model selected > select subtract #2 42 models selected > hide #!1 models > hide #!2 models > show #!1 models > show #!2 models > ui tool show ""Color Zone"" > color zone #1 near #2 distance 6.37 > color zone #1 near #2 distance 6.3 > color zone #1 near #2 distance 6 [Repeated 1 time(s)] > volume splitbyzone #1 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size 512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size 512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size 512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size 512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size 512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size 512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size 512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size 512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32 Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size 512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32 > volume #1 level 0.3 > volume #17.1 level 0.3 > volume #17.2 level 0.3 > volume #17.3 level 0.3 > volume #17.4 level 0.3 > volume #17.5 level 0.3 > volume #17.6 level 0.3 > volume #17.7 level 0.3 > volume #17.8 level 0.3 > volume #17.9 level 0.3 > surface dust #17.2 size 10.6 > surface dust #17.3 size 10.6 > surface dust #17.4 size 10.6 > surface dust #17.5 size 10.6 > surface dust #17.6 size 10.6 > surface dust #17.7 size 10.6 > surface dust #17.8 size 10.6 > surface dust #17.9 size 10.6 > hide #!2 models > lighting depthCue false > view > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/02_tail_tip_split_maps.cxs"" > view > hide #!17 models > show #!6 models > show #!5 models > select add #5 13584 atoms, 13884 bonds, 1800 residues, 1 model selected > hide #!5 models > select subtract #5 6 models selected > hide #!6 models > show #!12 models > hide #!12 models > show #!13 models > hide #!13 models > show #!14 models > hide #!14 models > show #!15 models > hide #!15 models > show #!16 models > hide #!16 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!5 models > select add #5 13584 atoms, 13884 bonds, 1800 residues, 1 model selected > ui tool show ""Color Actions"" > color sel gold > select subtract #5 6 models selected > hide #!5 models > show #!5 models > show #!6 models > hide #!5-6 surfaces > show #!5-6 cartoons > hide #!5-6 atoms > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!5 models > show #!5 models > select #6/q:39,73,131, 63,78,84,88,89,94,121 #6/r:40,54,56,59,284,288 | > select #5/P:74,75,76,83 Expected a keyword > hide #!5 models > show #!5 models > select #5/P:74,75,76,83 #6/p:124 #6/q:39,73,131, 63,78,84,88,89,94,121 > #6/r:40,54,56,59,284,288 210 atoms, 199 bonds, 21 residues, 2 models selected > style sel ball Changed 210 atom styles > show sel atoms > turn y 30 [Repeated 2 time(s)] > turn y -30 > turn y 30 > color (#!5-6 & sel) byhetero > ui tool show H-Bonds > hbonds sel color #000000 dashes 10 restrict both twoColors true slopColor > #000000 intraRes false select true reveal true 15 hydrogen bonds found 6 strict hydrogen bonds found > rename #18 ""hydrogen bonds gp13d-17"" > select clear > select #5/M-O,Q,R 11320 atoms, 11570 bonds, 1500 residues, 1 model selected > hide sel cartoons [Repeated 1 time(s)] > show sel cartoons > ui tool show ""Color Actions"" > color (#!5 & sel) #ebebebff > select clear > select #6/m-o 7062 atoms, 7287 bonds, 873 residues, 1 model selected > hide sel cartoons > show sel cartoons > ui tool show ""Color Actions"" > color (#!6 & sel) #ffffffff > color (#!6 & sel) #ebebebff > select clear > hide #!17.6 models > show #!17.6 models > transparency #5.1-6#6.1-6#17.3.1#17.6.1#17.7.1 50 > transparency #5.1-6#6.1-6#17.3.1#17.6.1#17.7.1 0 > lighting soft > lighting simple > lighting soft > lighting flat > lighting full > lighting soft > lighting depthCue false > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/13d-17_Map.png"" width 5000 height 4194 supersample 4 > hide #!17 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!5 models > show #!5 models > select #6/m-o 7062 atoms, 7287 bonds, 873 residues, 1 model selected > show sel surfaces > lighting flat > lighting soft > hide sel cartoons [Repeated 2 time(s)] > select #6/m-o 7062 atoms, 7287 bonds, 873 residues, 1 model selected > hide sel cartoons [Repeated 1 time(s)] > hide sel surfaces > select #5/M-O,Q,R 11320 atoms, 11570 bonds, 1500 residues, 1 model selected > hide sel cartoons > select add #5 13584 atoms, 13884 bonds, 1800 residues, 6 models selected > select add #6 27708 atoms, 28458 bonds, 9 pseudobonds, 3546 residues, 9 models selected > show sel cartoons > select clear > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/13d-17_Cartoon.png"" width 5000 height 4194 supersample 4 > select #5/M-O,Q,R 11320 atoms, 11570 bonds, 1500 residues, 1 model selected > hide sel cartoons > select #6/m-o 7062 atoms, 7287 bonds, 873 residues, 1 model selected > hide sel cartoons > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/13d-17-Interaction.cxs"" ——— End of log from Mon Apr 17 13:31:58 2023 ——— opened ChimeraX session > ui mousemode right distance > distance #6/q:121@OH #6/r:284@NH2 Distance between 05_gp17_6mer_ring_SS.pdb #6/q TYR 121 OH and /r ARG 284 NH2: 2.218Å > distance #6/q:88@NE #6/r:40@OD1 Distance between 05_gp17_6mer_ring_SS.pdb #6/q ARG 88 NE and /r ASP 40 OD1: 3.630Å > show #!1 models > hide #!1 models > hide #19.1 models > color #19 #212121ff models > color #19 black models > ui tool show Distances > distance style color black [Repeated 2 time(s)] > distance style dashes 8 [Repeated 2 time(s)] > distance style radius 0.08 [Repeated 2 time(s)] > rename #19 ""distances gp17-gp17"" > show #!13 models > show #!12 models > hide #!13 models > hide #!12 models > show #!11 models > view > view orient > turn x -90 > turn y 90 > hide #!11 models > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp13d-gp17-Interaction.cxs"" ——— End of log from Mon Apr 17 13:40:26 2023 ——— opened ChimeraX session > hide #!17.6 models > hide #!17.7 models > show #!17.7 models > show #!17.6 models > view orient > turn x -90 > turn y 90 > hide #!17.6 models > hide #!17.7 models > hide #!17.3 models > close #1 > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp13d-gp17-Interaction.cxs"" > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp13d-gp17_Interaction.png"" width 5000 height 4194 supersample > 4 > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp13d-gp17_Interaction2.png"" width 5000 height 4194 > supersample 4 > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp13d-gp17-Interaction2.cxs"" > view > show #!17.3 models > show #!17.6 models > show #!17.7 models > view > view orient > turn x -90 > hide #!17 models > hide #!17.3 models > show #!17.3 models > turn y 90 > hide #!17.3 models > hide #!17.6 models > hide #!17.7 models > show #!17.7 models > show #!17.6 models > hide #!17.6 models > show #!17.6 models > hide #!17.7 models > show #!17.7 models > hide #!17.6 models > hide #!17.7 models > show #!17.6 models > hide #!17.6 models > show #!17.6 models > transparency #5.1-6#6.1-6#17.6.1 50 > transparency #5.1-6#6.1-6#17.6.1 0 > hide #!17.6 models > view > view orient > show #!17.6 models > hide #!17.6 models > show #!17.6 models > show #!17.7 models > show #!17.3 models > view orient > turn x -90 > turn y 90 > hide #!17.6 models > hide #!17.7 models > hide #!17.3 models > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/13d-17_Cartoon__.png"" width 5000 height 4194 supersample 4 > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp13d-gp17-Interaction.cxs"" > show #!17.7 models > show #!17.6 models > show #!17.5 models > hide #!17.5 models > show #!17.8 models > hide #!17.8 models > show #!17.3 models > view > show #!17.8 models > view > hide #!17.8 models > hide #!17.7 models > hide #!17.6 models > hide #!17.3 models > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp13d-gp17-Interaction.cxs"" ——— End of log from Mon Apr 17 14:45:58 2023 ——— opened ChimeraX session > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/02_gp13d-gp17_cartoon_image.png"" width 5000 height 4194 > supersample 4 > show sel surfaces > hide sel surfaces > transparency c 30 Missing or invalid ""percent"" argument: Expected a number > transparency 30 cartoons > transparency 50 cartoons > transparency 50 r Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 50 > transparency 0 cartoons > transparency 10 cartoons > transparency 90 cartoons [Repeated 1 time(s)] > transparency 70 cartoons > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/02_gp13d-gp17_Int3.png"" width 4000 height 3355 supersample 4 > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/02_gp13d-gp17_Int1.png"" width 4000 height 3355 supersample 4 > turn y 10 > turn y -30 [Repeated 1 time(s)] > turn y 15 > turn y -15 > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/02_gp13d-gp17_Int2.png"" width 4000 height 3355 supersample 4 > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp13d-gp17-Interaction2.cxs"" ——— End of log from Mon Apr 17 14:56:24 2023 ——— opened ChimeraX session > show #!17.7 models > show #!17.6 models > show #!17.5 models > hide #!17.5 models > show #!17.3 models > view orient > lighting soft > lighting full > lighting soft > lighting simple > lighting soft > turn x -90 > transparency #5.1-6#6.1-6#17.3.1#17.6.1#17.7.1 0 > turn y 90 > lighting depthCue false > hide #!17.7 models > hide #!17.6 models > hide #!17.3 models > show #!17.8 models > show #!17.7 models > show #!17.6 models > show #!17.5 models > show #!17.4 models > hide #!17.4 models > hide #!17.5 models > show #!17.3 models > transparency #5.1-6#6.1-6#17.3.1#17.6.1#17.7.1#17.8.1 0 > view > hide #!17.8 models > hide #!17.6 models > hide #!17.3 models > hide #!17.7 models > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp13d-gp17-Interaction.cxs"" ——— End of log from Mon Apr 17 15:22:23 2023 ——— opened ChimeraX session > hide sel atoms [Repeated 1 time(s)] > hide sel cartoons > show #!7 models > hide sel atoms > hide sel cartoons > hide #!5 models > show #!5 models > hide #!6 models > select add #6 14124 atoms, 14574 bonds, 11 pseudobonds, 1746 residues, 3 models selected > select subtract #6 6 models selected > show #!6 models > hide #!5-7 cartoons > show #!5-7 cartoons > hide #!5-7 atoms > hide #!5-7 surfaces > hide #!19 models > hide #18 models > show #!17.7 models > show #!17.6 models > show #!17.4 models > hide #!17.4 models > show #!17.5 models > hide #!17.5 models > show #!17.3 models > show #!17.8 models > view > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/01_gp13d-gp17-gp18_full_map.png"" width 5000 height 4194 > supersample 4 > hide #!17.6 models > hide #!17.7 models > hide #!17.8 models > hide #!17 models > hide #!17.3 models > hide #!5 models > select #6/q:44,198,275,151,176,248 #6/p:51,52,199,248 > #7/s:382,459,518,519,364, 365,368,435,24,21 /u: > 368,62,45,128,137,194,98,89,139,244 285 atoms, 268 bonds, 30 residues, 2 models selected > show sel atoms > select #7/t 4582 atoms, 4700 bonds, 586 residues, 1 model selected > hide sel cartoons > select #7/s 4582 atoms, 4700 bonds, 586 residues, 1 model selected > color (#!7 & sel) light gray > select clear > turn y 30 [Repeated 1 time(s)] > select #7/s 4582 atoms, 4700 bonds, 586 residues, 1 model selected > ui tool show ""Color Actions"" > color sel cornflower blue > select #7/t 4582 atoms, 4700 bonds, 586 residues, 1 model selected > show sel cartoons > color sel sky blue > color sel light sky blue > color sel powder blue > color sel silver > color sel light cyan > color sel green yellow > color sel cyan > color sel chartreuse > hide sel cartoons > select #6/q:44,198,275,151,176,248 #6/p:51,52,199,248 > #7/s:382,459,518,519,364, 365,368,435,24,21 /u: > 368,62,45,128,137,194,98,89,139,244 285 atoms, 268 bonds, 30 residues, 2 models selected > show sel atoms > color (#!6-7 & sel) byhetero > ui tool show H-Bonds > hbonds sel color #000000 dashes 10 restrict both twoColors true slopColor > #000000 intraRes false select true reveal true 13 hydrogen bonds found 7 strict hydrogen bonds found > rename #1 id #20 > rename #20 ""hydrogen bonds gp17-gp18"" > hide #!6 models > select add #6 14140 atoms, 14574 bonds, 12 pseudobonds, 1759 residues, 9 models selected > select add #7 27870 atoms, 28674 bonds, 21 pseudobonds, 3504 residues, 13 models selected > select subtract #6 13746 atoms, 14100 bonds, 9 pseudobonds, 1758 residues, 11 models selected > select subtract #7 3 models selected > show #!6 models > show #!6-7 cartoons > select #7/t 4582 atoms, 4700 bonds, 586 residues, 1 model selected > color sel royal blue > color sel navy > hide sel cartoons > turn y -30 > select #6/m-r 14124 atoms, 14574 bonds, 12 pseudobonds, 1746 residues, 4 models selected > hide sel cartoons > show sel cartoons > select #6/m-o,r 9416 atoms, 9716 bonds, 1164 residues, 1 model selected > hide sel cartoons > show #!16 models > hide #!16 models > show #!15 models > hide #!15 models > show #!13 models > hide #!13 models > show #!17.7 models > show #!17.6 models > show #!17.3 models > show #!17.8 models > view orient > turn x 90 [Repeated 2 time(s)] > turn y 90 > view > hide #!17.8 models > hide #!17.7 models > hide #!17.6 models > hide #!17.3 models > hide #!17 models > turn y 30 > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > turn y 30 > turn y -30 [Repeated 1 time(s)] > select #6/p 2354 atoms, 2429 bonds, 291 residues, 1 model selected > hide sel cartoons > show sel cartoons > select #6/r 2354 atoms, 2429 bonds, 291 residues, 1 model selected > show sel cartoons > select clear > hide #!6-7 atoms > select #6/q:44,198,275,151,176,248 #6/r: 51,52,199,248 > #7/s:382,459,518,519,364, 365,368,435,24,21, 368,62,45 /u: > 128,137,194,98,89,139,244 271 atoms, 253 bonds, 12 pseudobonds, 29 residues, 3 models selected > show sel atoms > close #20 > color (#!6-7 & sel) byhetero > ui tool show H-Bonds > hbonds sel color #000000 dashes 10 restrict both twoColors true slopColor > #000000 intraRes false select true reveal true 13 hydrogen bonds found 6 strict hydrogen bonds found > rename #1 ""hydrogen bonds gp17-gp18"" > rename #1 id #20 > hide #20 models > show #20 models > select clear > select #6/q:44,198,275,151,176,248 #6/r:51,52,199,248 > #7/s:382,459,518,519,364, 365,368,435,24,21, 368,62,45,272 /u: > 128,137,194,98,89,139,244 279 atoms, 260 bonds, 13 pseudobonds, 30 residues, 3 models selected > show sel atoms > color (#!6-7 & sel) byhetero > hide sel atoms > select #6/q:44,198,275,151,176,248 #6/r:51,52,199,248 > #7/s:382,459,518,519,364, 365,368,435,24,21, 368,62,45 /u: > 128,137,194,98,89,139,244 271 atoms, 253 bonds, 13 pseudobonds, 29 residues, 3 models selected > show sel atoms > select #6/q:44,198,275,151,176,248 #6/r:51,52,60,199,248 > #7/s:382,459,518,519,364, 365,368,435,24,21, 368,62,45 /u: > 128,137,194,98,89,139,244 282 atoms, 263 bonds, 13 pseudobonds, 30 residues, 3 models selected > show sel atoms > select #6/q:44,198,275,151,176,248 #6/r:51,52,60,199,248 > #7/s:382,459,518,519,364,365,368,435,24,21, 368,62,45,539 /u: > 128,137,194,98,89,139,244 290 atoms, 270 bonds, 13 pseudobonds, 31 residues, 3 models selected > show sel atoms > hide sel atoms > select #6/q:44,198,275,151,176,248 #6/r:51,52,60,199,248 > #7/s:382,459,518,519,364,365,368,435,24,21, 368,62,539 /u: > 128,137,194,98,89,139,244 279 atoms, 260 bonds, 13 pseudobonds, 30 residues, 3 models selected > show sel atoms > close #20 > ui tool show H-Bonds > hbonds sel color #000000 dashes 10 restrict both twoColors true slopColor > #000000 intraRes false select true reveal true 13 hydrogen bonds found 6 strict hydrogen bonds found > select clear > ui mousemode right distance > distance #7/u:194@NH2 #7/s:459@OE2 Distance between 05_gp18_3mer_ring_SS.pdb #7/u ARG 194 NH2 and /s GLU 459 OE2: 2.224Å > distance #7/s:364@NH2 #6/q:248@OD1 Distance between 05_gp18_3mer_ring_SS.pdb #7/s ARG 364 NH2 and 05_gp17_6mer_ring_SS.pdb #6/q ASP 248 OD1: 3.104Å > distance #7/s:62@NH1 #6/r:248@OD1 Distance between 05_gp18_3mer_ring_SS.pdb #7/s ARG 62 NH1 and 05_gp17_6mer_ring_SS.pdb #6/r ASP 248 OD1: 2.924Å > select #6/q:44,198,275,151,176,248 #6/r:51,52,60,199,248 > #7/s:382,459,518,519,364,365,368,435,24,21, 368,62,539 /u: > 128,137,194,98,89,139,244 279 atoms, 260 bonds, 16 pseudobonds, 30 residues, 4 models selected > color (#!6-7 & sel) byhetero > select clear > distance #7/s:539@OD1 #6/r:60@NH1 Distance between 05_gp18_3mer_ring_SS.pdb #7/s ASN 539 OD1 and 05_gp17_6mer_ring_SS.pdb #6/r ARG 60 NH1: 3.148Å > show #!17.3 models > show #!17.5 models > hide #!17.5 models > show #!17.6 models > show #!17.7 models > view orient > show #!17.8 models > view orient > view > turn x -90 > view > turn y 90 > hide #!7 models > hide #!6 models > show #!6 models > show #!7 models > hide #!17 models > hide #!17.3 models > hide #!17.6 models > hide #!17.7 models > hide #!17.8 models > rename #20 id #21 > rename #1 id #20 > rename #20 ""hydrogen bonds gp17-gp18"" > rename #21 ""distances gp18-gp18"" > color #21 #212121ff models > color #21 black models > ui tool show Distances > distance style color black [Repeated 2 time(s)] > distance style dashes 8 [Repeated 2 time(s)] > distance style radius 0.08 [Repeated 2 time(s)] > color #21.1 black models > rename #21 distances Another pseudobond group is already named 'distances' > select add #21 4 pseudobonds, 2 models selected > ui tool show Distances Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/struct_measure/tool.py"", line 626, in clear_status if s.apc_status_label.text() == s.apc_status_tip: RuntimeError: wrapped C/C++ object of type QLabel has been deleted RuntimeError: wrapped C/C++ object of type QLabel has been deleted File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/struct_measure/tool.py"", line 626, in clear_status if s.apc_status_label.text() == s.apc_status_tip: See log for complete Python traceback. > select subtract #21 Nothing selected > select add #21.1 1 model selected > select subtract #21.1 Nothing selected > hide #21.1 models > show #!15 models > show #!14 models > hide #!14 models > hide #!15 models > show #!17.3 models > show #!17.6 models > show #!17.7 models > show #!17.8 models > view > hide #!17.8 models > hide #!17.7 models > hide #!17.6 models > hide #!17.3 models > turn y 45 > turn y -45 [Repeated 1 time(s)] > turn y 45 [Repeated 2 time(s)] > turn y -45 [Repeated 1 time(s)] > view orient > turn x -90 > turn y 90 > show #!17.3 models > show #!17.7 models > show #!17.8 models > show #!17.6 models > view > hide #!17.8 models > hide #!17.7 models > hide #!17.6 models > hide #!17.3 models > show #!17.3 models > hide #!17.3 models > show #!17.3 models > hide #!17.3 models > select #6/p 2354 atoms, 2429 bonds, 291 residues, 1 model selected > hide sel cartoons [Repeated 1 time(s)] > show sel cartoons > select clear > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp17-gp18_interaction.cxs"" > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_gp17-gp18_int1.png"" width 5000 height 4194 supersample 4 > distance #6/q:151@OE2 #7/s:21@NZ Distance between 05_gp17_6mer_ring_SS.pdb #6/q GLU 151 OE2 and 05_gp18_3mer_ring_SS.pdb #7/s LYS 21 NZ: 3.896Å > hide #!21 models > show #!21 models > distance #6/q:151@OE2 #7/s:21@NZ Distance already exists; modify distance properties with 'distance style' > show #21.1 models > hide #21.1 models > ui tool show Distances > distance style dashes 8 [Repeated 1 time(s)] > distance style color #212121 [Repeated 2 time(s)] > distance style color black [Repeated 2 time(s)] > ~distance #6/q:151@OE2 #7/s:21@NZ [Repeated 6 time(s)] > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_gp17-gp18_Int1.png"" width 5000 height 4194 supersample 4 > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/gp17-gp18_interaction1.cxs"" [Repeated 1 time(s)] ——— End of log from Mon Apr 17 17:14:38 2023 ——— opened ChimeraX session Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/dist_monitor/monitor.py"", line 106, in _changes_handler pbg = pb.group File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 100, in get_prop return astype(v.value) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/ctypes_support.py"", line 69, in pseudobond_group return PseudobondGroupData.c_ptr_to_py_inst(p) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 2326, in class_obj.c_ptr_to_py_inst = lambda ptr, *, fname=func_name: c_function(fname, File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py"", line 29, in __init__ session = s.session AttributeError: 'NoneType' object has no attribute 'session' Error processing trigger ""changes"": AttributeError: 'NoneType' object has no attribute 'session' File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py"", line 29, in __init__ session = s.session See log for complete Python traceback. Exception ignored in: Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1199, in __del__ if not self.was_deleted: AttributeError: 'PseudobondGroup' object has no attribute 'was_deleted' > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_gp17-gp18_Int1.png"" width 5000 height 4194 supersample 4 > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_gp17-gp18_Int2.png"" width 5000 height 4194 supersample 4 > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_gp17-gp18 Interaction2.cxs"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 249, in discovery if hasattr(sm, 'include_state') and not sm.include_state(value): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/attributes.py"", line 245, in include_state self._python_instances = [[inst for inst in inst_func(self.session) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/attributes.py"", line 245, in self._python_instances = [[inst for inst in inst_func(self.session) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 2504, in register_class(reg_class, lambda *args, cls=reg_class: python_instances_of_class(cls), File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 49, in python_instances_of_class return [x for x in instances if filt(x)] File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 49, in return [x for x in instances if filt(x)] File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 44, in filt = lambda x: (not x.group.structure) or x.group.structure.id File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 100, in get_prop return astype(v.value) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/ctypes_support.py"", line 69, in pseudobond_group return PseudobondGroupData.c_ptr_to_py_inst(p) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 2326, in class_obj.c_ptr_to_py_inst = lambda ptr, *, fname=func_name: c_function(fname, File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py"", line 29, in __init__ session = s.session AttributeError: 'NoneType' object has no attribute 'session' AttributeError: 'NoneType' object has no attribute 'session' File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py"", line 29, in __init__ session = s.session See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 165, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/__init__.py"", line 37, in run_provider providers.run_provider(session, name) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/providers.py"", line 45, in run_provider what(session) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/providers.py"", line 27, in _file_save show_save_file_dialog(session) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 249, in discovery if hasattr(sm, 'include_state') and not sm.include_state(value): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/attributes.py"", line 245, in include_state self._python_instances = [[inst for inst in inst_func(self.session) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/attributes.py"", line 245, in self._python_instances = [[inst for inst in inst_func(self.session) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 2504, in register_class(reg_class, lambda *args, cls=reg_class: python_instances_of_class(cls), File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 49, in python_instances_of_class return [x for x in instances if filt(x)] File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 49, in return [x for x in instances if filt(x)] File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 44, in filt = lambda x: (not x.group.structure) or x.group.structure.id File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 100, in get_prop return astype(v.value) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/ctypes_support.py"", line 69, in pseudobond_group return PseudobondGroupData.c_ptr_to_py_inst(p) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 2326, in class_obj.c_ptr_to_py_inst = lambda ptr, *, fname=func_name: c_function(fname, File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py"", line 29, in __init__ session = s.session AttributeError: 'NoneType' object has no attribute 'session' AttributeError: 'NoneType' object has no attribute 'session' File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py"", line 29, in __init__ session = s.session See log for complete Python traceback. > save > ""/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip > | Interaction/03_gp17-gp18 Interaction2.cxs"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 249, in discovery if hasattr(sm, 'include_state') and not sm.include_state(value): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/attributes.py"", line 245, in include_state self._python_instances = [[inst for inst in inst_func(self.session) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/attributes.py"", line 245, in self._python_instances = [[inst for inst in inst_func(self.session) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 2504, in register_class(reg_class, lambda *args, cls=reg_class: python_instances_of_class(cls), File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 49, in python_instances_of_class return [x for x in instances if filt(x)] File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 49, in return [x for x in instances if filt(x)] File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 44, in filt = lambda x: (not x.group.structure) or x.group.structure.id File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 100, in get_prop return astype(v.value) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/ctypes_support.py"", line 69, in pseudobond_group return PseudobondGroupData.c_ptr_to_py_inst(p) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 2326, in class_obj.c_ptr_to_py_inst = lambda ptr, *, fname=func_name: c_function(fname, File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py"", line 29, in __init__ session = s.session AttributeError: 'NoneType' object has no attribute 'session' AttributeError: 'NoneType' object has no attribute 'session' File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py"", line 29, in __init__ session = s.session See log for complete Python traceback. Exception ignored in: Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1199, in __del__ if not self.was_deleted: AttributeError: 'PseudobondGroup' object has no attribute 'was_deleted' Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 165, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/__init__.py"", line 37, in run_provider providers.run_provider(session, name) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/providers.py"", line 45, in run_provider what(session) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/providers.py"", line 27, in _file_save show_save_file_dialog(session) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 249, in discovery if hasattr(sm, 'include_state') and not sm.include_state(value): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/attributes.py"", line 245, in include_state self._python_instances = [[inst for inst in inst_func(self.session) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/attributes.py"", line 245, in self._python_instances = [[inst for inst in inst_func(self.session) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 2504, in register_class(reg_class, lambda *args, cls=reg_class: python_instances_of_class(cls), File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 49, in python_instances_of_class return [x for x in instances if filt(x)] File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 49, in return [x for x in instances if filt(x)] File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 44, in filt = lambda x: (not x.group.structure) or x.group.structure.id File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 100, in get_prop return astype(v.value) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/ctypes_support.py"", line 69, in pseudobond_group return PseudobondGroupData.c_ptr_to_py_inst(p) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 2326, in class_obj.c_ptr_to_py_inst = lambda ptr, *, fname=func_name: c_function(fname, File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py"", line 29, in __init__ session = s.session AttributeError: 'NoneType' object has no attribute 'session' AttributeError: 'NoneType' object has no attribute 'session' File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py"", line 29, in __init__ session = s.session See log for complete Python traceback. OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGT3CT/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 8422.100.650 OS Loader Version: 8422.100.650 Software: System Software Overview: System Version: macOS 13.3.1 (22E261) Kernel Version: Darwin 22.4.0 Time since boot: 1 day, 23 hours, 50 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 biopython: 1.81 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-ArtiaX: 0.3 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.19.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-Cytoscape: 0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.5 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBImages: 1.1 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.1.10 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-StrudelScore: 0.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 geomdl: 5.3.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 MolecularDynamicsViewer: 1.4 mrcfile: 1.4.3 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 pandas: 1.5.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 recordtype: 1.4 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 starfile: 0.4.11 superqt: 0.4.1 tables: 3.7.0 threed-strudel: 0.9.18 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect feedback normal Sessions all ChimeraX