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Opened 18 months ago
Closed 18 months ago
#15183 closed defect (fixed)
Restoring session: core tasks KeyError
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| 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-5.19.0-43-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/mn452228/Downloads/lab10_zad4-1(3).cxs
Log from Thu May 9 15:11:20 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /home/odol/Desktop/BioinformaticS/2024_lato/bioinfo/20_homology/lab10_zad3-2.cxs
> format session
Log from Thu May 9 15:05:14 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /home/odol/Desktop/BioinformaticS/2024_lato/bioinfo/20_homology/zad2_7.cxs
> format session
Log from Thu May 9 12:05:13 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /home/odol/Desktop/BioinformaticS/2024_lato/bioinfo/20_homology/zad2_6.cxs
> format session
Log from Thu May 9 11:23:21 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /home/odol/Desktop/BioinformaticS/2024_lato/bioinfo/20_homology/zad2_1.cxs
> format session
Log from Thu May 9 09:40:30 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show "Blast Protein"
> blastprotein
> MNFNNKTKYGKIQEFLRSNNEPDYRIKQITNAIFKQRISRFEDMKVLPKLLREDLINNFGETVLNIKLLAEQNSEQVTKVLFEVSKNERVETVNMKYKAGWESFCISSQCGCNFGCKFCATGDIGLKKNLTVDEITDQVLYFHLLGHQIDSISFMGMGEALANRQVFDALDSFTDPNLFALSPRRLSISTIGIIPSIKKITQEYPQVNLTFSLHSPYSEERSKLMPINDRYPIDEVMNILDEHIRLTSRKVYIAYIMLPGVNDSLEHANEVVSLLKSRYKSGKLYHVNLIRYNPTISAPEMYGEANEGQVEAFYKVLKSAGIHVTIRSQFGIDIDAACGQLYGNYQNSQ
> database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version None name bp1
Webservices job id: 8QCMBB7TJGAVYF67
> ui tool show "Blast Protein"
> ui dockable false bp1
> ui dockable true bp1
> ui dockable false bp1
Alignment identifier is bp1 [1]
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [1]
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f4f0, name="eDP-1")
wdgScreen: QScreen(0x130f4f0, name="eDP-1") orgWdgScreen QScreen(0x0)
[Repeated 56 time(s)]
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f4f0, name="eDP-1") orgWdgScreen QScreen(0x0)
[Repeated 10 time(s)]
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f560, name="HDMI-1") orgWdgScreen QScreen(0x0)
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f4f0, name="eDP-1") orgWdgScreen QScreen(0x0)
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f560, name="HDMI-1") orgWdgScreen QScreen(0x0)
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f4f0, name="eDP-1") orgWdgScreen QScreen(0x0)
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f560, name="HDMI-1") orgWdgScreen QScreen(0x0)
[Repeated 142 time(s)]
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f4f0, name="eDP-1") orgWdgScreen QScreen(0x0)
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f560, name="HDMI-1") orgWdgScreen QScreen(0x0)
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f4f0, name="eDP-1") orgWdgScreen QScreen(0x0)
[Repeated 1 time(s)]
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f560, name="HDMI-1") orgWdgScreen QScreen(0x0)
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f4f0, name="eDP-1") orgWdgScreen QScreen(0x0)
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f560, name="HDMI-1") orgWdgScreen QScreen(0x0)
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f4f0, name="eDP-1") orgWdgScreen QScreen(0x0)
[Repeated 1 time(s)]
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x130f4f0, name="eDP-1") screenTo: QScreen(0x130f560, name="HDMI-1")
wdgScreen: QScreen(0x130f560, name="HDMI-1") orgWdgScreen QScreen(0x0)
[Repeated 45 time(s)]
> select
Nothing selected
> select
Nothing selected
> select
Nothing selected
> select clear
[Repeated 2 time(s)]
> save
> /home/odol/Desktop/BioinformaticS/2024_lato/bioinfo/20_homology/zad2_1.cxs
——— End of log from Thu May 9 09:40:30 2024 ———
opened ChimeraX session
BLAST job failed
> sequence header consensus show
Showing consensus header ("seq_consensus" residue attribute) for alignment bp1
[1]
> sequence header consensus hide
Hiding consensus header for alignment bp1 [1]
> sequence identity "bp1 [1]" :1
query vs. query: 100.00% identity
6FZ6_A vs. query: 36.23% identity
3RF9_A vs. query: 35.24% identity
4PL2_A vs. query: 34.63% identity
3RFA_A vs. query: 34.96% identity
5HR7_A vs. query: 34.67% identity
4PL1_A vs. query: 34.33% identity
5HR6_A vs. query: 34.67% identity
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x203b190, name="eDP-1") screenTo: QScreen(0x203b190, name="eDP-1")
wdgScreen: QScreen(0x203b190, name="eDP-1") orgWdgScreen QScreen(0x0)
[Repeated 81 time(s)]
> open pdb:6FZ6
6fz6 title:
Crystal Structure of a radical SAM methyltransferase from Sphaerobacter
thermophilus [more info...]
Chain information for 6fz6 #1
---
Chain | Description | UniProt
A B | Probable dual-specificity RNA methyltransferase RlmN | D1C4T7_SPHTD
1-347
Non-standard residues in 6fz6 #1
---
BR — bromide ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
SAH — S-adenosyl-L-homocysteine
SF4 — iron/sulfur cluster
6fz6 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Associated 6fz6 chain A to 6FZ6_A with 0 mismatches
Associated 6fz6 chain B to 6FZ6_A with 0 mismatches
> select clear
> open pdb:3RF9
3rf9 title:
X-ray structure of RlmN from Escherichia coli [more info...]
Chain information for 3rf9 #2
---
Chain | Description | UniProt
A B | Ribosomal RNA large subunit methyltransferase N | RLMN_ECOLI 1-384
Non-standard residues in 3rf9 #2
---
MRD — (4R)-2-methylpentane-2,4-diol
SF4 — iron/sulfur cluster
3rf9 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Associated 3rf9 chain A to 3RF9_A with 0 mismatches
Associated 3rf9 chain B to 3RF9_A with 0 mismatches
> select clear
> open pdb:4PL2
4pl2 title:
X-ray crystal structure of C118A RlmN from Escherichia coli [more info...]
Chain information for 4pl2 #3
---
Chain | Description | UniProt
A B | Dual-specificity RNA methyltransferase RlmN | C9QPQ6_ECOD1 17-375
Non-standard residues in 4pl2 #3
---
SF4 — iron/sulfur cluster
4pl2 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Associated 4pl2 chain B to 4PL2_A with 0 mismatches
Associated 4pl2 chain A to 4PL2_A with 0 mismatches
> select clear
> open pdb:3RFA
3rfa title:
X-ray structure of RlmN from Escherichia coli in complex with
S-adenosylmethionine [more info...]
Chain information for 3rfa #4
---
Chain | Description | UniProt
A B | Ribosomal RNA large subunit methyltransferase N | RLMN_ECOLI 1-384
Non-standard residues in 3rfa #4
---
SAM — S-adenosylmethionine
SF4 — iron/sulfur cluster
3rfa mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Associated 3rfa chain A to 3RF9_A with 0 mismatches
Associated 3rfa chain B to 3RF9_A with 0 mismatches
> select clear
> open pdb:5HR7
5hr7 title:
X-ray crystal structure of C118A RlmN from Escherichia coli with cross-linked
in vitro transcribed tRNA [more info...]
Chain information for 5hr7 #5
---
Chain | Description | UniProt
A B | Dual-specificity RNA methyltransferase RlmN | RLMN_ECO24 1-384
C D | tRNA Glu |
Non-standard residues in 5hr7 #5
---
5AD — 5'-deoxyadenosine
CAS — S-(dimethylarsenic)cysteine
MET — methionine
MG — magnesium ion
SF4 — iron/sulfur cluster
5hr7 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Associated 5hr7 chain B to 5HR7_A with 1 mismatch
Associated 5hr7 chain A to 5HR7_A with 1 mismatch
> select clear
> open pdb:4PL1
4pl1 title:
X-ray crystal structure of C118A RlmN from Escherichia coli with
S-adenosylmethionine [more info...]
Chain information for 4pl1 #6
---
Chain | Description | UniProt
A B | Dual-specificity RNA methyltransferase RlmN | C9QPQ6_ECOD1 17-375
Non-standard residues in 4pl1 #6
---
SAM — S-adenosylmethionine
SF4 — iron/sulfur cluster
4pl1 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Associated 4pl1 chain B to 4PL2_A with 0 mismatches
Associated 4pl1 chain A to 4PL2_A with 0 mismatches
> select clear
> open pdb:5HR6
5hr6 title:
X-ray crystal structure of C118A RlmN with cross-linked tRNA purified from
Escherichia coli [more info...]
Chain information for 5hr6 #7
---
Chain | Description | UniProt
A B | RlmN methylase | RLMN_ECO24 1-384
C D | tRNA Glu |
Non-standard residues in 5hr6 #7
---
5AD — 5'-deoxyadenosine
MET — methionine
MG — magnesium ion
SF4 — iron/sulfur cluster
5hr6 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Associated 5hr6 chain A to 4PL2_A with 0 mismatches
Associated 5hr6 chain B to 4PL2_A with 0 mismatches
> select clear
> save
> /home/odol/Desktop/BioinformaticS/2024_lato/bioinfo/20_homology/zad2_2.cxs
QXcbConnection: XCB error: 3 (BadWindow), sequence: 64611, resource id:
17804078, major code: 40 (TranslateCoords), minor code: 0
> select #5/C#5/D#7/C#7/D
5867 atoms, 6490 bonds, 292 pseudobonds, 324 residues, 6 models selected
> delete atoms (#!5,7 & sel)
> delete bonds (#!5,7 & sel)
> select #3/B
2907 atoms, 2833 bonds, 4 pseudobonds, 474 residues, 3 models selected
> select #3/B
2907 atoms, 2833 bonds, 4 pseudobonds, 474 residues, 3 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #5/B
2898 atoms, 2925 bonds, 6 pseudobonds, 387 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select #6/B
2867 atoms, 2919 bonds, 5 pseudobonds, 361 residues, 2 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> select #1/B
2999 atoms, 2742 bonds, 5 pseudobonds, 652 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #2/B
2957 atoms, 2846 bonds, 4 pseudobonds, 512 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #4/B
2970 atoms, 2920 bonds, 5 pseudobonds, 463 residues, 2 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select #7/B
2842 atoms, 2872 bonds, 9 pseudobonds, 378 residues, 2 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> save
> /home/odol/Desktop/BioinformaticS/2024_lato/bioinfo/20_homology/zad2_3.cxs
> ui tool show Matchmaker
> matchmaker #!2-7 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 6fz6, chain A (#1) with 3rf9, chain A (#2), sequence alignment
score = 883.2
RMSD between 235 pruned atom pairs is 0.977 angstroms; (across all 328 pairs:
2.266)
Matchmaker 6fz6, chain A (#1) with 4pl2, chain A (#3), sequence alignment
score = 891.7
RMSD between 227 pruned atom pairs is 0.927 angstroms; (across all 330 pairs:
2.352)
Matchmaker 6fz6, chain A (#1) with 3rfa, chain A (#4), sequence alignment
score = 906.2
RMSD between 227 pruned atom pairs is 0.924 angstroms; (across all 326 pairs:
2.272)
Matchmaker 6fz6, chain A (#1) with 5hr7, chain A (#5), sequence alignment
score = 928.5
RMSD between 240 pruned atom pairs is 0.812 angstroms; (across all 338 pairs:
2.404)
Matchmaker 6fz6, chain A (#1) with 4pl1, chain A (#6), sequence alignment
score = 867.9
RMSD between 229 pruned atom pairs is 0.955 angstroms; (across all 325 pairs:
2.268)
Matchmaker 6fz6, chain A (#1) with 5hr6, chain A (#7), sequence alignment
score = 917.1
RMSD between 239 pruned atom pairs is 0.822 angstroms; (across all 337 pairs:
2.494)
> view
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select clear
[Repeated 3 time(s)]
> select #1/A:331
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:331-339
60 atoms, 59 bonds, 9 residues, 1 model selected
> select #1/A:330
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:316-330
116 atoms, 117 bonds, 15 residues, 1 model selected
> select #3/A:349-361 #7/A:349-361
127 atoms, 124 bonds, 1 pseudobond, 18 residues, 3 models selected
> select #1/A:330
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:330-331
14 atoms, 13 bonds, 2 residues, 1 model selected
> sequence header rmsd show
Chains used in RMSD evaluation for alignment bp1 [1]: 6fz6 #1/A, 3rf9 #2/A,
4pl2 #3/A, 3rfa #4/A, 5hr7 #5/A, 4pl1 #6/A, 5hr6 #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment bp1 [1]
> save
> /home/odol/Desktop/BioinformaticS/2024_lato/bioinfo/20_homology/zad2_4.cxs
> sym #2
3rf9 mmCIF Assemblies
---
1| author_and_software_defined_assembly| 1 copy of chain
2| author_and_software_defined_assembly| 1 copy of chain A
> log metadata #2
Metadata for 3rf9 #2
---
Title | X-ray structure of RlmN from Escherichia coli
Citation | Boal, A.K., Grove, T.L., McLaughlin, M.I., Yennawar, N.H., Booker,
S.J., Rosenzweig, A.C. (2011). Structural basis for methyl transfer by a
radical SAM enzyme. Science, 332, 1089-1092. PMID: 21527678. DOI:
10.1126/science.1205358
Non-standard residue | SF4 — iron/sulfur cluster
Gene source | Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.20Å
> log chains #2
Chain information for 3rf9 #2
---
Chain | Description | UniProt
A | Ribosomal RNA large subunit methyltransferase N | RLMN_ECOLI 1-384
> sym #3
4pl2 mmCIF Assemblies
---
1| author_defined_assembly| 1 copy of chain
2| author_defined_assembly| 1 copy of chain A
> log metadata #3
Metadata for 4pl2 #3
---
Title | X-ray crystal structure of C118A RlmN from Escherichia coli
Citation | Silakov, A., Grove, T.L., Radle, M.I., Bauerle, M.R., Green, M.T.,
Rosenzweig, A.C., Boal, A.K., Booker, S.J. (2014). Characterization of a
cross-linked protein-nucleic acid substrate radical in the reaction catalyzed
by RlmN. J.Am.Chem.Soc., 136, 8221-8228. PMID: 24806349. DOI:
10.1021/ja410560p
Non-standard residue | SF4 — iron/sulfur cluster
Gene source | Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.20Å
> log chains #3
Chain information for 4pl2 #3
---
Chain | Description | UniProt
A | Dual-specificity RNA methyltransferase RlmN | C9QPQ6_ECOD1 17-375
> sym #4
3rfa mmCIF Assemblies
---
1| author_and_software_defined_assembly| 1 copy of chain
2| author_and_software_defined_assembly| 1 copy of chain A
> log metadata #4
Metadata for 3rfa #4
---
Title | X-ray structure of RlmN from Escherichia coli in complex with
S-adenosylmethionine
Citation | Boal, A.K., Grove, T.L., McLaughlin, M.I., Yennawar, N.H., Booker,
S.J., Rosenzweig, A.C. (2011). Structural basis for methyl transfer by a
radical SAM enzyme. Science, 332, 1089-1092. PMID: 21527678. DOI:
10.1126/science.1205358
Non-standard residues | SAM — S-adenosylmethionine
SF4 — iron/sulfur cluster
Gene source | Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.05Å
> log chains #4
Chain information for 3rfa #4
---
Chain | Description | UniProt
A | Ribosomal RNA large subunit methyltransferase N | RLMN_ECOLI 1-384
> sym #5
5hr7 mmCIF Assemblies
---
1| author_and_software_defined_assembly| 1 copy of chain A
2| author_and_software_defined_assembly| 1 copy of chain
> log metadata #5
Metadata for 5hr7 #5
---
Title | X-ray crystal structure of C118A RlmN from Escherichia coli with
cross-linked in vitro transcribed tRNA
Citation | Schwalm, E.L., Grove, T.L., Booker, S.J., Boal, A.K. (2016).
Crystallographic capture of a radical S-adenosylmethionine enzyme in the act
of modifying tRNA. Science, 352, 309-312. PMID: 27081063. DOI:
10.1126/science.aad5367
Non-standard residues | 5AD — 5'-deoxyadenosine
CAS — S-(dimethylarsenic)cysteine
MET — methionine
SF4 — iron/sulfur cluster
Gene source | Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.4Å
> log chains #5
Chain information for 5hr7 #5
---
Chain | Description | UniProt
A | Dual-specificity RNA methyltransferase RlmN | RLMN_ECO24 1-384
> sym #6
4pl1 mmCIF Assemblies
---
1| author_defined_assembly| 1 copy of chain
2| author_defined_assembly| 1 copy of chain A
> log metadata #6
Metadata for 4pl1 #6
---
Title | X-ray crystal structure of C118A RlmN from Escherichia coli with
S-adenosylmethionine
Citation | Silakov, A., Grove, T.L., Radle, M.I., Bauerle, M.R., Green, M.T.,
Rosenzweig, A.C., Boal, A.K., Booker, S.J. (2014). Characterization of a
cross-linked protein-nucleic acid substrate radical in the reaction catalyzed
by RlmN. J.Am.Chem.Soc., 136, 8221-8228. PMID: 24806349. DOI:
10.1021/ja410560p
Non-standard residues | SAM — S-adenosylmethionine
SF4 — iron/sulfur cluster
Gene source | Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.58Å
> log chains #6
Chain information for 4pl1 #6
---
Chain | Description | UniProt
A | Dual-specificity RNA methyltransferase RlmN | C9QPQ6_ECOD1 17-375
> sym #7
5hr6 mmCIF Assemblies
---
1| author_and_software_defined_assembly| 1 copy of chain A
2| author_and_software_defined_assembly| 1 copy of chain
> log metadata #7
Metadata for 5hr6 #7
---
Title | X-ray crystal structure of C118A RlmN with cross-linked tRNA purified
from Escherichia coli
Citation | Schwalm, E.L., Grove, T.L., Booker, S.J., Boal, A.K. (2016).
Crystallographic capture of a radical S-adenosylmethionine enzyme in the act
of modifying tRNA. Science, 352, 309-312. PMID: 27081063. DOI:
10.1126/science.aad5367
Non-standard residues | 5AD — 5'-deoxyadenosine
MET — methionine
MG — magnesium ion
SF4 — iron/sulfur cluster
Source (natural) | Escherichia coli
Gene source | Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.850Å
> log chains #7
Chain information for 5hr6 #7
---
Chain | Description | UniProt
A | RlmN methylase | RLMN_ECO24 1-384
> close #2#3-7
> select clear
> ui tool show "Modeller Comparative"
> save
> /home/odol/Desktop/BioinformaticS/2024_lato/bioinfo/20_homology/zad2_5.cxs
QXcbConnection: XCB error: 3 (BadWindow), sequence: 13697, resource id:
17811746, major code: 40 (TranslateCoords), minor code: 0
Alignment identifier is bp1 [1]
Associated 6fz6 chain A to 6FZ6_A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [1]
Alignment identifier is bp1 [2]
Associated 6fz6 chain A to 6FZ6_A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [2]
Alignment identifier is bp1 [3]
Associated 6fz6 chain A to 6FZ6_A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [3]
Alignment identifier is bp1 [4]
Associated 6fz6 chain A to 6FZ6_A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [4]
> modeller comparative "bp1 [4]:1" numModels 1 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: 0XZZYFOWNFKTCCEX
Modeller job (ID 0XZZYFOWNFKTCCEX) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 72, in <module>
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 624, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 577, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.ModellerError: read_te_290E> Number of residues in the alignment and
pdb files are different: 341 342 For alignment entry: 1 6fz6_1
Modeller run output
MODELLER 10.5, 2024/01/19, r12711
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2024 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu
4.18.0-513.24.1.el8_9.x86_64 x86_64
Date and time of compilation : 2024/01/20 00:40:16
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2024/05/09 02:21:11
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v5}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v5}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183
openf___224_> Open ${MODINSTALL10v5}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL10v5}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v5}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v5}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v5}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v5}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v5}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v5}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282425 275.806
0.269
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297517 290.544
0.284
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 312917 305.583
0.298
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343717 335.661
0.328
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405317 395.817
0.387
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 406677 397.146 0.388
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 408069 398.505 0.389
read_al_374_> Non-standard residue type,position,sequence: . 352 1
Read the alignment from file : alignment.ali
Total number of alignment positions: 363
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 6fz6_1 341 1 6fz6_1
2 query 349 1 query
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./6fz6_1.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 512094 500.092
0.488
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 512094 500.092 0.488
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 512265 500.259
0.489
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 513115 501.089
0.489
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 514373 502.317
0.491
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 516277 504.177
0.492
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516277 504.177 0.492
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 516367 504.265
0.492
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 519223 507.054
0.495
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 519223 507.054 0.495
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 519358 507.186
0.495
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 523642 511.369
0.499
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 523642 511.369 0.499
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 523840 511.562
0.500
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 530266 517.838
0.506
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 530266 517.838 0.506
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 530563 518.128
0.506
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 540185 527.524
0.515
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 540185 527.524 0.515
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 540635 527.964
0.516
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 555085 542.075
0.529
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 555085 542.075 0.529
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 555760 542.734
0.530
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 577418 563.885
0.551
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 577418 563.885 0.551
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 578426 564.869
0.552
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 610930 596.611
0.583
read_pd_459W> Residue type SMC not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 610930 596.611 0.583
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 612442 598.088
0.584
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 612442 598.088 0.584
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 612442 598.088
0.584
rdpdb___459W> Residue type SAH not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 611279 596.952
0.583
read_te_290E> Number of residues in the alignment and pdb files are different:
341 342
For alignment entry: 1 6fz6_1
x (mismatch at alignment position 342)
Alignment TVRYSRGVDISAA.GQLRAE/ -
PDB TVRYSRGVDISAA.GQLRAE/./
Match *********************
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 6fz6_1
No output models from Modeller; see log for Modeller text output.
QXcbConnection: XCB error: 3 (BadWindow), sequence: 13899, resource id:
17816611, major code: 40 (TranslateCoords), minor code: 0
> save
> /home/odol/Desktop/BioinformaticS/2024_lato/bioinfo/20_homology/zad2_6.cxs
——— End of log from Thu May 9 11:23:21 2024 ———
opened ChimeraX session
BLAST job failed
> ui tool show "Modeller Comparative"
> modeller comparative "bp1 [4]:1" numModels 1 fast false multichain false
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: EGAPP4FQIMZJ8NFJ
Modeller job (ID EGAPP4FQIMZJ8NFJ) finished
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 6fz6, chain A (#1) with query, chain A (#), sequence alignment
score = 790.1
RMSD between 317 pruned atom pairs is 0.283 angstroms; (across all 335 pairs:
3.311)
Associated query chain A to query with 0 mismatches
Chain information for query
---
Chain | Description
2.1/A | No description available
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
Downloading file shown.png
> modeller scores #2.1 refresh false
> ui tool show Matchmaker
> matchmaker #2.1 to #1 showAlignment true
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 6fz6, chain A (#1) with query, chain A (#2.1), sequence alignment
score = 790.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 6fz6 #1/A, query #2.1/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 317 pruned atom pairs is 0.283 angstroms; (across all 335 pairs:
3.311)
> save
> /home/odol/Desktop/BioinformaticS/2024_lato/bioinfo/20_homology/zad2_7.cxs
——— End of log from Thu May 9 12:05:13 2024 ———
opened ChimeraX session
BLAST job failed
> save
> /home/odol/Desktop/BioinformaticS/2024_lato/bioinfo/20_homology/lab10_zad3-2.cxs
——— End of log from Thu May 9 15:05:14 2024 ———
opened ChimeraX session
BLAST job failed
> ui tool show Matchmaker
> matchmaker #!1 to #2.1 showAlignment true
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 query, chain A (#2.1) with 6fz6, chain A (#1), sequence alignment
score = 790.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 6fz6 #1/A, query #2.1/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 317 pruned atom pairs is 0.283 angstroms; (across all 335 pairs:
3.311)
> save
> /home/odol/Desktop/BioinformaticS/2024_lato/bioinfo/20_homology/lab10_zad4-1.cxs
——— End of log from Thu May 9 15:11:20 2024 ———
opened ChimeraX session
BLAST job failed
> ui tool show "Render by Attribute"
> color byattribute r:seq_rmsd #2.1 target csab palette
> 0.00641663,blue:3.09604,white:34.5495,red
2803 atoms, 349 residues, atom seq_rmsd range 0.00642 to 34.5
> select #2.1/A:99
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2.1/A:99-101 #1/A:98-99
42 atoms, 42 bonds, 5 residues, 2 models selected
MatchMaker Alignment [ID: 1] region query, chain A..6fz6, chain A [118-120]
RMSD: 3.733
> select #2.1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.1/A:1-8 #1/A:1-7
124 atoms, 124 bonds, 15 residues, 2 models selected
MatchMaker Alignment [ID: 1] region query, chain A..6fz6, chain A [20-27]
RMSD: 22.295
> show sel target ab
> ui tool show Clashes
> clashes ignoreHiddenModels true
14636 clashes
> hide sel cartoons
> select sideonly
2698 atoms, 2120 bonds, 4321 pseudobonds, 648 residues, 3 models selected
> hide (#2.1#!1 & sel) target a
> open /home/mn452228/Downloads/lab10_zad4-4(1).cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 713, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 641, in reset_state
task.terminate()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 208, in terminate
self.session.tasks.remove(self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 556, in remove
self.__delitem__(task.id)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 545, in __delitem__
task = self._tasks[key]
~~~~~~~~~~~^^^^^
KeyError: 1
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 713, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 641, in reset_state
task.terminate()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 208, in terminate
self.session.tasks.remove(self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 556, in remove
self.__delitem__(task.id)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 545, in __delitem__
task = self._tasks[key]
~~~~~~~~~~~^^^^^
KeyError: 1
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/open_command/dialog.py", line 334, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
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 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 514, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 37, in open
return cxs_open(session, data, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1017, in open
session.restore(stream, path=path, resize_window=resize_window,
combine=combine)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 755, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 641, in reset_state
task.terminate()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 208, in terminate
self.session.tasks.remove(self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 556, in remove
self.__delitem__(task.id)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 545, in __delitem__
task = self._tasks[key]
~~~~~~~~~~~^^^^^
KeyError: 1
KeyError: 1
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 545, in __delitem__
task = self._tasks[key]
~~~~~~~~~~~^^^^^
See log for complete Python traceback.
> open /home/mn452228/Downloads/lab10_zad4-3.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 713, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 641, in reset_state
task.terminate()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 208, in terminate
self.session.tasks.remove(self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 556, in remove
self.__delitem__(task.id)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 545, in __delitem__
task = self._tasks[key]
~~~~~~~~~~~^^^^^
KeyError: 1
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 713, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 641, in reset_state
task.terminate()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 208, in terminate
self.session.tasks.remove(self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 556, in remove
self.__delitem__(task.id)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 545, in __delitem__
task = self._tasks[key]
~~~~~~~~~~~^^^^^
KeyError: 1
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/open_command/dialog.py", line 334, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
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 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 514, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 37, in open
return cxs_open(session, data, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1017, in open
session.restore(stream, path=path, resize_window=resize_window,
combine=combine)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 755, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 641, in reset_state
task.terminate()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 208, in terminate
self.session.tasks.remove(self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 556, in remove
self.__delitem__(task.id)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 545, in __delitem__
task = self._tasks[key]
~~~~~~~~~~~^^^^^
KeyError: 1
KeyError: 1
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 545, in __delitem__
task = self._tasks[key]
~~~~~~~~~~~^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 510.108.03
OpenGL renderer: NVIDIA GeForce GTX 750 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Gigabyte Technology Co., Ltd.
Model: B450 AORUS ELITE
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 AMD Ryzen 5 5600G with Radeon Graphics
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 2.8Gi 10Gi 44Mi 1.7Gi 12Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107 [GeForce GTX 750 Ti] [10de:1380] (rev a2)
Subsystem: Gigabyte Technology Co., Ltd GM107 [GeForce GTX 750 Ti] [1458:362d]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 18 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Restoring session: core tasks KeyError |
comment:2 by , 18 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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