Opened 2 years ago

Closed 2 years ago

#10004 closed defect (fixed)

Reading SDF file: atoms[index].charge = charge IndexError: list index out of range

Reported by: rsepela@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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

rank1_confidence-0.69.sdf​

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rank1_confidence-0.69.sdf​ (4.3 KB ) - added by rsepela@… 2 years ago.
Added by email2trac

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Change History (3)

by rsepela@…, 2 years ago

Attachment: rank1_confidence-0.69.sdf​ added

Added by email2trac

comment:1 by Tom Goddard, 2 years ago

Component: Unassigned → Input/Output
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Reading SDF file: atoms[index].charge = charge IndexError: list index out of range

This appears to be a bad SDF file. The file list has 17 atoms but lists charges for 31 atoms. What code wrote that file?

The person who wrote the ChimeraX SDF reader is on vacation this week but can take a look next week and give a better analysis of the problem.

comment:2 by Eric Pettersen, 2 years ago

Resolution: → fixed
Status: assigned → closed

Yes, the charge section of the file has indices for atoms that don't exist in the file. Nonetheless, I have changed the SDF reader to warn about a bad charge section but still carry on with opening the structure, so if you get tomorrow's daily build you will be able to open this file.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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