![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Last modified 8 months ago
#17246 assigned defect
Session restore: LZ4F_decompress failed with code: ERROR_maxBlockSize_invalid
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.18.0-477.27.2.el8_8.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.7.dev202306010115 (2023-06-01 01:15:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.dev202306010115 (2023-06-01)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/home/laiqi@nidvd.org/AAA_model/RV ab complex/rv/view03.cxs"
Log from Fri Mar 21 21:20:02 2025UCSF ChimeraX version: 1.7.dev202306010115
(2023-06-01)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/home/laiqi@nidvd.org/AAA_model/RV ab complex/rv/view02.cxs"
Log from Fri Mar 21 20:35:31 2025 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.dev202306010115 (2023-06-01)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 4V7q format mmcif fromDatabase pdb
4v7q title:
Atomic model of an infectious rotavirus particle [more info...]
Chain information for 4v7q #1
---
Chain | Description | UniProt
AA AB | Core scaffold protein | B3F2X3_9REOV 81-880
AC AD AE AF AG AH AI AJ AK AL AM AN AO | Intermediate capsid protein VP6 |
VP6_ROTRH 1-397
BA BF BG BH BI BJ BK BL BM BN BO BP BQ | Outer layer protein VP7 |
C3RX25_9REOV 51-326
BX BY BZ | Outer capsid protein VP4 | C3RX20_9REOV 1-776
Non-standard residues in 4v7q #1
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
ZN — zinc ion
4v7q mmCIF Assemblies
---
1| complete icosahedral assembly
> show surfaces
> graphics silhouettes true
> set bgColor white
> ui mousemode right select
> select /BY:187@CD
1 atom, 1 residue, 1 model selected
> select /BY:187@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
53 atoms, 54 bonds, 6 residues, 2 models selected
> select up
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> show sel cartoons
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> open "/home/laiqi@nidvd.org/AAA_model/RV ab
> complex/2_VP8_6D8_5F10/VP8_6D8_5F10-ini-coot-36.pdb"
Summary of feedback from opening /home/laiqi@nidvd.org/AAA_model/RV ab
complex/2_VP8_6D8_5F10/VP8_6D8_5F10-ini-coot-36.pdb
---
warnings | Ignored bad PDB record found on line 114
SSBOND *** CYS C 22 CYS C 95
Ignored bad PDB record found on line 115
SSBOND *** CYS B 23 CYS B 88
Ignored bad PDB record found on line 116
SSBOND *** CYS A 22 CYS A 96
Ignored bad PDB record found on line 117
SSBOND *** CYS D 23 CYS D 88
Start residue of secondary structure not found: HELIX 4 4 ILE E 98 GLY E 100 1
3
Start residue of secondary structure not found: HELIX 5 5 ARG E 186 ASN E 198
1 13
Start residue of secondary structure not found: SHEET 20 2020 TRP E 58 ILE E
61 0
Start residue of secondary structure not found: SHEET 21 2121 TYR E 70 THR E
73 0
Start residue of secondary structure not found: SHEET 22 2222 TRP E 79 ILE E
85 0
9 messages similar to the above omitted
Chain information for VP8_6D8_5F10-ini-coot-36.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> lighting soft
> select add #2
6043 atoms, 6192 bonds, 765 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,1,0,0,-56.47,0,1,0,188.81,0,0,1,109.23,#2,1,0,0,-56.47,0,1,0,188.81,0,0,1,109.23
> view matrix models
> #1,1,0,0,74.637,0,1,0,-154.85,0,0,1,-84.533,#2,1,0,0,74.637,0,1,0,-154.85,0,0,1,-84.533
> select add #1
102058 atoms, 104247 bonds, 15 pseudobonds, 12823 residues, 5 models selected
> select subtract #1
4771 atoms, 4886 bonds, 605 residues, 32 models selected
> view matrix models #2,1,0,0,28.573,0,1,0,202.56,0,0,1,133.08
> hide sel atoms
> show sel cartoons
> view matrix models #2,1,0,0,2.9859,0,1,0,205.54,0,0,1,130.4
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.77696,-0.025615,0.62903,156.02,0.38801,-0.80632,0.44642,330.18,0.49577,0.59092,0.63641,36.774
> dssp
> view matrix models
> #2,-0.29259,0.93869,0.18236,26.487,0.031096,-0.18127,0.98294,226.07,0.95573,0.29327,0.023847,95.07
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.29259,0.93869,0.18236,74.917,0.031096,-0.18127,0.98294,127.37,0.95573,0.29327,0.023847,-10.267
> ui mousemode right select
> select clear
> sequence chain #2/A
Alignment identifier is 2/A
Drag select of 86 residues
> select up
955 atoms, 974 bonds, 122 residues, 1 model selected
> select up
1744 atoms, 1786 bonds, 224 residues, 1 model selected
> hide sel cartoons
Drag select of 99 residues
Drag select of 149 residues
> select up
1514 atoms, 1543 bonds, 193 residues, 1 model selected
> select up
1744 atoms, 1782 bonds, 223 residues, 1 model selected
> hide sel cartoons
Drag select of 158 residues
> color sel light gray
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.29259,0.93869,0.18236,76.701,0.031096,-0.18127,0.98294,123.27,0.95573,0.29327,0.023847,-13.43
> view matrix models
> #2,-0.29259,0.93869,0.18236,62.839,0.031096,-0.18127,0.98294,131.58,0.95573,0.29327,0.023847,-4.1183
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.83933,-0.42543,-0.33841,169.54,0.50914,0.83337,0.21511,29.654,0.19051,-0.35285,0.91608,68.667
> view matrix models
> #2,0.053127,-0.99407,-0.094848,319.42,0.57039,-0.047753,0.81998,63.51,-0.81965,-0.097664,0.56447,212.75
> view matrix models
> #2,0.34935,-0.92449,-0.15257,278.38,0.20868,-0.081967,0.97454,95.624,-0.91346,-0.3723,0.16429,315.31
> view matrix models
> #2,0.3683,-0.91779,-0.14841,274.42,0.25013,-0.055933,0.96659,87.624,-0.89543,-0.39312,0.20897,309.94
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.3683,-0.91779,-0.14841,331.08,0.25013,-0.055933,0.96659,69.11,-0.89543,-0.39312,0.20897,310.84
> view matrix models
> #2,0.3683,-0.91779,-0.14841,335.31,0.25013,-0.055933,0.96659,69.835,-0.89543,-0.39312,0.20897,302.42
> view matrix models
> #2,0.3683,-0.91779,-0.14841,333.36,0.25013,-0.055933,0.96659,70.807,-0.89543,-0.39312,0.20897,302.73
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.28048,-0.94566,-0.16452,350.87,0.27429,-0.085286,0.95786,72.805,-0.91983,-0.31378,0.23546,291.56
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4v7q, chain BX (#1) with VP8_6D8_5F10-ini-coot-36.pdb, chain E
(#2), sequence alignment score = 468.6
RMSD between 150 pruned atom pairs is 1.007 angstroms; (across all 158 pairs:
1.227)
> ui mousemode right select
> select #1/BX:171@ND2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
12 atoms, 11 bonds, 2 residues, 2 models selected
> select up
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4v7q, chain BX (#1) with VP8_6D8_5F10-ini-coot-36.pdb, chain E
(#2), sequence alignment score = 468.6
RMSD between 150 pruned atom pairs is 1.007 angstroms; (across all 158 pairs:
1.227)
> select clear
> show surfaces
> hide surfaces
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!1 surfaces
> show #!2 models
> select #1/BX:194@CE2
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
26 atoms, 26 bonds, 3 residues, 2 models selected
> select up
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> select up
1439 atoms, 1475 bonds, 183 residues, 2 models selected
> select down
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4v7q, chain BX (#1) with VP8_6D8_5F10-ini-coot-36.pdb, chain E
(#2), sequence alignment score = 468.6
RMSD between 150 pruned atom pairs is 1.007 angstroms; (across all 158 pairs:
1.227)
> transparency sel 75 surfaces
> select clear
> select #1/BY:111@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
44 atoms, 44 bonds, 6 residues, 2 models selected
> select up
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> hide sel cartoons
> hide sel surfaces
> select #1/AH:267@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
12 atoms, 11 bonds, 2 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> select up
97287 atoms, 99361 bonds, 12218 residues, 2 models selected
> select down
3163 atoms, 3233 bonds, 397 residues, 32 models selected
Drag select of 4v7q_AA SES surface, 768379 of 845108 triangles, 4v7q_AB SES
surface, 835249 of 865418 triangles, 4v7q_AC SES surface, 1901 of 345712
triangles, 4v7q_AD SES surface, 4119 of 343138 triangles, 4v7q_AF SES surface,
217717 of 345726 triangles, 4v7q_AG SES surface, 169103 of 346434 triangles,
4v7q_AH SES surface, 191701 of 350200 triangles, 4v7q_AI SES surface, 131582
of 346554 triangles, 4v7q_AJ SES surface, 89758 of 347202 triangles, 4v7q_AK
SES surface, 67137 of 348548 triangles, 4v7q_AL SES surface, 109954 of 344322
triangles, 4v7q_AM SES surface, 76179 of 346762 triangles, 4v7q_AN SES
surface, 113668 of 348624 triangles, 4v7q_AO SES surface, 50826 of 348624
triangles, 4v7q_BX SES surface, 255 of 703936 triangles, 22446 atoms, 2
pseudobonds
> select up
23471 atoms, 23775 bonds, 2 pseudobonds, 2889 residues, 16 models selected
> select up
26806 atoms, 27240 bonds, 2 pseudobonds, 3308 residues, 16 models selected
> select up
50881 atoms, 51956 bonds, 2 pseudobonds, 6346 residues, 16 models selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #1/AE:56@CG2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
69 atoms, 69 bonds, 10 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel cartoons
> hide sel surfaces
> hide sel atoms
> select #1/BX:460@OE1
1 atom, 1 residue, 1 model selected
> view name A1
> select clear
> view name A2
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes width 3
> select clear
> view name A1
> save "/home/laiqi@nidvd.org/AAA_model/RV ab complex/rv/view01.cxs"
> view name A2
> save "/home/laiqi@nidvd.org/AAA_model/RV ab complex/rv/view02.png" width
> 1979 height 1153 supersample 3 transparentBackground true
> view name A1
> view A1
> view A2
> view name A2
> save "/home/laiqi@nidvd.org/AAA_model/RV ab complex/rv/view01.png" width
> 1979 height 1153 supersample 3 transparentBackground true
> hide #!2 models
> hide #!1 models
> show #!1 models
Drag select of 4v7q_BI SES surface, 126063 of 280590 triangles, 4v7q_BK SES
surface, 63663 of 272824 triangles, 1518 atoms, 23 bonds
> select up
1520 atoms, 1530 bonds, 208 residues, 3 models selected
> select up
1675 atoms, 1707 bonds, 208 residues, 3 models selected
> select up
2234 atoms, 2282 bonds, 283 residues, 3 models selected
> select up
4305 atoms, 4403 bonds, 544 residues, 3 models selected
> select up
97287 atoms, 99361 bonds, 12218 residues, 3 models selected
> select down
4305 atoms, 4403 bonds, 544 residues, 32 models selected
> hide sel surfaces
> hide sel atoms
Drag select of 4v7q_BJ SES surface, 100006 of 278122 triangles, 4v7q_BL SES
surface, 83964 of 275038 triangles, 4v7q_BM SES surface, 103627 of 248250
triangles, 2401 atoms
> select up
2892 atoms, 2917 bonds, 360 residues, 4 models selected
> select up
4364 atoms, 4450 bonds, 554 residues, 4 models selected
> select up
6331 atoms, 6475 bonds, 802 residues, 4 models selected
> select up
9508 atoms, 9722 bonds, 1200 residues, 4 models selected
> hide sel cartoons
> hide sel surfaces
> hide sel atoms
Drag select of 4v7q_BA SES surface, 84780 of 253132 triangles, 4v7q_BN SES
surface, 62856 of 271870 triangles, 4v7q_BP SES surface, 83497 of 278692
triangles, 4v7q_BQ SES surface, 70616 of 253052 triangles, 2296 atoms, 59
bonds
> select up
2631 atoms, 2676 bonds, 328 residues, 5 models selected
> select up
3581 atoms, 3654 bonds, 453 residues, 5 models selected
> select up
8416 atoms, 8608 bonds, 1064 residues, 5 models selected
> select up
14742 atoms, 15074 bonds, 1858 residues, 5 models selected
> select down
8416 atoms, 8608 bonds, 1064 residues, 7 models selected
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> select clear
Drag select of 4v7q_BF SES surface, 107268 of 263022 triangles, 4v7q_BG SES
surface, 151612 of 275902 triangles, 4v7q_BH SES surface, 242890 of 251218
triangles, 4v7q_BO SES surface, 96074 of 280222 triangles, 4759 atoms, 87
bonds
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
Drag select of 4v7q_BF SES surface, 51377 of 263022 triangles, 4v7q_BG SES
surface, 54200 of 275902 triangles, 4v7q_BO SES surface, 57840 of 280222
triangles, 4v7q_BY SES surface, 13872 of 717050 triangles, 4v7q_BZ SES
surface, 11089 of 511878 triangles, 1619 atoms
> select up
2132 atoms, 2135 bonds, 259 residues, 6 models selected
> select up
4102 atoms, 4172 bonds, 514 residues, 6 models selected
> select up
12444 atoms, 12708 bonds, 1576 residues, 6 models selected
> select down
4102 atoms, 4172 bonds, 514 residues, 6 models selected
> undo
[Repeated 9 time(s)]Drag select of 256 atoms, 12 bonds
Drag select of 4v7q_BG SES surface, 310 of 275902 triangles, 4v7q_BH SES
surface, 8729 of 251218 triangles, 4v7q_BO SES surface, 25352 of 280222
triangles, 3613 atoms, 80 bonds
> select up
3615 atoms, 3646 bonds, 478 residues, 5 models selected
> select up
3873 atoms, 3937 bonds, 478 residues, 5 models selected
> select up
4846 atoms, 4950 bonds, 611 residues, 5 models selected
> select up
8498 atoms, 8693 bonds, 1071 residues, 5 models selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
Drag select of 29 atoms, 29 bonds
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> select #1/BX:118@O
1 atom, 1 residue, 1 model selected
Drag select of 4v7q_BX SES surface, 570338 of 703936 triangles, 4v7q_BY SES
surface, 551425 of 717050 triangles, 4v7q_BZ SES surface, 11691 atoms, 160
residues, 4 pseudobonds
Drag select of 4v7q_BX SES surface, 703153 of 703936 triangles, 4v7q_BY SES
surface, 595319 of 717050 triangles, 4v7q_BZ SES surface, 13105 atoms, 160
residues, 4 pseudobonds
> select clear
[Repeated 1 time(s)]
> show #!1 atoms
> hide #!1 atoms
> show #!1 surfaces
Drag select of 4v7q_AA SES surface, 740505 of 845108 triangles, 4v7q_AB SES
surface, 4v7q_AC SES surface, 38094 of 345712 triangles, 4v7q_AD SES surface,
73974 of 343138 triangles, 4v7q_AE SES surface, 37416 of 348406 triangles,
4v7q_AF SES surface, 81923 of 345726 triangles, 4v7q_AG SES surface, 126278 of
346434 triangles, 4v7q_AH SES surface, 70372 of 350200 triangles, 4v7q_AI SES
surface, 104259 of 346554 triangles, 4v7q_AJ SES surface, 193058 of 347202
triangles, 4v7q_AK SES surface, 159783 of 348548 triangles, 4v7q_AL SES
surface, 91713 of 344322 triangles, 4v7q_AM SES surface, 169008 of 346762
triangles, 4v7q_AN SES surface, 116155 of 348624 triangles, 4v7q_AO SES
surface, 285758 of 348624 triangles
Drag select of 4v7q_AA SES surface, 808129 of 845108 triangles, 4v7q_AB SES
surface, 4v7q_AC SES surface, 40245 of 345712 triangles, 4v7q_AD SES surface,
76050 of 343138 triangles, 4v7q_AE SES surface, 38982 of 348406 triangles,
4v7q_AF SES surface, 84560 of 345726 triangles, 4v7q_AG SES surface, 128343 of
346434 triangles, 4v7q_AH SES surface, 72384 of 350200 triangles, 4v7q_AI SES
surface, 106791 of 346554 triangles, 4v7q_AJ SES surface, 195579 of 347202
triangles, 4v7q_AK SES surface, 161981 of 348548 triangles, 4v7q_AL SES
surface, 94564 of 344322 triangles, 4v7q_AM SES surface, 171069 of 346762
triangles, 4v7q_AN SES surface, 118217 of 348624 triangles, 4v7q_AO SES
surface, 287678 of 348624 triangles
> hide #!1 surfaces
> undo
[Repeated 1 time(s)]
> show #!1 surfaces
> select clear
Drag select of 4v7q_AA SES surface, 252890 of 845108 triangles, 4v7q_AB SES
surface, 734657 of 865418 triangles, 4v7q_AF SES surface, 46438 of 345726
triangles, 4v7q_AG SES surface, 78820 of 346434 triangles, 4v7q_AH SES
surface, 27601 of 350200 triangles, 4v7q_AI SES surface, 21512 of 346554
triangles, 4v7q_AJ SES surface, 73990 of 347202 triangles, 4v7q_AK SES
surface, 62297 of 348548 triangles, 4v7q_AL SES surface, 79 of 344322
triangles, 4v7q_AM SES surface, 17760 of 346762 triangles, 4v7q_AN SES
surface, 9367 of 348624 triangles, 4v7q_AO SES surface, 73470 of 348624
triangles
> hide #!1 surfaces
> show #!1 surfaces
Drag select of 4v7q_AA SES surface, 410687 of 845108 triangles
> select clear
> select #1/AF:105@OE1
1 atom, 1 residue, 1 model selected
Drag select of 4v7q_AA SES surface, 231245 of 845108 triangles, 4v7q_AF SES
surface, 8502 of 345726 triangles, 4v7q_AG SES surface, 8584 of 346434
triangles
Drag select of 4v7q_AA SES surface, 602616 of 845108 triangles, 4v7q_AB SES
surface, 167480 of 865418 triangles, 4v7q_AF SES surface, 124652 of 345726
triangles, 4v7q_AG SES surface, 61683 of 346434 triangles, 4v7q_AH SES
surface, 19783 of 350200 triangles
Drag select of 4v7q_AA SES surface, 502573 of 845108 triangles, 4v7q_AF SES
surface, 190069 of 345726 triangles, 4v7q_AG SES surface, 179225 of 346434
triangles, 4v7q_AH SES surface, 54163 of 350200 triangles, 4v7q_AI SES
surface, 12531 of 346554 triangles, 4v7q_AJ SES surface, 94863 of 347202
triangles, 4v7q_AK SES surface, 7608 of 348548 triangles, 4v7q_BI SES surface,
36852 of 280590 triangles
> hide #!1 surfaces
> show #!1 surfaces
> select #1/BI:146@N
1 atom, 1 residue, 1 model selected
> select #1/BJ:144@O
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
40 atoms, 40 bonds, 5 residues, 2 models selected
> select up
2171 atoms, 2221 bonds, 274 residues, 2 models selected
> select #1/BI:94@O
1 atom, 1 residue, 1 model selected
Drag select of 4v7q_AA SES surface, 46750 of 845108 triangles
> select #1/AA:121@N
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
220 atoms, 222 bonds, 26 residues, 2 models selected
> select up
6379 atoms, 6495 bonds, 781 residues, 2 models selected
> select up
97287 atoms, 99361 bonds, 12218 residues, 2 models selected
> select down
6379 atoms, 6495 bonds, 781 residues, 32 models selected
> hide sel surfaces
> select #1/AB:116@CG1
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
130 atoms, 131 bonds, 15 residues, 2 models selected
> select up
6545 atoms, 6665 bonds, 800 residues, 2 models selected
> select up
97287 atoms, 99361 bonds, 12218 residues, 2 models selected
> select down
6545 atoms, 6665 bonds, 800 residues, 32 models selected
> hide sel surfaces
> select #1/AE:65@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
108 atoms, 109 bonds, 14 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> select up
97287 atoms, 99361 bonds, 12218 residues, 2 models selected
> select down
3163 atoms, 3233 bonds, 397 residues, 32 models selected
> hide sel surfaces
> select #1/AO:25@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
26 atoms, 26 bonds, 3 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
Drag select of 4v7q_AF SES surface, 19923 of 345726 triangles, 4v7q_AH SES
surface, 37270 of 350200 triangles, 4v7q_BI SES surface, 27341 of 280590
triangles, 4v7q_BK SES surface, 6228 of 272824 triangles
> ui mousemode right select
Drag select of 4v7q_AF SES surface, 45990 of 345726 triangles, 4v7q_AH SES
surface, 9009 of 350200 triangles, 4v7q_BI SES surface, 52712 of 280590
triangles
> select up
88586 atoms, 15 pseudobonds, 11131 residues, 34 models selected
> select up
88604 atoms, 90481 bonds, 15 pseudobonds, 11136 residues, 31 models selected
> select down
88586 atoms, 15 pseudobonds, 11131 residues, 31 models selected
> select up
88604 atoms, 90481 bonds, 15 pseudobonds, 11136 residues, 31 models selected
> select down
88586 atoms, 15 pseudobonds, 11131 residues, 31 models selected
> select clear
Drag select of 4v7q_AF SES surface, 26423 of 345726 triangles, 4v7q_AG SES
surface, 27663 of 346434 triangles, 4v7q_AH SES surface, 29614 of 350200
triangles, 4v7q_BI SES surface, 9586 of 280590 triangles
> select up
85423 atoms, 15 pseudobonds, 10734 residues, 34 models selected
> select clear
> select #1/AC:69@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
108 atoms, 109 bonds, 14 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AN:67@CA
1 atom, 1 residue, 1 model selected
> select #1/AD:44@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
20 atoms, 19 bonds, 3 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/BH:311@OG
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
28 atoms, 27 bonds, 4 residues, 2 models selected
> select up
2011 atoms, 2057 bonds, 255 residues, 2 models selected
> hide sel surfaces
> select #1/AN:57@NH2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
69 atoms, 69 bonds, 10 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AM:216@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
59 atoms, 58 bonds, 7 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AL:16@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
129 atoms, 129 bonds, 16 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AK:106@N
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
108 atoms, 108 bonds, 14 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AJ:72@ND2
1 atom, 1 residue, 1 model selected
> select #1/AG:28@C
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
115 atoms, 115 bonds, 14 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AH:118@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
27 atoms, 26 bonds, 4 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AF:29@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
115 atoms, 115 bonds, 14 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AJ:69@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
108 atoms, 109 bonds, 14 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AI:123@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
28 atoms, 28 bonds, 3 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/BI:308@OE1
1 atom, 1 residue, 1 model selected
> select #1/BK:264@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
142 atoms, 143 bonds, 20 residues, 2 models selected
> select up
2117 atoms, 2164 bonds, 269 residues, 2 models selected
> hide sel surfaces
> select #1/BJ:122@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
15 atoms, 14 bonds, 2 residues, 2 models selected
> select up
2171 atoms, 2221 bonds, 274 residues, 2 models selected
> hide sel surfaces
> select #1/BI:87@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
21 atoms, 20 bonds, 3 residues, 2 models selected
> select up
2160 atoms, 2210 bonds, 273 residues, 2 models selected
> hide sel surfaces
> select #1/BL:144@CE1
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
40 atoms, 40 bonds, 5 residues, 2 models selected
> select up
2148 atoms, 2197 bonds, 272 residues, 2 models selected
> hide sel surfaces
> select #1/BM:266@N
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
142 atoms, 143 bonds, 20 residues, 2 models selected
> select up
2011 atoms, 2057 bonds, 255 residues, 2 models selected
> hide sel surfaces
> select #1/BN:123@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
15 atoms, 14 bonds, 2 residues, 2 models selected
> select up
2179 atoms, 2229 bonds, 275 residues, 2 models selected
> hide sel surfaces
> select #1/BP:172@CD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
122 atoms, 124 bonds, 14 residues, 2 models selected
> select up
2157 atoms, 2206 bonds, 273 residues, 2 models selected
> hide sel surfaces
> select #1/BQ:124@N
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
30 atoms, 30 bonds, 4 residues, 2 models selected
> select up
2011 atoms, 2057 bonds, 255 residues, 2 models selected
> hide sel surfaces
> select #1/BA:91@OG1
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
29 atoms, 28 bonds, 4 residues, 2 models selected
> select up
2011 atoms, 2057 bonds, 255 residues, 2 models selected
> select up
97287 atoms, 99361 bonds, 12218 residues, 2 models selected
> select down
2011 atoms, 2057 bonds, 255 residues, 32 models selected
> hide sel surfaces
> select #1/BG:218@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
30 atoms, 29 bonds, 4 residues, 2 models selected
> select up
2160 atoms, 2210 bonds, 273 residues, 2 models selected
> hide sel surfaces
> select #1/BO:163@N
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> select up
60 atoms, 62 bonds, 7 residues, 2 models selected
> select up
2171 atoms, 2221 bonds, 274 residues, 2 models selected
> hide sel surfaces
> select #1/BF:91@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
29 atoms, 28 bonds, 4 residues, 2 models selected
> select up
2072 atoms, 2118 bonds, 263 residues, 2 models selected
> hide sel surfaces
> select #1/BX:171@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
12 atoms, 11 bonds, 2 residues, 2 models selected
> select up
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> transparency sel 0
Drag select of 4v7q_BX SES surface, 4v7q_BY SES surface, 4v7q_BZ SES surface,
510026 of 511878 triangles, 160 residues
Drag select of 4v7q_BX SES surface, 4v7q_BY SES surface, 4v7q_BZ SES surface,
160 residues
> select #1/BZ:611@NE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
131 atoms, 130 bonds, 16 residues, 2 models selected
> select up
2159 atoms, 2186 bonds, 278 residues, 2 models selected
> select up
2173 atoms, 2199 bonds, 280 residues, 2 models selected
> select up
3829 atoms, 3898 bonds, 488 residues, 2 models selected
> select up
3855 atoms, 3923 bonds, 492 residues, 2 models selected
> select up
4058 atoms, 4128 bonds, 517 residues, 2 models selected
> select up
97287 atoms, 99361 bonds, 12218 residues, 2 models selected
> color (#!1 & sel) light gray
> select 306,384,386,388,393,394,398,429,424,440,441,459
Expected an objects specifier or a keyword
> select clear
> select #1/306,384,386,388,393,394,398,429,424,440,441,459
Nothing selected
> select /BX:1-776
5783 atoms, 5897 bonds, 2 pseudobonds, 735 residues, 2 models selected
> sequence chain #1/BX#1/BY#1/BZ
Alignment identifier is 1
> select #1/BX,BY,BZ:在306,384,386,388,393,394,398,429,424,440,441,459
Expected an objects specifier or a keyword
> select #1/BX,BY,BZ:306,384,386,388,393,394,398,429,424,440,441,459
306 atoms, 282 bonds, 36 residues, 1 model selected
> color (#!1 & sel) red
> select clear
> select #1/BX,BY,BZ:306,384,386,388,393,394,398,429,434,440,441,459
309 atoms, 285 bonds, 36 residues, 1 model selected
> color (#!1 & sel) red
> color (#!1 & sel) cornflower blue
> select clear
> select
> #1/BX,BY,BZ:72,87,88,89,100,114,116,132,133,135,136,146,148,150,180,183,188,190,194,217
296 atoms, 268 bonds, 40 residues, 1 model selected
> color (#!1 & sel) forest green
> select clear
> select #1/BX,BY,BZ:97,98,199,133,195,197
88 atoms, 78 bonds, 12 residues, 1 model selected
> color (#!1 & sel) forest green
> select #1/BX,BY,BZ:109
18 atoms, 16 bonds, 2 residues, 1 model selected
> color (#!1 & sel) forest green
> select clear
> undo
[Repeated 6 time(s)]
> select #1/BX,BY,BZ:97,98,199,133,195,197
88 atoms, 78 bonds, 12 residues, 1 model selected
> color (#!1 & sel) cyan
> select clear
> select #1/BX,BY,BZ:109,389,393,197
83 atoms, 73 bonds, 10 residues, 1 model selected
> select #1/BX,BY,BZ:109,389,393,135
87 atoms, 77 bonds, 10 residues, 1 model selected
> undo
[Repeated 4 time(s)]
> select clear
> select #1/BX,BY,BZ:97,98,199,133,195,197
88 atoms, 78 bonds, 12 residues, 1 model selected
> color (#!1 & sel) forest green
> select #1/BX,BY,BZ:109,105
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #1/BX,BY,BZ:109,135
36 atoms, 32 bonds, 4 residues, 1 model selected
> color (#!1 & sel) forest green
> select #1/BX,BY,BZ:389.393
Expected an objects specifier or a keyword
> select #1/BX,BY,BZ:389,393
51 atoms, 45 bonds, 6 residues, 1 model selected
> color (#!1 & sel) cyan
> color (#!1 & sel) cornflower blue
> select clear
> select #1/BX,BY,BZ:374,266,270,417,463,467
159 atoms, 141 bonds, 18 residues, 1 model selected
> color (#!1 & sel) cornflower blue
> select #1/BX,BY,BZ:51
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/BY:354@CB
1 atom, 1 residue, 1 model selected
> select #1/BY:50@O
1 atom, 1 residue, 1 model selected
> select #1/BY:51@CA
1 atom, 1 residue, 1 model selected
> select #1/BY:421@CD2
1 atom, 1 residue, 1 model selected
> select #1/BX,BY,BZ:40
22 atoms, 22 bonds, 2 residues, 1 model selected
> show #!2 models
> select #1/BX,BY,BZ:51
4 atoms, 3 bonds, 1 residue, 1 model selected
> color (#!1 & sel) cornflower blue
> select #1/BX,BY,BZ:51
4 atoms, 3 bonds, 1 residue, 1 model selected
> color (#!1 & sel) purple
> color (#!1 & sel) cornflower blue
> select #1/BX,BY,BZ:376,464
45 atoms, 39 bonds, 6 residues, 1 model selected
> color (#!1 & sel) cornflower blue
> select add #2
4816 atoms, 4925 bonds, 611 residues, 5 models selected
> show sel cartoons
> select clear
> hide #!1 models
> select #2/E:81
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> show #!1 models
> select #1/BX,BY,BZ:63,64,65,
Expected an objects specifier or a keyword
> select #1/BX,BY,BZ:63,64,65
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/BX,BY,BZ:90
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #1/BX,BY,BZ:128
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/BX,BY,BZ:92
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/BY:110@CD
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
44 atoms, 44 bonds, 6 residues, 2 models selected
> select up
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> select clear
> select #1/BX,BY,BZ:92
14 atoms, 12 bonds, 2 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> show sel surfaces
> select clear
> show surfaces
> undo
Drag select of 4v7q_AF SES surface, 273393 of 345726 triangles, 4v7q_AG SES
surface, 224324 of 346434 triangles, 4v7q_AH SES surface, 194949 of 350200
triangles, 4v7q_AI SES surface, 79291 of 346554 triangles, 4v7q_AJ SES
surface, 100331 of 347202 triangles, 4v7q_BI SES surface, 4v7q_BJ SES surface,
115709 of 278122 triangles, 4v7q_BK SES surface, 95814 of 272824 triangles,
4v7q_BL SES surface, 37555 of 275038 triangles, 4v7q_BM SES surface, 27307 of
248250 triangles
> hide #!2 models
> select #1/BY:190@O
1 atom, 1 residue, 1 model selected
Drag select of 4v7q_AF SES surface, 34461 of 345726 triangles, 4v7q_AG SES
surface, 42829 of 346434 triangles, 4v7q_AH SES surface, 19032 of 350200
triangles, 4v7q_AI SES surface, 60603 of 346554 triangles, 4v7q_AJ SES
surface, 63600 of 347202 triangles, 4v7q_AK SES surface, 42284 of 348548
triangles, 4v7q_BA SES surface, 2750 of 253132 triangles, 4v7q_BI SES surface,
139352 of 280590 triangles, 4v7q_BJ SES surface, 144076 of 278122 triangles,
4v7q_BK SES surface, 90378 of 272824 triangles, 4v7q_BL SES surface, 120177 of
275038 triangles, 4v7q_BM SES surface, 87833 of 248250 triangles, 4v7q_BN SES
surface, 77733 of 271870 triangles, 4v7q_BP SES surface, 2199 of 278692
triangles, 4v7q_BX SES surface, 165 of 703936 triangles
> select #1/BI:112@CB
1 atom, 1 residue, 1 model selected
Drag select of 4v7q_AF SES surface, 12507 of 345726 triangles, 4v7q_AG SES
surface, 5519 of 346434 triangles, 4v7q_AH SES surface, 1536 of 350200
triangles, 4v7q_AI SES surface, 8441 of 346554 triangles, 4v7q_AJ SES surface,
10362 of 347202 triangles, 4v7q_BI SES surface, 10941 of 280590 triangles,
4v7q_BJ SES surface, 5419 of 278122 triangles, 4v7q_BL SES surface, 4272 of
275038 triangles
Drag select of 4v7q_AF SES surface, 180311 of 345726 triangles, 4v7q_AG SES
surface, 121174 of 346434 triangles, 4v7q_AH SES surface, 64903 of 350200
triangles, 4v7q_AI SES surface, 115186 of 346554 triangles, 4v7q_AJ SES
surface, 170270 of 347202 triangles, 4v7q_AK SES surface, 5885 of 348548
triangles, 4v7q_BI SES surface, 174165 of 280590 triangles, 4v7q_BJ SES
surface, 94873 of 278122 triangles, 4v7q_BK SES surface, 30414 of 272824
triangles, 4v7q_BL SES surface, 40889 of 275038 triangles, 4v7q_BM SES
surface, 71601 of 248250 triangles
> hide #!1 surfaces
> show #!1 surfaces
> select #1/AA:283@N
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
85 atoms, 85 bonds, 10 residues, 2 models selected
> select up
6379 atoms, 6495 bonds, 781 residues, 2 models selected
> hide sel surfaces
> select #1/AB:179@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
68 atoms, 69 bonds, 8 residues, 2 models selected
> select up
6545 atoms, 6665 bonds, 800 residues, 2 models selected
> hide sel surfaces
> select #1/AN:25@CA
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
26 atoms, 26 bonds, 3 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> select up
3164 atoms, 3233 bonds, 398 residues, 2 models selected
> select up
97287 atoms, 99361 bonds, 12218 residues, 2 models selected
> select down
3164 atoms, 3233 bonds, 398 residues, 32 models selected
> hide sel surfaces
> select #1/AJ:32@NE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
115 atoms, 115 bonds, 14 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> select up
97287 atoms, 99361 bonds, 12218 residues, 2 models selected
> select down
3163 atoms, 3233 bonds, 397 residues, 32 models selected
> hide sel surfaces
> select #1/AF:58@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
41 atoms, 42 bonds, 4 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AH:283@O
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
38 atoms, 38 bonds, 4 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AG:156@ND2
1 atom, 1 residue, 1 model selected
> select #1/AG:339@CA
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
70 atoms, 69 bonds, 10 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AI:40@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
115 atoms, 115 bonds, 14 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> select up
97287 atoms, 99361 bonds, 12218 residues, 2 models selected
> select down
3163 atoms, 3233 bonds, 397 residues, 32 models selected
> hide sel surfaces
> select #1/BI:99@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
95 atoms, 97 bonds, 11 residues, 2 models selected
> select up
2160 atoms, 2210 bonds, 273 residues, 2 models selected
> select up
97287 atoms, 99361 bonds, 12218 residues, 2 models selected
> select down
2160 atoms, 2210 bonds, 273 residues, 32 models selected
> hide sel surfaces
> select #1/BJ:263@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
31 atoms, 30 bonds, 4 residues, 2 models selected
> select up
2171 atoms, 2221 bonds, 274 residues, 2 models selected
> hide sel surfaces
> select #1/BK:242@CA
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
33 atoms, 32 bonds, 5 residues, 2 models selected
> select up
2117 atoms, 2164 bonds, 269 residues, 2 models selected
> hide sel surfaces
> select #1/BL:164@O
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
29 atoms, 29 bonds, 4 residues, 2 models selected
> select up
2148 atoms, 2197 bonds, 272 residues, 2 models selected
> hide sel surfaces
> select #1/AK:340@CG
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
88 atoms, 87 bonds, 13 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AO:118@O
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
50 atoms, 49 bonds, 6 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/BM:122@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
15 atoms, 14 bonds, 2 residues, 2 models selected
> select up
2011 atoms, 2057 bonds, 255 residues, 2 models selected
> hide sel surfaces
> select #1/BN:154@OE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
85 atoms, 84 bonds, 11 residues, 2 models selected
> select up
2179 atoms, 2229 bonds, 275 residues, 2 models selected
> hide sel surfaces
> select #1/AL:40@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
115 atoms, 115 bonds, 14 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AM:42@ND2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
20 atoms, 19 bonds, 3 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/BQ:145@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
40 atoms, 40 bonds, 5 residues, 2 models selected
> select up
2011 atoms, 2057 bonds, 255 residues, 2 models selected
> hide sel surfaces
> select #1/BA:189@O
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
25 atoms, 24 bonds, 4 residues, 2 models selected
> select up
2011 atoms, 2057 bonds, 255 residues, 2 models selected
> hide sel surfaces
> select #1/AC:51@CB
1 atom, 1 residue, 1 model selected
> select #1/AC:118@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
50 atoms, 49 bonds, 6 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> select up
3164 atoms, 3233 bonds, 398 residues, 2 models selected
> hide sel surfaces
> select #1/AE:33@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
115 atoms, 115 bonds, 14 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/AD:353@OH
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
75 atoms, 79 bonds, 10 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> hide sel surfaces
> select #1/BG:220@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
30 atoms, 29 bonds, 4 residues, 2 models selected
> select up
2160 atoms, 2210 bonds, 273 residues, 2 models selected
> hide sel surfaces
> select #1/BH:123@OD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
15 atoms, 14 bonds, 2 residues, 2 models selected
> select up
2011 atoms, 2057 bonds, 255 residues, 2 models selected
> hide sel surfaces
> select #1/BF:147@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
40 atoms, 40 bonds, 5 residues, 2 models selected
> select up
2072 atoms, 2118 bonds, 263 residues, 2 models selected
> hide sel surfaces
> select #1/BP:225@CG1
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
30 atoms, 29 bonds, 4 residues, 2 models selected
> select up
2157 atoms, 2206 bonds, 273 residues, 2 models selected
> hide sel surfaces
> select #1/BO:290@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
40 atoms, 41 bonds, 4 residues, 2 models selected
> select up
2171 atoms, 2221 bonds, 274 residues, 2 models selected
> hide sel surfaces
> select #1/BZ:603@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
75 atoms, 74 bonds, 11 residues, 2 models selected
> select up
2159 atoms, 2186 bonds, 278 residues, 2 models selected
> select up
2173 atoms, 2199 bonds, 280 residues, 2 models selected
> select up
3829 atoms, 3898 bonds, 488 residues, 2 models selected
> select up
3855 atoms, 3923 bonds, 492 residues, 2 models selected
> select up
4058 atoms, 4128 bonds, 517 residues, 2 models selected
> select up
97287 atoms, 99361 bonds, 12218 residues, 2 models selected
> select clear
[Repeated 1 time(s)]
> ui mousemode right rotate
> select #1/BX-BZ:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/BX-BZ:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/BX-BZ:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/BX-BZ
15650 atoms, 15950 bonds, 6 pseudobonds, 1990 residues, 2 models selected
> ui mousemode right select
> select clear
> select #1/BY:146@CB
1 atom, 1 residue, 1 model selected
> select #1/BY:148@N
1 atom, 1 residue, 1 model selected
> select #1/BY:147@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
53 atoms, 53 bonds, 7 residues, 2 models selected
> select up
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> select #1/BX-BZ:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/BX-BZ
15650 atoms, 15950 bonds, 6 pseudobonds, 1990 residues, 2 models selected
> select #1/BX-BZ:752-776
651 atoms, 654 bonds, 75 residues, 1 model selected
> select #1/BX-BZ:401-776
8612 atoms, 8737 bonds, 1 pseudobond, 1103 residues, 2 models selected
> select #1/BX-BZ:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/BX-BZ
15650 atoms, 15950 bonds, 6 pseudobonds, 1990 residues, 2 models selected
> select #1/BX-BZ:752-776
651 atoms, 654 bonds, 75 residues, 1 model selected
> select #1/BX-BZ
15650 atoms, 15950 bonds, 6 pseudobonds, 1990 residues, 2 models selected
> select #1/BX-BZ:752-776
651 atoms, 654 bonds, 75 residues, 1 model selected
> select #1/BX-BZ
15650 atoms, 15950 bonds, 6 pseudobonds, 1990 residues, 2 models selected
> select #1/BX-BZ:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/BX-BZ
15650 atoms, 15950 bonds, 6 pseudobonds, 1990 residues, 2 models selected
> select clear
> select #1/BX-BZ:752-776
651 atoms, 654 bonds, 75 residues, 1 model selected
> select #1/BX-BZ:405-430
636 atoms, 648 bonds, 78 residues, 1 model selected
> select #1/BX-BZ:405-430
636 atoms, 648 bonds, 78 residues, 1 model selected
> select #1/BX-BZ:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/BX-BZ
15650 atoms, 15950 bonds, 6 pseudobonds, 1990 residues, 2 models selected
> show #!2 models
> sequence chain #2/E
Alignment identifier is 2/E
> select #2/E:198
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/E
1283 atoms, 1318 bonds, 158 residues, 1 model selected
> hide #!2 models
> select #1/BZ:424@CD2
1 atom, 1 residue, 1 model selected
> color (#!1 & sel) light gray
> select clear
> open 7ums
Summary of feedback from opening 7ums fetched from pdb
---
warnings | Atom H1 is not in the residue template for MET /A:1
Atom H1 is not in the residue template for MET /B:1
Atom H1 is not in the residue template for MET /C:1
Atom H1 is not in the residue template for MET /D:1
Atom H1 is not in the residue template for MET /E:1
4 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
note | Fetching compressed mmCIF 7ums from
http://files.rcsb.org/download/7ums.cif
7ums title:
Structure of the VP5*/VP8* assembly from the human rotavirus strain CDC-9 in
complex with antibody 41 - Upright conformation [more info...]
Chain information for 7ums #3
---
Chain | Description | UniProt
1 2 3 | Outer capsid protein VP5* | X4YMN0_9REOV 247-775
4 6 | Fab 41 heavy chain |
5 7 | Fab 41 light chain |
A B C D E F G H I J K L M N O P Q R | Intermediate capsid protein VP6 |
A0A223GHC7_9REOV 1-397
T U V | Outer capsid protein VP8* | X4YMN0_9REOV 1-230
a b c d e f g h i j k l m n o p q r | Outer capsid glycoprotein VP7 |
B1NP55_9REOV 1-326
Non-standard residues in 7ums #3
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
CA — calcium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7ums
Summary of feedback from opening 7ums fetched from pdb
---
warnings | Atom H1 is not in the residue template for MET /A:1
Atom H1 is not in the residue template for MET /B:1
Atom H1 is not in the residue template for MET /C:1
Atom H1 is not in the residue template for MET /D:1
Atom H1 is not in the residue template for MET /E:1
4 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
7ums title:
Structure of the VP5*/VP8* assembly from the human rotavirus strain CDC-9 in
complex with antibody 41 - Upright conformation [more info...]
Chain information for 7ums #4
---
Chain | Description | UniProt
1 2 3 | Outer capsid protein VP5* | X4YMN0_9REOV 247-775
4 6 | Fab 41 heavy chain |
5 7 | Fab 41 light chain |
A B C D E F G H I J K L M N O P Q R | Intermediate capsid protein VP6 |
A0A223GHC7_9REOV 1-397
T U V | Outer capsid protein VP8* | X4YMN0_9REOV 1-230
a b c d e f g h i j k l m n o p q r | Outer capsid glycoprotein VP7 |
B1NP55_9REOV 1-326
Non-standard residues in 7ums #4
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
CA — calcium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> hide #!1,3-4 atoms
> show #!1,3-4 cartoons
> select #3/U:177
17 atoms, 17 bonds, 1 residue, 1 model selected
> select up
137 atoms, 140 bonds, 8 residues, 1 model selected
> select up
3553 atoms, 3602 bonds, 227 residues, 1 model selected
> select #4/U:2-228
3553 atoms, 3602 bonds, 227 residues, 1 model selected
> sequence chain #4/T#4/U#4/V
Alignment identifier is 2
> select #4/T-V
7507 atoms, 7607 bonds, 479 residues, 1 model selected
> select clear
> close #4
> select add #3
236285 atoms, 238902 bonds, 368 pseudobonds, 15030 residues, 3 models selected
Drag select of 25 residues
> select add #3
236285 atoms, 238902 bonds, 368 pseudobonds, 15030 residues, 3 models selected
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-141.61,0,1,0,-69.682,0,0,1,105.91
> select subtract #3
Nothing selected
> ui mousemode right select
> select #3/2:302
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/2:302
21 atoms, 21 bonds, 1 residue, 1 model selected
Drag select of 259 residues
> select up
4241 atoms, 4290 bonds, 290 residues, 1 model selected
> select up
6598 atoms, 6691 bonds, 447 residues, 1 model selected
> hide sel cartoons
Drag select of 247 residues
> select up
4019 atoms, 4063 bonds, 277 residues, 1 model selected
> select up
6598 atoms, 6691 bonds, 447 residues, 1 model selected
> hide sel cartoons
> select clear
> select #3/2:392
10 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]Drag select of 540 residues
> select clear
Drag select of 1542 residues
> select up
30505 atoms, 30795 bonds, 1922 residues, 1 model selected
> select up
55314 atoms, 55941 bonds, 3487 residues, 1 model selected
> select up
55330 atoms, 55941 bonds, 3503 residues, 1 model selected
> select up
236285 atoms, 238902 bonds, 15030 residues, 1 model selected
> select down
55330 atoms, 55941 bonds, 3503 residues, 1 model selected
> hide sel cartoons
Drag select of 1756 residues
> select up
34086 atoms, 34417 bonds, 2138 residues, 1 model selected
> select up
62565 atoms, 63262 bonds, 3940 residues, 1 model selected
> select up
67524 atoms, 68256 bonds, 4275 residues, 1 model selected
> select down
62565 atoms, 63262 bonds, 3940 residues, 1 model selected
> select up
67524 atoms, 68256 bonds, 4275 residues, 1 model selected
> select down
62565 atoms, 63262 bonds, 3940 residues, 1 model selected
> hide sel cartoons
Drag select of 209 residues
> select up
3680 atoms, 3719 bonds, 231 residues, 1 model selected
> select up
4413 atoms, 4465 bonds, 278 residues, 1 model selected
> hide sel cartoons
Drag select of 192 residues
> select up
11198 atoms, 11275 bonds, 706 residues, 1 model selected
> select up
44663 atoms, 45174 bonds, 2817 residues, 1 model selected
> hide sel cartoons
Drag select of 98 residues
> select up
2355 atoms, 2381 bonds, 148 residues, 1 model selected
> select up
8826 atoms, 8930 bonds, 556 residues, 1 model selected
> hide sel cartoons
Drag select of 571 residues
> select clear
Drag select of 163 residues
> select up
3942 atoms, 3964 bonds, 246 residues, 1 model selected
> select up
18886 atoms, 19096 bonds, 1191 residues, 1 model selected
> hide sel cartoons
Drag select of 884 residues
Drag select of 1792 residues, 2 pseudobonds
> select clear
Drag select of 1792 residues, 2 pseudobonds
> show sel surfaces
> color (#!3 & sel) light gray
> select up
31054 atoms, 31370 bonds, 2 pseudobonds, 1963 residues, 8 models selected
> select down
28274 atoms, 2 pseudobonds, 1792 residues, 8 models selected
> select #1/1,2,3:306,384,386,388,393,394,398,429,434,440,441,459
Nothing selected
> select #3/2:300@CE1
1 atom, 1 residue, 1 model selected
> select #3/1,2,3:306,384,386,388,393,394,398,429,434,440,441,459
645 atoms, 633 bonds, 36 residues, 1 model selected
> color (#!3 & sel) cornflower blue
> select clear
> select #3/1:247-775
7914 atoms, 7986 bonds, 1 pseudobond, 499 residues, 2 models selected
> sequence chain #3/1#3/2#3/3
Alignment identifier is 2
> select clear
> select #1/BX-BZ
15650 atoms, 15950 bonds, 6 pseudobonds, 1990 residues, 2 models selected
> select #1/BX-BZ
15650 atoms, 15950 bonds, 6 pseudobonds, 1990 residues, 2 models selected
> select clear
> select #1/BX-BZ
15650 atoms, 15950 bonds, 6 pseudobonds, 1990 residues, 2 models selected
> select #1/BX-BZ
15650 atoms, 15950 bonds, 6 pseudobonds, 1990 residues, 2 models selected
> select #1/BX-BZ
15650 atoms, 15950 bonds, 6 pseudobonds, 1990 residues, 2 models selected
> select #1/BX-BZ
15650 atoms, 15950 bonds, 6 pseudobonds, 1990 residues, 2 models selected
> select clear
> select #3/2:304@CA
1 atom, 1 residue, 1 model selected
> select /BY:1-776
5809 atoms, 5925 bonds, 2 pseudobonds, 738 residues, 2 models selected
> sequence chain #1/BX#1/BY#1/BZ
Alignment identifier is 1
Drag select of 633 residues
> select up
7333 atoms, 7440 bonds, 915 residues, 5 models selected
> select up
15868 atoms, 16194 bonds, 1972 residues, 5 models selected
> select up
15869 atoms, 16194 bonds, 1973 residues, 5 models selected
> hide sel cartoons
Drag select of 581 residues
> select up
5424 atoms, 5534 bonds, 688 residues, 6 models selected
> select up
10607 atoms, 10849 bonds, 1343 residues, 6 models selected
> select up
10621 atoms, 10863 bonds, 1344 residues, 6 models selected
> hide sel cartoons
Drag select of 652 residues
> select up
7799 atoms, 7906 bonds, 964 residues, 6 models selected
> select up
19197 atoms, 19597 bonds, 2388 residues, 6 models selected
> select up
19199 atoms, 19597 bonds, 2390 residues, 6 models selected
> hide sel cartoons
Drag select of 249 residues
> select up
2738 atoms, 2764 bonds, 342 residues, 4 models selected
> select up
9489 atoms, 9699 bonds, 1191 residues, 4 models selected
> select up
9490 atoms, 9699 bonds, 1192 residues, 4 models selected
> hide sel cartoons
Drag select of 105 residues
> select up
1207 atoms, 1227 bonds, 156 residues, 4 models selected
> select up
6347 atoms, 6492 bonds, 803 residues, 4 models selected
> hide sel cartoons
Drag select of 88 residues
> select up
1270 atoms, 1285 bonds, 155 residues, 3 models selected
> select up
6326 atoms, 6466 bonds, 794 residues, 3 models selected
> select up
97287 atoms, 99361 bonds, 12218 residues, 3 models selected
> select down
6326 atoms, 6466 bonds, 794 residues, 32 models selected
> hide sel cartoons
Drag select of 36 residues
> select up
378 atoms, 381 bonds, 48 residues, 2 models selected
> select up
3163 atoms, 3233 bonds, 397 residues, 2 models selected
> select up
3164 atoms, 3233 bonds, 398 residues, 2 models selected
> hide sel cartoons
Drag select of 81 residues
> select up
1189 atoms, 1207 bonds, 156 residues, 5 models selected
> select up
8353 atoms, 8545 bonds, 1057 residues, 5 models selected
> hide sel cartoons
Drag select of 15 residues
> select up
271 atoms, 280 bonds, 32 residues, 2 models selected
> select up
2072 atoms, 2118 bonds, 263 residues, 2 models selected
> hide sel cartoons
> select #3/2:688@HD3
1 atom, 1 residue, 1 model selected
Drag select of 7ums_1 SES surface, 622557 of 627392 triangles, 7ums_2 SES
surface, 630937 of 646866 triangles, 7ums_3 SES surface, 337694 of 558052
triangles, 7ums_T SES surface, 309465 of 332100 triangles, 7ums_U SES surface,
328212 of 331002 triangles, 7ums_V SES surface, 1768 residues, 2 pseudobonds
> select clear
Drag select of 4v7q_BX SES surface, 4v7q_BY SES surface, 4v7q_BZ SES surface,
1990 residues, 6 pseudobonds
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.89335,0.38688,0.22859,-77.591,-0.36339,0.92121,-0.13896,-54.616,-0.26434,0.041069,0.96355,-55.208
> view matrix models
> #1,0.48749,0.78109,0.3902,-178.77,-0.66822,0.6214,-0.40908,132.93,-0.562,-0.061318,0.82486,43.729
> view matrix models
> #1,0.57606,-0.63277,-0.51745,431.79,0.72613,0.68684,-0.031516,-146.31,0.37535,-0.35758,0.85513,6.776
> view matrix models
> #1,0.98963,-0.1189,-0.080609,128.05,0.12119,0.99234,0.024045,-173.32,0.077133,-0.033565,0.99646,-83.852
> view matrix models
> #1,0.73165,-0.53839,-0.41811,360.82,0.59749,0.80177,0.013129,-176.15,0.32816,-0.25942,0.9083,-29.862
> view matrix models
> #1,0.99894,-0.038432,-0.025505,89.272,0.038666,0.99921,0.0087614,-168.71,0.025149,-0.0097383,0.99964,-90.132
> view matrix models
> #1,0.33487,-0.70633,-0.62366,505.7,0.85282,0.50866,-0.11818,-97.011,0.40071,-0.49229,0.77271,56.9
> view matrix models
> #1,-0.79396,0.60716,-0.031554,126.58,-0.21207,-0.32521,-0.92156,463.36,-0.56979,-0.72498,0.38696,334.09
> view matrix models
> #1,0.99999,0.002988,0.0019617,75.147,-0.0029866,0.99999,-0.0007196,-173.24,-0.0019637,0.00071401,1,-96.495
> ui mousemode right "rotate selected models"
> select
> #1/T,U,V:72,87,88,89,100,114,116,132,133,135,136,146,148,150,180,183,188,190,194,217
Nothing selected
> select
> #3/T,U,V:72,87,88,89,100,114,116,132,133,135,136,146,148,150,180,183,188,190,194,217
554 atoms, 524 bonds, 40 residues, 1 model selected
> select
> #1/:BX,BY,BZ,100,114,116,132,133,135,136,146,148,150,180,183,188,190,194,217
Expected an objects specifier or a keyword
> select
> #1/:BX,BY,BZ:72,87,88,89,100,114,116,132,133,135,136,146,148,150,180,183,188,190,194,217
Expected an objects specifier or a keyword
> select
> #1/:BX,BY,BZ:72,87,88,89,100,114,116,132,133,135,136,146,148,150,180,183,188,190,194,217
Expected an objects specifier or a keyword
> select
> #1/BX,BY,BZ:72,87,88,89,100,114,116,132,133,135,136,146,148,150,180,183,188,190,194,217
296 atoms, 268 bonds, 40 residues, 1 model selected
> view matrix models
> #1,0.97197,-0.20514,-0.11483,167.61,0.20392,0.97873,-0.022336,-191.58,0.11697,-0.0017055,0.99313,-111.22
> hide #!3 models
> view matrix models
> #1,0.042888,-0.75055,0.65942,309.34,0.84536,0.37903,0.37643,-167.94,-0.53247,0.5413,0.65074,-127.14
> view matrix models
> #1,0.25263,-0.93839,0.23581,424.47,0.90109,0.31696,0.29593,-139.89,-0.35244,0.13773,0.92564,-78.857
> select /BX:1-776
5783 atoms, 5897 bonds, 2 pseudobonds, 735 residues, 2 models selected
> sequence chain #1/BX#1/BY#1/BZ
Alignment identifier is 1
> sequence chain #2/E
Alignment identifier is 2/E
> select #2/E:198
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/E
1283 atoms, 1318 bonds, 158 residues, 1 model selected
> select #1/BX,BY,BZ:66,68,69,72,75
84 atoms, 80 bonds, 10 residues, 1 model selected
> ui tool show "Color Actions"
> color sel teal
> view matrix models
> #1,0.25013,-0.94168,0.22509,427.95,0.91121,0.30754,0.27406,-133.97,-0.3273,0.13656,0.935,-83.672
> ui mousemode right select
> select clear
> undo
[Repeated 3 time(s)]
> select clear
> show #!2 models
Drag select of VP8_6D8_5F10-ini-coot-36.pdb_A SES surface, 45576 of 104150
triangles, VP8_6D8_5F10-ini-coot-36.pdb_D SES surface, 65701 of 95130
triangles, 132 residues
> select up
1661 atoms, 1700 bonds, 214 residues, 3 models selected
> hide sel surfaces
> hide sel cartoons
Drag select of VP8_6D8_5F10-ini-coot-36.pdb_A SES surface, 1184 of 104150
triangles, 4 residues
> select up
48 atoms, 48 bonds, 6 residues, 2 models selected
> select up
919 atoms, 941 bonds, 118 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
Drag select of VP8_6D8_5F10-ini-coot-36.pdb_B SES surface, 15662 of 96002
triangles, VP8_6D8_5F10-ini-coot-36.pdb_C SES surface, 8405 of 109430
triangles, 42 residues
> select up
747 atoms, 761 bonds, 94 residues, 3 models selected
> select up
1744 atoms, 1782 bonds, 223 residues, 3 models selected
> hide sel surfaces
> hide sel cartoons
Drag select of 4v7q_BX SES surface, 3906 of 703936 triangles, 4 residues
Drag select of 4v7q_BX SES surface, 20075 of 703936 triangles, 47 residues
> select up
494 atoms, 505 bonds, 62 residues, 2 models selected
> select up
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> hide sel surfaces
Drag select of VP8_6D8_5F10-ini-coot-36.pdb_E SES surface, 7816 of 139434
triangles, 13 residues
> select up
216 atoms, 223 bonds, 26 residues, 2 models selected
> select up
1283 atoms, 1318 bonds, 158 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> select clear
Drag select of 3 residues
Drag select of 72 residues
> select up
785 atoms, 804 bonds, 95 residues, 2 models selected
> select up
1283 atoms, 1318 bonds, 158 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.20381,0.56946,0.79635,108.36,-0.43173,-0.78234,0.44895,310.88,0.87868,-0.2523,0.4053,29.852
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.78237,0.43715,-0.44363,365.26,0.29715,-0.36399,-0.88273,331.79,-0.54736,-0.82244,0.15488,328.98
> view matrix models
> #2,-0.63528,0.50653,-0.58296,354.6,0.5649,-0.20994,-0.79801,264.22,-0.5266,-0.83627,-0.15277,368.46
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.63528,0.50653,-0.58296,301.8,0.5649,-0.20994,-0.79801,309.26,-0.5266,-0.83627,-0.15277,340.69
> view matrix models
> #2,-0.63528,0.50653,-0.58296,287.59,0.5649,-0.20994,-0.79801,286.44,-0.5266,-0.83627,-0.15277,331.06
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.32238,0.33197,-0.88649,310.14,0.68088,-0.56927,-0.46079,276.39,-0.65762,-0.75215,-0.042506,322.31
> view matrix models
> #2,-0.84408,0.0075404,-0.53616,377.6,0.43222,-0.5822,-0.68864,340.78,-0.31734,-0.81301,0.48817,216.31
> view matrix models
> #2,-0.078784,0.98321,-0.16461,93.892,-0.31178,0.13254,0.94086,127.01,0.94688,0.12545,0.29611,-54.171
> view matrix models
> #2,-0.27345,0.95763,0.090392,89.648,-0.58316,-0.23978,0.77617,235.55,0.76495,0.15953,0.62402,-77.852
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.27345,0.95763,0.090392,87.069,-0.58316,-0.23978,0.77617,228.5,0.76495,0.15953,0.62402,-70.841
> view matrix models
> #2,-0.27345,0.95763,0.090392,82.855,-0.58316,-0.23978,0.77617,235.21,0.76495,0.15953,0.62402,-79.333
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.20009,0.9729,-0.11586,45.383,-0.54622,0.20893,0.81117,164.04,0.8134,-0.099019,0.57322,-43.502
> view matrix models
> #2,0.335,0.94105,0.046963,10.654,-0.52641,0.14559,0.83767,166.67,0.78145,-0.30534,0.54415,-7.1087
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.335,0.94105,0.046963,15.144,-0.52641,0.14559,0.83767,162.04,0.78145,-0.30534,0.54415,-0.57824
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.30142,0.87786,0.37217,-14.353,-0.46264,-0.20665,0.86213,198.87,0.83373,-0.43205,0.34384,36.206
> view matrix models
> #2,0.52616,0.73771,0.42302,-31.353,-0.40308,-0.22166,0.88791,189.71,0.74879,-0.63769,0.18073,97.053
> view matrix models
> #2,0.41185,0.79358,0.4479,-27.234,-0.42968,-0.26433,0.86343,202.29,0.80359,-0.54805,0.23212,70.77
> view matrix models
> #2,0.49065,0.67934,0.54568,-34.718,-0.40843,-0.37388,0.8327,218.58,0.76971,-0.63143,0.094016,104.8
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4v7q, chain BX (#1) with VP8_6D8_5F10-ini-coot-36.pdb, chain E
(#2), sequence alignment score = 468.6
RMSD between 150 pruned atom pairs is 1.007 angstroms; (across all 158 pairs:
1.227)
> hide sel surfaces
> hide sel cartoons
> show sel surfaces
> transparency sel 75 surfaces
> transparency #2/E：41,42,43,44,45,46,47,48,49,50,51,53,180,182
Missing or invalid "percent" argument: Expected a number
> transparency #2/E:41,42,43,44,45,46,47,48,49,50,51,53,180,182
Missing or invalid "percent" argument: Expected a number
> select #2/E:41,42,43,44,45,46,47,48,49,50,51,53,180,182
113 atoms, 115 bonds, 14 residues, 1 model selected
> color sel teal surfaces
> select up
188 atoms, 196 bonds, 23 residues, 2 models selected
> ui mousemode right select
> select #2/E:190@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
75 atoms, 75 bonds, 9 residues, 2 models selected
> select up
1283 atoms, 1318 bonds, 158 residues, 2 models selected
> transparency sel 50
> select clear
> ui mousemode right clip
[Repeated 1 time(s)]
> ui mousemode right "clip rotate"
> ui mousemode right zone
> ui tool show "Side View"
> zone #2/E:170
> zone label false
> zone #2/E:170 residueDistance 3.62 labelDistance 2.89 surfaceDistance 5.79
> zone label false
> zone #2/A:68
> zone #2/A:82
> undo
[Repeated 1 time(s)]
> ui mousemode right zone
> ui mousemode right clip
> ui mousemode right select
Drag select of 75 residues
> select up
892 atoms, 911 bonds, 113 residues, 3 models selected
> select up
1744 atoms, 1786 bonds, 224 residues, 3 models selected
> hide sel cartoons
Drag select of 47 atoms
> hide sel atoms
Drag select of 7 atoms
> hide sel atoms
> select #2/E:188@CD
1 atom, 1 residue, 1 model selected
> select #1/B,C
56 atoms, 58 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #2/B,C
1744 atoms, 1782 bonds, 223 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> select #2/e
1283 atoms, 1318 bonds, 158 residues, 1 model selected
> hide sel cartoons
> select clear
> select
> #2/e:63,64.65,85,86,87,88,89,91,92,93,94,103,108,109,111,112,113,136,138
Expected an objects specifier or a keyword
> select
> #2/e:63,64,65,85,86,87,88,89,91,92,93,94,103,108,109,111,112,113,136,138
174 atoms, 170 bonds, 20 residues, 1 model selected
> color sel darkred organge s
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel dark orange surfaces
> select clear
[Repeated 1 time(s)]
> select #2/e:90,92,94,100,102,103,104,105,116,118,122,124,125,126,127,128,129
149 atoms, 144 bonds, 17 residues, 1 model selected
> color (#!2 & sel) magenta
> select clear
> save "/home/laiqi@nidvd.org/AAA_model/RV ab complex/rv/view02.cxs"
——— End of log from Fri Mar 21 20:35:31 2025 ———
opened ChimeraX session
> select #2/E:189@CB
1 atom, 1 residue, 1 model selected
> select #2/E:190@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
75 atoms, 75 bonds, 9 residues, 2 models selected
> select up
1283 atoms, 1318 bonds, 158 residues, 2 models selected
> color (#!2 & sel) light gray
> transparency sel 50
> select #2/e:42,44,45,46,48,51
50 atoms, 48 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
> color sel teal
> select clear
> select #2/e:90,100,102,103,105,125,126,128,129
79 atoms, 75 bonds, 9 residues, 1 model selected
> color (#!2 & sel) magenta
> select #2/e:65,85,89,92,93,94,108,109,111,138
88 atoms, 81 bonds, 10 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select #2/e:63,65,87,92,94,138
54 atoms, 49 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select #2/E:190@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
75 atoms, 75 bonds, 9 residues, 2 models selected
> select up
1283 atoms, 1318 bonds, 158 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> select clear
> select #2/E:165
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/E:163
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #2/E:192
20 atoms, 17 bonds, 3 residues, 2 models selected
> select add #2/E:158
31 atoms, 27 bonds, 4 residues, 2 models selected
> select add #2/E:170
39 atoms, 34 bonds, 5 residues, 2 models selected
> select add #2/E:172
47 atoms, 41 bonds, 6 residues, 2 models selected
> select add #2/E:174
55 atoms, 48 bonds, 7 residues, 2 models selected
> select add #2/E:49
62 atoms, 54 bonds, 8 residues, 2 models selected
> select subtract #2/E:49
55 atoms, 48 bonds, 7 residues, 2 models selected
> select add #1/BX:72
62 atoms, 54 bonds, 8 residues, 3 models selected
> select subtract #1/BX:72
55 atoms, 48 bonds, 7 residues, 3 models selected
> select add #2/E:48
62 atoms, 54 bonds, 8 residues, 2 models selected
> select add #2/E:74
70 atoms, 61 bonds, 9 residues, 2 models selected
> select add #2/E:123
76 atoms, 66 bonds, 10 residues, 2 models selected
> select add #2/E:121
82 atoms, 71 bonds, 11 residues, 2 models selected
> select add #2/E:125
90 atoms, 78 bonds, 12 residues, 2 models selected
> select add #2/E:92
98 atoms, 85 bonds, 13 residues, 2 models selected
> select add #2/E:90
105 atoms, 92 bonds, 14 residues, 2 models selected
> select add #2/E:109
113 atoms, 99 bonds, 15 residues, 2 models selected
> select add #2/E:108
121 atoms, 106 bonds, 16 residues, 2 models selected
> select add #2/E:111
129 atoms, 113 bonds, 17 residues, 2 models selected
> select add #2/E:65
137 atoms, 120 bonds, 18 residues, 2 models selected
> select add #2/E:64
144 atoms, 126 bonds, 19 residues, 2 models selected
> select add #2/E:63
152 atoms, 133 bonds, 20 residues, 2 models selected
> color (#!2 & sel) forest green
> select
338343 atoms, 343149 bonds, 383 pseudobonds, 27853 residues, 8 models selected
> select #2/E
1283 atoms, 1318 bonds, 158 residues, 1 model selected
> show sel surfaces
> transparency sel 0
> undo
[Repeated 9 time(s)]
> select clear
> select #2/E:124@OE1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
66 atoms, 66 bonds, 8 residues, 2 models selected
> select up
1283 atoms, 1318 bonds, 158 residues, 2 models selected
> hide sel surfaces
> select clear
> select #1/BX:151
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/BX:153
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #1/BX:154
21 atoms, 18 bonds, 3 residues, 2 models selected
> select add #1/BX:124
28 atoms, 24 bonds, 4 residues, 2 models selected
> select add #1/BX:126
37 atoms, 32 bonds, 5 residues, 2 models selected
> select add #1/BX:127
46 atoms, 40 bonds, 6 residues, 2 models selected
> select add #1/BX:129
53 atoms, 46 bonds, 7 residues, 2 models selected
> color (#!1 & sel) magenta
> select add #1/BX:118
59 atoms, 51 bonds, 8 residues, 2 models selected
> select add #1/BX:111
67 atoms, 58 bonds, 9 residues, 2 models selected
> select add #1/BX:163
76 atoms, 66 bonds, 10 residues, 2 models selected
> color (#!1 & sel) medium blue
> undo
> select #1/BY:289@OH
1 atom, 1 residue, 1 model selected
> select add #1/BX:118
7 atoms, 5 bonds, 2 residues, 2 models selected
> select add #1/BX:111
15 atoms, 12 bonds, 3 residues, 3 models selected
> select add #1/BX:163
24 atoms, 20 bonds, 4 residues, 3 models selected
> color (#!1 & sel) medium blue
> select #1/BY:289@OH
1 atom, 1 residue, 1 model selected
> color (#!1 & sel) light gray
> select #1/BX:117
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1/BX:113
18 atoms, 16 bonds, 2 residues, 2 models selected
> select add #2/E:108
26 atoms, 23 bonds, 3 residues, 3 models selected
> select add #2/E:109
34 atoms, 30 bonds, 4 residues, 4 models selected
> select clear
> select add #1/BX:113
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1/BX:117
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #2/e:65,85,89,92,93,94,108,109,111,138
88 atoms, 81 bonds, 10 residues, 1 model selected
> select clear
> select add #1/BX:113
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1/BX:117
18 atoms, 16 bonds, 2 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark orange
> select add #1/BX:66
26 atoms, 23 bonds, 3 residues, 2 models selected
> select add #1/BX:68
33 atoms, 30 bonds, 4 residues, 2 models selected
> select add #1/BX:69
45 atoms, 42 bonds, 5 residues, 2 models selected
> select add #1/BX:70
54 atoms, 50 bonds, 6 residues, 2 models selected
> select add #1/BX:75
62 atoms, 57 bonds, 7 residues, 2 models selected
> ui tool show "Color Actions"
> color sel teal
> select #1/BX:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/BX:66
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/BX:89
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
29 atoms, 29 bonds, 5 residues, 2 models selected
> select up
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> select up
1439 atoms, 1475 bonds, 183 residues, 2 models selected
> show sel surfaces
> hide #!2 models
> select #1/BX:113@CB
1 atom, 1 residue, 1 model selected
> select #1/BX:113@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
44 atoms, 44 bonds, 6 residues, 2 models selected
> select up
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> hide sel surfaces
> select clear
> select #1/BX:113
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1/BX:117
18 atoms, 16 bonds, 2 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark orange
> select #1/BX:156
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 2 residues, 2 models selected
> select #1/BX:156
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/BX:113
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/BX:117
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
60 atoms, 60 bonds, 7 residues, 2 models selected
> select up
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> show sel surfaces
> select clear
> hide #!2 models
> save "/home/laiqi@nidvd.org/AAA_model/RV ab complex/rv/view06.png" width
> 1979 height 1153 supersample 3 transparentBackground true
> save "/home/laiqi@nidvd.org/AAA_model/RV ab complex/rv/view07.png" width
> 1979 height 1153 supersample 3
> select #1/BX:135@N
1 atom, 1 residue, 1 model selected
> select #1/BX:137@NE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
49 atoms, 48 bonds, 7 residues, 2 models selected
> select up
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> hide ~sel
Drag select of 4v7q_BX SES surface, 443320 of 703936 triangles, 4v7q_BY SES
surface, 476973 of 717050 triangles, 4v7q_BZ SES surface, 1381 residues, 2
pseudobonds
Drag select of 4v7q_BX SES surface, 487686 of 703936 triangles, 4v7q_BY SES
surface, 541088 of 717050 triangles, 4v7q_BZ SES surface, 1501 residues, 4
pseudobonds
Drag select of 4v7q_BX SES surface, 500185 of 703936 triangles, 4v7q_BY SES
surface, 550420 of 717050 triangles, 4v7q_BZ SES surface, 1527 residues, 5
pseudobonds
> hide sel surfaces
> hide sel cartoons
Drag select of 4v7q_BX SES surface, 15188 of 703936 triangles, 4v7q_BY SES
surface, 109860 of 717050 triangles, 178 residues
> hide sel surfaces
> hide sel cartoons
Drag select of 4v7q_BX SES surface, 12902 of 703936 triangles, 4v7q_BY SES
surface, 12238 of 717050 triangles, 50 residues
> select up
909 atoms, 932 bonds, 118 residues, 3 models selected
> hide sel surfaces
> hide sel cartoons
Drag select of 4v7q_BX SES surface, 7136 of 703936 triangles, 4v7q_BY SES
surface, 1955 of 717050 triangles, 16 residues
> select up
198 atoms, 202 bonds, 25 residues, 3 models selected
> select up
8284 atoms, 8434 bonds, 1054 residues, 3 models selected
> hide sel surfaces
> hide sel cartoons
Drag select of 4v7q_BY SES surface, 5968 of 717050 triangles, 10 residues
> select up
343 atoms, 351 bonds, 44 residues, 2 models selected
> hide sel surfaces
Drag select of 10 residues
> hide sel cartoons
> undo
[Repeated 9 time(s)]
> select #1/BX:157@CG
1 atom, 1 residue, 1 model selected
> select #1/BX:73@O
1 atom, 1 residue, 1 model selected
> select #1/BX:184
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/BX:69@CD2
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
217 atoms, 222 bonds, 29 residues, 2 models selected
> select up
1641 atoms, 1680 bonds, 208 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
Drag select of 16 residues
> select up
171 atoms, 175 bonds, 22 residues, 2 models selected
> hide sel surfaces
[Repeated 1 time(s)]
> hide sel cartoons
Drag select of 8 residues
> hide sel cartoons
> select clear
> select #1/BY:442
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 10 residues
> hide sel cartoons
Drag select of 160 residues
> show sel surfaces
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> select clear
> show #!1 surfaces
Drag select of 4v7q_AA SES surface, 603036 of 845108 triangles, 4v7q_AB SES
surface, 4v7q_AC SES surface, 4v7q_AD SES surface, 336922 of 343138 triangles,
4v7q_AE SES surface, 347491 of 348406 triangles, 4v7q_AF SES surface, 4v7q_AG
SES surface, 4v7q_AH SES surface, 4v7q_AI SES surface, 4v7q_AJ SES surface,
4v7q_AK SES surface, 4v7q_AL SES surface, 4v7q_AM SES surface, 4v7q_AN SES
surface, 4v7q_AO SES surface, 4v7q_BA SES surface, 4v7q_BF SES surface, 34665
of 263022 triangles, 4v7q_BG SES surface, 190912 of 275902 triangles, 4v7q_BH
SES surface, 79072 of 251218 triangles, 4v7q_BI SES surface, 280577 of 280590
triangles, 4v7q_BJ SES surface, 277162 of 278122 triangles, 4v7q_BK SES
surface, 232959 of 272824 triangles, 4v7q_BL SES surface, 4v7q_BM SES surface,
4v7q_BN SES surface, 4v7q_BO SES surface, 269932 of 280222 triangles, 4v7q_BP
SES surface, 4v7q_BQ SES surface, 4v7q_BX SES surface, 356924 of 703936
triangles, 4v7q_BY SES surface, 318120 of 717050 triangles, 4v7q_BZ SES
surface, 297621 of 511878 triangles
Drag select of 4v7q_AA SES surface, 810610 of 845108 triangles, 4v7q_AB SES
surface, 4v7q_AC SES surface, 4v7q_AD SES surface, 4v7q_AE SES surface,
4v7q_AF SES surface, 4v7q_AG SES surface, 4v7q_AH SES surface, 4v7q_AI SES
surface, 4v7q_AJ SES surface, 4v7q_AK SES surface, 4v7q_AL SES surface,
4v7q_AM SES surface, 4v7q_AN SES surface, 4v7q_AO SES surface, 4v7q_BA SES
surface, 246409 of 253132 triangles, 4v7q_BF SES surface, 258761 of 263022
triangles, 4v7q_BG SES surface, 4v7q_BH SES surface, 243657 of 251218
triangles, 4v7q_BI SES surface, 4v7q_BJ SES surface, 4v7q_BK SES surface,
4v7q_BL SES surface, 4v7q_BM SES surface, 4v7q_BN SES surface, 4v7q_BO SES
surface, 4v7q_BP SES surface, 4v7q_BQ SES surface, 4v7q_BX SES surface, 489360
of 703936 triangles, 4v7q_BY SES surface, 470334 of 717050 triangles, 4v7q_BZ
SES surface, 508123 of 511878 triangles
> ui mousemode right select
> select #1/AF:266@OD1
1 atom, 1 residue, 1 model selected
Drag select of 4v7q_AA SES surface, 551536 of 845108 triangles, 4v7q_AB SES
surface, 4v7q_AC SES surface, 304577 of 345712 triangles, 4v7q_AD SES surface,
257213 of 343138 triangles, 4v7q_AE SES surface, 272561 of 348406 triangles,
4v7q_AF SES surface, 4v7q_AG SES surface, 4v7q_AH SES surface, 349917 of
350200 triangles, 4v7q_AI SES surface, 4v7q_AJ SES surface, 4v7q_AK SES
surface, 4v7q_AL SES surface, 4v7q_AM SES surface, 4v7q_AN SES surface,
4v7q_AO SES surface, 4v7q_BA SES surface, 4v7q_BG SES surface, 29402 of 275902
triangles, 4v7q_BH SES surface, 12940 of 251218 triangles, 4v7q_BI SES
surface, 224050 of 280590 triangles, 4v7q_BJ SES surface, 210118 of 278122
triangles, 4v7q_BK SES surface, 56212 of 272824 triangles, 4v7q_BL SES
surface, 261421 of 275038 triangles, 4v7q_BM SES surface, 4v7q_BN SES surface,
234435 of 271870 triangles, 4v7q_BO SES surface, 139314 of 280222 triangles,
4v7q_BP SES surface, 235395 of 278692 triangles, 4v7q_BQ SES surface, 246914
of 253052 triangles, 4v7q_BX SES surface, 276786 of 703936 triangles, 4v7q_BY
SES surface, 155967 of 717050 triangles, 4v7q_BZ SES surface, 184785 of 511878
triangles
Drag select of 4v7q_AA SES surface, 721725 of 845108 triangles, 4v7q_AB SES
surface, 4v7q_AC SES surface, 312892 of 345712 triangles, 4v7q_AD SES surface,
269766 of 343138 triangles, 4v7q_AE SES surface, 282593 of 348406 triangles,
4v7q_AF SES surface, 4v7q_AG SES surface, 4v7q_AH SES surface, 4v7q_AI SES
surface, 4v7q_AJ SES surface, 4v7q_AK SES surface, 4v7q_AL SES surface,
4v7q_AM SES surface, 4v7q_AN SES surface, 4v7q_AO SES surface, 4v7q_BA SES
surface, 251431 of 253132 triangles, 4v7q_BG SES surface, 34901 of 275902
triangles, 4v7q_BH SES surface, 16041 of 251218 triangles, 4v7q_BI SES
surface, 233899 of 280590 triangles, 4v7q_BJ SES surface, 223181 of 278122
triangles, 4v7q_BK SES surface, 77498 of 272824 triangles, 4v7q_BL SES
surface, 267045 of 275038 triangles, 4v7q_BM SES surface, 4v7q_BN SES surface,
243030 of 271870 triangles, 4v7q_BO SES surface, 161492 of 280222 triangles,
4v7q_BP SES surface, 245033 of 278692 triangles, 4v7q_BQ SES surface, 251006
of 253052 triangles, 4v7q_BX SES surface, 286700 of 703936 triangles, 4v7q_BY
SES surface, 175619 of 717050 triangles, 4v7q_BZ SES surface, 198348 of 511878
triangles
> hide #!1 surfaces
> select #1/BX:175
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
56 atoms, 57 bonds, 6 residues, 2 models selected
> select up
1272 atoms, 1306 bonds, 160 residues, 2 models selected
> select up
1439 atoms, 1475 bonds, 183 residues, 2 models selected
> show sel surfaces
> select clear
Drag select of 4v7q_BX SES surface, 35197 of 703936 triangles
[Repeated 1 time(s)]
> select clear
> select #1/BX:46@CB
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
217 atoms, 222 bonds, 29 residues, 2 models selected
> select down
5 atoms, 4 bonds, 1 residue, 2 models selected
> save "/home/laiqi@nidvd.org/AAA_model/RV ab complex/rv/view08.png" width
> 1979 height 1153 supersample 3
> save "/home/laiqi@nidvd.org/AAA_model/RV ab complex/rv/view03.cxs"
——— End of log from Fri Mar 21 21:20:02 2025 ———
opened ChimeraX session
> open "/home/laiqi@nidvd.org/AAA_model/RV ab complex/rv/view04.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 708, in restore
data = fdeserialize(stream)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/core/serialize.py", line 70, in msgpack_deserialize
return next(stream)
File "msgpack/_unpacker.pyx", line 540, in msgpack._cmsgpack.Unpacker.__next__
File "msgpack/_unpacker.pyx", line 474, in msgpack._cmsgpack.Unpacker._unpack
File "msgpack/_unpacker.pyx", line 448, in
msgpack._cmsgpack.Unpacker.read_from_file
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/lz4/frame/__init__.py", line 668, in read
return self._buffer.read(size)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/_compression.py", line
68, in readinto
data = self.read(len(byte_view))
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/_compression.py", line
103, in read
data = self._decompressor.decompress(rawblock, size)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/lz4/frame/__init__.py", line 414, in decompress
decompressed, bytes_read, eoframe = decompress_chunk(
RuntimeError: LZ4F_decompress failed with code: ERROR_maxBlockSize_invalid
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 535.104.05
OpenGL renderer: NVIDIA RTX A4500/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 3660
OS: AlmaLinux 8.10 Cerulean Leopard
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 12th Gen Intel(R) Core(TM) i9-12900K
Cache Size: 30720 KB
Memory:
total used free shared buff/cache available
Mem: 30Gi 6.1Gi 18Gi 389Mi 6.6Gi 23Gi
Swap: 15Gi 0B 15Gi
Graphics:
0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102GL [RTX A4500] [10de:2232] (rev a1)
Subsystem: Dell Device [1028:163c]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
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: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
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: 1.45.7
ChimeraX-AtomicLibrary: 10.0.7
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: 2.10.3
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.dev202306010115
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: 1.1.2
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-LinuxSupport: 1.0.1
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-MCopy: 1.0
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: 1.12
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: 1.2.2
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-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
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.4
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
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
openvr: 1.23.701
packaging: 23.1
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: 3.5.1
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: 25.1.0
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.9.3
setuptools: 67.4.0
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: 6.3.2
traitlets: 5.9.0
typing-extensions: 4.6.2
tzdata: 2023.3
urllib3: 2.0.2
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (1)
comment:1 by , 8 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session restore: LZ4F_decompress failed with code: ERROR_maxBlockSize_invalid |
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