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Opened 3 years ago
Last modified 3 years ago
#8472 assigned defect
Various simulation errors
| Reported by: | 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-10-10.0.22621
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.
> open
> C:/Users/nganga/Desktop/Peter/WT_HiRes/Session_isolde_TcdA1wt_pentamer_complete_1622.cxs
Opened relion_locres_filtered_job045_Bfac74.mrc as #2.1.1.1, grid size
560,560,560, pixel 0.68, shown at level 0.637, step 1, values float32
Log from Fri Feb 10 16:24:02 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> C:\Users\nganga\Desktop\Peter\WT_HiRes\Session_isolde_TcdA1wt_pentamer_complete_1022.cxs
> format session
Opened relion_locres_filtered_job045_Bfac74.mrc as #2.1.1.1, grid size
560,560,560, pixel 0.68, shown at level 0.594, step 1, values float32
Log from Wed Feb 8 15:45:41 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> C:\Users\nganga\Desktop\Peter\WT_HiRes\Session_isolde_TcdA1wt_pentamer_complete_544.cxs
> format session
Opened relion_locres_filtered_job045_Bfac74.mrc as #2.1.1.1, grid size
560,560,560, pixel 0.68, shown at level 0.538, step 1, values float32
Log from Tue Feb 7 15:54:43 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> C:\Users\nganga\Desktop\Peter\WT_HiRes\Session_isolde_TcdA1wt_pentamer_complete_438.cxs
> format session
Opened relion_locres_filtered_job045_Bfac74.mrc as #2.1.1.1, grid size
560,560,560, pixel 0.68, shown at level 0.569, step 1, values float32
Log from Thu Feb 2 19:32:17 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> C:/Users/nganga/Desktop/Peter/WT_HiRes/Session_isolde_TcdA1wt_pentamer_complete_188.cxs
Opened relion_locres_filtered_job045_Bfac74.mrc as #2.1.1.1, grid size
560,560,560, pixel 0.68, shown at level 0.952, step 1, values float32
Log from Thu Feb 2 16:47:47 2023 Startup Messages
---
note | Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json
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 C:/Users/belyy/Desktop/TcdA-
> HighRes/relion_locres_filtered_job045_Bfac74.mrc
> C:/Users/belyy/Desktop/TcdA-
> HighRes/Session_isolde_TcdA1wt_pentamer_complete.pdb
> C:/Users/belyy/Desktop/TcdA-HighRes/postprocess.mrc
Opened relion_locres_filtered_job045_Bfac74.mrc as #1, grid size 560,560,560,
pixel 0.68, shown at level 0.493, step 4, values float32
Chain information for Session_isolde_TcdA1wt_pentamer_complete.pdb #2
---
Chain | Description
A B C D E | No description available
Opened postprocess.mrc as #3, grid size 560,560,560, pixel 0.68, shown at
level 0.262, step 4, values float32
> volume #1 step 1
> volume #3 step 1
> close #3
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for Session_isolde_TcdA1wt_pentamer_complete.pdb
---
Chain | Description
2.2/A 2.2/B 2.2/C 2.2/D 2.2/E | No description available
> clipper associate #1 toModel #2
Opened relion_locres_filtered_job045_Bfac74.mrc as #2.1.1.1, grid size
560,560,560, pixel 0.68, shown at step 1, values float32
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\matplotlib\cbook\\__init__.py", line 287, in process
func(*args, **kwargs)
File "C:\Users\belyy\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\validation\ramaplot\ramaplot.py", line 292, in
on_resize
c.draw()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\matplotlib\backends\backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\matplotlib\artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\matplotlib\artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\matplotlib\figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\matplotlib\figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\matplotlib\axes\\_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\matplotlib\transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> select clear
> volume #2.1.1.1 level 0.5255
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> volume #2.1.1.1 level 0.4253
> volume #2.1.1.1 level 0.4854
> volume #2.1.1.1 level 0.4954
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
[Repeated 5 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7627
> volume #2.1.1.1 level 0.5214
> volume #2.1.1.1 level 0.6995
> volume #2.1.1.1 level 0.5563
> volume #2.1.1.1 level 0.5176
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6966
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.773
> volume #2.1.1.1 level 0.4862
> volume #2.1.1.1 level 0.5374
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> volume #2.1.1.1 level 0.394
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4777
> save C:/Users/belyy/Desktop/TcdA-
> HighRes/Session_isolde_TcdA1wt_pentamer_complete_86.pdb
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7317
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4761
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4596
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.8824
> volume #2.1.1.1 level 1.109
> volume #2.1.1.1 level 0.7881
> volume #2.1.1.1 level 0.5728
> volume #2.1.1.1 level 0.9252
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.8215
> isolde sim start sel
ISOLDE: started sim
> select clear
> volume #2.1.1.1 level 0.6648
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.5097
> volume #2.1.1.1 level 0.7072
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 1.124
> volume #2.1.1.1 level 0.9524
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> save C:/Users/belyy/Desktop/TcdA-
> HighRes/Session_isolde_TcdA1wt_pentamer_complete_188.pdb
> save C:/Users/belyy/Desktop/TcdA-
> HighRes/Session_isolde_TcdA1wt_pentamer_complete_188.cxs
——— End of log from Thu Feb 2 16:47:47 2023 ———
opened ChimeraX session
> isolde start
> set selectionWidth 4
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> ui tool show "Volume Viewer"
> volume #2.1.1.1 level 0.7318
> volume #2.1.1.1 level 0.6419
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.757
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
[Repeated 1 time(s)]
> 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
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.5224
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4406
> volume #2.1.1.1 level 0.3916
> volume #2.1.1.1 level 0.4161
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 1.005
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.8984
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 1.005
> volume #2.1.1.1 level 0.5715
> select clear
[Repeated 2 time(s)]
> isolde sim start sel
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 clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.882
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.8575
> volume #2.1.1.1 level 0.596
> volume #2.1.1.1 level 0.9474
> volume #2.1.1.1 level 0.6614
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.5143
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5919
> volume #2.1.1.1 level 0.4438
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.3781
> volume #2.1.1.1 level 0.5678
> volume #2.1.1.1 level 0.4745
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.3437
> volume #2.1.1.1 level 0.4336
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.308
> volume #2.1.1.1 level 0.2577
> volume #2.1.1.1 level 0.4399
> volume #2.1.1.1 level 0.3765
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4243
> volume #2.1.1.1 level 0.5622
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4396
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.749
> volume #2.1.1.1 level 0.5647
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5906
[Repeated 1 time(s)]
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4925
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7997
> volume #2.1.1.1 level 0.7559
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4944
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.4636
> volume #2.1.1.1 level 0.479
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.5607
> volume #2.1.1.1 level 0.3809
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4692
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> volume #2.1.1.1 level 0.3303
> volume #2.1.1.1 level 0.4038
> volume #2.1.1.1 level 0.4365
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.8778
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.9154
> volume #2.1.1.1 level 0.7854
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4422
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.4361
> volume #2.1.1.1 level 0.4068
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.3308
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4709
> volume #2.1.1.1 level 0.6285
> volume #2.1.1.1 level 0.5925
> volume #2.1.1.1 level 0.5127
> volume #2.1.1.1 level 0.5748
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4153
> volume #2.1.1.1 level 0.4033
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> 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
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.3905
> volume #2.1.1.1 level 0.5893
> volume #2.1.1.1 level 0.4935
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6318
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4994
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.422
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6986
> volume #2.1.1.1 level 0.5701
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.6143
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.6707
> volume #2.1.1.1 level 0.4946
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5212
> volume #2.1.1.1 level 0.6449
> volume #2.1.1.1 level 0.6016
> volume #2.1.1.1 level 0.3852
> volume #2.1.1.1 level 0.4037
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4602
> 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 clear
[Repeated 1 time(s)]
> 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
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.4324
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
ISOLDE: started sim
> select clear
> volume #2.1.1.1 level 0.529
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.5211
> select clear
> 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: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5381
> select clear
> 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 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6662
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5902
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4016
> volume #2.1.1.1 level 0.4075
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4985
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.5139
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.539
> volume #2.1.1.1 level 0.4974
> select clear
> volume #2.1.1.1 level 0.4142
> 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 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> volume #2.1.1.1 level 0.4222
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.2884
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5053
> volume #2.1.1.1 level 0.3788
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.3969
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.2662
> 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: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> 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
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.447
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5103
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.3431
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4425
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.3649
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> 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
> volume #2.1.1.1 level 0.5055
> volume #2.1.1.1 level 0.355
> volume #2.1.1.1 level 0.5417
> volume #2.1.1.1 level 0.4573
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> volume #2.1.1.1 level 0.4761
> volume #2.1.1.1 level 0.3888
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4999
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5687
> save
> C:/Users/nganga/Desktop/Peter/WT_HiRes/Session_isolde_TcdA1wt_pentamer_complete_438.cxs
——— End of log from Thu Feb 2 19:32:17 2023 ———
opened ChimeraX session
> ui tool show "Volume Viewer"
> isolde start
> set selectionWidth 4
> select clear
> volume #2.1.1.1 level 0.7941
> volume #2.1.1.1 level 0.5147
> volume #2.1.1.1 level 0.4918
> volume #2.1.1.1 level 0.6986
> volume #2.1.1.1 level 0.6022
> volume #2.1.1.1 level 0.8311
> volume #2.1.1.1 level 0.5292
> volume #2.1.1.1 level 0.4437
> volume #2.1.1.1 level 0.3697
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.3233
> volume #2.1.1.1 level 0.5087
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6193
> volume #2.1.1.1 level 0.5666
> volume #2.1.1.1 level 0.6368
> volume #2.1.1.1 level 0.4672
> volume #2.1.1.1 level 0.5783
> volume #2.1.1.1 level 0.4204
> volume #2.1.1.1 level 0.3502
> volume #2.1.1.1 level 0.631
> volume #2.1.1.1 level 0.8474
> volume #2.1.1.1 level 0.7289
> volume #2.1.1.1 level 0.5855
> volume #2.1.1.1 level 0.8287
> volume #2.1.1.1 level 0.7536
> volume #2.1.1.1 level 1.01
> volume #2.1.1.1 level 0.7784
> volume #2.1.1.1 level 0.5863
> volume #2.1.1.1 level 0.4538
> volume #2.1.1.1 level 0.6459
> volume #2.1.1.1 level 0.4984
> volume #2.1.1.1 level 0.6677
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.3817
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7349
> volume #2.1.1.1 level 0.7474
> volume #2.1.1.1 level 0.486
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4262
> volume #2.1.1.1 level 0.584
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4563
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.5564
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4411
> volume #2.1.1.1 level 0.7304
> select clear
> volume #2.1.1.1 level 0.6172
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> volume #2.1.1.1 level 0.4782
> volume #2.1.1.1 level 0.6417
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.8839
> volume #2.1.1.1 level 0.5276
> volume #2.1.1.1 level 0.7312
> volume #2.1.1.1 level 0.4258
> volume #2.1.1.1 level 0.763
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.688
> 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: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6629
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> volume #2.1.1.1 level 0.5485
> volume #2.1.1.1 level 0.7412
> volume #2.1.1.1 level 0.6446
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.5641
> volume #2.1.1.1 level 0.5077
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6281
> volume #2.1.1.1 level 0.415
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> volume #2.1.1.1 level 0.5439
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.4343
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> volume #2.1.1.1 level 0.7002
> volume #2.1.1.1 level 0.4423
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6049
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4447
> volume #2.1.1.1 level 0.786
> volume #2.1.1.1 level 0.5669
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4863
> select clear
[Repeated 1 time(s)]
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.6303
> select clear
> volume #2.1.1.1 level 0.5361
> volume #2.1.1.1 level 0.6994
> volume #2.1.1.1 level 0.4779
> select clear
[Repeated 1 time(s)]
> 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 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.3491
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4472
> volume #2.1.1.1 level 0.4673
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5377
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> C:/Users/nganga/Desktop/Peter/WT_HiRes/Session_isolde_TcdA1wt_pentamer_complete_544.cxs
——— End of log from Tue Feb 7 15:54:43 2023 ———
opened ChimeraX session
> select clear
> ui tool show "Volume Viewer"
> isolde start
> set selectionWidth 4
> select clear
> volume #2.1.1.1 level 0.518
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> 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
> volume #2.1.1.1 level 0.5604
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4926
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.8821
> volume #2.1.1.1 level 0.4561
> volume #2.1.1.1 level 0.7549
> volume #2.1.1.1 level 0.5131
> volume #2.1.1.1 level 0.4559
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.7231
> volume #2.1.1.1 level 0.7604
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.5188
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.7115
> select clear
> volume #2.1.1.1 level 0.4972
> volume #2.1.1.1 level 0.5157
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 2 time(s)]
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6619
> volume #2.1.1.1 level 0.4404
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.5995
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4722
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7415
> volume #2.1.1.1 level 0.5115
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.9009
> volume #2.1.1.1 level 0.6087
> volume #2.1.1.1 level 0.8054
> volume #2.1.1.1 level 0.5683
> volume #2.1.1.1 level 0.8246
> volume #2.1.1.1 level 1.009
> volume #2.1.1.1 level 0.5707
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4949
> volume #2.1.1.1 level 0.5623
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.8656
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6474
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 1.301
> volume #2.1.1.1 level 0.9317
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.718
> volume #2.1.1.1 level 0.6111
> volume #2.1.1.1 level 0.9317
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4907
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6283
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.3952
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.6724
> volume #2.1.1.1 level 0.4808
> volume #2.1.1.1 level 0.525
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6503
> volume #2.1.1.1 level 0.5744
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7704
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.5319
> volume #2.1.1.1 level 0.8817
> volume #2.1.1.1 level 0.4473
> volume #2.1.1.1 level 0.3642
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4877
> select clear
[Repeated 1 time(s)]
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7102
> volume #2.1.1.1 level 0.4488
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7506
> volume #2.1.1.1 level 0.4403
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7112
> clipper spotlight
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5448
> volume #2.1.1.1 level 0.7507
> volume #2.1.1.1 level 0.53
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7758
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4744
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.8645
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 1.257
> volume #2.1.1.1 level 0.6587
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.5931
> 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: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4961
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6062
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.5942
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> save
> C:/Users/nganga/Desktop/Peter/WT_HiRes/Session_isolde_TcdA1wt_pentamer_complete_1022.cxs
——— End of log from Wed Feb 8 15:45:41 2023 ———
opened ChimeraX session
> ui tool show "Volume Viewer"
> isolde start
> set selectionWidth 4
> select clear
> volume #2.1.1.1 level 0.5745
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.9732
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.664
> volume #2.1.1.1 level 0.4236
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.6234
> select clear
> volume #2.1.1.1 level 0.9425
> volume #2.1.1.1 level 0.5782
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.9297
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7225
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.9907
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.5641
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.8141
> volume #2.1.1.1 level 1.07
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.7983
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4515
> volume #2.1.1.1 level 0.336
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5382
> volume #2.1.1.1 level 0.4007
> volume #2.1.1.1 level 0.6561
> volume #2.1.1.1 level 0.8657
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.3121
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.5193
> select clear
> volume #2.1.1.1 level 0.8134
> volume #2.1.1.1 level 0.4355
> volume #2.1.1.1 level 0.9718
> select clear
> 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 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4706
> volume #2.1.1.1 level 0.954
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4664
> volume #2.1.1.1 level 0.3323
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.7589
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 1.177
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> volume #2.1.1.1 level 0.64
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4777
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7684
> volume #2.1.1.1 level 0.6438
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4985
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4185
> volume #2.1.1.1 level 0.6497
> volume #2.1.1.1 level 0.5084
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 2 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.389
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5945
> volume #2.1.1.1 level 0.5313
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6892
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4366
> volume #2.1.1.1 level 0.6577
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.9507
> volume #2.1.1.1 level 0.549
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.3041
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.6876
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> volume #2.1.1.1 level 0.4926
> 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\nganga\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\nganga\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\nganga\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\nganga\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\nganga\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\nganga\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\nganga\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\nganga\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.
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.3547
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7006
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.5909
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.9831
> select clear
> volume #2.1.1.1 level 0.5827
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6917
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.3383
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.5176
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.337
> volume #2.1.1.1 level 0.3
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.454
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5719
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.3178
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4662
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.3556
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4605
> volume #2.1.1.1 level 0.3797
> volume #2.1.1.1 level 0.5514
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> volume #2.1.1.1 level 0.4343
> volume #2.1.1.1 level 0.5305
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.3191
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4155
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> 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
> select clear
> volume #2.1.1.1 level 0.545
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> 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
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.3414
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.3172
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4139
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> 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
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.623
> volume #2.1.1.1 level 0.4705
> select clear
> 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 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6145
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.3926
> select clear
> volume #2.1.1.1 level 0.4695
> volume #2.1.1.1 level 0.8462
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4999
> select clear
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> select clear
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> select clear
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> select clear
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7141
> volume #2.1.1.1 level 0.3818
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\nganga\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 187, in run_provider
toolbar_command(session, name)
File "C:\Users\nganga\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\toolbar.py", line 37, in toolbar_command
_rota_command(session, name)
File "C:\Users\nganga\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\toolbar.py", line 63, in _rota_command
rrmgr.next_preview(rota)
File "C:\Users\nganga\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\nganga\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\nganga\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 12 does not match objects array length 14
ValueError: Values array length 12 does not match objects array length 14
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.
> select clear
> volume #2.1.1.1 level 0.6365
> select clear
> save
> C:/Users/nganga/Desktop/Peter/WT_HiRes/Session_isolde_TcdA1wt_pentamer_complete_1622.cxs
——— End of log from Fri Feb 10 16:24:02 2023 ———
opened ChimeraX session
> ui tool show "Volume Viewer"
> isolde start
> set selectionWidth 4
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.8692
> volume #2.1.1.1 level 0.542
> volume #2.1.1.1 level 0.4812
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.5381
> volume #2.1.1.1 level 0.4349
> volume #2.1.1.1 level 0.5934
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4968
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7039
> volume #2.1.1.1 level 0.5321
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4757
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4109
> volume #2.1.1.1 level 0.5016
> volume #2.1.1.1 level 0.4582
> volume #2.1.1.1 level 0.3975
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7397
> volume #2.1.1.1 level 0.5406
> volume #2.1.1.1 level 0.4411
> volume #2.1.1.1 level 0.5392
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.4099
> volume #2.1.1.1 level 0.4484
> volume #2.1.1.1 level 0.5554
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4573
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> 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
> select clear
> volume #2.1.1.1 level 0.5557
> volume #2.1.1.1 level 0.6725
> volume #2.1.1.1 level 0.3842
> volume #2.1.1.1 level 0.3575
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> select clear
> 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
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.521
> volume #2.1.1.1 level 0.4175
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6294
> volume #2.1.1.1 level 1.051
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7175
> select clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.6175
> select clear
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.4832
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.7163
> 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 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #2.1.1.1 level 0.494
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
reverting to start
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\nganga\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\nganga\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\nganga\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\nganga\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\nganga\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\nganga\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\nganga\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\nganga\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.
> select clear
> volume #2.1.1.1 level 0.8366
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
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\nganga\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 187, in run_provider
toolbar_command(session, name)
File "C:\Users\nganga\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\toolbar.py", line 37, in toolbar_command
_rota_command(session, name)
File "C:\Users\nganga\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\toolbar.py", line 63, in _rota_command
rrmgr.next_preview(rota)
File "C:\Users\nganga\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\nganga\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\nganga\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 17 does not match objects array length 16
ValueError: Values array length 17 does not match objects array length 16
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.
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
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\nganga\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 187, in run_provider
toolbar_command(session, name)
File "C:\Users\nganga\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\toolbar.py", line 37, in toolbar_command
_rota_command(session, name)
File "C:\Users\nganga\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\toolbar.py", line 63, in _rota_command
rrmgr.next_preview(rota)
File "C:\Users\nganga\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\nganga\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\nganga\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 17 does not match objects array length 16
ValueError: Values array length 17 does not match objects array length 16
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 NVIDIA 425.46
OpenGL renderer: GeForce GTX 1080 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
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: ASUSTeK COMPUTER INC.
Model: Zephyrus GX501GI
OS: Microsoft Windows 11 Enterprise (Build 22621)
Memory: 25,689,001,984
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz
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 (1)
comment:1 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Various simulation errors |
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