Opened 3 years ago

Closed 3 years ago

#7394 closed defect (fixed)

Stop simulation: model is None

Reported by: a.m.borowska@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "G:/My Drive/Sodium binding sites paper/cryo-EM_map.cxc.cxc"

> set bgColor white

> lighting soft

> lighting depthCue true

> graphics silhouettes true

> open "G:\My Drive\Cryo-EM\data processing\ASCT2-2N2-gln
> NeCEN\final_final_final\cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc"

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc as #1, grid
size 240,240,240, pixel 0.836, shown at level 3.08, step 1, values float32  

> volume #1 level 3

> turn x 180

> open "G:\My Drive\Cryo-EM\model refinement\ASCT2-2N2-gln-
> NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb"

Summary of feedback from opening G:\My Drive\Cryo-EM\model
refinement\ASCT2-2N2-gln-NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
13367 messages similar to the above omitted  
  
Chain information for v3-isolde.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> select #2 /A-C:49-120,179-294

8721 atoms, 8790 bonds, 564 residues, 1 model selected  

> color sel yellow

> select #2 /A-C:121-178,295-488

11268 atoms, 11367 bonds, 756 residues, 1 model selected  

> color sel blue

> hide #!2 models

> color zone #1 near #2 distance 4

> volume splitbyzone #1

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 0 as #3.1,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 1 as #3.2,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 2 as #3.3,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 3 as #3.4,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 4 as #3.5,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 5 as #3.6,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 6 as #3.7,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 7 as #3.8,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  

> volume #3.1 transparency 75

executed cryo-EM_map.cxc.cxc  

> volume #1 level 3.481

> volume #3.1 color #b2b2b2

> volume #3.1 color white

> volume #3.1 color #e7e7e7

> close session

> open "G:/My Drive/Sodium binding sites paper/cryo-EM_map.cxc.cxc"

> set bgColor white

> lighting soft

> lighting depthCue true

> graphics silhouettes true

> open "G:\My Drive\Cryo-EM\data processing\ASCT2-2N2-gln
> NeCEN\final_final_final\cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc"

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc as #1, grid
size 240,240,240, pixel 0.836, shown at level 3.08, step 1, values float32  

> volume #1 level 3

> turn x 180

> open "G:\My Drive\Cryo-EM\model refinement\ASCT2-2N2-gln-
> NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb"

Summary of feedback from opening G:\My Drive\Cryo-EM\model
refinement\ASCT2-2N2-gln-NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
13367 messages similar to the above omitted  
  
Chain information for v3-isolde.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> select #2 /A-C:49-120,179-294

8721 atoms, 8790 bonds, 564 residues, 1 model selected  

> color sel yellow

> select #2 /A-C:121-178,295-488

11268 atoms, 11367 bonds, 756 residues, 1 model selected  

> color sel blue

> hide #!2 models

> color zone #1 near #2 distance 4

> volume splitbyzone #1

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 0 as #3.1,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 1 as #3.2,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 2 as #3.3,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 3 as #3.4,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 4 as #3.5,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 5 as #3.6,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 6 as #3.7,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 7 as #3.8,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  

> volume #3.1 color #e7e7e7 transparency 25

executed cryo-EM_map.cxc.cxc  

> close session

> open "G:/My Drive/Sodium binding sites paper/cryo-EM_map.cxc.cxc"

> set bgColor white

> lighting soft

> lighting depthCue true

> graphics silhouettes true

> open "G:\My Drive\Cryo-EM\data processing\ASCT2-2N2-gln
> NeCEN\final_final_final\cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc"

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc as #1, grid
size 240,240,240, pixel 0.836, shown at level 3.08, step 1, values float32  

> volume #1 level 3

> turn x 180

> open "G:\My Drive\Cryo-EM\model refinement\ASCT2-2N2-gln-
> NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb"

Summary of feedback from opening G:\My Drive\Cryo-EM\model
refinement\ASCT2-2N2-gln-NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
13367 messages similar to the above omitted  
  
Chain information for v3-isolde.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> select #2 /A-C:49-120,179-294

8721 atoms, 8790 bonds, 564 residues, 1 model selected  

> color sel yellow

> select #2 /A-C:121-178,295-488

11268 atoms, 11367 bonds, 756 residues, 1 model selected  

> color sel blue

> hide #!2 models

> color zone #1 near #2 distance 4

> volume splitbyzone #1

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 0 as #3.1,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 1 as #3.2,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 2 as #3.3,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 3 as #3.4,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 4 as #3.5,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 5 as #3.6,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 6 as #3.7,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 7 as #3.8,
grid size 240,240,240, pixel 0.836, shown at level 3, step 1, values float32  

> volume #3.1 color #e7e7e7

executed cryo-EM_map.cxc.cxc  

> volume #1 level 1.174

> volume #1 level 2.327

> volume #1 level 2.5

> ui tool show "Color Actions"

> close session

> open "G:/My Drive/Sodium binding sites paper/cryo-EM_map.cxc.cxc"

> set bgColor white

> lighting soft

> lighting depthCue true

> graphics silhouettes true

> open "G:\My Drive\Cryo-EM\data processing\ASCT2-2N2-gln
> NeCEN\final_final_final\cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc"

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc as #1, grid
size 240,240,240, pixel 0.836, shown at level 3.08, step 1, values float32  

> volume #1 level 2.5

> turn x 90

> open "G:\My Drive\Cryo-EM\model refinement\ASCT2-2N2-gln-
> NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb"

Summary of feedback from opening G:\My Drive\Cryo-EM\model
refinement\ASCT2-2N2-gln-NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
13367 messages similar to the above omitted  
  
Chain information for v3-isolde.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> select #2 /A-C:49-120,179-294

8721 atoms, 8790 bonds, 564 residues, 1 model selected  

> color sel yellow

> select #2 /A-C:121-178,295-488

11268 atoms, 11367 bonds, 756 residues, 1 model selected  

> color sel blue

> hide #!2 models

> color zone #1 near #2 distance 4

> volume splitbyzone #1

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 0 as #3.1,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 1 as #3.2,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 2 as #3.3,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 3 as #3.4,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 4 as #3.5,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 5 as #3.6,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 6 as #3.7,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 7 as #3.8,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  

> volume #3.1 color #e7e7e7 transparency 50

executed cryo-EM_map.cxc.cxc  

> close session

> open "G:/My Drive/Sodium binding sites paper/cryo-EM_map.cxc.cxc"

> set bgColor white

> lighting soft

> lighting depthCue true

> graphics silhouettes true

> open "G:\My Drive\Cryo-EM\data processing\ASCT2-2N2-gln
> NeCEN\final_final_final\cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc"

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc as #1, grid
size 240,240,240, pixel 0.836, shown at level 3.08, step 1, values float32  

> volume #1 level 2.5

> turn x 90

> open "G:\My Drive\Cryo-EM\model refinement\ASCT2-2N2-gln-
> NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb"

Summary of feedback from opening G:\My Drive\Cryo-EM\model
refinement\ASCT2-2N2-gln-NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
13367 messages similar to the above omitted  
  
Chain information for v3-isolde.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> select #2 /A-C:49-120,179-294

8721 atoms, 8790 bonds, 564 residues, 1 model selected  

> color sel yellow

> select #2 /A-C:121-178,295-488

11268 atoms, 11367 bonds, 756 residues, 1 model selected  

> color sel blue

> hide #!2 models

> color zone #1 near #2 distance 4

> volume splitbyzone #1

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 0 as #3.1,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 1 as #3.2,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 2 as #3.3,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 3 as #3.4,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 4 as #3.5,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 5 as #3.6,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 6 as #3.7,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 7 as #3.8,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  

> volume #3.1 color #e7e7e7 transparency 0.5

executed cryo-EM_map.cxc.cxc  

> volume #!3.1-8 style surface

> hide #!3.1 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.1 models

> volume #!3.1-8 style mesh

> volume #!3.1-8 style surface

[Repeated 1 time(s)]

> volume #!3.1-8 style mesh

> volume #!3.1-8 style surface

> transparency #3.1.1#3.2.1#3.3.1#3.4.1#3.5.1#3.6.1#3.7.1#3.8.1 0

> transparency #3.1.1#3.2.1#3.3.1#3.4.1#3.5.1#3.6.1#3.7.1#3.8.1 50

> transparency #3.1.1#3.2.1#3.3.1#3.4.1#3.5.1#3.6.1#3.7.1#3.8.1 0

> transparency #3.1.1#3.2.1#3.3.1#3.4.1#3.5.1#3.6.1#3.7.1#3.8.1 50

> transparency #3.1.1#3.2.1#3.3.1#3.4.1#3.5.1#3.6.1#3.7.1#3.8.1 0

> close session

> open "G:/My Drive/Sodium binding sites paper/cryo-EM_map.cxc.cxc"

> set bgColor white

> lighting soft

> lighting depthCue true

> graphics silhouettes true

> open "G:\My Drive\Cryo-EM\data processing\ASCT2-2N2-gln
> NeCEN\final_final_final\cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc"

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc as #1, grid
size 240,240,240, pixel 0.836, shown at level 3.08, step 1, values float32  

> volume #1 level 2.5

> turn x 90

> open "G:\My Drive\Cryo-EM\model refinement\ASCT2-2N2-gln-
> NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb"

Summary of feedback from opening G:\My Drive\Cryo-EM\model
refinement\ASCT2-2N2-gln-NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
13367 messages similar to the above omitted  
  
Chain information for v3-isolde.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> select #2 /A-C:49-120,179-294

8721 atoms, 8790 bonds, 564 residues, 1 model selected  

> color sel yellow

> select #2 /A-C:121-178,295-488

11268 atoms, 11367 bonds, 756 residues, 1 model selected  

> color sel blue

> hide #!2 models

> color zone #1 near #2 distance 4

> volume splitbyzone #1

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 0 as #3.1,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 1 as #3.2,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 2 as #3.3,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 3 as #3.4,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 4 as #3.5,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 5 as #3.6,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 6 as #3.7,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 7 as #3.8,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  

> volume #3.1 color #e7e7e7 transparency 25

executed cryo-EM_map.cxc.cxc  

> volume #3.1 color #e7e7e7 transparency 100

> volume #3.1 color #e7e7e7 transparency 0

> volume #3.1 color #e7e7e7 transparency 1

> volume #3.1 color #e7e7e7 transparency 0.5

> volume #3.1 color #e7e7e7 transparency 0.25

> volume #3.1 color #e7e7e7 transparency 0

> volume #3.1 color #e7e7e7 transparency 0.8

> volume #3.1 color #e7e7e7 transparency 0.5

> volume #3.1 color #e7e7e7 transparency 0.8

> volume #3.1 color #e7e7e7 transparency 0.9

> volume #3.1 color #e7e7e7 transparency 1

> volume #3.1 color #e7e7e7 transparency 0.9

> volume #3.1 color #ffffff19

> volume #3.1 color #e7e7e7 transparency 1

> volume #3.1 color #e7e7e7 transparency 0.5

> volume #3.1 color #9090907f

> volume #3.1 color #e7e7e7 transparency 0.8

> volume #3.1 color #adadad32

> volume #3.1 color #96969632

> close session

> save C:\Users\aboro\Desktop\image2.png supersample 3

> open "G:/My Drive/Sodium binding sites paper/cryo-EM_map.cxc.cxc"

> set bgColor white

> lighting soft

> lighting depthCue true

> graphics silhouettes true

> open "G:\My Drive\Cryo-EM\data processing\ASCT2-2N2-gln
> NeCEN\final_final_final\cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc"

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc as #1, grid
size 240,240,240, pixel 0.836, shown at level 3.08, step 1, values float32  

> volume #1 level 2.5

> turn x 90

> open "G:\My Drive\Cryo-EM\model refinement\ASCT2-2N2-gln-
> NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb"

Summary of feedback from opening G:\My Drive\Cryo-EM\model
refinement\ASCT2-2N2-gln-NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
13367 messages similar to the above omitted  
  
Chain information for v3-isolde.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> select #2 /A-C:49-120,179-294

8721 atoms, 8790 bonds, 564 residues, 1 model selected  

> color sel yellow

> select #2 /A-C:121-178,295-488

11268 atoms, 11367 bonds, 756 residues, 1 model selected  

> color sel blue

> hide #!2 models

> color zone #1 near #2 distance 4

> volume splitbyzone #1

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 0 as #3.1,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 1 as #3.2,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 2 as #3.3,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 3 as #3.4,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 4 as #3.5,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 5 as #3.6,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 6 as #3.7,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 7 as #3.8,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  

> volume #3.1 color #969696 transparency 0.8

> save "G:\My Drive\Sodium binding sites paper\cryo-EM_map.png" supersample 3

executed cryo-EM_map.cxc.cxc  

> close session

> open "G:/My Drive/Sodium binding sites paper/cryo-EM_map.cxc.cxc"

> set bgColor white

> lighting soft

> lighting depthCue true

> graphics silhouettes true

> open "G:\My Drive\Cryo-EM\data processing\ASCT2-2N2-gln
> NeCEN\final_final_final\cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc"

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc as #1, grid
size 240,240,240, pixel 0.836, shown at level 3.08, step 1, values float32  

> volume #1 level 2.5

> turn x 90

> open "G:\My Drive\Cryo-EM\model refinement\ASCT2-2N2-gln-
> NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb"

Summary of feedback from opening G:\My Drive\Cryo-EM\model
refinement\ASCT2-2N2-gln-NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
13367 messages similar to the above omitted  
  
Chain information for v3-isolde.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> select #2 /A-C:49-120,179-294

8721 atoms, 8790 bonds, 564 residues, 1 model selected  

> color sel yellow

> select #2 /A-C:121-178,295-488

11268 atoms, 11367 bonds, 756 residues, 1 model selected  

> color sel blue

> hide #!2 models

> color zone #1 near #2 distance 4

> volume splitbyzone #1

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 0 as #3.1,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 1 as #3.2,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 2 as #3.3,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 3 as #3.4,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 4 as #3.5,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 5 as #3.6,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 6 as #3.7,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 7 as #3.8,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  

> volume #3.1 color #969696 transparency 0.8

> windowsize 2000 2000

QWindowsWindow::setGeometry: Unable to set geometry 2579x2198+92-1002 (frame:
2595x2237+84-1033) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1924x2141+92-1002 (frame:
1940x2180+84-1033) margins: 8, 31, 8, 8 minimum size: 422x465
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=504)))  

> save "G:\My Drive\Sodium binding sites paper\cryo-EM_map.png"
> transparentBackground

Missing "transparentBackground" keyword's argument  

> close session

> open "G:/My Drive/Sodium binding sites paper/cryo-EM_map.cxc.cxc"

> set bgColor white

> lighting soft

> lighting depthCue true

> graphics silhouettes true

> open "G:\My Drive\Cryo-EM\data processing\ASCT2-2N2-gln
> NeCEN\final_final_final\cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc"

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc as #1, grid
size 240,240,240, pixel 0.836, shown at level 3.08, step 1, values float32  

> volume #1 level 2.5

> turn x 90

> open "G:\My Drive\Cryo-EM\model refinement\ASCT2-2N2-gln-
> NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb"

Summary of feedback from opening G:\My Drive\Cryo-EM\model
refinement\ASCT2-2N2-gln-NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
13367 messages similar to the above omitted  
  
Chain information for v3-isolde.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> select #2 /A-C:49-120,179-294

8721 atoms, 8790 bonds, 564 residues, 1 model selected  

> color sel yellow

> select #2 /A-C:121-178,295-488

11268 atoms, 11367 bonds, 756 residues, 1 model selected  

> color sel blue

> hide #!2 models

> color zone #1 near #2 distance 4

> volume splitbyzone #1

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 0 as #3.1,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 1 as #3.2,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 2 as #3.3,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 3 as #3.4,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 4 as #3.5,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 5 as #3.6,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 6 as #3.7,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 7 as #3.8,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  

> volume #3.1 color #969696 transparency 0.8

> save "G:\My Drive\Sodium binding sites paper\cryo-EM_map.png"
> transparentBackground true

executed cryo-EM_map.cxc.cxc  

> close session

> open "G:/My Drive/Sodium binding sites paper/cryo-EM_map.cxc.cxc"

> set bgColor white

> lighting soft

> lighting depthCue true

> graphics silhouettes true

> open "G:\My Drive\Cryo-EM\data processing\ASCT2-2N2-gln
> NeCEN\final_final_final\cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc"

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc as #1, grid
size 240,240,240, pixel 0.836, shown at level 3.08, step 1, values float32  

> volume #1 level 2.5

> turn x 90

> open "G:\My Drive\Cryo-EM\model refinement\ASCT2-2N2-gln-
> NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb"

Summary of feedback from opening G:\My Drive\Cryo-EM\model
refinement\ASCT2-2N2-gln-NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
13367 messages similar to the above omitted  
  
Chain information for v3-isolde.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> select #2 /A-C:49-120,179-294

8721 atoms, 8790 bonds, 564 residues, 1 model selected  

> color sel #d9d9b7b70d0d

> select #2 /A-C:121-178,295-488

11268 atoms, 11367 bonds, 756 residues, 1 model selected  

> color sel #2d2d4b4b7373

> hide #!2 models

> color zone #1 near #2 distance 4

> volume splitbyzone #1

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 0 as #3.1,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 1 as #3.2,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 2 as #3.3,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 3 as #3.4,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 4 as #3.5,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 5 as #3.6,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 6 as #3.7,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 7 as #3.8,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  

> volume #3.1 color #969696 transparency 0.8

> save "G:\My Drive\Sodium binding sites paper\cryo-EM_map.png"
> transparentBackground true

executed cryo-EM_map.cxc.cxc  

> turn x 90

> close session

> open "G:/My Drive/Sodium binding sites paper/cryo-EM_map.cxc.cxc"

> set bgColor white

> lighting soft

> lighting depthCue true

> graphics silhouettes true

> open "G:\My Drive\Cryo-EM\data processing\ASCT2-2N2-gln
> NeCEN\final_final_final\cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc"

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc as #1, grid
size 240,240,240, pixel 0.836, shown at level 3.08, step 1, values float32  

> volume #1 level 2.5

> turn x 90

> open "G:\My Drive\Cryo-EM\model refinement\ASCT2-2N2-gln-
> NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb"

Summary of feedback from opening G:\My Drive\Cryo-EM\model
refinement\ASCT2-2N2-gln-NeCEN-v2\RealSpaceRefine_14\v3-isolde.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
13367 messages similar to the above omitted  
  
Chain information for v3-isolde.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> select #2 /A-C:49-120,179-294

8721 atoms, 8790 bonds, 564 residues, 1 model selected  

> color sel #d9d9b7b70d0d

> select #2 /A-C:121-178,295-488

11268 atoms, 11367 bonds, 756 residues, 1 model selected  

> color sel #2d2d4b4b7373

> hide #!2 models

> color zone #1 near #2 distance 4

> volume splitbyzone #1

Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 0 as #3.1,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 1 as #3.2,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 2 as #3.3,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 3 as #3.4,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 4 as #3.5,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 5 as #3.6,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 6 as #3.7,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  
Opened cryosparc_P43_J354_009_volume_map_phenix_autosharpen.mrc 7 as #3.8,
grid size 240,240,240, pixel 0.836, shown at level 2.5, step 1, values float32  

> volume #3.1 color #969696 transparency 0.8

> save "G:\My Drive\Sodium binding sites paper\cryo-
> EM_map_nanodisc_bottom.png" transparentBackground true

> turn x 90

> save "G:\My Drive\Sodium binding sites paper\cryo-EM_map_nanodisc_top.png"
> transparentBackground true

executed cryo-EM_map.cxc.cxc  

> volume #1 level 4.326

> hide #!1 models

> hide #!3 models

> show #!1 models

> volume #1 level 4.615

> volume #1 level 4.038

> volume #1 level 4

> open "G:/My Drive/Cryo-EM/data processing/ASCT2-2N2-gln
> NeCEN/final_final_final/run_ct18_half1_class001_unfil.mrc"

Opened run_ct18_half1_class001_unfil.mrc as #4, grid size 240,240,240, pixel
0.836, shown at level 0.011, step 1, values float32  

> volume #3.2 level 4.422

> hide #!1 models

> volume #4 level 0.01456

> open "G:/My Drive/Cryo-EM/data processing/ASCT2-2N2-gln
> NeCEN/final_final_final/1102_mask.mrc"

Opened 1102_mask.mrc as #5, grid size 240,240,240, pixel 0.836, shown at level
1, step 1, values float32  

> hide #!5 models

> show #!5 models

> volume #5 level 0.9093

> volume #5 level 1

> open "G:/My Drive/Cryo-EM/data processing/ASCT2-2N2-gln
> NeCEN/final_final_final/run_class001_unfil_localdeblur.mrc"

Opened run_class001_unfil_localdeblur.mrc as #6, grid size 240,240,240, pixel
0.836, shown at level 0.0229, step 1, values float32  

> volume #6 level 0.03037

> hide #!4 models

> hide #!5 models

> volume #6 level 0.03441

> close session

> open "G:/My Drive/Cryo-EM/model refinement/ASCT2-2N2-gln-
> NeCEN-v2/RealSpaceRefine_19/v6-chopped-retr-loop_real_space_refined_019.pdb"

Chain information for v6-chopped-retr-loop_real_space_refined_019.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> open "G:/My Drive/Cryo-EM/data processing/ASCT2-2N2-gln
> NeCEN/final_final_final/1112_postprocess.mrc"

Opened 1112_postprocess.mrc as #2, grid size 240,240,240, pixel 0.836, shown
at level 0.0224, step 1, values float32  

> clipper associate #2 toModel #1

Opened 1112_postprocess.mrc as #1.1.1.1, grid size 240,240,240, pixel 0.836,
shown at level 0.0399, step 1, values float32  
Chain information for v6-chopped-retr-loop_real_space_refined_019.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 48 residues in model #1.2 to IUPAC-IUB
standards.  

> volume #1.1.1.1 color #ffaaff

> volume style surface

> transparency 50

> volume #1.1.1.1 level 0.07064

> select /A

6546 atoms, 6600 bonds, 4 pseudobonds, 436 residues, 3 models selected  

> ui tool show "Ramachandran Plot"

> select #1/A:475

12 atoms, 11 bonds, 1 residue, 1 model selected  

> volume #1.1.1.1 level 0.03556

> select #1/A:385

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

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> isolde restrain ligands #1

> isolde sim resume

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select #1/A:386

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:387

17 atoms, 16 bonds, 1 residue, 1 model selected  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select #1/A:367-403

547 atoms, 551 bonds, 37 residues, 1 model selected  

> clipper spotlight

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> ui mousemode right "isolde tug residue"

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select /A

6546 atoms, 6600 bonds, 4 pseudobonds, 436 residues, 3 models selected  

> select clear

> select #1/A:471

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:475

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/A:382

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:386

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:387

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #1/A:425

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:428

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #1/A:135

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #1/A:138

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:139

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:388

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/A:467

11 atoms, 10 bonds, 1 residue, 1 model selected  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.02454

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\isolde.py", line 1009, in _sim_end_cb  
run(self.session, f'clipper spot #{self.selected_model.id_string}', log=False)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\clipper\cmd.py", line 109, in spotlight  
sh = get_symmetry_handler(m, create=create, auto_add_to_session=True)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\clipper\symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\clipper\symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\clipper\symmetry.py", line 594, in __init__  
self.add_model(model, ignore_model_symmetry=ignore_model_symmetry,  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\clipper\symmetry.py", line 649, in add_model  
self.set_default_atom_display(mode=self._hydrogen_mode)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\clipper\symmetry.py", line 922, in set_default_atom_display  
atoms = model.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "sim terminated":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\clipper\symmetry.py", line 922, in set_default_atom_display  
atoms = model.atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4490, in next_preview  
return self._incr_preview(rotamer, 1)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4474, in _incr_preview  
self._create_preview(rotamer, target_def, new_target)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4583, in _create_preview  
pm.atoms.coords = master_atoms.coords  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 19 does not match objects array length 17  
  
ValueError: Values array length 19 does not match objects array length 17  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4490, in next_preview  
return self._incr_preview(rotamer, 1)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4474, in _incr_preview  
self._create_preview(rotamer, target_def, new_target)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4583, in _create_preview  
pm.atoms.coords = master_atoms.coords  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 19 does not match objects array length 17  
  
ValueError: Values array length 19 does not match objects array length 17  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  

> save "G:/My Drive/Cryo-EM/model refinement/ASCT2-2N2-gln-
> NeCEN-v2/RealSpaceRefine_19/v7-isolde.pdb"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4490, in next_preview  
return self._incr_preview(rotamer, 1)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4474, in _incr_preview  
self._create_preview(rotamer, target_def, new_target)  
File "C:\Users\aboro\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4583, in _create_preview  
pm.atoms.coords = master_atoms.coords  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 19 does not match objects array length 17  
  
ValueError: Values array length 19 does not match objects array length 17  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 24.20.100.6346
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: LENOVO
Model: 81C4
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 17,014,951,936
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Stop simulation: model is None

Reported by Anna Borowska

in reply to:  2 ; comment:2 by Tristan Croll, 3 years ago 

Off on holiday so won’t be able to look properly until late last week, but that is a *very* strange series of errors. A little mystified right now.

comment:3 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

This was happening if the simulation was stopped with the rotamer preview still running. Fixed in ISOLDE 1.5.

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