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Opened 3 years ago
Closed 3 years ago
#7983 closed defect (can't reproduce)
open PDB file: 'utf-8' codec can't decode byte
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/shrugs/Documents/UCL/Year four/4th year project
> /5ht2a/5ht2a-active.pdb" format pdb
Summary of feedback from opening /Users/shrugs/Documents/UCL/Year four/4th
year project /5ht2a/5ht2a-active.pdb
---
warnings | Ignored bad PDB record found on line 1
FREMARK 1 MODEL FOR 6wha CREATED WITH GPCRDB HOMOLOGY MODELING PIPELINE,
VERSION 2022-03-28
Ignored bad PDB record found on line 2
REMARK 2 MAIN TEMPLATE: 6WHA
Ignored bad PDB record found on line 3
SSBOND 1 CYS R 148 CYS R 227
Ignored bad PDB record found on line 4
SSBOND 2 CYS R 349 CYS R 353
Chain information for 5ht2a-active.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
R | No description available
> save "/Users/shrugs/Documents/UCL/Year four/4th year project /5ht2a/5HT2a-
> CLEAN.cxs"
> select /A
2908 atoms, 2966 bonds, 349 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /B
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /G
395 atoms, 401 bonds, 51 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save "/Users/shrugs/Documents/UCL/Year four/4th year project /5ht2a/5HT2a-
> CLEAN.cxs"
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> ui tool show Toolbar
[Repeated 1 time(s)]
> ui tool show "Show Sequence Viewer"
> sequence chain /R
Alignment identifier is 1/R
> select /R:273
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /R:273-277
37 atoms, 36 bonds, 5 residues, 1 model selected
> ui tool show "Model Loops"
> modeller refine 1/R:1:210-214 numModels 10 fast false adjacentFlexible 1
> protocol standard
Webservices job id: WQ212H52J3MLZ7UB
> ui tool show Log
Modeller job ID WQ212H52J3MLZ7UB 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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 306 pruned atom pairs is 0.093 angstroms; (across all 310 pairs:
1.161)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 306 pruned atom pairs is 0.119 angstroms; (across all 310 pairs:
0.796)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 306 pruned atom pairs is 0.057 angstroms; (across all 310 pairs:
0.950)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 305 pruned atom pairs is 0.062 angstroms; (across all 310 pairs:
1.224)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 305 pruned atom pairs is 0.075 angstroms; (across all 310 pairs:
1.460)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 306 pruned atom pairs is 0.079 angstroms; (across all 310 pairs:
1.060)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 305 pruned atom pairs is 0.082 angstroms; (across all 310 pairs:
1.385)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 306 pruned atom pairs is 0.104 angstroms; (across all 310 pairs:
1.221)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 306 pruned atom pairs is 0.095 angstroms; (across all 310 pairs:
1.020)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 307 pruned atom pairs is 0.127 angstroms; (across all 310 pairs:
0.862)
Associated chain_R chain R to chain R with 0 mismatches
[Repeated 9 time(s)] Chain information for chain_R
---
Chain | Description
2.1/R 2.2/R 2.3/R 2.4/R 2.5/R 2.6/R 2.7/R 2.8/R 2.9/R 2.10/R | No description
available
> select ::name="CYS"
660 atoms, 552 bonds, 110 residues, 11 models selected
> hide #!2 models
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> hide #2.6 models
> hide #2.7 models
> hide #2.9 models
> hide #2.10 models
> hide #2.8 models
> show #2.1 models
> hide #2.1 models
> show (#!1 & sel) target ab
> select
> #1/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.1/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.2/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.3/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.4/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.5/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.6/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.7/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.8/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.9/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.10/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
20988 atoms, 21351 bonds, 2673 residues, 11 models selected
> select #1/R:273 #2.1/R:273 #2.2/R:273 #2.3/R:273 #2.4/R:273 #2.5/R:273
> #2.6/R:273 #2.7/R:273 #2.8/R:273 #2.9/R:273 #2.10/R:273
44 atoms, 33 bonds, 11 residues, 11 models selected
> select #1/R:273-311 #2.1/R:273-311 #2.2/R:273-311 #2.3/R:273-311
> #2.4/R:273-311 #2.5/R:273-311 #2.6/R:273-311 #2.7/R:273-311 #2.8/R:273-311
> #2.9/R:273-311 #2.10/R:273-311
837 atoms, 825 bonds, 1 pseudobond, 110 residues, 12 models selected
5ht2a-Active.pdb (#1) Chain R [ID: 1/R] region chain R [210-219] RMSD: 4.624
> select #1/R:273 #2.1/R:273 #2.2/R:273 #2.3/R:273 #2.4/R:273 #2.5/R:273
> #2.6/R:273 #2.7/R:273 #2.8/R:273 #2.9/R:273 #2.10/R:273
44 atoms, 33 bonds, 11 residues, 11 models selected
> select #1/R:273-277 #2.1/R:273-277 #2.2/R:273-277 #2.3/R:273-277
> #2.4/R:273-277 #2.5/R:273-277 #2.6/R:273-277 #2.7/R:273-277 #2.8/R:273-277
> #2.9/R:273-277 #2.10/R:273-277
397 atoms, 386 bonds, 55 residues, 11 models selected
5ht2a-Active.pdb (#1) Chain R [ID: 1/R] region chain R [210-214] RMSD: 6.513
> select #1/R:272 #2.1/R:272 #2.2/R:272 #2.3/R:272 #2.4/R:272 #2.5/R:272
> #2.6/R:272 #2.7/R:272 #2.8/R:272 #2.9/R:272 #2.10/R:272
88 atoms, 77 bonds, 11 residues, 11 models selected
> select #1/R:272-275 #2.1/R:272-275 #2.2/R:272-275 #2.3/R:272-275
> #2.4/R:272-275 #2.5/R:272-275 #2.6/R:272-275 #2.7/R:272-275 #2.8/R:272-275
> #2.9/R:272-275 #2.10/R:272-275
330 atoms, 319 bonds, 44 residues, 11 models selected
5ht2a-Active.pdb (#1) Chain R [ID: 1/R] region chain R [209-212] RMSD: 4.571
> select
> #1/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.1/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.2/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.3/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.4/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.5/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.6/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.7/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.8/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.9/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
> #2.10/R:70-101,108-137,145-176,181-185,191-207,209-216,218-221,232-243,245-271,312-348,355-382,385-395
20988 atoms, 21351 bonds, 2673 residues, 11 models selected
> select #1/R:277 #2.1/R:277 #2.2/R:277 #2.3/R:277 #2.4/R:277 #2.5/R:277
> #2.6/R:277 #2.7/R:277 #2.8/R:277 #2.9/R:277 #2.10/R:277
100 atoms, 89 bonds, 11 residues, 11 models selected
> select #1/R:275-277 #2.1/R:275-277 #2.2/R:275-277 #2.3/R:275-277
> #2.4/R:275-277 #2.5/R:275-277 #2.6/R:275-277 #2.7/R:275-277 #2.8/R:275-277
> #2.9/R:275-277 #2.10/R:275-277
276 atoms, 265 bonds, 33 residues, 11 models selected
5ht2a-Active.pdb (#1) Chain R [ID: 1/R] region chain R [212-214] RMSD: 7.914
> select #1/R:307-308 #2.1/R:307-308 #2.2/R:307-308 #2.3/R:307-308
> #2.4/R:307-308 #2.5/R:307-308 #2.6/R:307-308 #2.7/R:307-308 #2.8/R:307-308
> #2.9/R:307-308 #2.10/R:307-308
121 atoms, 110 bonds, 22 residues, 11 models selected
> select #1/R:307-309 #2.1/R:307-309 #2.2/R:307-309 #2.3/R:307-309
> #2.4/R:307-309 #2.5/R:307-309 #2.6/R:307-309 #2.7/R:307-309 #2.8/R:307-309
> #2.9/R:307-309 #2.10/R:307-309
242 atoms, 231 bonds, 33 residues, 11 models selected
5ht2a-Active.pdb (#1) Chain R [ID: 1/R] region chain R [215-217] RMSD: 0.743
> select #1/R:309 #2.1/R:309 #2.2/R:309 #2.3/R:309 #2.4/R:309 #2.5/R:309
> #2.6/R:309 #2.7/R:309 #2.8/R:309 #2.9/R:309 #2.10/R:309
121 atoms, 110 bonds, 11 residues, 11 models selected
> select #1/R:275-309 #2.1/R:275-309 #2.2/R:275-309 #2.3/R:275-309
> #2.4/R:275-309 #2.5/R:275-309 #2.6/R:275-309 #2.7/R:275-309 #2.8/R:275-309
> #2.9/R:275-309 #2.10/R:275-309
518 atoms, 506 bonds, 1 pseudobond, 66 residues, 12 models selected
5ht2a-Active.pdb (#1) Chain R [ID: 1/R] region chain R [212-217] RMSD: 5.621
> select #1/R:356 #2.1/R:356 #2.2/R:356 #2.3/R:356 #2.4/R:356 #2.5/R:356
> #2.6/R:356 #2.7/R:356 #2.8/R:356 #2.9/R:356 #2.10/R:356
88 atoms, 77 bonds, 11 residues, 11 models selected
> select #1/R:356-365 #2.1/R:356-365 #2.2/R:356-365 #2.3/R:356-365
> #2.4/R:356-365 #2.5/R:356-365 #2.6/R:356-365 #2.7/R:356-365 #2.8/R:356-365
> #2.9/R:356-365 #2.10/R:356-365
814 atoms, 814 bonds, 110 residues, 11 models selected
5ht2a-Active.pdb (#1) Chain R [ID: 1/R] region chain R [264-273] RMSD: 0.012
> select #1/R:307 #2.1/R:307 #2.2/R:307 #2.3/R:307 #2.4/R:307 #2.5/R:307
> #2.6/R:307 #2.7/R:307 #2.8/R:307 #2.9/R:307 #2.10/R:307
77 atoms, 66 bonds, 11 residues, 11 models selected
> select #1/R:277-307 #2.1/R:277-307 #2.2/R:277-307 #2.3/R:277-307
> #2.4/R:277-307 #2.5/R:277-307 #2.6/R:277-307 #2.7/R:277-307 #2.8/R:277-307
> #2.9/R:277-307 #2.10/R:277-307
177 atoms, 165 bonds, 1 pseudobond, 22 residues, 12 models selected
5ht2a-Active.pdb (#1) Chain R [ID: 1/R] region chain R [214-215] RMSD: 5.848
> ui tool show "Model Loops"
> modeller refine 1/R:1:214-215 numModels 10 fast false adjacentFlexible 1
> protocol standard
Webservices job id: UZ81CO83K4VX105V
Webservices job id: L3Y8LF2V3RIUWVV1
Webservices job id: RBR5BLPEL801B5G8
Webservices job id: VYJ9188NVA956CQX
Webservices job id: YA2ZWL0ALBKKM8CD
Webservices job id: KVHAEEB9PYA65V5M
Webservices job id: 5HFBVEPY20P5N0CT
Webservices job id: 6ZEAKWAI4URZJEK3
Webservices job id: WDOUBFEE4L1PTT70
Webservices job id: 72EK91X4TIW6S07A
Webservices job id: LXU4GO6NDX27EKZQ
Modeller job ID UZ81CO83K4VX105V 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 chain_R, chain R (#2.2) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.042 angstroms; (across all 310 pairs:
0.139)
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 chain_R, chain R (#2.2) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 308 pruned atom pairs is 0.028 angstroms; (across all 310 pairs:
0.232)
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 chain_R, chain R (#2.2) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 308 pruned atom pairs is 0.029 angstroms; (across all 310 pairs:
0.244)
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 chain_R, chain R (#2.2) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.052 angstroms; (across all 310 pairs:
0.052)
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 chain_R, chain R (#2.2) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.053 angstroms; (across all 310 pairs:
0.053)
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 chain_R, chain R (#2.2) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.053 angstroms; (across all 310 pairs:
0.053)
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 chain_R, chain R (#2.2) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.081 angstroms; (across all 310 pairs:
0.081)
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 chain_R, chain R (#2.2) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.046 angstroms; (across all 310 pairs:
0.046)
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 chain_R, chain R (#2.2) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.059 angstroms; (across all 310 pairs:
0.059)
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 chain_R, chain R (#2.2) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.048 angstroms; (across all 310 pairs:
0.048)
Associated chain_R chain R to chain R with 0 mismatches
[Repeated 9 time(s)] Chain information for chain_R
---
Chain | Description
3.1/R 3.2/R 3.3/R 3.4/R 3.5/R 3.6/R 3.7/R 3.8/R 3.9/R 3.10/R | No description
available
Modeller job ID L3Y8LF2V3RIUWVV1 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 chain_R, chain R (#2.3) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.063 angstroms; (across all 310 pairs:
0.063)
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 chain_R, chain R (#2.3) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.033 angstroms; (across all 310 pairs:
0.033)
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 chain_R, chain R (#2.3) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.125 angstroms; (across all 310 pairs:
0.173)
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 chain_R, chain R (#2.3) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.032 angstroms; (across all 310 pairs:
0.032)
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 chain_R, chain R (#2.3) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.051 angstroms; (across all 310 pairs:
0.051)
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 chain_R, chain R (#2.3) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.113 angstroms; (across all 310 pairs:
0.113)
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 chain_R, chain R (#2.3) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.101 angstroms; (across all 310 pairs:
0.178)
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 chain_R, chain R (#2.3) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.109 angstroms; (across all 310 pairs:
0.109)
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 chain_R, chain R (#2.3) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.094 angstroms; (across all 310 pairs:
0.094)
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 chain_R, chain R (#2.3) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.100 angstroms; (across all 310 pairs:
0.100)
Associated chain_R chain R to chain R with 0 mismatches
[Repeated 9 time(s)] Chain information for chain_R
---
Chain | Description
4.1/R 4.2/R 4.3/R 4.4/R 4.5/R 4.6/R 4.7/R 4.8/R 4.9/R 4.10/R | No description
available
Modeller job ID RBR5BLPEL801B5G8 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 chain_R, chain R (#2.5) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.049 angstroms; (across all 310 pairs:
0.049)
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 chain_R, chain R (#2.5) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.042 angstroms; (across all 310 pairs:
0.042)
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 chain_R, chain R (#2.5) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.053 angstroms; (across all 310 pairs:
0.053)
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 chain_R, chain R (#2.5) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.090 angstroms; (across all 310 pairs:
0.244)
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 chain_R, chain R (#2.5) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.064 angstroms; (across all 310 pairs:
0.064)
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 chain_R, chain R (#2.5) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.126 angstroms; (across all 310 pairs:
0.126)
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 chain_R, chain R (#2.5) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.043 angstroms; (across all 310 pairs:
0.043)
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 chain_R, chain R (#2.5) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.088 angstroms; (across all 310 pairs:
0.187)
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 chain_R, chain R (#2.5) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.094 angstroms; (across all 310 pairs:
0.094)
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 chain_R, chain R (#2.5) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.091 angstroms; (across all 310 pairs:
0.220)
Associated chain_R chain R to chain R with 0 mismatches
[Repeated 9 time(s)] Chain information for chain_R
---
Chain | Description
5.1/R 5.2/R 5.3/R 5.4/R 5.5/R 5.6/R 5.7/R 5.8/R 5.9/R 5.10/R | No description
available
Modeller job ID 72EK91X4TIW6S07A 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 chain_R, chain R (#2.8) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.128 angstroms; (across all 310 pairs:
0.128)
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 chain_R, chain R (#2.8) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.075 angstroms; (across all 310 pairs:
0.139)
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 chain_R, chain R (#2.8) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.129 angstroms; (across all 310 pairs:
0.129)
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 chain_R, chain R (#2.8) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.019 angstroms; (across all 310 pairs:
0.019)
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 chain_R, chain R (#2.8) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.030 angstroms; (across all 310 pairs:
0.030)
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 chain_R, chain R (#2.8) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.110 angstroms; (across all 310 pairs:
0.110)
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 chain_R, chain R (#2.8) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.121 angstroms; (across all 310 pairs:
0.121)
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 chain_R, chain R (#2.8) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.024 angstroms; (across all 310 pairs:
0.024)
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 chain_R, chain R (#2.8) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.103 angstroms; (across all 310 pairs:
0.103)
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 chain_R, chain R (#2.8) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 308 pruned atom pairs is 0.043 angstroms; (across all 310 pairs:
0.242)
Associated chain_R chain R to chain R with 0 mismatches
[Repeated 9 time(s)] Chain information for chain_R
---
Chain | Description
6.1/R 6.2/R 6.3/R 6.4/R 6.5/R 6.6/R 6.7/R 6.8/R 6.9/R 6.10/R | No description
available
Modeller job ID VYJ9188NVA956CQX 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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 307 pruned atom pairs is 0.051 angstroms; (across all 310 pairs:
0.589)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 307 pruned atom pairs is 0.047 angstroms; (across all 310 pairs:
0.587)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 307 pruned atom pairs is 0.050 angstroms; (across all 310 pairs:
0.587)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 307 pruned atom pairs is 0.047 angstroms; (across all 310 pairs:
0.597)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 307 pruned atom pairs is 0.048 angstroms; (across all 310 pairs:
0.601)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 307 pruned atom pairs is 0.041 angstroms; (across all 310 pairs:
0.564)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 307 pruned atom pairs is 0.051 angstroms; (across all 310 pairs:
0.592)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 307 pruned atom pairs is 0.049 angstroms; (across all 310 pairs:
0.581)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 307 pruned atom pairs is 0.041 angstroms; (across all 310 pairs:
0.565)
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 5ht2a-active.pdb, chain R (#1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 307 pruned atom pairs is 0.042 angstroms; (across all 310 pairs:
0.563)
Associated chain_R chain R to chain R with 0 mismatches
[Repeated 9 time(s)] Chain information for chain_R
---
Chain | Description
7.1/R 7.2/R 7.3/R 7.4/R 7.5/R 7.6/R 7.7/R 7.8/R 7.9/R 7.10/R | No description
available
Modeller job ID 5HFBVEPY20P5N0CT 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 chain_R, chain R (#2.7) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.115 angstroms; (across all 310 pairs:
0.115)
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 chain_R, chain R (#2.7) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.080 angstroms; (across all 310 pairs:
0.080)
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 chain_R, chain R (#2.7) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.059 angstroms; (across all 310 pairs:
0.210)
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 chain_R, chain R (#2.7) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.064 angstroms; (across all 310 pairs:
0.217)
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 chain_R, chain R (#2.7) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.104 angstroms; (across all 310 pairs:
0.104)
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 chain_R, chain R (#2.7) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.092 angstroms; (across all 310 pairs:
0.193)
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 chain_R, chain R (#2.7) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.070 angstroms; (across all 310 pairs:
0.209)
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 chain_R, chain R (#2.7) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.074 angstroms; (across all 310 pairs:
0.213)
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 chain_R, chain R (#2.7) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.073 angstroms; (across all 310 pairs:
0.073)
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 chain_R, chain R (#2.7) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.075 angstroms; (across all 310 pairs:
0.215)
Associated chain_R chain R to chain R with 0 mismatches
[Repeated 9 time(s)] Chain information for chain_R
---
Chain | Description
8.1/R 8.2/R 8.3/R 8.4/R 8.5/R 8.6/R 8.7/R 8.8/R 8.9/R 8.10/R | No description
available
Modeller job ID KVHAEEB9PYA65V5M 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 chain_R, chain R (#2.4) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.099 angstroms; (across all 310 pairs:
0.099)
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 chain_R, chain R (#2.4) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.154 angstroms; (across all 310 pairs:
0.154)
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 chain_R, chain R (#2.4) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.103 angstroms; (across all 310 pairs:
0.159)
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 chain_R, chain R (#2.4) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.089 angstroms; (across all 310 pairs:
0.157)
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 chain_R, chain R (#2.4) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.072 angstroms; (across all 310 pairs:
0.072)
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 chain_R, chain R (#2.4) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.105 angstroms; (across all 310 pairs:
0.105)
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 chain_R, chain R (#2.4) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.108 angstroms; (across all 310 pairs:
0.164)
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 chain_R, chain R (#2.4) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.088 angstroms; (across all 310 pairs:
0.162)
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 chain_R, chain R (#2.4) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.086 angstroms; (across all 310 pairs:
0.086)
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 chain_R, chain R (#2.4) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.096 angstroms; (across all 310 pairs:
0.155)
Associated chain_R chain R to chain R with 0 mismatches
[Repeated 9 time(s)] Chain information for chain_R
---
Chain | Description
9.1/R 9.2/R 9.3/R 9.4/R 9.5/R 9.6/R 9.7/R 9.8/R 9.9/R 9.10/R | No description
available
Modeller job ID YA2ZWL0ALBKKM8CD 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 chain_R, chain R (#2.1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.119 angstroms; (across all 310 pairs:
0.119)
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 chain_R, chain R (#2.1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.031 angstroms; (across all 310 pairs:
0.031)
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 chain_R, chain R (#2.1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.081 angstroms; (across all 310 pairs:
0.081)
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 chain_R, chain R (#2.1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.093 angstroms; (across all 310 pairs:
0.093)
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 chain_R, chain R (#2.1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.118 angstroms; (across all 310 pairs:
0.118)
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 chain_R, chain R (#2.1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 308 pruned atom pairs is 0.045 angstroms; (across all 310 pairs:
0.237)
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 chain_R, chain R (#2.1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.006 angstroms; (across all 310 pairs:
0.006)
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 chain_R, chain R (#2.1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.071 angstroms; (across all 310 pairs:
0.071)
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 chain_R, chain R (#2.1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.016 angstroms; (across all 310 pairs:
0.016)
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 chain_R, chain R (#2.1) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.074 angstroms; (across all 310 pairs:
0.074)
Associated chain_R chain R to chain R with 0 mismatches
[Repeated 9 time(s)] Chain information for chain_R
---
Chain | Description
10.1/R 10.2/R 10.3/R 10.4/R 10.5/R 10.6/R 10.7/R 10.8/R 10.9/R 10.10/R | No
description available
Modeller job ID 6ZEAKWAI4URZJEK3 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 chain_R, chain R (#2.6) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 308 pruned atom pairs is 0.085 angstroms; (across all 310 pairs:
0.299)
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 chain_R, chain R (#2.6) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.132 angstroms; (across all 310 pairs:
0.186)
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 chain_R, chain R (#2.6) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.079 angstroms; (across all 310 pairs:
0.157)
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 chain_R, chain R (#2.6) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.054 angstroms; (across all 310 pairs:
0.054)
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 chain_R, chain R (#2.6) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.064 angstroms; (across all 310 pairs:
0.064)
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 chain_R, chain R (#2.6) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.059 angstroms; (across all 310 pairs:
0.059)
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 chain_R, chain R (#2.6) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 309 pruned atom pairs is 0.078 angstroms; (across all 310 pairs:
0.146)
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 chain_R, chain R (#2.6) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.060 angstroms; (across all 310 pairs:
0.060)
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 chain_R, chain R (#2.6) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.100 angstroms; (across all 310 pairs:
0.100)
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 chain_R, chain R (#2.6) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.062 angstroms; (across all 310 pairs:
0.062)
Associated chain_R chain R to chain R with 0 mismatches
[Repeated 9 time(s)] Chain information for chain_R
---
Chain | Description
11.1/R 11.2/R 11.3/R 11.4/R 11.5/R 11.6/R 11.7/R 11.8/R 11.9/R 11.10/R | No
description available
Modeller job ID WDOUBFEE4L1PTT70 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 chain_R, chain R (#2.9) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.081 angstroms; (across all 310 pairs:
0.081)
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 chain_R, chain R (#2.9) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.041 angstroms; (across all 310 pairs:
0.041)
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 chain_R, chain R (#2.9) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.045 angstroms; (across all 310 pairs:
0.045)
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 chain_R, chain R (#2.9) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.035 angstroms; (across all 310 pairs:
0.035)
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 chain_R, chain R (#2.9) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.022 angstroms; (across all 310 pairs:
0.022)
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 chain_R, chain R (#2.9) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.030 angstroms; (across all 310 pairs:
0.030)
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 chain_R, chain R (#2.9) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.034 angstroms; (across all 310 pairs:
0.034)
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 chain_R, chain R (#2.9) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.026 angstroms; (across all 310 pairs:
0.026)
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 chain_R, chain R (#2.9) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 308 pruned atom pairs is 0.028 angstroms; (across all 310 pairs:
0.250)
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 chain_R, chain R (#2.9) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.033 angstroms; (across all 310 pairs:
0.033)
Associated chain_R chain R to chain R with 0 mismatches
[Repeated 9 time(s)] Chain information for chain_R
---
Chain | Description
12.1/R 12.2/R 12.3/R 12.4/R 12.5/R 12.6/R 12.7/R 12.8/R 12.9/R 12.10/R | No
description available
Modeller job ID LXU4GO6NDX27EKZQ 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 chain_R, chain R (#2.10) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.037 angstroms; (across all 310 pairs:
0.037)
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 chain_R, chain R (#2.10) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.040 angstroms; (across all 310 pairs:
0.040)
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 chain_R, chain R (#2.10) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.036 angstroms; (across all 310 pairs:
0.036)
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 chain_R, chain R (#2.10) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.055 angstroms; (across all 310 pairs:
0.055)
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 chain_R, chain R (#2.10) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.025 angstroms; (across all 310 pairs:
0.025)
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 chain_R, chain R (#2.10) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.030 angstroms; (across all 310 pairs:
0.030)
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 chain_R, chain R (#2.10) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 308 pruned atom pairs is 0.035 angstroms; (across all 310 pairs:
0.268)
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 chain_R, chain R (#2.10) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.044 angstroms; (across all 310 pairs:
0.044)
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 chain_R, chain R (#2.10) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.041 angstroms; (across all 310 pairs:
0.041)
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 chain_R, chain R (#2.10) with chain_R, chain R (#), sequence
alignment score = 1629.4
RMSD between 310 pruned atom pairs is 0.055 angstroms; (across all 310 pairs:
0.055)
Associated chain_R chain R to chain R with 0 mismatches
[Repeated 9 time(s)] Chain information for chain_R
---
Chain | Description
13.1/R 13.2/R 13.3/R 13.4/R 13.5/R 13.6/R 13.7/R 13.8/R 13.9/R 13.10/R | No
description available
> hide #!3 models
> hide #3.1 models
> hide #3.2 models
> hide #3.3 models
> hide #3.4 models
> hide #3.5 models
> hide #3.6 models
> hide #3.7 models
> hide #3.8 models
> hide #3.9 models
> hide #3.10 models
> hide #!4 models
> hide #4.1 models
> hide #4.2 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.3 models
> hide #2.3 models
> show #2.4 models
> hide #2.4 models
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> hide #2.5 models
> show #2.6 models
> hide #2.6 models
> show #2.7 models
> hide #2.7 models
> show #2.8 models
> hide #2.8 models
> show #2.9 models
> hide #2.9 models
> show #2.10 models
> hide #2.10 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.3 models
> hide #2.3 models
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> hide #2.5 models
> show #2.6 models
> show #2.7 models
> hide #2.7 models
> hide #2.6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #3.1 models
> hide #3.1 models
> show #3.2 models
> hide #3.2 models
> hide #!3 models
> show #3.3 models
> hide #3.3 models
> show #3.4 models
> hide #3.4 models
> show #3.6 models
> hide #!3 models
> show #!3 models
> show #2.1 models
> hide #2.1 models
> show #2.6 models
> hide #2.6 models
> open "/Users/shrugs/Documents/UCL/Year four/4th year project /5ht2a/5HT2a-
> CLEAN.pdb"
Traceback (most recent call last):
File
"/private/var/folders/jm/jn8k7dmn2kj86c4kp1685qlc0000gn/T/AppTranslocation/10D8F15D-A5F5-45AD-B682-D154C5AFF0A9/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 284, in event
_open_dropped_file(self.session, event.file())
File
"/private/var/folders/jm/jn8k7dmn2kj86c4kp1685qlc0000gn/T/AppTranslocation/10D8F15D-A5F5-45AD-B682-D154C5AFF0A9/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1945, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/private/var/folders/jm/jn8k7dmn2kj86c4kp1685qlc0000gn/T/AppTranslocation/10D8F15D-A5F5-45AD-B682-D154C5AFF0A9/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/jm/jn8k7dmn2kj86c4kp1685qlc0000gn/T/AppTranslocation/10D8F15D-A5F5-45AD-B682-D154C5AFF0A9/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/jm/jn8k7dmn2kj86c4kp1685qlc0000gn/T/AppTranslocation/10D8F15D-A5F5-45AD-B682-D154C5AFF0A9/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/private/var/folders/jm/jn8k7dmn2kj86c4kp1685qlc0000gn/T/AppTranslocation/10D8F15D-A5F5-45AD-B682-D154C5AFF0A9/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/jm/jn8k7dmn2kj86c4kp1685qlc0000gn/T/AppTranslocation/10D8F15D-A5F5-45AD-B682-D154C5AFF0A9/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/private/var/folders/jm/jn8k7dmn2kj86c4kp1685qlc0000gn/T/AppTranslocation/10D8F15D-A5F5-45AD-B682-D154C5AFF0A9/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open
return remember_data_format()
File
"/private/var/folders/jm/jn8k7dmn2kj86c4kp1685qlc0000gn/T/AppTranslocation/10D8F15D-A5F5-45AD-B682-D154C5AFF0A9/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/private/var/folders/jm/jn8k7dmn2kj86c4kp1685qlc0000gn/T/AppTranslocation/10D8F15D-A5F5-45AD-B682-D154C5AFF0A9/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/pdb/__init__.py", line 34, in open
return pdb.open_pdb(session, data, file_name, **kw)
File
"/private/var/folders/jm/jn8k7dmn2kj86c4kp1685qlc0000gn/T/AppTranslocation/10D8F15D-A5F5-45AD-B682-D154C5AFF0A9/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/pdb/pdb.py", line 77, in open_pdb
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,
File
"/private/var/folders/jm/jn8k7dmn2kj86c4kp1685qlc0000gn/T/AppTranslocation/10D8F15D-A5F5-45AD-B682-D154C5AFF0A9/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/codecs.py",
line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc0 in position 6:
invalid start byte
Populating font family aliases took 915 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc0 in position 6:
invalid start byte
File
"/private/var/folders/jm/jn8k7dmn2kj86c4kp1685qlc0000gn/T/AppTranslocation/10D8F15D-A5F5-45AD-B682-D154C5AFF0A9/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/codecs.py",
line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-18.8.4
OpenGL renderer: Intel(R) UHD Graphics 617
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir8,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1.6 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16064.0.0,0)
OS Loader Version: 540.120.3~19
Software:
System Software Overview:
System Version: macOS 12.5 (21G72)
Kernel Version: Darwin 21.6.0
Time since boot: 6:02
Graphics/Displays:
Intel UHD Graphics 617:
Chipset Model: Intel UHD Graphics 617
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x87c0
Revision ID: 0x0002
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL P2423:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: BTMCVJ3
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 8.63
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → open PDB file: 'utf-8' codec can't decode byte |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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Would need the PDB file to assess whether this has already been fixed and/or how to fix it.