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#9078 closed defect (fixed)
AlphaFold sequence search web service failed (500) "Internal Server Error"
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
When I execute the command: "alphafold match .......". I get this error:
AlphaFold sequence search web service failed (500) "Internal Server Error"
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search3_cgi.py
However, few weeks ago I took the same sequence using the same command.
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "I:\\\Mi
> unidad\\\Santiago\\\BIO_INF_TEC_URP\\\Bacillus\\\Resultados\\\Bioinf\\\Tesis_David\\\id_char_muts\\\par1_vs_CynD.cxs"
Log from Sun Apr 30 21:29:43 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "I:/Mi
> unidad/Santiago/BIO_INF_TEC_URP/Bacillus/Resultados/Bioinf/Tesis_David/id_char_muts/par2_vs_CynD.cxs"
Log from Sun Apr 30 01:02:17 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
No sequence chosen for AlphaFold match
Fetching A0A1D7XF17 UniProt info from
https://www.uniprot.org/uniprot/A0A1D7XF17.xml
> alphafold match A0A1D7XF17
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
1 UniProt id does not have an AlphaFold database model: A0A1D7XF17 (UniProt
A0A1D7XF17)
Fetching compressed AlphaFold A0A1D7XF17 from
https://alphafold.ebi.ac.uk/files/AF-A0A1D7XF17-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A1D7XF17
(UniProt A0A1D7XF17)
Opened 1 AlphaFold model
Fetching U7U7F7 UniProt info from https://www.uniprot.org/uniprot/U7U7F7.xml
> alphafold match U7U7F7
1 UniProt id does not have an AlphaFold database model: U7U7F7 (UniProt
U7U7F7)
Fetching compressed AlphaFold U7U7F7 from
https://alphafold.ebi.ac.uk/files/AF-U7U7F7-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: U7U7F7 (UniProt
U7U7F7)
Opened 1 AlphaFold model
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold
U7U7F7_9BURK, chain A (#2), sequence alignment score = 767
RMSD between 256 pruned atom pairs is 0.740 angstroms; (across all 325 pairs:
13.043)
> mmaker #2 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold
U7U7F7_9BURK, chain A (#2), sequence alignment score = 767
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: AlphaFold A0A1D7XF17_ALCSP
#1/A, AlphaFold U7U7F7_9BURK #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 256 pruned atom pairs is 0.740 angstroms; (across all 325 pairs:
13.043)
> select #1/A:229
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:229-237 #2/A:240-248
146 atoms, 148 bonds, 18 residues, 2 models selected
MatchMaker Alignment [ID: 1] region AlphaFold A0A1D7XF17_ALCSP, chain
A..AlphaFold U7U7F7_9BURK, chain A [241-249] RMSD: 4.627
> select #1/A:293
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:293-300
64 atoms, 66 bonds, 8 residues, 1 model selected
Fetching A3LPM9 UniProt info from https://www.uniprot.org/uniprot/A3LPM9.xml
> alphafold match A3LPM9
1 UniProt id does not have an AlphaFold database model: A3LPM9 (UniProt
A3LPM9)
Fetching compressed AlphaFold A3LPM9 from
https://alphafold.ebi.ac.uk/files/AF-A3LPM9-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A3LPM9 (UniProt
A3LPM9)
Opened 1 AlphaFold model
Fetching A8FEX8 UniProt info from https://www.uniprot.org/uniprot/A8FEX8.xml
> alphafold match A8FEX8
1 UniProt id does not have an AlphaFold database model: A8FEX8 (UniProt
A8FEX8)
Fetching compressed AlphaFold A8FEX8 from
https://alphafold.ebi.ac.uk/files/AF-A8FEX8-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A8FEX8 (UniProt
A8FEX8)
Opened 1 AlphaFold model
> mmaker #3 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold
A3LPM9_PICST, chain A (#3), sequence alignment score = 1365.7
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: AlphaFold A0A1D7XF17_ALCSP
#1/A, AlphaFold A3LPM9_PICST #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 260 pruned atom pairs is 0.454 angstroms; (across all 324 pairs:
15.791)
> mmaker #4 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold
A8FEX8_BACP2, chain A (#4), sequence alignment score = 1458.2
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: AlphaFold A0A1D7XF17_ALCSP
#1/A, AlphaFold A8FEX8_BACP2 #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 309 pruned atom pairs is 0.468 angstroms; (across all 326 pairs:
1.749)
> select #1/A:1-238,240-308,311-312 #4/A:2-239,241-309,312-313
4895 atoms, 5024 bonds, 618 residues, 2 models selected
> select #1/A:290 #4/A:291
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/A:196
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:196-205
72 atoms, 72 bonds, 10 residues, 1 model selected
> select #1/A:287
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:287-298
94 atoms, 95 bonds, 12 residues, 1 model selected
> select #3/A:289
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:289-300
89 atoms, 89 bonds, 12 residues, 1 model selected
> select #1/A:287
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:287-298
94 atoms, 95 bonds, 12 residues, 1 model selected
> select #2/A:300
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:300-303
32 atoms, 31 bonds, 4 residues, 1 model selected
> select #2/A:304
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:304-306
23 atoms, 22 bonds, 3 residues, 1 model selected
Fetching A0A6I3IK90 UniProt info from
https://www.uniprot.org/uniprot/A0A6I3IK90.xml
> alphafold match A0A6I3IK90
1 UniProt id does not have an AlphaFold database model: A0A6I3IK90 (UniProt
A0A6I3IK90)
Fetching compressed AlphaFold A0A6I3IK90 from
https://alphafold.ebi.ac.uk/files/AF-A0A6I3IK90-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A6I3IK90
(UniProt A0A6I3IK90)
Opened 1 AlphaFold model
> mmaker #5 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold
A0A6I3IK90_9MICO, chain A (#5), sequence alignment score = 815.5
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4: AlphaFold A0A1D7XF17_ALCSP
#1/A, AlphaFold A0A6I3IK90_9MICO #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
RMSD between 267 pruned atom pairs is 0.757 angstroms; (across all 326 pairs:
9.022)
> mmaker #2 to #5 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 AlphaFold A0A6I3IK90_9MICO, chain A (#5) with AlphaFold
U7U7F7_9BURK, chain A (#2), sequence alignment score = 932.2
Alignment identifier is 5
Showing conservation header ("seq_conservation" residue attribute) for
alignment 5
Hiding conservation header for alignment 5
Chains used in RMSD evaluation for alignment 5: AlphaFold U7U7F7_9BURK #2/A,
AlphaFold A0A6I3IK90_9MICO #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 5
RMSD between 290 pruned atom pairs is 0.708 angstroms; (across all 354 pairs:
13.030)
> hide #1 models
> hide #3 models
> hide #4 models
> hide #5 models
> select clear
> show #5 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #1 models
> hide #1 models
> show #1 models
> show #3 models
> show #4 models
> hide #4 models
> hide #3 models
> hide #1 models
Fetching V4Y1C7 UniProt info from https://www.uniprot.org/uniprot/V4Y1C7.xml
> alphafold match V4Y1C7
1 UniProt id does not have an AlphaFold database model: V4Y1C7 (UniProt
V4Y1C7)
Fetching compressed AlphaFold V4Y1C7 from
https://alphafold.ebi.ac.uk/files/AF-V4Y1C7-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: V4Y1C7 (UniProt
V4Y1C7)
Opened 1 AlphaFold model
> hide #5 models
> show #5 models
> mmaker #6 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold
V4Y1C7_9PROT, chain A (#6), sequence alignment score = 862.6
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: AlphaFold A0A1D7XF17_ALCSP
#1/A, AlphaFold V4Y1C7_9PROT #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 272 pruned atom pairs is 0.789 angstroms; (across all 329 pairs:
8.216)
> show #4 models
> hide #4 models
> hide #2 models
> show #2 models
> hide #2 models
> hide #5 models
> show #5 models
> show #1 models
> hide #1 models
> show #3 models
> hide #3 models
> show #4 models
Fetching A0A4Y9PQA1 UniProt info from
https://www.uniprot.org/uniprot/A0A4Y9PQA1.xml
> alphafold match A0A4Y9PQA1
1 UniProt id does not have an AlphaFold database model: A0A4Y9PQA1 (UniProt
A0A4Y9PQA1)
Fetching compressed AlphaFold A0A6D1IBG6 from
https://alphafold.ebi.ac.uk/files/AF-A0A6D1IBG6-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A6D1IBG6
(UniProt A0A4Y9PQA1)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
A0A6D1IBG6_9MICO | A0A4Y9PQA1 | 100.0 | 100.0
Opened 1 AlphaFold model
> mmaker #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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold
A0A6D1IBG6_9MICO, chain A (#7), sequence alignment score = 847.1
RMSD between 276 pruned atom pairs is 0.805 angstroms; (across all 327 pairs:
10.285)
> show #1 models
> hide #1 models
> hide #5 models
> hide #6 models
> hide #7 models
> show #7 models
> show #6 models
> show #5 models
Fetching A0A1X3P4Z3 UniProt info from
https://www.uniprot.org/uniprot/A0A1X3P4Z3.xml
> alphafold match A0A1X3P4Z3
1 UniProt id does not have an AlphaFold database model: A0A1X3P4Z3 (UniProt
A0A1X3P4Z3)
Fetching compressed AlphaFold A0A1X3P4Z3 from
https://alphafold.ebi.ac.uk/files/AF-A0A1X3P4Z3-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A1X3P4Z3
(UniProt A0A1X3P4Z3)
Opened 1 AlphaFold model
> mmaker #8 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold
A0A1X3P4Z3_9MICC, chain A (#8), sequence alignment score = 842.2
RMSD between 279 pruned atom pairs is 0.781 angstroms; (across all 333 pairs:
8.300)
Fetching A0A399JD64 UniProt info from
https://www.uniprot.org/uniprot/A0A399JD64.xml
> alphafold match A0A399JD64
1 UniProt id does not have an AlphaFold database model: A0A399JD64 (UniProt
A0A399JD64)
Fetching compressed AlphaFold A0A399JD64 from
https://alphafold.ebi.ac.uk/files/AF-A0A399JD64-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A399JD64
(UniProt A0A399JD64)
Opened 1 AlphaFold model
> mmaker #9 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold
A0A399JD64_9MICC, chain A (#9), sequence alignment score = 791.3
RMSD between 256 pruned atom pairs is 0.839 angstroms; (across all 333 pairs:
17.953)
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
Fetching M0QIC5 UniProt info from https://www.uniprot.org/uniprot/M0QIC5.xml
> alphafold match M0QIC5
1 UniProt id does not have an AlphaFold database model: M0QIC5 (UniProt
M0QIC5)
Fetching compressed AlphaFold M0QIC5 from
https://alphafold.ebi.ac.uk/files/AF-M0QIC5-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: M0QIC5 (UniProt
M0QIC5)
Opened 1 AlphaFold model
> hide #9 models
> mmaker #10 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold
M0QIC5_9ACTN, chain A (#10), sequence alignment score = 840.5
RMSD between 281 pruned atom pairs is 0.824 angstroms; (across all 332 pairs:
14.761)
Fetching A0A0N1NB04 UniProt info from
https://www.uniprot.org/uniprot/A0A0N1NB04.xml
> alphafold match A0A0N1NB04
1 UniProt id does not have an AlphaFold database model: A0A0N1NB04 (UniProt
A0A0N1NB04)
Fetching compressed AlphaFold A0A0N1NB04 from
https://alphafold.ebi.ac.uk/files/AF-A0A0N1NB04-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A0N1NB04
(UniProt A0A0N1NB04)
Opened 1 AlphaFold model
> mmaker #11 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold
A0A0N1NB04_9ACTN, chain A (#11), sequence alignment score = 791
RMSD between 278 pruned atom pairs is 0.785 angstroms; (across all 329 pairs:
7.826)
> hide #10 models
Fetching A0A3A4KI50 UniProt info from
https://www.uniprot.org/uniprot/A0A3A4KI50.xml
> alphafold match A0A3A4KI50
1 UniProt id does not have an AlphaFold database model: A0A3A4KI50 (UniProt
A0A3A4KI50)
Fetching compressed AlphaFold A0A3A4KI50 from
https://alphafold.ebi.ac.uk/files/AF-A0A3A4KI50-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A3A4KI50
(UniProt A0A3A4KI50)
Opened 1 AlphaFold model
> mmaker #12 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold
A0A3A4KI50_9NOCA, chain A (#12), sequence alignment score = 813.4
RMSD between 272 pruned atom pairs is 0.781 angstroms; (across all 319 pairs:
8.900)
> hide #11 models
Fetching A0A6G4V0U3 UniProt info from
https://www.uniprot.org/uniprot/A0A6G4V0U3.xml
> alphafold match A0A6G4V0U3
1 UniProt id does not have an AlphaFold database model: A0A6G4V0U3 (UniProt
A0A6G4V0U3)
Fetching compressed AlphaFold A0A6G4V0U3 from
https://alphafold.ebi.ac.uk/files/AF-A0A6G4V0U3-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A6G4V0U3
(UniProt A0A6G4V0U3)
Opened 1 AlphaFold model
> mmaker #13 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold
A0A6G4V0U3_9ACTN, chain A (#13), sequence alignment score = 875.3
RMSD between 272 pruned atom pairs is 0.711 angstroms; (across all 325 pairs:
5.931)
> hide #12 models
> close #1
> close #2
> close #3
> hide #4 models
> hide #13 models
> open "I:/Mi
> unidad/Santiago/BIO_INF_TEC_URP/Bacillus/Resultados/Cryo_EM/QHYN/pdb_analysis_sessions/CynD_chainA.pdb"
Chain information for CynD_chainA.pdb #1
---
Chain | Description
A | No description available
> mmaker #1 to #4
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 AlphaFold A8FEX8_BACP2, chain A (#4) with CynD_chainA.pdb, chain A
(#1), sequence alignment score = 1595.4
RMSD between 295 pruned atom pairs is 0.684 angstroms; (across all 315 pairs:
1.961)
> show #4 models
> mmaker #1 to #4 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 AlphaFold A8FEX8_BACP2, chain A (#4) with CynD_chainA.pdb, chain A
(#1), sequence alignment score = 1595.4
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: CynD_chainA.pdb #1/A,
AlphaFold A8FEX8_BACP2 #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 295 pruned atom pairs is 0.684 angstroms; (across all 315 pairs:
1.961)
> select #4/A:321
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #4/A:321-330
84 atoms, 84 bonds, 10 residues, 1 model selected
> hide #4 models
> show #4 models
> hide #4 models
> mmaker #4 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A8FEX8_BACP2, chain A
(#4), sequence alignment score = 1595.4
RMSD between 295 pruned atom pairs is 0.684 angstroms; (across all 315 pairs:
1.961)
> mmaker #5 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A6I3IK90_9MICO,
chain A (#5), sequence alignment score = 757.8
RMSD between 247 pruned atom pairs is 0.876 angstroms; (across all 314 pairs:
9.178)
> mmaker #6 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 CynD_chainA.pdb, chain A (#1) with AlphaFold V4Y1C7_9PROT, chain A
(#6), sequence alignment score = 816.2
RMSD between 256 pruned atom pairs is 0.876 angstroms; (across all 314 pairs:
3.929)
> mmaker #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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A6D1IBG6_9MICO,
chain A (#7), sequence alignment score = 784.9
RMSD between 264 pruned atom pairs is 0.895 angstroms; (across all 312 pairs:
6.515)
> mmaker #8 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1X3P4Z3_9MICC,
chain A (#8), sequence alignment score = 806.5
RMSD between 258 pruned atom pairs is 0.951 angstroms; (across all 310 pairs:
3.320)
> mmaker #9 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A399JD64_9MICC,
chain A (#9), sequence alignment score = 741.7
RMSD between 245 pruned atom pairs is 0.944 angstroms; (across all 310 pairs:
7.132)
> mmaker #10 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 CynD_chainA.pdb, chain A (#1) with AlphaFold M0QIC5_9ACTN, chain A
(#10), sequence alignment score = 763.9
RMSD between 257 pruned atom pairs is 0.904 angstroms; (across all 314 pairs:
8.327)
> mmaker #11 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A0N1NB04_9ACTN,
chain A (#11), sequence alignment score = 738.5
RMSD between 271 pruned atom pairs is 0.909 angstroms; (across all 314 pairs:
3.426)
> mmaker #12 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A3A4KI50_9NOCA,
chain A (#12), sequence alignment score = 759.5
RMSD between 264 pruned atom pairs is 0.972 angstroms; (across all 309 pairs:
5.336)
> mmaker #13 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A6G4V0U3_9ACTN,
chain A (#13), sequence alignment score = 801.2
RMSD between 270 pruned atom pairs is 0.856 angstroms; (across all 310 pairs:
3.292)
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #12 models
> show #13 models
> show #4 models
> hide #4 models
> mmaker #5 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A6I3IK90_9MICO,
chain A (#5), sequence alignment score = 757.8
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: CynD_chainA.pdb #1/A,
AlphaFold A0A6I3IK90_9MICO #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 247 pruned atom pairs is 0.876 angstroms; (across all 314 pairs:
9.178)
> select #5/A:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:61-69
58 atoms, 57 bonds, 9 residues, 1 model selected
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #12 models
> hide #11 models
> hide #13 models
> show #5 models
> select #5/A:109
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/A:109-110
9 atoms, 8 bonds, 2 residues, 1 model selected
> select #5/A:192
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:192-207
129 atoms, 132 bonds, 16 residues, 1 model selected
> select #1/A:232
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/A:232-239
148 atoms, 150 bonds, 8 residues, 1 model selected
> show #6 models
> show #7 models
> show #8 models
> show #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> show #5 models
> show #6 models
> hide #6 models
> hide #4 models
> hide #5 models
> select #5/A:300
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:300-314
119 atoms, 121 bonds, 15 residues, 1 model selected
> show #5 models
> hide #5 models
> hide #1 models
> show #1 models
> hide #1 models
> save "I:/Mi
> unidad/Santiago/BIO_INF_TEC_URP/Bacillus/Resultados/Bioinf/Tesis_David/id_char_muts/par2_vs_CynD.cxs"
——— End of log from Sun Apr 30 01:02:17 2023 ———
opened ChimeraX session
> rainbow structures
> select add #5
2878 atoms, 2949 bonds, 378 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
2878 atoms, 2949 bonds, 378 residues, 1 model selected
> select subtract #5
Nothing selected
> show #1 models
> show #4 models
> hide #4 models
> show #5 models
> show #6 models
> hide #5 models
> hide #6 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #11 models
> hide #11 models
> show #12 models
> hide #12 models
> show #13 models
> hide #13 models
> ui tool show Shell
QWindowsWindow::setGeometry: Unable to set geometry 579x370+2009+834 (frame:
601x426+1998+789) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 573x353+2012+848 (frame:
595x409+2001+803) margins: 11, 45, 11, 11 minimum size: 78x1 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=139, y=58)))
> ui tool show AlphaFold
Fetching A0A0J8YTP9 UniProt info from
https://www.uniprot.org/uniprot/A0A0J8YTP9.xml
> alphafold match A0A0J8YTP9
1 UniProt id does not have an AlphaFold database model: A0A0J8YTP9 (UniProt
A0A0J8YTP9)
Fetching compressed AlphaFold A0A0J8YTP9 from
https://alphafold.ebi.ac.uk/files/AF-A0A0J8YTP9-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A0J8YTP9
(UniProt A0A0J8YTP9)
Opened 1 AlphaFold model
> alphafold match A0A0J8YTP9
1 UniProt id does not have an AlphaFold database model: A0A0J8YTP9 (UniProt
A0A0J8YTP9)
1 AlphaFold model found using sequence similarity searches: A0A0J8YTP9
(UniProt A0A0J8YTP9)
Opened 1 AlphaFold model
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> close 2
Expected a models specifier or a keyword
> close #2
> close #3
> close #4
> close #5
> close #6
> close #7
> close #8
> close #9
> close #10
> close #11
> close #12
> close #13
Fetching A0A0J8YTP9 UniProt info from
https://www.uniprot.org/uniprot/A0A0J8YTP9.xml
> alphafold match A0A0J8YTP9
1 UniProt id does not have an AlphaFold database model: A0A0J8YTP9 (UniProt
A0A0J8YTP9)
Fetching compressed AlphaFold A0A0J8YTP9 from
https://alphafold.ebi.ac.uk/files/AF-A0A0J8YTP9-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A0J8YTP9
(UniProt A0A0J8YTP9)
Opened 1 AlphaFold model
Fetching D2TWZ9 UniProt info from https://www.uniprot.org/uniprot/D2TWZ9.xml
> alphafold match D2TWZ9
1 UniProt id does not have an AlphaFold database model: D2TWZ9 (UniProt
D2TWZ9)
Fetching compressed AlphaFold D2TWZ9 from
https://alphafold.ebi.ac.uk/files/AF-D2TWZ9-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: D2TWZ9 (UniProt
D2TWZ9)
Opened 1 AlphaFold model
Fetching V2TN35 UniProt info from https://www.uniprot.org/uniprot/V2TN35.xml
> alphafold match V2TN35
1 UniProt id does not have an AlphaFold database model: V2TN35 (UniProt
V2TN35)
Fetching compressed AlphaFold V2TN35 from
https://alphafold.ebi.ac.uk/files/AF-V2TN35-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: V2TN35 (UniProt
V2TN35)
Opened 1 AlphaFold model
Fetching B8KVK8 UniProt info from https://www.uniprot.org/uniprot/B8KVK8.xml
> alphafold match B8KVK8
1 UniProt id does not have an AlphaFold database model: B8KVK8 (UniProt
B8KVK8)
Fetching compressed AlphaFold B8KVK8 from
https://alphafold.ebi.ac.uk/files/AF-B8KVK8-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: B8KVK8 (UniProt
B8KVK8)
Opened 1 AlphaFold model
Fetching B1KMA0 UniProt info from https://www.uniprot.org/uniprot/B1KMA0.xml
> alphafold match B1KMA0
1 UniProt id does not have an AlphaFold database model: B1KMA0 (UniProt
B1KMA0)
Fetching compressed AlphaFold B1KMA0 from
https://alphafold.ebi.ac.uk/files/AF-B1KMA0-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: B1KMA0 (UniProt
B1KMA0)
Opened 1 AlphaFold model
Fetching A0A4V2ZFV7 UniProt info from
https://www.uniprot.org/uniprot/A0A4V2ZFV7.xml
> alphafold match A0A4V2ZFV7
1 UniProt id does not have an AlphaFold database model: A0A4V2ZFV7 (UniProt
A0A4V2ZFV7)
Fetching compressed AlphaFold A0A4V2ZFV7 from
https://alphafold.ebi.ac.uk/files/AF-A0A4V2ZFV7-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A4V2ZFV7
(UniProt A0A4V2ZFV7)
Opened 1 AlphaFold model
Fetching A0A5S3PMU3 UniProt info from
https://www.uniprot.org/uniprot/A0A5S3PMU3.xml
> alphafold match A0A5S3PMU3
1 UniProt id does not have an AlphaFold database model: A0A5S3PMU3 (UniProt
A0A5S3PMU3)
Fetching compressed AlphaFold A0A5S3PMU3 from
https://alphafold.ebi.ac.uk/files/AF-A0A5S3PMU3-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A5S3PMU3
(UniProt A0A5S3PMU3)
Opened 1 AlphaFold model
Fetching A5V4Y8 UniProt info from https://www.uniprot.org/uniprot/A5V4Y8.xml
> alphafold match A5V4Y8
Fetching A0A3A1P588 UniProt info from
https://www.uniprot.org/uniprot/A0A3A1P588.xml
> alphafold match A0A3A1P588
1 UniProt id does not have an AlphaFold database model: A0A3A1P588 (UniProt
A0A3A1P588)
Fetching compressed AlphaFold A0A3A1P588 from
https://alphafold.ebi.ac.uk/files/AF-A0A3A1P588-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A3A1P588
(UniProt A0A3A1P588)
Opened 1 AlphaFold model
Fetching F6IEF9 UniProt info from https://www.uniprot.org/uniprot/F6IEF9.xml
> alphafold match F6IEF9
1 UniProt id does not have an AlphaFold database model: F6IEF9 (UniProt
F6IEF9)
Fetching compressed AlphaFold F6IEF9 from
https://alphafold.ebi.ac.uk/files/AF-F6IEF9-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: F6IEF9 (UniProt
F6IEF9)
Opened 1 AlphaFold model
Fetching A0A480AHR2 UniProt info from
https://www.uniprot.org/uniprot/A0A480AHR2.xml
> alphafold match A0A480AHR2
1 UniProt id does not have an AlphaFold database model: A0A480AHR2 (UniProt
A0A480AHR2)
Fetching compressed AlphaFold A0A480AHR2 from
https://alphafold.ebi.ac.uk/files/AF-A0A480AHR2-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A480AHR2
(UniProt A0A480AHR2)
Opened 1 AlphaFold model
Fetching A0A4R7PEM6 UniProt info from
https://www.uniprot.org/uniprot/A0A4R7PEM6.xml
> alphafold match A0A4R7PEM6
1 UniProt id does not have an AlphaFold database model: A0A4R7PEM6 (UniProt
A0A4R7PEM6)
Fetching compressed AlphaFold A0A4R7PEM6 from
https://alphafold.ebi.ac.uk/files/AF-A0A4R7PEM6-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A4R7PEM6
(UniProt A0A4R7PEM6)
Opened 1 AlphaFold model
Fetching L1M139 UniProt info from https://www.uniprot.org/uniprot/L1M139.xml
> alphafold match L1M139
1 UniProt id does not have an AlphaFold database model: L1M139 (UniProt
L1M139)
Fetching compressed AlphaFold L1M139 from
https://alphafold.ebi.ac.uk/files/AF-L1M139-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: L1M139 (UniProt
L1M139)
Opened 1 AlphaFold model
Fetching A0A4Q8URY2 UniProt info from
https://www.uniprot.org/uniprot/A0A4Q8URY2.xml
> alphafold match A0A4Q8URY2
1 UniProt id does not have an AlphaFold database model: A0A4Q8URY2 (UniProt
A0A4Q8URY2)
Fetching compressed AlphaFold A0A4Q8URY2 from
https://alphafold.ebi.ac.uk/files/AF-A0A4Q8URY2-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A4Q8URY2
(UniProt A0A4Q8URY2)
Opened 1 AlphaFold model
Fetching A9D6L7 UniProt info from https://www.uniprot.org/uniprot/A9D6L7.xml
> alphafold match A9D6L7
1 UniProt id does not have an AlphaFold database model: A9D6L7 (UniProt
A9D6L7)
Fetching compressed AlphaFold A9D6L7 from
https://alphafold.ebi.ac.uk/files/AF-A9D6L7-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A9D6L7 (UniProt
A9D6L7)
Opened 1 AlphaFold model
Fetching I4CEN7 UniProt info from https://www.uniprot.org/uniprot/I4CEN7.xml
> alphafold match I4CEN7
1 UniProt id does not have an AlphaFold database model: I4CEN7 (UniProt
I4CEN7)
Fetching compressed AlphaFold I4CEN7 from
https://alphafold.ebi.ac.uk/files/AF-I4CEN7-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: I4CEN7 (UniProt
I4CEN7)
Opened 1 AlphaFold model
Fetching A0A370N3U6 UniProt info from
https://www.uniprot.org/uniprot/A0A370N3U6.xml
> alphafold match A0A370N3U6
1 UniProt id does not have an AlphaFold database model: A0A370N3U6 (UniProt
A0A370N3U6)
Fetching compressed AlphaFold A0A370N3U6 from
https://alphafold.ebi.ac.uk/files/AF-A0A370N3U6-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A370N3U6
(UniProt A0A370N3U6)
Opened 1 AlphaFold model
Fetching A0A1L9B491 UniProt info from
https://www.uniprot.org/uniprot/A0A1L9B491.xml
> alphafold match A0A1L9B491
1 UniProt id does not have an AlphaFold database model: A0A1L9B491 (UniProt
A0A1L9B491)
Fetching compressed AlphaFold A0A1L9B491 from
https://alphafold.ebi.ac.uk/files/AF-A0A1L9B491-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A1L9B491
(UniProt A0A1L9B491)
Opened 1 AlphaFold model
Fetching A0A1H0LGU0 UniProt info from
https://www.uniprot.org/uniprot/A0A1H0LGU0.xml
> alphafold match A0A1H0LGU0
1 UniProt id does not have an AlphaFold database model: A0A1H0LGU0 (UniProt
A0A1H0LGU0)
Fetching compressed AlphaFold A0A1H0LGU0 from
https://alphafold.ebi.ac.uk/files/AF-A0A1H0LGU0-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A1H0LGU0
(UniProt A0A1H0LGU0)
Opened 1 AlphaFold model
Fetching A0A1G5QFQ9 UniProt info from
https://www.uniprot.org/uniprot/A0A1G5QFQ9.xml
> alphafold match A0A1G5QFQ9
1 UniProt id does not have an AlphaFold database model: A0A1G5QFQ9 (UniProt
A0A1G5QFQ9)
Fetching compressed AlphaFold A0A1G5QFQ9 from
https://alphafold.ebi.ac.uk/files/AF-A0A1G5QFQ9-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A1G5QFQ9
(UniProt A0A1G5QFQ9)
Opened 1 AlphaFold model
Fetching A0A4Q1KIU1 UniProt info from
https://www.uniprot.org/uniprot/A0A4Q1KIU1.xml
> alphafold match A0A4Q1KIU1
1 UniProt id does not have an AlphaFold database model: A0A4Q1KIU1 (UniProt
A0A4Q1KIU1)
Fetching compressed AlphaFold A0A4Q1KIU1 from
https://alphafold.ebi.ac.uk/files/AF-A0A4Q1KIU1-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A4Q1KIU1
(UniProt A0A4Q1KIU1)
Opened 1 AlphaFold model
Fetching A0A0N0VI24 UniProt info from
https://www.uniprot.org/uniprot/A0A0N0VI24.xml
> alphafold match A0A0N0VI24
1 UniProt id does not have an AlphaFold database model: A0A0N0VI24 (UniProt
A0A0N0VI24)
Fetching compressed AlphaFold A0A0N0VI24 from
https://alphafold.ebi.ac.uk/files/AF-A0A0N0VI24-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A0N0VI24
(UniProt A0A0N0VI24)
Opened 1 AlphaFold model
Fetching A0A060QHL9 UniProt info from
https://www.uniprot.org/uniprot/A0A060QHL9.xml
> alphafold match A0A060QHL9
1 UniProt id does not have an AlphaFold database model: A0A060QHL9 (UniProt
A0A060QHL9)
Fetching compressed AlphaFold A0A060QHL9 from
https://alphafold.ebi.ac.uk/files/AF-A0A060QHL9-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A060QHL9
(UniProt A0A060QHL9)
Opened 1 AlphaFold model
Fetching A0A1N6UIB7 UniProt info from
https://www.uniprot.org/uniprot/A0A1N6UIB7.xml
> alphafold match A0A1N6UIB7
1 UniProt id does not have an AlphaFold database model: A0A1N6UIB7 (UniProt
A0A1N6UIB7)
Fetching compressed AlphaFold A0A1N6UIB7 from
https://alphafold.ebi.ac.uk/files/AF-A0A1N6UIB7-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A1N6UIB7
(UniProt A0A1N6UIB7)
Opened 1 AlphaFold model
Fetching A0A1I4SMV6 UniProt info from
https://www.uniprot.org/uniprot/A0A1I4SMV6.xml
> alphafold match A0A1I4SMV6
1 UniProt id does not have an AlphaFold database model: A0A1I4SMV6 (UniProt
A0A1I4SMV6)
Fetching compressed AlphaFold A0A1I4SMV6 from
https://alphafold.ebi.ac.uk/files/AF-A0A1I4SMV6-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A1I4SMV6
(UniProt A0A1I4SMV6)
Opened 1 AlphaFold model
Fetching A0A1I5SZE4 UniProt info from
https://www.uniprot.org/uniprot/A0A1I5SZE4.xml
> alphafold match A0A1I5SZE4
1 UniProt id does not have an AlphaFold database model: A0A1I5SZE4 (UniProt
A0A1I5SZE4)
Fetching compressed AlphaFold A0A1I5SZE4 from
https://alphafold.ebi.ac.uk/files/AF-A0A1I5SZE4-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A1I5SZE4
(UniProt A0A1I5SZE4)
Opened 1 AlphaFold model
Fetching A0P008 UniProt info from https://www.uniprot.org/uniprot/A0P008.xml
> alphafold match A0P008
1 UniProt id does not have an AlphaFold database model: A0P008 (UniProt
A0P008)
Fetching compressed AlphaFold A0P008 from
https://alphafold.ebi.ac.uk/files/AF-A0P008-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0P008 (UniProt
A0P008)
Opened 1 AlphaFold model
Fetching A0A2R4MHN4 UniProt info from
https://www.uniprot.org/uniprot/A0A2R4MHN4.xml
> alphafold match A0A2R4MHN4
1 UniProt id does not have an AlphaFold database model: A0A2R4MHN4 (UniProt
A0A2R4MHN4)
Fetching compressed AlphaFold A0A2R4MHN4 from
https://alphafold.ebi.ac.uk/files/AF-A0A2R4MHN4-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A2R4MHN4
(UniProt A0A2R4MHN4)
Opened 1 AlphaFold model
Fetching Q28KW0 UniProt info from https://www.uniprot.org/uniprot/Q28KW0.xml
> alphafold match Q28KW0
1 UniProt id does not have an AlphaFold database model: Q28KW0 (UniProt
Q28KW0)
Fetching compressed AlphaFold Q28KW0 from
https://alphafold.ebi.ac.uk/files/AF-Q28KW0-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: Q28KW0 (UniProt
Q28KW0)
Opened 1 AlphaFold model
Fetching A0A1H4HM05 UniProt info from
https://www.uniprot.org/uniprot/A0A1H4HM05.xml
> alphafold match A0A1H4HM05
1 UniProt id does not have an AlphaFold database model: A0A1H4HM05 (UniProt
A0A1H4HM05)
Fetching compressed AlphaFold A0A1H4HM05 from
https://alphafold.ebi.ac.uk/files/AF-A0A1H4HM05-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A1H4HM05
(UniProt A0A1H4HM05)
Opened 1 AlphaFold model
Fetching A0A2Z2NN35 UniProt info from
https://www.uniprot.org/uniprot/A0A2Z2NN35.xml
> alphafold match A0A2Z2NN35
1 UniProt id does not have an AlphaFold database model: A0A2Z2NN35 (UniProt
A0A2Z2NN35)
Fetching compressed AlphaFold A0A2Z2NN35 from
https://alphafold.ebi.ac.uk/files/AF-A0A2Z2NN35-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A2Z2NN35
(UniProt A0A2Z2NN35)
Opened 1 AlphaFold model
Fetching U7U7F7 UniProt info from https://www.uniprot.org/uniprot/U7U7F7.xml
> alphafold match U7U7F7
1 UniProt id does not have an AlphaFold database model: U7U7F7 (UniProt
U7U7F7)
Fetching compressed AlphaFold U7U7F7 from
https://alphafold.ebi.ac.uk/files/AF-U7U7F7-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: U7U7F7 (UniProt
U7U7F7)
Opened 1 AlphaFold model
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CynD_chainA.pdb, chain A (#1) with AlphaFold A0A0J8YTP9_9GAMM,
chain A (#2), sequence alignment score = 758.8
RMSD between 244 pruned atom pairs is 0.895 angstroms; (across all 309 pairs:
6.331)
> mmaker #3 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 CynD_chainA.pdb, chain A (#1) with AlphaFold D2TWZ9_9GAMM, chain A
(#3), sequence alignment score = 764.3
RMSD between 244 pruned atom pairs is 0.881 angstroms; (across all 312 pairs:
9.634)
> mmaker #4 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 CynD_chainA.pdb, chain A (#1) with AlphaFold V2TN35_9GAMM, chain A
(#4), sequence alignment score = 805.5
RMSD between 260 pruned atom pairs is 0.918 angstroms; (across all 305 pairs:
5.915)
> mmaker #5 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 CynD_chainA.pdb, chain A (#1) with AlphaFold B8KVK8_9GAMM, chain A
(#5), sequence alignment score = 819.3
RMSD between 258 pruned atom pairs is 0.874 angstroms; (across all 313 pairs:
8.557)
> mmaker #6 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 CynD_chainA.pdb, chain A (#1) with AlphaFold B1KMA0_SHEWM, chain A
(#6), sequence alignment score = 810.8
RMSD between 261 pruned atom pairs is 0.915 angstroms; (across all 313 pairs:
7.161)
> mmaker #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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A4V2ZFV7_9ALTE,
chain A (#7), sequence alignment score = 824.8
RMSD between 270 pruned atom pairs is 0.883 angstroms; (across all 314 pairs:
6.307)
> mmaker #8 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A5S3PMU3_9FLAO,
chain A (#8), sequence alignment score = 808.4
RMSD between 259 pruned atom pairs is 0.924 angstroms; (across all 311 pairs:
11.357)
> mmaker #9 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A3A1P588_9SPHN,
chain A (#9), sequence alignment score = 798.1
RMSD between 254 pruned atom pairs is 0.891 angstroms; (across all 311 pairs:
5.373)
> mmaker #10 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 CynD_chainA.pdb, chain A (#1) with AlphaFold F6IEF9_9SPHN, chain A
(#10), sequence alignment score = 545.8
RMSD between 194 pruned atom pairs is 0.944 angstroms; (across all 243 pairs:
7.281)
> mmaker #11 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A480AHR2_9BURK,
chain A (#11), sequence alignment score = 809.6
RMSD between 255 pruned atom pairs is 0.872 angstroms; (across all 312 pairs:
6.300)
> mmaker #12 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A4R7PEM6_9GAMM,
chain A (#12), sequence alignment score = 773
RMSD between 255 pruned atom pairs is 0.859 angstroms; (across all 314 pairs:
9.132)
> mmaker #13 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 CynD_chainA.pdb, chain A (#1) with AlphaFold L1M139_PSEPU, chain A
(#13), sequence alignment score = 819.7
RMSD between 259 pruned atom pairs is 0.880 angstroms; (across all 314 pairs:
11.981)
> mmaker #14 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A4Q8URY2_9MICC,
chain A (#14), sequence alignment score = 827.9
RMSD between 249 pruned atom pairs is 0.899 angstroms; (across all 308 pairs:
6.811)
> mmaker #15 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A9D6L7_HOEPD, chain A
(#15), sequence alignment score = 828
RMSD between 261 pruned atom pairs is 0.894 angstroms; (across all 309 pairs:
6.317)
> mmaker #16 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 CynD_chainA.pdb, chain A (#1) with AlphaFold I4CEN7_DESTA, chain A
(#16), sequence alignment score = 861.5
RMSD between 263 pruned atom pairs is 0.858 angstroms; (across all 309 pairs:
8.262)
> mmaker #17 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A370N3U6_9BURK,
chain A (#17), sequence alignment score = 776.1
RMSD between 252 pruned atom pairs is 0.881 angstroms; (across all 310 pairs:
6.668)
> mmaker #18 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1L9B491_9DELT,
chain A (#18), sequence alignment score = 803.5
RMSD between 258 pruned atom pairs is 0.827 angstroms; (across all 310 pairs:
8.245)
> mmaker #19 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1H0LGU0_9BRAD,
chain A (#19), sequence alignment score = 767.2
RMSD between 245 pruned atom pairs is 0.827 angstroms; (across all 304 pairs:
6.407)
> mmaker #20 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1G5QFQ9_9RHOB,
chain A (#20), sequence alignment score = 812.5
RMSD between 248 pruned atom pairs is 0.841 angstroms; (across all 305 pairs:
7.987)
> mmaker #21 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A4Q1KIU1_9SPHN,
chain A (#21), sequence alignment score = 803.3
RMSD between 266 pruned atom pairs is 0.927 angstroms; (across all 309 pairs:
3.649)
> mmaker #22 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A0N0VI24_9PSED,
chain A (#22), sequence alignment score = 813
RMSD between 258 pruned atom pairs is 0.854 angstroms; (across all 314 pairs:
11.371)
> mmaker #23 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A060QHL9_9PROT,
chain A (#23), sequence alignment score = 762.8
RMSD between 256 pruned atom pairs is 0.919 angstroms; (across all 307 pairs:
6.450)
> mmaker #24 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1N6UIB7_9GAMM,
chain A (#24), sequence alignment score = 822.9
RMSD between 266 pruned atom pairs is 0.892 angstroms; (across all 314 pairs:
11.556)
> mmaker #25 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1I4SMV6_9RHOB,
chain A (#25), sequence alignment score = 769.3
RMSD between 246 pruned atom pairs is 0.824 angstroms; (across all 295 pairs:
4.488)
> mmaker #26 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1I5SZE4_9BURK,
chain A (#26), sequence alignment score = 735.4
RMSD between 260 pruned atom pairs is 0.908 angstroms; (across all 305 pairs:
4.645)
> mmaker #27 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0P008_LABAI, chain A
(#27), sequence alignment score = 803.6
RMSD between 257 pruned atom pairs is 0.890 angstroms; (across all 313 pairs:
2.941)
> mmaker #28 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A2R4MHN4_9HYPH,
chain A (#28), sequence alignment score = 790.9
RMSD between 264 pruned atom pairs is 0.908 angstroms; (across all 314 pairs:
6.709)
> mmaker #29 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 CynD_chainA.pdb, chain A (#1) with AlphaFold Q28KW0_JANSC, chain A
(#29), sequence alignment score = 806.6
RMSD between 248 pruned atom pairs is 0.888 angstroms; (across all 311 pairs:
8.054)
> mmaker #30 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1H4HM05_9BURK,
chain A (#30), sequence alignment score = 800.8
RMSD between 262 pruned atom pairs is 0.935 angstroms; (across all 309 pairs:
3.307)
> mmaker #31 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A2Z2NN35_9GAMM,
chain A (#31), sequence alignment score = 774.6
RMSD between 253 pruned atom pairs is 0.896 angstroms; (across all 305 pairs:
6.732)
> mmaker #32 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 CynD_chainA.pdb, chain A (#1) with AlphaFold U7U7F7_9BURK, chain A
(#32), sequence alignment score = 726.3
RMSD between 256 pruned atom pairs is 0.900 angstroms; (across all 313 pairs:
9.758)
> rainbow structures
> hide ~#1 ribbons
> show #2 ribbons
> hide #2 models
> show #3 ribbons
> hide #3 models
> show #4 ribbons
> hide #4 models
> show #5 ribbons
> hide #5 models
> show #5 ribbons
> show #6 ribbons
> show #2 models
> hide #2 models
> show #2 models
> show #3 models
> hide #3 models
> show #3 models
> show #4 models
> hide #4 models
> show #4 models
> hide #3 models
> hide #4 models
> hide #2 models
> hide #6 models
> show #7 ribbons
> hide #7 models
> show #8 ribbons
> hide #8 models
> show #9 ribbons
> hide #9 models
> show #10 ribbons
> hide #10 models
> show #11 ribbons
> hide #11 models
> show #12 ribbons
> hide #12 models
> show #13 ribbons
> hide #13 models
> show #14 ribbons
> hide #14 models
> show #15 ribbons
> show #15 atoms,ribbons
> hide #15 atoms,ribbons
> alphafold pae #15 uniprotId A9D6L7
Fetching compressed AlphaFold PAE A9D6L7 from
https://alphafold.ebi.ac.uk/files/AF-A9D6L7-F1-predicted_aligned_error_v4.json
> hide #15 models
> show #16 ribbons
> hide #16 models
> show #17 ribbons
> show #18 ribbons
> hide #17 models
> show #19 ribbons
> hide #18 models
> show #20 ribbons
> show #21 ribbons
> show #22 ribbons
> show #23 ribbons
> show #24 ribbons
> show #25 ribbons
> hide #19 models
> hide #20 models
> hide #21 models
> hide #22 models
> hide #23 models
> hide #24 models
> show #26 ribbons
> show #27 ribbons
> show #278 ribbons
> show #28 ribbons
> show #29 ribbons
> show #30 ribbons
> show #31 ribbons
> hide #25 models
> hide #26 models
> hide #27 models
> hide #28 models
> hide #29 models
> hide #30 models
> show #32 ribbons
> hide #31 models
> hide #32 models
> save "I:/Mi
> unidad/Santiago/BIO_INF_TEC_URP/Bacillus/Resultados/Bioinf/Tesis_David/id_char_muts/par1_vs_CynD.cxs"
——— End of log from Sun Apr 30 21:29:43 2023 ———
opened ChimeraX session
QWindowsWindow::setGeometry: Unable to set geometry 581x149+2010+1205 (frame:
603x205+1999+1160) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 575x132+2013+1219 (frame:
597x188+2002+1174) margins: 11, 45, 11, 11 minimum size: 142x72 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=235, y=164)))
> show #2 models
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\matplotlib\cbook\\__init__.py", line 287, in process
func(*args, **kwargs)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\validation\ramaplot\ramaplot.py", line 307, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 143, in step_to
self._new_camera_position(residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 232, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 217, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 360, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
UnboundLocalError: local variable 'o' referenced before assignment
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\matplotlib\cbook\\__init__.py", line 287, in process
func(*args, **kwargs)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\validation\ramaplot\ramaplot.py", line 307, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 143, in step_to
self._new_camera_position(residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 232, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 217, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 360, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
UnboundLocalError: local variable 'o' referenced before assignment
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\matplotlib\cbook\\__init__.py", line 287, in process
func(*args, **kwargs)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\validation\ramaplot\ramaplot.py", line 307, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 143, in step_to
self._new_camera_position(residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 232, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 217, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 360, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
UnboundLocalError: local variable 'o' referenced before assignment
> hide #2 models
> ui tool show "Ramachandran Plot"
> show #!2 models
> hide #!2 models
> hide #1 models
> show #1 models
> show ribbons
> select add #1
4908 atoms, 4976 bonds, 315 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
4908 atoms, 4976 bonds, 315 residues, 1 model selected
> view sel
> hide #1 models
> show #1 models
> show #!2 models
> select clear
> show #3 models
> hide #!2 models
> show #4 models
> hide #3 models
> show #5 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #5 models
> ui tool show "Ramachandran Plot"
> select #1/A:36
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
223 atoms, 222 bonds, 15 residues, 1 model selected
> select clear
> select #1/A:200
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
175 atoms, 176 bonds, 11 residues, 1 model selected
> select clear
> select #1/A:104
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
149 atoms, 149 bonds, 10 residues, 1 model selected
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\matplotlib\cbook\\__init__.py", line 287, in process
func(*args, **kwargs)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\validation\ramaplot\ramaplot.py", line 307, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 143, in step_to
self._new_camera_position(residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 232, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 217, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 360, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
UnboundLocalError: local variable 'o' referenced before assignment
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\matplotlib\cbook\\__init__.py", line 287, in process
func(*args, **kwargs)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\validation\ramaplot\ramaplot.py", line 307, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 143, in step_to
self._new_camera_position(residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 232, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 217, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 360, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
UnboundLocalError: local variable 'o' referenced before assignment
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\matplotlib\cbook\\__init__.py", line 287, in process
func(*args, **kwargs)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\validation\ramaplot\ramaplot.py", line 307, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 143, in step_to
self._new_camera_position(residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 232, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 217, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 360, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
UnboundLocalError: local variable 'o' referenced before assignment
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\matplotlib\cbook\\__init__.py", line 287, in process
func(*args, **kwargs)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\validation\ramaplot\ramaplot.py", line 307, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 143, in step_to
self._new_camera_position(residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 232, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 217, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 360, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
UnboundLocalError: local variable 'o' referenced before assignment
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\matplotlib\cbook\\__init__.py", line 287, in process
func(*args, **kwargs)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\validation\ramaplot\ramaplot.py", line 307, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 143, in step_to
self._new_camera_position(residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 232, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 217, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 360, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
UnboundLocalError: local variable 'o' referenced before assignment
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\matplotlib\cbook\\__init__.py", line 287, in process
func(*args, **kwargs)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\validation\ramaplot\ramaplot.py", line 307, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 143, in step_to
self._new_camera_position(residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 232, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 217, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 360, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
UnboundLocalError: local variable 'o' referenced before assignment
> view sel
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\matplotlib\cbook\\__init__.py", line 287, in process
func(*args, **kwargs)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\validation\ramaplot\ramaplot.py", line 307, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 143, in step_to
self._new_camera_position(residue)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 232, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 217, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
File "C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\navigate.py", line 360, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
UnboundLocalError: local variable 'o' referenced before assignment
> view sel
> show sel target ab
> show #!2 models
> select #1
4908 atoms, 4976 bonds, 315 residues, 1 model selected
> view sel
> select clear
> show #3 models
> hide #1 models
> show #4 models
Fetching G7M953 UniProt info from https://www.uniprot.org/uniprot/G7M953.xml
> alphafold match G7M953
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
1 UniProt id does not have an AlphaFold database model: G7M953 (UniProt
G7M953)
AlphaFold sequence search web service failed (500) "Internal Server Error"
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search3_cgi.py
No AlphaFold model with similar sequence for UniProt G7M953
Opened 0 AlphaFold model
OpenGL version: 3.3.0 NVIDIA 531.68
OpenGL renderer: NVIDIA GeForce RTX 4080 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: es_ES.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Alienware
Model: Alienware m18 R1
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 34,033,319,936
MaxProcessMemory: 137,438,953,344
CPU: 32 13th Gen Intel(R) Core(TM) i9-13900HX
OSLanguage: es-ES
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
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: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
Change History (3)
comment:1 by , 2 years ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → AlphaFold sequence search web service failed (500) "Internal Server Error" |
comment:2 by , 2 years ago
| Cc: | added |
|---|---|
| Resolution: | → fixed |
| Status: | assigned → closed |
Fixed.
Thanks for reporting the problem. The AlphaFold search capability broke because of an update of the operating system on our servers. The search script used Python and the location of Python changed (/usr/local/bin to /usr/bin). I've updated the scripts but do not have permission to put them on the live server. Another developer will put them on the live server or they will update automatically overnight tonight (Pacific time), about 15 hours from now.
comment:3 by , 2 years ago
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Reported by Santiago Justo Arevalo