Opened 5 months ago

Closed 5 months ago

#17893 closed defect (duplicate)

ISOLDE: ResidueStepper holding reference to dead model

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-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/vol_000_250604.cxs"

Opened vol_000.mrc as #1.1.1.1, grid size 256,256,256, pixel 1.23, shown at
level 0.00119, step 1, values float32  
Restoring stepper: fold_2024_09_04_13_34_spcas9_model_3.cif  
Log from Wed Jun 4 13:11:02 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "E:/CryoDRGN atomic model/202505_local refinement/Rigid body
> fitting_202505/OC-1 no Mg/vol_008_250515.cxs"

Error opening map "E:\CryoDRGN atomic model\202505_local refinement\Rigid body
fitting_202505\OC-1 no Mg\vol_008_250515.cxs": File vol_008_250515.cxs, format
mrc  
MRC header value nsymbt (1953787962) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Redust" returned None  

Log from Thu May 15 13:43:06 2025 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Volumes/Charmaine/CryoDRGN atomic model/202505_local
> refinement/CryoSPARC files_202505 /openCRISPR_xMgCl2/OC-1_HNH.pdb"
> "/Volumes/Charmaine/CryoDRGN atomic model/202505_local refinement/CryoSPARC
> files_202505 /openCRISPR_xMgCl2/OC-1_REC2.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1_REC3.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_000_isolde_0318.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_000_sharp.mrc" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_000.mrc.cif"

Summary of feedback from opening /Volumes/Charmaine/CryoDRGN atomic
model/202505_local refinement/CryoSPARC files_202505
/openCRISPR_xMgCl2/vol_000.mrc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for OC-1_HNH.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC2.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC3.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for vol_000_isolde_0318.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Opened vol_000_sharp.mrc as #6, grid size 256,256,256, pixel 1.23, shown at
level 0.122, step 1, values float32  
Chain information for vol_000.mrc.cif #7  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ba | No description available  
Bb Bc | No description available  
Bd | No description available  
Be | No description available  
Ca | No description available  
Cb | No description available  
Cc | No description available  
  

> hide #!7 models

> transparency 50

> matchmaker #1 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_000_isolde_0318.pdb, chain A (#5) with OC-1_HNH.pdb, chain A
(#1), sequence alignment score = 637.4  
RMSD between 131 pruned atom pairs is 0.502 angstroms; (across all 131 pairs:
0.502)  
  

> matchmaker #2 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_000_isolde_0318.pdb, chain A (#5) with OC-1_REC2.pdb, chain A
(#2), sequence alignment score = 650.5  
RMSD between 133 pruned atom pairs is 0.666 angstroms; (across all 133 pairs:
0.666)  
  

> matchmaker #3 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_000_isolde_0318.pdb, chain A (#5) with OC-1_REC3.pdb, chain A
(#3), sequence alignment score = 1128.9  
RMSD between 222 pruned atom pairs is 0.369 angstroms; (across all 222 pairs:
0.369)  
  

> matchmaker #4 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_000_isolde_0318.pdb, chain A (#5) with OC-1.pdb, chain A (#4),
sequence alignment score = 3970.7  
RMSD between 877 pruned atom pairs is 0.856 angstroms; (across all 894 pairs:
0.924)  
  

> surface dust #6 size 12.3

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_000_HNH_250515.pdb" models #1 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_000_REC2_250515.pdb" models #2 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_000_REC3_250515.pdb" models #3 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_000_OC1_250515.pdb" models #4 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_000_250515.cxs"

> close

> open "/Volumes/Charmaine/CryoDRGN atomic model/202505_local
> refinement/CryoSPARC files_202505 /openCRISPR_xMgCl2/OC-1_HNH.pdb"
> "/Volumes/Charmaine/CryoDRGN atomic model/202505_local refinement/CryoSPARC
> files_202505 /openCRISPR_xMgCl2/OC-1_REC2.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1_REC3.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_001_isolde_0318.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_001_sharp.mrc" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_001.mrc.cif"

Summary of feedback from opening /Volumes/Charmaine/CryoDRGN atomic
model/202505_local refinement/CryoSPARC files_202505
/openCRISPR_xMgCl2/vol_001.mrc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for OC-1_HNH.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC2.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC3.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for vol_001_isolde_0318.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Opened vol_001_sharp.mrc as #6, grid size 256,256,256, pixel 1.23, shown at
level 0.108, step 1, values float32  
Chain information for vol_001.mrc.cif #7  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ba | No description available  
Bb | No description available  
Bc | No description available  
Ca | No description available  
Cb | No description available  
Cc | No description available  
Cd | No description available  
  

> hide #5 models

> surface dust #6 size 12.3

> matchmaker #4 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_001_isolde_0318.pdb, chain A (#5) with OC-1.pdb, chain A (#4),
sequence alignment score = 3946.1  
RMSD between 808 pruned atom pairs is 1.028 angstroms; (across all 894 pairs:
5.390)  
  

> matchmaker #3 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_001_isolde_0318.pdb, chain A (#5) with OC-1_REC3.pdb, chain A
(#3), sequence alignment score = 1142.7  
RMSD between 222 pruned atom pairs is 0.335 angstroms; (across all 222 pairs:
0.335)  
  

> matchmaker #2 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_001_isolde_0318.pdb, chain A (#5) with OC-1_REC2.pdb, chain A
(#2), sequence alignment score = 646.9  
RMSD between 125 pruned atom pairs is 0.609 angstroms; (across all 133 pairs:
1.081)  
  

> matchmaker #1 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_001_isolde_0318.pdb, chain A (#5) with OC-1_HNH.pdb, chain A
(#1), sequence alignment score = 594.8  
RMSD between 123 pruned atom pairs is 0.861 angstroms; (across all 131 pairs:
1.415)  
  

> transparency 50

> show #5 models

> hide #!7 models

> show #!7 models

> hide #5 models

> hide #1-3#!4,7 atoms

> show #1-3#!4,7 cartoons

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_001_250515.cxs"

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_001_HNH_250515.pdb" models #1 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_001_OC1_250515.pdb" models #4 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_001_REC2_250515.pdb" models #2 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_001_REC3_250515.pdb" models #3 relModel #6

> close

> open "/Volumes/Charmaine/CryoDRGN atomic model/202505_local
> refinement/CryoSPARC files_202505 /openCRISPR_xMgCl2/OC-1_HNH.pdb"
> "/Volumes/Charmaine/CryoDRGN atomic model/202505_local refinement/CryoSPARC
> files_202505 /openCRISPR_xMgCl2/OC-1_REC2.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1_REC3.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_002_isolde_0318.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_002_sharp.mrc" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_002.mrc.cif"

Summary of feedback from opening /Volumes/Charmaine/CryoDRGN atomic
model/202505_local refinement/CryoSPARC files_202505
/openCRISPR_xMgCl2/vol_002.mrc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for OC-1_HNH.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC2.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC3.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for vol_002_isolde_0318.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Opened vol_002_sharp.mrc as #6, grid size 256,256,256, pixel 1.23, shown at
level 0.145, step 1, values float32  
Chain information for vol_002.mrc.cif #7  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ba Bb Bc | No description available  
Bd | No description available  
Be | No description available  
Ca | No description available  
Cb | No description available  
Cc | No description available  
Cd | No description available  
  

> transparency 50

[Repeated 1 time(s)]

> hide #5 models

> hide #1-3#!4,7 atoms

> show #1-3#!4,7 cartoons

> surface dust #6 size 12.3

> matchmaker #1 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_002_isolde_0318.pdb, chain A (#5) with OC-1_HNH.pdb, chain A
(#1), sequence alignment score = 601.4  
RMSD between 123 pruned atom pairs is 0.804 angstroms; (across all 131 pairs:
1.410)  
  

> matchmaker #2 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_002_isolde_0318.pdb, chain A (#5) with OC-1_REC2.pdb, chain A
(#2), sequence alignment score = 646.9  
RMSD between 124 pruned atom pairs is 0.527 angstroms; (across all 133 pairs:
1.224)  
  

> matchmaker #3 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_002_isolde_0318.pdb, chain A (#5) with OC-1_REC3.pdb, chain A
(#3), sequence alignment score = 1142.7  
RMSD between 222 pruned atom pairs is 0.343 angstroms; (across all 222 pairs:
0.343)  
  

> matchmaker #4 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_002_isolde_0318.pdb, chain A (#5) with OC-1.pdb, chain A (#4),
sequence alignment score = 3946.7  
RMSD between 810 pruned atom pairs is 1.024 angstroms; (across all 894 pairs:
5.401)  
  

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_002_HNH_250515.pdb" models #1 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_002_OC1_250515.pdb" models #4 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_002_REC2_250515.pdb" models #2 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_002_REC3_250515.pdb" models #3 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_002_250515.cxs"

> close

> open "/Volumes/Charmaine/CryoDRGN atomic model/202505_local
> refinement/CryoSPARC files_202505 /openCRISPR_xMgCl2/OC-1_HNH.pdb"
> "/Volumes/Charmaine/CryoDRGN atomic model/202505_local refinement/CryoSPARC
> files_202505 /openCRISPR_xMgCl2/OC-1_REC2.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1_REC3.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_003_isolde_0318.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_003_sharp.mrc" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_003.mrc.cif"

Summary of feedback from opening /Volumes/Charmaine/CryoDRGN atomic
model/202505_local refinement/CryoSPARC files_202505
/openCRISPR_xMgCl2/vol_003.mrc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for OC-1_HNH.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC2.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC3.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for vol_003_isolde_0318.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Opened vol_003_sharp.mrc as #6, grid size 256,256,256, pixel 1.23, shown at
level 0.122, step 1, values float32  
Chain information for vol_003.mrc.cif #7  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ba | No description available  
Bb | No description available  
Bc | No description available  
Ca | No description available  
Cb | No description available  
Cc | No description available  
Cd | No description available  
  

> matchmaker #4 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_003_isolde_0318.pdb, chain A (#5) with OC-1.pdb, chain A (#4),
sequence alignment score = 3946.7  
RMSD between 811 pruned atom pairs is 1.039 angstroms; (across all 894 pairs:
5.387)  
  

> matchmaker #3 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_003_isolde_0318.pdb, chain A (#5) with OC-1_REC3.pdb, chain A
(#3), sequence alignment score = 1135.5  
RMSD between 220 pruned atom pairs is 0.365 angstroms; (across all 222 pairs:
0.441)  
  

> matchmaker #2 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_003_isolde_0318.pdb, chain A (#5) with OC-1_REC2.pdb, chain A
(#2), sequence alignment score = 646.9  
RMSD between 123 pruned atom pairs is 0.532 angstroms; (across all 133 pairs:
1.259)  
  

> matchmaker #1 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_003_isolde_0318.pdb, chain A (#5) with OC-1_HNH.pdb, chain A
(#1), sequence alignment score = 597.8  
RMSD between 123 pruned atom pairs is 0.916 angstroms; (across all 131 pairs:
1.434)  
  

> surface dust #6 size 12.3

> hide #5 models

> hide #1-3#!4,7 atoms

> show #1-3#!4,7 cartoons

> transparency 50

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_003_250515.cxs"

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_003_HNH_250515.pdb" models #1 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_003_OC1_250515.pdb" models #4 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_003_REC2_250515.pdb" models #2 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_003_REC3_250515.pdb" models #3 relModel #6

> close

> open "/Volumes/Charmaine/CryoDRGN atomic model/202505_local
> refinement/CryoSPARC files_202505 /openCRISPR_xMgCl2/OC-1_HNH.pdb"
> "/Volumes/Charmaine/CryoDRGN atomic model/202505_local refinement/CryoSPARC
> files_202505 /openCRISPR_xMgCl2/OC-1_REC2.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1_REC3.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_004_isolde_0318.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_004_sharp.mrc" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_004.mrc.cif"

Summary of feedback from opening /Volumes/Charmaine/CryoDRGN atomic
model/202505_local refinement/CryoSPARC files_202505
/openCRISPR_xMgCl2/vol_004.mrc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for OC-1_HNH.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC2.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC3.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for vol_004_isolde_0318.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Opened vol_004_sharp.mrc as #6, grid size 256,256,256, pixel 1.23, shown at
level 0.0765, step 1, values float32  
Chain information for vol_004.mrc.cif #7  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
Ba | No description available  
Bb Bc | No description available  
Bd Be | No description available  
Bf | No description available  
Bg | No description available  
Ca | No description available  
Cb | No description available  
Cc | No description available  
  

> transparency 50

> surface dust #6 size 12.3

> hide #5 models

> hide #1-3#!4,7 atoms

> show #1-3#!4,7 cartoons

> transparency 50

> matchmaker #1 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_004_isolde_0318.pdb, chain A (#5) with OC-1_HNH.pdb, chain A
(#1), sequence alignment score = 638.6  
RMSD between 129 pruned atom pairs is 0.619 angstroms; (across all 131 pairs:
0.674)  
  

> matchmaker #2 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_004_isolde_0318.pdb, chain A (#5) with OC-1_REC2.pdb, chain A
(#2), sequence alignment score = 653.5  
RMSD between 133 pruned atom pairs is 0.640 angstroms; (across all 133 pairs:
0.640)  
  

> matchmaker #3 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_004_isolde_0318.pdb, chain A (#5) with OC-1_REC3.pdb, chain A
(#3), sequence alignment score = 1132.5  
RMSD between 222 pruned atom pairs is 0.228 angstroms; (across all 222 pairs:
0.228)  
  

> matchmaker #4 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_004_isolde_0318.pdb, chain A (#5) with OC-1.pdb, chain A (#4),
sequence alignment score = 3999.5  
RMSD between 884 pruned atom pairs is 0.884 angstroms; (across all 894 pairs:
0.910)  
  

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_004_HNH_250515.pdb" models #1 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_004_OC1_250515.pdb" models #4 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_004_REC2_250515.pdb" models #2 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_004_REC3_250515.pdb" models #3 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_004_250515.cxs"

> close

> open "/Volumes/Charmaine/CryoDRGN atomic model/202505_local
> refinement/CryoSPARC files_202505 /openCRISPR_xMgCl2/OC-1_HNH.pdb"
> "/Volumes/Charmaine/CryoDRGN atomic model/202505_local refinement/CryoSPARC
> files_202505 /openCRISPR_xMgCl2/OC-1_REC2.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1_REC3.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_005_isolde_0318.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_005_sharp.mrc" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_005.mrc.cif"

Summary of feedback from opening /Volumes/Charmaine/CryoDRGN atomic
model/202505_local refinement/CryoSPARC files_202505
/openCRISPR_xMgCl2/vol_005.mrc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for OC-1_HNH.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC2.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC3.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for vol_005_isolde_0318.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Opened vol_005_sharp.mrc as #6, grid size 256,256,256, pixel 1.23, shown at
level 0.0392, step 1, values float32  
Chain information for vol_005.mrc.cif #7  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Ba | No description available  
Bb | No description available  
Bc | No description available  
Bd | No description available  
Ca | No description available  
Cb | No description available  
Cc | No description available  
Cd | No description available  
  

> transparency 50

> matchmaker #1 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_005_isolde_0318.pdb, chain A (#5) with OC-1_HNH.pdb, chain A
(#1), sequence alignment score = 621.2  
RMSD between 123 pruned atom pairs is 0.630 angstroms; (across all 131 pairs:
0.897)  
  

> matchmaker #2 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_005_isolde_0318.pdb, chain A (#5) with OC-1_REC2.pdb, chain A
(#2), sequence alignment score = 646.9  
RMSD between 131 pruned atom pairs is 0.613 angstroms; (across all 133 pairs:
0.667)  
  

> matchmaker #3 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_005_isolde_0318.pdb, chain A (#5) with OC-1_REC3.pdb, chain A
(#3), sequence alignment score = 1135.5  
RMSD between 222 pruned atom pairs is 0.404 angstroms; (across all 222 pairs:
0.404)  
  

> matchmaker #4 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_005_isolde_0318.pdb, chain A (#5) with OC-1.pdb, chain A (#4),
sequence alignment score = 4009.1  
RMSD between 849 pruned atom pairs is 0.919 angstroms; (across all 894 pairs:
1.252)  
  

> surface dust #6 size 12.3

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_005_250515.cxs"

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_005_HNH_250515.pdb" models #1 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_005_OC1_250515.pdb" models #4 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_005_REC2_250515.pdb" models #2 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_005_REC3_250515.pdb" models #3 relModel #6

> close

> open "/Volumes/Charmaine/CryoDRGN atomic model/202505_local
> refinement/CryoSPARC files_202505 /openCRISPR_xMgCl2/OC-1_HNH.pdb"
> "/Volumes/Charmaine/CryoDRGN atomic model/202505_local refinement/CryoSPARC
> files_202505 /openCRISPR_xMgCl2/OC-1_REC2.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1_REC3.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_006_isolde_0318.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_006_sharp.mrc" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_006.mrc.cif"

Summary of feedback from opening /Volumes/Charmaine/CryoDRGN atomic
model/202505_local refinement/CryoSPARC files_202505
/openCRISPR_xMgCl2/vol_006.mrc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for OC-1_HNH.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC2.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC3.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for vol_006_isolde_0318.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Opened vol_006_sharp.mrc as #6, grid size 256,256,256, pixel 1.23, shown at
level 0.103, step 1, values float32  
Chain information for vol_006.mrc.cif #7  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Ba Bb | No description available  
Bc | No description available  
Bd | No description available  
Be | No description available  
Ca | No description available  
Cb | No description available  
Cc | No description available  
Cd | No description available  
  

> surface dust #6 size 12.3

> hide #5 models

> hide #1-3#!4,7 atoms

> show #1-3#!4,7 cartoons

> transparency 50

> matchmaker #4 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_006_isolde_0318.pdb, chain A (#5) with OC-1.pdb, chain A (#4),
sequence alignment score = 3956.3  
RMSD between 806 pruned atom pairs is 1.013 angstroms; (across all 894 pairs:
5.430)  
  

> matchmaker #3 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_006_isolde_0318.pdb, chain A (#5) with OC-1_REC3.pdb, chain A
(#3), sequence alignment score = 1142.7  
RMSD between 222 pruned atom pairs is 0.334 angstroms; (across all 222 pairs:
0.334)  
  

> matchmaker #2 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_006_isolde_0318.pdb, chain A (#5) with OC-1_REC2.pdb, chain A
(#2), sequence alignment score = 646.9  
RMSD between 120 pruned atom pairs is 0.561 angstroms; (across all 133 pairs:
1.274)  
  

> matchmaker #1 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_006_isolde_0318.pdb, chain A (#5) with OC-1_HNH.pdb, chain A
(#1), sequence alignment score = 600.2  
RMSD between 123 pruned atom pairs is 0.861 angstroms; (across all 131 pairs:
1.420)  
  

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_006_OC1_250515.pdb" models #4 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_006_HNH_250515.pdb" models #1 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_006_REC2_250515.pdb" models #2 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_006_REC3_250515.pdb" models #3 relModel #6

> close

> open "/Volumes/Charmaine/CryoDRGN atomic model/202505_local
> refinement/CryoSPARC files_202505 /openCRISPR_xMgCl2/OC-1_HNH.pdb"
> "/Volumes/Charmaine/CryoDRGN atomic model/202505_local refinement/CryoSPARC
> files_202505 /openCRISPR_xMgCl2/OC-1_REC2.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1_REC3.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_007_isolde_0318.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_007_sharp.mrc" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_007.mrc.cif"

Summary of feedback from opening /Volumes/Charmaine/CryoDRGN atomic
model/202505_local refinement/CryoSPARC files_202505
/openCRISPR_xMgCl2/vol_007.mrc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for OC-1_HNH.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC2.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC3.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for vol_007_isolde_0318.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Opened vol_007_sharp.mrc as #6, grid size 256,256,256, pixel 1.23, shown at
level 0.128, step 1, values float32  
Chain information for vol_007.mrc.cif #7  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Ba | No description available  
Bb | No description available  
Bc | No description available  
Bd | No description available  
Be | No description available  
Ca | No description available  
Cb | No description available  
Cc | No description available  
  

> transparency 50

> hide atoms

> show cartoons

> hide #5 models

> matchmaker #1 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_007_isolde_0318.pdb, chain A (#5) with OC-1_HNH.pdb, chain A
(#1), sequence alignment score = 642.2  
RMSD between 124 pruned atom pairs is 0.572 angstroms; (across all 131 pairs:
0.891)  
  

> matchmaker #12to #5

Missing or invalid "matchAtoms" argument: only initial part "#12" of atom
specifier valid  

> matchmaker #2 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_007_isolde_0318.pdb, chain A (#5) with OC-1_REC2.pdb, chain A
(#2), sequence alignment score = 653.5  
RMSD between 131 pruned atom pairs is 0.437 angstroms; (across all 133 pairs:
0.603)  
  

> matchmaker #3 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_007_isolde_0318.pdb, chain A (#5) with OC-1_REC3.pdb, chain A
(#3), sequence alignment score = 1128.3  
RMSD between 210 pruned atom pairs is 0.411 angstroms; (across all 222 pairs:
0.702)  
  

> matchmaker #4 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_007_isolde_0318.pdb, chain A (#5) with OC-1.pdb, chain A (#4),
sequence alignment score = 4006.1  
RMSD between 849 pruned atom pairs is 0.937 angstroms; (across all 894 pairs:
1.274)  
  

> surface dust #6 size 12.3

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_007_HNH_250515.pdb" models #1 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_007_OC1_250515.pdb" models #4 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_007_REC2_250515.pdb" models #2 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_007_REC3_250515.pdb" models #3 relModel #6

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_007_250515.cxs"

> close

> open "/Volumes/Charmaine/CryoDRGN atomic model/202505_local
> refinement/CryoSPARC files_202505 /openCRISPR_xMgCl2/OC-1_HNH.pdb"
> "/Volumes/Charmaine/CryoDRGN atomic model/202505_local refinement/CryoSPARC
> files_202505 /openCRISPR_xMgCl2/OC-1_REC2.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1_REC3.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_006_isolde_0318.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_006_sharp.mrc" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_006.mrc.cif"

Summary of feedback from opening /Volumes/Charmaine/CryoDRGN atomic
model/202505_local refinement/CryoSPARC files_202505
/openCRISPR_xMgCl2/vol_006.mrc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for OC-1_HNH.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC2.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC3.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for vol_006_isolde_0318.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Opened vol_006_sharp.mrc as #6, grid size 256,256,256, pixel 1.23, shown at
level 0.103, step 1, values float32  
Chain information for vol_006.mrc.cif #7  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Ba Bb | No description available  
Bc | No description available  
Bd | No description available  
Be | No description available  
Ca | No description available  
Cb | No description available  
Cc | No description available  
Cd | No description available  
  

> hide #5 models

> surface dust #6 size 12.3

> hide #1-3#!4,7 atoms

> show #1-3#!4,7 cartoons

> transparency 50

> matchmaker #4 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_006_isolde_0318.pdb, chain A (#5) with OC-1.pdb, chain A (#4),
sequence alignment score = 3956.3  
RMSD between 806 pruned atom pairs is 1.013 angstroms; (across all 894 pairs:
5.430)  
  

> matchmaker #3 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_006_isolde_0318.pdb, chain A (#5) with OC-1_REC3.pdb, chain A
(#3), sequence alignment score = 1142.7  
RMSD between 222 pruned atom pairs is 0.334 angstroms; (across all 222 pairs:
0.334)  
  

> matchmaker # to #5

Missing or invalid "matchAtoms" argument: invalid atoms specifier  

> matchmaker #2 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_006_isolde_0318.pdb, chain A (#5) with OC-1_REC2.pdb, chain A
(#2), sequence alignment score = 646.9  
RMSD between 120 pruned atom pairs is 0.561 angstroms; (across all 133 pairs:
1.274)  
  

> matchmaker #1 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_006_isolde_0318.pdb, chain A (#5) with OC-1_HNH.pdb, chain A
(#1), sequence alignment score = 600.2  
RMSD between 123 pruned atom pairs is 0.861 angstroms; (across all 131 pairs:
1.420)  
  

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_006_250515.cxs"

> close

> open "/Volumes/Charmaine/CryoDRGN atomic model/202505_local
> refinement/CryoSPARC files_202505 /openCRISPR_xMgCl2/OC-1_HNH.pdb"
> "/Volumes/Charmaine/CryoDRGN atomic model/202505_local refinement/CryoSPARC
> files_202505 /openCRISPR_xMgCl2/OC-1_REC2.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1_REC3.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/OC-1.pdb" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_008_isolde_0319.pdb" "/Volumes/Charmaine/CryoDRGN
> atomic model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_008_sharp.mrc" "/Volumes/Charmaine/CryoDRGN atomic
> model/202505_local refinement/CryoSPARC files_202505
> /openCRISPR_xMgCl2/vol_008.mrc.cif"

Summary of feedback from opening /Volumes/Charmaine/CryoDRGN atomic
model/202505_local refinement/CryoSPARC files_202505
/openCRISPR_xMgCl2/vol_008.mrc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for OC-1_HNH.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC2.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1_REC3.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for OC-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for vol_008_isolde_0319.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Opened vol_008_sharp.mrc as #6, grid size 256,256,256, pixel 1.23, shown at
level 0.0837, step 1, values float32  
Chain information for vol_008.mrc.cif #7  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
Ba Bb | No description available  
Bc | No description available  
Bd | No description available  
Be | No description available  
Ca | No description available  
Cb | No description available  
Cc | No description available  
Cd | No description available  
Ce | No description available  
  

> hide atoms

> show cartoons

> hide #5 models

> surface dust #6 size 12.3

> matchmaker #1 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_008_isolde_0319.pdb, chain A (#5) with OC-1_HNH.pdb, chain A
(#1), sequence alignment score = 604.4  
RMSD between 123 pruned atom pairs is 1.158 angstroms; (across all 131 pairs:
1.250)  
  

> matchmaker #2 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_008_isolde_0319.pdb, chain A (#5) with OC-1_REC2.pdb, chain A
(#2), sequence alignment score = 639.7  
RMSD between 98 pruned atom pairs is 1.057 angstroms; (across all 133 pairs:
1.772)  
  

> matchmaker #3 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_008_isolde_0319.pdb, chain A (#5) with OC-1_REC3.pdb, chain A
(#3), sequence alignment score = 1111.5  
RMSD between 158 pruned atom pairs is 1.133 angstroms; (across all 222 pairs:
2.042)  
  

> matchmaker #4 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_008_isolde_0319.pdb, chain A (#5) with OC-1.pdb, chain A (#4),
sequence alignment score = 3978.5  
RMSD between 861 pruned atom pairs is 1.119 angstroms; (across all 894 pairs:
1.244)  
  

> transparency 50

> save "/Users/charmaine/Desktop/Rigid body fitting_202505/OC-1 no
> Mg/vol_008_250515.cxs"

——— End of log from Thu May 15 13:43:06 2025 ———

opened ChimeraX session  

> open "E:/CryoDRGN atomic model/202505_local refinement/CryoSPARC
> files_202505/openCRISPR_xMgCl2/vol_008_sharp.mrc"

Opened vol_008_sharp.mrc as #6, grid size 256,256,256, pixel 1.23, shown at
level 0.0837, step 1, values float32  

> surface dust #6 size 12.3

> save "E:/CryoDRGN atomic model/202505_local refinement/Rigid body
> fitting_202505/OC-1 no Mg/vol_008_250515.cxs"

> save "E:/CryoDRGN atomic model/202505_local refinement/Rigid body
> fitting_202505/OC-1 no Mg/vol_008_HNH_250515.pdb" models #1 relModel #6

> save "E:/CryoDRGN atomic model/202505_local refinement/Rigid body
> fitting_202505/OC-1 no Mg/vol_008_REC2_250515.pdb" models #2 relModel #6

> save "E:/CryoDRGN atomic model/202505_local refinement/Rigid body
> fitting_202505/OC-1 no Mg/vol_008_HNH_250515.pdb" models #1 relModel #6

> save "E:/CryoDRGN atomic model/202505_local refinement/Rigid body
> fitting_202505/OC-1 no Mg/vol_008_OC1_250515.pdb" models #4 relModel #6

> save "E:/CryoDRGN atomic model/202505_local refinement/Rigid body
> fitting_202505/OC-1 no Mg/vol_008_REC2_250515.pdb" models #2 relModel #6

> save "E:/CryoDRGN atomic model/202505_local refinement/Rigid body
> fitting_202505/OC-1 no Mg/vol_008_REC3_250515.pdb" models #3 relModel #6

> close

> open "E:\CryoDRGN atomic model\202505_local refinement\Rigid body
> fitting_202505\OC-1 no Mg\vol_008_OC1_250515.pdb" format pdb

Chain information for vol_008_OC1_250515.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> close

> open "C:/Users/User/Desktop/HOMOGENEOUS REFINEMENT/SpCas9/vol_000.mrc.cif"

Summary of feedback from opening C:/Users/User/Desktop/HOMOGENEOUS
REFINEMENT/SpCas9/vol_000.mrc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for vol_000.mrc.cif #1  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
Aj | No description available  
Ba Bb Bc Bd Be | No description available  
Bf | No description available  
Bg Bi | No description available  
Bh Bj Bk Bl Bm | No description available  
Bn Bo | No description available  
Bp Bq | No description available  
Br | No description available  
Bs | No description available  
Bt | No description available  
  

> open "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_0.cif"

Chain information for fold_2024_09_04_13_34_spcas9_model_0.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_1.cif"

Chain information for fold_2024_09_04_13_34_spcas9_model_1.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_2.cif"

Chain information for fold_2024_09_04_13_34_spcas9_model_2.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_3.cif"

Chain information for fold_2024_09_04_13_34_spcas9_model_3.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_4.cif"

Chain information for fold_2024_09_04_13_34_spcas9_model_4.cif #6  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open "C:/Users/User/Desktop/HOMOGENEOUS REFINEMENT/SpCas9/vol_000.mrc"

Opened vol_000.mrc as #7, grid size 256,256,256, pixel 1.23, shown at level
0.00283, step 1, values float32  

> close

> open "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_0.cif"

Chain information for fold_2024_09_04_13_34_spcas9_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_1.cif"

Chain information for fold_2024_09_04_13_34_spcas9_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_2.cif"

Chain information for fold_2024_09_04_13_34_spcas9_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_3.cif"

Chain information for fold_2024_09_04_13_34_spcas9_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_4.cif"

Chain information for fold_2024_09_04_13_34_spcas9_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open "C:/Users/User/Desktop/HOMOGENEOUS REFINEMENT/SpCas9/vol_000.mrc"

Opened vol_000.mrc as #6, grid size 256,256,256, pixel 1.23, shown at level
0.00283, step 1, values float32  

> open "C:/Users/User/Desktop/HOMOGENEOUS REFINEMENT/SpCas9/vol_000.mrc.cif"

Summary of feedback from opening C:/Users/User/Desktop/HOMOGENEOUS
REFINEMENT/SpCas9/vol_000.mrc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for vol_000.mrc.cif #7  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
Aj | No description available  
Ba Bb Bc Bd Be | No description available  
Bf | No description available  
Bg Bi | No description available  
Bh Bj Bk Bl Bm | No description available  
Bn Bo | No description available  
Bp Bq | No description available  
Br | No description available  
Bs | No description available  
Bt | No description available  
  

> matchmaker #1 to #7

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_000.mrc.cif, chain Ad (#7) with
fold_2024_09_04_13_34_spcas9_model_0.cif, chain A (#1), sequence alignment
score = 723  
RMSD between 159 pruned atom pairs is 1.025 angstroms; (across all 171 pairs:
2.140)  
  

> matchmaker #2 to #7

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_000.mrc.cif, chain Ad (#7) with
fold_2024_09_04_13_34_spcas9_model_1.cif, chain A (#2), sequence alignment
score = 723  
RMSD between 158 pruned atom pairs is 1.037 angstroms; (across all 171 pairs:
2.121)  
  

> matchmaker #3 to #7

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_000.mrc.cif, chain Ad (#7) with
fold_2024_09_04_13_34_spcas9_model_2.cif, chain A (#3), sequence alignment
score = 723  
RMSD between 155 pruned atom pairs is 1.044 angstroms; (across all 171 pairs:
2.181)  
  

> matchmaker #4 to #7

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_000.mrc.cif, chain Ad (#7) with
fold_2024_09_04_13_34_spcas9_model_3.cif, chain A (#4), sequence alignment
score = 723  
RMSD between 160 pruned atom pairs is 0.988 angstroms; (across all 171 pairs:
2.116)  
  

> matchmaker #5 to #7

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_000.mrc.cif, chain Ad (#7) with
fold_2024_09_04_13_34_spcas9_model_4.cif, chain A (#5), sequence alignment
score = 723  
RMSD between 156 pruned atom pairs is 1.007 angstroms; (across all 171 pairs:
2.142)  
  

> view clip false

> surface dust #6 size 12.3

> view clip false

> hide #!6 models

> show #!6 models

> volume #6 style mesh

> volume #6 level 0.001467

> close #7

> hide #!6 models

> show #!6 models

> hide #5 models

> close #5

> hide #3 models

> close #3

> hide #1 models

> hide #!6 models

> show #!6 models

> close #2

> show #1 models

> close #1

> addh

Summary of feedback from adding hydrogens to
fold_2024_09_04_13_34_spcas9_model_3.cif #4  
---  
notes | Termini for fold_2024_09_04_13_34_spcas9_model_3.cif (#4) chain A determined from SEQRES records  
Termini for fold_2024_09_04_13_34_spcas9_model_3.cif (#4) chain B determined
from SEQRES records  
Termini for fold_2024_09_04_13_34_spcas9_model_3.cif (#4) chain C determined
from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASP 1368  
Chain-final residues that are not actual C termini:  
1569 hydrogen bonds  
12908 hydrogens added  
  

> clipper associate #6 toModel #4

Opened vol_000.mrc as #1.1.1.1, grid size 256,256,256, pixel 1.23, shown at
level 0.00965, step 1, values float32  
Chain information for fold_2024_09_04_13_34_spcas9_model_3.cif  
---  
Chain | Description  
1.2/A | .  
1.2/B | .  
1.2/C | .  
  

> addh

Summary of feedback from adding hydrogens to
fold_2024_09_04_13_34_spcas9_model_3.cif #1.2  
---  
notes | Termini for fold_2024_09_04_13_34_spcas9_model_3.cif (#1.2) chain A determined from SEQRES records  
Termini for fold_2024_09_04_13_34_spcas9_model_3.cif (#1.2) chain B determined
from SEQRES records  
Termini for fold_2024_09_04_13_34_spcas9_model_3.cif (#1.2) chain C determined
from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASP 1368  
Chain-final residues that are not actual C termini:  
1504 hydrogen bonds  
0 hydrogens added  
  

> hbonds

1504 hydrogen bonds found  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 232 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> volume #1.1.1.1 level 0.001189

> view clip false

> surface dust #1.1.1.1 size 12.3

Deleted the following atoms from residue DA B1: OP1  
Deleted the following atoms from residue G C1: OP1  

> isolde sim start /A:638

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 /A:530

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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  

> isolde sim start /A:1299

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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  

> isolde sim start /B:13-16,18-21

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /C:83-84,96-98

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 /A:94,96,100

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /A:70,460,462/C:61-62

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 /A:1272/C:90

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 /A:450,464,491/B:37-39/C:15-16

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /A:1205-1207,1210,1341

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:721,735,738,742/C:66-68

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /A:340/C:41-42

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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  

> isolde sim start /A:1118,1135-1136/B:5-6

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 /A:215,307,373,392,396-397,400,404,406

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:5-10,25-28

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:1017,1019,1031

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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  

> isolde sim start /B:6-9,25-27

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:1342

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:139,161,318,418

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:37-38/C:15-16

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:450/B:37-38/C:15-16

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:6-9,25-27

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/vol000_isolde_250604.pdb"

> save "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/vol_000_isolde_250604.pdb"

> save "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/vol_000_250604.cxs"

Taking snapshot of stepper: fold_2024_09_04_13_34_spcas9_model_3.cif  

——— End of log from Wed Jun 4 13:11:02 2025 ———

opened ChimeraX session  

> save "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/vol_000_isolde_250604.pdb" relModel #1.1.1.1

> close

> open "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_0.cif"
> "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_1.cif"
> "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_2.cif"
> "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_3.cif"
> "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/fold_2024_09_04_13_34_spcas9_model_4.cif"
> "C:/Users/User/Desktop/HOMOGENEOUS REFINEMENT/SpCas9/vol_002.mrc"
> "C:/Users/User/Desktop/HOMOGENEOUS REFINEMENT/SpCas9/vol_002.mrc.cif"

Summary of feedback from opening C:/Users/User/Desktop/HOMOGENEOUS
REFINEMENT/SpCas9/vol_002.mrc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for fold_2024_09_04_13_34_spcas9_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Chain information for fold_2024_09_04_13_34_spcas9_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Chain information for fold_2024_09_04_13_34_spcas9_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Chain information for fold_2024_09_04_13_34_spcas9_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Chain information for fold_2024_09_04_13_34_spcas9_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Opened vol_002.mrc as #6, grid size 256,256,256, pixel 1.23, shown at level
0.00173, step 1, values float32  
Chain information for vol_002.mrc.cif #7  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
Aj | No description available  
Ak | No description available  
Al | No description available  
Am | No description available  
An | No description available  
Ao | No description available  
Ba Bb Bc Bd Be Bf Bg | No description available  
Bh Bi Bj Bk Bl | No description available  
Bm | No description available  
Bn Bo Bp | No description available  
Bq | No description available  
Br | No description available  
Bs | No description available  
Bt | No description available  
Bu | No description available  
Bv | No description available  
Bw | No description available  
  

> matchmaker #5 to #7

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_002.mrc.cif, chain Ad (#7) with
fold_2024_09_04_13_34_spcas9_model_4.cif, chain A (#5), sequence alignment
score = 622  
RMSD between 140 pruned atom pairs is 1.034 angstroms; (across all 153 pairs:
1.375)  
  

> matchmaker 45 to #7

Missing or invalid "matchAtoms" argument: invalid atoms specifier  

> matchmaker #4 to #7

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_002.mrc.cif, chain Ad (#7) with
fold_2024_09_04_13_34_spcas9_model_3.cif, chain A (#4), sequence alignment
score = 622  
RMSD between 141 pruned atom pairs is 1.009 angstroms; (across all 153 pairs:
1.350)  
  

> matchmaker #3 to #7

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_002.mrc.cif, chain Ad (#7) with
fold_2024_09_04_13_34_spcas9_model_2.cif, chain A (#3), sequence alignment
score = 622  
RMSD between 141 pruned atom pairs is 1.078 angstroms; (across all 153 pairs:
1.403)  
  

> matchmaker #2 to #7

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_002.mrc.cif, chain Ad (#7) with
fold_2024_09_04_13_34_spcas9_model_1.cif, chain A (#2), sequence alignment
score = 622  
RMSD between 140 pruned atom pairs is 1.062 angstroms; (across all 153 pairs:
1.397)  
  

> matchmaker #1 to #7

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vol_002.mrc.cif, chain Ad (#7) with
fold_2024_09_04_13_34_spcas9_model_0.cif, chain A (#1), sequence alignment
score = 622  
RMSD between 141 pruned atom pairs is 1.045 angstroms; (across all 153 pairs:
1.375)  
  

> close #7

> view clip false

> volume #6 style mesh

> close #5

> close #3

> close #1

> hide #!6 models

> hide #2 models

> show #2 models

> show #!6 models

> hide #4 models

> close #4

> clipper associate #6 toModel #2

Opened vol_002.mrc as #1.1.1.1, grid size 256,256,256, pixel 1.23, shown at
level 0.00853, step 1, values float32  
Chain information for fold_2024_09_04_13_34_spcas9_model_1.cif  
---  
Chain | Description  
1.2/A | .  
1.2/B | .  
1.2/C | .  
  

> addh

Summary of feedback from adding hydrogens to
fold_2024_09_04_13_34_spcas9_model_1.cif #1.2  
---  
notes | Termini for fold_2024_09_04_13_34_spcas9_model_1.cif (#1.2) chain A determined from SEQRES records  
Termini for fold_2024_09_04_13_34_spcas9_model_1.cif (#1.2) chain B determined
from SEQRES records  
Termini for fold_2024_09_04_13_34_spcas9_model_1.cif (#1.2) chain C determined
from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASP 1368  
Chain-final residues that are not actual C termini:  
1575 hydrogen bonds  
12908 hydrogens added  
  

> hbonds

1506 hydrogen bonds found  

> view clip false

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 233 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> volume #1.1.1.1 level 0.006931

> volume #1.1.1.1 level 0.001338

> surface dust #1.1.1.1 size 12.3

Deleted the following atoms from residue DA B1: OP1  
Deleted the following atoms from residue G C1: OP1  

> isolde sim start /A:308

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 /A:551

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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  

> isolde sim start /A:651

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 /B:6-7,27-28

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:1109/B:32-33

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 /A:139,161,318,418

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 /A:515,519,661-662/C:6

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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  

> isolde sim start /A:561,583-586

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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  

> isolde sim start /A:90,93-97,100

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /A:918,1007,1039/C:1

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /A:1260,1263,1302

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /A:1205-1207,1210,1341

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:450-451,464,488,491,626,631/B:36-38/C:15-16

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 6 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /A:1272/C:90

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 /A:738,742/C:67-68

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 /A:63,66,70/C:14-16

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:512,514,613,615-626,639

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /B:13-15,18-21

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:3/C:83-85,96-97

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 /A:63,66,70/C:14-16

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /C:30-32,39-41

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 /C:34,36-37

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:63,66,70/C:14-16

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /C:34,36-37

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /C:34,36-37

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/vol_002_isolde_250604.pdb" relModel #1.1.1.1

> save "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/vol_002_250604.cxs"

Taking snapshot of stepper: fold_2024_09_04_13_34_spcas9_model_1.cif  
Taking snapshot of stepper: fold_2024_09_04_13_34_spcas9_model_3.cif  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1418, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> <chimerax.isolde.navigate.ResidueStepper
object at 0x0000029543800950> -> <chimerax.atomic.structure.AtomicStructure
object at 0x000002958AC5FFD0> 'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1418, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> <chimerax.isolde.navigate.ResidueStepper
object at 0x0000029543800950> -> <chimerax.atomic.structure.AtomicStructure
object at 0x000002958AC5FFD0> 'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/vol_002_250604.cxs"

Taking snapshot of stepper: fold_2024_09_04_13_34_spcas9_model_1.cif  
Taking snapshot of stepper: fold_2024_09_04_13_34_spcas9_model_3.cif  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1418, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> <chimerax.isolde.navigate.ResidueStepper
object at 0x0000029543800950> -> <chimerax.atomic.structure.AtomicStructure
object at 0x000002958AC5FFD0> 'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1418, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> <chimerax.isolde.navigate.ResidueStepper
object at 0x0000029543800950> -> <chimerax.atomic.structure.AtomicStructure
object at 0x000002958AC5FFD0> 'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/vol_002_250604.cxs"

Taking snapshot of stepper: fold_2024_09_04_13_34_spcas9_model_1.cif  
Taking snapshot of stepper: fold_2024_09_04_13_34_spcas9_model_3.cif  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1418, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> <chimerax.isolde.navigate.ResidueStepper
object at 0x0000029543800950> -> <chimerax.atomic.structure.AtomicStructure
object at 0x000002958AC5FFD0> 'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1418, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> <chimerax.isolde.navigate.ResidueStepper
object at 0x0000029543800950> -> <chimerax.atomic.structure.AtomicStructure
object at 0x000002958AC5FFD0> 'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/User/Desktop/HOMOGENEOUS
> REFINEMENT/SpCas9/vol_002_250604.cxs"

Taking snapshot of stepper: fold_2024_09_04_13_34_spcas9_model_1.cif  
Taking snapshot of stepper: fold_2024_09_04_13_34_spcas9_model_3.cif  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1418, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> <chimerax.isolde.navigate.ResidueStepper
object at 0x0000029543800950> -> <chimerax.atomic.structure.AtomicStructure
object at 0x000002958AC5FFD0> 'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1418, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> <chimerax.isolde.navigate.ResidueStepper
object at 0x0000029543800950> -> <chimerax.atomic.structure.AtomicStructure
object at 0x000002958AC5FFD0> 'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/User/Desktop/HOMOGENEOUS REFINEMENT/SpCas9/d.cxs"

Taking snapshot of stepper: fold_2024_09_04_13_34_spcas9_model_1.cif  
Taking snapshot of stepper: fold_2024_09_04_13_34_spcas9_model_3.cif  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1418, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> <chimerax.isolde.navigate.ResidueStepper
object at 0x0000029543800950> -> <chimerax.atomic.structure.AtomicStructure
object at 0x000002958AC5FFD0> 'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1418, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x0000029543800950> ->
<chimerax.atomic.structure.AtomicStructure object at 0x000002958AC5FFD0>
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> <chimerax.isolde.navigate.ResidueStepper
object at 0x0000029543800950> -> <chimerax.atomic.structure.AtomicStructure
object at 0x000002958AC5FFD0> 'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif': Error while saving session data
for 'isolde residue stepper 0' -> ->
'fold_2024_09_04_13_34_spcas9_model_3.cif'  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 561.09
OpenGL renderer: NVIDIA GeForce RTX 4090 D/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 137,132,670,976
MaxProcessMemory: 137,438,953,344
CPU: 32 Intel(R) Core(TM) i9-14900K
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 5 months ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: ResidueStepper holding reference to dead model

comment:2 by pett, 5 months ago

Resolution: → duplicate
Status: assigned → closed
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