Opened 18 months ago

Closed 18 months ago

#15027 closed defect (not a bug)

Update atomic bundle

Reported by: nm7155@… Owned by: pett
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
where to update atomic bundle

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/interaction.cxs"

> To restore session:
>
>   * update Atomic bundle to version 1.56 or newer (have 1.49.1)
>

Unable to restore session: need to update bundle  

> open "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/10.pdb"

Summary of feedback from opening D:/Studies/NM_Research/Helix/Cupric
cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
gui-1337438842/gromacs/10.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
10.pdb title:  
Title t= 10000.00000 step= 5000000 [more info...]  
  
Chain information for 10.pdb #1  
---  
Chain | Description  
A C E G I K M O | No description available  
B D F H J L N P | No description available  
  
Non-standard residues in 10.pdb #1  
---  
CTHR — (CTHR)  
CU — (CU)  
NGLN — (NGLN)  
NHID — (nhid)  
NILE — (nile)  
  

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> lighting soft

> graphics silhouettes true

> ui tool show "Color Actions"

> open "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/100.pdb"

Summary of feedback from opening D:/Studies/NM_Research/Helix/Cupric
cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
gui-1337438842/gromacs/100.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
100.pdb title:  
Title t= 100000.00000 step= 50000000 [more info...]  
  
Chain information for 100.pdb #2  
---  
Chain | Description  
A C E G I K M O | No description available  
B D F H J L N P | No description available  
  
Non-standard residues in 100.pdb #2  
---  
CTHR — (CTHR)  
CU — (CU)  
NGLN — (NGLN)  
NHID — (nhid)  
NILE — (nile)  
  

> select

17486 atoms, 17534 bonds, 1216 residues, 2 models selected  

> ui tool show "Color Actions"

> select protein

17390 atoms, 17534 bonds, 1120 residues, 2 models selected  

> color sel cornflower blue

> hide sel atoms

> show sel cartoons

> hide #2 models

> ui mousemode right select

> select clear

[Repeated 1 time(s)]

> cd "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs"

Current working directory is: D:\Studies\NM_Research\Helix\Cupric
cation_insulin\Trial3\insulin_fibril_50mM_cucl2_wo_water\charmm-
gui-1337438842\gromacs  

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/50_1.png" width 12000 height 7687 supersample 4
> transparentBackground true

> show #2 models

> hide #1 models

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/100_1.png" width 12000 height 7687 supersample 4
> transparentBackground true

> select clear

> select protein

17390 atoms, 17534 bonds, 1120 residues, 2 models selected  

> color sel light gray

> select clear

> select ::name="CU"

96 atoms, 96 residues, 2 models selected  

> color sel magenta

> select clear

[Repeated 1 time(s)]

> select #2/N:21

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #4/?:21,24,26

Nothing selected  

> select clear

> select #4/?:21,24,26

Nothing selected  

> select #4/?:21,24,26

Nothing selected  

> select #4/?:21

Nothing selected  

> show #2 atoms

> undo

> select clear

> select #2/N:21

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2/N:21,24,26

56 atoms, 55 bonds, 3 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 56 atom styles  

> hide sel cartoons

> select clear

> select #2/N:21,24,26

56 atoms, 55 bonds, 3 residues, 1 model selected  

> view sel

> select clear

> select #2/N:21,24,26

56 atoms, 55 bonds, 3 residues, 1 model selected  

> color sel cornflower blue

> color sel byhetero

> select clear

> select #2/?:56@CU

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> style sel stick

Changed 1 atom style  

> select clear

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/21,24,26.png" width 12000 height 7687 supersample 4
> transparentBackground true

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/21,24,26.png" width 12000 height 7687 supersample 4
> transparentBackground true

> select

17486 atoms, 17534 bonds, 1216 residues, 2 models selected  

> view sel

Drag select of 3 atoms, 16 residues  

> select clear

> select protein

17390 atoms, 17534 bonds, 1120 residues, 2 models selected  

> hide sel & #2 atoms

> select clear

> select #2/E:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select clear

Drag select of 3 residues  

> select clear

Drag select of 2 residues  

> select #2/E:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 34 atom styles  

> select #2/E:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select clear

Drag select of 2 atoms, 2 residues, 2 bonds  

> show sel cartoons

> hide sel atoms

> select clear

[Repeated 1 time(s)]Drag select of 3 atoms, 2 residues, 2 bonds  

> select clear

> select #2/G:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select clear

Drag select of 1 residues  

> show sel atoms

> style sel ball

Changed 15 atom styles  

> select clear

> select #2/G:18

30 atoms, 28 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 30 atom styles  

> select #2@@serial_number=2624

1 atom, 1 residue, 1 model selected  

> color sel byhetero

> select #2@@serial_number=2624

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 2 time(s)]Drag select of 3 atoms  

> hide sel atoms

Drag select of 2 atoms  

> hide sel atoms

> select #2/?:62@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

Drag select of 1 atoms  

> hide sel atoms

> select clear

> select #2@@serial_number=3727

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #2@@serial_number=3732

1 atom, 1 residue, 1 model selected  

> hide sel atoms

Drag select of 2 atoms, 2 bonds  

> hide sel atoms

Drag select of 2 atoms, 1 bonds  
Drag select of 3 atoms, 2 bonds  

> hide sel atoms

> select clear

> select #2@@serial_number=3736

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #2@@serial_number=3733

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #2/?:89@CU

1 atom, 1 residue, 1 model selected  

> select #2/?:85@CU

1 atom, 1 residue, 1 model selected  

> show sel atoms

> select #2/?:59@CU

1 atom, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #2@@serial_number=3712

1 atom, 1 residue, 1 model selected  

> color sel byhetero

> color sel cornflower blue

> color sel byhetero

Drag select of 10 atoms, 5 residues, 9 bonds  

> color sel byhetero

> color sel cornflower blue target a

> color sel byhetero target a

Drag select of 15 atoms, 11 residues, 13 bonds  

> color sel cornflower blue target a

> color sel byhetero target a

> select clear

[Repeated 1 time(s)]Drag select of 11 atoms, 7 residues, 10 bonds  

> show sel cartoons

> hide sel atoms

> select #2/G:18

30 atoms, 28 bonds, 2 residues, 1 model selected  

> select clear

Drag select of 1 atoms, 1 residues  

> show sel atoms

> style sel ball

Changed 15 atom styles  

> hide sel cartoons

> select clear

> select #2@@serial_number=3712

1 atom, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #2/G:19

21 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select clear

> undo

[Repeated 2 time(s)]

> select clear

> select #2@@serial_number=3712

1 atom, 1 residue, 1 model selected  
Drag select of 17 atoms, 8 residues, 18 bonds  

> hide sel cartoons

> show sel cartoons

> select #2@@serial_number=3727

1 atom, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/17,17,18.png" width 12000 height 7687 supersample 4
> transparentBackground true

Drag select of 1 atoms  

> select #2/A:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select #2/C:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select protein

17390 atoms, 17534 bonds, 1120 residues, 2 models selected  

> hide sel & #2 atoms

> select #2/A:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 34 atom styles  
Drag select of 15 atoms, 7 residues, 13 bonds  

> hide sel atoms

> select #2/C:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select #2@@serial_number=452

1 atom, 1 residue, 1 model selected  

> color sel cornflower blue target a

> color sel light gray target a

> color sel byhetero target c

> color sel cornflower blue target c

> color sel byhetero target c

> color sel cornflower blue target ac

> select clear

Drag select of 7 atoms, 14 residues, 8 bonds  

> select clear

Drag select of 9 atoms, 15 residues, 9 bonds  

> color sel byhetero target ac

Drag select of 1 residues  
Drag select of 3 atoms  

> hide sel atoms

Drag select of 1 atoms  

> hide sel atoms

Drag select of 1 atoms, 2 residues  

> hide sel atoms

> select #2/C:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 34 atom styles  

> select clear

> select #2/C:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> color sel cornflower blue target ac

> color sel byhetero target ac

Drag select of 15 atoms, 5 residues, 13 bonds  

> hide sel atoms

Drag select of 5 residues  

> color sel light gray target ac

> select clear

[Repeated 1 time(s)]

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/6_dative.png" width 12000 height 7687 supersample 4
> transparentBackground true

Drag select of 1 residues  
Drag select of 20 atoms, 47 residues, 18 bonds  

> select

17486 atoms, 17534 bonds, 1216 residues, 2 models selected  

> show sel & #2 atoms

> select protein

17390 atoms, 17534 bonds, 1120 residues, 2 models selected  

> hide sel & #2 atoms

> select clear

> select protein

17390 atoms, 17534 bonds, 1120 residues, 2 models selected  

> color sel light gray target ac

Drag select of 1 residues  

> select clear

Drag select of 1 atoms, 5 residues  

> select #2/E:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

Drag select of 3 residues  

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> show sel atoms

Drag select of 1 residues  

> undo

[Repeated 1 time(s)]

> select protein

17390 atoms, 17534 bonds, 1120 residues, 2 models selected  

> show sel & #2 cartoons

Drag select of 17 atoms, 24 residues, 13 bonds  

> hide sel atoms

> select clear

> select #2/G:18

30 atoms, 28 bonds, 2 residues, 1 model selected  

> select #2/G:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 34 atom styles  

> select clear

[Repeated 1 time(s)]

> select #2@@serial_number=3712

1 atom, 1 residue, 1 model selected  

> select #2/G:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select #2/G:18

30 atoms, 28 bonds, 2 residues, 1 model selected  

> select #2/G:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> show sel atoms

Drag select of 12 atoms, 10 residues, 13 bonds  

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select clear

[Repeated 1 time(s)]Drag select of 1 residues  
Drag select of 3 residues  

> select clear

[Repeated 1 time(s)]

> select #2/C:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 34 atom styles  

> select #2/A:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 34 atom styles  

> select clear

> select #2/?:96@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #2/?:100@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #2/?:61@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #2/?:71@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

Drag select of 21 atoms, 15 residues, 18 bonds  
[Repeated 1 time(s)]

> color sel byhetero target ac

> select clear

[Repeated 1 time(s)]

> select #2/?:68@CU

1 atom, 1 residue, 1 model selected  

> color sel magenta target ac

Drag select of 21 atoms, 6 residues, 18 bonds  

> select clear

Drag select of 21 atoms, 8 residues, 18 bonds  

> color sel cornflower blue target a

> select #2/?:68@CU

1 atom, 1 residue, 1 model selected  

> color sel magenta target a

Drag select of 21 atoms, 8 residues, 18 bonds  

> color sel byhetero target a

> select #2/?:68@CU

1 atom, 1 residue, 1 model selected  

> color sel magenta target a

> select clear

Drag select of 21 atoms, 7 residues, 18 bonds  

> select #2/A:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select #2/A:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> view sel

> select clear

[Repeated 1 time(s)]

> select #2/A:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> style sel stick

Changed 34 atom styles  

> select #2/C:17

34 atoms, 32 bonds, 2 residues, 1 model selected  

> style sel stick

Changed 34 atom styles  

> select clear

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/6_dative.png" width 12000 height 7687 supersample 4
> transparentBackground true

> select

17486 atoms, 17534 bonds, 1216 residues, 2 models selected  

> view sel

Drag select of 6 residues  

> select ::name="CU"

96 atoms, 96 residues, 2 models selected  

> show sel & #2 atoms

> select clear

Drag select of 2 residues  
[Repeated 1 time(s)]Drag select of 3 residues  
Drag select of 1 residues  

> select clear

> select nucleic-acid

Nothing selected  

> select protein

17390 atoms, 17534 bonds, 1120 residues, 2 models selected  

> hide sel & #2 atoms

Drag select of 4 atoms, 1 residues  

> hide sel atoms

Drag select of 1 atoms, 1 residues  

> hide sel atoms

> select #2/A:16

40 atoms, 39 bonds, 2 residues, 1 model selected  

> close session

> open "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/interaction.cxs"

> To restore session:
>
>   * update Atomic bundle to version 1.56 or newer (have 1.49.1)
>

Unable to restore session: need to update bundle  

> open "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/100.pdb"

Summary of feedback from opening D:/Studies/NM_Research/Helix/Cupric
cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
gui-1337438842/gromacs/100.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
100.pdb title:  
Title t= 100000.00000 step= 50000000 [more info...]  
  
Chain information for 100.pdb #1  
---  
Chain | Description  
A C E G I K M O | No description available  
B D F H J L N P | No description available  
  
Non-standard residues in 100.pdb #1  
---  
CTHR — (CTHR)  
CU — (CU)  
NGLN — (NGLN)  
NHID — (nhid)  
NILE — (nile)  
  

> select protein

8695 atoms, 8767 bonds, 560 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> color sel cornflower blue target a

> color sel medium aquamarine target ac

> color sel cornflower blue target ac

> select clear

[Repeated 1 time(s)]

> select ::name="CU"

48 atoms, 48 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 48 atom styles  

> color sel magenta target ac

> select clear

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/100_1.png" width 12000 height 7687 supersample 4
> transparentBackground true

> select ::name="CU"

48 atoms, 48 residues, 1 model selected  

> style sel sphere

Changed 48 atom styles  

> select clear

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/100_1.png" width 12000 height 7687 supersample 4
> transparentBackground true

> select ::name="CU"

48 atoms, 48 residues, 1 model selected  

> ui tool show "Selection Inspector"

> size sel atomRadius 0.58

Changed 48 atom radii  

> size sel atomRadius 0.59

Changed 48 atom radii  

> size sel atomRadius 0.6

Changed 48 atom radii  

> size sel atomRadius 0.61

Changed 48 atom radii  

> size sel atomRadius 0.62

Changed 48 atom radii  

> size sel atomRadius 0.63

Changed 48 atom radii  

> size sel atomRadius 0.64

Changed 48 atom radii  

> size sel atomRadius 0.65

Changed 48 atom radii  

> size sel atomRadius 0.66

Changed 48 atom radii  

> size sel atomRadius 0.67

Changed 48 atom radii  

> size sel atomRadius 0.68

Changed 48 atom radii  

> size sel atomRadius 0.69

Changed 48 atom radii  

> size sel atomRadius 0.7

Changed 48 atom radii  

> size sel atomRadius 0.71

Changed 48 atom radii  

> size sel atomRadius 0.72

Changed 48 atom radii  

> size sel atomRadius 0.73

Changed 48 atom radii  

> size sel atomRadius 0.74

Changed 48 atom radii  

> size sel atomRadius 0.75

Changed 48 atom radii  

> size sel atomRadius 0.76

Changed 48 atom radii  

> size sel atomRadius 0.77

Changed 48 atom radii  

> size sel atomRadius 0.78

Changed 48 atom radii  

> size sel atomRadius 0.79

Changed 48 atom radii  

> size sel atomRadius 0.8

Changed 48 atom radii  

> size sel atomRadius 0.81

Changed 48 atom radii  

> size sel atomRadius 0.82

Changed 48 atom radii  

> size sel atomRadius 0.83

Changed 48 atom radii  

> size sel atomRadius 0.84

Changed 48 atom radii  

> size sel atomRadius 0.85

Changed 48 atom radii  

> size sel atomRadius 0.86

Changed 48 atom radii  

> size sel atomRadius 0.87

Changed 48 atom radii  

> size sel atomRadius 0.88

Changed 48 atom radii  

> size sel atomRadius 0.89

Changed 48 atom radii  

> size sel atomRadius 0.9

Changed 48 atom radii  

> size sel atomRadius 0.91

Changed 48 atom radii  

> size sel atomRadius 0.92

Changed 48 atom radii  

> size sel atomRadius 0.93

Changed 48 atom radii  

> size sel atomRadius 0.94

Changed 48 atom radii  

> size sel atomRadius 0.95

Changed 48 atom radii  

> size sel atomRadius 0.96

Changed 48 atom radii  

> size sel atomRadius 0.97

Changed 48 atom radii  

> size sel atomRadius 0.98

Changed 48 atom radii  

> size sel atomRadius 0.99

Changed 48 atom radii  

> size sel atomRadius 1

Changed 48 atom radii  

> size sel atomRadius 1.01

Changed 48 atom radii  

> size sel atomRadius 1.02

Changed 48 atom radii  

> size sel atomRadius 1.03

Changed 48 atom radii  

> size sel atomRadius 1.04

Changed 48 atom radii  

> size sel atomRadius 1.05

Changed 48 atom radii  

> size sel atomRadius 1.06

Changed 48 atom radii  

> size sel atomRadius 1.07

Changed 48 atom radii  

> size sel atomRadius 1.08

Changed 48 atom radii  

> size sel atomRadius 1.09

Changed 48 atom radii  

> size sel atomRadius 1.1

Changed 48 atom radii  

> size sel atomRadius 1.11

Changed 48 atom radii  

> size sel atomRadius 1.12

Changed 48 atom radii  

> size sel atomRadius 1.13

Changed 48 atom radii  

> size sel atomRadius 1.14

Changed 48 atom radii  

> size sel atomRadius 1.15

Changed 48 atom radii  

> size sel atomRadius 1.16

Changed 48 atom radii  

> size sel atomRadius 1.17

Changed 48 atom radii  

> size sel atomRadius 1.18

Changed 48 atom radii  

> size sel atomRadius 1.19

Changed 48 atom radii  

> size sel atomRadius 1.2

Changed 48 atom radii  

> size sel atomRadius 1.21

Changed 48 atom radii  

> size sel atomRadius 1.22

Changed 48 atom radii  

> size sel atomRadius 1.23

Changed 48 atom radii  

> size sel atomRadius 1.24

Changed 48 atom radii  

> size sel atomRadius 1.25

Changed 48 atom radii  

> size sel atomRadius 1.26

Changed 48 atom radii  

> size sel atomRadius 1.27

Changed 48 atom radii  

> size sel atomRadius 1.28

Changed 48 atom radii  

> size sel atomRadius 1.29

Changed 48 atom radii  

> size sel atomRadius 1.3

Changed 48 atom radii  

> size sel atomRadius 1.31

Changed 48 atom radii  

> size sel atomRadius 1.32

Changed 48 atom radii  

> size sel atomRadius 1.33

Changed 48 atom radii  

> size sel atomRadius 1.34

Changed 48 atom radii  

> size sel atomRadius 1.35

Changed 48 atom radii  

> size sel atomRadius 1.36

Changed 48 atom radii  

> size sel atomRadius 1.37

Changed 48 atom radii  

> size sel atomRadius 1.38

Changed 48 atom radii  

> size sel atomRadius 1.39

Changed 48 atom radii  

> size sel atomRadius 1.4

Changed 48 atom radii  

> size sel atomRadius 1.41

Changed 48 atom radii  

> size sel atomRadius 1.42

Changed 48 atom radii  

> size sel atomRadius 1.43

Changed 48 atom radii  

> size sel atomRadius 1.44

Changed 48 atom radii  

> size sel atomRadius 1.45

Changed 48 atom radii  

> size sel atomRadius 1.46

Changed 48 atom radii  

> size sel atomRadius 1.47

Changed 48 atom radii  

> size sel atomRadius 1.48

Changed 48 atom radii  

> size sel atomRadius 1.49

Changed 48 atom radii  

> size sel atomRadius 1.5

Changed 48 atom radii  

> size sel atomRadius 1.51

Changed 48 atom radii  

> size sel atomRadius 1.52

Changed 48 atom radii  

> size sel atomRadius 1.53

Changed 48 atom radii  

> size sel atomRadius 1.54

Changed 48 atom radii  

> size sel atomRadius 1.55

Changed 48 atom radii  

> size sel atomRadius 1.56

Changed 48 atom radii  
Drag select of 2 residues  

> ui tool show "Selection Inspector"

> size sel atomRadius 1

Changed 31 atom radii  

> select ::name="CU"

48 atoms, 48 residues, 1 model selected  

> size sel atomRadius 1

Changed 48 atom radii  

> select clear

[Repeated 1 time(s)]Drag select of 5 residues  

> select clear

> select /?:53@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select /?:90@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #2/?:59@CU

Nothing selected  

> select #2/?:59@CU

Nothing selected  

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

[Repeated 1 time(s)]

> lighting flat

[Repeated 1 time(s)]

> lighting full

> lighting soft

[Repeated 1 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> cofr frontCenter

> ui tool show "Selection Inspector"

> toolshed show

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> view orient

[Repeated 3 time(s)]

> ui tool show "Side View"

Drag select of 2 atoms, 4 residues  
Drag select of 71 residues  

> select clear

> ui tool show "Side View"

> select clear

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/100_1.png" width 12000 height 7628 supersample 4
> transparentBackground true

> view orient

> select /?:54@CU

1 atom, 1 residue, 1 model selected  

> select ::name="CU"

48 atoms, 48 residues, 1 model selected  

> style sel sphere

Changed 48 atom styles  

> style sel stick

Changed 48 atom styles  

> style sel sphere

Changed 48 atom styles  

> style sel sphere

Changed 48 atom styles  

> style sel ball

Changed 48 atom styles  

> style sel sphere

Changed 48 atom styles  

> select clear

> select /?:98@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select /?:61@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select /?:96@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select /?:69@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/100_1.png" width 12000 height 7687 supersample 4
> transparentBackground true

> open "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/10.pdb"

Summary of feedback from opening D:/Studies/NM_Research/Helix/Cupric
cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
gui-1337438842/gromacs/10.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
10.pdb title:  
Title t= 10000.00000 step= 5000000 [more info...]  
  
Chain information for 10.pdb #2  
---  
Chain | Description  
A C E G I K M O | No description available  
B D F H J L N P | No description available  
  
Non-standard residues in 10.pdb #2  
---  
CTHR — (CTHR)  
CU — (CU)  
NGLN — (NGLN)  
NHID — (nhid)  
NILE — (nile)  
  

> open "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/step4_input.pdb"

Chain information for step4_input.pdb #3  
---  
Chain | Description  
? | No description available  
  

> select add #1

8743 atoms, 8767 bonds, 608 residues, 1 model selected  

> select add #2

17486 atoms, 17534 bonds, 1216 residues, 2 models selected  

> select subtract #1

8743 atoms, 8767 bonds, 608 residues, 1 model selected  

> select add #3

17871 atoms, 17798 bonds, 1361 residues, 2 models selected  

> select protein

26349 atoms, 26565 bonds, 1704 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> ui tool show "Color Actions"

> color sel cornflower blue target ac

> select ::name="CU"

144 atoms, 144 residues, 3 models selected  

> color sel magenta target ac

> select add #1

8839 atoms, 8767 bonds, 704 residues, 3 models selected  

> select subtract #1

96 atoms, 96 residues, 2 models selected  

> select add #2

8791 atoms, 8767 bonds, 656 residues, 2 models selected  

> select add #3

17871 atoms, 17798 bonds, 1361 residues, 2 models selected  

> select subtract #2

9128 atoms, 9031 bonds, 753 residues, 1 model selected  

> select subtract #3

Nothing selected  

> hide #2 models

> hide #1 models

> hide #3 models

> show #2 models

> select ::name="CU"

144 atoms, 144 residues, 3 models selected  

> style sel & #2 sphere

Changed 48 atom styles  

> select clear

> select #2/?:53@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #2/?:65@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #2/?:69@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/50_1.png" width 12000 height 7687 supersample 4
> transparentBackground true

> select add #2

8743 atoms, 8767 bonds, 608 residues, 1 model selected  

> select subtract #2

Nothing selected  

> hide #2 models

> show #3 models

> select ::name="CL-"

96 atoms, 96 residues, 1 model selected  

> hide sel atoms

> select ::name="K+"

25 atoms, 25 residues, 1 model selected  

> hide sel atoms

> select ::name="CU"

144 atoms, 144 residues, 3 models selected  

> style sel & #3 sphere

Changed 48 atom styles  

> show sel & #3 atoms

> style sel & #3 sphere

Changed 48 atom styles  

> select ::name="CU"

144 atoms, 144 residues, 3 models selected  

> select clear

[Repeated 1 time(s)]

> select ::name="CU"

144 atoms, 144 residues, 3 models selected  

> style sel & #3 stick

Changed 48 atom styles  

> style sel & #3 sphere

Changed 48 atom styles  

> select clear

> select ::name="CU"

144 atoms, 144 residues, 3 models selected  

> ui tool show "Selection Inspector"

> size sel atomRadius 2

Changed 144 atom radii  

> select clear

> select #3/?:64@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #3/?:61@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #3/?:45@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #3/?:57@CU

1 atom, 1 residue, 1 model selected  

> select clear

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/0_1.png" width 12000 height 7687 supersample 4
> transparentBackground true

> show #2 models

> hide #3 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> select ::name="CU"

144 atoms, 144 residues, 3 models selected  

> style sel & #2 sphere

Changed 48 atom styles  

> ui tool show "Selection Inspector"

> size sel atomRadius 1

Changed 144 atom radii  

> select clear

> select #2/?:80@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #2/?:98@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #2/?:96@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #2/?:100@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #2/?:75@CU

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> save "D:/Studies/NM_Research/Helix/Cupric
> cation_insulin/Trial3/insulin_fibril_50mM_cucl2_wo_water/charmm-
> gui-1337438842/gromacs/50_1.png" width 12000 height 7687 supersample 4
> transparentBackground true

> toolshed show




OpenGL version: 3.3.0 NVIDIA 545.84
OpenGL renderer: NVIDIA GeForce RTX 3050 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_IN.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: LENOVO
Model: 82JW
OS: Microsoft Windows 11 Home Single Language (Build 22631)
Memory: 17,024,741,376
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800H with Radeon Graphics         
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 18 months ago

Cc: Greg Couch added
Component: Unassigned → Sessions
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Update atomic bundle

comment:2 by pett, 18 months ago

Resolution: → not a bug
Status: accepted → closed

Hi Nishant,

The Atomic bundle is shipped as part of the ChimeraX app, so to get a newer version you need to get a newer version of ChimeraX. The session you are trying to open must have been written from a ChimeraX daily build, so you will need to install the daily build in order to open it.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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