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Opened 18 months ago
Last modified 18 months ago
#15126 assigned defect
XMAS: CSV file: Unsupported evidence file format: 'Tabular' object has no attribute 'peptide_pairs'
| Reported by: | Owned by: | Richard Scheltema | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202304302138 (2023-04-30 21:38:49 UTC)
Description
I wanted to map identified crosslinks onto the protein structure using a csv-file with four columns (abspos1, abspos2, Protein1, Protein2), but that error keeps occurring. Is there something wrong with my column nomenclature? Help would be highly appreciated.
Log:
UCSF ChimeraX version: 1.7.dev202304302138 (2023-04-30)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/Timo/Documents/PhD/Data/Lisa/ClpG-RS+Hex_240221.cxs format
> session
Log from Mon Apr 15 15:55:19 2024UCSF ChimeraX version: 1.7.dev202304302138
(2023-04-30)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/Timo/Documents/PhD/Data/Lisa/ClpG-RS+Hex_240221.cxs format
> session
Log from Thu Feb 22 14:42:20 2024UCSF ChimeraX version: 1.7.dev202304302138
(2023-04-30)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/Timo/Documents/PhD/Data/Mass-spectrometry/DHSO_X-
> Link_WT+Y541A.cxs
Opened ClpGwt-peptide-dodecamer_NUref-P17J66002_volume_map.mrc as #3, grid
size 128,128,128, pixel 3.31, shown at step 1, values float32
Log from Mon Feb 19 19:11:29 2024UCSF ChimeraX version: 1.7.dev202304302138
(2023-04-30)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/Timo/Documents/PhD/Data/cryo-EM/P17_Dodecamer_Map_Model
> (1).cxs"
Opened ClpGwt-peptide-dodecamer_NUref-P17J66002_volume_map.mrc as #4, grid
size 128,128,128, pixel 3.31, shown at level 0.499, step 1, values float32
Log from Wed Jul 26 15:27:17 2023UCSF ChimeraX version: 1.6rc202304202331
(2023-04-20)
© 2016-2023 Regents of the University of California. All rights reserved.
> open C:/Users/Administrator/OneDrive/Desktop/P17_Dodecamer_colour_movie.cxs
SHGetFileInfo() timed out for C:\Users\Administrator\Downloads\chimerax-rc.exe
Opened ClpGwt-peptide-dodecamer_NUref-P17J66002_volume_map.mrc as #4, grid
size 128,128,128, pixel 3.31, shown at level 0.499, step 1, values float32
Log from Fri Jul 21 16:00:24 2023You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /nethome/engel/Downloads/ClpGwt-peptide-
> dodecamer_NUref-P17J66002_volume_map.mrc
Opened ClpGwt-peptide-dodecamer_NUref-P17J66002_volume_map.mrc as #1, grid
size 128,128,128, pixel 3.31, shown at level 0.499, step 1, values float32
> open /nethome/engel/Downloads/ClpGwt-peptide-
> dodecamer_Homoref-P17J66002_volume_map_sharp.mrc
Opened ClpGwt-peptide-dodecamer_Homoref-P17J66002_volume_map_sharp.mrc as #2,
grid size 128,128,128, pixel 3.31, shown at level 0.677, step 1, values
float32
> surface dust #1 size 33.1
> surface dust #2 size 33.1
> hide #!1 models
> show #!1 models
> set bgColor white
> lighting soft
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui mousemode right "translate selected models"
> select add #2
2 models selected
> view matrix models #2,1,0,0,9.2759,0,1,0,-163.35,0,0,1,-1.5411
> select subtract #2
Nothing selected
> close #1
> color #2 #9141acff models
> color #2 #99c1f1ff models
> color #2 #77767bff models
> color #2 #9a9996ff models
> color #2 #c0bfbcff models
> color #2 #9a9996ff models
> open
> "/nethome/engel/Downloads/ClpG_AF_AAA1_AAA2_M_N1_N2_tetradecamer_proper_names-
> merged_models - Copy.pdb"
Summary of feedback from opening
/nethome/engel/Downloads/ClpG_AF_AAA1_AAA2_M_N1_N2_tetradecamer_proper_names-
merged_models - Copy.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
80305 messages similar to the above omitted
Chain information for ClpG_AF_AAA1_AAA2_M_N1_N2_tetradecamer_proper_names-
merged_models - Copy.pdb #1
---
Chain | Description
A | No description available
B C D E F G | No description available
H | No description available
I J K L M N | No description available
> hide surfaces
> hide cartoons
> show atoms
> hide atoms
> show atoms
[Repeated 1 time(s)]
> hide atoms
> show cartoons
> select #2/A
Nothing selected
> select #2
2 models selected
> select clear
> select add /A:793
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
140 atoms, 141 bonds, 17 residues, 1 model selected
> select up
2533 atoms, 2573 bonds, 322 residues, 1 model selected
> select up
2545 atoms, 2584 bonds, 324 residues, 1 model selected
> select /A
6291 atoms, 6378 bonds, 807 residues, 1 model selected
> select clear
> select add #2
2 models selected
> select add #1
85414 atoms, 86624 bonds, 10948 residues, 3 models selected
> select subtract #2
85414 atoms, 86624 bonds, 10948 residues, 1 model selected
> view matrix models #1,1,0,0,28.027,0,1,0,-161.87,0,0,1,-27.819
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99999,0.00093132,0.0045335,26.8,-0.0010722,0.99951,0.031165,-168.6,-0.0045023,-0.031169,0.9995,-19.989
> view matrix models
> #1,-0.6091,-0.79181,0.045128,521.34,0.79233,-0.60503,0.078433,7.1081,-0.034801,0.08353,0.9959,-37.932
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.6091,-0.79181,0.045128,523.45,0.79233,-0.60503,0.078433,-5.349,-0.034801,0.08353,0.9959,-21.837
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule ClpG_AF_AAA1_AAA2_M_N1_N2_tetradecamer_proper_names-merged_models
- Copy.pdb (#1) to map ClpGwt-peptide-
dodecamer_Homoref-P17J66002_volume_map_sharp.mrc (#2) using 85414 atoms
average map value = 0.5278, steps = 100
shifted from previous position = 10.6
rotated from previous position = 16 degrees
atoms outside contour = 56195, contour level = 0.67738
Position of ClpG_AF_AAA1_AAA2_M_N1_N2_tetradecamer_proper_names-merged_models
- Copy.pdb (#1) relative to ClpGwt-peptide-
dodecamer_Homoref-P17J66002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.36998960 -0.92748872 0.05359437 480.54846785
0.92539568 -0.36282433 0.10955059 68.21705868
-0.08216159 0.09012858 0.99253529 -6.08996077
Axis -0.01045345 0.07306751 0.99727221
Axis point 216.90111678 197.66525896 0.00000000
Rotation angle (degrees) 111.72420973
Shift along axis -6.11228582
> open /nethome/engel/Downloads/ClpG_dodecamer_flipped_map.pdb
Summary of feedback from opening
/nethome/engel/Downloads/ClpG_dodecamer_flipped_map.pdb
---
warnings | End residue of secondary structure not found: HELIX 1 1 GLN A 11
GLU A 20 1 10
Start residue of secondary structure not found: HELIX 2 2 GLY A 30 LEU A 38 1
9
Start residue of secondary structure not found: HELIX 3 3 THR A 56 GLY A 69 1
14
Start residue of secondary structure not found: HELIX 4 4 THR A 81 LEU A 98 1
18
Start residue of secondary structure not found: HELIX 5 5 GLY A 104 LEU A 109
1 6
Start residue of secondary structure not found: HELIX 6 6 LYS A 133 ALA A 141
1 9
6 messages similar to the above omitted
End residue of secondary structure not found: HELIX 13 13 ALA A 329 ARG A 332
1 4
Start residue of secondary structure not found: HELIX 14 14 SER A 343 GLY A
353 1 11
Start residue of secondary structure not found: HELIX 15 15 LEU A 354 ARG A
363 1 10
Start residue of secondary structure not found: HELIX 16 16 SER A 367 VAL A
382 1 16
Start residue of secondary structure not found: HELIX 17 17 PHE A 386 SER A
406 1 21
Start residue of secondary structure not found: HELIX 18 18 ASN A 412 ALA A
433 1 22
336 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 GLY A 313 THR A 315
0
Start residue of secondary structure not found: SHEET 6 6 1 PHE A 334 GLN A
338 0
Start residue of secondary structure not found: SHEET 7 7 1 SER A 540 LEU A
544 0
Start residue of secondary structure not found: SHEET 8 8 1 MET A 569 VAL A
572 0
Start residue of secondary structure not found: SHEET 9 9 1 SER A 612 PHE A
616 0
End residue of secondary structure not found: SHEET 10 10 1 THR A 652 SER A
658 0
Start residue of secondary structure not found: SHEET 11 11 1 ASP A 707 VAL A
710 0
Start residue of secondary structure not found: SHEET 12 12 1 ALA B 120 ALA B
121 0
Start residue of secondary structure not found: SHEET 13 13 1 ALA B 125 ASN B
126 0
Start residue of secondary structure not found: SHEET 14 14 1 ARG B 168 ASP B
169 0
Start residue of secondary structure not found: SHEET 15 15 1 ASN B 203 GLY B
208 0
98 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 GLN A 11 GLU A 20 1 10
Start residue of secondary structure not found: HELIX 2 2 GLY A 30 LEU A 38 1
9
Start residue of secondary structure not found: HELIX 3 3 THR A 56 GLY A 69 1
14
Start residue of secondary structure not found: HELIX 4 4 THR A 81 LEU A 98 1
18
Start residue of secondary structure not found: HELIX 5 5 GLY A 104 LEU A 109
1 6
Start residue of secondary structure not found: HELIX 6 6 LYS A 133 ALA A 141
1 9
816 messages similar to the above omitted
End residue of secondary structure not found: SHEET 10 10 1 THR A 652 SER A
658 0
Start residue of secondary structure not found: SHEET 11 11 1 ASP A 707 VAL A
710 0
Start residue of secondary structure not found: SHEET 12 12 1 ALA B 120 ALA B
121 0
Start residue of secondary structure not found: SHEET 13 13 1 ALA B 125 ASN B
126 0
Start residue of secondary structure not found: SHEET 14 14 1 ARG B 168 ASP B
169 0
Start residue of secondary structure not found: SHEET 15 15 1 ASN B 203 GLY B
208 0
110 messages similar to the above omitted
End residue of secondary structure not found: HELIX 13 13 ALA A 329 ARG A 332
1 4
Start residue of secondary structure not found: HELIX 14 14 SER A 343 GLY A
353 1 11
Start residue of secondary structure not found: HELIX 15 15 LEU A 354 ARG A
363 1 10
Start residue of secondary structure not found: HELIX 16 16 SER A 367 VAL A
382 1 16
Start residue of secondary structure not found: HELIX 17 17 PHE A 386 SER A
406 1 21
Start residue of secondary structure not found: HELIX 18 18 ASN A 412 ALA A
433 1 22
336 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 GLY A 313 THR A 315
0
Start residue of secondary structure not found: SHEET 6 6 1 PHE A 334 GLN A
338 0
Start residue of secondary structure not found: SHEET 7 7 1 SER A 540 LEU A
544 0
Start residue of secondary structure not found: SHEET 8 8 1 MET A 569 VAL A
572 0
Start residue of secondary structure not found: SHEET 9 9 1 SER A 612 PHE A
616 0
Start residue of secondary structure not found: SHEET 10 10 1 THR A 652 SER A
658 0
103 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 GLN A 11 GLU A 20 1 10
Start residue of secondary structure not found: HELIX 2 2 GLY A 30 LEU A 38 1
9
Start residue of secondary structure not found: HELIX 3 3 THR A 56 GLY A 69 1
14
Start residue of secondary structure not found: HELIX 4 4 THR A 81 LEU A 98 1
18
Start residue of secondary structure not found: HELIX 5 5 GLY A 104 LEU A 109
1 6
Start residue of secondary structure not found: HELIX 6 6 LYS A 133 ALA A 141
1 9
1246 messages similar to the above omitted
End residue of secondary structure not found: HELIX 327 327 ALA L 329 ARG L
332 1 4
Start residue of secondary structure not found: HELIX 328 328 SER L 343 LEU L
354 1 12
Start residue of secondary structure not found: HELIX 329 329 ARG L 355 ARG L
363 1 9
Start residue of secondary structure not found: HELIX 330 330 SER L 367 VAL L
382 1 16
Start residue of secondary structure not found: HELIX 331 331 PHE L 386 THR L
408 1 23
Start residue of secondary structure not found: HELIX 332 332 ASN L 412 ASN L
425 1 14
3 messages similar to the above omitted
End residue of secondary structure not found: HELIX 336 336 GLU L 473 GLY L
482 1 10
Start residue of secondary structure not found: HELIX 337 337 GLU L 495 SER L
501 1 7
Start residue of secondary structure not found: HELIX 338 338 GLU L 503 HIS L
507 1 5
Start residue of secondary structure not found: HELIX 339 339 GLN L 513 ILE L
520 1 8
Start residue of secondary structure not found: HELIX 340 340 SER L 521 ALA L
527 1 7
Start residue of secondary structure not found: HELIX 341 341 GLY L 550 MET L
562 1 13
1313 messages similar to the above omitted
End residue of secondary structure not found: HELIX 266 266 GLU I 579 SER I
584 1 6
Start residue of secondary structure not found: HELIX 267 267 THR I 603 ARG I
608 1 6
Start residue of secondary structure not found: HELIX 268 268 ASP I 625 ASP I
635 1 11
Start residue of secondary structure not found: HELIX 269 269 ASP I 636 HIS I
638 1 3
Start residue of secondary structure not found: HELIX 270 270 VAL I 660 ARG I
669 1 10
Start residue of secondary structure not found: HELIX 271 271 ASP I 681 ASN I
695 1 15
Start residue of secondary structure not found: HELIX 272 272 ARG I 698 ASN I
703 1 6
474 messages similar to the above omitted
End residue of secondary structure not found: HELIX 284 284 ALA H 329 ARG H
333 1 5
Start residue of secondary structure not found: HELIX 285 285 VAL H 344 GLY H
353 1 10
Start residue of secondary structure not found: HELIX 286 286 LEU H 354 ALA H
360 1 7
Start residue of secondary structure not found: HELIX 287 287 HIS H 361 ARG H
363 1 3
Start residue of secondary structure not found: HELIX 288 288 SER H 367 VAL H
382 1 16
Start residue of secondary structure not found: HELIX 289 289 PHE H 386 THR H
408 1 23
2 messages similar to the above omitted
End residue of secondary structure not found: HELIX 292 292 GLU H 473 GLY H
485 1 13
Start residue of secondary structure not found: HELIX 293 293 THR H 489 GLU H
493 1 5
Start residue of secondary structure not found: HELIX 294 294 GLU H 497 VAL H
510 1 14
Start residue of secondary structure not found: HELIX 295 295 GLN H 513 ASN H
518 1 6
Start residue of secondary structure not found: HELIX 296 296 SER H 521 ARG H
526 1 6
Start residue of secondary structure not found: HELIX 297 297 ALA H 527 LEU H
531 1 5
2 messages similar to the above omitted
End residue of secondary structure not found: HELIX 300 300 GLU H 579 LEU H
586 1 8
Start residue of secondary structure not found: HELIX 301 301 LEU H 602 ARG H
608 1 7
Start residue of secondary structure not found: HELIX 302 302 GLU H 618 ALA H
622 1 5
Start residue of secondary structure not found: HELIX 303 303 ASP H 625 ASP H
635 1 11
Start residue of secondary structure not found: HELIX 304 304 ARG H 650 THR H
652 1 3
Start residue of secondary structure not found: HELIX 305 305 GLY H 661 GLN H
668 1 8
746 messages similar to the above omitted
End residue of secondary structure not found: HELIX 126 126 GLU D 579 SER D
584 1 6
Start residue of secondary structure not found: HELIX 127 127 THR D 603 ARG D
608 1 6
Start residue of secondary structure not found: HELIX 128 128 ILE D 619 ALA D
622 1 4
Start residue of secondary structure not found: HELIX 129 129 ASP D 625 ASP D
635 1 11
Start residue of secondary structure not found: HELIX 130 130 ASP D 648 THR D
652 1 5
Start residue of secondary structure not found: HELIX 131 131 VAL D 660 ARG D
669 1 10
Start residue of secondary structure not found: HELIX 132 132 ASP D 681 ASN D
695 1 15
491 messages similar to the above omitted
End residue of secondary structure not found: HELIX 161 161 GLU E 473 GLY E
482 1 10
Start residue of secondary structure not found: HELIX 162 162 LYS E 498 VAL E
510 1 13
Start residue of secondary structure not found: HELIX 163 163 GLN E 513 ARG E
526 1 14
Start residue of secondary structure not found: HELIX 164 164 GLY E 550 PHE E
563 1 14
Start residue of secondary structure not found: HELIX 165 165 ASP E 565 ASP E
567 1 3
Start residue of secondary structure not found: HELIX 166 166 ASP E 573 GLU E
579 1 7
239 messages similar to the above omitted
End residue of secondary structure not found: SHEET 56 56 1 THR E 652 SER E
658 0
Start residue of secondary structure not found: SHEET 57 57 1 ASP E 707 VAL E
710 0
Start residue of secondary structure not found: SHEET 58 58 1 ALA F 167 ASP F
169 0
Start residue of secondary structure not found: SHEET 59 59 1 ASN F 203 ILE F
207 0
Start residue of secondary structure not found: SHEET 60 60 1 ARG F 238 LEU F
242 0
Start residue of secondary structure not found: SHEET 61 61 1 VAL F 274 LEU F
276 0
239 messages similar to the above omitted
End residue of secondary structure not found: HELIX 188 188 ALA F 329 ARG F
332 1 4
Start residue of secondary structure not found: HELIX 189 189 SER F 343 GLY F
353 1 11
Start residue of secondary structure not found: HELIX 190 190 LEU F 354 ALA F
360 1 7
Start residue of secondary structure not found: HELIX 191 191 HIS F 361 ARG F
363 1 3
Start residue of secondary structure not found: HELIX 192 192 SER F 367 LYS F
376 1 10
Start residue of secondary structure not found: HELIX 193 193 PHE F 386 SER F
406 1 21
4 messages similar to the above omitted
End residue of secondary structure not found: HELIX 198 198 LEU F 499 VAL F
510 1 12
Start residue of secondary structure not found: HELIX 199 199 GLN F 513 ALA F
527 1 15
Start residue of secondary structure not found: HELIX 200 200 GLY F 550 PHE F
563 1 14
Start residue of secondary structure not found: HELIX 201 201 ASP F 573 PHE F
577 1 5
Start residue of secondary structure not found: HELIX 202 202 LYS F 580 ARG F
585 1 6
Start residue of secondary structure not found: HELIX 203 203 THR F 603 ARG F
608 1 6
208 messages similar to the above omitted
End residue of secondary structure not found: SHEET 62 62 1 GLY F 313 ALA F
314 0
Start residue of secondary structure not found: SHEET 63 63 1 PHE F 334 GLN F
338 0
Start residue of secondary structure not found: SHEET 64 64 1 ASN F 365 ILE F
366 0
Start residue of secondary structure not found: SHEET 65 65 1 THR F 469 SER F
470 0
Start residue of secondary structure not found: SHEET 66 66 1 ILE F 542 PHE F
543 0
Start residue of secondary structure not found: SHEET 67 67 1 SER F 612 ILE F
614 0
End residue of secondary structure not found: SHEET 68 68 1 THR F 652 ILE F
654 0
Start residue of secondary structure not found: SHEET 69 69 1 ILE F 708 ILE F
709 0
Start residue of secondary structure not found: SHEET 70 70 1 ASN F 740 ILE F
741 0
Start residue of secondary structure not found: SHEET 71 71 1 LYS F 791 VAL F
792 0
Start residue of secondary structure not found: SHEET 72 72 1 ASN G 203 LEU G
206 0
Start residue of secondary structure not found: SHEET 73 73 1 ARG G 238 SER G
241 0
52 messages similar to the above omitted
End residue of secondary structure not found: HELIX 13 13 ALA A 329 ARG A 332
1 4
Start residue of secondary structure not found: HELIX 14 14 SER A 343 GLY A
353 1 11
Start residue of secondary structure not found: HELIX 15 15 LEU A 354 ARG A
363 1 10
Start residue of secondary structure not found: HELIX 16 16 SER A 367 VAL A
382 1 16
Start residue of secondary structure not found: HELIX 17 17 PHE A 386 SER A
406 1 21
Start residue of secondary structure not found: HELIX 18 18 ASN A 412 ALA A
433 1 22
336 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 GLY A 313 THR A 315
0
Start residue of secondary structure not found: SHEET 6 6 1 PHE A 334 GLN A
338 0
Start residue of secondary structure not found: SHEET 7 7 1 SER A 540 LEU A
544 0
Start residue of secondary structure not found: SHEET 8 8 1 MET A 569 VAL A
572 0
Start residue of secondary structure not found: SHEET 9 9 1 SER A 612 PHE A
616 0
End residue of secondary structure not found: SHEET 10 10 1 THR A 652 SER A
658 0
Start residue of secondary structure not found: SHEET 11 11 1 ASP A 707 VAL A
710 0
Start residue of secondary structure not found: SHEET 12 12 1 ALA B 120 ALA B
121 0
Start residue of secondary structure not found: SHEET 13 13 1 ALA B 125 ASN B
126 0
Start residue of secondary structure not found: SHEET 14 14 1 ARG B 168 ASP B
169 0
Start residue of secondary structure not found: SHEET 15 15 1 ASN B 203 GLY B
208 0
157 messages similar to the above omitted
End residue of secondary structure not found: HELIX 60 60 ALA B 329 ARG B 332
1 4
Start residue of secondary structure not found: HELIX 61 61 VAL B 344 TYR B
358 1 15
Start residue of secondary structure not found: HELIX 62 62 GLU B 359 ARG B
363 1 5
Start residue of secondary structure not found: HELIX 63 63 ASP B 368 TYR B
381 1 14
Start residue of secondary structure not found: HELIX 64 64 PHE B 386 SER B
406 1 21
Start residue of secondary structure not found: HELIX 65 65 ASN B 412 VAL B
423 1 12
409 messages similar to the above omitted
End residue of secondary structure not found: HELIX 13 13 ALA A 329 ARG A 332
1 4
Start residue of secondary structure not found: HELIX 14 14 SER A 343 GLY A
353 1 11
Start residue of secondary structure not found: HELIX 15 15 LEU A 354 ARG A
363 1 10
Start residue of secondary structure not found: HELIX 16 16 SER A 367 VAL A
382 1 16
Start residue of secondary structure not found: HELIX 17 17 PHE A 386 SER A
406 1 21
Start residue of secondary structure not found: HELIX 18 18 ASN A 412 ALA A
433 1 22
336 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 GLY A 313 THR A 315
0
Start residue of secondary structure not found: SHEET 6 6 1 PHE A 334 GLN A
338 0
Start residue of secondary structure not found: SHEET 7 7 1 SER A 540 LEU A
544 0
Start residue of secondary structure not found: SHEET 8 8 1 MET A 569 VAL A
572 0
Start residue of secondary structure not found: SHEET 9 9 1 SER A 612 PHE A
616 0
End residue of secondary structure not found: SHEET 10 10 1 THR A 652 SER A
658 0
Start residue of secondary structure not found: SHEET 11 11 1 ASP A 707 VAL A
710 0
Start residue of secondary structure not found: SHEET 12 12 1 ALA B 120 ALA B
121 0
Start residue of secondary structure not found: SHEET 13 13 1 ALA B 125 ASN B
126 0
Start residue of secondary structure not found: SHEET 14 14 1 ARG B 168 ASP B
169 0
Start residue of secondary structure not found: SHEET 15 15 1 ASN B 203 GLY B
208 0
326 messages similar to the above omitted
End residue of secondary structure not found: HELIX 229 229 ALA G 329 ARG G
332 1 4
Start residue of secondary structure not found: HELIX 230 230 VAL G 344 GLY G
353 1 10
Start residue of secondary structure not found: HELIX 231 231 LEU G 354 ARG G
363 1 10
Start residue of secondary structure not found: HELIX 232 232 SER G 367 VAL G
382 1 16
Start residue of secondary structure not found: HELIX 233 233 PHE G 386 LEU G
404 1 19
Start residue of secondary structure not found: HELIX 234 234 ASN G 412 GLU G
426 1 15
555 messages similar to the above omitted
End residue of secondary structure not found: HELIX 327 327 ALA L 329 ARG L
332 1 4
Start residue of secondary structure not found: HELIX 328 328 SER L 343 LEU L
354 1 12
Start residue of secondary structure not found: HELIX 329 329 ARG L 355 ARG L
363 1 9
Start residue of secondary structure not found: HELIX 330 330 SER L 367 VAL L
382 1 16
Start residue of secondary structure not found: HELIX 331 331 PHE L 386 THR L
408 1 23
Start residue of secondary structure not found: HELIX 332 332 ASN L 412 ASN L
425 1 14
3 messages similar to the above omitted
End residue of secondary structure not found: HELIX 336 336 GLU L 473 GLY L
482 1 10
Start residue of secondary structure not found: HELIX 337 337 GLU L 495 SER L
501 1 7
Start residue of secondary structure not found: HELIX 338 338 GLU L 503 HIS L
507 1 5
Start residue of secondary structure not found: HELIX 339 339 GLN L 513 ILE L
520 1 8
Start residue of secondary structure not found: HELIX 340 340 SER L 521 ALA L
527 1 7
Start residue of secondary structure not found: HELIX 341 341 GLY L 550 MET L
562 1 13
1776 messages similar to the above omitted
End residue of secondary structure not found: HELIX 266 266 GLU I 579 SER I
584 1 6
Start residue of secondary structure not found: HELIX 267 267 THR I 603 ARG I
608 1 6
Start residue of secondary structure not found: HELIX 268 268 ASP I 625 ASP I
635 1 11
Start residue of secondary structure not found: HELIX 269 269 ASP I 636 HIS I
638 1 3
Start residue of secondary structure not found: HELIX 270 270 VAL I 660 ARG I
669 1 10
Start residue of secondary structure not found: HELIX 271 271 ASP I 681 ASN I
695 1 15
Start residue of secondary structure not found: HELIX 272 272 ARG I 698 ASN I
703 1 6
474 messages similar to the above omitted
End residue of secondary structure not found: HELIX 284 284 ALA H 329 ARG H
333 1 5
Start residue of secondary structure not found: HELIX 285 285 VAL H 344 GLY H
353 1 10
Start residue of secondary structure not found: HELIX 286 286 LEU H 354 ALA H
360 1 7
Start residue of secondary structure not found: HELIX 287 287 HIS H 361 ARG H
363 1 3
Start residue of secondary structure not found: HELIX 288 288 SER H 367 VAL H
382 1 16
Start residue of secondary structure not found: HELIX 289 289 PHE H 386 THR H
408 1 23
2 messages similar to the above omitted
End residue of secondary structure not found: HELIX 292 292 GLU H 473 GLY H
485 1 13
Start residue of secondary structure not found: HELIX 293 293 THR H 489 GLU H
493 1 5
Start residue of secondary structure not found: HELIX 294 294 GLU H 497 VAL H
510 1 14
Start residue of secondary structure not found: HELIX 295 295 GLN H 513 ASN H
518 1 6
Start residue of secondary structure not found: HELIX 296 296 SER H 521 ARG H
526 1 6
Start residue of secondary structure not found: HELIX 297 297 ALA H 527 LEU H
531 1 5
2 messages similar to the above omitted
End residue of secondary structure not found: HELIX 300 300 GLU H 579 LEU H
586 1 8
Start residue of secondary structure not found: HELIX 301 301 LEU H 602 ARG H
608 1 7
Start residue of secondary structure not found: HELIX 302 302 GLU H 618 ALA H
622 1 5
Start residue of secondary structure not found: HELIX 303 303 ASP H 625 ASP H
635 1 11
Start residue of secondary structure not found: HELIX 304 304 ARG H 650 THR H
652 1 3
Start residue of secondary structure not found: HELIX 305 305 GLY H 661 GLN H
668 1 8
746 messages similar to the above omitted
End residue of secondary structure not found: HELIX 126 126 GLU D 579 SER D
584 1 6
Start residue of secondary structure not found: HELIX 127 127 THR D 603 ARG D
608 1 6
Start residue of secondary structure not found: HELIX 128 128 ILE D 619 ALA D
622 1 4
Start residue of secondary structure not found: HELIX 129 129 ASP D 625 ASP D
635 1 11
Start residue of secondary structure not found: HELIX 130 130 ASP D 648 THR D
652 1 5
Start residue of secondary structure not found: HELIX 131 131 VAL D 660 ARG D
669 1 10
Start residue of secondary structure not found: HELIX 132 132 ASP D 681 ASN D
695 1 15
491 messages similar to the above omitted
End residue of secondary structure not found: HELIX 161 161 GLU E 473 GLY E
482 1 10
Start residue of secondary structure not found: HELIX 162 162 LYS E 498 VAL E
510 1 13
Start residue of secondary structure not found: HELIX 163 163 GLN E 513 ARG E
526 1 14
Start residue of secondary structure not found: HELIX 164 164 GLY E 550 PHE E
563 1 14
Start residue of secondary structure not found: HELIX 165 165 ASP E 565 ASP E
567 1 3
Start residue of secondary structure not found: HELIX 166 166 ASP E 573 GLU E
579 1 7
239 messages similar to the above omitted
End residue of secondary structure not found: SHEET 56 56 1 THR E 652 SER E
658 0
Start residue of secondary structure not found: SHEET 57 57 1 ASP E 707 VAL E
710 0
Start residue of secondary structure not found: SHEET 58 58 1 ALA F 167 ASP F
169 0
Start residue of secondary structure not found: SHEET 59 59 1 ASN F 203 ILE F
207 0
Start residue of secondary structure not found: SHEET 60 60 1 ARG F 238 LEU F
242 0
Start residue of secondary structure not found: SHEET 61 61 1 VAL F 274 LEU F
276 0
239 messages similar to the above omitted
End residue of secondary structure not found: HELIX 188 188 ALA F 329 ARG F
332 1 4
Start residue of secondary structure not found: HELIX 189 189 SER F 343 GLY F
353 1 11
Start residue of secondary structure not found: HELIX 190 190 LEU F 354 ALA F
360 1 7
Start residue of secondary structure not found: HELIX 191 191 HIS F 361 ARG F
363 1 3
Start residue of secondary structure not found: HELIX 192 192 SER F 367 LYS F
376 1 10
Start residue of secondary structure not found: HELIX 193 193 PHE F 386 SER F
406 1 21
4 messages similar to the above omitted
End residue of secondary structure not found: HELIX 198 198 LEU F 499 VAL F
510 1 12
Start residue of secondary structure not found: HELIX 199 199 GLN F 513 ALA F
527 1 15
Start residue of secondary structure not found: HELIX 200 200 GLY F 550 PHE F
563 1 14
Start residue of secondary structure not found: HELIX 201 201 ASP F 573 PHE F
577 1 5
Start residue of secondary structure not found: HELIX 202 202 LYS F 580 ARG F
585 1 6
Start residue of secondary structure not found: HELIX 203 203 THR F 603 ARG F
608 1 6
208 messages similar to the above omitted
End residue of secondary structure not found: SHEET 62 62 1 GLY F 313 ALA F
314 0
Start residue of secondary structure not found: SHEET 63 63 1 PHE F 334 GLN F
338 0
Start residue of secondary structure not found: SHEET 64 64 1 ASN F 365 ILE F
366 0
Start residue of secondary structure not found: SHEET 65 65 1 THR F 469 SER F
470 0
Start residue of secondary structure not found: SHEET 66 66 1 ILE F 542 PHE F
543 0
Start residue of secondary structure not found: SHEET 67 67 1 SER F 612 ILE F
614 0
End residue of secondary structure not found: SHEET 68 68 1 THR F 652 ILE F
654 0
Start residue of secondary structure not found: SHEET 69 69 1 ILE F 708 ILE F
709 0
Start residue of secondary structure not found: SHEET 70 70 1 ASN F 740 ILE F
741 0
Start residue of secondary structure not found: SHEET 71 71 1 LYS F 791 VAL F
792 0
Start residue of secondary structure not found: SHEET 72 72 1 ASN G 203 LEU G
206 0
Start residue of secondary structure not found: SHEET 73 73 1 ARG G 238 SER G
241 0
268 messages similar to the above omitted
End residue of secondary structure not found: HELIX 229 229 ALA G 329 ARG G
332 1 4
Start residue of secondary structure not found: HELIX 230 230 VAL G 344 GLY G
353 1 10
Start residue of secondary structure not found: HELIX 231 231 LEU G 354 ARG G
363 1 10
Start residue of secondary structure not found: HELIX 232 232 SER G 367 VAL G
382 1 16
Start residue of secondary structure not found: HELIX 233 233 PHE G 386 LEU G
404 1 19
Start residue of secondary structure not found: HELIX 234 234 ASN G 412 GLU G
426 1 15
288 messages similar to the above omitted
End residue of secondary structure not found: HELIX 60 60 ALA B 329 ARG B 332
1 4
Start residue of secondary structure not found: HELIX 61 61 VAL B 344 TYR B
358 1 15
Start residue of secondary structure not found: HELIX 62 62 GLU B 359 ARG B
363 1 5
Start residue of secondary structure not found: HELIX 63 63 ASP B 368 TYR B
381 1 14
Start residue of secondary structure not found: HELIX 64 64 PHE B 386 SER B
406 1 21
Start residue of secondary structure not found: HELIX 65 65 ASN B 412 VAL B
423 1 12
456 messages similar to the above omitted
End residue of secondary structure not found: HELIX 60 60 ALA B 329 ARG B 332
1 4
Start residue of secondary structure not found: HELIX 61 61 VAL B 344 TYR B
358 1 15
Start residue of secondary structure not found: HELIX 62 62 GLU B 359 ARG B
363 1 5
Start residue of secondary structure not found: HELIX 63 63 ASP B 368 TYR B
381 1 14
Start residue of secondary structure not found: HELIX 64 64 PHE B 386 SER B
406 1 21
Start residue of secondary structure not found: HELIX 65 65 ASN B 412 VAL B
423 1 12
456 messages similar to the above omitted
End residue of secondary structure not found: HELIX 60 60 ALA B 329 ARG B 332
1 4
Start residue of secondary structure not found: HELIX 61 61 VAL B 344 TYR B
358 1 15
Start residue of secondary structure not found: HELIX 62 62 GLU B 359 ARG B
363 1 5
Start residue of secondary structure not found: HELIX 63 63 ASP B 368 TYR B
381 1 14
Start residue of secondary structure not found: HELIX 64 64 PHE B 386 SER B
406 1 21
Start residue of secondary structure not found: HELIX 65 65 ASN B 412 VAL B
423 1 12
409 messages similar to the above omitted
End residue of secondary structure not found: HELIX 13 13 ALA A 329 ARG A 332
1 4
Start residue of secondary structure not found: HELIX 14 14 SER A 343 GLY A
353 1 11
Start residue of secondary structure not found: HELIX 15 15 LEU A 354 ARG A
363 1 10
Start residue of secondary structure not found: HELIX 16 16 SER A 367 VAL A
382 1 16
Start residue of secondary structure not found: HELIX 17 17 PHE A 386 SER A
406 1 21
Start residue of secondary structure not found: HELIX 18 18 ASN A 412 ALA A
433 1 22
41 messages similar to the above omitted
End residue of secondary structure not found: HELIX 60 60 ALA B 329 ARG B 332
1 4
Start residue of secondary structure not found: HELIX 61 61 VAL B 344 TYR B
358 1 15
Start residue of secondary structure not found: HELIX 62 62 GLU B 359 ARG B
363 1 5
Start residue of secondary structure not found: HELIX 63 63 ASP B 368 TYR B
381 1 14
Start residue of secondary structure not found: HELIX 64 64 PHE B 386 SER B
406 1 21
Start residue of secondary structure not found: HELIX 65 65 ASN B 412 VAL B
423 1 12
60 messages similar to the above omitted
End residue of secondary structure not found: HELIX 126 126 GLU D 579 SER D
584 1 6
Start residue of secondary structure not found: HELIX 127 127 THR D 603 ARG D
608 1 6
Start residue of secondary structure not found: HELIX 128 128 ILE D 619 ALA D
622 1 4
Start residue of secondary structure not found: HELIX 129 129 ASP D 625 ASP D
635 1 11
Start residue of secondary structure not found: HELIX 130 130 ASP D 648 THR D
652 1 5
Start residue of secondary structure not found: HELIX 131 131 VAL D 660 ARG D
669 1 10
Start residue of secondary structure not found: HELIX 132 132 ASP D 681 ASN D
695 1 15
28 messages similar to the above omitted
End residue of secondary structure not found: HELIX 161 161 GLU E 473 GLY E
482 1 10
Start residue of secondary structure not found: HELIX 162 162 LYS E 498 VAL E
510 1 13
Start residue of secondary structure not found: HELIX 163 163 GLN E 513 ARG E
526 1 14
Start residue of secondary structure not found: HELIX 164 164 GLY E 550 PHE E
563 1 14
Start residue of secondary structure not found: HELIX 165 165 ASP E 565 ASP E
567 1 3
Start residue of secondary structure not found: HELIX 166 166 ASP E 573 GLU E
579 1 7
21 messages similar to the above omitted
End residue of secondary structure not found: HELIX 188 188 ALA F 329 ARG F
332 1 4
Start residue of secondary structure not found: HELIX 189 189 SER F 343 GLY F
353 1 11
Start residue of secondary structure not found: HELIX 190 190 LEU F 354 ALA F
360 1 7
Start residue of secondary structure not found: HELIX 191 191 HIS F 361 ARG F
363 1 3
Start residue of secondary structure not found: HELIX 192 192 SER F 367 LYS F
376 1 10
Start residue of secondary structure not found: HELIX 193 193 PHE F 386 SER F
406 1 21
4 messages similar to the above omitted
End residue of secondary structure not found: HELIX 198 198 LEU F 499 VAL F
510 1 12
Start residue of secondary structure not found: HELIX 199 199 GLN F 513 ALA F
527 1 15
Start residue of secondary structure not found: HELIX 200 200 GLY F 550 PHE F
563 1 14
Start residue of secondary structure not found: HELIX 201 201 ASP F 573 PHE F
577 1 5
Start residue of secondary structure not found: HELIX 202 202 LYS F 580 ARG F
585 1 6
Start residue of secondary structure not found: HELIX 203 203 THR F 603 ARG F
608 1 6
25 messages similar to the above omitted
End residue of secondary structure not found: HELIX 229 229 ALA G 329 ARG G
332 1 4
Start residue of secondary structure not found: HELIX 230 230 VAL G 344 GLY G
353 1 10
Start residue of secondary structure not found: HELIX 231 231 LEU G 354 ARG G
363 1 10
Start residue of secondary structure not found: HELIX 232 232 SER G 367 VAL G
382 1 16
Start residue of secondary structure not found: HELIX 233 233 PHE G 386 LEU G
404 1 19
Start residue of secondary structure not found: HELIX 234 234 ASN G 412 GLU G
426 1 15
31 messages similar to the above omitted
End residue of secondary structure not found: HELIX 266 266 GLU I 579 SER I
584 1 6
Start residue of secondary structure not found: HELIX 267 267 THR I 603 ARG I
608 1 6
Start residue of secondary structure not found: HELIX 268 268 ASP I 625 ASP I
635 1 11
Start residue of secondary structure not found: HELIX 269 269 ASP I 636 HIS I
638 1 3
Start residue of secondary structure not found: HELIX 270 270 VAL I 660 ARG I
669 1 10
Start residue of secondary structure not found: HELIX 271 271 ASP I 681 ASN I
695 1 15
Start residue of secondary structure not found: HELIX 272 272 ARG I 698 ASN I
703 1 6
11 messages similar to the above omitted
End residue of secondary structure not found: HELIX 284 284 ALA H 329 ARG H
333 1 5
Start residue of secondary structure not found: HELIX 285 285 VAL H 344 GLY H
353 1 10
Start residue of secondary structure not found: HELIX 286 286 LEU H 354 ALA H
360 1 7
Start residue of secondary structure not found: HELIX 287 287 HIS H 361 ARG H
363 1 3
Start residue of secondary structure not found: HELIX 288 288 SER H 367 VAL H
382 1 16
Start residue of secondary structure not found: HELIX 289 289 PHE H 386 THR H
408 1 23
2 messages similar to the above omitted
End residue of secondary structure not found: HELIX 292 292 GLU H 473 GLY H
485 1 13
Start residue of secondary structure not found: HELIX 293 293 THR H 489 GLU H
493 1 5
Start residue of secondary structure not found: HELIX 294 294 GLU H 497 VAL H
510 1 14
Start residue of secondary structure not found: HELIX 295 295 GLN H 513 ASN H
518 1 6
Start residue of secondary structure not found: HELIX 296 296 SER H 521 ARG H
526 1 6
Start residue of secondary structure not found: HELIX 297 297 ALA H 527 LEU H
531 1 5
2 messages similar to the above omitted
End residue of secondary structure not found: HELIX 300 300 GLU H 579 LEU H
586 1 8
Start residue of secondary structure not found: HELIX 301 301 LEU H 602 ARG H
608 1 7
Start residue of secondary structure not found: HELIX 302 302 GLU H 618 ALA H
622 1 5
Start residue of secondary structure not found: HELIX 303 303 ASP H 625 ASP H
635 1 11
Start residue of secondary structure not found: HELIX 304 304 ARG H 650 THR H
652 1 3
Start residue of secondary structure not found: HELIX 305 305 GLY H 661 GLN H
668 1 8
21 messages similar to the above omitted
End residue of secondary structure not found: HELIX 327 327 ALA L 329 ARG L
332 1 4
Start residue of secondary structure not found: HELIX 328 328 SER L 343 LEU L
354 1 12
Start residue of secondary structure not found: HELIX 329 329 ARG L 355 ARG L
363 1 9
Start residue of secondary structure not found: HELIX 330 330 SER L 367 VAL L
382 1 16
Start residue of secondary structure not found: HELIX 331 331 PHE L 386 THR L
408 1 23
Start residue of secondary structure not found: HELIX 332 332 ASN L 412 ASN L
425 1 14
3 messages similar to the above omitted
End residue of secondary structure not found: HELIX 336 336 GLU L 473 GLY L
482 1 10
Start residue of secondary structure not found: HELIX 337 337 GLU L 495 SER L
501 1 7
Start residue of secondary structure not found: HELIX 338 338 GLU L 503 HIS L
507 1 5
Start residue of secondary structure not found: HELIX 339 339 GLN L 513 ILE L
520 1 8
Start residue of secondary structure not found: HELIX 340 340 SER L 521 ALA L
527 1 7
Start residue of secondary structure not found: HELIX 341 341 GLY L 550 MET L
562 1 13
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 GLY A 313 THR A 315
0
Start residue of secondary structure not found: SHEET 6 6 1 PHE A 334 GLN A
338 0
Start residue of secondary structure not found: SHEET 7 7 1 SER A 540 LEU A
544 0
Start residue of secondary structure not found: SHEET 8 8 1 MET A 569 VAL A
572 0
Start residue of secondary structure not found: SHEET 9 9 1 SER A 612 PHE A
616 0
End residue of secondary structure not found: SHEET 10 10 1 THR A 652 SER A
658 0
Start residue of secondary structure not found: SHEET 11 11 1 ASP A 707 VAL A
710 0
Start residue of secondary structure not found: SHEET 12 12 1 ALA B 120 ALA B
121 0
Start residue of secondary structure not found: SHEET 13 13 1 ALA B 125 ASN B
126 0
Start residue of secondary structure not found: SHEET 14 14 1 ARG B 168 ASP B
169 0
Start residue of secondary structure not found: SHEET 15 15 1 ASN B 203 GLY B
208 0
39 messages similar to the above omitted
End residue of secondary structure not found: SHEET 56 56 1 THR E 652 SER E
658 0
Start residue of secondary structure not found: SHEET 57 57 1 ASP E 707 VAL E
710 0
Start residue of secondary structure not found: SHEET 58 58 1 ALA F 167 ASP F
169 0
Start residue of secondary structure not found: SHEET 59 59 1 ASN F 203 ILE F
207 0
Start residue of secondary structure not found: SHEET 60 60 1 ARG F 238 LEU F
242 0
Start residue of secondary structure not found: SHEET 61 61 1 VAL F 274 LEU F
276 0
End residue of secondary structure not found: SHEET 62 62 1 GLY F 313 ALA F
314 0
Start residue of secondary structure not found: SHEET 63 63 1 PHE F 334 GLN F
338 0
Start residue of secondary structure not found: SHEET 64 64 1 ASN F 365 ILE F
366 0
Start residue of secondary structure not found: SHEET 65 65 1 THR F 469 SER F
470 0
Start residue of secondary structure not found: SHEET 66 66 1 ILE F 542 PHE F
543 0
Start residue of secondary structure not found: SHEET 67 67 1 SER F 612 ILE F
614 0
End residue of secondary structure not found: SHEET 68 68 1 THR F 652 ILE F
654 0
Start residue of secondary structure not found: SHEET 69 69 1 ILE F 708 ILE F
709 0
Start residue of secondary structure not found: SHEET 70 70 1 ASN F 740 ILE F
741 0
Start residue of secondary structure not found: SHEET 71 71 1 LYS F 791 VAL F
792 0
Start residue of secondary structure not found: SHEET 72 72 1 ASN G 203 LEU G
206 0
Start residue of secondary structure not found: SHEET 73 73 1 ARG G 238 SER G
241 0
52 messages similar to the above omitted
End residue of secondary structure not found: HELIX 13 13 ALA A 329 ARG A 332
1 4
Start residue of secondary structure not found: HELIX 14 14 SER A 343 GLY A
353 1 11
Start residue of secondary structure not found: HELIX 15 15 LEU A 354 ARG A
363 1 10
Start residue of secondary structure not found: HELIX 16 16 SER A 367 VAL A
382 1 16
Start residue of secondary structure not found: HELIX 17 17 PHE A 386 SER A
406 1 21
Start residue of secondary structure not found: HELIX 18 18 ASN A 412 ALA A
433 1 22
41 messages similar to the above omitted
End residue of secondary structure not found: HELIX 60 60 ALA B 329 ARG B 332
1 4
Start residue of secondary structure not found: HELIX 61 61 VAL B 344 TYR B
358 1 15
Start residue of secondary structure not found: HELIX 62 62 GLU B 359 ARG B
363 1 5
Start residue of secondary structure not found: HELIX 63 63 ASP B 368 TYR B
381 1 14
Start residue of secondary structure not found: HELIX 64 64 PHE B 386 SER B
406 1 21
Start residue of secondary structure not found: HELIX 65 65 ASN B 412 VAL B
423 1 12
26 messages similar to the above omitted
End residue of secondary structure not found: HELIX 92 92 ALA C 329 ARG C 332
1 4
Start residue of secondary structure not found: HELIX 93 93 VAL C 344 LEU C
354 1 11
Start residue of secondary structure not found: HELIX 94 94 ASP C 368 VAL C
382 1 15
Start residue of secondary structure not found: HELIX 95 95 PHE C 386 THR C
408 1 23
Start residue of secondary structure not found: HELIX 96 96 ASN C 412 ALA C
429 1 18
Start residue of secondary structure not found: HELIX 97 97 ALA C 439 GLN C
464 1 26
End residue of secondary structure not found: HELIX 98 98 GLU C 473 GLY C 485
1 13
Start residue of secondary structure not found: HELIX 99 99 GLU C 497 VAL C
510 1 14
Start residue of secondary structure not found: HELIX 100 100 GLN C 513 SER C
519 1 7
Start residue of secondary structure not found: HELIX 101 101 GLY C 550 GLY C
564 1 15
Start residue of secondary structure not found: HELIX 102 102 SER C 575 PHE C
577 1 3
End residue of secondary structure not found: HELIX 103 103 GLU C 579 LEU C
586 1 8
Start residue of secondary structure not found: HELIX 104 104 LEU C 602 ARG C
608 1 7
Start residue of secondary structure not found: HELIX 105 105 GLU C 618 ALA C
622 1 5
Start residue of secondary structure not found: HELIX 106 106 ASP C 625 ASP C
635 1 11
Start residue of secondary structure not found: HELIX 107 107 ARG C 650 THR C
652 1 3
Start residue of secondary structure not found: HELIX 108 108 GLY C 661 GLN C
668 1 8
17 messages similar to the above omitted
End residue of secondary structure not found: HELIX 126 126 GLU D 579 SER D
584 1 6
Start residue of secondary structure not found: HELIX 127 127 THR D 603 ARG D
608 1 6
Start residue of secondary structure not found: HELIX 128 128 ILE D 619 ALA D
622 1 4
Start residue of secondary structure not found: HELIX 129 129 ASP D 625 ASP D
635 1 11
Start residue of secondary structure not found: HELIX 130 130 ASP D 648 THR D
652 1 5
Start residue of secondary structure not found: HELIX 131 131 VAL D 660 ARG D
669 1 10
Start residue of secondary structure not found: HELIX 132 132 ASP D 681 ASN D
695 1 15
28 messages similar to the above omitted
End residue of secondary structure not found: HELIX 161 161 GLU E 473 GLY E
482 1 10
Start residue of secondary structure not found: HELIX 162 162 LYS E 498 VAL E
510 1 13
Start residue of secondary structure not found: HELIX 163 163 GLN E 513 ARG E
526 1 14
Start residue of secondary structure not found: HELIX 164 164 GLY E 550 PHE E
563 1 14
Start residue of secondary structure not found: HELIX 165 165 ASP E 565 ASP E
567 1 3
Start residue of secondary structure not found: HELIX 166 166 ASP E 573 GLU E
579 1 7
21 messages similar to the above omitted
End residue of secondary structure not found: HELIX 188 188 ALA F 329 ARG F
332 1 4
Start residue of secondary structure not found: HELIX 189 189 SER F 343 GLY F
353 1 11
Start residue of secondary structure not found: HELIX 190 190 LEU F 354 ALA F
360 1 7
Start residue of secondary structure not found: HELIX 191 191 HIS F 361 ARG F
363 1 3
Start residue of secondary structure not found: HELIX 192 192 SER F 367 LYS F
376 1 10
Start residue of secondary structure not found: HELIX 193 193 PHE F 386 SER F
406 1 21
4 messages similar to the above omitted
End residue of secondary structure not found: HELIX 198 198 LEU F 499 VAL F
510 1 12
Start residue of secondary structure not found: HELIX 199 199 GLN F 513 ALA F
527 1 15
Start residue of secondary structure not found: HELIX 200 200 GLY F 550 PHE F
563 1 14
Start residue of secondary structure not found: HELIX 201 201 ASP F 573 PHE F
577 1 5
Start residue of secondary structure not found: HELIX 202 202 LYS F 580 ARG F
585 1 6
Start residue of secondary structure not found: HELIX 203 203 THR F 603 ARG F
608 1 6
25 messages similar to the above omitted
End residue of secondary structure not found: HELIX 229 229 ALA G 329 ARG G
332 1 4
Start residue of secondary structure not found: HELIX 230 230 VAL G 344 GLY G
353 1 10
Start residue of secondary structure not found: HELIX 231 231 LEU G 354 ARG G
363 1 10
Start residue of secondary structure not found: HELIX 232 232 SER G 367 VAL G
382 1 16
Start residue of secondary structure not found: HELIX 233 233 PHE G 386 LEU G
404 1 19
Start residue of secondary structure not found: HELIX 234 234 ASN G 412 GLU G
426 1 15
31 messages similar to the above omitted
End residue of secondary structure not found: HELIX 266 266 GLU I 579 SER I
584 1 6
Start residue of secondary structure not found: HELIX 267 267 THR I 603 ARG I
608 1 6
Start residue of secondary structure not found: HELIX 268 268 ASP I 625 ASP I
635 1 11
Start residue of secondary structure not found: HELIX 269 269 ASP I 636 HIS I
638 1 3
Start residue of secondary structure not found: HELIX 270 270 VAL I 660 ARG I
669 1 10
Start residue of secondary structure not found: HELIX 271 271 ASP I 681 ASN I
695 1 15
Start residue of secondary structure not found: HELIX 272 272 ARG I 698 ASN I
703 1 6
11 messages similar to the above omitted
End residue of secondary structure not found: HELIX 284 284 ALA H 329 ARG H
333 1 5
Start residue of secondary structure not found: HELIX 285 285 VAL H 344 GLY H
353 1 10
Start residue of secondary structure not found: HELIX 286 286 LEU H 354 ALA H
360 1 7
Start residue of secondary structure not found: HELIX 287 287 HIS H 361 ARG H
363 1 3
Start residue of secondary structure not found: HELIX 288 288 SER H 367 VAL H
382 1 16
Start residue of secondary structure not found: HELIX 289 289 PHE H 386 THR H
408 1 23
2 messages similar to the above omitted
End residue of secondary structure not found: HELIX 292 292 GLU H 473 GLY H
485 1 13
Start residue of secondary structure not found: HELIX 293 293 THR H 489 GLU H
493 1 5
Start residue of secondary structure not found: HELIX 294 294 GLU H 497 VAL H
510 1 14
Start residue of secondary structure not found: HELIX 295 295 GLN H 513 ASN H
518 1 6
Start residue of secondary structure not found: HELIX 296 296 SER H 521 ARG H
526 1 6
Start residue of secondary structure not found: HELIX 297 297 ALA H 527 LEU H
531 1 5
2 messages similar to the above omitted
End residue of secondary structure not found: HELIX 300 300 GLU H 579 LEU H
586 1 8
Start residue of secondary structure not found: HELIX 301 301 LEU H 602 ARG H
608 1 7
Start residue of secondary structure not found: HELIX 302 302 GLU H 618 ALA H
622 1 5
Start residue of secondary structure not found: HELIX 303 303 ASP H 625 ASP H
635 1 11
Start residue of secondary structure not found: HELIX 304 304 ARG H 650 THR H
652 1 3
Start residue of secondary structure not found: HELIX 305 305 GLY H 661 GLN H
668 1 8
21 messages similar to the above omitted
End residue of secondary structure not found: HELIX 327 327 ALA L 329 ARG L
332 1 4
Start residue of secondary structure not found: HELIX 328 328 SER L 343 LEU L
354 1 12
Start residue of secondary structure not found: HELIX 329 329 ARG L 355 ARG L
363 1 9
Start residue of secondary structure not found: HELIX 330 330 SER L 367 VAL L
382 1 16
Start residue of secondary structure not found: HELIX 331 331 PHE L 386 THR L
408 1 23
Start residue of secondary structure not found: HELIX 332 332 ASN L 412 ASN L
425 1 14
3 messages similar to the above omitted
End residue of secondary structure not found: HELIX 336 336 GLU L 473 GLY L
482 1 10
Start residue of secondary structure not found: HELIX 337 337 GLU L 495 SER L
501 1 7
Start residue of secondary structure not found: HELIX 338 338 GLU L 503 HIS L
507 1 5
Start residue of secondary structure not found: HELIX 339 339 GLN L 513 ILE L
520 1 8
Start residue of secondary structure not found: HELIX 340 340 SER L 521 ALA L
527 1 7
Start residue of secondary structure not found: HELIX 341 341 GLY L 550 MET L
562 1 13
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 GLY A 313 THR A 315
0
Start residue of secondary structure not found: SHEET 6 6 1 PHE A 334 GLN A
338 0
Start residue of secondary structure not found: SHEET 7 7 1 SER A 540 LEU A
544 0
Start residue of secondary structure not found: SHEET 8 8 1 MET A 569 VAL A
572 0
Start residue of secondary structure not found: SHEET 9 9 1 SER A 612 PHE A
616 0
End residue of secondary structure not found: SHEET 10 10 1 THR A 652 SER A
658 0
Start residue of secondary structure not found: SHEET 11 11 1 ASP A 707 VAL A
710 0
Start residue of secondary structure not found: SHEET 12 12 1 ALA B 120 ALA B
121 0
Start residue of secondary structure not found: SHEET 13 13 1 ALA B 125 ASN B
126 0
Start residue of secondary structure not found: SHEET 14 14 1 ARG B 168 ASP B
169 0
Start residue of secondary structure not found: SHEET 15 15 1 ASN B 203 GLY B
208 0
39 messages similar to the above omitted
End residue of secondary structure not found: SHEET 56 56 1 THR E 652 SER E
658 0
Start residue of secondary structure not found: SHEET 57 57 1 ASP E 707 VAL E
710 0
Start residue of secondary structure not found: SHEET 58 58 1 ALA F 167 ASP F
169 0
Start residue of secondary structure not found: SHEET 59 59 1 ASN F 203 ILE F
207 0
Start residue of secondary structure not found: SHEET 60 60 1 ARG F 238 LEU F
242 0
Start residue of secondary structure not found: SHEET 61 61 1 VAL F 274 LEU F
276 0
End residue of secondary structure not found: SHEET 62 62 1 GLY F 313 ALA F
314 0
Start residue of secondary structure not found: SHEET 63 63 1 PHE F 334 GLN F
338 0
Start residue of secondary structure not found: SHEET 64 64 1 ASN F 365 ILE F
366 0
Start residue of secondary structure not found: SHEET 65 65 1 THR F 469 SER F
470 0
Start residue of secondary structure not found: SHEET 66 66 1 ILE F 542 PHE F
543 0
Start residue of secondary structure not found: SHEET 67 67 1 SER F 612 ILE F
614 0
End residue of secondary structure not found: SHEET 68 68 1 THR F 652 ILE F
654 0
Start residue of secondary structure not found: SHEET 69 69 1 ILE F 708 ILE F
709 0
Start residue of secondary structure not found: SHEET 70 70 1 ASN F 740 ILE F
741 0
Start residue of secondary structure not found: SHEET 71 71 1 LYS F 791 VAL F
792 0
Start residue of secondary structure not found: SHEET 72 72 1 ASN G 203 LEU G
206 0
Start residue of secondary structure not found: SHEET 73 73 1 ARG G 238 SER G
241 0
40 messages similar to the above omitted
Chain information for ClpG_dodecamer_flipped_map.pdb
---
Chain | Description
3.1/A 3.1/B 3.1/C 3.1/D 3.1/E 3.1/F 3.1/G 3.1/H 3.1/I 3.1/L | No description
available
3.2/A | No description available
3.3/A | No description available
3.4/A | No description available
3.5/A | No description available
3.6/A | No description available
3.17/A 3.19/A 3.36/A 3.18/B 3.32/B 3.33/B 3.34/B 3.35/B 3.36/B 3.36/C 3.14/D
3.28/D 3.35/D 3.36/D 3.15/E 3.29/E 3.35/E 3.36/E 3.16/F 3.30/F 3.35/F 3.36/F
3.20/G 3.31/G 3.35/G 3.36/G 3.12/H 3.26/H 3.35/H 3.36/H 3.11/I 3.25/I 3.35/I
3.36/I 3.10/J 3.24/J 3.35/J 3.36/J 3.7/K 3.22/K 3.35/K 3.36/K 3.8/L 3.21/L
3.35/L 3.36/L 3.9/M 3.23/M 3.35/M 3.36/M 3.13/N 3.27/N 3.35/N 3.36/N | No
description available
3.35/A | No description available
> select add #3
412040 atoms, 417421 bonds, 74 pseudobonds, 55755 residues, 39 models selected
> select subtract #1
326626 atoms, 330797 bonds, 74 pseudobonds, 44807 residues, 38 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,143.55,0,1,0,-108.28,0,0,1,-20.82
> view matrix models #3,1,0,0,237.17,0,1,0,-111.18,0,0,1,32.78
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> close #3
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color zone #2 near #1 distance 19.9
> color #1 #813d9cff
> color zone #2 near #1 distance 19.9
[Repeated 1 time(s)]
> color #1 #461212ff
> color zone #2 near #1 distance 19.9
> color zone #2 near #1 distance 10
> color zone #2 near #1 distance 5
> color zone #2 near #1 distance 1
> color zone #2 near #1 distance 2
> color zone #2 near #1 distance 3
> color #1 #c061cbff
> color zone #2 near #1 distance 19.9
> color zone #2 near #1 distance 3
> hide #!2 models
> show #!2 models
> hide #1 models
> hide #!2 models
> show #1 models
> select add /C:546
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #1 models
> hide #!2 models
> show #1 models
> show #!2 models
> hide #1 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> close #2
> show #1 models
> close
> open /nethome/engel/Downloads/ClpG_AF_AAA1_MD.pdb
Summary of feedback from opening /nethome/engel/Downloads/ClpG_AF_AAA1_MD.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 32
GLN A 41 1 10
Start residue of secondary structure not found: HELIX 2 2 GLU A 50 LEU A 52 1
3
Start residue of secondary structure not found: HELIX 3 3 LEU A 59 PHE A 63 1
5
Start residue of secondary structure not found: HELIX 4 4 SER A 66 PHE A 69 1
4
Start residue of secondary structure not found: HELIX 5 5 ALA A 109 ARG A 111
1 3
46 messages similar to the above omitted
Chain information for ClpG_AF_AAA1_MD.pdb #1
---
Chain | Description
A | No description available
> open /nethome/engel/Downloads/ClpG_AF_AAA2.pdb
Summary of feedback from opening /nethome/engel/Downloads/ClpG_AF_AAA2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 32
GLN A 41 1 10
Start residue of secondary structure not found: HELIX 2 2 GLU A 50 LEU A 52 1
3
Start residue of secondary structure not found: HELIX 3 3 LEU A 59 PHE A 63 1
5
Start residue of secondary structure not found: HELIX 4 4 SER A 66 PHE A 69 1
4
Start residue of secondary structure not found: HELIX 5 5 ALA A 109 ARG A 111
1 3
39 messages similar to the above omitted
Chain information for ClpG_AF_AAA2.pdb #2
---
Chain | Description
A | No description available
> open /nethome/engel/Downloads/ClpG_AF_N1N2.pdb
Summary of feedback from opening /nethome/engel/Downloads/ClpG_AF_N1N2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 16 16 PRO A
263 LEU A 265 1 3
Start residue of secondary structure not found: HELIX 17 17 ASP A 266 TYR A
268 1 3
Start residue of secondary structure not found: HELIX 18 18 LEU A 272 GLU A
278 1 7
Start residue of secondary structure not found: HELIX 19 19 ALA A 288 LEU A
298 1 11
Start residue of secondary structure not found: HELIX 20 20 LYS A 316 ALA A
329 1 14
53 messages similar to the above omitted
Chain information for ClpG_AF_N1N2.pdb #3
---
Chain | Description
A | No description available
> select add #2
2533 atoms, 2573 bonds, 322 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
2533 atoms, 2573 bonds, 322 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-247.32,0,1,0,114.39,0,0,1,-63.6
> view matrix models #2,1,0,0,-108.02,0,1,0,435.53,0,0,1,-223.07
> view matrix models #2,1,0,0,-17.229,0,1,0,516.13,0,0,1,-159.39
> open /nethome/engel/Downloads/ClpGwt-peptide-
> dodecamer_NUref-P17J66002_volume_map.mrc
Opened ClpGwt-peptide-dodecamer_NUref-P17J66002_volume_map.mrc as #4, grid
size 128,128,128, pixel 3.31, shown at level 0.499, step 1, values float32
> select subtract #2
Nothing selected
> select add #4
2 models selected
> view matrix models #4,1,0,0,-125.08,0,1,0,28.823,0,0,1,-110.15
> view matrix models #4,1,0,0,-154.67,0,1,0,48.236,0,0,1,-85.736
> volume sel style surface
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> surface dust #4 size 33.1
> select subtract #4
Nothing selected
> select add #1
2571 atoms, 2603 bonds, 329 residues, 1 model selected
> view matrix models #1,1,0,0,-110.46,0,1,0,-0.5963,0,0,1,45.771
> view matrix models #1,1,0,0,-140.69,0,1,0,74.607,0,0,1,22.892
> view matrix models #1,1,0,0,-113.94,0,1,0,81.166,0,0,1,39.605
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.9842,0.13397,-0.11573,257.7,0.016294,-0.58239,-0.81275,621.63,-0.17628,-0.8018,0.57101,352.3
> view matrix models
> #1,-0.50629,-0.79895,0.32459,306.85,-0.7265,0.19236,-0.6597,546.13,0.46463,-0.5698,-0.67782,416.26
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.50629,-0.79895,0.32459,291.69,-0.7265,0.19236,-0.6597,553.18,0.46463,-0.5698,-0.67782,390.03
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.7831,-0.55012,-0.29002,404.32,-0.35886,0.78062,-0.51171,310.46,0.5079,-0.29664,-0.80873,340.78
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.7831,-0.55012,-0.29002,395.32,-0.35886,0.78062,-0.51171,297,0.5079,-0.29664,-0.80873,348.64
> view matrix models
> #1,-0.7831,-0.55012,-0.29002,399.7,-0.35886,0.78062,-0.51171,281.79,0.5079,-0.29664,-0.80873,335.47
> view matrix models
> #1,-0.7831,-0.55012,-0.29002,404.96,-0.35886,0.78062,-0.51171,282.11,0.5079,-0.29664,-0.80873,340.89
> ui mousemode right "move picked models"
> view matrix models #4,1,0,0,-152.22,0,1,0,46.258,0,0,1,-82.688
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.66876,-0.53579,-0.51545,423.47,-0.49854,0.8375,-0.22373,238.94,0.55156,0.10735,-0.8272,237.8
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.66876,-0.53579,-0.51545,432.33,-0.49854,0.8375,-0.22373,241.93,0.55156,0.10735,-0.8272,238.88
> view matrix models
> #1,-0.66876,-0.53579,-0.51545,434.27,-0.49854,0.8375,-0.22373,240.57,0.55156,0.10735,-0.8272,236.49
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.89896,-0.37607,-0.22459,382.93,-0.41197,0.90009,0.14184,137.36,0.14881,0.22003,-0.96408,313.25
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.89896,-0.37607,-0.22459,371.27,-0.41197,0.90009,0.14184,134.36,0.14881,0.22003,-0.96408,309.15
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.695,-0.66798,-0.26605,411.15,-0.58762,0.74091,-0.32519,298,0.41434,-0.06967,-0.90745,317.52
> view matrix models
> #1,-0.67071,-0.72755,-0.14428,397.21,-0.71175,0.68605,-0.15081,301.19,0.2087,0.001546,-0.97798,353.5
> view matrix models
> #1,-0.75811,-0.64899,0.063956,354.28,-0.6469,0.73601,-0.19952,286.07,0.082413,-0.19263,-0.9778,425
> fitmap #1 inMap #4
Fit molecule ClpG_AF_AAA1_MD.pdb (#1) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 2571 atoms
average map value = 0.4814, steps = 84
shifted from previous position = 12.7
rotated from previous position = 18.8 degrees
atoms outside contour = 1393, contour level = 0.49865
Position of ClpG_AF_AAA1_MD.pdb (#1) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.67966130 -0.73248653 -0.03903838 540.45100428
-0.73244562 0.67481083 0.09029820 211.09510860
-0.03979870 0.08996568 -0.99514936 462.57420739
Axis -0.40021198 0.91509842 0.04924681
Axis point 316.43849734 0.00000000 225.54564885
Rotation angle (degrees) 179.97619757
Shift along axis -0.34185932
> select subtract #1
Nothing selected
> select add #2
2533 atoms, 2573 bonds, 322 residues, 1 model selected
> transparency 50
> transparency 60
> transparency 30
> volume style surface
> transparency 0
> transparency 50
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting soft
> lighting full
> view matrix models
> #2,0.90079,0.17021,0.39952,-95.96,-0.1875,0.98226,0.0042827,556.5,-0.3917,-0.078767,0.91672,-51.83
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.90079,0.17021,0.39952,-245.93,-0.1875,0.98226,0.0042827,581.09,-0.3917,-0.078767,0.91672,-10.425
> view matrix models
> #2,0.90079,0.17021,0.39952,-264.52,-0.1875,0.98226,0.0042827,608.3,-0.3917,-0.078767,0.91672,-24.441
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.35972,0.5767,0.73349,39.569,-0.32329,0.66039,-0.67777,810.37,-0.87526,-0.48094,-0.05111,350.64
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.35972,0.5767,0.73349,34.594,-0.32329,0.66039,-0.67777,816.02,-0.87526,-0.48094,-0.05111,342.75
> fitmap #1 inMap #4
Fit molecule ClpG_AF_AAA1_MD.pdb (#1) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 2571 atoms
average map value = 0.4814, steps = 44
shifted from previous position = 0.0521
rotated from previous position = 0.065 degrees
atoms outside contour = 1394, contour level = 0.49865
Position of ClpG_AF_AAA1_MD.pdb (#1) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.67956029 -0.73263808 -0.03793761 540.24460351
-0.73250620 0.67477293 0.09008976 211.17824809
-0.04040392 0.08901096 -0.99521082 462.96733739
Axis -0.40027437 0.91508814 0.04892984
Axis point 316.47914445 0.00000000 225.63896692
Rotation angle (degrees) 179.92278945
Shift along axis -0.34644198
> fitmap #2 inMap #4
Fit molecule ClpG_AF_AAA2.pdb (#2) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 2533 atoms
average map value = 0.4606, steps = 164
shifted from previous position = 19.6
rotated from previous position = 56.4 degrees
atoms outside contour = 1445, contour level = 0.49865
Position of ClpG_AF_AAA2.pdb (#2) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.11928599 0.55013540 0.82651187 10.32300975
-0.93394899 0.34465540 -0.09461462 601.17003260
-0.33691264 -0.76063374 0.55491096 -13.58946953
Axis -0.33302436 0.58173810 -0.74207517
Axis point 276.09888489 207.51476926 0.00000000
Rotation angle (degrees) 89.45991202
Shift along axis 356.37010929
> select subtract #2
Nothing selected
> select add #3
1994 atoms, 2023 bonds, 262 residues, 1 model selected
> view matrix models #3,1,0,0,-176.3,0,1,0,-28.898,0,0,1,-3.9692
> view matrix models #3,1,0,0,-120.35,0,1,0,48.201,0,0,1,-8.1059
> view matrix models #3,1,0,0,-133.98,0,1,0,46.084,0,0,1,4.4459
> view matrix models #3,1,0,0,-116.53,0,1,0,50.701,0,0,1,6.3978
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.6,0.72163,0.34533,-283.28,-0.63587,0.69213,-0.34152,295.94,-0.48547,-0.014675,0.87413,116.34
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.6,0.72163,0.34533,-287.6,-0.63587,0.69213,-0.34152,292.38,-0.48547,-0.014675,0.87413,108.74
> view matrix models
> #3,0.6,0.72163,0.34533,-302.88,-0.63587,0.69213,-0.34152,304.83,-0.48547,-0.014675,0.87413,117.26
> view matrix models
> #3,0.6,0.72163,0.34533,-300.85,-0.63587,0.69213,-0.34152,304.29,-0.48547,-0.014675,0.87413,120.16
> fitmap #2 inMap #4
Fit molecule ClpG_AF_AAA2.pdb (#2) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 2533 atoms
average map value = 0.4606, steps = 64
shifted from previous position = 0.071
rotated from previous position = 0.0493 degrees
atoms outside contour = 1445, contour level = 0.49865
Position of ClpG_AF_AAA2.pdb (#2) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.11998155 0.55050190 0.82616709 10.42263084
-0.93391173 0.34487703 -0.09417379 601.10165252
-0.33676891 -0.76026803 0.55549906 -13.70166690
Axis -0.33306438 0.58149813 -0.74224527
Axis point 276.37772919 207.34652656 0.00000000
Rotation angle (degrees) 89.41678632
Shift along axis 356.23807663
> view matrix models
> #3,0.6,0.72163,0.34533,-301.81,-0.63587,0.69213,-0.34152,302.17,-0.48547,-0.014675,0.87413,123.25
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.26382,0.50816,-0.81986,109.81,0.89743,0.44089,-0.015512,39.193,0.35359,-0.73986,-0.57235,415.5
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.26382,0.50816,-0.81986,111.96,0.89743,0.44089,-0.015512,41.582,0.35359,-0.73986,-0.57235,413.04
> view matrix models
> #3,-0.26382,0.50816,-0.81986,104.07,0.89743,0.44089,-0.015512,50.678,0.35359,-0.73986,-0.57235,425.24
> fitmap #2 inMap #4
Fit molecule ClpG_AF_AAA2.pdb (#2) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 2533 atoms
average map value = 0.4606, steps = 64
shifted from previous position = 0.00556
rotated from previous position = 0.0375 degrees
atoms outside contour = 1448, contour level = 0.49865
Position of ClpG_AF_AAA2.pdb (#2) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.12054250 0.55072926 0.82593388 10.42966938
-0.93389044 0.34504330 -0.09377500 600.99175461
-0.33662759 -0.76002789 0.55591317 -13.82365625
Axis -0.33314570 0.58131433 -0.74235275
Axis point 276.52675236 207.20375007 0.00000000
Rotation angle (degrees) 89.38408773
Shift along axis 356.15254600
> fitmap #3 inMap #4
Fit molecule ClpG_AF_N1N2.pdb (#3) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 1994 atoms
average map value = 0.5018, steps = 104
shifted from previous position = 11.7
rotated from previous position = 51 degrees
atoms outside contour = 955, contour level = 0.49865
Position of ClpG_AF_N1N2.pdb (#3) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.08939751 0.19414663 -0.97689056 340.20480651
0.31995369 0.93443020 0.15642838 -56.35536533
0.94320609 -0.29857543 -0.14565366 216.98807481
Axis -0.23011630 -0.97108093 0.06362640
Axis point 80.48248050 0.00000000 256.20335130
Rotation angle (degrees) 98.64492018
Shift along axis -9.75487943
> select subtract #3
Nothing selected
> select add #3
1994 atoms, 2023 bonds, 262 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.38278,0.90023,0.20754,-145.94,-0.91284,-0.334,-0.23488,576.92,-0.14213,-0.27936,0.94961,117.34
> fitmap #3 inMap #4
Fit molecule ClpG_AF_N1N2.pdb (#3) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 1994 atoms
average map value = 0.4872, steps = 140
shifted from previous position = 8.3
rotated from previous position = 38.5 degrees
atoms outside contour = 981, contour level = 0.49865
Position of ClpG_AF_N1N2.pdb (#3) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.48808828 0.69776276 0.52430616 19.49460041
-0.75805162 -0.04117238 -0.65089367 508.38805099
-0.43258244 -0.71514471 0.54903595 421.99334686
Axis -0.03685559 0.54888913 -0.83508226
Axis point 192.73343331 387.00778025 0.00000000
Rotation angle (degrees) 119.34796661
Shift along axis -74.06896764
> close #3
> open /nethome/engel/Downloads/ClpG_AF_N1N2.pdb
Summary of feedback from opening /nethome/engel/Downloads/ClpG_AF_N1N2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 16 16 PRO A
263 LEU A 265 1 3
Start residue of secondary structure not found: HELIX 17 17 ASP A 266 TYR A
268 1 3
Start residue of secondary structure not found: HELIX 18 18 LEU A 272 GLU A
278 1 7
Start residue of secondary structure not found: HELIX 19 19 ALA A 288 LEU A
298 1 11
Start residue of secondary structure not found: HELIX 20 20 LYS A 316 ALA A
329 1 14
53 messages similar to the above omitted
Chain information for ClpG_AF_N1N2.pdb #3
---
Chain | Description
A | No description available
> select add #3
1994 atoms, 2023 bonds, 262 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #3
1994 atoms, 2023 bonds, 262 residues, 1 model selected
> view matrix models
> #3,0.75588,-0.60783,0.2433,143.32,0.60808,0.7895,0.083217,-69.369,-0.24267,0.085046,0.96637,27.51
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.75588,-0.60783,0.2433,-24.347,0.60808,0.7895,0.083217,-74.774,-0.24267,0.085046,0.96637,25.069
> view matrix models
> #3,0.75588,-0.60783,0.2433,-1.3485,0.60808,0.7895,0.083217,-7.5007,-0.24267,0.085046,0.96637,19.757
> view matrix models
> #3,0.75588,-0.60783,0.2433,-5.7722,0.60808,0.7895,0.083217,-8.6223,-0.24267,0.085046,0.96637,16.665
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.48512,-0.59931,0.63678,-32.758,0.72162,0.68566,0.095563,-5.5415,-0.49389,0.41315,0.7651,17.925
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.48512,-0.59931,0.63678,-34.215,0.72162,0.68566,0.095563,-5.38,-0.49389,0.41315,0.7651,13.739
> fitmap #3 inMap #4
Fit molecule ClpG_AF_N1N2.pdb (#3) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 1994 atoms
average map value = 0.4589, steps = 80
shifted from previous position = 6.01
rotated from previous position = 28.4 degrees
atoms outside contour = 1083, contour level = 0.49865
Position of ClpG_AF_N1N2.pdb (#3) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.30495358 -0.89819298 0.31662727 285.15162290
0.81619981 0.41779690 0.39907865 -57.36430991
-0.49073548 0.13673068 0.86051360 142.92817133
Axis -0.13713516 0.42202659 0.89615150
Axis point 217.32490533 159.18987428 0.00000000
Rotation angle (degrees) 73.04431243
Shift along axis 64.77171670
> select add #2
4527 atoms, 4596 bonds, 584 residues, 2 models selected
> select add #1
7098 atoms, 7199 bonds, 913 residues, 3 models selected
> select add #4
7098 atoms, 7199 bonds, 913 residues, 5 models selected
> select subtract #4
7098 atoms, 7199 bonds, 913 residues, 3 models selected
> hide #!4 models
> save /nethome/engel/Desktop/P17_ClpG_dodecamer_chainA.pdb displayedOnly true
> selectedOnly true relModel #4
> open /nethome/engel/Desktop/P17_ClpG_dodecamer_chainA.pdb
> hide #4.1 models
> hide #3 models
> hide #2 models
> hide #1 models
> select subtract #3
5104 atoms, 5176 bonds, 651 residues, 2 models selected
> select subtract #2
2571 atoms, 2603 bonds, 329 residues, 1 model selected
> select subtract #1
Nothing selected
> open /nethome/engel/Desktop/P17_ClpG_dodecamer_chainA.pdb
[Repeated 1 time(s)]
> view
[Repeated 1 time(s)]
> show #!4 models
> show #4.1 models
> show #3 models
> show #2 models
> show #1 models
> save /nethome/engel/Desktop/P17_ChainA.pdb selectedOnly true relModel #4
> open /nethome/engel/Desktop/P17_ChainA.pdb
> save /nethome/engel/Desktop/P17_ChainA.pdb displayedOnly true relModel #4
QXcbConnection: XCB error: 3 (BadWindow), sequence: 61342, resource id:
13597099, major code: 40 (TranslateCoords), minor code: 0
> open /nethome/engel/Desktop/P17_ChainA.pdb
[Repeated 1 time(s)]
> hide #!4 models
> hide #4.1 models
> save /nethome/engel/Desktop/test.pdb displayedOnly true relModel #4
> open /nethome/engel/Desktop/test.pdb
> save /nethome/engel/Desktop/test.pdb displayedOnly true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 5182, resource id:
13628072, major code: 40 (TranslateCoords), minor code: 0
> open /nethome/engel/Desktop/test.pdb
> save /nethome/engel/Desktop/test.pdb
> open /nethome/engel/Desktop/test.pdb
Summary of feedback from opening /nethome/engel/Desktop/test.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 263
LEU A 265 1 3
Start residue of secondary structure not found: HELIX 2 2 ASP A 266 TYR A 268
1 3
Start residue of secondary structure not found: HELIX 3 3 LEU A 272 GLU A 278
1 7
Start residue of secondary structure not found: HELIX 4 4 ALA A 288 LEU A 298
1 11
Start residue of secondary structure not found: HELIX 5 5 LYS A 316 ALA A 329
1 14
45 messages similar to the above omitted
Chain information for test.pdb
---
Chain | Description
5.1/A | No description available
5.2/A | No description available
5.3/A | No description available
> select add #5
7098 atoms, 7199 bonds, 913 residues, 4 models selected
> view matrix models #5,1,0,0,-114.41,0,1,0,-70.175,0,0,1,-25.754
[part of log deleted to fit within ticket limits]
> changechains sel I
Chain IDs of 0 residues changed
> select subtract #10
Nothing selected
> select add #11
7098 atoms, 7199 bonds, 913 residues, 1 model selected
> changechains sel J
Chain IDs of 0 residues changed
> select add #12
14196 atoms, 14398 bonds, 1826 residues, 2 models selected
> select subtract #11
7098 atoms, 7199 bonds, 913 residues, 1 model selected
> changechains sel K
Chain IDs of 0 residues changed
> select subtract #12
Nothing selected
> select add #13
7098 atoms, 7199 bonds, 913 residues, 1 model selected
> changechains sel L
Chain IDs of 0 residues changed
> select subtract #13
Nothing selected
> select add #14
7098 atoms, 7199 bonds, 913 residues, 1 model selected
> changechains sel M
Chain IDs of 0 residues changed
> select add #15
14196 atoms, 14398 bonds, 1826 residues, 2 models selected
> select subtract #14
7098 atoms, 7199 bonds, 913 residues, 1 model selected
> changechains sel N
Chain IDs of 0 residues changed
> select subtract #15
Nothing selected
> select #1/A#2/A#3/A#16.12/A#16.13/A#16.14/A
18184 atoms, 18444 bonds, 2350 residues, 4 models selected
> select #2/B#3/B#16.12/B#16.13/B
17306 atoms, 17551 bonds, 2215 residues, 3 models selected
> select #5/D#5/D#16.1/D
14196 atoms, 14398 bonds, 1826 residues, 2 models selected
> select add #16
102482 atoms, 103940 bonds, 13171 residues, 16 models selected
> select subtract #16
7098 atoms, 7199 bonds, 913 residues, 1 model selected
> select subtract #5
Nothing selected
> close #16
> show atoms
> save /nethome/engel/Desktop/FL_1.pdb displayedOnly true
> hide #7 models
> hide #9 models
> hide #11 models
> show #11 models
> hide #10 models
> hide #11 models
> hide #8 models
> hide #12 models
> hide #14 models
> hide #13 models
> hide #15 models
> hide #6 models
> hide #5 models
> hide #3 models
> hide #2 models
> hide #1 models
> open "/nethome/engel/Desktop/FL_1 (copy 1).pdb"
Summary of feedback from opening /nethome/engel/Desktop/FL_1 (copy 1).pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
88279 messages similar to the above omitted
Chain information for FL_1 (copy 1).pdb #16
---
Chain | Description
A B C D E F I J K L M N | No description available
G | No description available
H | No description available
> color #16 bychain
> hide #16 surfaces
> hide #16 atoms
> hide #16 cartoons
> show #16 cartoons
> show #!4 models
> hide #!4 models
> show #!4 models
> volume show
> volume style surface
> select #16/A:1-49
390 atoms, 394 bonds, 49 residues, 1 model selected
> color sel red
> select add #16
95384 atoms, 96741 bonds, 12258 residues, 1 model selected
> select subtract #16
Nothing selected
> select #16/B:1-49
390 atoms, 394 bonds, 49 residues, 1 model selected
> select #16/B:1-200
1528 atoms, 1549 bonds, 200 residues, 1 model selected
> select #16/B:1-236
1803 atoms, 1831 bonds, 236 residues, 1 model selected
> select #16/C
7098 atoms, 7199 bonds, 913 residues, 1 model selected
> select #16/C:1-46
369 atoms, 372 bonds, 46 residues, 1 model selected
> select #16/D
7098 atoms, 7199 bonds, 913 residues, 1 model selected
> select #16/E
7098 atoms, 7199 bonds, 913 residues, 1 model selected
> select #16/E:1-49
390 atoms, 394 bonds, 49 residues, 1 model selected
> select #16/F:1-49
390 atoms, 394 bonds, 49 residues, 1 model selected
> select #16/G:1-49
Nothing selected
> select #16/G
5104 atoms, 5176 bonds, 651 residues, 1 model selected
> select #16/I
7098 atoms, 7199 bonds, 913 residues, 1 model selected
> select #16/I:1-49
390 atoms, 394 bonds, 49 residues, 1 model selected
> select #16/J:1-49
390 atoms, 394 bonds, 49 residues, 1 model selected
> select #16/J:1-239
1825 atoms, 1853 bonds, 239 residues, 1 model selected
> select #16/K
7098 atoms, 7199 bonds, 913 residues, 1 model selected
> select #16/K:1-49
390 atoms, 394 bonds, 49 residues, 1 model selected
> select #16/L:1-49
390 atoms, 394 bonds, 49 residues, 1 model selected
> select #16/M:1-49
390 atoms, 394 bonds, 49 residues, 1 model selected
> hide #16 models
> show #16 models
> select #16/N:1-49
390 atoms, 394 bonds, 49 residues, 1 model selected
> hide #16 models
> show #16 models
> hide #16 models
> select add #16
95384 atoms, 96741 bonds, 12258 residues, 1 model selected
> select subtract #16
Nothing selected
> open "/nethome/engel/Desktop/FL_1 (copy 1) (copy 1).pdb"
Summary of feedback from opening /nethome/engel/Desktop/FL_1 (copy 1) (copy
1).pdb
---
warnings | Duplicate atom serial number found: 391
Duplicate atom serial number found: 392
Duplicate atom serial number found: 393
Duplicate atom serial number found: 394
Duplicate atom serial number found: 395
80781 messages similar to the above omitted
Chain information for FL_1 (copy 1) (copy 1).pdb #17
---
Chain | Description
A C D E I K L M N | No description available
B J | No description available
F | No description available
G | No description available
H | No description available
> hide #17 surfaces
> hide #17 atoms
> show #17 cartoons
> color #17 bychain
> color zone #4 near #17 distance 19.9
> lighting flat
> lighting soft
> close #1-3,5-15
> graphics silhouettes false
> turn -1
Expected an axis vector or a keyword
> turn -1 x
Expected an axis vector or a keyword
> turn x -1
> turn 90 -1
Expected an axis vector or a keyword
> turn x 90 -1
Missing or invalid "frames" argument: Must be greater than or equal to 1
> Turn x 90 model #4
Unknown command: Turn x 90 model #4
> turn y -1 90 models #4
> turn y +1 90 models #4
> turn y +1 90 models #4 #17
> turn y -1 90 models #4 #17
> undo
[Repeated 3 time(s)]
> fitmap #17 inMap #4 shift false
Fit molecule FL_1 (copy 1) (copy 1).pdb (#17) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 87886 atoms
average map value = 0.3001, steps = 60
shifted from previous position = 7.69e-14
rotated from previous position = 9.61 degrees
atoms outside contour = 66930, contour level = 0.49865
Position of FL_1 (copy 1) (copy 1).pdb (#17) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.98636756 0.02653870 -0.16240297 182.28229233
-0.02191005 0.99930292 0.03022624 -51.08977031
0.16309193 -0.02625592 0.98626145 79.08188702
Axis -0.16916252 -0.97484832 -0.14510268
Axis point -393.56927888 0.00000000 1163.25073971
Rotation angle (degrees) 9.61032560
Shift along axis 7.49445167
> undo
> fitmap #17 inMap #4 shift false
Fit molecule FL_1 (copy 1) (copy 1).pdb (#17) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 87886 atoms
average map value = 0.3001, steps = 28
shifted from previous position = 1.18e-13
rotated from previous position = 0.0309 degrees
atoms outside contour = 66925, contour level = 0.49865
Position of FL_1 (copy 1) (copy 1).pdb (#17) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.98637520 0.02652306 -0.16235916 182.28059325
-0.02180814 0.99928905 0.03075399 -51.15614857
0.16305942 -0.02679422 0.98625235 79.22470614
Axis -0.17230857 -0.97435537 -0.14471135
Axis point -393.98381721 0.00000000 1163.16019285
Rotation angle (degrees) 9.61295801
Shift along axis 6.97104604
> select add #17
87886 atoms, 89135 bonds, 11297 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.98638,0.026523,-0.16236,10.883,-0.021808,0.99929,0.030754,-1.5896,0.16306,-0.026794,0.98625,-6.5966
> view matrix models
> #17,0.98638,0.026523,-0.16236,10.463,-0.021808,0.99929,0.030754,-0.7728,0.16306,-0.026794,0.98625,1.2689
> fitmap #17 inMap #4 shift false
Fit molecule FL_1 (copy 1) (copy 1).pdb (#17) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 87886 atoms
average map value = 0.4447, steps = 68
shifted from previous position = 1.39e-13
rotated from previous position = 10.4 degrees
atoms outside contour = 53100, contour level = 0.49865
Position of FL_1 (copy 1) (copy 1).pdb (#17) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99990911 0.00341620 0.01304215 146.60784556
-0.00333421 0.99997458 -0.00630271 -43.78397304
-0.01306335 0.00625865 0.99989508 83.94437789
Axis 0.42228074 0.87759961 -0.22693150
Axis point 6591.75244968 0.00000000 -11051.53835010
Rotation angle (degrees) 0.85220527
Shift along axis 4.43524851
> select subtract #17
Nothing selected
> fitmap #17 inMap #4
Fit molecule FL_1 (copy 1) (copy 1).pdb (#17) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 87886 atoms
average map value = 0.4934, steps = 64
shifted from previous position = 4.09
rotated from previous position = 0.848 degrees
atoms outside contour = 45821, contour level = 0.49865
Position of FL_1 (copy 1) (copy 1).pdb (#17) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999970 0.00062708 -0.00046243 152.14676352
-0.00062750 0.99999940 -0.00089483 -46.12879167
0.00046186 0.00089512 0.99999949 82.46653834
Axis 0.75422702 -0.38946505 -0.52863841
Axis point 0.00000000 -144770.37576151 -12663.52510124
Rotation angle (degrees) 0.06798808
Shift along axis 89.12377250
> hide #!4 models
> turn y -2 20 models #17
> turn y +2 20 models #17
> turn y -2 20 models #17
> turn y -2 30 models #17
> show #!4 models
> hide #!4 models
> show #!4 models
> fitmap #17 inMap #4
Fit molecule FL_1 (copy 1) (copy 1).pdb (#17) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 87886 atoms
average map value = 0.2828, steps = 88
shifted from previous position = 26.5
rotated from previous position = 10.6 degrees
atoms outside contour = 68614, contour level = 0.49865
Position of FL_1 (copy 1) (copy 1).pdb (#17) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.08003018 -0.98649821 -0.14288614 488.94338841
0.98561485 -0.09972230 0.13645084 167.57132635
-0.14885744 -0.12991051 0.98028808 135.31922652
Axis -0.13384800 0.00300061 0.99099733
Axis point 177.20864475 311.00876761 0.00000000
Rotation angle (degrees) 95.72374955
Shift along axis 69.15971437
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select add #17
87886 atoms, 89135 bonds, 11297 residues, 1 model selected
> view matrix models
> #17,-0.14706,-0.96858,-0.20055,355.8,0.98911,-0.14284,-0.035406,242.56,0.0056471,-0.20357,0.97904,73.883
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.84811,-0.48823,-0.20577,170.04,0.4907,0.87029,-0.042442,11.867,0.1998,-0.064975,0.97768,26.054
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.84811,-0.48823,-0.20577,175.43,0.4907,0.87029,-0.042442,16.137,0.1998,-0.064975,0.97768,7.0117
> view matrix models
> #17,0.84811,-0.48823,-0.20577,161.34,0.4907,0.87029,-0.042442,13.649,0.1998,-0.064975,0.97768,7.5018
> fitmap #17 inMap #4
Fit molecule FL_1 (copy 1) (copy 1).pdb (#17) to map ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) using 87886 atoms
average map value = 0.4934, steps = 136
shifted from previous position = 3.47
rotated from previous position = 32 degrees
atoms outside contour = 45845, contour level = 0.49865
Position of FL_1 (copy 1) (copy 1).pdb (#17) relative to ClpGwt-peptide-
dodecamer_NUref-P17J66002_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999982 0.00057460 -0.00018825 152.09778963
-0.00057475 0.99999950 -0.00081539 -46.17428629
0.00018778 0.00081550 0.99999965 82.53505295
Axis 0.80326706 -0.18520918 -0.56609151
Axis point 0.00000000 -159537.13150926 -37450.06039655
Rotation angle (degrees) 0.05816447
Shift along axis 84.00465331
> select subtract #17
Nothing selected
> turn y 4 360 models #4 #17 center #4
> show #16 models
> hide #16 models
> close #16
> hide #!4 models
> select /A
6708 atoms, 6804 bonds, 864 residues, 1 model selected
> ui tool show "Color Actions"
> color #17 #0a192fff
> select add #17
87886 atoms, 89135 bonds, 11297 residues, 1 model selected
> select subtract #17
Nothing selected
> color #17/A #0A192F
> color #17 #77767bff
> color #17/A #0A192F
> color #17/B #556B2F
> color #17/C #B8860B
> color #17/D #800000
> color #17/E #708090
> color #17/F #4B0082
> color #17/G #8A9A5B
> color #17/H #006D66
> color #17/I #E97451
> color #17/J #8E4585
> color #17/K #367588
> color #17/L #B7410E
> color #17/M #5D3954
> color #17/N #64543B
> color #17/A #708090
> color #17/B #0A192F
> color #17/C #006D66
> color #17/D #8E4585
> color #17/E #4B0082
> color #17/F #5D3954
> color #17/ G #556B2F
> color #17/ H #8A9A5B
> color #17/I #64543B
> color #17/J #B8860B
> color #17/K #800000
> color #17/L #B7410E
> color #17/M #E97451
> color #17/N #367588
> show #!4 models
> color zone #4 near #17 distance 19.9
> color #17/A #008080
> hide #!4 models
> color #17/B #000080
> color #17/C #008B8B
> color #17/D #4B0082
> color #17/E #4682B4
> color #17F #DA70D6
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #17/F #DA70D6
> color #17/G #228B22
> color #17/H #40E0D0
> color #17/I #E9967A
> color #17/J #FF7F50
> color #17/K #8B008B
> color #17/L #8B0000
> color #17/m #FF8C00
> color #17/n #7851A9
> show #!4 models
> color zone #4 near #17 distance 19.9
> color #17/A #708090
> color #17/B #0A192F
> color #17/C #006D66
> color #17/d#8E4585
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #17/d #8E4585
> hide #!4 models
> show #!4 models
> color zone #4 near #17 distance 19.9
> color #17/e #4B0082
> hide #!4 models
> color #17/f #5D3954
> color #17/g #556B2F
> color #17/h #8A9A5B
> color #17/i #64543B
> color #17/j #B8860B
> color #17/k #800000
> color #17/l #B7410E
> color #17/n #367588
> show #!4 models
> color zone #4 near #17 distance 19.9
> hide #!4 models
> color #17/j #B7410E
> color #17/k #B8860B
> color #17/j #800000
> color #17/k #B7410E
> color #17/l #B8860B
> show #!4 models
> color zone #4 near #17 distance 19.9
> color #17/a #000080
> color zone #4 near #17 distance 19.9
> color #17/a #0A192F
> color zone #4 near #17 distance 19.9
> color #17/b #4B0082
> color zone #4 near #17 distance 19.9
> color #17/b #4682B4
> color zone #4 near #17 distance 19.9
> color #17/b #228B22
> color zone #4 near #17 distance 19.9
> color #17/b #2f6280
> color zone #4 near #17 distance 19.9
> color #17/m #E97451
> color zone #4 near #17 distance 19.9
> undo
[Repeated 1 time(s)]
> color zone #4 near #17 distance 19.9
> color #17/n #E97451
> color zone #4 near #17 distance 19.9
> color #17/n #daa520
> color zone #4 near #17 distance 19.9
> color #17/n ##B8860B
> color zone #4 near #17 distance 19.9
> color #17/n #B8860B
> color zone #4 near #17 distance 19.9
> color #17/n #dabb20
> color zone #4 near #17 distance 19.9
> color #17/n #ad9518
> color zone #4 near #17 distance 19.9
> color #17/m #a87e39
> color zone #4 near #17 distance 19.9
> color #17/m #b59702
> color zone #4 near #17 distance 19.9
> color #17/m #b57f02
> color zone #4 near #17 distance 19.9
> undo
> color #17/l #b55e02
> color zone #4 near #17 distance 19.9
> save /nethome/engel/Desktop/P17_Dodecamer_colour_movie.cxs includeMaps true
> transparency 50
> graphics silhouettes true
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> turn -2 180 #4 #17 center #4
Expected an axis vector or a keyword
> turn y -2 180 #4 #17 center #4
Expected a keyword
> turn y -2 180 models #4 #17 center #4
> turn y -2 90 models #4 #17 center #4
[Repeated 1 time(s)]
> turn y -2 180 models #4 #17 center #4
> hide #17 models
> turn y -2 180 models #4 #17 center #4
> turn y -1 180 models #4 #17 center #4
[Repeated 3 time(s)]
> show #17/A
> show #17 models
> show cartoons #17/A
Expected ',' or a keyword
> hide surfaces
> hide cartoons
> hide atoms
> show cartoons
> hide cartoons #17
Expected ',' or a keyword
> show #17/A cartoons
> show #17/B cartoons
> show #17/C cartoons
> hide #17 cartoons
> show #17/A cartoons
> turn y -2 30 models #4 #17 center #4
> show #1/B cartoons
> show #17/B cartoons
> turn y -2 30 models #4 #17 center #4
> show #17/C cartoons
> show #17 cartoons
> turn x -2 180 models #4 #17 center #4
> hide #4
> turn y -3 180 models #4 #17 center #4
> turn x -3 180 models #4 #17 center #4
> turn x 3 90 models #4 #17 center #4
> view
> turn x 3 90 models #4 #17 center #4
> turn x 3 95 models #4 #17 center #4
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #17 models
> volume show
> show #17 models
> show #4
> hide #17 models
> show #17/D cartoons
> show #17/E cartoons
> show #17/F cartoons
> show #17/G cartoons
> show #17/H cartoons
> show #17/I cartoons
> show #17/J cartoons
> show #17/K cartoons
> show #17/L cartoons
> show #17/M cartoons
> show #17/N cartoons
> show #17 models
> save /nethome/engel/Desktop/P17_Dodecamer_colour_movie.cxs
——— End of log from Fri Jul 21 16:00:24 2023 ———
opened ChimeraX session
> view
> hide #17 models
> show #17 models
> hide #17
> hide #17 cartoons
> movie record
> turn y -2 90 models #4 #17 center #4
> stop
> wait
wait requires a frame count argument unless motion is in progress
> movie encode
Movie saved to C:\Users\Administrator/Desktop/movie.mp4
> turn y 2 90 models #4 #17 center #4
> turn y 2 180 models #4 #17 center #4
> turn y -2 180 models #4 #17 center #4
> movie record
> turn y -2 180 models #4 #17 center #4
> stop
> wait
wait requires a frame count argument unless motion is in progress
> show #17/A cartoons
> stop
> wait
wait requires a frame count argument unless motion is in progress
> turn y -2 40 models #4 #17 center #4
> stop
> show #17/B cartoons
> turn y -2 40 models #4 #17 center #4
> show #17/C cartoons
> movie encode
Movie saved to C:\Users\Administrator/Desktop/movie.mp4
> hide #17 cartoons
> turn y -2 90 models #4 #17 center #4
> movie record
> turn y -2 90 models #4 #17 center #4
> movie encode
Movie saved to C:\Users\Administrator/Desktop/movie.mp4
> movie record
> turn y -2 180 models #4 #17 center #4
> movie encode
Movie saved to C:\Users\Administrator/Desktop/movie.mp4
> turn y -2 180 models #4 #17 center #4
> turn y 2 60 models #4 #17 center #4
> turn y 2 20 models #4 #17 center #4
> movie record
> turn y -2 180 models #4 #17 center #4
> stop
> wait
wait requires a frame count argument unless motion is in progress
> show #17/A cartoons
> stop
> wait
wait requires a frame count argument unless motion is in progress
> turn y -2 30 models #4 #17 center #4
> stop
> wait
wait requires a frame count argument unless motion is in progress
> show #17/B cartoons
> stop
> wait
wait requires a frame count argument unless motion is in progress
> turn y -2 30 models #4 #17 center #4
> stop
> wait
wait requires a frame count argument unless motion is in progress
> show #17/C cartoons
> stop
> wait
wait requires a frame count argument unless motion is in progress
> show #17/D cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/E cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/F cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/G cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/H cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/I cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/J cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/K cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/L cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/M cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/N cartoons
> wait
wait requires a frame count argument unless motion is in progress
> wait
wait requires a frame count argument unless motion is in progress
> turn x -2 180 models #4 #17 center #4
> stop
> wait
wait requires a frame count argument unless motion is in progress
> hide #4
> wait
wait requires a frame count argument unless motion is in progress
> turn x 3 90 models #17 #4 center #17
> stop
> wait
wait requires a frame count argument unless motion is in progress
> movie encode
Movie saved to C:\Users\Administrator/Desktop/movie.mp4
> show #!4 models
> hide #17 cartoons
> hide #!4 models
> show #!4 models
> show #4
> movie record
> movie record stop
Expected a keyword
> movie stop
> turn y -2 10 models #4 #17 center #4
> turn y 2 10 models #4 #17 center #4
[Repeated 5 time(s)]
> movie record
> turn y -2 180 models #4 #17 center #4
> show #17/A cartoons
> turn y -2 30 models #4 #17 center #4
> show #17/B cartoons
> turn y -2 30 models #4 #17 center #4
> show #17/C cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17 carton
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #17 cartoons
> turn x -2 90 models #4 #17 center #4
> hide #4
> turn x -2 90 models #4 #17 center #4
> stop
> turn y -2 180 models #4 #17 center #4
> stop
> movie record
Already recording a movie
> movie encode
Movie saved to C:\Users\Administrator/Desktop/movie.mp4
> show #!4 models
> show #4
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> movie encode
No frames have been recorded
> movie record
> turn y -2 180 models #4 #17 center #4
> stop
> movie stop
> hide #17 cartoons
> graphics silhouettes true
> movie record
> turn y -2 180 models #4 #17 center #4
> wait 5
> show #17/A cartoons
> wait 5
> turn y -2 30 models #4 #17 center #4
> wait 5
> show #17/B cartoons
> turn y -2 30 models #4 #17 center #4
> wait 5
> show #17/C cartoons
> movie encode
Movie saved to C:\Users\Administrator/Desktop/movie.mp4
> hide #17
> hide #17 cartoons
> view orient
[Repeated 1 time(s)]
> view
[Repeated 1 time(s)]
> view orient
> movie record
> turn y -2 180 models #4 #17 center #4
> wait
wait requires a frame count argument unless motion is in progress
> show #17/A cartoons
> wait 5
> turn y -2 30 models #4 #17 center #4
> wait
wait requires a frame count argument unless motion is in progress
> show #17/B cartoons
> wait 5
> turn y -2 30 models #4 #17 center #4
> show #17/C cartoons
> wait 5
> show #17/C
> movie stop
> show #17 cartoons
> hide surfaces
> hide atoms
> hide cartoons
> show cartoons
> hide atoms
> movie record
> movie stop
> hide #17 cartoons
> movie record
> turn y -2 180 models #4 #17 center #4
> movie stop
> movie record
> turn y -2 180 models #4 #17 center #4
> wait 5
> show #17/A cartoons
> wait 5
> turn y -2 30 models #4 #17 center #4
> wait 5
> show #17/B cartoons
> wait 5
> turn y -2 30 models #4 #17 center #4
> wait 5
> show #17/C cartoons
> wait 5
> show #17/D cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/E cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/F cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/G cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/H cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/I cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/J cartoons
[Repeated 1 time(s)]
> wait
wait requires a frame count argument unless motion is in progress
> show #17/K cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/L cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/M cartoons
> wait
wait requires a frame count argument unless motion is in progress
> show #17/N cartoons
> wait
wait requires a frame count argument unless motion is in progress
> turn x -2 45 models #4 #17 center #4
[Repeated 1 time(s)]
> hide #4
> wait
wait requires a frame count argument unless motion is in progress
> turn y -2 90 models #4 #17 center #4
> turn x 3 90 models #17 #4 center #17
> stop
> movie encode
Movie saved to C:\Users\Administrator/Desktop/movie.mp4
> show #!4 models
> show #4
> select #17:1-200
11388 atoms, 11548 bonds, 1511 residues, 1 model selected
> select #17:1-100
3698 atoms, 3778 bonds, 511 residues, 1 model selected
> select clear
> hide #!4 models
> select add /A:538
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #17:1-60
838 atoms, 848 bonds, 111 residues, 1 model selected
> select #17:1-100
3698 atoms, 3778 bonds, 511 residues, 1 model selected
> show #!4 models
> select #17:1-150
7478 atoms, 7588 bonds, 1011 residues, 1 model selected
> select #17:1-180
9948 atoms, 10088 bonds, 1311 residues, 1 model selected
> select #17:1-200
11388 atoms, 11548 bonds, 1511 residues, 1 model selected
> select ~sel
76498 atoms, 77577 bonds, 9786 residues, 3 models selected
> select clear
> hide #17 cartoons
> hide #!4 models
> show #17/A cartoons
> show #17/B cartoons
> show #17/C cartoons
> select #17/C:540-262
Nothing selected
> select #17:540-262
Nothing selected
> select 537-262
Expected an objects specifier or a keyword
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> show #17 cartoons
> show #17/C:262-540 cartoons
> show #17/C262-540 cartoons
> show #17:262-540 cartoons
> show #17:262 cartoons
> show #17:100 cartoons
> show #17/100 cartoons
> select #17/100 cartoon
Expected a keyword
> select #17/A:100 cartoon
Expected a keyword
> select #17/A:100
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #17:262-540
30464 atoms, 30830 bonds, 3904 residues, 1 model selected
> select #17:262-150
Nothing selected
> select #17/C:262-150
Nothing selected
> select #17/C:150-262
864 atoms, 876 bonds, 113 residues, 1 model selected
> select #17/C:150-280
1012 atoms, 1025 bonds, 131 residues, 1 model selected
> select #17/C:150-262
864 atoms, 876 bonds, 113 residues, 1 model selected
> select #17/C:100-262
1242 atoms, 1257 bonds, 163 residues, 1 model selected
> select add #17
87886 atoms, 89135 bonds, 11297 residues, 1 model selected
> select subtract #17
Nothing selected
> show #!4 models
> hide #17 models
> hide #!4 models
> show #17 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 87886 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> show #!4 models
> hide #!4 models
> show #!4 models
> save C:/Users/Administrator/Downloads/P17_Dodecamer_Map_Model.cxs
> includeMaps true
——— End of log from Wed Jul 26 15:27:17 2023 ———
opened ChimeraX session
> volume hide
> color :1-106 cornflower blue
> color :107-260 light sea green
> color :261-514 light gray
> color :515-572 orange
> color :573-592 light gray
> color :573-909 gray
> color :910-949 purple
> select #2
Nothing selected
> show cartoons
> hide cartoons
> show cartoons
> select clear
> show #!4 models
> hide #!4 models
> hide #4.1 models
> open "/Users/Timo/Documents/Master Biosciences/Master-THESIS/EM/ClpG_AF.pdb"
> format pdb
Chain information for ClpG_AF.pdb #1
---
Chain | Description
A B C D E F | No description available
> rename #4 id #2
> rename #2 id #3
> rename #17 id #2
> select #1
44106 atoms, 44760 bonds, 5694 residues, 1 model selected
> renumber start 1
16042 residues renumbered
> color :1-106 cornflower blue
> color :107-260 light sea green
> color :261-514 light gray
> color :515-572 orange
> color :573-592 light gray
> color :573-909 gray
> color :910-949 purple
> select clear
> select #2
87886 atoms, 89135 bonds, 11297 residues, 1 model selected
> close #2
> open /Users/Timo/Documents/PhD/Data/cryo-EM/P17_ClpG-wild-type_Dodecamer.pdb
> format pdb
Chain information for P17_ClpG-wild-type_Dodecamer.pdb #2
---
Chain | Description
A C D E I K L M N | No description available
B J | No description available
F | No description available
G | No description available
H | No description available
> 3
Unknown command: 3
> select #3
2 models selected
> select add #2
87886 atoms, 89135 bonds, 11297 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select clear
> select #2
87886 atoms, 89135 bonds, 11297 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #2/C #2/D #2/E #2/I #2/K #2/L #2/M #2/N
Alignment identifier is 1
> sequence chain #2/B #2/J
Alignment identifier is 2
> sequence chain #2/F
Alignment identifier is 2/F
> sequence chain #2/G
Alignment identifier is 2/G
> sequence chain #2/H
Alignment identifier is 2/H
> color :1-106 cornflower blue
> color :107-260 light sea green
> color :261-514 light gray
> color :515-572 orange
> color :573-592 light gray
> color :573-909 gray
> color :910-949 purple
> select clear
> select #1
44106 atoms, 44760 bonds, 5694 residues, 1 model selected
> ui mousemode right "move picked models"
> view matrix models #1,1,0,0,-6.7828,0,1,0,-19.175,0,0,1,-10.693
> view matrix models #1,1,0,0,-13.455,0,1,0,-38.68,0,0,1,-20.792
> view matrix models #1,1,0,0,-12.295,0,1,0,-57.34,0,0,1,-26.276
> ui mousemode right translate
> select #1
44106 atoms, 44760 bonds, 5694 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> select :282
160 atoms, 140 bonds, 20 residues, 2 models selected
> style sel sphere
Changed 160 atom styles
> show sel atoms
> undo
[Repeated 1 time(s)]
> select :290
180 atoms, 160 bonds, 20 residues, 2 models selected
> select :413
180 atoms, 160 bonds, 20 residues, 2 models selected
> select :33
48 atoms, 42 bonds, 6 residues, 1 model selected
> show :33 atoms
> color :33 blue
> select :413
180 atoms, 160 bonds, 20 residues, 2 models selected
> show :413 atoms
> color :413 red
> set bgColor black
> set bgColor gray
> set bgColor black
> select :32
48 atoms, 42 bonds, 6 residues, 1 model selected
> show :32 atoms
> color :32 blue
> select :114
144 atoms, 128 bonds, 16 residues, 2 models selected
> show :114 atoms
> color :114 red
> undo
[Repeated 9 time(s)]
> hide sel atoms
> save /Users/Timo/Documents/PhD/Data/Mass-spectrometry/DHSO_X-
> Link_WT+Y541A.cxs
——— End of log from Mon Feb 19 19:11:29 2024 ———
opened ChimeraX session
> select clear
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> close #3
> open /Users/Timo/Documents/PhD/Data/Lisa/ClpG-RS_fur_Timo-coot-0_240221.pdb
> format pdb
Summary of feedback from opening /Users/Timo/Documents/PhD/Data/Lisa/ClpG-
RS_fur_Timo-coot-0_240221.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
25217 messages similar to the above omitted
Ignored bad PDB record found on line 113769
Duplicate atom serial number found: 25224
Duplicate atom serial number found: 25225
Duplicate atom serial number found: 25226
Duplicate atom serial number found: 25227
Duplicate atom serial number found: 25228
63311 messages similar to the above omitted
Chain information for ClpG-RS_fur_Timo-coot-0_240221.pdb #3
---
Chain | Description
A B C D E F I J K L M N | No description available
G | No description available
H | No description available
> close #2
> rename #3 id #2
> select #2
177096 atoms, 178337 bonds, 11293 residues, 1 model selected
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,10.845,0,1,0,-56.237,0,0,1,-56.392
> show sel atoms
> show sel cartoons
> hide sel atoms
> view matrix models #2,1,0,0,19.017,0,1,0,-64.567,0,0,1,-96.563
> view matrix models #2,1,0,0,3.6794,0,1,0,-88.046,0,0,1,-120.8
> color :1-106 cornflower blue
> color :107-260 light sea green
> color :261-514 light gray
> color :515-572 orange
> color :573-592 light gray
> color :573-909 gray
> color :910-949 purple
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #2/B #2/C #2/D #2/E #2/F #2/I #2/J #2/K #2/L #2/M #2/N
Alignment identifier is 1
> renumber start 106
16987 residues renumbered
> color :1-106 cornflower blue
> color :107-260 light sea green
> color :261-514 light gray
> color :515-572 orange
> color :573-592 light gray
> color :573-909 gray
> color :910-949 purple
> select clear
> select #1
44106 atoms, 44760 bonds, 5694 residues, 1 model selected
> renumber #1 start 1
5694 residues renumbered
> color :1-106 cornflower blue
> color :107-260 light sea green
> color :261-514 light gray
> color :515-572 orange
> color :573-592 light gray
> color :573-909 gray
> color :910-949 purple
> select clear
> save /Users/Timo/Documents/PhD/Data/Lisa/ClpG-RS_240221.cxs
——— End of log from Thu Feb 22 14:42:20 2024 ———
opened ChimeraX session
> lighting flat
> ui mousemode right "rotate selected models"
> select #2
177096 atoms, 178337 bonds, 11293 residues, 1 model selected
> view matrix models
> #2,0.99412,-0.024439,-0.10552,25.438,0.013153,0.99424,-0.10636,-72.469,0.10751,0.10435,0.98871,-154.49
> ui mousemode right "move picked models"
> view matrix models #1,1,0,0,32.977,0,1,0,-9.2215,0,0,1,-7.3555
> select clear
> save /Users/Timo/Documents/PhD/Data/Lisa/ClpG-RS+Hex_240221.cxs
——— End of log from Mon Apr 15 15:55:19 2024 ———
opened ChimeraX session
> select :543
348 atoms, 328 bonds, 20 residues, 2 models selected
> show :543 atoms
> color :543 blue
> select :571
188 atoms, 168 bonds, 20 residues, 2 models selected
> show :571 atoms
> color :571 red
> lighting simple
> set bgColor white
> set bgColor black
> rename #1 ClpG-Hex_AF.pdb
> ui tool show XMAS
Unsupported evidence file format
Traceback (most recent call last):
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/tool.py", line 290, in <lambda>
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/tool.py", line 447, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/tool.py", line 460, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
See log for complete Python traceback.
Unsupported evidence file format
Traceback (most recent call last):
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/tool.py", line 290, in <lambda>
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/tool.py", line 447, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/tool.py", line 460, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
See log for complete Python traceback.
Please select pseudobonds
Please select pseudobonds
Unsupported evidence file format
Traceback (most recent call last):
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/tool.py", line 290, in <lambda>
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/tool.py", line 447, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/tool.py", line 460, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-20.5.7
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2,4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
OS Loader Version: 577~129
Software:
System Software Overview:
System Version: macOS 13.3.1 (a) (22E772610a)
Kernel Version: Darwin 22.4.0
Time since boot: 4 Tage und 24 Minuten
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LEN T24d-10:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: V5LRV735
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 2,60
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.4
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.45.4
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202304302138
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.2
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.11.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-XMAS: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
et-xmlfile: 1.1.0
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openpyxl: 3.1.2
openvr: 1.23.701
packaging: 21.3
pandas: 2.2.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
seaborn: 0.13.2
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
File attachment: Mappe11.csv
Attachments (1)
Change History (2)
by , 18 months ago
| Attachment: | Mappe11.csv added |
|---|
comment:1 by , 18 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → XMAS: CSV file: Unsupported evidence file format: 'Tabular' object has no attribute 'peptide_pairs' |
Reported by Timo Jenne
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