id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16968 Session restore: Similar Structures: 'NoneType' object has no attribute 'hits' chimerax-bug-report@… Tom Goddard "{{{ 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' -> 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' -> : Error while saving session data for 'tools' -> 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' -> 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 *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' -> : Error while saving session data for 'tools' -> 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' -> 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' -> : Error while saving session data for 'tools' -> 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' -> 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 *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' -> : Error while saving session data for 'tools' -> 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 }}} " defect closed normal Sessions fixed all ChimeraX