ResidueStepper refers to dead Structure

[mille153@…]

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

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

> open /Users/mille153/Downloads/practice-fnv-E-fit.cxs format session

Opened cryosparc_P102_J43_008_volume_map.mrc as #1.1.1.1, grid size
600,600,600, pixel 1.33, shown at level 0.0897, step 1, values float32  
Restoring stepper: best-model-fit-sorta-2.pdb  
Log from Wed Nov 2 16:37:45 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select #1/A:414-493

1182 atoms, 1195 bonds, 80 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> select #1/A:418-493

1143 atoms, 1156 bonds, 76 residues, 1 model selected  

> select #1/A:420-493

1107 atoms, 1118 bonds, 74 residues, 1 model selected  

> select #1/A:446-493

747 atoms, 752 bonds, 48 residues, 1 model selected  

> select clear

> open
> /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best_model_fit-
> sorta.pdb

Chain information for best_model_fit-sorta.pdb #2  
---  
Chain | Description  
A | No description available  
  

> matchmaker #2 to #1

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 best_model.pdb, chain A (#1) with best_model_fit-sorta.pdb, chain A
(#2), sequence alignment score = 2425.5  
RMSD between 283 pruned atom pairs is 1.125 angstroms; (across all 493 pairs:
5.309)  
  

> hide #2 models

> show #2 models

> hide #2 models

> select #1/A:413-493

1199 atoms, 1212 bonds, 81 residues, 1 model selected  

> show #2 models

> select #1/A:413-423

144 atoms, 146 bonds, 11 residues, 1 model selected  

> select #1/A:392-493

1515 atoms, 1529 bonds, 102 residues, 1 model selected  

> select #1/A:421-446

360 atoms, 365 bonds, 26 residues, 1 model selected  

> select #1/A:413-420

112 atoms, 114 bonds, 8 residues, 1 model selected  

> select #1/A:413-422

134 atoms, 136 bonds, 10 residues, 1 model selected  

> select #1/A:413-421

123 atoms, 125 bonds, 9 residues, 1 model selected  

> select #1/A:413-420

112 atoms, 114 bonds, 8 residues, 1 model selected  

> select #1/A:413-421

123 atoms, 125 bonds, 9 residues, 1 model selected  

> select #1/A:421

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

> select clear

Populating font family aliases took 757 ms. Replace uses of missing font
family ".SF NS Text" with one that exists to avoid this cost.  

> save /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-model-
> fit-sorta-2.pdb models #1 relModel #2

> close #1

> close

> open /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-model-
> fit-sorta-2.pdb format pdb

Chain information for best-model-fit-sorta-2.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /Users/mille153/Downloads/cryosparc_P102_J43_008_volume_map.mrc format
> mrc

Opened cryosparc_P102_J43_008_volume_map.mrc as #2, grid size 600,600,600,
pixel 1.33, shown at level 0.108, step 4, values float32  

> volume #2 step 1

> select #1/A:413

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

> hide #!2 models

> select #1/A:414

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

> show #!2 models

> select #1/A:414-423

127 atoms, 129 bonds, 10 residues, 1 model selected  

> select #1/A:414

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

> select #1/A:415

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

> select #1/A:414

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

> select #1/A:416

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

> select #1/A:417

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

> select #1/A:417-423

98 atoms, 100 bonds, 7 residues, 1 model selected  

> select #1/A:418

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:418-421

67 atoms, 69 bonds, 4 residues, 1 model selected  

> volume #2 level 0.09638

> volume #2 level 0.08963

> select clear

> hide #!2 models

> select #1/A:4115

Nothing selected  

> select #1/A:4115

Nothing selected  

> select #1/A:415

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

> select #1/A:413

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

> select #1/A:414

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

> select #1/A:415

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

> select #1/A:416

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

> select #1/A:417

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

> select #1/A:418

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:415

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

> select #1/A:414

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

> select #1/A:415

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

> select clear

> show #!2 models

> volume #2 level 0.06116

> volume #2 level 0.08625

> volume #2 color #bcbcbc

> volume #2 color #bcbcbca1

[Repeated 1 time(s)]

> view orient

> ui tool show "Fit in Map"

> fitmap #1 inMap #2

Fit molecule best-model-fit-sorta-2.pdb (#1) to map
cryosparc_P102_J43_008_volume_map.mrc (#2) using 7449 atoms  
average map value = 0.09499, steps = 68  
shifted from previous position = 0.886  
rotated from previous position = 2.97 degrees  
atoms outside contour = 3224, contour level = 0.086248  
  
Position of best-model-fit-sorta-2.pdb (#1) relative to
cryosparc_P102_J43_008_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99890344 0.01542641 0.04420343 -33.17003156  
-0.01444810 0.99964543 -0.02236672 19.33198915  
-0.04453279 0.02170353 0.99877214 8.10464247  
Axis 0.42586831 0.85749328 -0.28868920  
Axis point 161.88374769 -0.00000000 755.48281196  
Rotation angle (degrees) 2.96590210  
Shift along axis 0.11126255  
  

> view orient

> save /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-model-
> fit-sorta-2.pdb relModel #2

> close #1

> close #2

> isolde start

> set selectionWidth 4

> open /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-model-
> fit-sorta-2.pdb format pdb

Chain information for best-model-fit-sorta-2.pdb #1  
---  
Chain | Description  
A | No description available  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 49 residues in model #1 to IUPAC-IUB
standards.  
Chain information for best-model-fit-sorta-2.pdb  
---  
Chain | Description  
1.2/A | No description available  
  
ISOLDE: created disulfide bonds between the following residues:  
A74-A105; A60-A121; A182-A283; A92-A116; A3-A30; A300-A330  

> ui mousemode right "translate selected atoms"

> isolde cisflip #1.2/A:329

Performing cis<\-->trans flip for 1 residues  

> distance restraints

Unknown command: isolde distance restraints  

> distancerestraints

Unknown command: isolde distancerestraints  

> isolde cisflip #1.2/A:329

Performing cis<\-->trans flip for 1 residues  

> isolde restrain distances

Missing or invalid "atoms" argument: empty atom specifier  

> isolde restrain distances #1

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

> addh

Summary of feedback from adding hydrogens to best-model-fit-sorta-2.pdb #1.2  
---  
notes | No usable SEQRES records for best-model-fit-sorta-2.pdb (#1.2) chain
A; guessing termini instead  
Chain-initial residues that are actual N termini: /A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ALA 493  
Chain-final residues that are not actual C termini:  
374 hydrogen bonds  
0 hydrogens added  
  

> isolde cisflip #1.2/A:329

Performing cis<\-->trans flip for 1 residues  

> select clear

> close #1.2.5

> isolde restrain distances #1

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

> alphafold pae #1.2 file
> /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best_model_pae.json
> plot false

> open /Users/mille153/Downloads/cryosparc_P102_J43_008_volume_map.mrc format
> mrc

Opened cryosparc_P102_J43_008_volume_map.mrc as #2, grid size 600,600,600,
pixel 1.33, shown at level 0.108, step 4, values float32  

> volume #2 step 1

> transparency 50

> isolde cisflip #1.2/A:329

Performing cis<\-->trans flip for 1 residues  

> hide #!2 models

> ui tool show "Ramachandran Plot"

[Repeated 1 time(s)]

> save /Users/mille153/Downloads/practice-fnv-E-fit.cxs

Taking snapshot of stepper: best-model-fit-sorta-2.pdb  

> close #1.2.5

> select clear

> show cartoons

> hide atoms

> view orient

> clipper associate #2 toModel #1

Opened cryosparc_P102_J43_008_volume_map.mrc as #1.1.1.1, grid size
600,600,600, pixel 1.33, shown at step 1, values float32  

> hide #!1.2 models

> show #!1.2 models

> volume #1.1.1.1 level 0.08965

> select add #1.2

7449 atoms, 7530 bonds, 493 residues, 6 models selected  

> clipper isolate sel maskRadius 7.0 focus false

> show sel atoms

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 style surface

> transparency 50

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 15 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> clipper isolate sel maskRadius 7.0 focus false

> isolde cisflip #1.2/A:329

Performing cis<\-->trans flip for 1 residues  
ISOLDE: started sim  

> isolde sim stop discardTo start

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

> isolde cisflip #1.2/A:329

Performing cis<\-->trans flip for 1 residues  
ISOLDE: started sim  

> isolde sim stop discardTo start

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

> isolde cisflip #1.2/A:329

Performing cis<\-->trans flip for 1 residues  
ISOLDE: started sim  

> isolde sim stop discardTo start

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

> ui tool show "Ramachandran Plot"

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  
ISOLDE: started sim  

> isolde sim stop discardTo start

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

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  
ISOLDE: started sim  

> isolde sim stop discardTo start

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

> clipper isolate sel maskRadius 7.0 focus false

> select add #1.2

7449 atoms, 7530 bonds, 493 residues, 11 models selected  

> clipper isolate sel maskRadius 7.0 focus false

> ui mousemode right "translate selected atoms"

[Repeated 1 time(s)]

> isolde release torsions #1.2&sel

> select clear

[Repeated 4 time(s)]

> save /Users/mille153/Downloads/practice-fnv-E-fit.cxs

Taking snapshot of stepper: best-model-fit-sorta-2.pdb  

——— End of log from Wed Nov 2 16:37:45 2022 ———

opened ChimeraX session  

> clipper isolate sel maskRadius 7.0 focus false

> save /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-model-
> fit-2.pdb relModel #1.1.1.1

> close session

> open /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-model-
> fit-2.pdb format pdb

Chain information for best-model-fit-2.pdb #1  
---  
Chain | Description  
A | No description available  
  

> close session

> open /Users/mille153/Downloads/cryosparc_P102_J43_008_volume_map.mrc format
> mrc

Opened cryosparc_P102_J43_008_volume_map.mrc as #1, grid size 600,600,600,
pixel 1.33, shown at level 0.108, step 4, values float32  

> volume #1 step 1

> open /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-model-
> fit-2.pdb

Chain information for best-model-fit-2.pdb #2  
---  
Chain | Description  
A | No description available  
  

> volume #1 level 0.09841

> volume #1 level 0.1019

> transparency 50

> ui mousemode right "clip rotate"

[Repeated 1 time(s)]

> close #1

> close

> open /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-model-
> fit-2.pdb format pdb

Chain information for best-model-fit-2.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /Users/mille153/Downloads/cryosparc_P102_J43_008_volume_map.mrc format
> mrc

Opened cryosparc_P102_J43_008_volume_map.mrc as #2, grid size 600,600,600,
pixel 1.33, shown at level 0.108, step 4, values float32  

> volume #2 step 1

> transparency 50

> open /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-model-
> fit-2.pdb

Chain information for best-model-fit-2.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> select #3

7449 atoms, 7530 bonds, 493 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.95696,0.19236,0.21733,-198.49,-0.15415,0.97133,-0.18098,184.2,-0.24591,0.13969,0.95917,62.576

> view matrix models
> #3,-0.96989,-0.20713,-0.12808,985.75,0.11151,-0.84527,0.52257,482.25,-0.2165,0.49256,0.84292,-40.972

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.96989,-0.20713,-0.12808,986.38,0.11151,-0.84527,0.52257,411.65,-0.2165,0.49256,0.84292,-27.917

> view matrix models
> #3,-0.98033,-0.15412,0.1233,817.5,0.1946,-0.85905,0.47347,412.63,0.032945,0.48815,0.87214,-146.53

> view matrix models
> #3,-0.98033,-0.15412,0.1233,817.38,0.1946,-0.85905,0.47347,409.58,0.032945,0.48815,0.87214,-145.96

> show #1 models

> hide #1 models

> view matrix models
> #3,-0.98033,-0.15412,0.1233,811.96,0.1946,-0.85905,0.47347,409.17,0.032945,0.48815,0.87214,-145.3

> view matrix models
> #3,-0.97178,-0.1246,0.20028,749.35,0.21462,-0.81934,0.53162,348.35,0.097861,0.5596,0.82297,-175.48

> view matrix models
> #3,-0.96911,-0.14466,0.19976,757.67,0.20161,-0.93117,0.30377,539.7,0.14206,0.33466,0.93157,-156

> view matrix models
> #3,-0.96911,-0.14466,0.19976,765.16,0.20161,-0.93117,0.30377,544.23,0.14206,0.33466,0.93157,-157.37

> view matrix models
> #3,-0.97123,-0.14133,0.19166,769.32,0.20225,-0.91443,0.35059,508.59,0.12571,0.37927,0.91671,-162.05

> view matrix models
> #3,-0.93156,-0.081064,0.35443,628.96,0.21713,-0.90594,0.36348,490.92,0.29163,0.41557,0.86154,-214.52

> view matrix models
> #3,-0.95599,-0.1019,0.27513,695.58,0.21065,-0.89114,0.40186,464.12,0.20423,0.44213,0.87339,-197.43

> view matrix models
> #3,-0.95765,-0.15982,0.23953,743.7,0.24466,-0.89024,0.3842,460.1,0.15184,0.42654,0.89163,-179.47

> view matrix models
> #3,-0.95834,-0.16991,0.22959,754.47,0.25908,-0.85553,0.44827,400.36,0.12025,0.48907,0.86391,-178.37

> view matrix models
> #3,-0.95279,-0.2646,0.14889,843.07,0.29657,-0.91611,0.26979,518.23,0.065014,0.30121,0.95134,-122

> volume #2 color #b2b2b2

> volume #2 color #9b9b9b

> lighting simple

> lighting soft

> lighting simple

> volume #2 color #9b9b9b73

> set bgColor white

> view matrix models
> #3,-0.95279,-0.2646,0.14889,835.35,0.29657,-0.91611,0.26979,515.15,0.065014,0.30121,0.95134,-122.67

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.94962,-0.31165,-0.033171,963.41,0.28951,-0.91281,0.28803,505.76,-0.12004,0.26391,0.95705,-32.488

> view matrix models
> #3,-0.91355,-0.37295,-0.1623,1052.9,0.30884,-0.8957,0.3199,471.08,-0.26468,0.24212,0.93345,51.302

> view matrix models
> #3,-0.92983,-0.3546,-0.098417,1013.4,0.31673,-0.9073,0.27657,498.78,-0.18736,0.22599,0.95594,13.273

> view matrix models
> #3,-0.92542,-0.36026,-0.1175,1025.5,0.31436,-0.90301,0.29282,488.17,-0.2116,0.23404,0.94892,23.813

> view matrix models
> #3,-0.96951,-0.16598,-0.18027,992.71,0.11168,-0.95411,0.27785,604.19,-0.21811,0.24924,0.94356,22.786

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.96951,-0.16598,-0.18027,997.93,0.11168,-0.95411,0.27785,607.12,-0.21811,0.24924,0.94356,23.255

> show #1 models

> ui tool show "Fit in Map"

> fitmap #3 inMap #2

Fit molecule best-model-fit-2.pdb (#3) to map
cryosparc_P102_J43_008_volume_map.mrc (#2) using 7449 atoms  
average map value = 0.1092, steps = 124  
shifted from previous position = 2.95  
rotated from previous position = 25.3 degrees  
atoms outside contour = 3675, contour level = 0.10844  
  
Position of best-model-fit-2.pdb (#3) relative to
cryosparc_P102_J43_008_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.97718955 0.02857663 0.21043756 678.77355886  
0.04034551 -0.94787861 0.31606708 609.98999935  
0.20850139 0.31734766 0.92510412 -174.19712113  
Axis 0.10675351 0.16140610 0.98109722  
Axis point 347.93172272 320.36150537 0.00000000  
Rotation angle (degrees) 179.65634826  
Shift along axis 0.01325755  
  

> save /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-model-
> fit-2a.pdb models #3 relModel #2

> select subtract #3

Nothing selected  

> volume #2 level 0.1036

> open /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-model-
> fit-2a.pdb

Chain information for best-model-fit-2a.pdb #4  
---  
Chain | Description  
A | No description available  
  

> select #4

7449 atoms, 7530 bonds, 493 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.96923,-0.23007,0.087515,851.73,0.22725,-0.97297,-0.041006,693.56,0.094584,-0.019856,0.99532,-28.67

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.96923,-0.23007,0.087515,813.42,0.22725,-0.97297,-0.041006,710.51,0.094584,-0.019856,0.99532,-26.636

> view matrix models
> #4,-0.96923,-0.23007,0.087515,812.98,0.22725,-0.97297,-0.041006,716.53,0.094584,-0.019856,0.99532,-27.946

> view matrix models
> #4,-0.96923,-0.23007,0.087515,814.17,0.22725,-0.97297,-0.041006,721.8,0.094584,-0.019856,0.99532,-28.371

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.99279,-0.046172,0.11057,738.98,0.045759,-0.99893,-0.006273,786.16,0.11075,-0.0011681,0.99385,-41.408

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.99279,-0.046172,0.11057,746.08,0.045759,-0.99893,-0.006273,784.66,0.11075,-0.0011681,0.99385,-40.522

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.99313,0.0090064,0.11669,721.21,-0.0084159,-0.99995,0.0055522,800.39,0.11674,0.004532,0.99315,-44.79

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.99313,0.0090064,0.11669,720.32,-0.0084159,-0.99995,0.0055522,799.25,0.11674,0.004532,0.99315,-44.753

> fitmap #4 inMap #2

Fit molecule best-model-fit-2a.pdb (#4) to map
cryosparc_P102_J43_008_volume_map.mrc (#2) using 7449 atoms  
average map value = 0.1092, steps = 80  
shifted from previous position = 2.12  
rotated from previous position = 6.71 degrees  
atoms outside contour = 3328, contour level = 0.10364  
  
Position of best-model-fit-2a.pdb (#4) relative to
cryosparc_P102_J43_008_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99999995 -0.00014202 0.00028279 799.08138936  
0.00014207 -0.99999998 0.00016721 799.03759374  
0.00028276 0.00016725 0.99999995 -0.18224161  
Axis 0.00013980 0.00008223 0.99999999  
Axis point 399.51233207 399.54718127 0.00000000  
Rotation angle (degrees) 179.99186127  
Shift along axis -0.00482932  
  

> select clear

> save /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-model-
> fit-2b.pdb models #4 relModel #2

> save /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/asu-
> fittodensity.cxs

Taking snapshot of stepper: best-model-fit-sorta-2.pdb  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1389, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, 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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> -> 'best-model-fit-sorta-2.pdb'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1389, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, 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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> -> 'best-model-fit-sorta-2.pdb'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> open /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-model-
> fit-2a.pdb /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/best-
> model-fit-2b.pdb

Chain information for best-model-fit-2a.pdb #5  
---  
Chain | Description  
A | No description available  
  
Chain information for best-model-fit-2b.pdb #6  
---  
Chain | Description  
A | No description available  
  

> hide #4 models

> hide #1 models

> hide #3 models

> show #3 models

> hide #!2 models

> hide #3 models

> hide #5 models

> hide #6 models

> show #1 models

> show #5 models

> show #6 models

> show #!2 models

> close #3

> close #4

> save /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/FNV-asu-
> fittodensity.cxs

Taking snapshot of stepper: best-model-fit-sorta-2.pdb  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1389, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, 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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> -> 'best-model-fit-sorta-2.pdb'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1389, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, 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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> -> 'best-model-fit-sorta-2.pdb'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> view orient

> save /Users/mille153/Downloads/ChimeraX/AlphaFold/prediction_1/fnv-asu-
> fittodensity.cxs

Taking snapshot of stepper: best-model-fit-sorta-2.pdb  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1389, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, 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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> -> 'best-model-fit-sorta-2.pdb'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1389, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, 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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> -> 'best-model-fit-sorta-2.pdb'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save /Users/mille153/Downloads/fnv-fit.cxs

Taking snapshot of stepper: best-model-fit-sorta-2.pdb  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1389, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, 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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> -> 'best-model-fit-sorta-2.pdb'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1389, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, 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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> <chimerax.isolde.navigate.ResidueStepper object at 0x13ab75a30> ->
<chimerax.atomic.structure.AtomicStructure object at 0x13d8de7c0> 'best-model-
fit-sorta-2.pdb'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'best-model-
fit-sorta-2.pdb': Error while saving session data for 'isolde residue stepper
0' -> -> 'best-model-fit-sorta-2.pdb'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 575X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 220.270.93.0.0
      SMC Version (system): 2.46f12

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G95)
      Kernel Version: Darwin 18.7.0
      Time since boot: 14 days 8:26

Graphics/Displays:

    Radeon Pro 575X:

      Chipset Model: Radeon Pro 575X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c4
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A14GP-003
      EFI Driver Version: 01.01.042
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[pett]

Reported by Andrew Miller

[Tristan Croll]

Sorry for the ridiculously long wait, but this will be fixed in the next ISOLDE release. See #14894 for details.