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Opened 3 years ago
Closed 3 years ago
#7205 closed defect (can't reproduce)
Morph: index out of bounds
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19043
ChimeraX Version: 1.4.dev202201150102 (2022-01-15 01:02:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4.dev202201150102 (2022-01-15)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> "C:\\\Users\\\nxb318\\\Documents\\\EM_related\\\rGluK2-3m-domoic_acid_processing\\\FROM_EXX\\\Manuscript-
> figures\\\Figure 3\\\gating-ring-TMD.cxs"
registering illegal selector name "B-D-gating ring"
registering illegal selector name "B D gating ring"
registering illegal selector name "BDgating ring"
Log from Wed Jun 29 16:33:53 2022UCSF ChimeraX version: 1.4.dev202201150102
(2022-01-15)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\Users\nxb318\Documents\EM_related\rGluK2-3m-domoic_acid_processing\FROM_EXX\Class_comparison\all-
> models-video-TOP.cxs format session
Log from Tue Jun 28 15:51:52 2022UCSF ChimeraX version: 1.4.dev202201150102
(2022-01-15)
© 2016-2021 Regents of the University of California. All rights reserved.
> set bgColor transparent
Log from Mon Jun 27 12:57:28 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/apo-
> NEW/apo-fitted-050622_rsr_004-coot-0.pdb format pdb
Chain information for apo-fitted-050622_rsr_004-coot-0.pdb #1
---
Chain | Description
A B C D | No description available
> close #1
> open /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/apo-
> fitted-050622_rsr_004-coot-1.pdb
Chain information for apo-fitted-050622_rsr_004-coot-1.pdb #1
---
Chain | Description
A B C D | No description available
> lighting soft
> open "/mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/CLS1-FINAL
> - rsr_018-BETA-ABCD_real_space_refined_019-noloops-noH-
> TODAY_real_space_refined_030-rep_real_space_refined_031.pdb"
Chain information for CLS1-FINAL - rsr_018-BETA-
ABCD_real_space_refined_019-noloops-noH-
TODAY_real_space_refined_030-rep_real_space_refined_031.pdb #2
---
Chain | Description
A B C | No description available
D | No description available
> open /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/FINAL-
> cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
Chain information for FINAL-cls2-rsr_031-DOQ-
refined-D1_real_space_refined_032.pdb #3
---
Chain | Description
A B C D | No description available
> open /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/FINAL-
> cls4-fromcls5-input_real_space_refined_002.pdb
Chain information for FINAL-cls4-fromcls5-input_real_space_refined_002.pdb #4
---
Chain | Description
A B C D | No description available
> open
> /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/FINAL_cls5_real_space_refined_001.pdb
Chain information for FINAL_cls5_real_space_refined_001.pdb #5
---
Chain | Description
A B C D | No description available
> mmaker #1 to #2
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 CLS1-FINAL - rsr_018-BETA-ABCD_real_space_refined_019-noloops-noH-
TODAY_real_space_refined_030-rep_real_space_refined_031.pdb, chain A (#2) with
apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1), sequence alignment score =
3549.1
RMSD between 366 pruned atom pairs is 1.017 angstroms; (across all 741 pairs:
3.984)
> color #147bf3ff
> cartoon style modeHelix tube sides 20
> select ligand
3311 atoms, 3443 bonds, 247 residues, 5 models selected
> color sel yellow
> select clear
> select DOQ
Expected an objects specifier or a keyword
> select ::name="DOQ"
330 atoms, 330 bonds, 15 residues, 4 models selected
> color sel magenta
> select clear
> select #1/A:661-680
155 atoms, 155 bonds, 20 residues, 1 model selected
> select #1/A:632-661
239 atoms, 246 bonds, 30 residues, 1 model selected
> select #1/A:631-661
247 atoms, 254 bonds, 31 residues, 1 model selected
> mmaker #2/A:631-661 to #1/A:631-661
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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with CLS1-FINAL
- rsr_018-BETA-ABCD_real_space_refined_019-noloops-noH-
TODAY_real_space_refined_030-rep_real_space_refined_031.pdb, chain A (#2),
sequence alignment score = 162.8
RMSD between 31 pruned atom pairs is 0.648 angstroms; (across all 31 pairs:
0.648)
> mmaker #3/A:631-661 to #1/A:631-661
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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with FINAL-
cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb, chain A (#3), sequence
alignment score = 165.8
RMSD between 31 pruned atom pairs is 0.786 angstroms; (across all 31 pairs:
0.786)
> mmaker #4/A:631-661 to #1/A:631-661
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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with FINAL-
cls4-fromcls5-input_real_space_refined_002.pdb, chain A (#4), sequence
alignment score = 165.8
RMSD between 31 pruned atom pairs is 0.741 angstroms; (across all 31 pairs:
0.741)
> mmaker #5/A:631-661 to #1/A:631-661
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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with
FINAL_cls5_real_space_refined_001.pdb, chain A (#5), sequence alignment score
= 165.8
RMSD between 31 pruned atom pairs is 0.767 angstroms; (across all 31 pairs:
0.767)
> save
> /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Figures/Whole-
> struct/all-models-video.cxs
> select #3/B,D:400-514,637-805
4442 atoms, 4526 bonds, 560 residues, 1 model selected
> select #3/B,D:400-514
1820 atoms, 1852 bonds, 230 residues, 1 model selected
> select #7/D:431-545,668-809
Nothing selected
> select #1/D:431-545,668-809
1995 atoms, 2031 bonds, 249 residues, 1 model selected
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> select #1/D:431-545
934 atoms, 953 bonds, 115 residues, 1 model selected
> select #1/D:668-809
1061 atoms, 1078 bonds, 134 residues, 1 model selected
> select #1-5/D:668-809
5367 atoms, 5455 bonds, 678 residues, 5 models selected
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> select #1-5/D:668-809
5367 atoms, 5455 bonds, 678 residues, 5 models selected
> color sel #fcaf3eff
> color sel #f57900ff
> color sel #ef2929ff
> color sel #ad7fa8ff
> color sel #75507bff
> color sel #dda0ddff
> color sel #fcaf3eff
> select #1-5/D:431-545
4668 atoms, 4763 bonds, 575 residues, 5 models selected
> color sel #a40000ff
> color sel #5c3566ff
> color sel #bf5040ff
> color sel #5740bfff
> color sel #7040bfff
> color sel #9640bfff
[Repeated 1 time(s)]
> color sel #bf5040ff
> color sel #7dbf40ff
> color sel #40bf98ff
> color sel #40bf9aff
> color sel #4087bfff
> color sel #404cbfff
> color sel #5740bfff
> color sel #8040bfff
> color sel #9e40bfff
> color sel #a140bfff
> color sel #a440bfff
> color sel #a640bfff
> color sel #bc40bfff
[Repeated 2 time(s)]
> color sel cyan
> select clear
> save
> /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Figures/Whole-
> struct/all-models-video.cxs
——— End of log from Mon Jun 27 12:57:28 2022 ———
opened ChimeraX session
> morph #1,3 same true
Computed 51 frame morph #6
> coordset #6 1,51
> hide #!5 models
> hide #!4 models
> hide #!2 models
> help morph
> morph #1,3 frames 20
Computed 21 frame morph #7
> coordset #7 1,21
> hide #!6 models
> lighting simple
> mmaker #2-5/A,D:631-661 to #1/A,D:631-661
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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with CLS1-FINAL
- rsr_018-BETA-ABCD_real_space_refined_019-noloops-noH-
TODAY_real_space_refined_030-rep_real_space_refined_031.pdb, chain A (#2),
sequence alignment score = 162.8
RMSD between 31 pruned atom pairs is 0.648 angstroms; (across all 31 pairs:
0.648)
Matchmaker apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with FINAL-
cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb, chain A (#3), sequence
alignment score = 165.8
RMSD between 31 pruned atom pairs is 0.786 angstroms; (across all 31 pairs:
0.786)
Matchmaker apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with FINAL-
cls4-fromcls5-input_real_space_refined_002.pdb, chain A (#4), sequence
alignment score = 165.8
RMSD between 31 pruned atom pairs is 0.741 angstroms; (across all 31 pairs:
0.741)
Matchmaker apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with
FINAL_cls5_real_space_refined_001.pdb, chain A (#5), sequence alignment score
= 165.8
RMSD between 31 pruned atom pairs is 0.767 angstroms; (across all 31 pairs:
0.767)
> hide #!7 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> select protein
164931 atoms, 168528 bonds, 55 pseudobonds, 20804 residues, 14 models selected
> cartoon style (#!1 & sel) xsection oval modeHelix default
> hide #!1 models
> show #!2 models
> hide #!2 models
> morph #1,3 same true frames 20
Computed 21 frame morph #8
> coordset #8 1,21
> hide #!8 models
> show #!1 models
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> morph #3-5,2 same true frames 20
Computed 61 frame morph #9
> coordset #9 1,61
> cartoon style #9 xsection oval modeHelix default
> lighting soft
> hide #!9 models
> morph #3-5,2 same true frames 50
Computed 151 frame morph #10
> coordset #10 1,151
> close #10
> show #!9 models
> ui tool show "Side View"
> hide #!9 models
> morph #1,3-5,2 same true frames 15
Computed 61 frame morph #10
> coordset #10 1,61
> hide #!10 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> show #!1 models
> cartoon style #1-5 xsection oval modeHelix default
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> show #!10 models
> hide #!10 models
> show #!1 models
> ui mousemode right distance
[Repeated 1 time(s)]
> distance #1/B:302@CA #1/B:631@CA
Distance between apo-fitted-050622_rsr_004-coot-1.pdb #1/B GLN 302 CA and LEU
631 CA: 153.638Å
> distance #1/B:302@CA #1/B:664@CA
Distance between apo-fitted-050622_rsr_004-coot-1.pdb #1/B GLN 302 CA and MET
664 CA: 107.168Å
> hide #!1 models
> show #!3 models
> distance #3/B:302@CA #3/B:664@CA
Distance between FINAL-cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
#3/B GLN 302 CA and MET 664 CA: 113.579Å
> distance #3/B:302@CA #3/B:631@CA
Distance between FINAL-cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
#3/B GLN 302 CA and LEU 631 CA: 162.045Å
> hide #!3 models
> distance #4/B:302@CA #4/B:631@CA
Distance between FINAL-cls4-fromcls5-input_real_space_refined_002.pdb #4/B GLN
302 CA and LEU 631 CA: 160.657Å
> show #!4 models
> distance #4/B:302@CA #4/B:664@CA
Distance between FINAL-cls4-fromcls5-input_real_space_refined_002.pdb #4/B GLN
302 CA and MET 664 CA: 114.545Å
> hide #!4 models
> show #!5 models
> distance #5/B:302@CA #5/B:631@CA
Distance between FINAL_cls5_real_space_refined_001.pdb #5/B GLN 302 CA and LEU
631 CA: 161.761Å
> distance #5/B:302@CA #5/B:664@CA
Distance between FINAL_cls5_real_space_refined_001.pdb #5/B GLN 302 CA and MET
664 CA: 113.248Å
> hide #!5 models
> show #!10 models
> hide #!10 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> morph #1,3same true frames 15
Missing or invalid "structures" argument: only initial part "#1,3" of atom
specifier valid
> morph #1,3 same true frames 15
Computed 16 frame morph #12
> coordset #12 1,16
> mmaker #3/A,C:631-664 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 apo-fitted-050622_rsr_004-coot-1.pdb, chain B (#1) with FINAL-
cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb, chain A (#3), sequence
alignment score = 181.7
RMSD between 34 pruned atom pairs is 0.841 angstroms; (across all 34 pairs:
0.841)
> hide #!12 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> morph #1,3 same true frames 15
Computed 16 frame morph #13
> coordset #13 1,16
> close #13
> show #!12 models
> mmaker #3/A,C:631-664 to #1/A,C:631-664
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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with FINAL-
cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb, chain C (#3), sequence
alignment score = 181.1
RMSD between 33 pruned atom pairs is 0.631 angstroms; (across all 34 pairs:
0.744)
> morph #1,3 same true frames 15
Computed 16 frame morph #13
> coordset #13 1,16
> hide #!12 models
> close #13
> mmaker #3/A631-664 to #1/A631-664
No 'to' model specified
> mmaker #3/A:631-664 to #1/A631-664
No 'to' model specified
> mmaker #3/A:631-664 to #1/A:631-664
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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with FINAL-
cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb, chain A (#3), sequence
alignment score = 178.1
RMSD between 34 pruned atom pairs is 0.805 angstroms; (across all 34 pairs:
0.805)
> morph #1,3 same true frames 15
Computed 16 frame morph #13
> coordset #13 1,16
> hide #!13 models
> show #!3 models
> show #!13 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #!13 models
> hide #!11 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> distance #1/B:413@CA #1/B:433@CA
Distance between apo-fitted-050622_rsr_004-coot-1.pdb #1/B MET 413 CA and LEU
433 CA: 35.328Å
> show #!11 models
> hide #!1 models
> show #!3 models
> distance #3/B:413@CA #3/B:433@CA
Distance between FINAL-cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
#3/B MET 413 CA and LEU 433 CA: 40.208Å
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> distance #1/D:413@CA #1/D:433@CA
Distance between apo-fitted-050622_rsr_004-coot-1.pdb #1/D MET 413 CA and LEU
433 CA: 34.704Å
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> distance #3/D:413@CA #3/D:433@CA
Distance between FINAL-cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
#3/D MET 413 CA and LEU 433 CA: 40.399Å
> view #3
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> distance #1/A:413@CA #1/A:433@CA
Distance between apo-fitted-050622_rsr_004-coot-1.pdb #1/A MET 413 CA and LEU
433 CA: 30.295Å
> distance #3/A:413@CA #3/A:433@CA
Distance between FINAL-cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
#3/A MET 413 CA and LEU 433 CA: 32.357Å
> show #!3 models
> hide #!1 models
> measure center #1/A:34-413 mark true radius 0.5 color red
Center of mass of 3028 atoms = (202.40, 271.92, 278.34)
> hide #14 models
> show #14 models
> measure center #1/A:431-546,668-810 mark true color red
Center of mass of 2003 atoms = (214.85, 254.14, 227.96)
> distance #14 #15
Distance between apo-fitted-050622_rsr_004-coot-1.pdb center 3028 atoms #14/M
mark 1 M and apo-fitted-050622_rsr_004-coot-1.pdb center 2003 atoms #15/M mark
1 M: 54.859Å
> hide #!3 models
> show #!1 models
> measure center #3/A:34-413 mark true radius color red
Invalid "radius" argument: Expected a number
> measure center #3/A:34-413 mark true color red
Center of mass of 3028 atoms = (200.29, 273.95, 283.49)
> hide #!1 models
> show #!3 models
> hide #14 models
> hide #15 models
> measure center #3/A:431-546,668-810 mark true color red
Center of mass of 2003 atoms = (217.42, 255.42, 230.98)
> distance #16 #17
Distance between FINAL-cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
center 3028 atoms #16/M mark 1 M and FINAL-cls2-rsr_031-DOQ-
refined-D1_real_space_refined_032.pdb center 2003 atoms #17/M mark 1 M:
58.260Å
> hide #!3 models
> show #!1 models
> hide #17 models
> hide #16 models
> measure center #1/C:34-413 mark true radius color green
Invalid "radius" argument: Expected a number
> measure center #1/C:34-413 mark true color green
Center of mass of 3028 atoms = (248.04, 190.33, 286.42)
> measure center #1/C:431-546,668-810 mark true color green
Center of mass of 2003 atoms = (233.51, 196.83, 233.90)
> distance #18 #19
Distance between apo-fitted-050622_rsr_004-coot-1.pdb center 3028 atoms #18/M
mark 1 M and apo-fitted-050622_rsr_004-coot-1.pdb center 2003 atoms #19/M mark
1 M: 54.878Å
> show #17 models
> show #16 models
> measure center #3/C:34-413 mark true color green
Center of mass of 3028 atoms = (230.23, 179.85, 290.76)
> hide #!1 models
> show #!3 models
> measure center #3/C:431-546,668-810 mark true color green
Center of mass of 2003 atoms = (221.99, 192.47, 234.54)
> distance #20 #21
Distance between FINAL-cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
center 3028 atoms #20/M mark 1 M and FINAL-cls2-rsr_031-DOQ-
refined-D1_real_space_refined_032.pdb center 2003 atoms #21/M mark 1 M:
58.207Å
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ui mousemode right distance
> distance #1/C:801-817
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
11
> distance #1/C:801 #1/C:817
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
11
> distance #1/C:801@CA #1/C:817@CA
Distance between apo-fitted-050622_rsr_004-coot-1.pdb #1/C GLY 801 CA and VAL
817 CA: 32.737Å
> distance #3/C:801@CA #3/C:817@CA
Distance between FINAL-cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
#3/C GLY 801 CA and VAL 817 CA: 33.458Å
> distance #1/A:801@CA #1/A:817@CA
Distance between apo-fitted-050622_rsr_004-coot-1.pdb #1/A GLY 801 CA and VAL
817 CA: 33.027Å
> distance #3/A:801@CA #3/A:817@CA
Distance between FINAL-cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
#3/A GLY 801 CA and VAL 817 CA: 34.588Å
> distance #1/B:801@CA #1/B:817@CA
Distance between apo-fitted-050622_rsr_004-coot-1.pdb #1/B GLY 801 CA and VAL
817 CA: 34.574Å
> distance #3/B:801@CA #3/B:817@CA
Distance between FINAL-cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
#3/B GLY 801 CA and VAL 817 CA: 35.026Å
> distance #1/D:801@CA #1/D:817@CA
Distance between apo-fitted-050622_rsr_004-coot-1.pdb #1/D GLY 801 CA and VAL
817 CA: 30.335Å
> distance #3/D:801@CA #3/D:817@CA
Distance between FINAL-cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
#3/D GLY 801 CA and VAL 817 CA: 31.117Å
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Presentation/05102022/Figures/Whole-
> struct/all-classes-measurement-of-distances.cxs
> hide #!3 models
> show #!6 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 #!1 models
> set bgColor white
> set bgColor #ffffff00
> show #!3 models
> hide #!10 models
> hide #17 models
> hide #16 target m
> hide #18 models
> hide #19 models
> hide #20 models
> hide #21 models
> hide #!11 models
> hide #11.1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!5 models
> set bgColor black
> set bgColor transparent
> morph #4,5 same true
Computed 51 frame morph #22
> coordset #22 1,51
> morph #5,2 same true
Computed 51 frame morph #23
> coordset #23 1,51
> hide #!22 models
> hide #!23 models
> show #!12 models
> show #!10 models
> hide #!12 models
> ui tool show "Side View"
> select #10/A:631-664
275 atoms, 282 bonds, 34 residues, 1 model selected
> color sel yellow
> select clear
> hide #!10 models
> show #!1 models
> hide #!1 models
> show #!10 models
> show #17 models
> hide #17 models
> show #16 models
> hide #16 models
> show #15 models
> show #16 models
> show #17 models
> show #14 models
> measure center #1/D:431-546,668-810 mark true color pink
Center of mass of 2003 atoms = (197.37, 218.37, 231.97)
> show #!1 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> measure center #3/D:431-546,668-810 mark true color pink
Center of mass of 2003 atoms = (189.47, 223.15, 229.71)
> hide #!10 models
> measure center #1 mark true color yellow radius 5
Center of mass of 24152 atoms = (224.70, 228.12, 254.77)
> measure center #3 mark true color marine radius 5
Invalid "color" argument: Invalid color name or specifier
> measure center #3 mark true color blue radius 5
Center of mass of 24216 atoms = (217.58, 225.36, 257.96)
> hide #25 models
> show #25 models
> distance #25 #26
Distance between FINAL-cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
center 2003 atoms #25/M mark 1 M and apo-fitted-050622_rsr_004-coot-1.pdb
center #26/M mark 1 M: 43.520Å
> show #!11 models
> hide #26 models
> show #26 models
> hide #27 models
> show #27 models
> hide #24 models
> show #24 models
> distance #24 #26
Distance between apo-fitted-050622_rsr_004-coot-1.pdb center 2003 atoms #24/M
mark 1 M and apo-fitted-050622_rsr_004-coot-1.pdb center #26/M mark 1 M:
36.902Å
> distance #25 #27
Distance between FINAL-cls2-rsr_031-DOQ-refined-D1_real_space_refined_032.pdb
center 2003 atoms #25/M mark 1 M and FINAL-cls2-rsr_031-DOQ-
refined-D1_real_space_refined_032.pdb center #27/M mark 1 M: 39.915Å
> close #24-27
> show #!10 models
> hide #!1 models
> show #!23 models
> hide #!23 models
> show #!22 models
> hide #!10 models
> hide #!22 models
> show #!6 models
> hide #!6 models
> show #!10 models
> hide #!10 models
> show #!1 models
> show #!2 models
> measure rotation #1/D:431-546,665-810 #2/D:431-546,665-810 show axis true
> showSlabs true
Missing or invalid "model" argument: Must specify 1 model, got 2
> measure rotation #1/D:431-546,665-810 toModel #2/D:431-546,665-810 show axis
> true showSlabs true
Expected keyword "showAxis" or "showSlabs"
> measure rotation #1/D:431-546,665-810 toModel #2/D:431-546,665-810 showAxis
> true showSlabs true
Position of apo-fitted-050622_rsr_004-coot-1.pdb #1 relative to CLS1-FINAL -
rsr_018-BETA-ABCD_real_space_refined_019-noloops-noH-
TODAY_real_space_refined_030-rep_real_space_refined_031.pdb #2 coordinates:
Matrix rotation and translation
0.97388204 -0.17769361 0.14134624 30.83988752
0.17777492 0.98399611 0.01215468 -28.23686041
-0.14124396 0.01329059 0.98988560 44.56542205
Axis 0.00250138 0.62229384 0.78277974
Axis point 232.23851612 139.17659123 0.00000000
Rotation angle (degrees) 13.12376483
Shift along axis 17.39042730
> hide #25.1 models
> hide #25.2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> define axis #1/D:700-711
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/axis' centered at [214.91650211
225.10384267 224.5482905 ] with direction [-0.35507097 0.93477467 0.01099632],
radius 3.4549, and length 20.4172
> define axis fromPoint #1/D:700@CA toPoint #1/D:711@CA
Invalid "fromPoint" argument: Expected a number
> define axis fromPoint #1/D:700 toPoint #1/D:711
Invalid "fromPoint" argument: Expected a number
> define axis #1/D:700-711 perHelix true
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 1'
centered at [193.98481554 284.76470992 284.80576263] with direction
[-0.89786482 0.08093191 0.43276876], radius 1.87166, and length 22.0219
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 2'
centered at [211.00035222 281.43112675 296.88598428] with direction
[-0.74436069 0.24232833 0.62225729], radius 1.87487, and length 19.253
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 3'
centered at [210.29764405 271.78741718 294.26847042] with direction
[-0.3907709 -0.14373592 0.9091964 ], radius 1.85819, and length 20.6536
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 4'
centered at [202.27376003 257.24605114 270.63127627] with direction
[-0.19961039 -0.32327786 -0.92501196], radius 1.84364, and length 20.3357
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 5'
centered at [212.82105697 261.49568992 275.28438115] with direction
[-0.43120985 -0.84554036 -0.31483259], radius 1.96759, and length 15.3522
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 6'
centered at [211.40880255 249.73470924 269.80075896] with direction [
0.29720087 -0.92764948 -0.22613733], radius 1.17374, and length 5.7813
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 7'
centered at [219.67330696 271.48362671 259.69272951] with direction
[0.03922125 0.77976353 0.6248444 ], radius 1.74043, and length 20.29
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 8'
centered at [210.93546545 276.00002153 261.16870475] with direction [
0.28797194 -0.03142812 -0.957123 ], radius 1.84737, and length 19.7513
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 9'
centered at [199.5412965 275.29591202 266.23614894] with direction
[-0.20150042 0.9792817 -0.020123 ], radius 1.16059, and length 5.72343
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 10'
centered at [200.95315744 275.97625205 253.34436731] with direction
[0.23093029 0.67446428 0.70126253], radius 1.80734, and length 7.70794
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 11'
centered at [190.43952195 284.7104888 273.94878385] with direction [
0.63363207 0.77358799 -0.00848653], radius 1.80916, and length 25.3334
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 12'
centered at [193.05738558 275.24053192 287.17160451] with direction
[-0.55563032 -0.17213133 0.8134161 ], radius 1.9049, and length 28.2019
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 13'
centered at [194.2105382 266.9634544 298.05713203] with direction [-0.42681623
-0.22977137 -0.87466166], radius 1.87039, and length 15.1949
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 14'
centered at [195.93690994 268.71648024 240.84277342] with direction
[0.84879016 0.47834984 0.2252481 ], radius 1.45706, and length 12.1957
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 15'
centered at [202.78086243 266.70479188 230.2222764 ] with direction
[-0.75522409 0.30011248 0.58272555], radius 1.93271, and length 16.3317
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 16'
centered at [218.51907176 257.49821212 241.46340697] with direction
[-0.49958568 0.15258989 0.85271946], radius 1.73365, and length 11.2275
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 17'
centered at [212.82833625 247.25965374 241.76025254] with direction [
0.03308444 -0.68082456 -0.73169894], radius 1.8119, and length 9.4392
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 18'
centered at [239.34955649 228.96510284 174.86579333] with direction [
0.07853685 -0.37810573 -0.92242507], radius 1.85716, and length 30.88
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 19'
centered at [230.56024249 221.70873405 182.57140342] with direction
[-0.31113071 0.39002558 0.86664741], radius 1.89029, and length 47.8526
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 20'
centered at [221.76642561 234.01729896 219.24113095] with direction [
0.94467355 -0.3270203 -0.02548748], radius 1.65931, and length 10.3598
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 21'
centered at [219.4880794 243.96124458 232.55948412] with direction [ 0.1331654
-0.87185656 0.47131001], radius 1.83343, and length 11.7058
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 22'
centered at [225.40568877 236.85499221 228.20457265] with direction
[0.80584205 0.5909932 0.03668276], radius 1.8574, and length 18.2655
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 23'
centered at [224.67650753 253.77767888 217.5129626 ] with direction [
0.37675042 -0.4451889 -0.81232135], radius 1.82013, and length 13.7114
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 24'
centered at [212.81830769 253.13109641 215.77958245] with direction [
0.24022197 0.44768498 -0.86131967], radius 1.78725, and length 15.5239
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 25'
centered at [198.25993943 258.88940226 236.78451767] with direction
[-0.43201204 -0.11029891 -0.89509762], radius 1.84412, and length 22.884
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 26'
centered at [201.48192482 260.64748967 219.56683714] with direction [
0.74166924 0.01474586 -0.67060368], radius 1.96097, and length 14.6318
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 27'
centered at [224.03952596 240.30866085 172.65738342] with direction [
0.17838299 0.01803656 -0.98379581], radius 1.85785, and length 30.4705
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 1'
centered at [237.16617311 261.55134789 303.3133257 ] with direction
[0.87214361 0.44053742 0.2128199 ], radius 1.88403, and length 19.7068
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 2'
centered at [221.02987643 274.07551835 302.82320825] with direction
[0.69066675 0.59197112 0.41539094], radius 1.87289, and length 19.4069
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 3'
centered at [221.85948381 273.77573705 293.00569599] with direction
[0.33391553 0.93714628 0.10127815], radius 1.88288, and length 19.6833
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 4'
centered at [231.99722724 254.89914489 272.23205525] with direction [
0.24045429 -0.77898748 -0.57910297], radius 1.86167, and length 21.8946
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 5'
centered at [219.23860006 258.81352519 280.65536757] with direction [
0.7958984 0.24401571 -0.55407768], radius 1.57248, and length 10.3962
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 6'
centered at [223.67769595 257.85676436 267.95758049] with direction [
0.00214918 -0.1775455 -0.98411025], radius 1.8587, and length 14.5154
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 7'
centered at [214.13917585 243.29704486 289.19626605] with direction
[-0.49503205 -0.65557549 -0.57023157], radius 1.15086, and length 5.79357
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 8'
centered at [215.00330147 238.70019078 276.14448515] with direction [
0.2509718 -0.19761774 -0.94760772], radius 1.81105, and length 16.928
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 9'
centered at [223.00344708 241.59220165 287.84250917] with direction
[-0.23789082 -0.90608216 -0.3498901 ], radius 1.84219, and length 19.2191
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 10'
centered at [234.54630161 232.52961964 282.41126523] with direction
[0.38235985 0.42163339 0.82220814], radius 1.08314, and length 6.3545
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 11'
centered at [242.22506193 251.66438772 300.49882437] with direction
[-0.69397971 -0.24570584 0.67677234], radius 1.82049, and length 25.1255
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 12'
centered at [239.65942981 267.33539798 294.85693965] with direction
[0.51276327 0.85226856 0.10349945], radius 1.82547, and length 29.5471
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 13'
centered at [237.85000762 281.12946617 290.8221439 ] with direction [
0.55520206 -0.69809317 -0.45212453], radius 1.85215, and length 12.2474
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 14'
centered at [263.27597176 242.60685708 234.74041144] with direction
[0.25122547 0.59576898 0.76285325], radius 1.84218, and length 17.3337
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 15'
centered at [251.33021697 228.71124497 242.37507583] with direction
[-0.08937342 0.38384658 0.91906158], radius 1.79486, and length 9.03229
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 16'
centered at [233.92853279 204.73011456 180.63537738] with direction
[-0.24398915 -0.22166756 -0.94410422], radius 1.84302, and length 30.1239
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 17'
centered at [224.51918339 213.57411597 185.07005544] with direction
[0.33782067 0.4593414 0.82151243], radius 1.91458, and length 48.304
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 18'
centered at [232.94428123 228.49292189 215.35459241] with direction
[-0.50777964 -0.81827316 -0.26942321], radius 1.63739, and length 10.1728
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 19'
centered at [235.26743532 229.46910826 231.56006987] with direction
[-0.86514119 -0.28376428 0.4135318 ], radius 1.52163, and length 6.23978
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 20'
centered at [231.84916542 224.52320891 224.15537137] with direction [
0.37595456 -0.92459484 0.06150247], radius 1.82184, and length 15.4486
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 21'
centered at [252.11230418 222.63758284 218.63421699] with direction
[-0.24422393 -0.3102717 -0.91874161], radius 1.86896, and length 14.155
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 22'
centered at [253.1365247 234.64229979 216.97282001] with direction [
0.62079424 -0.14462045 -0.77051894], radius 1.8316, and length 15.6125
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 23'
centered at [256.84101279 250.79342108 234.8965689 ] with direction
[-0.20857665 -0.35116744 0.91278541], radius 1.84721, and length 7.25131
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 24'
centered at [259.23594722 246.22670588 226.24771997] with direction
[-0.15821157 -0.7215939 -0.67399655], radius 1.71546, and length 9.46516
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 25'
centered at [244.05098554 217.68180768 175.37408554] with direction [
0.1789684 -0.41850912 -0.89040464], radius 1.81716, and length 30.2462
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 1'
centered at [255.91000843 178.86839158 295.16628696] with direction
[0.90983586 0.01586905 0.41466477], radius 1.87084, and length 20.6229
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 2'
centered at [240.23821055 185.1988814 306.89579577] with direction [
0.78051179 -0.07099128 0.62109709], radius 1.86513, and length 19.0541
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 3'
centered at [240.08118175 193.3943401 301.25376855] with direction [0.46280344
0.28522471 0.83932106], radius 1.90635, and length 17.59
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 4'
centered at [247.75349319 203.03712326 274.88243527] with direction [
0.16122511 0.13222093 -0.9780205 ], radius 1.85395, and length 21.8474
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 5'
centered at [236.159359 197.50947875 283.24162981] with direction [ 0.78628116
0.57991436 -0.21321648], radius 1.57162, and length 10.223
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 6'
centered at [239.14410022 207.89418169 276.18971302] with direction
[-0.19959384 0.78663347 -0.58426884], radius 1.68122, and length 13.4996
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 7'
centered at [229.67253469 187.22698904 268.00876537] with direction
[-0.06597014 -0.65286524 0.75459587], radius 1.68002, and length 18.577
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 8'
centered at [238.69340178 182.76945393 270.81948282] with direction
[-0.33574556 -0.17708683 -0.92515684], radius 1.85623, and length 19.6722
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 9'
centered at [250.6883554 184.42273585 275.43773038] with direction [
0.17741796 -0.96842698 0.17513438], radius 1.19277, and length 5.50434
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 10'
centered at [261.98164665 179.20637816 283.6960239 ] with direction
[-0.56941815 -0.79982151 0.18986447], radius 1.83943, and length 18.0675
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 11'
centered at [257.18032616 188.63783471 294.89139673] with direction
[0.59158596 0.29984834 0.74840966], radius 1.87762, and length 27.1634
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 12'
centered at [257.76505775 199.64437207 303.67503084] with direction [
0.33985409 -0.01193775 -0.94040241], radius 1.85886, and length 14.1603
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 13'
centered at [235.37757212 176.8733672 237.47543053] with direction
[-0.55193373 0.05192209 -0.83226994], radius 1.1357, and length 6.0577
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 14'
centered at [245.2342473 184.69159486 237.29359318] with direction [
0.78508532 -0.25498771 0.5644664 ], radius 1.86541, and length 17.6205
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 15'
centered at [230.75466638 195.99682732 248.38698934] with direction [
0.35898627 -0.04070069 0.93245499], radius 1.75622, and length 10.187
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 16'
centered at [235.94040173 206.47609419 245.88002341] with direction [
0.07862268 -0.45780224 0.88557077], radius 1.69022, and length 9.96181
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 17'
centered at [217.67548581 202.17822358 193.58390626] with direction
[-0.18288672 -0.97870651 -0.09319885], radius 1.51452, and length 6.61955
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 18'
centered at [207.49878915 210.65404979 177.78583811] with direction [-0.111329
0.13715761 -0.98427315], radius 1.81648, and length 28.1613
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 19'
centered at [216.09776602 218.54956157 183.44078092] with direction [
0.35264927 -0.18451493 0.91738363], radius 1.90733, and length 47.7447
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 20'
centered at [227.30683584 213.7134111 220.73362753] with direction
[-0.99876399 0.0461129 0.01854956], radius 1.80864, and length 7.53596
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 21'
centered at [222.31460106 213.99265834 231.20842389] with direction
[-0.81262733 -0.54387206 0.20938005], radius 1.83193, and length 18.5158
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 22'
centered at [222.54123061 194.75311233 222.9717879 ] with direction
[-0.25694937 0.4345925 -0.86319545], radius 1.78138, and length 12.1802
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 23'
centered at [234.98358882 194.20904901 221.01767879] with direction
[-0.1773707 -0.5575154 -0.81099705], radius 1.83583, and length 13.5417
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 24'
centered at [251.02154523 193.8893051 242.24917273] with direction [
0.44672168 -0.10207146 -0.88883134], radius 1.84978, and length 24.5058
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 25'
centered at [247.92820678 188.88739891 227.00185266] with direction
[-0.7252418 -0.28997966 -0.62444866], radius 1.76161, and length 13.4458
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 26'
centered at [222.9378959 199.32160956 180.10053773] with direction
[-0.36399599 -0.28804469 -0.88574103], radius 1.78034, and length 30.7628
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 1'
centered at [212.79944055 205.30336158 310.48314232] with direction
[-0.87062616 -0.35864981 0.33672007], radius 1.87617, and length 22.4359
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 2'
centered at [229.71700259 193.15629768 312.06998452] with direction
[-0.71710334 -0.49270344 0.4929565 ], radius 1.85118, and length 17.6384
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 3'
centered at [229.08925581 191.58807222 301.8400684 ] with direction
[-0.35426011 -0.86542145 0.35432398], radius 1.89478, and length 19.7263
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 4'
centered at [218.26667895 205.17167092 278.233367 ] with direction
[-0.26668432 0.62360749 -0.73484227], radius 1.86702, and length 20.5559
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 5'
centered at [231.40842417 203.80415046 286.4378922 ] with direction
[-0.80622285 -0.37025954 -0.46142453], radius 1.58244, and length 10.2733
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 6'
centered at [226.64166749 201.73884327 276.64288382] with direction
[-0.00698737 -0.12345558 0.9923255 ], radius 1.69739, and length 9.73842
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 7'
centered at [235.91980101 222.17576188 280.9895046 ] with direction
[-0.25165912 0.03305062 -0.96725144], radius 1.88393, and length 14.214
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 8'
centered at [227.39447211 221.95327076 289.67993396] with direction [
0.2243256 0.8204896 -0.52580874], radius 1.8503, and length 19.2746
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 9'
centered at [206.72222212 213.71915108 303.88795149] with direction
[0.64050603 0.36665816 0.67476946], radius 1.83346, and length 20.0971
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 10'
centered at [211.76645819 199.09500511 302.83897896] with direction
[-0.48957579 -0.81228267 0.31703691], radius 1.87565, and length 27.1831
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 11'
centered at [212.9568191 184.23520254 301.49277436] with direction
[-0.53902911 0.6580588 -0.5257435 ], radius 1.83085, and length 12.1801
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 12'
centered at [184.98143967 209.08506538 239.17002066] with direction
[-0.19119529 -0.50599879 0.84107644], radius 1.84583, and length 18.2802
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 13'
centered at [198.16896261 225.0240385 246.76429802] with direction
[-0.10513417 -0.11006057 0.98834886], radius 1.73917, and length 10.3226
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 14'
centered at [207.59600239 218.45842244 243.01535667] with direction
[-0.28452317 0.06212372 0.95665417], radius 1.7854, and length 8.79173
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 15'
centered at [213.3674985 234.52030459 172.1437188 ] with direction [
0.21362338 -0.02032621 -0.97670461], radius 1.83833, and length 25.52
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 16'
centered at [221.42307898 227.08707244 183.6276594 ] with direction
[-0.25517771 -0.24925799 0.93421346], radius 1.85723, and length 50.6561
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 17'
centered at [213.8446965 218.48250354 216.63642021] with direction [
0.26248562 0.91828636 -0.29639749], radius 1.82404, and length 7.79299
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 18'
centered at [210.26382156 222.00755761 232.12553922] with direction
[0.96814421 0.10005429 0.22953414], radius 1.75151, and length 11.9856
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 19'
centered at [214.52248636 226.73296879 224.51957349] with direction
[-0.32756279 0.94096067 -0.08541449], radius 1.84131, and length 15.2813
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 20'
centered at [196.03930614 225.80224443 218.83410379] with direction [
0.25502434 0.04810305 -0.96573738], radius 1.82331, and length 13.7264
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 21'
centered at [194.40845759 213.41000988 220.997525 ] with direction
[-0.68161688 0.11139552 -0.72318011], radius 1.7917, and length 15.5127
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 22'
centered at [197.54687955 210.56294806 249.04758237] with direction
[-0.65131476 -0.63403604 -0.41687814], radius 1.83435, and length 12.0356
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 23'
centered at [187.56941961 203.92980013 227.6170707 ] with direction
[-0.3177051 0.72206849 -0.61455721], radius 1.85109, and length 11.815
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 24'
centered at [202.302393 221.26029089 175.86120193] with direction [-0.17742078
0.15115515 -0.97245771], radius 1.8209, and length 25.9266
> define axis #1/D:700-711 perHelix true primary false secondary true tertiary
> false
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 1'
centered at [194.04566875 284.69681037 284.92523214] with direction [
0.35510379 -0.44796223 0.82050664], radius 5.73775, and length 4.87406
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 2'
centered at [211.02274338 281.38909219 296.84478567] with direction
[0.47942251 0.84258492 0.24536647], radius 4.99488, and length 4.78839
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 3'
centered at [210.21672199 271.81760405 294.48282445] with direction
[0.09269773 0.97656677 0.19422789], radius 5.45229, and length 5.02513
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 4'
centered at [202.34325785 257.32559946 270.95848679] with direction [
0.03584854 -0.94578715 0.32280264], radius 5.2381, and length 4.63106
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 5'
centered at [212.51148729 260.7602637 274.97377413] with direction [
0.79609793 -0.19234902 -0.57378562], radius 4.3783, and length 7.11339
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 6'
centered at [211.58806614 249.68847755 269.56239351] with direction
[-0.51425732 -0.35506865 0.78068282], radius 1.82192, and length 3.45381
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 7'
centered at [219.61758005 271.18695224 259.52780332] with direction
[-0.5990609 -0.4821349 0.63927457], radius 5.18344, and length 5.15101
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 8'
centered at [210.89548082 276.0205338 261.37807485] with direction
[-0.81572705 -0.53161774 -0.22797358], radius 5.10911, and length 4.48519
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 9'
centered at [199.34337786 275.03368156 266.16508718] with direction
[-0.93550945 -0.19849941 -0.29226708], radius 1.90543, and length 3.29705
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 10'
centered at [201.20946349 276.02996693 253.50862755] with direction
[-0.91774547 0.39036075 -0.07322387], radius 2.40416, and length 4.56735
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 11'
centered at [190.16722928 284.36526223 273.98520504] with direction
[-0.19138506 0.1461125 -0.97057864], radius 6.25862, and length 4.56001
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 12'
centered at [193.03332489 275.22126481 287.20117661] with direction
[0.11092039 0.95424277 0.27770019], radius 7.23453, and length 5.63916
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 13'
centered at [194.31313654 267.19176049 297.93199411] with direction [
0.38720522 0.82761334 -0.40635979], radius 4.03461, and length 4.70365
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 14'
centered at [196.07193741 268.67110202 240.91028817] with direction [
0.37710981 -0.8463095 0.37622921], radius 3.27247, and length 4.04675
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 15'
centered at [202.45550995 266.79040403 230.58558927] with direction [
0.36409605 -0.54717564 0.75367956], radius 4.62738, and length 5.37067
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 16'
centered at [218.79251195 257.36474392 241.28177903] with direction [
0.69905861 -0.51032892 0.50088068], radius 3.04008, and length 4.56136
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 17'
centered at [212.76350176 247.12810765 241.62204171] with direction
[-0.99899352 -0.0447127 -0.00356653], radius 2.71451, and length 4.42375
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 18'
centered at [239.39854287 228.94446789 174.5900245 ] with direction
[-0.31206718 -0.88810453 0.33746767], radius 7.75248, and length 5.20795
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 19'
centered at [230.16570449 221.79579189 182.78677751] with direction
[0.94994747 0.15472712 0.27140252], radius 12.0308, and length 6.07655
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 20'
centered at [221.56519791 233.83652337 219.09939618] with direction
[0.29150346 0.80136441 0.52234166], radius 2.70078, and length 4.53395
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 21'
centered at [219.59122406 243.81612939 232.56362745] with direction
[-0.78553391 0.19711647 0.58658467], radius 3.34365, and length 4.53911
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 22'
centered at [225.20875617 236.87823803 228.11246449] with direction
[-0.48182173 0.69047126 -0.53953429], radius 4.74829, and length 4.80288
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 23'
centered at [224.70070326 253.7311722 217.45907336] with direction
[-0.22983656 -0.89444265 0.38359809], radius 3.67057, and length 4.72455
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 24'
centered at [212.78362098 253.05785617 215.89163435] with direction
[-0.12107774 -0.86655387 -0.48417411], radius 4.1216, and length 4.8376
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 25'
centered at [198.04989577 258.79051429 236.58975087] with direction [
0.72561377 0.54689326 -0.41760318], radius 5.74924, and length 5.15744
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 26'
centered at [201.72323371 260.66127062 219.34779443] with direction
[-0.05822582 0.99739988 -0.04246439], radius 3.9674, and length 4.77571
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain A helix 27'
centered at [223.80787383 240.51498007 173.03309667] with direction
[-0.59442512 0.79873905 -0.09313805], radius 7.98822, and length 5.99312
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 1'
centered at [237.22826866 261.56873437 303.32787087] with direction [
0.43869228 -0.89673362 0.05846281], radius 5.08427, and length 4.54989
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 2'
centered at [221.09197207 274.1269672 302.85594897] with direction
[-0.51848172 0.00491214 0.8550746 ], radius 5.02872, and length 4.47409
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 3'
centered at [221.78744963 273.67718435 293.02875163] with direction
[-0.69002376 0.1698265 0.70358096], radius 5.08195, and length 4.61669
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 4'
centered at [231.94204193 255.04451838 272.3579851 ] with direction
[-0.44757722 -0.61837725 0.6459754 ], radius 5.70686, and length 4.53981
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 5'
centered at [219.44653376 258.97921943 280.3035969 ] with direction
[-0.60455788 0.36943125 -0.70571263], radius 2.84472, and length 3.89373
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 6'
centered at [223.7024834 257.86141219 267.80849186] with direction [
0.61910312 0.77306824 -0.1381189 ], radius 4.04863, and length 5.11152
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 7'
centered at [214.30321024 243.24653764 289.45130157] with direction [
0.28567919 -0.74260559 0.6057428 ], radius 1.92935, and length 3.30122
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 8'
centered at [215.03890846 238.71107513 276.2885387 ] with direction
[-0.93539001 0.20242192 -0.28994981], radius 4.56563, and length 4.38501
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 9'
centered at [223.08009749 241.616486 287.80581563] with direction [ 0.83463068
-0.00644667 -0.55077225], radius 5.06443, and length 4.64657
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 10'
centered at [234.77108206 232.507331 282.64120735] with direction [-0.67476696
0.73531305 -0.06327928], radius 1.97342, and length 3.29538
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 11'
centered at [242.55452969 251.96425218 300.55577695] with direction
[0.40278096 0.64663707 0.647787 ], radius 6.33734, and length 5.41287
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 12'
centered at [239.47129307 267.13333489 294.98895682] with direction
[-0.33913867 0.090326 0.93638997], radius 7.28093, and length 4.83958
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 13'
centered at [237.81567611 281.19525988 290.84668481] with direction
[-0.44191177 -0.70812429 0.55070317], radius 3.34466, and length 4.71022
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 14'
centered at [263.22958875 242.35674094 234.57911076] with direction
[-0.24606115 0.80154755 -0.54495453], radius 4.61548, and length 5.03587
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 15'
centered at [251.4955587 228.7674707 242.54432626] with direction [-0.99328951
0.03365737 -0.11064868], radius 2.5219, and length 4.49956
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 16'
centered at [233.79821336 204.57309312 180.10637497] with direction [
0.23640124 -0.95775322 0.16377798], radius 7.27192, and length 5.43683
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 17'
centered at [224.55468173 213.77268489 185.18065111] with direction
[-0.24330965 0.88577692 -0.39522102], radius 12.1473, and length 5.76655
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 18'
centered at [233.09351978 228.43186028 215.45801249] with direction [
0.66334499 -0.57092066 0.48375926], radius 2.70385, and length 3.81589
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 19'
centered at [235.02860114 229.47141329 231.75540642] with direction
[0.08114494 0.7344811 0.67376035], radius 2.29751, and length 3.74686
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 20'
centered at [231.73417675 224.79670455 224.17203412] with direction
[-0.1156162 0.01904873 0.99311129], radius 4.04003, and length 4.66368
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 21'
centered at [252.17043555 222.37891371 218.53873021] with direction [
0.40524906 -0.8933886 0.19398455], radius 3.691, and length 4.99022
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 22'
centered at [253.18513473 234.64714279 216.83937462] with direction
[-0.64615834 0.46217926 -0.60734647], radius 4.07004, and length 4.98013
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 23'
centered at [256.45448458 250.94173977 234.9126919 ] with direction [
0.9161498 -0.39680767 0.05668531], radius 2.22604, and length 4.84125
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 24'
centered at [259.31587026 246.43212477 226.41315195] with direction
[-0.87677053 -0.21128082 0.43201141], radius 2.76429, and length 4.07927
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain B helix 25'
centered at [244.04073308 217.81722393 175.51346298] with direction
[-0.33352661 -0.87723478 0.34528126], radius 7.69274, and length 5.12234
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 1'
centered at [256.00058636 178.85269922 295.25874435] with direction [
0.38280891 0.35361392 -0.85347204], radius 5.40787, and length 4.86148
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 2'
centered at [240.16730695 185.2398739 306.79144937] with direction
[-0.50782924 -0.65140907 0.56371596], radius 4.99106, and length 4.2932
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 3'
centered at [240.00937234 193.31967113 301.19666378] with direction
[-0.41257493 -0.7687185 0.4887267 ], radius 4.71498, and length 4.92444
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 4'
centered at [247.69333711 202.95284501 274.9854126 ] with direction
[-0.50113676 -0.84275256 -0.19654532], radius 5.73286, and length 4.61049
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 5'
centered at [236.25511083 197.82725567 283.19347363] with direction
[-0.5846025 0.80995199 0.04709229], radius 2.86565, and length 3.95205
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 6'
centered at [239.13382463 207.89203359 276.02388993] with direction [
0.06779926 -0.58375084 -0.80909716], radius 3.6849, and length 4.32112
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 7'
centered at [229.63283411 187.49967402 267.59890667] with direction
[0.75562207 0.46121584 0.46509701], radius 4.64616, and length 4.807
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 8'
centered at [238.76763636 182.81023708 270.98069816] with direction [
0.77639882 0.50411205 -0.37825377], radius 5.09736, and length 4.75541
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 9'
centered at [250.89701204 184.52831694 275.33064946] with direction [
0.91960134 0.09975649 -0.37997633], radius 1.86549, and length 3.37504
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 10'
centered at [261.99047698 179.2539974 283.71526115] with direction [
0.40078141 -0.4717639 -0.78537448], radius 4.74362, and length 4.63795
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 11'
centered at [257.20042142 188.64524391 294.91567177] with direction
[-0.40295475 0.91397789 -0.04766425], radius 6.86671, and length 5.52388
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 12'
centered at [257.68331067 199.65579514 303.86118409] with direction
[-0.78222946 0.55153878 -0.28969302], radius 3.75819, and length 4.48369
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 13'
centered at [235.64385616 176.63771213 237.42676126] with direction
[-0.59275942 0.67756202 0.43536879], radius 1.9377, and length 3.03621
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 14'
centered at [245.25840606 184.61950114 237.36539952] with direction [
0.52989282 0.74837534 -0.39893352], radius 4.67436, and length 4.69301
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 15'
centered at [230.67075816 195.82479285 248.20482757] with direction
[-0.08106473 -0.99663303 -0.01229285], radius 2.68723, and length 4.79629
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 16'
centered at [236.05949779 206.57939599 245.76664604] with direction
[-0.95367173 -0.29330366 -0.06695665], radius 2.85163, and length 4.1426
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 17'
centered at [217.77526411 202.31063744 193.52713733] with direction [
0.72307844 -0.0696748 -0.68724304], radius 2.29099, and length 3.81008
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 18'
centered at [207.58898884 210.64325046 177.52666445] with direction
[-0.92472806 0.34845762 0.15315125], radius 6.97517, and length 4.98991
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 19'
centered at [216.43565365 218.50014925 183.43101143] with direction
[-0.92409907 0.08558855 0.37244531], radius 12.0171, and length 6.06404
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 20'
centered at [226.74247043 213.70208851 220.59889441] with direction
[0.02943541 0.24803027 0.96830498], radius 2.34792, and length 4.97786
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 21'
centered at [222.69669184 214.13869793 231.06011361] with direction [
0.36365023 -0.75396382 -0.5470805 ], radius 4.74351, and length 4.59857
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 22'
centered at [222.47841045 194.85386519 222.92123695] with direction [
0.47031286 -0.72405036 -0.50453632], radius 3.33799, and length 4.36602
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 23'
centered at [234.94035787 194.20742929 221.04234354] with direction
[-0.93377507 -0.1649174 0.31759465], radius 3.68967, and length 4.58107
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 24'
centered at [251.14394868 193.89472764 242.06117724] with direction
[-0.62688215 -0.74452493 -0.22956785], radius 6.19988, and length 5.07275
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 25'
centered at [248.01811473 189.16765012 226.96341255] with direction [
0.0040271 0.90517513 -0.42501973], radius 3.61083, and length 4.63646
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain C helix 26'
centered at [223.11988687 199.44323102 180.11394735] with direction [
0.74954293 0.47392581 -0.46214686], radius 7.83727, and length 4.67524
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 1'
centered at [212.8044388 205.27763882 310.4839693 ] with direction [
0.36894587 -0.92877957 -0.03531921], radius 5.77063, and length 4.79879
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 2'
centered at [229.57975957 193.35304722 311.98497501] with direction [
0.66156621 -0.70373849 0.25900249], radius 4.68816, and length 4.64571
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 3'
centered at [229.24944259 191.8767245 301.774879 ] with direction [0.64281334
0.04982811 0.76440053], radius 5.13785, and length 4.93146
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 4'
centered at [218.39952939 204.9678189 278.54643863] with direction [0.50756533
0.73902978 0.44295871], radius 5.36742, and length 4.88089
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 5'
centered at [231.10733193 203.55922652 286.11962415] with direction [
0.5906847 -0.46013176 -0.66285017], radius 2.88437, and length 4.02254
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 6'
centered at [226.48546916 201.86145079 276.70202152] with direction [
0.77047748 -0.63323252 -0.07335545], radius 2.62283, and length 4.64282
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 7'
centered at [236.18180474 222.17753242 280.65390802] with direction
[-0.96741836 0.02005315 0.25238776], radius 3.67966, and length 4.71181
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 8'
centered at [227.42046281 221.86536814 289.78023317] with direction
[-0.80411863 -0.14896019 -0.57550333], radius 5.04389, and length 4.54066
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 9'
centered at [206.72625204 213.7345569 303.89850188] with direction
[-0.51017069 0.859905 0.0170076 ], radius 5.15535, and length 4.73711
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 10'
centered at [211.88608448 199.30093549 302.77997347] with direction [
0.00491638 -0.36615648 -0.93054031], radius 6.87336, and length 4.86852
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 11'
centered at [212.8764355 184.17708141 301.43070877] with direction [0.54217444
0.74875792 0.3813246 ], radius 3.34524, and length 4.73731
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 12'
centered at [184.87148356 209.06389798 239.39016886] with direction [
0.57964551 -0.74971818 -0.31927063], radius 4.76055, and length 4.76393
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 13'
centered at [198.31833719 225.12159297 246.88618184] with direction
[0.81865471 0.55466063 0.14884911], radius 2.65889, and length 5.30261
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 14'
centered at [207.63631592 218.39923884 242.84767663] with direction
[-0.19575245 -0.98063813 0.00546151], radius 2.55764, and length 4.62096
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 15'
centered at [213.34336654 234.58899325 172.19829352] with direction
[-0.16555767 0.9845688 -0.0567004 ], radius 6.48869, and length 4.45878
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 16'
centered at [221.42725656 227.0761145 183.62610103] with direction [
0.35769837 -0.92198776 -0.14829177], radius 12.6381, and length 5.62922
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 17'
centered at [213.79961025 218.51452009 216.32380841] with direction
[0.24862039 0.23243605 0.94029856], radius 2.34253, and length 4.63753
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 18'
centered at [209.91781845 222.05197435 231.98094634] with direction
[-0.06045448 -0.79617268 0.60204179], radius 3.49124, and length 4.91429
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 19'
centered at [214.46395106 226.56238333 224.53349879] with direction
[-0.94473756 -0.32745034 0.01572312], radius 4.02015, and length 4.84924
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 20'
centered at [196.09731035 225.78841108 218.78297428] with direction [
0.90436593 -0.36530556 0.2206221 ], radius 3.6692, and length 4.38227
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 21'
centered at [194.34043333 213.43198581 220.95634418] with direction [
0.57632481 -0.5272183 -0.62441219], radius 4.14608, and length 4.91379
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 22'
centered at [197.36106511 210.37198941 248.94747723] with direction [
0.04467955 0.51638833 -0.85518819], radius 3.3223, and length 4.35488
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 23'
centered at [187.53200464 204.13372793 227.50392476] with direction
[0.59576813 0.65623695 0.46304795], radius 3.36348, and length 4.61916
Axis 'apo-fitted-050622_rsr_004-coot-1.pdb #1/helix axes/chain D helix 24'
centered at [202.29265996 221.25722053 175.83336459] with direction
[0.53877836 0.84181844 0.03255125], radius 6.57097, and length 4.96538
> hide #!25 models
> hide #24 models
> hide #11.1 models
> show #11.1 models
> hide #!11 models
> show #!11 models
> hide axus
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide axis
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui tool show Angles/Torsions
> hide #!1.4 models
> show #!1.4 models
> hide #1.2 models
> show #1.2 models
> close #1.2#1.3-4
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> hide #!11 models
Either three or four atoms must be selected!
> hide #1.1 models
> show #!2 models
> hide #!2 models
> select #1/D:701
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1/D:712
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #2/D:701
25 atoms, 22 bonds, 3 residues, 2 models selected
> select add #2/D:712
36 atoms, 32 bonds, 4 residues, 2 models selected
Either three or four atoms must be selected!
> show #!2 models
Either three or four atoms must be selected!
[Repeated 1 time(s)]
> hide #!2 models
> hide #!1 models
> morph #1,3,5,4,2 same true frames 20
Computed 81 frame morph #26
> coordset #26 1,81
> hide #!26 models
> show #!10 models
> hide #!10 models
> show #!26 models
> hide #!26 models
> show #!10 models
> hide #!10 models
> show #!26 models
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Presentation/05102022/Figures/Whole-
> struct/all-classes-measurement-of-distances-morph.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\session.py", line 894, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\session.py", line 628, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\lz4\frame\\__init__.py", line 719, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\lz4\frame\\__init__.py", line 719, in write
self._fp.write(compressed)
See log for complete Python traceback.
Cannot save
'C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Presentation/05102022/Figures/Whole-
struct/all-classes-measurement-of-distances-morph.cxs': [Errno 28] No space
left on device
> show #!10 models
> hide #!26 models
> hide #!10 models
> show #!26 models
> hide #!26 models
> show #!10 models
> hide #!10 models
> open 5kuf
5kuf title:
GluK2EM with 2S,4R-4-methylglutamate [more info...]
Chain information for 5kuf #27
---
Chain | Description | UniProt
A B C D | Glutamate receptor ionotropic, kainate 2 | GRIK2_RAT
Non-standard residues in 5kuf #27
---
SYM — 2S,4R-4-methylglutamate
> 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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with 5kuf, chain
A (#27), sequence alignment score = 3450.8
RMSD between 533 pruned atom pairs is 1.336 angstroms; (across all 741 pairs:
2.320)
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> mmaker #27/A:600-633 to #1/A:631-664
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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with 5kuf, chain
A (#27), sequence alignment score = 178.1
RMSD between 34 pruned atom pairs is 0.709 angstroms; (across all 34 pairs:
0.709)
> show #!1 models
> hide #!1 models
> hide #!27 models
> morph #1,27 same true
Computed 51 frame morph #28
> coordset #28 1,51
> close #28
> close #27
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Class_comparison/5kuf-
> renumbered-to-match.pdb
Chain information for 5kuf-renumbered-to-match.pdb #27
---
Chain | Description
A B C D | No description available
> view #27
> show #!1 models
> 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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with 5kuf-
renumbered-to-match.pdb, chain A (#27), sequence alignment score = 3504.8
RMSD between 533 pruned atom pairs is 1.336 angstroms; (across all 742 pairs:
2.407)
> mmaker #27/A:631-664 to #1/A:631-664
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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with 5kuf-
renumbered-to-match.pdb, chain A (#27), sequence alignment score = 23.2
RMSD between 9 pruned atom pairs is 0.526 angstroms; (across all 26 pairs:
12.010)
> mmaker #27/A:631-664 to #1/A
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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with 5kuf-
renumbered-to-match.pdb, chain A (#27), sequence alignment score = 178
RMSD between 34 pruned atom pairs is 0.683 angstroms; (across all 34 pairs:
0.683)
> select clear
> mmaker #27/A:631-664 to #1/A:631-664
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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with 5kuf-
renumbered-to-match.pdb, chain A (#27), sequence alignment score = 23.2
RMSD between 9 pruned atom pairs is 0.526 angstroms; (across all 26 pairs:
12.010)
> mmaker #27/A:631-664 to #1/A
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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with 5kuf-
renumbered-to-match.pdb, chain A (#27), sequence alignment score = 178
RMSD between 34 pruned atom pairs is 0.683 angstroms; (across all 34 pairs:
0.683)
> hide #!1 models
> select #27/A:631-664
276 atoms, 282 bonds, 34 residues, 1 model selected
> select #27/A:585-617
254 atoms, 261 bonds, 33 residues, 1 model selected
> mmaker #27/A:585-617 ti #1/A:631-664
> matchmaker #27/A:585-617 ti #1/A:631-664
Expected a keyword
> mmaker #27/A:585-617 to #1/A:631-664
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 apo-fitted-050622_rsr_004-coot-1.pdb, chain A (#1) with 5kuf-
renumbered-to-match.pdb, chain A (#27), sequence alignment score = 173.4
RMSD between 33 pruned atom pairs is 0.655 angstroms; (across all 33 pairs:
0.655)
> show #!1 models
> select clear
> hide #27 models
> hide #!1 models
> morph #1,27 same true
Computed 51 frame morph #28
> coordset #28 1,51
> close #28
> morph #1,27 frame20
Expected a keyword
> morph #1,27 frames 20
Computed 21 frame morph #28
> coordset #28 1,21
> hide #!28 models
> show #!10 models
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Class_comparison/all-
> models-video-TOP.cxs
——— End of log from Tue Jun 28 15:51:52 2022 ———
opened ChimeraX session
> hide #!10 models
> show #!10 models
> toolshed show
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\nxb318\Desktop\movie6.mp4
Movie saved to \C:Users\\...\Desktop\movie6.mp4
> ui mousemode right "play coordinates"
> ui tool show "Side View"
> view #10
> morph #1,3,4,5,2 same true frames 50
Computed 201 frame morph #29
> coordset #29 1,201
> hide #!10 models
> set bgColor white
> mlp #!29
Map values for surface "Morph - apo-fitted-050622_rsr_004-coot-1.pdb_A SES
surface": minimum -29.52, mean -3.951, maximum 25.18
Map values for surface "Morph - apo-fitted-050622_rsr_004-coot-1.pdb_B SES
surface": minimum -27.98, mean -3.411, maximum 24.7
Map values for surface "Morph - apo-fitted-050622_rsr_004-coot-1.pdb_C SES
surface": minimum -29.25, mean -3.806, maximum 24.09
Map values for surface "Morph - apo-fitted-050622_rsr_004-coot-1.pdb_D SES
surface": minimum -29.67, mean -3.561, maximum 24.13
To also show corresponding color key, enter the above mlp command and add key
true
> surface hidePatches #29
> cartoon style #29 modeHelix tube sides 20
> close #29
> morph #1,3,4,5,2 same true frames 20
Computed 81 frame morph #29
> coordset #29 1,81
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> graphics silhouettes true
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\nxb318\Desktop\movie7.mp4
Movie saved to \C:Users\\...\Desktop\movie7.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\nxb318\Desktop\movie8.mp4
Movie saved to \C:Users\\...\Desktop\movie8.mp4
> select #29
23486 atoms, 23994 bonds, 8 pseudobonds, 2965 residues, 2 models selected
> color sel #147bf3
> select clear
> select #29:700-712
444 atoms, 456 bonds, 52 residues, 1 model selected
> select #29:700-710
376 atoms, 388 bonds, 44 residues, 1 model selected
> select #29:700-712
444 atoms, 456 bonds, 52 residues, 1 model selected
> cartoon style sel modeHelix tube sides 20
[Repeated 1 time(s)]
> select #29/A:631-664
275 atoms, 282 bonds, 34 residues, 1 model selected
> color sel orange
> select clear
> undo
> select clear
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> select #29/A,C:700-712
222 atoms, 228 bonds, 26 residues, 1 model selected
> color sel hot pink
> select #29/B,D:700-712
222 atoms, 228 bonds, 26 residues, 1 model selected
> color sel orange
> color sel yellow
> select clear
> select #29/A,C:463-473
174 atoms, 172 bonds, 22 residues, 1 model selected
> select #29/A,C:462-473
198 atoms, 198 bonds, 24 residues, 1 model selected
> color sel purple
> select #29/B,D:462-473
198 atoms, 198 bonds, 24 residues, 1 model selected
> color sel orange red
> color sel orange
> color sel #ff4343ff
> color sel #ff4141ff
> color sel #ff792bff
> color sel #ff842cff
> color sel #ff9b29ff
> color sel #ffa527ff
> color sel #ffab25ff
> color sel #ffac26ff
> color sel #ffa72cff
> color sel #ffa12eff
> color sel #ff8c27ff
> color sel #ff7d27ff
> color sel #ff7627ff
> select clear
> ui tool show "Side View"
> graphics silhouettes true
> movie record
> movie encode C:\Users\nxb318/Desktop/movie.mp4 framerate 25.0
Movie saved to C:\Users\nxb318/Desktop/movie.mp4
> graphics silhouettes false
> view #29
> movie record
> movie encode C:\Users\nxb318/Desktop/movie.mp4 framerate 25.0
Movie saved to C:\Users\nxb318/Desktop/movie.mp4
> view orient
> movie record movie encode C:\Users\nxb318/Desktop/movie.mp4 framerate 10
Expected a keyword
> movie record
> movie encode C:\Users\nxb318/Desktop/movie.mp4 framerate 25.0
Movie saved to C:\Users\nxb318/Desktop/movie.mp4
> movie record
> coordset #29 1,21
> wait 25
> movie encode C:\Users\nxb318/Desktop/side.mp4
Movie saved to C:\Users\nxb318/Desktop/side.mp4
> movie record
> coordset #29 1,51
> wait 25
> movie encode C:\Users\nxb318/Desktop/side.mp4
Movie saved to C:\Users\nxb318/Desktop/side.mp4
> morph #1,3,4,5,2 frames 50
Computed 201 frame morph #30
> coordset #30 1,201
> hide #10.1 models
> hide #!29 models
> movie record
> movie encode C:\Users\nxb318/Desktop/movie.mp4 framerate 25.0
Movie saved to C:\Users\nxb318/Desktop/movie.mp4
> hide #30.1 models
> show #!29 models
> hide #!29 models
> select #30
23628 atoms, 24147 bonds, 8 pseudobonds, 2976 residues, 2 models selected
> color sel #147bf3
> select #29/A,C:700-712
222 atoms, 228 bonds, 26 residues, 1 model selected
> select #30/A,C:700-712
222 atoms, 228 bonds, 26 residues, 1 model selected
> color sel yellow
> select #29/B,D:700-712
222 atoms, 228 bonds, 26 residues, 1 model selected
> color #!30 hot pink
> undo
> select #29/B,D:700-712
222 atoms, 228 bonds, 26 residues, 1 model selected
> select #30/B,D:700-712
222 atoms, 228 bonds, 26 residues, 1 model selected
> color sel hot pink
> select #30/B,D:463-472
158 atoms, 156 bonds, 20 residues, 1 model selected
> color sel purple
> select #30/A,C:463-472
158 atoms, 156 bonds, 20 residues, 1 model selected
> color sel orange
> select clear
> graphics silhouettes true
> movie record
> movie encode C:\Users\nxb318/Desktop/movie.mp4 framerate 25.0
Movie saved to C:\Users\nxb318/Desktop/movie.mp4
> movie record
> movie encode C:\Users\nxb318/Desktop/movie.mp4 framerate 25.0
Movie saved to C:\Users\nxb318/Desktop/movie.mp4
> select #30/A:631-664
275 atoms, 282 bonds, 34 residues, 1 model selected
> color sel yellow
> select clear
> movie record
> movie encode C:\Users\nxb318/Desktop/movie.mp4 framerate 25.0
Movie saved to C:\Users\nxb318/Desktop/movie.mp4
> select #30/A:644
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #!30 models
> show #!30 models
> select #30/A:664
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:645-664
155 atoms, 156 bonds, 20 residues, 1 model selected
> show sel target ab
> select clear
> select #30/A:664@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:660@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
9 atoms, 7 bonds, 2 residues, 1 model selected
> select up
11 atoms, 8 bonds, 3 residues, 1 model selected
> select up
19 atoms, 16 bonds, 3 residues, 1 model selected
> select up
21 atoms, 17 bonds, 4 residues, 1 model selected
> color sel red
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #30/A:652,656,660,664
27 atoms, 23 bonds, 4 residues, 1 model selected
> select #30:652,656,660,664
108 atoms, 92 bonds, 16 residues, 1 model selected
> cartoon sel
> show sel target ab
> color sel red
> style sel ball
Changed 108 atom styles
> select #30/A:645-664
155 atoms, 156 bonds, 20 residues, 1 model selected
> hide sel target a
> select #30:652,656,660,664
108 atoms, 92 bonds, 16 residues, 1 model selected
> show sel target ab
> select clear
> select #30/B,C,D:652,656,660,664
81 atoms, 69 bonds, 12 residues, 1 model selected
> name frozen "B-D-gating ring" sel
registering illegal selector name "B-D-gating ring"
> name frozen "B D gating ring" sel
registering illegal selector name "B D gating ring"
> name frozen "BDgating ring" sel
registering illegal selector name "BDgating ring"
> name frozen "BDgating ring" sel
registering illegal selector name "BDgating ring"
> select #30/B-D
17664 atoms, 18049 bonds, 6 pseudobonds, 2228 residues, 2 models selected
> cartoon hide sel
> hide (#!30 & sel) target a
> hide #!30 models
> morph #1,4,5,3,2 same true frames 20
Computed 81 frame morph #31
> coordset #31 1,81
> hide #!31 models
> show #!30 models
> select #30
23628 atoms, 24147 bonds, 8 pseudobonds, 2976 residues, 2 models selected
> cartoon (#!30 & sel)
> select clear
> hide #!30 models
> show #!31 models
> help help:contact.html
[Repeated 1 time(s)]
> hide #!31 models
> show #!1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!3 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!31 models
> morph #1,5,4,3,2 same true frames 20
Computed 81 frame morph #32
> coordset #32 1,81
> hide #!31 models
> hide #!32 models
> show #!31 models
> select #1:700-712
444 atoms, 456 bonds, 52 residues, 1 model selected
> select #1:700-712
444 atoms, 456 bonds, 52 residues, 1 model selected
> select #31:700-712
444 atoms, 456 bonds, 52 residues, 1 model selected
> select #31
23486 atoms, 23994 bonds, 8 pseudobonds, 2965 residues, 2 models selected
> cartoon hide sel
> select #31:700-712
444 atoms, 456 bonds, 52 residues, 1 model selected
> select #31:700-712
444 atoms, 456 bonds, 52 residues, 1 model selected
> cartoon sel
> select clear
> select #31
23486 atoms, 23994 bonds, 8 pseudobonds, 2965 residues, 2 models selected
> hide (#!31 & sel) target a
> select clear
> select #31:700-712
444 atoms, 456 bonds, 52 residues, 1 model selected
> cartoon style sel modeHelix tube sides 20
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select clear
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!31 models
> show #!32 models
> hide #!2 models
> Gitarra300
Unknown command: Gitarra300
> select #32/A:631-664
275 atoms, 282 bonds, 34 residues, 1 model selected
> color yellow sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> cartoon yellow sel
Expected an atoms specifier or a keyword
> cartoon color yellow sel
Expected an atoms specifier or a keyword
> color sel yellow
> select clear
> pwd
Current working directory is: C:\ProgramData\ChimeraX
> hide #!32 models
> show #!31 models
> hide #!31 models
> show #!32 models
> open mfHydrophobicity.defattr
Summary of feedback from opening mfHydrophobicity.defattr
---
note | Assigned attribute 'mfHydrophobicity' to 62364 residues using match
mode: any
> select #32/A:631-664
275 atoms, 282 bonds, 34 residues, 1 model selected
> color sel byattribute mfHydrophobicity palette ^RdYlBu
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color sel byattribute mfHydrophobicity palette ^RdYlBu
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> select clear
> hide #!32 models
> close #31-32
> morph #1,5,4,3,2 same true frames 20
Computed 81 frame morph #31
> coordset #31 1,81
> morph #1,2,3,4,5 same true frames 20
Computed 81 frame morph #32
> coordset #32 1,81
> hide #!31 models
> close #32
> show #!31 models
> morph #1,3,5,4,2 same true frames 20
Computed 81 frame morph #32
> coordset #32 1,81
> hide #!31 models
> close #32
> show #!30 models
> hide #!30 models
> show #!31 models
> hide #!31 models
> show #!30 models
> show #!31 models
> hide #!30 models
> hide #!31 models
> show #!30 models
> select #30:652,656,660,664
108 atoms, 92 bonds, 16 residues, 1 model selected
> show sel target ab
> select clear
> save
> "C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Manuscript-
> figures/Figure 3/gating-ring-TMD.cxs"
——— End of log from Wed Jun 29 16:33:53 2022 ———
opened ChimeraX session
> hide #!30 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> morph #13,4,5,2 same true frames 20
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\morph\morph.py", line 73, in morph
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph
res_groups = motion.interpolate(mol, res_interp)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\morph\motion.py", line 144, in interpolate
coords0[maindices] = matoms.coords
IndexError: index 24068 is out of bounds for axis 0 with size 24068
IndexError: index 24068 is out of bounds for axis 0 with size 24068
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\morph\motion.py", line 144, in interpolate
coords0[maindices] = matoms.coords
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 512.77
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Locale: en_US.cp1252
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex 7071
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 34,140,291,072
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.10
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.32.2
ChimeraX-AtomicLibrary: 5.0
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
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: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202201150102
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: 1.0
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: 1.1
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
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: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.1
ChimeraX-ModelPanel: 1.3.1
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: 1.8
ChimeraX-PDB: 2.6.5
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
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
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: 1.7.4
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
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.16
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
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: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.5.1
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.3
filelock: 3.4.2
fonttools: 4.28.5
funcparserlib: 1.0.0a0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.25
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.0.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.4
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.0
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 9.0.0
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.24
psutil: 5.9.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 303
pyzmq: 22.3.0
qtconsole: 5.2.2
QtPy: 2.0.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.1
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: 1.26.8
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (3)
comment:1 by , 3 years ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Morph: index out of bounds |
comment:2 by , 3 years ago
I fixed a ChimeraX morph bug similar to this last month that involved morphing between more than 2 structures. Can you try the ChimeraX daily build and see if that fixes your morphing problem?
comment:3 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Reported by Nebojsa Bogdanovic