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#16968 closed defect (fixed)

Session restore: Similar Structures: 'NoneType' object has no attribute 'hits'

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Sessions	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-6.8.0-52-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Trying to save file

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1KFS fromDatabase pdb format mmcif

Summary of feedback from opening 1KFS fetched from pdb  
---  
warning | Atom HO5' is not in the residue template for DA /B:1005  
note | Fetching compressed mmCIF 1kfs from http://files.rcsb.org/download/1kfs.cif  
  
1kfs title:  
Dna polymerase I klenow fragment (E.C.2.7.7.7) mutant/DNA complex [more
info...]  
  
Chain information for 1kfs #1  
---  
Chain | Description | UniProt  
A | PROTEIN (DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7)) | DPO1_ECOLI 324-928  
B | DNA (5'-D(*GP*CP*TP*TP*AP*CP*G)-3') |   
  
Non-standard residues in 1kfs #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> open 1KRP fromDatabase pdb format mmcif

Summary of feedback from opening 1KRP fetched from pdb  
---  
notes | Fetching compressed mmCIF 1krp from http://files.rcsb.org/download/1krp.cif  
Fetching CCD PST from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/PST/PST.cif  
  
1krp title:  
DNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex [more
info...]  
  
Chain information for 1krp #2  
---  
Chain | Description | UniProt  
A | PROTEIN (DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7)) | DPO1_ECOLI 324-928  
B | DNA (5'-D(P*TP*TP*PST)-3') |   
  
Non-standard residues in 1krp #2  
---  
ZN — zinc ion  
  

> open 1KSP fromDatabase pdb format mmcif

Summary of feedback from opening 1KSP fetched from pdb  
---  
note | Fetching compressed mmCIF 1ksp from http://files.rcsb.org/download/1ksp.cif  
  
1ksp title:  
DNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex [more
info...]  
  
Chain information for 1ksp #3  
---  
Chain | Description | UniProt  
A | PROTEIN (DNA POLYMERASE I-KLENOW FRAGMENT (E.C.2.7.7.7)) | DPO1_ECOLI 324-928  
B | DNA (5'-D(P*TP*TP*PST)-3') |   
  
Non-standard residues in 1ksp #3  
---  
ZN — zinc ion  
  

> open 7N0B fromDatabase pdb format mmcif

Summary of feedback from opening 7N0B fetched from pdb  
---  
notes | Fetching compressed mmCIF 7n0b from http://files.rcsb.org/download/7n0b.cif  
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif  
  
7n0b title:  
Cryo-EM structure of SARS-CoV-2 nsp10-nsp14 (WT)-RNA complex [more info...]  
  
Chain information for 7n0b #4  
---  
Chain | Description | UniProt  
A | Non-structural protein 10 | R1AB_SARS2 1-139  
B | Proofreading exoribonuclease | R1AB_SARS2 1-527  
D | RNA (5'-R(*AP*GP*AP*AP*GP*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*C)-3') |   
T | RNA (5'-R(*AP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*U)-3') |   
  
Non-standard residues in 7n0b #4  
---  
CA — calcium ion  
ZN — zinc ion  
  

> style stick

Changed 21123 atom styles  

> ui tool show "Similar Structures"

> ui tool show "Modeller Comparative"

> ui tool show Matchmaker

> matchmaker #!4 to #1

Computing secondary structure  
[Repeated 1 time(s)]  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 1kfs, chain A (#1) with 7n0b, chain A (#4), sequence alignment
score = 42.4  
RMSD between 4 pruned atom pairs is 1.104 angstroms; (across all 107 pairs:
24.089)  
  

> select #4/A

957 atoms, 976 bonds, 8 pseudobonds, 133 residues, 2 models selected  

> delete atoms (#!4 & sel)

> delete bonds (#!4 & sel)

> ui tool show Matchmaker

> matchmaker #!4 to #1

Computing secondary structure  
[Repeated 1 time(s)]  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 1kfs, chain A (#1) with 7n0b, chain B (#4), sequence alignment
score = 24  
RMSD between 6 pruned atom pairs is 1.024 angstroms; (across all 165 pairs:
23.826)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/B

Alignment identifier is 4/B  

> open 7N0B format mmcif fromDatabase pdb

7n0b title:  
Cryo-EM structure of SARS-CoV-2 nsp10-nsp14 (WT)-RNA complex [more info...]  
  
Chain information for 7n0b #5  
---  
Chain | Description | UniProt  
A | Non-structural protein 10 | R1AB_SARS2 1-139  
B | Proofreading exoribonuclease | R1AB_SARS2 1-527  
D | RNA (5'-R(*AP*GP*AP*AP*GP*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*C)-3') |   
T | RNA (5'-R(*AP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*U)-3') |   
  
Non-standard residues in 7n0b #5  
---  
CA — calcium ion  
ZN — zinc ion  
  

> select clear

> select #4/B:288-523

1829 atoms, 1884 bonds, 1 pseudobond, 226 residues, 2 models selected  

> select #4/B:289

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

> select #4/B:289-523

1820 atoms, 1875 bonds, 1 pseudobond, 225 residues, 2 models selected  

> delete atoms (#!4 & sel)

> delete bonds (#!4 & sel)

> ui tool show Matchmaker

> matchmaker #!2-5 to #1

Computing secondary structure  
[Repeated 4 time(s)]  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 1kfs, chain A (#1) with 1krp, chain A (#2), sequence alignment
score = 3085.3  
RMSD between 601 pruned atom pairs is 0.314 angstroms; (across all 601 pairs:
0.314)  
  
Matchmaker 1kfs, chain A (#1) with 1ksp, chain A (#3), sequence alignment
score = 3037.3  
RMSD between 601 pruned atom pairs is 0.314 angstroms; (across all 601 pairs:
0.314)  
  
Matchmaker 1kfs, chain B (#1) with 7n0b, chain D (#4), sequence alignment
score = 19.7  
RMSD between 3 pruned atom pairs is 0.499 angstroms; (across all 3 pairs:
0.499)  
  
Matchmaker 1kfs, chain A (#1) with 7n0b, chain A (#5), sequence alignment
score = 42.4  
RMSD between 4 pruned atom pairs is 1.104 angstroms; (across all 107 pairs:
24.089)  
  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #4.3 models

> hide #4.2 models

> hide #4.1 models

> show #!4 models

> show #!5 models

> close #5

> show #!1 models

> show #!2 models

> show #!3 models

> matchmaker #!4 to #1

Computing secondary structure  
[Repeated 1 time(s)]  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 1kfs, chain B (#1) with 7n0b, chain D (#4), sequence alignment
score = 19.7  
RMSD between 3 pruned atom pairs is 0.499 angstroms; (across all 3 pairs:
0.499)  
  
No reference and/or match structure/chain chosen  

> matchmaker #4/B to #1/A pairing ss

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | ss  
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 1kfs, chain A (#1) with 7n0b, chain B (#4), sequence alignment
score = 4  
Fewer than 3 residues aligned; cannot match 1kfs, chain A with 7n0b, chain B  

> close #4

> open 7N0B fromDatabase pdb format mmcif

7n0b title:  
Cryo-EM structure of SARS-CoV-2 nsp10-nsp14 (WT)-RNA complex [more info...]  
  
Chain information for 7n0b #4  
---  
Chain | Description | UniProt  
A | Non-structural protein 10 | R1AB_SARS2 1-139  
B | Proofreading exoribonuclease | R1AB_SARS2 1-527  
D | RNA (5'-R(*AP*GP*AP*AP*GP*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*C)-3') |   
T | RNA (5'-R(*AP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*U)-3') |   
  
Non-standard residues in 7n0b #4  
---  
CA — calcium ion  
ZN — zinc ion  
  

> nucleotides atoms

> style nucleic stick

Changed 1008 atom styles  

> select #4/D:70

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #4/D:71

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #4/D:69

62 atoms, 66 bonds, 3 residues, 1 model selected  

> color sel bynucleotide

> nucleotides sel atoms

> style nucleic & sel stick

Changed 62 atom styles  

> style sel stick

Changed 62 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 62 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 62 atom styles  

> nucleotides sel slab

> style nucleic & sel stick

Changed 62 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel tube/slab shape ellipsoid

> nucleotides sel tube/slab shape muffler

> nucleotides sel ladder

> nucleotides sel stubs

> color sel bynucleotide

> nucleotides sel atoms

> style nucleic & sel stick

Changed 62 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel ladder

> nucleotides sel atoms

> style nucleic & sel stick

Changed 62 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 62 atom styles  

> show sel target ab

> nucleotides sel atoms

> hide sel cartoons

> color sel byhetero

> open 7N0D fromDatabase pdb format mmcif

Summary of feedback from opening 7N0D fetched from pdb  
---  
notes | Fetching compressed mmCIF 7n0d from http://files.rcsb.org/download/7n0d.cif  
Fetching CCD 1N7 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/7/1N7/1N7.cif  
  
7n0d title:  
Cryo-EM structure of the tetrameric form of SARS-CoV-2 nsp10-nsp14 (E191A)-RNA
complex [more info...]  
  
Chain information for 7n0d #5  
---  
Chain | Description | UniProt  
A C E G | Non-structural protein 10 | R1AB_SARS2 1-139  
B D F H | Proofreading exoribonuclease | R1AB_SARS2 1-527  
I T | RNA (5'-R(*GP*GP*GP*GP*AP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*G)-3') |   
J P | RNA (5'-R(*CP*CP*CP*CP*C)-3') |   
K L | RNA (5'-R(*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*C)-3') |   
  
Non-standard residues in 7n0d #5  
---  
1N7 — chapso
(2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium)  
MG — magnesium ion  
ZN — zinc ion  
  

> ui tool show Matchmaker

> matchmaker #!5 to #4

Computing secondary structure  
[Repeated 1 time(s)]  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 7n0b, chain B (#4) with 7n0d, chain D (#5), sequence alignment
score = 2539.9  
RMSD between 385 pruned atom pairs is 0.784 angstroms; (across all 512 pairs:
1.737)  
  

> style sel stick

Changed 62 atom styles  

> style sel sphere

Changed 62 atom styles  

> hide sel surfaces

> hide #5.1 models

> hide #5.2 models

> hide #5.3 models

> hide #!5 models

> show #!5 models

> show sel cartoons

> show sel atoms

> hide sel surfaces

> style sel sphere

Changed 62 atom styles  

> color sel byhetero

> hide sel target a

> select #3/A

4961 atoms, 4839 bonds, 4 pseudobonds, 809 residues, 3 models selected  

> select #5/B

4091 atoms, 4203 bonds, 18 pseudobonds, 518 residues, 3 models selected  

> style sel sphere

Changed 4091 atom styles  

> style sel stick

Changed 4091 atom styles  

> hide sel atoms

> show sel cartoons

> select #5/D

4115 atoms, 4231 bonds, 17 pseudobonds, 518 residues, 3 models selected  

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> select #4/B#5/B#5/D#5/F#5/H

20506 atoms, 21075 bonds, 87 pseudobonds, 2589 residues, 6 models selected  

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> select #4/B

4094 atoms, 4207 bonds, 17 pseudobonds, 517 residues, 3 models selected  

> select #4/A#5/A#5/C#5/E#5/G

4785 atoms, 4880 bonds, 40 pseudobonds, 665 residues, 4 models selected  

> delete atoms (#!4-5 & sel)

> delete bonds (#!4-5 & sel)

> select #4/D

405 atoms, 452 bonds, 20 residues, 1 model selected  

> select #4/T

419 atoms, 466 bonds, 20 residues, 1 model selected  

> select #5/J#5/P

200 atoms, 218 bonds, 10 residues, 1 model selected  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 200 atom styles  

> hide sel cartoons

> hide sel atoms

> hide sel surfaces

> show sel cartoons

> show sel atoms

> select #5/K#5/L

584 atoms, 650 bonds, 28 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> show sel cartoons

> show sel atoms

> hide sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 584 atom styles  

> show sel atoms

> color sel byhetero

> select #5/I#5/T

822 atoms, 920 bonds, 38 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> show sel cartoons

> nucleotides sel atoms

> style nucleic & sel stick

Changed 822 atom styles  

> show sel atoms

> color sel byhetero

> view #5 clip false

> log metadata #5

Metadata for 7n0d #5  
---  
Title | Cryo-EM structure of the tetrameric form of SARS-CoV-2 nsp10-nsp14 (E191A)-RNA complex  
Citation | Liu, C., Shi, W., Becker, S.T., Schatz, D.G., Liu, B., Yang, Y. (2021). Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Science, 373, 1142-1146. PMID: 34315827. DOI: 10.1126/science.abi9310  
Non-standard residues | 1N7 — chapso (2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium)  
MG — magnesium ion  
ZN — zinc ion  
Gene source | Severe acute respiratory syndrome coronavirus 2 (2019-ncov, sars-cov-2)  
CryoEM Map | EMDB 24104 — open map  
Experimental method | Electron microscopy  
Resolution | 2.5Å  
  
> log chains #5

Chain information for 7n0d #5  
---  
Chain | Description | UniProt  
B D F H | Proofreading exoribonuclease | R1AB_SARS2 1-527  
I T | RNA (5'-R(*GP*GP*GP*GP*AP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*G)-3') |   
J P | RNA (5'-R(*CP*CP*CP*CP*C)-3') |   
K L | RNA (5'-R(*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*C)-3') |   
  

> select #5/B:2-523

4085 atoms, 4203 bonds, 1 pseudobond, 512 residues, 2 models selected  

> select #5/D:2-523

4085 atoms, 4203 bonds, 1 pseudobond, 512 residues, 2 models selected  

> select #5/B:2-523

4085 atoms, 4203 bonds, 1 pseudobond, 512 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #5/F:2-523

4085 atoms, 4203 bonds, 1 pseudobond, 512 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #5/H:2-523

4085 atoms, 4203 bonds, 1 pseudobond, 512 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #5/J:67-71

100 atoms, 109 bonds, 5 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #5/P:67-71

100 atoms, 109 bonds, 5 residues, 1 model selected  

> select #5/P:67-71

100 atoms, 109 bonds, 5 residues, 1 model selected  

> select #5/P:67-71

100 atoms, 109 bonds, 5 residues, 1 model selected  

> select #5/K:58-71

292 atoms, 325 bonds, 14 residues, 1 model selected  

> select #5/K:58-71

292 atoms, 325 bonds, 14 residues, 1 model selected  

> select #5/K:58-71

292 atoms, 325 bonds, 14 residues, 1 model selected  

> select #5/L:58-71

292 atoms, 325 bonds, 14 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> view #5 clip false

> log metadata #5

Metadata for 7n0d #5  
---  
Title | Cryo-EM structure of the tetrameric form of SARS-CoV-2 nsp10-nsp14 (E191A)-RNA complex  
Citation | Liu, C., Shi, W., Becker, S.T., Schatz, D.G., Liu, B., Yang, Y. (2021). Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Science, 373, 1142-1146. PMID: 34315827. DOI: 10.1126/science.abi9310  
Non-standard residues | 1N7 — chapso (2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium)  
MG — magnesium ion  
ZN — zinc ion  
Gene source | Severe acute respiratory syndrome coronavirus 2 (2019-ncov, sars-cov-2)  
CryoEM Map | EMDB 24104 — open map  
Experimental method | Electron microscopy  
Resolution | 2.5Å  
  
> log chains #5

Chain information for 7n0d #5  
---  
Chain | Description | UniProt  
D | Proofreading exoribonuclease | R1AB_SARS2 1-527  
I T | RNA (5'-R(*GP*GP*GP*GP*AP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*G)-3') |   
K | RNA (5'-R(*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*C)-3') |   
P | RNA (5'-R(*CP*CP*CP*CP*C)-3') |   
  

> select #5/P:67-71

100 atoms, 109 bonds, 5 residues, 1 model selected  

> select #5/K:58-71

292 atoms, 325 bonds, 14 residues, 1 model selected  

> select #5/T:1-19

411 atoms, 460 bonds, 19 residues, 1 model selected  

> select #5/I:1-19

411 atoms, 460 bonds, 19 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #5/P:71

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #4/D:71

40 atoms, 42 bonds, 2 residues, 2 models selected  

> select add #4/D:70

60 atoms, 63 bonds, 3 residues, 2 models selected  

> select add #5/P:70

80 atoms, 84 bonds, 4 residues, 2 models selected  

> select add #4/D:69

102 atoms, 108 bonds, 5 residues, 2 models selected  

> select add #5/P:69

122 atoms, 129 bonds, 6 residues, 2 models selected  

> hide sel cartoons

> show sel atoms

> hide sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 122 atom styles  

> show sel atoms

> select ::name="MG"

7 atoms, 7 residues, 2 models selected  

> show sel target ab

> select #5/D:601@MG

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> undo

[Repeated 1 time(s)]

> select ions

21 atoms, 21 residues, 5 models selected  

> show sel target ab

> select clear

> select #5/D:601@MG

1 atom, 1 residue, 1 model selected  

> select #5/D:601@MG

1 atom, 1 residue, 1 model selected  

> select #4/D:71@OP2

1 atom, 1 residue, 1 model selected  

> select #4/D:71@OP2

1 atom, 1 residue, 1 model selected  

> select #4/D:71@OP2

1 atom, 1 residue, 1 model selected  

> select #4/D:71@OP2

1 atom, 1 residue, 1 model selected  
Drag select of 1 atoms  

> ui tool show Angles/Torsions

> select #5/D:601@MG

1 atom, 1 residue, 1 model selected  

> select add #4/D:71@OP1

2 atoms, 2 residues, 2 models selected  

> distance #5/D:601@MG #4/D:71@OP1

Distance between 7n0d #5/D MG 601 MG and 7n0b #4/D C 71 OP1: 1.932Å  

> select #5/D:601@MG

1 atom, 1 residue, 1 model selected  

> select add #4/D:71@OP2

2 atoms, 2 residues, 2 models selected  

> distance #5/D:601@MG #4/D:71@OP2

Distance between 7n0d #5/D MG 601 MG and 7n0b #4/D C 71 OP2: 3.127Å  

> select clear

> select #4/B:601@CA

1 atom, 1 residue, 1 model selected  

> select clear

> hide #!4 models

> select #5/P:71@OP1

1 atom, 1 residue, 1 model selected  

> select add #5/D:601@MG

2 atoms, 2 residues, 1 model selected  

> distance #5/P:71@OP1 #5/D:601@MG

Distance between 7n0d #5/P C 71 OP1 and /D MG 601 MG: 2.180Å  

> select #5/P:71@OP2

1 atom, 1 residue, 1 model selected  

> select add #5/D:601@MG

2 atoms, 2 residues, 1 model selected  

> distance #5/P:71@OP2 #5/D:601@MG

Distance between 7n0d #5/P C 71 OP2 and /D MG 601 MG: 4.052Å  

> select clear

> select #5/P:71@OP1

1 atom, 1 residue, 1 model selected  

> select #5/P:71@OP2

1 atom, 1 residue, 1 model selected  

> select #5/P:71@OP2

1 atom, 1 residue, 1 model selected  

> select #5/P:71@OP1

1 atom, 1 residue, 1 model selected  

> hide #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> show #!2 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> log metadata #3

Metadata for 1ksp #3  
---  
Title | DNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex  
Citations | Brautigam, C.A., Steitz, T.A. (1998). Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates. J.Mol.Biol., 277, 363-377. PMID: 9514742. DOI: 10.1006/jmbi.1997.1586  
Beese, L.S., Steitz, T.A. (1991). Structural Basis for the 3'-5' Exonuclease
Activity of Escherichia Coli DNA Polymerase I: A Two Metal Ion Mechanism. Embo
J., 10, 25  
Non-standard residue | ZN — zinc ion  
Gene source | Escherichia coli  
Experimental method | X-ray diffraction  
Resolution | 2.300Å  
  
> log chains #3

Chain information for 1ksp #3  
---  
Chain | Description | UniProt  
A | PROTEIN (DNA POLYMERASE I-KLENOW FRAGMENT (E.C.2.7.7.7)) | DPO1_ECOLI 324-928  
B | DNA (5'-D(P*TP*TP*PST)-3') |   
  

> select #3/B:1001-1003

61 atoms, 66 bonds, 3 residues, 1 model selected  

> select #3/B:1001-1003

61 atoms, 66 bonds, 3 residues, 1 model selected  

> select #3/B:1001-1003

61 atoms, 66 bonds, 3 residues, 1 model selected  

> select #3/B:1001-1003

61 atoms, 66 bonds, 3 residues, 1 model selected  

> sequence chain #3/B

Alignment identifier is 3/B  

> show #!3 models

> hide #!2 models

> show #!2 models

> show #!1 models

> show #!4 models

> save "/home/ash/Amubox/Papers/in
> progress/InversionConfig/ExoStructures/DNAKlenowExovsSARS.cxs"

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tools.py", line 278, in take_snapshot  
if not tool_inst.SESSION_SAVE:  
^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/similarstructures/gui.py", line 395, in SESSION_SAVE  
return len(self.hits) > 0  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/similarstructures/gui.py", line 101, in hits  
return self.results.hits  
^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'hits'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x714f5cba4050>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x714f5cba4050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x714f5cba4050>  
  
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tools.py", line 278, in take_snapshot  
if not tool_inst.SESSION_SAVE:  
^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/similarstructures/gui.py", line 395, in SESSION_SAVE  
return len(self.hits) > 0  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/similarstructures/gui.py", line 101, in hits  
return self.results.hits  
^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'hits'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x714f5cba4050>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x714f5cba4050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x714f5cba4050>  
  
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  

> save "/home/ash/Amubox/Papers/in
> progress/InversionConfig/ExoStructures/KlenowSARS.cxs"

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tools.py", line 278, in take_snapshot  
if not tool_inst.SESSION_SAVE:  
^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/similarstructures/gui.py", line 395, in SESSION_SAVE  
return len(self.hits) > 0  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/similarstructures/gui.py", line 101, in hits  
return self.results.hits  
^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'hits'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x714f5cba4050>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x714f5cba4050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x714f5cba4050>  
  
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tools.py", line 278, in take_snapshot  
if not tool_inst.SESSION_SAVE:  
^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/similarstructures/gui.py", line 395, in SESSION_SAVE  
return len(self.hits) > 0  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/similarstructures/gui.py", line 101, in hits  
return self.results.hits  
^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'hits'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x714f5cba4050>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x714f5cba4050>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x714f5cba4050>  
  
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.256.02
OpenGL renderer: NVIDIA RTX A2000 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 7560
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 11th Gen Intel(R) Core(TM) i7-11850H @ 2.50GHz
Cache Size: 24576 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            30Gi       8.0Gi        14Gi        94Mi       8.2Gi        21Gi
	Swap:           15Gi          0B        15Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation TigerLake-H GT1 [UHD Graphics] [8086:9a60] (rev 01)	
	Subsystem: Dell TigerLake-H GT1 [UHD Graphics] [1028:0a69]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    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: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    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-MutationScores: 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: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    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: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (2)

comment:1 by Eric Pettersen, 9 months ago

Component:	Unassigned → Sessions
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Session restore: Similar Structures: 'NoneType' object has no attribute 'hits'

comment:2 by Tom Goddard, 9 months ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed.

Yikes. Session save fails if the Similar Structures gui is shown but no search was ever done. It fails because the test to save sessions assumes that results from a search are present.

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