Opened 3 years ago

Closed 3 years ago

#8372 closed defect (duplicate)

isolde sim stop discardTo start: 'NoneType' object has no attribute 'atoms'

Reported by: chimerax-bug-report@… 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_aa803.cxs format
> session

Opened postprocess.mrc as #1.1.1.1, grid size 560,560,560, pixel 0.68, shown
at level 0.333, step 1, values float32  
Restoring stepper: 6rw6_fit_monomer.pdb  
Log from Wed Jan 25 14:13:31 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_aa356.cxs

Opened postprocess.mrc as #1.1.1.1, grid size 560,560,560, pixel 0.68, shown
at level 0.248, step 1, values float32  
Restoring stepper: 6rw6_fit_monomer.pdb  
Log from Tue Jan 24 18:05:53 2023 Startup Messages  
---  
note | Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
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\\\nganga\\\Desktop\\\Peter\\\WT_HiRes\\\6rw6_fit_monomer.pdb

6rw6_fit_monomer.pdb title:  
Cryo-em structure of photorhabdus luminescens TCDA1 [more info...]  
  
Chain information for 6rw6_fit_monomer.pdb #1  
---  
Chain | Description | UniProt  
A | toxin A | Q9RN43_PHOLU  
  

> open C:\\\Users\\\nganga\\\Desktop\\\Peter\\\WT_HiRes\\\postprocess.mrc

Opened postprocess.mrc as #2, grid size 560,560,560, pixel 0.68, shown at
level 0.262, step 4, values float32  

> volume #2 step 1

> volume #2 level 0.4345

> volume #2 level 0.4468

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 83 residues in model #1 to IUPAC-IUB
standards.  
6rw6_fit_monomer.pdb title:  
Cryo-em structure of photorhabdus luminescens TCDA1 [more info...]  
  
Chain information for 6rw6_fit_monomer.pdb  
---  
Chain | Description | UniProt  
1.2/A | toxin A | Q9RN43_PHOLU  
  

> isolde sim start sel

> clipper associate #2 toModel #1

Opened postprocess.mrc as #1.1.1.1, grid size 560,560,560, pixel 0.68, shown
at step 1, values float32  

> volume #1.1.1.1 level 0.1584

> volume #1.1.1.1 level 0.1254

> volume #1.1.1.1 level 0.09466

> volume #1.1.1.1 level 0.2726

> volume #1.1.1.1 level 0.3155

> ui tool show "Ramachandran Plot"

> volume #1.1.1.1 level 0.4098

> select clear

> select #1.2:21

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

> volume #1.1.1.1 level 0.3719

> volume #1.1.1.1 level 0.3427

> select clear

> volume #1.1.1.1 level 0.2846

> select clear

> isolde sim start sel

ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to 6rw6_fit_monomer.pdb #1.2  
---  
notes | No usable SEQRES records for 6rw6_fit_monomer.pdb (#1.2) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: /A LEU 21  
Chain-initial residues that are not actual N termini: /A TYR 1188, /A ARG 1939  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A LYS 2516, /A GLY 1182,
/A THR 1932  
2059 hydrogen bonds  
Adding 'H' to /A TYR 1188  
Adding 'H' to /A ARG 1939  
/A LYS 2516 is not terminus, removing H atom from 'C'  
19281 hydrogens added  
  

> 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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.2687

> select clear

> volume #1.1.1.1 level 0.3104

> volume #1.1.1.1 level 0.3016

> 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 #1.1.1.1 level 0.2575

> select clear

> volume #1.1.1.1 level 0.2238

> 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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.2815

> select clear

[Repeated 3 time(s)]

> volume #1.1.1.1 level 0.3444

> volume #1.1.1.1 level 0.2904

> select clear

[Repeated 1 time(s)]

> volume #1.1.1.1 level 0.2804

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> select clear

> volume #1.1.1.1 level 0.2513

> select clear

> volume #1.1.1.1 level 0.2633

> volume #1.1.1.1 level 0.1993

> volume #1.1.1.1 level 0.2433

> volume #1.1.1.1 level 0.2233

> 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\nganga\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  

> ui tool show "Ramachandran Plot"

> volume #1.1.1.1 level 0.2026

> volume #1.1.1.1 level 0.2441

> select clear

> volume #1.1.1.1 level 0.2209

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> select clear

[Repeated 2 time(s)]

> volume #1.1.1.1 level 0.2642

> 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 2 time(s)]

> volume #1.1.1.1 level 0.189

> 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 #1.1.1.1 level 0.3293

> volume #1.1.1.1 level 0.249

> 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: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.2898

> select clear

> volume #1.1.1.1 level 0.2274

> volume #1.1.1.1 level 0.3376

> 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 #1.1.1.1 level 0.3757

> volume #1.1.1.1 level 0.3292

> 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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.4227

> volume #1.1.1.1 level 0.2484

> volume #1.1.1.1 level 0.3377

> 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 #1.1.1.1 level 0.5733

> 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  

> ui tool show "Ramachandran Plot"

> volume #1.1.1.1 level 0.4405

> volume #1.1.1.1 level 0.3473

> volume #1.1.1.1 level 0.2714

> volume #1.1.1.1 level 0.3231

> volume #1.1.1.1 level 0.3269

> 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 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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

[Repeated 3 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  

> select clear

> volume #1.1.1.1 level 0.3009

> select clear

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.2842

> volume #1.1.1.1 level 0.2422

> isolde sim stop

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

> select clear

> volume #1.1.1.1 level 0.3687

> 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  

> isolde sim stop

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

> volume #1.1.1.1 level 0.4058

> volume #1.1.1.1 level 0.3018

> select clear

[Repeated 2 time(s)]

> volume #1.1.1.1 level 0.2218

> select clear

> volume #1.1.1.1 level 0.3537

> 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 #1.1.1.1 level 0.2662

> volume #1.1.1.1 level 0.2881

> volume #1.1.1.1 level 0.3331

> 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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

[Repeated 2 time(s)]

> 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

[Repeated 1 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.2993

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.2502

> volume #1.1.1.1 level 0.3308

> 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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.2478

> 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: Corrected atom nomenclature of 2 residues in model #1.2 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 2 time(s)]

> save C:/Users/nganga/Desktop/Peter/6rw6_fit_monomer_isolde_aa356.pdb
> relModel #1.2

> save C:/Users/nganga/Desktop/Peter/WT_HiRes/Session_isolde_aa356.cxs

Taking snapshot of stepper: 6rw6_fit_monomer.pdb  

——— End of log from Tue Jan 24 18:05:53 2023 ———

opened ChimeraX session  

> isolde start

> set selectionWidth 4

> ui tool show "Ramachandran Plot"

> select clear

> ui tool show "Volume Viewer"

> volume #1.1.1.1 level 0.2455

> volume #1.1.1.1 level 0.2296

> volume #1.1.1.1 level 0.191

> volume #1.1.1.1 level 0.2364

> volume #1.1.1.1 level 0.3389

> select clear

> volume #1.1.1.1 level 0.2962

> volume #1.1.1.1 level 0.3674

> 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 #1.2 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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

[Repeated 1 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.3632

> isolde sim stop

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

> select clear

> volume #1.1.1.1 level 0.3392

> volume #1.1.1.1 level 0.3191

> volume #1.1.1.1 level 0.3311

> 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 #1.1.1.1 level 0.2419

> volume #1.1.1.1 level 0.2055

> volume #1.1.1.1 level 0.4062

> 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  

> isolde sim stop

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

> 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 #1.2 to IUPAC-IUB
standards.  
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 sim stop

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

> 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 #1.1.1.1 level 0.427

> 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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.2571

> 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 discardTo start

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

> select clear

> volume #1.1.1.1 level 0.3272

> 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 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 #1.1.1.1 level 0.3313

> volume #1.1.1.1 level 0.2987

> volume #1.1.1.1 level 0.3272

> select clear

> 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 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  

> 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 #1.2 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: stopped sim  

> select clear

[Repeated 1 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.2716

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> select clear

[Repeated 1 time(s)]

> volume #1.1.1.1 level 0.3533

> 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 #1.1.1.1 level 0.2604

> volume #1.1.1.1 level 0.4117

> volume #1.1.1.1 level 0.3335

> 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 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save C:/Users/nganga/Desktop/Peter/WT_HiRes/Session_isolde_aa803.cxs

Taking snapshot of stepper: 6rw6_fit_monomer.pdb  

——— End of log from Wed Jan 25 14:13:31 2023 ———

opened ChimeraX session  

> isolde start

> set selectionWidth 4

> ui tool show "Volume Viewer"

> 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 #1.1.1.1 level 0.3972

> 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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.3448

> 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 #1.1.1.1 level 0.4388

> volume #1.1.1.1 level 0.4689

> volume #1.1.1.1 level 0.405

> 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  

> isolde sim stop

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

> select clear

> volume #1.1.1.1 level 0.3243

> volume #1.1.1.1 level 0.2633

> volume #1.1.1.1 level 0.3668

> 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 #1.1.1.1 level 0.3668

> select clear

[Repeated 1 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.343

> isolde sim stop

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

> select clear

[Repeated 3 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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

[Repeated 1 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> 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 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 #1.1.1.1 level 0.2905

> isolde sim stop

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

> 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  

> isolde sim stop discardTo start

reverting to start  
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: stopped sim  

> select clear

[Repeated 1 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.3608

> isolde sim stop

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

> 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

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.2937

> 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  

> volume #1.1.1.1 level 0.3453

> volume #1.1.1.1 level 0.335

> select clear

[Repeated 2 time(s)]

> isolde sim stop

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

> select clear

> volume #1.1.1.1 level 0.3161

> 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 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 sim stop

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

> 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

> save C:/Users/nganga/Desktop/Peter/WT_HiRes/Session_isolde_aa1065.cxs

Taking snapshot of stepper: 6rw6_fit_monomer.pdb  

> 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 #1.2 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: stopped sim  

> select clear

[Repeated 1 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  

> 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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

[Repeated 2 time(s)]

> volume #1.1.1.1 level 0.414

> 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 #1.1.1.1 level 0.3749

> select clear

> volume #1.1.1.1 level 0.2739

> volume #1.1.1.1 level 0.3384

> 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  

> isolde sim stop

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

> select clear

> volume #1.1.1.1 level 0.2734

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> select clear

> volume #1.1.1.1 level 0.4437

> volume #1.1.1.1 level 0.3398

> 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 #1.1.1.1 level 0.3209

> 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  

> isolde sim stop

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

> select clear

> volume #1.1.1.1 level 0.3017

> 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 #1.1.1.1 level 0.4671

> 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 #1.1.1.1 level 0.3631

> 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 #1.1.1.1 level 0.2693

> 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 #1.1.1.1 level 0.1931

> isolde sim stop discardTo start

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

> select clear

> volume #1.1.1.1 level 0.3099

> 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 #1.2 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: 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 2 residues in model #1.2 to IUPAC-IUB
standards.  
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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

[Repeated 1 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: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.2533

> volume #1.1.1.1 level 0.2758

> volume #1.1.1.1 level 0.3183

> 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 #1.2 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 #1.2 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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

[Repeated 1 time(s)]

> volume #1.1.1.1 level 0.2425

> 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 #1.1.1.1 level 0.2813

> 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 #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

[Repeated 1 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.2288

> isolde sim stop

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

> select clear

[Repeated 1 time(s)]

> 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 #1.1.1.1 level 0.2482

> volume #1.1.1.1 level 0.2924

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.2533

> 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 24 does not match objects array length 14  
  
ValueError: Values array length 24 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.  
  
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 24 does not match objects array length 14  
  
ValueError: Values array length 24 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.  
  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
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 24 does not match objects array length 14  
  
ValueError: Values array length 24 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.  
  




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 (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → isolde sim stop discardTo start: 'NoneType' object has no attribute 'atoms'

comment:2 by Tristan Croll, 3 years ago

Resolution: → duplicate
Status: assigned → closed

Stopping a simulation with the rotamer preview visible. Fixed a while back.

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