id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10004 Reading SDF file: atoms[index].charge = charge IndexError: list index out of range rsepela@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.2.3 (2021-05-13 06:57:20 UTC) Description (Describe the actions that caused this problem to occur here) Trying to load the attached file into chimeraX causes this errror. Log: UCSF ChimeraX version: 1.2.3 (2021-05-13) © 2016-2021 Regents of the University of California. All rights reserved. > open ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/1A3COOHBC.cxs"" Log from Tue Oct 17 13:52:20 2023UCSF ChimeraX version: 1.2.3 (2021-05-13) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/protein_no_ligands.pdb"" > format pdb Summary of feedback from opening /Users/rebeckasepela/Library/CloudStorage/OneDrive- HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule files/neurosnap-652da2320d833bed9c70195f-norharmane/protein_no_ligands.pdb --- warnings | CONECT record to nonexistent atom: (450, 23925) CONECT record to nonexistent atom: (1297, 23911) CONECT record to nonexistent atom: (2991, 23952) CONECT record to nonexistent atom: (3076, 23979) CONECT record to nonexistent atom: (5232, 24109) 15 messages similar to the above omitted CONECT record for nonexistent atom: 23911 Cannot find LINK/SSBOND residue NAG (402 ) Cannot find LINK/SSBOND residue NAG (401 ) Cannot find LINK/SSBOND residue NAG (403 ) Cannot find LINK/SSBOND residue NAG (404 ) Cannot find LINK/SSBOND residue NAG (402 ) 15 messages similar to the above omitted protein_no_ligands.pdb title: Cryo-em structure of octopus sensory receptor CRT1 [more info...] Chain information for protein_no_ligands.pdb #1 --- Chain | Description A B C D E | octopus sensory receptor > close > open ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/protein_no_ligands.pdb"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank1_confidence-0.42.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank2_confidence-0.44.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank3_confidence-0.45.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank4_confidence-0.65.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank5_confidence-0.65.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank6_confidence-0.78.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank7_confidence-0.86.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank8_confidence-0.86.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank9_confidence-0.88.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank10_confidence-0.94.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank11_confidence-1.01.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank12_confidence-1.06.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank13_confidence-1.14.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank14_confidence-1.15.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank15_confidence-1.20.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank16_confidence-1.21.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank18_confidence-1.24.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank20_confidence-1.31.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank19_confidence-1.26.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank17_confidence-1.21.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank21_confidence-1.32.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank23_confidence-1.33.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank24_confidence-1.34.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank25_confidence-1.37.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652da2320d833bed9c70195f-norharmane/rank22_confidence-1.33.sdf"" Summary of feedback from opening /Users/rebeckasepela/Library/CloudStorage/OneDrive- HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule files/neurosnap-652da2320d833bed9c70195f-norharmane/protein_no_ligands.pdb --- warnings | CONECT record to nonexistent atom: (450, 23925) CONECT record to nonexistent atom: (1297, 23911) CONECT record to nonexistent atom: (2991, 23952) CONECT record to nonexistent atom: (3076, 23979) CONECT record to nonexistent atom: (5232, 24109) 15 messages similar to the above omitted CONECT record for nonexistent atom: 23911 Cannot find LINK/SSBOND residue NAG (402 ) Cannot find LINK/SSBOND residue NAG (401 ) Cannot find LINK/SSBOND residue NAG (403 ) Cannot find LINK/SSBOND residue NAG (404 ) Cannot find LINK/SSBOND residue NAG (402 ) 15 messages similar to the above omitted protein_no_ligands.pdb title: Cryo-em structure of octopus sensory receptor CRT1 [more info...] Chain information for protein_no_ligands.pdb #1 --- Chain | Description A B C D E | octopus sensory receptor PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 PubChem entry 64961 > show surfaces > show surfaces > surface > view #2-26 clip false > select #2 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #3 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #4 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #5 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #6 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #7 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #8 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #9 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #10 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #11 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #12 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #13 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #14 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #15 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #16 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #17 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #18 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > surface sel > select #19 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select#20 Unknown command: select#20 > select #20 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select#21 Unknown command: select#21 > select #21 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #22 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #23 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #24 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > select #25 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > surface style #25 solid > select #26 13 atoms, 15 bonds, 1 residue, 1 model selected > surface sel > movie record > turn y 2 180 > wait 180 > movie encode /Users/rebeckasepela/Desktop/movie1.mp4 Movie saved to /Users/rebeckasepela/Desktop/movie1.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/rebeckasepela/Desktop/movie2.mp4 Movie saved to /Users/rebeckasepela/Desktop/movie2.mp4 > lighting soft > set bgColor white > ~select #26 1 model selected > preset ""molecular surfaces"" ""ghostly white"" Changed 23905 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > undo > undo > undo > movie record > turn y 2 180 > wait 180 > movie encode /Users/rebeckasepela/Desktop/movie3.mp4 Movie saved to /Users/rebeckasepela/Desktop/movie3.mp4 > save ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/norharmane.png"" width 553 height 638 supersample 3 > save ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/norharmane.cxs"" > open ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/protein_no_ligands.pdb"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank1_confidence-0.43.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank2_confidence-0.54.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank3_confidence-0.63.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank4_confidence-0.72.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank5_confidence-0.85.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank6_confidence-0.91.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank7_confidence-0.96.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank8_confidence-0.98.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank12_confidence-1.03.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank14_confidence-1.09.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank17_confidence-1.14.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank18_confidence-1.14.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank19_confidence-1.17.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank16_confidence-1.14.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank15_confidence-1.12.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank13_confidence-1.05.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank11_confidence-1.02.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank10_confidence-1.00.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank9_confidence-0.99.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank24_confidence-1.28.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank22_confidence-1.23.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank21_confidence-1.20.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank20_confidence-1.17.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank23_confidence-1.27.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank25_confidence-1.35.sdf"" Summary of feedback from opening /Users/rebeckasepela/Library/CloudStorage/OneDrive- HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/protein_no_ligands.pdb --- warnings | CONECT record to nonexistent atom: (450, 23925) CONECT record to nonexistent atom: (1297, 23911) CONECT record to nonexistent atom: (2991, 23952) CONECT record to nonexistent atom: (3076, 23979) CONECT record to nonexistent atom: (5232, 24109) 15 messages similar to the above omitted CONECT record for nonexistent atom: 23911 Cannot find LINK/SSBOND residue NAG (402 ) Cannot find LINK/SSBOND residue NAG (401 ) Cannot find LINK/SSBOND residue NAG (403 ) Cannot find LINK/SSBOND residue NAG (404 ) Cannot find LINK/SSBOND residue NAG (402 ) 15 messages similar to the above omitted protein_no_ligands.pdb title: Cryo-em structure of octopus sensory receptor CRT1 [more info...] Chain information for protein_no_ligands.pdb #27 --- Chain | Description A B C D E | octopus sensory receptor PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 > close #1-26 > show surfaces > close #28-52#27 > open ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/protein_no_ligands.pdb"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank1_confidence-0.43.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank2_confidence-0.54.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank3_confidence-0.63.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank4_confidence-0.72.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank5_confidence-0.85.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank6_confidence-0.91.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank7_confidence-0.96.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank8_confidence-0.98.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank9_confidence-0.99.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank10_confidence-1.00.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank11_confidence-1.02.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank12_confidence-1.03.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank13_confidence-1.05.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank14_confidence-1.09.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank15_confidence-1.12.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank16_confidence-1.14.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank17_confidence-1.14.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank18_confidence-1.14.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank19_confidence-1.17.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank20_confidence-1.17.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank21_confidence-1.20.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank22_confidence-1.23.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank23_confidence-1.27.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank24_confidence-1.28.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/rank25_confidence-1.35.sdf"" Summary of feedback from opening /Users/rebeckasepela/Library/CloudStorage/OneDrive- HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule files/neurosnap-652db04b0d833bed9c701975-1A3COOHBC/protein_no_ligands.pdb --- warnings | CONECT record to nonexistent atom: (450, 23925) CONECT record to nonexistent atom: (1297, 23911) CONECT record to nonexistent atom: (2991, 23952) CONECT record to nonexistent atom: (3076, 23979) CONECT record to nonexistent atom: (5232, 24109) 15 messages similar to the above omitted CONECT record for nonexistent atom: 23911 Cannot find LINK/SSBOND residue NAG (402 ) Cannot find LINK/SSBOND residue NAG (401 ) Cannot find LINK/SSBOND residue NAG (403 ) Cannot find LINK/SSBOND residue NAG (404 ) Cannot find LINK/SSBOND residue NAG (402 ) 15 messages similar to the above omitted protein_no_ligands.pdb title: Cryo-em structure of octopus sensory receptor CRT1 [more info...] Chain information for protein_no_ligands.pdb #1 --- Chain | Description A B C D E | octopus sensory receptor PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 PubChem entry 5488588 > show surfaces > select #2 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #3 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #4 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #5 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #6 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #7 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #8 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #9 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #10 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #11 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #12 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #13 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #14 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > ;ect#15 Incomplete command: segmentation > select #15 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #16 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #17 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #18 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #19 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #20 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #21 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #22 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #23 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #24 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > select #25 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > lighting soft > view orient > view orient > ui tool show ""Side View"" > view orient > movie record > turn y 2 180 > wait 180 > movie encode /Users/rebeckasepela/Desktop/movie4.mp4 Movie saved to /Users/rebeckasepela/Desktop/movie4.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/rebeckasepela/Desktop/movie5.mp4 Movie saved to /Users/rebeckasepela/Desktop/movie5.mp4 > save ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/1A3COOHBC.cxs"" ——— End of log from Tue Oct 17 13:52:20 2023 ——— opened ChimeraX session > select #25 19 atoms, 21 bonds, 1 residue, 1 model selected > ~select #25 1 model selected > select #26 19 atoms, 21 bonds, 1 residue, 1 model selected > surface sel > ~select #26 1 model selected > movie record > turn y 2 180 > wait 180 > movie encode /Users/rebeckasepela/Desktop/movie7.mp4 Movie saved to /Users/rebeckasepela/Desktop/movie7.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/rebeckasepela/Desktop/movie8.mp4 Movie saved to /Users/rebeckasepela/Desktop/movie8.mp4 > save ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/1A3COOHBC.cxs"" > open ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652dc8b556b921542b73c2d8-1234THH3CA/protein_no_ligands.pdb"" Summary of feedback from opening /Users/rebeckasepela/Library/CloudStorage/OneDrive- HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule files/neurosnap-652dc8b556b921542b73c2d8-1234THH3CA/protein_no_ligands.pdb --- warnings | CONECT record to nonexistent atom: (450, 23925) CONECT record to nonexistent atom: (1297, 23911) CONECT record to nonexistent atom: (2991, 23952) CONECT record to nonexistent atom: (3076, 23979) CONECT record to nonexistent atom: (5232, 24109) 15 messages similar to the above omitted CONECT record for nonexistent atom: 23911 Cannot find LINK/SSBOND residue NAG (402 ) Cannot find LINK/SSBOND residue NAG (401 ) Cannot find LINK/SSBOND residue NAG (403 ) Cannot find LINK/SSBOND residue NAG (404 ) Cannot find LINK/SSBOND residue NAG (402 ) 15 messages similar to the above omitted protein_no_ligands.pdb title: Cryo-em structure of octopus sensory receptor CRT1 [more info...] Chain information for protein_no_ligands.pdb #27 --- Chain | Description A B C D E | octopus sensory receptor > close #27#1-26 > open ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652dc8b556b921542b73c2d8-1234THH3CA/protein_no_ligands.pdb"" > format pdb Summary of feedback from opening /Users/rebeckasepela/Library/CloudStorage/OneDrive- HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule files/neurosnap-652dc8b556b921542b73c2d8-1234THH3CA/protein_no_ligands.pdb --- warnings | CONECT record to nonexistent atom: (450, 23925) CONECT record to nonexistent atom: (1297, 23911) CONECT record to nonexistent atom: (2991, 23952) CONECT record to nonexistent atom: (3076, 23979) CONECT record to nonexistent atom: (5232, 24109) 15 messages similar to the above omitted CONECT record for nonexistent atom: 23911 Cannot find LINK/SSBOND residue NAG (402 ) Cannot find LINK/SSBOND residue NAG (401 ) Cannot find LINK/SSBOND residue NAG (403 ) Cannot find LINK/SSBOND residue NAG (404 ) Cannot find LINK/SSBOND residue NAG (402 ) 15 messages similar to the above omitted protein_no_ligands.pdb title: Cryo-em structure of octopus sensory receptor CRT1 [more info...] Chain information for protein_no_ligands.pdb #1 --- Chain | Description A B C D E | octopus sensory receptor > close > open ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652dc8b556b921542b73c2d8-1234THH3CA/protein_no_ligands.pdb"" Summary of feedback from opening /Users/rebeckasepela/Library/CloudStorage/OneDrive- HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule files/neurosnap-652dc8b556b921542b73c2d8-1234THH3CA/protein_no_ligands.pdb --- warnings | CONECT record to nonexistent atom: (450, 23925) CONECT record to nonexistent atom: (1297, 23911) CONECT record to nonexistent atom: (2991, 23952) CONECT record to nonexistent atom: (3076, 23979) CONECT record to nonexistent atom: (5232, 24109) 15 messages similar to the above omitted CONECT record for nonexistent atom: 23911 Cannot find LINK/SSBOND residue NAG (402 ) Cannot find LINK/SSBOND residue NAG (401 ) Cannot find LINK/SSBOND residue NAG (403 ) Cannot find LINK/SSBOND residue NAG (404 ) Cannot find LINK/SSBOND residue NAG (402 ) 15 messages similar to the above omitted protein_no_ligands.pdb title: Cryo-em structure of octopus sensory receptor CRT1 [more info...] Chain information for protein_no_ligands.pdb #1 --- Chain | Description A B C D E | octopus sensory receptor > open ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652dc8b556b921542b73c2d8-1234THH3CA/rank1_confidence-0.69.sdf"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/dialog.py"", line 155, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 179, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 421, in collated_open return func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/__init__.py"", line 25, in open return read_sdf(session, data, file_name, **kw) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 37, in read_sdf parse_v2000(session, file_name, lines, structures, auto_style) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 128, in parse_v2000 state, reading_data, indexed_charges, data_name, orig_data_name = read_data_line(s, state, File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 276, in read_data_line atoms[index].charge = charge IndexError: list index out of range IndexError: list index out of range File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 276, in read_data_line atoms[index].charge = charge See log for complete Python traceback. > open ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652dc8b556b921542b73c2d8-1234THH3CA/rank2_confidence-0.81.sdf"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/dialog.py"", line 155, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 179, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 421, in collated_open return func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/__init__.py"", line 25, in open return read_sdf(session, data, file_name, **kw) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 37, in read_sdf parse_v2000(session, file_name, lines, structures, auto_style) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 128, in parse_v2000 state, reading_data, indexed_charges, data_name, orig_data_name = read_data_line(s, state, File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 276, in read_data_line atoms[index].charge = charge IndexError: list index out of range IndexError: list index out of range File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 276, in read_data_line atoms[index].charge = charge See log for complete Python traceback. > open ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652dc8b556b921542b73c2d8-1234THH3CA/rank1.sdf"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/dialog.py"", line 155, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 179, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 421, in collated_open return func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/__init__.py"", line 25, in open return read_sdf(session, data, file_name, **kw) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 37, in read_sdf parse_v2000(session, file_name, lines, structures, auto_style) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 128, in parse_v2000 state, reading_data, indexed_charges, data_name, orig_data_name = read_data_line(s, state, File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 276, in read_data_line atoms[index].charge = charge IndexError: list index out of range IndexError: list index out of range File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 276, in read_data_line atoms[index].charge = charge See log for complete Python traceback. > close > open ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/protein_no_ligands.pdb"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank1_confidence-0.71.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank2_confidence-0.72.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank3_confidence-0.76.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank4_confidence-0.82.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank5_confidence-0.85.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank6_confidence-0.86.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank7_confidence-0.90.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank8_confidence-0.92.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank9_confidence-0.93.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank10_confidence-0.98.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank11_confidence-1.01.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank12_confidence-1.03.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank13_confidence-1.05.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank14_confidence-1.05.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank15_confidence-1.05.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank16_confidence-1.15.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank17_confidence-1.16.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank18_confidence-1.17.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank19_confidence-1.19.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank20_confidence-1.19.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank21_confidence-1.21.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank22_confidence-1.25.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank23_confidence-1.27.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank24_confidence-1.33.sdf"" > ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/rank25_confidence-1.38.sdf"" Summary of feedback from opening /Users/rebeckasepela/Library/CloudStorage/OneDrive- HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule files/neurosnap-652eca0a56b921542b73c3d2-1M3COOHBC/protein_no_ligands.pdb --- warnings | CONECT record to nonexistent atom: (450, 23925) CONECT record to nonexistent atom: (1297, 23911) CONECT record to nonexistent atom: (2991, 23952) CONECT record to nonexistent atom: (3076, 23979) CONECT record to nonexistent atom: (5232, 24109) 15 messages similar to the above omitted CONECT record for nonexistent atom: 23911 Cannot find LINK/SSBOND residue NAG (402 ) Cannot find LINK/SSBOND residue NAG (401 ) Cannot find LINK/SSBOND residue NAG (403 ) Cannot find LINK/SSBOND residue NAG (404 ) Cannot find LINK/SSBOND residue NAG (402 ) 15 messages similar to the above omitted protein_no_ligands.pdb title: Cryo-em structure of octopus sensory receptor CRT1 [more info...] Chain information for protein_no_ligands.pdb #1 --- Chain | Description A B C D E | octopus sensory receptor PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 PubChem entry 5406157 > show surfaces > select #2 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel No atoms specified by sel > select #2 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #3 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #4 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #5 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #6 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #7 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #8 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #9 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #10 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #11 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select#12 Unknown command: select#12 > select #12 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #13 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #14 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select#15 Unknown command: select#15 > select #15 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #16 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #17 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #18 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #19 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #20 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #21 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #22 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #23 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #24 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #25 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > select #26 17 atoms, 19 bonds, 1 residue, 1 model selected > surface sel > ~select #26 1 model selected > lighting soft > ui tool show ""Side View"" > movie record > turn y 2 180 > wait 180 > movie encode /Users/rebeckasepela/Desktop/movie1.mp4 Movie saved to /Users/rebeckasepela/Desktop/movie1.mp4 > save ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/1M3COOHBC.cxs"" > lighting soft > save ""/Users/rebeckasepela/Library/CloudStorage/OneDrive- > HarvardUniversity/microbes/Crabs and Eggs/Diffdock/Molecule > files/1M3COOHBC.png"" width 553 height 638 supersample 3 > close #1-26 > open > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/protein_no_ligands.pdb > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank1_confidence-0.69.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank2_confidence-0.81.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank3_confidence-0.86.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank4_confidence-0.97.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank5_confidence-0.97.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank6_confidence-0.98.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank7_confidence-1.01.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank8_confidence-1.04.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank9_confidence-1.08.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank10_confidence-1.14.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank11_confidence-1.14.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank12_confidence-1.18.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank13_confidence-1.19.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank14_confidence-1.20.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank15_confidence-1.22.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank16_confidence-1.22.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank17_confidence-1.27.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank18_confidence-1.32.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank19_confidence-1.33.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank20_confidence-1.37.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank21_confidence-1.47.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank22_confidence-1.56.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank23_confidence-1.57.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank24_confidence-1.65.sdf > /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/rank25_confidence-1.66.sdf Summary of feedback from opening /Users/rebeckasepela/Downloads/neurosnap-652dc8b556b921542b73c2d8-2/protein_no_ligands.pdb --- warnings | CONECT record to nonexistent atom: (450, 23925) CONECT record to nonexistent atom: (1297, 23911) CONECT record to nonexistent atom: (2991, 23952) CONECT record to nonexistent atom: (3076, 23979) CONECT record to nonexistent atom: (5232, 24109) 15 messages similar to the above omitted CONECT record for nonexistent atom: 23911 Cannot find LINK/SSBOND residue NAG (402 ) Cannot find LINK/SSBOND residue NAG (401 ) Cannot find LINK/SSBOND residue NAG (403 ) Cannot find LINK/SSBOND residue NAG (404 ) Cannot find LINK/SSBOND residue NAG (402 ) 15 messages similar to the above omitted Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/dialog.py"", line 155, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 200, in provider_open models, status = collated_open(session, None, [data], fi.data_format, _add_models, log_errors, File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 421, in collated_open return func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/__init__.py"", line 25, in open return read_sdf(session, data, file_name, **kw) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 37, in read_sdf parse_v2000(session, file_name, lines, structures, auto_style) File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 128, in parse_v2000 state, reading_data, indexed_charges, data_name, orig_data_name = read_data_line(s, state, File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 276, in read_data_line atoms[index].charge = charge IndexError: list index out of range IndexError: list index out of range File ""/Applications/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/sdf/sdf.py"", line 276, in read_data_line atoms[index].charge = charge See log for complete Python traceback. OpenGL version: 4.1 INTEL-22.1.27 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2020.0.1.0.0 (iBridge: 21.16.365.0.0,0) OS Loader Version: 580~439 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 5 hours, 28 minutes Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL ST2220L: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: G25N628U087L Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Adapter Firmware Version: 15.30 Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.4.1 chardet: 3.0.4 ChimeraX-AddCharge: 1.0 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.3 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.3 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.2 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.4 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.7 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.0 matplotlib: 3.3.2 matplotlib-inline: 0.1.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 File attachment: rank1_confidence-0.69.sdf }}} [attachment:""rank1_confidence-0.69.sdf""] " defect closed normal Input/Output fixed all ChimeraX