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Opened 3 years ago
Last modified 3 years ago
#8850 feedback defect
Problem creating pseudobond group during session restore
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.3.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_gp17-gp18 Interaction2.cxs"
Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level
0.5, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Log from Mon Apr 17 17:14:38 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp13d-gp17-Interaction.cxs"
Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level
0.5, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Log from Mon Apr 17 15:22:23 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp13d-gp17-Interaction2.cxs"
Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level
0.5, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Log from Mon Apr 17 14:56:24 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp13d-gp17-Interaction.cxs"
Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level
0.5, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Log from Mon Apr 17 14:45:58 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp13d-gp17-Interaction.cxs"
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level
0.5, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Log from Mon Apr 17 13:40:26 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/13d-17-Interaction.cxs"
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level
0.5, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size
512,512,512, pixel 1.06, shown at level 0.3, step 1, values float32
Log from Mon Apr 17 13:31:58 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/01_tail_tip_colored.cxs"
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32
Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level
0.5, step 1, values float32
Log from Mon Apr 17 13:03:15 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/cryosparc_P2_J765_009_volume_map_sharp.mrc
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.06, shown at level 0.287, step 2, values float32
> open
> /Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/06_tail_tip_refined_real_space_refined_012_VV_SS.pdb
Chain information for 06_tail_tip_refined_real_space_refined_012_VV_SS.pdb #2
---
Chain | Description
A B C D E F G H I J K L M N O P Q R | No description available
a b c d e f g h i j k l | No description available
m n o p q r | No description available
s t u | No description available
v w x | No description available
> open
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/02_Tail_tip
> | Structures/03_Small Map | alphafold/00_Small_.mrc"
Opened 00_Small_.mrc as #3, grid size 512,512,512, pixel 1.06, shown at level
0.000118, step 2, values float32
> color #3 #941100ff models
> color #1 #d6d6d6ff models
> select /A-L
27168 atoms, 27768 bonds, 3600 residues, 1 model selected
No map chosen to save
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/06_gp13_12mer_ring_SS.pdb" selectedOnly true
> relModel #1
> select /M-R
13584 atoms, 13884 bonds, 1800 residues, 1 model selected
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/06_gp13d_6mer_ring_SS.pdb" selectedOnly true
> relModel #1
> select /m-r
14124 atoms, 14574 bonds, 1746 residues, 1 model selected
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/06_gp17_17mer_ring_SS.pdb" selectedOnly true
> relModel #1
> select /a-l
28464 atoms, 29268 bonds, 3732 residues, 1 model selected
> select /a,c,e,g,i,k
14232 atoms, 14634 bonds, 1866 residues, 1 model selected
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/06_gp23_ring_a_SS.pdb" selectedOnly true
> relModel #1
> select /b,d,f,h,j,l
14232 atoms, 14634 bonds, 1866 residues, 1 model selected
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/06_gp23_ring_b_SS.pdb" selectedOnly true
> relModel #1
> select clear
> select /s-u
13746 atoms, 14100 bonds, 1758 residues, 1 model selected
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/06_gp18_3mer_ring_SS.pdb" selectedOnly true
> relModel #1
> select /v-x
2592 atoms, 2649 bonds, 345 residues, 1 model selected
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/06_gp20_3mer_ring_SS.pdb" selectedOnly true
> relModel #1
> select add #2
99678 atoms, 102243 bonds, 12981 residues, 1 model selected
> select subtract #2
Nothing selected
> hide cartoons
> hide atoms
> volume #3 step 1
> volume #1 step 1
> set bgColor white
> set bgColor #ffffff00
> surface dust #1 size 10.6
> surface dust #3 size 10.6
> hide #2 models
> hide #!1 models
> volume #3 level 0.5
> volume #3 level 0.4
> volume #3 level 0.5
> show #2 models
> lighting depthCue false
> camera ortho
> show #!1 models
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> graphics silhouettes true
> hide #!1 models
> hide #!3 models
> hide #2 models
> show #2 models
> select add #2
99678 atoms, 102243 bonds, 12981 residues, 1 model selected
> hide #2 models
> select subtract #2
Nothing selected
> show #2 models
> show atoms
> show cartoons
> style ball
Changed 99678 atom styles
> style stick
Changed 99678 atom styles
> hide cartoons
> show cartoons
> hide atoms
> open
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/05_gp13_12mer_ring_SS.pdb"
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/05_gp13d_6mer_ring_SS.pdb"
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/05_gp17_6mer_ring_SS.pdb"
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/05_gp18_3mer_ring_SS.pdb"
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/05_gp20_3mer_ring_SS.pdb"
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/05_gp23_ring_a_SS.pdb"
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/05_gp23_ring_b_SS.pdb"
Summary of feedback from opening
/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip |
Interaction/03_TT | rings/05_gp13_12mer_ring_SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 56 56 PHE M 4
LYS M 8 1 5
Start residue of secondary structure not found: HELIX 57 57 ALA M 12 LEU M 14
1 3
Start residue of secondary structure not found: HELIX 58 58 ARG M 102 TRP M
109 1 8
Start residue of secondary structure not found: HELIX 59 59 PRO M 202 ARG M
205 1 4
Start residue of secondary structure not found: HELIX 60 60 VAL M 208 ALA M
211 1 4
709 messages similar to the above omitted
Summary of feedback from opening
/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip |
Interaction/03_TT | rings/05_gp13d_6mer_ring_SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4
LYS A 8 1 5
Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109
1 8
Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211
1 10
Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5
846 messages similar to the above omitted
Summary of feedback from opening
/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip |
Interaction/03_TT | rings/05_gp17_6mer_ring_SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4
LYS A 8 1 5
Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109
1 8
Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211
1 10
Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5
840 messages similar to the above omitted
Summary of feedback from opening
/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip |
Interaction/03_TT | rings/05_gp18_3mer_ring_SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4
LYS A 8 1 5
Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109
1 8
Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211
1 10
Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5
861 messages similar to the above omitted
Summary of feedback from opening
/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip |
Interaction/03_TT | rings/05_gp20_3mer_ring_SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4
LYS A 8 1 5
Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109
1 8
Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211
1 10
Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5
953 messages similar to the above omitted
Summary of feedback from opening
/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip |
Interaction/03_TT | rings/05_gp23_ring_a_SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4
LYS A 8 1 5
Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109
1 8
Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211
1 10
Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5
840 messages similar to the above omitted
Summary of feedback from opening
/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip |
Interaction/03_TT | rings/05_gp23_ring_b_SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4
LYS A 8 1 5
Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109
1 8
Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211
1 10
Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5
838 messages similar to the above omitted
Chain information for 05_gp13_12mer_ring_SS.pdb #4
---
Chain | Description
A B C D E F G H I J K L | No description available
Chain information for 05_gp13d_6mer_ring_SS.pdb #5
---
Chain | Description
M N O P Q R | No description available
Chain information for 05_gp17_6mer_ring_SS.pdb #6
---
Chain | Description
m n o p q r | No description available
Chain information for 05_gp18_3mer_ring_SS.pdb #7
---
Chain | Description
s t u | No description available
Chain information for 05_gp20_3mer_ring_SS.pdb #8
---
Chain | Description
v w x | No description available
Chain information for 05_gp23_ring_a_SS.pdb #9
---
Chain | Description
a c e g i k | No description available
Chain information for 05_gp23_ring_b_SS.pdb #10
---
Chain | Description
b d f h j l | No description available
> open
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/06_gp13d-gp17_model_SS.pdb"
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/06_gp13d-gp23_model_SS.pdb"
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/06_gp17-gp18_model_SS.pdb"
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/06_gp17-gp23_model_SS.pdb"
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/06_gp18-gp20_model_SS.pdb"
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_TT | rings/06_gp18-gp23_model_SS.pdb"
Summary of feedback from opening
/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip |
Interaction/03_TT | rings/06_gp13d-gp17_model_SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4
LYS A 8 1 5
Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109
1 8
Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211
1 10
Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5
704 messages similar to the above omitted
Summary of feedback from opening
/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip |
Interaction/03_TT | rings/06_gp13d-gp23_model_SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4
LYS A 8 1 5
Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109
1 8
Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211
1 10
Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5
560 messages similar to the above omitted
Summary of feedback from opening
/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip |
Interaction/03_TT | rings/06_gp17-gp18_model_SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4
LYS A 8 1 5
Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109
1 8
Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211
1 10
Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5
719 messages similar to the above omitted
Summary of feedback from opening
/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip |
Interaction/03_TT | rings/06_gp17-gp23_model_SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4
LYS A 8 1 5
Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109
1 8
Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211
1 10
Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5
554 messages similar to the above omitted
Summary of feedback from opening
/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip |
Interaction/03_TT | rings/06_gp18-gp20_model_SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4
LYS A 8 1 5
Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109
1 8
Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211
1 10
Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5
832 messages similar to the above omitted
Summary of feedback from opening
/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip |
Interaction/03_TT | rings/06_gp18-gp23_model_SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 4
LYS A 8 1 5
Start residue of secondary structure not found: HELIX 2 2 ALA A 12 LEU A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 102 TRP A 109
1 8
Start residue of secondary structure not found: HELIX 4 4 PRO A 202 ALA A 211
1 10
Start residue of secondary structure not found: HELIX 5 5 PHE B 4 LYS B 8 1 5
575 messages similar to the above omitted
Chain information for 06_gp13d-gp17_model_SS.pdb #11
---
Chain | Description
M N O P Q R | No description available
m n o p q r | No description available
Chain information for 06_gp13d-gp23_model_SS.pdb #12
---
Chain | Description
M N O P Q R | No description available
a b c d e f g h i j k l | No description available
Chain information for 06_gp17-gp18_model_SS.pdb #13
---
Chain | Description
m n o p q r | No description available
s t u | No description available
Chain information for 06_gp17-gp23_model_SS.pdb #14
---
Chain | Description
a b c d e f g h i j k l | No description available
m n o p q r | No description available
Chain information for 06_gp18-gp20_model_SS.pdb #15
---
Chain | Description
s t u | No description available
v w x | No description available
Chain information for 06_gp18-gp23_model_SS.pdb #16
---
Chain | Description
a b c d e f g h i j k l | No description available
s t u | No description available
> ui tool show "Color Actions"
> color dark gray
> color light gray
> color #2,4-16 #d6d6d6ff
> color #2,4-16 #ebebebff
> style ball
Changed 398118 atom styles
> show surfaces
> show #!3 models
> show #!1 models
> ui tool show "Color Actions"
> color #ffffffff
> color #ebebebff
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting soft
> lighting simple
> lighting soft
> hide #!1 models
> hide #!3 models
> select /A-L
54336 atoms, 55536 bonds, 7200 residues, 2 models selected
> color (#!2,4 & sel) light gray
> select /M-R
54336 atoms, 55536 bonds, 7200 residues, 4 models selected
> ui tool show "Color Actions"
> color sel gold
> select /v-x
7776 atoms, 7947 bonds, 1035 residues, 3 models selected
> color sel orange red
> select /s-u
68730 atoms, 70500 bonds, 8790 residues, 5 models selected
> color sel deep sky blue
> color sel cornflower blue
> select /m-r
84204 atoms, 86754 bonds, 10530 residues, 6 models selected
> select /m, o, q
42102 atoms, 43377 bonds, 5265 residues, 6 models selected
> color sel deep pink
> color sel hot pink
> select /n, p, r
42102 atoms, 43377 bonds, 5265 residues, 6 models selected
> color sel blue violet
> select /s-u
68730 atoms, 70500 bonds, 8790 residues, 5 models selected
> color sel deep sky blue
> select /a,c,e,g,i,k
84744 atoms, 87054 bonds, 11130 residues, 6 models selected
> select /a
14124 atoms, 14509 bonds, 1855 residues, 6 models selected
> select add #2
111430 atoms, 114313 bonds, 14525 residues, 12 models selected
> select subtract #2
11752 atoms, 12070 bonds, 1544 residues, 52 models selected
> select add #12
51428 atoms, 52783 bonds, 6765 residues, 10 models selected
> select subtract #12
9380 atoms, 9631 bonds, 1233 residues, 26 models selected
> select add #4
34284 atoms, 35085 bonds, 4533 residues, 8 models selected
> select subtract #4
7116 atoms, 7317 bonds, 933 residues, 18 models selected
> select add #9
18976 atoms, 19512 bonds, 2488 residues, 6 models selected
> select subtract #9
4744 atoms, 4878 bonds, 622 residues, 10 models selected
> select add #9
18976 atoms, 19512 bonds, 2488 residues, 5 models selected
> select /a
14124 atoms, 14509 bonds, 1855 residues, 6 models selected
> select add #4
39028 atoms, 39963 bonds, 5155 residues, 12 models selected
> select subtract #4
11860 atoms, 12195 bonds, 1555 residues, 22 models selected
> select add #2
109166 atoms, 111999 bonds, 14225 residues, 10 models selected
> select subtract #2
9488 atoms, 9756 bonds, 1244 residues, 50 models selected
> select /a,c,e,g,i,k
84744 atoms, 87054 bonds, 11130 residues, 6 models selected
> select add #4
98328 atoms, 100938 bonds, 12930 residues, 42 models selected
> select subtract #4
71160 atoms, 73170 bonds, 9330 residues, 47 models selected
> select add #2
156606 atoms, 160779 bonds, 20445 residues, 35 models selected
> select subtract #2
56928 atoms, 58536 bonds, 7464 residues, 70 models selected
> color sel chartreuse
> select /b,d,f,h,j,l
84744 atoms, 87054 bonds, 11130 residues, 6 models selected
> select add #4
98328 atoms, 100938 bonds, 12930 residues, 42 models selected
> select subtract #4
71160 atoms, 73170 bonds, 9330 residues, 47 models selected
> select add #2
156606 atoms, 160779 bonds, 20445 residues, 35 models selected
> select subtract #2
56928 atoms, 58536 bonds, 7464 residues, 70 models selected
> color sel tomato
> color sel dark orange
> color sel orange
> color sel light salmon
> color sel green yellow
> color sel gold
> color sel yellow
> color sel coral
> color sel azure
> color sel cyan
> color sel orange
> show #!1 models
> show #!3 models
> view orient
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/01_tail_tip_colored.cxs" includeMaps true
——— End of log from Mon Apr 17 13:03:15 2023 ———
opened ChimeraX session
> turn x -90
> view
> hide #!16 models
> select add #16
84906 atoms, 87270 bonds, 11088 residues, 4 models selected
> select add #14
113262 atoms, 116478 bonds, 14700 residues, 19 models selected
> select subtract #16
71052 atoms, 73110 bonds, 9210 residues, 36 models selected
> select subtract #14
28464 atoms, 29268 bonds, 3732 residues, 20 models selected
> select add #12
56280 atoms, 57786 bonds, 7398 residues, 2 models selected
> select subtract #12
14232 atoms, 14634 bonds, 1866 residues, 19 models selected
> select add #10
14232 atoms, 14634 bonds, 1866 residues, 1 model selected
> hide #!15 models
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> select add #10
14232 atoms, 14634 bonds, 1866 residues, 1 model selected
> select subtract #10
Nothing selected
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!1 models
> select #2/a,c,e,g,i,k
14232 atoms, 14634 bonds, 1866 residues, 1 model selected
> show #!9 models
> hide #!9 models
> ui tool show "Color Actions"
> color sel lime
> color sel lawn green
> show #!9 models
> hide #!2 models
> show #!2 models
> select #2/b,d,f,h,j,l
14232 atoms, 14634 bonds, 1866 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orange
> select clear
> show #!1 models
> hide #!9 models
> select add #2
99678 atoms, 102243 bonds, 12981 residues, 1 model selected
> select subtract #2
42 models selected
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> ui tool show "Color Zone"
> color zone #1 near #2 distance 6.37
> color zone #1 near #2 distance 6.3
> color zone #1 near #2 distance 6
[Repeated 1 time(s)]
> volume splitbyzone #1
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 0 as #17.1, grid size
512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 1 as #17.2, grid size
512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 2 as #17.3, grid size
512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 3 as #17.4, grid size
512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 4 as #17.5, grid size
512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 5 as #17.6, grid size
512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 6 as #17.7, grid size
512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 7 as #17.8, grid size
512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32
Opened cryosparc_P2_J765_009_volume_map_sharp.mrc 8 as #17.9, grid size
512,512,512, pixel 1.06, shown at level 0.287, step 1, values float32
> volume #1 level 0.3
> volume #17.1 level 0.3
> volume #17.2 level 0.3
> volume #17.3 level 0.3
> volume #17.4 level 0.3
> volume #17.5 level 0.3
> volume #17.6 level 0.3
> volume #17.7 level 0.3
> volume #17.8 level 0.3
> volume #17.9 level 0.3
> surface dust #17.2 size 10.6
> surface dust #17.3 size 10.6
> surface dust #17.4 size 10.6
> surface dust #17.5 size 10.6
> surface dust #17.6 size 10.6
> surface dust #17.7 size 10.6
> surface dust #17.8 size 10.6
> surface dust #17.9 size 10.6
> hide #!2 models
> lighting depthCue false
> view
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/02_tail_tip_split_maps.cxs"
> view
> hide #!17 models
> show #!6 models
> show #!5 models
> select add #5
13584 atoms, 13884 bonds, 1800 residues, 1 model selected
> hide #!5 models
> select subtract #5
6 models selected
> hide #!6 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!5 models
> select add #5
13584 atoms, 13884 bonds, 1800 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold
> select subtract #5
6 models selected
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!5-6 surfaces
> show #!5-6 cartoons
> hide #!5-6 atoms
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> select #6/q:39,73,131, 63,78,84,88,89,94,121 #6/r:40,54,56,59,284,288 |
> select #5/P:74,75,76,83
Expected a keyword
> hide #!5 models
> show #!5 models
> select #5/P:74,75,76,83 #6/p:124 #6/q:39,73,131, 63,78,84,88,89,94,121
> #6/r:40,54,56,59,284,288
210 atoms, 199 bonds, 21 residues, 2 models selected
> style sel ball
Changed 210 atom styles
> show sel atoms
> turn y 30
[Repeated 2 time(s)]
> turn y -30
> turn y 30
> color (#!5-6 & sel) byhetero
> ui tool show H-Bonds
> hbonds sel color #000000 dashes 10 restrict both twoColors true slopColor
> #000000 intraRes false select true reveal true
15 hydrogen bonds found
6 strict hydrogen bonds found
> rename #18 "hydrogen bonds gp13d-17"
> select clear
> select #5/M-O,Q,R
11320 atoms, 11570 bonds, 1500 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> ui tool show "Color Actions"
> color (#!5 & sel) #ebebebff
> select clear
> select #6/m-o
7062 atoms, 7287 bonds, 873 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> ui tool show "Color Actions"
> color (#!6 & sel) #ffffffff
> color (#!6 & sel) #ebebebff
> select clear
> hide #!17.6 models
> show #!17.6 models
> transparency #5.1-6#6.1-6#17.3.1#17.6.1#17.7.1 50
> transparency #5.1-6#6.1-6#17.3.1#17.6.1#17.7.1 0
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting full
> lighting soft
> lighting depthCue false
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/13d-17_Map.png" width 5000 height 4194 supersample 4
> hide #!17 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> select #6/m-o
7062 atoms, 7287 bonds, 873 residues, 1 model selected
> show sel surfaces
> lighting flat
> lighting soft
> hide sel cartoons
[Repeated 2 time(s)]
> select #6/m-o
7062 atoms, 7287 bonds, 873 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel surfaces
> select #5/M-O,Q,R
11320 atoms, 11570 bonds, 1500 residues, 1 model selected
> hide sel cartoons
> select add #5
13584 atoms, 13884 bonds, 1800 residues, 6 models selected
> select add #6
27708 atoms, 28458 bonds, 9 pseudobonds, 3546 residues, 9 models selected
> show sel cartoons
> select clear
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/13d-17_Cartoon.png" width 5000 height 4194 supersample 4
> select #5/M-O,Q,R
11320 atoms, 11570 bonds, 1500 residues, 1 model selected
> hide sel cartoons
> select #6/m-o
7062 atoms, 7287 bonds, 873 residues, 1 model selected
> hide sel cartoons
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/13d-17-Interaction.cxs"
——— End of log from Mon Apr 17 13:31:58 2023 ———
opened ChimeraX session
> ui mousemode right distance
> distance #6/q:121@OH #6/r:284@NH2
Distance between 05_gp17_6mer_ring_SS.pdb #6/q TYR 121 OH and /r ARG 284 NH2:
2.218Å
> distance #6/q:88@NE #6/r:40@OD1
Distance between 05_gp17_6mer_ring_SS.pdb #6/q ARG 88 NE and /r ASP 40 OD1:
3.630Å
> show #!1 models
> hide #!1 models
> hide #19.1 models
> color #19 #212121ff models
> color #19 black models
> ui tool show Distances
> distance style color black
[Repeated 2 time(s)]
> distance style dashes 8
[Repeated 2 time(s)]
> distance style radius 0.08
[Repeated 2 time(s)]
> rename #19 "distances gp17-gp17"
> show #!13 models
> show #!12 models
> hide #!13 models
> hide #!12 models
> show #!11 models
> view
> view orient
> turn x -90
> turn y 90
> hide #!11 models
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp13d-gp17-Interaction.cxs"
——— End of log from Mon Apr 17 13:40:26 2023 ———
opened ChimeraX session
> hide #!17.6 models
> hide #!17.7 models
> show #!17.7 models
> show #!17.6 models
> view orient
> turn x -90
> turn y 90
> hide #!17.6 models
> hide #!17.7 models
> hide #!17.3 models
> close #1
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp13d-gp17-Interaction.cxs"
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp13d-gp17_Interaction.png" width 5000 height 4194 supersample
> 4
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp13d-gp17_Interaction2.png" width 5000 height 4194
> supersample 4
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp13d-gp17-Interaction2.cxs"
> view
> show #!17.3 models
> show #!17.6 models
> show #!17.7 models
> view
> view orient
> turn x -90
> hide #!17 models
> hide #!17.3 models
> show #!17.3 models
> turn y 90
> hide #!17.3 models
> hide #!17.6 models
> hide #!17.7 models
> show #!17.7 models
> show #!17.6 models
> hide #!17.6 models
> show #!17.6 models
> hide #!17.7 models
> show #!17.7 models
> hide #!17.6 models
> hide #!17.7 models
> show #!17.6 models
> hide #!17.6 models
> show #!17.6 models
> transparency #5.1-6#6.1-6#17.6.1 50
> transparency #5.1-6#6.1-6#17.6.1 0
> hide #!17.6 models
> view
> view orient
> show #!17.6 models
> hide #!17.6 models
> show #!17.6 models
> show #!17.7 models
> show #!17.3 models
> view orient
> turn x -90
> turn y 90
> hide #!17.6 models
> hide #!17.7 models
> hide #!17.3 models
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/13d-17_Cartoon__.png" width 5000 height 4194 supersample 4
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp13d-gp17-Interaction.cxs"
> show #!17.7 models
> show #!17.6 models
> show #!17.5 models
> hide #!17.5 models
> show #!17.8 models
> hide #!17.8 models
> show #!17.3 models
> view
> show #!17.8 models
> view
> hide #!17.8 models
> hide #!17.7 models
> hide #!17.6 models
> hide #!17.3 models
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp13d-gp17-Interaction.cxs"
——— End of log from Mon Apr 17 14:45:58 2023 ———
opened ChimeraX session
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/02_gp13d-gp17_cartoon_image.png" width 5000 height 4194
> supersample 4
> show sel surfaces
> hide sel surfaces
> transparency c 30
Missing or invalid "percent" argument: Expected a number
> transparency 30 cartoons
> transparency 50 cartoons
> transparency 50 r
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 50
> transparency 0 cartoons
> transparency 10 cartoons
> transparency 90 cartoons
[Repeated 1 time(s)]
> transparency 70 cartoons
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/02_gp13d-gp17_Int3.png" width 4000 height 3355 supersample 4
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/02_gp13d-gp17_Int1.png" width 4000 height 3355 supersample 4
> turn y 10
> turn y -30
[Repeated 1 time(s)]
> turn y 15
> turn y -15
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/02_gp13d-gp17_Int2.png" width 4000 height 3355 supersample 4
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp13d-gp17-Interaction2.cxs"
——— End of log from Mon Apr 17 14:56:24 2023 ———
opened ChimeraX session
> show #!17.7 models
> show #!17.6 models
> show #!17.5 models
> hide #!17.5 models
> show #!17.3 models
> view orient
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> turn x -90
> transparency #5.1-6#6.1-6#17.3.1#17.6.1#17.7.1 0
> turn y 90
> lighting depthCue false
> hide #!17.7 models
> hide #!17.6 models
> hide #!17.3 models
> show #!17.8 models
> show #!17.7 models
> show #!17.6 models
> show #!17.5 models
> show #!17.4 models
> hide #!17.4 models
> hide #!17.5 models
> show #!17.3 models
> transparency #5.1-6#6.1-6#17.3.1#17.6.1#17.7.1#17.8.1 0
> view
> hide #!17.8 models
> hide #!17.6 models
> hide #!17.3 models
> hide #!17.7 models
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp13d-gp17-Interaction.cxs"
——— End of log from Mon Apr 17 15:22:23 2023 ———
opened ChimeraX session
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> show #!7 models
> hide sel atoms
> hide sel cartoons
> hide #!5 models
> show #!5 models
> hide #!6 models
> select add #6
14124 atoms, 14574 bonds, 11 pseudobonds, 1746 residues, 3 models selected
> select subtract #6
6 models selected
> show #!6 models
> hide #!5-7 cartoons
> show #!5-7 cartoons
> hide #!5-7 atoms
> hide #!5-7 surfaces
> hide #!19 models
> hide #18 models
> show #!17.7 models
> show #!17.6 models
> show #!17.4 models
> hide #!17.4 models
> show #!17.5 models
> hide #!17.5 models
> show #!17.3 models
> show #!17.8 models
> view
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/01_gp13d-gp17-gp18_full_map.png" width 5000 height 4194
> supersample 4
> hide #!17.6 models
> hide #!17.7 models
> hide #!17.8 models
> hide #!17 models
> hide #!17.3 models
> hide #!5 models
> select #6/q:44,198,275,151,176,248 #6/p:51,52,199,248
> #7/s:382,459,518,519,364, 365,368,435,24,21 /u:
> 368,62,45,128,137,194,98,89,139,244
285 atoms, 268 bonds, 30 residues, 2 models selected
> show sel atoms
> select #7/t
4582 atoms, 4700 bonds, 586 residues, 1 model selected
> hide sel cartoons
> select #7/s
4582 atoms, 4700 bonds, 586 residues, 1 model selected
> color (#!7 & sel) light gray
> select clear
> turn y 30
[Repeated 1 time(s)]
> select #7/s
4582 atoms, 4700 bonds, 586 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> select #7/t
4582 atoms, 4700 bonds, 586 residues, 1 model selected
> show sel cartoons
> color sel sky blue
> color sel light sky blue
> color sel powder blue
> color sel silver
> color sel light cyan
> color sel green yellow
> color sel cyan
> color sel chartreuse
> hide sel cartoons
> select #6/q:44,198,275,151,176,248 #6/p:51,52,199,248
> #7/s:382,459,518,519,364, 365,368,435,24,21 /u:
> 368,62,45,128,137,194,98,89,139,244
285 atoms, 268 bonds, 30 residues, 2 models selected
> show sel atoms
> color (#!6-7 & sel) byhetero
> ui tool show H-Bonds
> hbonds sel color #000000 dashes 10 restrict both twoColors true slopColor
> #000000 intraRes false select true reveal true
13 hydrogen bonds found
7 strict hydrogen bonds found
> rename #1 id #20
> rename #20 "hydrogen bonds gp17-gp18"
> hide #!6 models
> select add #6
14140 atoms, 14574 bonds, 12 pseudobonds, 1759 residues, 9 models selected
> select add #7
27870 atoms, 28674 bonds, 21 pseudobonds, 3504 residues, 13 models selected
> select subtract #6
13746 atoms, 14100 bonds, 9 pseudobonds, 1758 residues, 11 models selected
> select subtract #7
3 models selected
> show #!6 models
> show #!6-7 cartoons
> select #7/t
4582 atoms, 4700 bonds, 586 residues, 1 model selected
> color sel royal blue
> color sel navy
> hide sel cartoons
> turn y -30
> select #6/m-r
14124 atoms, 14574 bonds, 12 pseudobonds, 1746 residues, 4 models selected
> hide sel cartoons
> show sel cartoons
> select #6/m-o,r
9416 atoms, 9716 bonds, 1164 residues, 1 model selected
> hide sel cartoons
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!13 models
> hide #!13 models
> show #!17.7 models
> show #!17.6 models
> show #!17.3 models
> show #!17.8 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> turn y 90
> view
> hide #!17.8 models
> hide #!17.7 models
> hide #!17.6 models
> hide #!17.3 models
> hide #!17 models
> turn y 30
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> turn y 30
> turn y -30
[Repeated 1 time(s)]
> select #6/p
2354 atoms, 2429 bonds, 291 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #6/r
2354 atoms, 2429 bonds, 291 residues, 1 model selected
> show sel cartoons
> select clear
> hide #!6-7 atoms
> select #6/q:44,198,275,151,176,248 #6/r: 51,52,199,248
> #7/s:382,459,518,519,364, 365,368,435,24,21, 368,62,45 /u:
> 128,137,194,98,89,139,244
271 atoms, 253 bonds, 12 pseudobonds, 29 residues, 3 models selected
> show sel atoms
> close #20
> color (#!6-7 & sel) byhetero
> ui tool show H-Bonds
> hbonds sel color #000000 dashes 10 restrict both twoColors true slopColor
> #000000 intraRes false select true reveal true
13 hydrogen bonds found
6 strict hydrogen bonds found
> rename #1 "hydrogen bonds gp17-gp18"
> rename #1 id #20
> hide #20 models
> show #20 models
> select clear
> select #6/q:44,198,275,151,176,248 #6/r:51,52,199,248
> #7/s:382,459,518,519,364, 365,368,435,24,21, 368,62,45,272 /u:
> 128,137,194,98,89,139,244
279 atoms, 260 bonds, 13 pseudobonds, 30 residues, 3 models selected
> show sel atoms
> color (#!6-7 & sel) byhetero
> hide sel atoms
> select #6/q:44,198,275,151,176,248 #6/r:51,52,199,248
> #7/s:382,459,518,519,364, 365,368,435,24,21, 368,62,45 /u:
> 128,137,194,98,89,139,244
271 atoms, 253 bonds, 13 pseudobonds, 29 residues, 3 models selected
> show sel atoms
> select #6/q:44,198,275,151,176,248 #6/r:51,52,60,199,248
> #7/s:382,459,518,519,364, 365,368,435,24,21, 368,62,45 /u:
> 128,137,194,98,89,139,244
282 atoms, 263 bonds, 13 pseudobonds, 30 residues, 3 models selected
> show sel atoms
> select #6/q:44,198,275,151,176,248 #6/r:51,52,60,199,248
> #7/s:382,459,518,519,364,365,368,435,24,21, 368,62,45,539 /u:
> 128,137,194,98,89,139,244
290 atoms, 270 bonds, 13 pseudobonds, 31 residues, 3 models selected
> show sel atoms
> hide sel atoms
> select #6/q:44,198,275,151,176,248 #6/r:51,52,60,199,248
> #7/s:382,459,518,519,364,365,368,435,24,21, 368,62,539 /u:
> 128,137,194,98,89,139,244
279 atoms, 260 bonds, 13 pseudobonds, 30 residues, 3 models selected
> show sel atoms
> close #20
> ui tool show H-Bonds
> hbonds sel color #000000 dashes 10 restrict both twoColors true slopColor
> #000000 intraRes false select true reveal true
13 hydrogen bonds found
6 strict hydrogen bonds found
> select clear
> ui mousemode right distance
> distance #7/u:194@NH2 #7/s:459@OE2
Distance between 05_gp18_3mer_ring_SS.pdb #7/u ARG 194 NH2 and /s GLU 459 OE2:
2.224Å
> distance #7/s:364@NH2 #6/q:248@OD1
Distance between 05_gp18_3mer_ring_SS.pdb #7/s ARG 364 NH2 and
05_gp17_6mer_ring_SS.pdb #6/q ASP 248 OD1: 3.104Å
> distance #7/s:62@NH1 #6/r:248@OD1
Distance between 05_gp18_3mer_ring_SS.pdb #7/s ARG 62 NH1 and
05_gp17_6mer_ring_SS.pdb #6/r ASP 248 OD1: 2.924Å
> select #6/q:44,198,275,151,176,248 #6/r:51,52,60,199,248
> #7/s:382,459,518,519,364,365,368,435,24,21, 368,62,539 /u:
> 128,137,194,98,89,139,244
279 atoms, 260 bonds, 16 pseudobonds, 30 residues, 4 models selected
> color (#!6-7 & sel) byhetero
> select clear
> distance #7/s:539@OD1 #6/r:60@NH1
Distance between 05_gp18_3mer_ring_SS.pdb #7/s ASN 539 OD1 and
05_gp17_6mer_ring_SS.pdb #6/r ARG 60 NH1: 3.148Å
> show #!17.3 models
> show #!17.5 models
> hide #!17.5 models
> show #!17.6 models
> show #!17.7 models
> view orient
> show #!17.8 models
> view orient
> view
> turn x -90
> view
> turn y 90
> hide #!7 models
> hide #!6 models
> show #!6 models
> show #!7 models
> hide #!17 models
> hide #!17.3 models
> hide #!17.6 models
> hide #!17.7 models
> hide #!17.8 models
> rename #20 id #21
> rename #1 id #20
> rename #20 "hydrogen bonds gp17-gp18"
> rename #21 "distances gp18-gp18"
> color #21 #212121ff models
> color #21 black models
> ui tool show Distances
> distance style color black
[Repeated 2 time(s)]
> distance style dashes 8
[Repeated 2 time(s)]
> distance style radius 0.08
[Repeated 2 time(s)]
> color #21.1 black models
> rename #21 distances
Another pseudobond group is already named 'distances'
> select add #21
4 pseudobonds, 2 models selected
> ui tool show Distances
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 626, in clear_status
if s.apc_status_label.text() == s.apc_status_tip:
RuntimeError: wrapped C/C++ object of type QLabel has been deleted
RuntimeError: wrapped C/C++ object of type QLabel has been deleted
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 626, in clear_status
if s.apc_status_label.text() == s.apc_status_tip:
See log for complete Python traceback.
> select subtract #21
Nothing selected
> select add #21.1
1 model selected
> select subtract #21.1
Nothing selected
> hide #21.1 models
> show #!15 models
> show #!14 models
> hide #!14 models
> hide #!15 models
> show #!17.3 models
> show #!17.6 models
> show #!17.7 models
> show #!17.8 models
> view
> hide #!17.8 models
> hide #!17.7 models
> hide #!17.6 models
> hide #!17.3 models
> turn y 45
> turn y -45
[Repeated 1 time(s)]
> turn y 45
[Repeated 2 time(s)]
> turn y -45
[Repeated 1 time(s)]
> view orient
> turn x -90
> turn y 90
> show #!17.3 models
> show #!17.7 models
> show #!17.8 models
> show #!17.6 models
> view
> hide #!17.8 models
> hide #!17.7 models
> hide #!17.6 models
> hide #!17.3 models
> show #!17.3 models
> hide #!17.3 models
> show #!17.3 models
> hide #!17.3 models
> select #6/p
2354 atoms, 2429 bonds, 291 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> select clear
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp17-gp18_interaction.cxs"
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_gp17-gp18_int1.png" width 5000 height 4194 supersample 4
> distance #6/q:151@OE2 #7/s:21@NZ
Distance between 05_gp17_6mer_ring_SS.pdb #6/q GLU 151 OE2 and
05_gp18_3mer_ring_SS.pdb #7/s LYS 21 NZ: 3.896Å
> hide #!21 models
> show #!21 models
> distance #6/q:151@OE2 #7/s:21@NZ
Distance already exists; modify distance properties with 'distance style'
> show #21.1 models
> hide #21.1 models
> ui tool show Distances
> distance style dashes 8
[Repeated 1 time(s)]
> distance style color #212121
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> ~distance #6/q:151@OE2 #7/s:21@NZ
[Repeated 6 time(s)]
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_gp17-gp18_Int1.png" width 5000 height 4194 supersample 4
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/gp17-gp18_interaction1.cxs"
[Repeated 1 time(s)]
——— End of log from Mon Apr 17 17:14:38 2023 ———
opened ChimeraX session
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dist_monitor/monitor.py", line 106, in _changes_handler
pbg = pb.group
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 100, in get_prop
return astype(v.value)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ctypes_support.py", line 69, in pseudobond_group
return PseudobondGroupData.c_ptr_to_py_inst(p)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 2326, in <lambda>
class_obj.c_ptr_to_py_inst = lambda ptr, *, fname=func_name: c_function(fname,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 29, in __init__
session = s.session
AttributeError: 'NoneType' object has no attribute 'session'
Error processing trigger "changes":
AttributeError: 'NoneType' object has no attribute 'session'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 29, in __init__
session = s.session
See log for complete Python traceback.
Exception ignored in: <function Drawing.__del__ at 0x1014dc820>
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1199, in __del__
if not self.was_deleted:
AttributeError: 'PseudobondGroup' object has no attribute 'was_deleted'
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_gp17-gp18_Int1.png" width 5000 height 4194 supersample 4
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_gp17-gp18_Int2.png" width 5000 height 4194 supersample 4
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_gp17-gp18 Interaction2.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 245, in include_state
self._python_instances = [[inst for inst in inst_func(self.session)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 245, in <listcomp>
self._python_instances = [[inst for inst in inst_func(self.session)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2504, in <lambda>
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 49, in python_instances_of_class
return [x for x in instances if filt(x)]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 49, in <listcomp>
return [x for x in instances if filt(x)]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 44, in <lambda>
filt = lambda x: (not x.group.structure) or x.group.structure.id
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 100, in get_prop
return astype(v.value)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ctypes_support.py", line 69, in pseudobond_group
return PseudobondGroupData.c_ptr_to_py_inst(p)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 2326, in <lambda>
class_obj.c_ptr_to_py_inst = lambda ptr, *, fname=func_name: c_function(fname,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 29, in __init__
session = s.session
AttributeError: 'NoneType' object has no attribute 'session'
AttributeError: 'NoneType' object has no attribute 'session'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 29, in __init__
session = s.session
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 245, in include_state
self._python_instances = [[inst for inst in inst_func(self.session)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 245, in <listcomp>
self._python_instances = [[inst for inst in inst_func(self.session)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2504, in <lambda>
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 49, in python_instances_of_class
return [x for x in instances if filt(x)]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 49, in <listcomp>
return [x for x in instances if filt(x)]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 44, in <lambda>
filt = lambda x: (not x.group.structure) or x.group.structure.id
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 100, in get_prop
return astype(v.value)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ctypes_support.py", line 69, in pseudobond_group
return PseudobondGroupData.c_ptr_to_py_inst(p)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 2326, in <lambda>
class_obj.c_ptr_to_py_inst = lambda ptr, *, fname=func_name: c_function(fname,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 29, in __init__
session = s.session
AttributeError: 'NoneType' object has no attribute 'session'
AttributeError: 'NoneType' object has no attribute 'session'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 29, in __init__
session = s.session
See log for complete Python traceback.
> save
> "/Users/jitendramaharana/Desktop/02_Douge/02_CryoEM/04_Tail_tip/03_Tail_tip
> | Interaction/03_gp17-gp18 Interaction2.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 245, in include_state
self._python_instances = [[inst for inst in inst_func(self.session)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 245, in <listcomp>
self._python_instances = [[inst for inst in inst_func(self.session)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2504, in <lambda>
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 49, in python_instances_of_class
return [x for x in instances if filt(x)]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 49, in <listcomp>
return [x for x in instances if filt(x)]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 44, in <lambda>
filt = lambda x: (not x.group.structure) or x.group.structure.id
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 100, in get_prop
return astype(v.value)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ctypes_support.py", line 69, in pseudobond_group
return PseudobondGroupData.c_ptr_to_py_inst(p)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 2326, in <lambda>
class_obj.c_ptr_to_py_inst = lambda ptr, *, fname=func_name: c_function(fname,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 29, in __init__
session = s.session
AttributeError: 'NoneType' object has no attribute 'session'
AttributeError: 'NoneType' object has no attribute 'session'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 29, in __init__
session = s.session
See log for complete Python traceback.
Exception ignored in: <function Drawing.__del__ at 0x1014dc820>
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1199, in __del__
if not self.was_deleted:
AttributeError: 'PseudobondGroup' object has no attribute 'was_deleted'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 245, in include_state
self._python_instances = [[inst for inst in inst_func(self.session)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 245, in <listcomp>
self._python_instances = [[inst for inst in inst_func(self.session)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2504, in <lambda>
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 49, in python_instances_of_class
return [x for x in instances if filt(x)]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 49, in <listcomp>
return [x for x in instances if filt(x)]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 44, in <lambda>
filt = lambda x: (not x.group.structure) or x.group.structure.id
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 100, in get_prop
return astype(v.value)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ctypes_support.py", line 69, in pseudobond_group
return PseudobondGroupData.c_ptr_to_py_inst(p)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 2326, in <lambda>
class_obj.c_ptr_to_py_inst = lambda ptr, *, fname=func_name: c_function(fname,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 29, in __init__
session = s.session
AttributeError: 'NoneType' object has no attribute 'session'
AttributeError: 'NoneType' object has no attribute 'session'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 29, in __init__
session = s.session
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGT3CT/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8422.100.650
OS Loader Version: 8422.100.650
Software:
System Software Overview:
System Version: macOS 13.3.1 (22E261)
Kernel Version: Darwin 22.4.0
Time since boot: 1 day, 23 hours, 50 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
biopython: 1.81
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-ArtiaX: 0.3
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-Cytoscape: 0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBImages: 1.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.1.10
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-StrudelScore: 0.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
geomdl: 5.3.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.4
mrcfile: 1.4.3
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
pandas: 1.5.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
recordtype: 1.4
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
starfile: 0.4.11
superqt: 0.4.1
tables: 3.7.0
threed-strudel: 0.9.18
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Problem creating pseudobond group during session restore |
comment:2 by , 3 years ago
| Status: | accepted → feedback |
|---|
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Hi Jitendra,
--Eric