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Opened 3 years ago
Closed 3 years ago
#8775 closed defect (can't reproduce)
saving image: glClear: invalid framebuffer operation
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-21.2.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/Arenavirumab_3.cxs" format session
Log from Thu Mar 23 14:45:14 2023UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022_4NAbgroups.cxs"
Log from Sun Jun 5 17:18:41 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022_4NAbgroups.cxs" format
> session
Log from Sun Jun 5 15:53:35 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022.cxs"
Log from Sun May 29 16:57:14 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022.cxs" format session
Log from Sun May 29 14:30:12 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/haoyangli/Google Drive/LASVGP_Arevirumab/EMmaps/final
> models/89F/GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb"
Chain information for
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1
---
Chain | Description
A B C | No description available
H | No description available
L | No description available
O Q S | No description available
P R T | No description available
a b c | No description available
> open "/Users/haoyangli/Google Drive/LASVGP_Arevirumab/EMmaps/final
> models/121F/GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb"
Chain information for
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb #2
---
Chain | Description
A B C | No description available
D F H | No description available
E G L | No description available
O Q S | No description available
P R T | No description available
a b c | No description available
> lighting soft
> set bgColor white
> hide #!2 models
> show #!2 models
> select #1/a#2/a
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> graphics silhouettes true
> color (#!1-2 & sel) #f6c7e3ff
> select #1/b#2/b
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> color (#!1-2 & sel) #ddd4cfff
> select #1/c#2/c
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> color (#!1-2 & sel) #f2e1ffff
> select #1/b#2/b
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> color (#!1-2 & sel) #f6c7e3ff
> select #1/a#2/a
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> color (#!1-2 & sel) #fd6fcfff
> color (#!1-2 & sel) #fd66ffff
> undo
> undo
> color (#!1-2 & sel) #fd67ffff
> color (#!1-2 & sel) #fd70ffff
> color (#!1-2 & sel) #fd80ffff
> color (#!1-2 & sel) #fd84ffff
> color (#!1-2 & sel) #fd8affff
> color (#!1-2 & sel) #fd91ffff
> color (#!1-2 & sel) #fd9fffff
> color (#!1-2 & sel) #fda1ffff
> color (#!1-2 & sel) #fda1ffff
> color (#!1-2 & sel) #fda4ffff
> color (#!1-2 & sel) #fda6ffff
> color (#!1-2 & sel) #feaaffff
> color (#!1-2 & sel) #feb0ffff
> color (#!1-2 & sel) #feb6ffff
> color (#!1-2 & sel) #feb8ffff
> color (#!1-2 & sel) #febaffff
> color (#!1-2 & sel) #febaffff
> color (#!1-2 & sel) #fec2ffff
> color (#!1-2 & sel) #fecdffff
> color (#!1-2 & sel) #fed2ffff
> color (#!1-2 & sel) #ffd8ffff
> color (#!1-2 & sel) #ffdcffff
> color (#!1-2 & sel) #ffe2ffff
> color (#!1-2 & sel) #ffe3ffff
> color (#!1-2 & sel) #ffe5ffff
> color (#!1-2 & sel) #ffe4ffff
> color (#!1-2 & sel) #ffdeffff
> color (#!1-2 & sel) #fecdffff
> color (#!1-2 & sel) #feb6ffff
> color (#!1-2 & sel) #feabffff
> color (#!1-2 & sel) #fda4ffff
> color (#!1-2 & sel) #fd95ffff
> color (#!1-2 & sel) #fd90ffff
> color (#!1-2 & sel) #fd8dffff
> color (#!1-2 & sel) #fd8bffff
> color (#!1-2 & sel) #fd8affff
> color (#!1-2 & sel) #fd90ffff
> color (#!1-2 & sel) #fd91ffff
> color (#!1-2 & sel) #fd96ffff
> color (#!1-2 & sel) #fd98ffff
> color (#!1-2 & sel) #fd9affff
> color (#!1-2 & sel) #fd9cffff
> color (#!1-2 & sel) #fd9dffff
> color (#!1-2 & sel) #fd9dffff
> color (#!1-2 & sel) #fda0ffff
> color (#!1-2 & sel) #fda0ffff
> color (#!1-2 & sel) #f9a0ffff
> color (#!1-2 & sel) #f5a0ffff
> color (#!1-2 & sel) #efa0ffff
> color (#!1-2 & sel) #e9a0ffff
> color (#!1-2 & sel) #e6a0ffff
> color (#!1-2 & sel) #e3a0ffff
> color (#!1-2 & sel) #e2a0ffff
> color (#!1-2 & sel) #e1a0ffff
> color (#!1-2 & sel) #d9a1ffff
> color (#!1-2 & sel) #d6a1ffff
> color (#!1-2 & sel) #d0a1ffff
> color (#!1-2 & sel) #cfa1ffff
> color (#!1-2 & sel) #cea1ffff
> color (#!1-2 & sel) #cea1ffff
> color (#!1-2 & sel) #d8a1ffff
> color (#!1-2 & sel) #efa0ffff
> color (#!1-2 & sel) #fda0ffff
> color (#!1-2 & sel) #c66467ff
> color (#!1-2 & sel) #f67b7eff
> select #1/O#2/O
1944 atoms, 1996 bonds, 250 residues, 2 models selected
> color sel #fecc66ff
> color sel #fd8008ff
> select #1/P#2/P
1586 atoms, 1624 bonds, 208 residues, 2 models selected
> color sel #ffff66ff
> color sel #ffff0aff
> select #1/O#2/O
1944 atoms, 1996 bonds, 250 residues, 2 models selected
> color sel #fecc66ff
> hide sel atoms
> show sel cartoons
Drag select of 34647 atoms, 250 residues, 30 pseudobonds, 3285 bonds
> show sel cartoons
> select #1/a#2/a
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> color (#!1-2 & sel) #fb7c80ff
> color (#!1-2 & sel) #fb7c81ff
> color (#!1-2 & sel) #fb7c87ff
> color (#!1-2 & sel) #fb7c97ff
> color (#!1-2 & sel) #fb7b9eff
> color (#!1-2 & sel) #fb7ba0ff
> color (#!1-2 & sel) #fb7ab0ff
> color (#!1-2 & sel) #fb7ab9ff
> color (#!1-2 & sel) #fb7abeff
> color (#!1-2 & sel) #fb79c6ff
> color (#!1-2 & sel) #fb79c6ff
> color (#!1-2 & sel) #fb7ac3ff
> color (#!1-2 & sel) #fb7ac2ff
> color (#!1-2 & sel) #fb7ac1ff
> color (#!1-2 & sel) #fb7abbff
> color (#!1-2 & sel) #fb7abbff
> color (#!1-2 & sel) #fb7ebbff
> color (#!1-2 & sel) #fb8cbbff
> color (#!1-2 & sel) #fb9dbbff
> color (#!1-2 & sel) #fba5bbff
> color (#!1-2 & sel) #fcb0bbff
> color (#!1-2 & sel) #fcb9bbff
> color (#!1-2 & sel) #fcb7bbff
> color (#!1-2 & sel) #fcb4bbff
> color (#!1-2 & sel) #fbabbbff
> color (#!1-2 & sel) #fba1bbff
> color (#!1-2 & sel) #fb9dbbff
> select #1/P#2/P
1586 atoms, 1624 bonds, 208 residues, 2 models selected
> hide sel atoms
> select clear
> select #1/O#2/O
1944 atoms, 1996 bonds, 250 residues, 2 models selected
> color sel orange
> select #1/P#2/P
1586 atoms, 1624 bonds, 208 residues, 2 models selected
> color sel yellow
Drag select of 21499 atoms, 4260 residues, 30 pseudobonds, 3285 bonds
> show sel surfaces
> select #1/O#2/O
1944 atoms, 1996 bonds, 250 residues, 2 models selected
> color (#!1-2 & sel) orange
> select #1/P#2/P
1586 atoms, 1624 bonds, 208 residues, 2 models selected
> color (#!1-2 & sel) yellow
> select #1/Q#2/Q
1944 atoms, 1996 bonds, 250 residues, 2 models selected
> color (#!1-2 & sel) orange
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select #1/P#2/P
1586 atoms, 1624 bonds, 208 residues, 2 models selected
> hide sel surfaces
> hide sel atoms
> select #1/O#2/O
1944 atoms, 1996 bonds, 250 residues, 2 models selected
> hide sel surfaces
> select #1/R#2/R
1586 atoms, 1624 bonds, 208 residues, 2 models selected
> color (#!1-2 & sel) yellow
> hide sel surfaces
> hide sel atoms
> select #1/S#2/S
1944 atoms, 1996 bonds, 250 residues, 2 models selected
> color (#!1-2 & sel) orange
> hide sel surfaces
> hide sel atoms
> select #1/T#2/T
1586 atoms, 1624 bonds, 208 residues, 2 models selected
> color (#!1-2 & sel) yellow
> hide sel surfaces
> hide sel atoms
> sequence chain #2/D#2/F#2/H
Alignment identifier is 1
> color (#!2 & sel) forest green
> hide sel surfaces
> hide sel atoms
> color (#!2 & sel) #fb9dbbff
> color (#!2 & sel) #146626ff
> show sel surfaces
> show sel atoms
> color (#!2 & sel) #146625ff
> color (#!2 & sel) #146626ff
> hide sel atoms
> hide sel surfaces
> sequence chain #2/E#2/G#2/L
Alignment identifier is 1
> color (#!2 & sel) #389c87ff
> hide sel surfaces
> hide sel atoms
> show sel surfaces
> color (#!2 & sel) #21ff80ff
> color (#!2 & sel) #21ff06ff
> color (#!2 & sel) #80ff07ff
> hide sel surfaces
> select #1/H
1048 atoms, 1077 bonds, 135 residues, 1 model selected
> color (#!1 & sel) #80ff07ff
> color (#!1 & sel) #8000ffff
> color (#!1 & sel) #8000ffff
> hide sel surfaces
> hide sel surfaces
> hide sel atoms
> select #1/L
794 atoms, 811 bonds, 108 residues, 1 model selected
> color (#!1 & sel) #8000ffff
> color (#!1 & sel) #982b87ff
> color (#!1 & sel) #fd6fcfff
> color (#!1 & sel) #fc0280ff
> color (#!1 & sel) #fc02ffff
> color (#!1 & sel) #fd66ffff
> color (#!1 & sel) #cc66ffff
> hide sel surfaces
> hide sel surfaces
> hide sel atoms
> select #1/a#2/a
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> color (#!1-2 & sel) #cc66ffff
> color (#!1-2 & sel) #fb9dbbff
> hide sel atoms
> show sel atoms
> select #1/b#2/b
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> color (#!1-2 & sel) #f3b9ddff
> select #1/c#2/c
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> color (#!1-2 & sel) #efd8ffff
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022.cxs"
> select #1/A#2/A
3584 atoms, 3699 bonds, 6 pseudobonds, 422 residues, 4 models selected
> color (#!1-2 & sel) #47a4e4ff
> color (#!1-2 & sel) #47a4e4ff
> color (#!1-2 & sel) #43a4e4ff
> color (#!1-2 & sel) #35a4e4ff
> color (#!1-2 & sel) #24a4e4ff
> color (#!1-2 & sel) #21a4e4ff
> color (#!1-2 & sel) #1ea4e4ff
> color (#!1-2 & sel) #1aa4e4ff
> color (#!1-2 & sel) #1aa4e4ff
> color (#!1-2 & sel) #15a4e4ff
> color (#!1-2 & sel) #14a4e4ff
> color (#!1-2 & sel) #14a4e4ff
> color (#!1-2 & sel) #14a4ecff
> color (#!1-2 & sel) #14a3ffff
> color (#!1-2 & sel) #14a4ffff
> color (#!1-2 & sel) #18c4ffff
> color (#!1-2 & sel) #18c5ffff
> color (#!1-2 & sel) #19cbffff
> color (#!1-2 & sel) #19caffff
> color (#!1-2 & sel) #1bdbffff
> color (#!1-2 & sel) #1de9ffff
> color (#!1-2 & sel) #1de9ffff
> color (#!1-2 & sel) #1fe9ffff
> color (#!1-2 & sel) #5fe8ffff
> color (#!1-2 & sel) #a7e7ffff
> color (#!1-2 & sel) #afe7ffff
> color (#!1-2 & sel) #afe6ffff
> color (#!1-2 & sel) #aeceffff
> color (#!1-2 & sel) #aeceffff
> color (#!1-2 & sel) #aeccffff
> color (#!1-2 & sel) #aecdffff
> select #1/B#2/B
3565 atoms, 3678 bonds, 6 pseudobonds, 420 residues, 4 models selected
> color (#!1-2 & sel) #aecdffff
> color (#!1-2 & sel) #9bb9ffff
> select #1/A#2/A
3584 atoms, 3699 bonds, 6 pseudobonds, 422 residues, 4 models selected
> color (#!1-2 & sel) #9bb9feff
> color (#!1-2 & sel) #9bb9ffff
> select #1/B#2/B
3565 atoms, 3678 bonds, 6 pseudobonds, 420 residues, 4 models selected
> color (#!1-2 & sel) #a5afc4ff
> color (#!1-2 & sel) #d2d6e1ff
> select #1/C#2/C
3609 atoms, 3726 bonds, 6 pseudobonds, 424 residues, 4 models selected
> color (#!1-2 & sel) #d2d6e0ff
> color (#!1-2 & sel) #d2d6e1ff
> select #1/B#2/B
3565 atoms, 3678 bonds, 6 pseudobonds, 420 residues, 4 models selected
> color (#!1-2 & sel) #d2d6e2ff
> color (#!1-2 & sel) #d2d5f5ff
> color (#!1-2 & sel) #d2d5ffff
> color (#!1-2 & sel) #d1d5ffff
> color (#!1-2 & sel) #bad6ffff
> color (#!1-2 & sel) #b6d6ffff
> color (#!1-2 & sel) #b2d6ffff
> color (#!1-2 & sel) #b1d6ffff
> color (#!1-2 & sel) #b1d6ffff
> color (#!1-2 & sel) #b6d6ffff
> color (#!1-2 & sel) #b9d6ffff
> color (#!1-2 & sel) #b9d6ffff
> color (#!1-2 & sel) #b9dbffff
> color (#!1-2 & sel) #baf0ffff
> color (#!1-2 & sel) #baf5ffff
> color (#!1-2 & sel) #baf6ffff
> color (#!1-2 & sel) #bbf6ffff
> color (#!1-2 & sel) #c1f6ffff
> color (#!1-2 & sel) #c7f6ffff
> color (#!1-2 & sel) #caf6ffff
> color (#!1-2 & sel) #cdf6ffff
> color (#!1-2 & sel) #d1f6ffff
> color (#!1-2 & sel) #d3f6ffff
> color (#!1-2 & sel) #d4f6ffff
> color (#!1-2 & sel) #d8f6ffff
> color (#!1-2 & sel) #e3f5ffff
> color (#!1-2 & sel) #e5f5ffff
> color (#!1-2 & sel) #e9f5ffff
> color (#!1-2 & sel) #e8f5ffff
> color (#!1-2 & sel) #d7f6ffff
> color (#!1-2 & sel) #c6f6ffff
> color (#!1-2 & sel) #c6f6ffff
> color (#!1-2 & sel) #c5f6ffff
> color (#!1-2 & sel) #b9f6ffff
> color (#!1-2 & sel) #b8f6ffff
> color (#!1-2 & sel) #b8f6ffff
> color (#!1-2 & sel) #b8f6fcff
> color (#!1-2 & sel) #b8f6f6ff
> color (#!1-2 & sel) #b8f7e9ff
> color (#!1-2 & sel) #b8f7eaff
> color (#!1-2 & sel) #b8f6ffff
> color (#!1-2 & sel) #b8f6ffff
> color (#!1-2 & sel) #b8f3ffff
> color (#!1-2 & sel) #b8efffff
> color (#!1-2 & sel) #b8e8ffff
> color (#!1-2 & sel) #b8e8ffff
> color (#!1-2 & sel) #bce8ffff
> color (#!1-2 & sel) #c2e8ffff
> color (#!1-2 & sel) #cbe8ffff
> color (#!1-2 & sel) #cfe8ffff
> select clear
> hide #!2 models
> select ::name="BMA"::name="FUC"::name="MAN"::name="NAG"
3042 atoms, 3219 bonds, 243 residues, 2 models selected
> show #!2 models
Drag select of
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_A SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_a SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_B SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_b SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_C SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_c SES surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_a SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_b SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface, 13215 atoms, 4260 residues, 30 pseudobonds, 3285 bonds
> hide sel atoms
> show sel cartoons
> select ::name="BMA"::name="FUC"::name="MAN"::name="NAG"
3042 atoms, 3219 bonds, 243 residues, 2 models selected
> show sel atoms
> show sel surfaces
> select #1/A#2/A
3584 atoms, 3699 bonds, 6 pseudobonds, 422 residues, 4 models selected
> color (#!1-2 & sel) #cfe7ffff
> color (#!1-2 & sel) #9bb9ffff
> select #1/B#2/B
3565 atoms, 3678 bonds, 6 pseudobonds, 420 residues, 4 models selected
> color (#!1-2 & sel) #cfe7ffff
> select #1/C#2/C
3609 atoms, 3726 bonds, 6 pseudobonds, 424 residues, 4 models selected
> color (#!1-2 & sel) #d2d6e1ff
> select #1/a#2/a
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> color (#!1-2 & sel) #fb9dbbff
> select #1/b#2/b
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> color (#!1-2 & sel) #f3b9ddff
> select #1/c#2/c
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> color (#!1-2 & sel) #efd8ffff
> select clear
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022.cxs"
> select ::name="BMA"::name="FUC"::name="MAN"::name="NAG"
3042 atoms, 3219 bonds, 243 residues, 2 models selected
> transparency (#!1-2 & sel) 50
> transparency (#!1-2 & sel) 90
> transparency (#!1-2 & sel) 80
> select clear
> hide #!2 models
> graphics silhouettes false
> graphics silhouettes true
> show #!2 models
> hide #!1 models
> mmaker #2/A to #1/A showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain A (#1) with
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb, chain
A (#2), sequence alignment score = 951.2
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 184 pruned atom pairs is 0.396 angstroms; (across all 185 pairs:
0.431)
> show #!1 models
> hide #!2 models
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022.cxs"
> select ::name="BMA"::name="FUC"::name="MAN"::name="NAG"
3042 atoms, 3219 bonds, 243 residues, 2 models selected
> style sel & #!1 sphere
Changed 1462 atom styles
> style sel & #!1 ball
Changed 1462 atom styles
> style sel & #!1 stick
Changed 1462 atom styles
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting shadows false
> lighting simple
> lighting full
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> select clear
> graphics silhouettes true
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022.cxs"
> preset cartoons/nucleotides licorice/ovals
Changed 33549 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> show #!2 models
> hide #!1 models
> show #!1 models
> select #1/a#2/a
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> show sel surfaces
> select #1/A#2/A
3584 atoms, 3699 bonds, 6 pseudobonds, 422 residues, 4 models selected
> show sel surfaces
> select #1/B#2/B
3565 atoms, 3678 bonds, 6 pseudobonds, 420 residues, 4 models selected
> show sel surfaces
> select #1/C#2/C
3609 atoms, 3726 bonds, 6 pseudobonds, 424 residues, 4 models selected
> show sel surfaces
> select #1/b#2/b
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> show sel surfaces
> select #1/c#2/c
2877 atoms, 2968 bonds, 4 pseudobonds, 337 residues, 4 models selected
> show sel surfaces
> select clear
> hide #!2 models
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> lighting full
> lighting shadows false
> lighting flat
> lighting soft
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> lighting full
> lighting shadows false
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> show #!2 models
> hide #!1 models
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022.cxs"
opened ChimeraX session
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save /Users/haoyangli/Desktop/image1.png supersample 3
> show #!1 models
> hide #!2 models
> save /Users/haoyangli/Desktop/image2.png supersample 3
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> lighting soft
> lighting full
> lighting soft
> save /Users/haoyangli/Desktop/image3.png supersample 3
> hide #!1 models
> show #!2 models
> save /Users/haoyangli/Desktop/image4.png supersample 3
> show #!1 models
> hide #!2 models
> save /Users/haoyangli/Desktop/image5.png supersample 3
> lighting simple
> lighting full
> lighting shadows false
> show #!2 models
> select ::name="BMA"::name="FUC"::name="MAN"::name="NAG"
3042 atoms, 3219 bonds, 243 residues, 2 models selected
> surface hidePatches (#!1-2 & sel)
> style sel ball
Changed 3042 atom styles
> style sel sphere
Changed 3042 atom styles
> hide #!2 models
> style sel & #!1 ball
Changed 1462 atom styles
> color sel & #!1 byhetero
> style sel & #!1 stick
Changed 1462 atom styles
> undo
> undo
> style sel & #!1 stick
Changed 1462 atom styles
> color sel & #!1 byhetero
> show #!2 models
> style sel stick
Changed 3042 atom styles
> color sel byhetero
> hide #!1 models
> undo
> undo
> undo
> undo
> undo
> select clear
> show #!2 models
> select #2
19757 atoms, 20352 bonds, 18 pseudobonds, 2431 residues, 2 models selected
> style sel stick
Changed 19757 atom styles
> select clear
> hide #!1 models
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/7pvd_matriglycan.pdb"
7pvd_matriglycan.pdb title:
Structure of the membrane soluble spike complex from the lassa virus In A
C1-symmetric map focused on the ectodomain [more info...]
Chain information for 7pvd_matriglycan.pdb #3
---
Chain | Description
A B C | PRE-GP-C
a b c | GP2
Non-standard residues in 7pvd_matriglycan.pdb #3
---
BDP — β-D-glucopyranuronic acid (β-D-glucuronic acid; D-glucuronic acid;
glucuronicacid)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
XYS — α-D-xylopyranose (α-D-xylose; D-xylose; xylose; xylopyranose)
> mmaker #3/A to #1/A showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain A (#1) with 7pvd_matriglycan.pdb, chain A (#3), sequence alignment score
= 938.5
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
7pvd_matriglycan.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 164 pruned atom pairs is 0.684 angstroms; (across all 183 pairs:
1.309)
> show #!1 models
> hide #!2 models
> hide #!1 models
Drag select of 8902 atoms, 12 pseudobonds, 450 bonds
> hide sel atoms
> select
> ::name="BDP"::name="BMA"::name="FUC"::name="MAN"::name="NAG"::name="XYS"
3598 atoms, 3796 bonds, 286 residues, 3 models selected
> show sel & #!3 atoms
Drag select of 234 atoms, 239 bonds
> hide sel atoms
Drag select of 32 atoms, 30 bonds
> hide sel atoms
Drag select of 69 atoms, 72 bonds
> hide sel atoms
Drag select of 28 atoms, 29 bonds
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
Drag select of 28 atoms, 29 bonds
> hide sel atoms
Drag select of 28 atoms, 29 bonds
> hide sel atoms
> show #!1 models
> select #3
8902 atoms, 9139 bonds, 12 pseudobonds, 1078 residues, 2 models selected
> hide #!1 models
Drag select of 136 atoms
> style sel stick
Changed 136 atom styles
> select clear
Drag select of 136 atoms, 148 bonds
> color sel byhetero
> select clear
> show #!1 models
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/7pvd_matriglycan1.pdb"
7pvd_matriglycan1.pdb title:
Structure of the membrane soluble spike complex from the lassa virus In A
C1-symmetric map focused on the ectodomain [more info...]
Chain information for 7pvd_matriglycan1.pdb #4
---
Chain | Description
A B C | PRE-GP-C
a b c | GP2
Non-standard residues in 7pvd_matriglycan1.pdb #4
---
BDP — β-D-glucopyranuronic acid (β-D-glucuronic acid; D-glucuronic acid;
glucuronicacid)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
XYS — α-D-xylopyranose (α-D-xylose; D-xylose; xylose; xylopyranose)
Associated 7pvd_matriglycan1.pdb chain A to 7pvd_matriglycan.pdb, chain A with
0 mismatches
Associated 7pvd_matriglycan1.pdb chain B to 7pvd_matriglycan.pdb, chain A with
0 mismatches
Associated 7pvd_matriglycan1.pdb chain C to 7pvd_matriglycan.pdb, chain A with
0 mismatches
Chains used in RMSD evaluation for alignment 1:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
7pvd_matriglycan.pdb #3/A, 7pvd_matriglycan1.pdb #4/C
> mmaker #4/A to #1/A showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain A (#1) with 7pvd_matriglycan1.pdb, chain A (#4), sequence alignment
score = 938.5
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
7pvd_matriglycan1.pdb #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 164 pruned atom pairs is 0.684 angstroms; (across all 183 pairs:
1.309)
Chains used in RMSD evaluation for alignment 1:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
7pvd_matriglycan.pdb #3/A, 7pvd_matriglycan1.pdb #4/A
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> select #4
8902 atoms, 9139 bonds, 12 pseudobonds, 1078 residues, 2 models selected
> hide #!3 models
> interfaces sel & ~solvent
15 buried areas: C c 2495, B b 2457, A a 2421, B C 1133, A B 1112, A C 1105, a
b 670, c a 659, c b 650, C a 515, B c 499, A b 468, B M 373, A M 369, C M 361
> hide sel atoms
> show sel cartoons
> select ::name="NAG"
2674 atoms, 2757 bonds, 191 residues, 4 models selected
> show sel & #!4 atoms
> hide sel & #!4 atoms
> undo
> show #!1 models
> hide #!4 models
> select clear
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> show #!4 models
Drag select of 272 atoms, 148 bonds
> style sel stick
Changed 272 atom styles
> color sel yellow
> select clear
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!4 models
> show #!4 models
> select #4
8902 atoms, 9139 bonds, 12 pseudobonds, 1078 residues, 2 models selected
> show sel cartoons
> color sel red
> color sel yellow
> select #4
8902 atoms, 9139 bonds, 12 pseudobonds, 1078 residues, 2 models selected
> show sel cartoons
> select #4/A:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/B:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 287 atoms, 296 bonds, 1035 residues, 12 pseudobonds
> style sel stick
Changed 8618 atom styles
> select clear
> select #3/a#3/b#3/c#4/a#4/b#4/c
7956 atoms, 8148 bonds, 972 residues, 2 models selected
> hide sel cartoons
> select #4/C:150
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/C:117
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/B:117
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/B:150
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/A:150
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/A:117
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/A:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/B:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/C:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/B:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> show sel atoms
> select clear
> style sel sphere
Changed 136 atom styles
> style sel ball
Changed 136 atom styles
> color sel byhetero
> show #!1 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> select #4
8902 atoms, 9139 bonds, 12 pseudobonds, 1078 residues, 2 models selected
> hide #!3 models
> select #1
16834 atoms, 17320 bonds, 12 pseudobonds, 2072 residues, 2 models selected
> interfaces sel & ~solvent
22 buried areas: B b 2729, A a 2689, C c 2678, A B 1223, C A 1187, C B 1171, c
S 929, b Q 917, a O 900, H L 822, Q R 799, O P 794, S T 793, b c 704, a c 687,
a b 687, A b 615, B c 615, C a 580, C L 558, A H 549, C H 394
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022.cxs"
> select clear
> show #!3 models
> select clear
> mmaker #3/c to #1/A showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain A (#1) with 7pvd_matriglycan.pdb, chain c (#3), sequence alignment score
= 32.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
7pvd_matriglycan.pdb #3/c
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 5 pruned atom pairs is 1.243 angstroms; (across all 129 pairs:
20.414)
> undo
> select clear
> mmaker #3/C to #1/A showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain A (#1) with 7pvd_matriglycan.pdb, chain C (#3), sequence alignment score
= 938.5
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
7pvd_matriglycan.pdb #3/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 164 pruned atom pairs is 0.684 angstroms; (across all 183 pairs:
1.309)
> mmaker #3/B to #1/A showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain A (#1) with 7pvd_matriglycan.pdb, chain B (#3), sequence alignment score
= 938.5
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
7pvd_matriglycan.pdb #3/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 164 pruned atom pairs is 0.684 angstroms; (across all 183 pairs:
1.309)
> mmaker #3/A to #1/A showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain A (#1) with 7pvd_matriglycan.pdb, chain A (#3), sequence alignment score
= 938.5
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
7pvd_matriglycan.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 164 pruned atom pairs is 0.684 angstroms; (across all 183 pairs:
1.309)
> mmaker #3/C to #1/A showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain A (#1) with 7pvd_matriglycan.pdb, chain C (#3), sequence alignment score
= 938.5
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
7pvd_matriglycan.pdb #3/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 164 pruned atom pairs is 0.684 angstroms; (across all 183 pairs:
1.309)
> mmaker #4/C to #1/A showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain A (#1) with 7pvd_matriglycan1.pdb, chain C (#4), sequence alignment
score = 938.5
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
7pvd_matriglycan1.pdb #4/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 164 pruned atom pairs is 0.684 angstroms; (across all 183 pairs:
1.309)
> select #3
8902 atoms, 9139 bonds, 12 pseudobonds, 1078 residues, 2 models selected
> style sel ball
Changed 8902 atom styles
> select clear
> show #!4 models
> hide #!3 models
> hide #!1 models
> select #4/A
1512 atoms, 1549 bonds, 4 pseudobonds, 187 residues, 2 models selected
> color (#!4 & sel) #ffff0aff
> color (#!4 & sel) #cfe7ffff
> select #4/B
1512 atoms, 1549 bonds, 4 pseudobonds, 187 residues, 2 models selected
> color (#!4 & sel) #d2d6e1ff
> select #4/C
1512 atoms, 1549 bonds, 4 pseudobonds, 187 residues, 2 models selected
> lighting soft
> color (#!4 & sel) #9bb9ffff
> select clear
Drag select of 282 atoms, 455 residues, 6 pseudobonds, 277 bonds
> style sel sphere
Changed 3795 atom styles
> select clear
> style sel ball
Changed 136 atom styles
> color sel yellow
> select clear
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022.cxs"
opened ChimeraX session
> show #!1 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/2510C-LIV-LASV-12bGP.pdb"
Summary of feedback from opening /Users/haoyangli/Google
Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/2510C-LIV-LASV-12bGP.pdb
---
warnings | Start residue of secondary structure not found: HELIX 46 46 ASN 1
162 GLY 1 164 5 3
Start residue of secondary structure not found: HELIX 47 47 SER 1 193 GLY 1
197 5 5
Start residue of secondary structure not found: HELIX 48 48 ASN 2 162 GLY 2
164 5 3
Start residue of secondary structure not found: HELIX 49 49 SER 2 193 GLY 2
197 5 5
Start residue of secondary structure not found: HELIX 50 50 ASN 3 162 GLY 3
164 5 3
22 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (147 )
Cannot find LINK/SSBOND residue CYS (147 )
Cannot find LINK/SSBOND residue CYS (147 )
Chain information for 2510C-LIV-LASV-12bGP.pdb #5
---
Chain | Description
A B C | No description available
D G J | No description available
E H K | No description available
> preset cartoons/nucleotides licorice/ovals
Changed 20321 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
Drag select of 198 residues, 2 pseudobonds
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
Drag select of 204 residues, 2 pseudobonds
Drag select of 197 residues, 2 pseudobonds
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
Drag select of 198 residues, 2 pseudobonds
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select clear
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> hide #!5 models
> show #!1 models
> show #!2 models
> mmaker #2/A to #1/A showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain A (#1) with
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb, chain
A (#2), sequence alignment score = 951.2
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 184 pruned atom pairs is 0.396 angstroms; (across all 185 pairs:
0.431)
> mmaker #5/A to #1/A showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain A (#1) with 2510C-LIV-LASV-12bGP.pdb, chain A (#5), sequence alignment
score = 712
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
2510C-LIV-LASV-12bGP.pdb #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 143 pruned atom pairs is 0.779 angstroms; (across all 162 pairs:
11.121)
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> mmaker #5 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain C (#1) with 2510C-LIV-LASV-12bGP.pdb, chain A (#5), sequence alignment
score = 713.8
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/C,
2510C-LIV-LASV-12bGP.pdb #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 142 pruned atom pairs is 0.722 angstroms; (across all 162 pairs:
11.225)
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> ui mousemode right "rotate selected models"
> select #5
12664 atoms, 12961 bonds, 36 pseudobonds, 1573 residues, 2 models selected
> mmaker #5/A to #1/A showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain A (#1) with 2510C-LIV-LASV-12bGP.pdb, chain A (#5), sequence alignment
score = 712
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/A,
2510C-LIV-LASV-12bGP.pdb #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 143 pruned atom pairs is 0.779 angstroms; (across all 162 pairs:
11.121)
> select clear
> show #!2 models
> hide #!1 models
Drag select of 2066 atoms, 3841 residues, 54 pseudobonds, 2175 bonds
> show #!1 models
> select clear
Drag select of 3528 atoms, 5797 residues, 66 pseudobonds, 3720 bonds
> show sel surfaces
> select clear
> hide #!2 models
> hide #!1 models
> select #5
12664 atoms, 12961 bonds, 36 pseudobonds, 1573 residues, 2 models selected
> hide sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
Drag select of 324 atoms, 1055 residues, 26 pseudobonds, 334 bonds
Drag select of 118 atoms, 251 residues, 123 bonds
Drag select of 324 atoms, 1087 residues, 26 pseudobonds, 334 bonds
> hide sel cartoons
> hide sel atoms
> select #5/A
2527 atoms, 2590 bonds, 12 pseudobonds, 305 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select clear
Drag select of 220 residues
> select clear
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
Drag select of 220 residues
Alignment identifier is 5/D
Alignment identifier is 5/E
> show #!1 models
> hide #!1 models
> color (#!5 & sel) dim gray
> show sel surfaces
> color (#!5 & sel) #808003ff
> color (#!5 & sel) #996633ff
> color (#!5 & sel) #808003ff
> color (#!5 & sel) #808003ff
> color (#!5 & sel) #838003ff
> color (#!5 & sel) #8d8004ff
> color (#!5 & sel) #928004ff
> color (#!5 & sel) #977f04ff
> color (#!5 & sel) #9a7f04ff
> color (#!5 & sel) #9b7f04ff
> color (#!5 & sel) #9d7f04ff
> color (#!5 & sel) #a27f04ff
> color (#!5 & sel) #a27f04ff
> color (#!5 & sel) #a47f04ff
> color (#!5 & sel) #a47f05ff
> color (#!5 & sel) #a47f08ff
> color (#!5 & sel) #a47f0dff
> color (#!5 & sel) #a47f15ff
> color (#!5 & sel) #a47f19ff
> color (#!5 & sel) #a47f1cff
> color (#!5 & sel) #a47f24ff
> color (#!5 & sel) #a47f25ff
> color (#!5 & sel) #a47f2cff
> color (#!5 & sel) #a47f2fff
> color (#!5 & sel) #a47f30ff
> color (#!5 & sel) #a47f31ff
> color (#!5 & sel) #a47f35ff
> color (#!5 & sel) #a47f35ff
> color (#!5 & sel) #a47f35ff
> color (#!5 & sel) #a48635ff
> color (#!5 & sel) #a48e35ff
> color (#!5 & sel) #a59b35ff
> color (#!5 & sel) #a5ad36ff
> color (#!5 & sel) #a6ba36ff
> color (#!5 & sel) #a6b936ff
> color (#!5 & sel) #a5b636ff
> color (#!5 & sel) #a59b35ff
> color (#!5 & sel) #a48835ff
> color (#!5 & sel) #a48635ff
> color (#!5 & sel) #a48535ff
> color (#!5 & sel) #a48435ff
> color (#!5 & sel) #a48435ff
> color (#!5 & sel) #a18435ff
> color (#!5 & sel) #9a8435ff
> color (#!5 & sel) #928435ff
> color (#!5 & sel) #8e8435ff
> color (#!5 & sel) #8c8435ff
> show sel surfaces
> color (#!5 & sel) dim gray
> select clear
> show #!2 models
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/D #5/G #5/J
Alignment identifier is 1
> sequence chain #5/E #5/H #5/K
Alignment identifier is 2
> hide #!1 models
> hide #!2 models
> show sel cartoons
> show sel surfaces
> color (#!5 & sel) dim gray
> show sel cartoons
> show sel surfaces
> color (#!5 & sel) light gray
> select clear
> show #!1 models
> show #!2 models
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022_4NAbgroups.cxs"
> hide #!2 models
> mmaker #5/B to #1/B showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb,
chain B (#1) with 2510C-LIV-LASV-12bGP.pdb, chain B (#5), sequence alignment
score = 710.2
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3:
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb #1/B,
2510C-LIV-LASV-12bGP.pdb #5/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 141 pruned atom pairs is 0.727 angstroms; (across all 162 pairs:
11.175)
> show #!2 models
> hide #!5 models
> hide #!1 models
> show #!5 models
> hide #!2 models
Drag select of 2510C-LIV-LASV-12bGP.pdb_D SES surface, 2510C-LIV-
LASV-12bGP.pdb_E SES surface, 2510C-LIV-LASV-12bGP.pdb_G SES surface,
2510C-LIV-LASV-12bGP.pdb_H SES surface, 2510C-LIV-LASV-12bGP.pdb_J SES
surface, 2510C-LIV-LASV-12bGP.pdb_K SES surface, 658 residues
> hide sel surfaces
> select clear
> show #!2 models
> hide #!2 models
> hide #!5 models
> show #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/D #2/F #2/H
Alignment identifier is 3
> sequence chain #2/E #2/G #2/L
Alignment identifier is 4
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> ui tool show "Show Sequence Viewer"
> sequence chain #1/H
Alignment identifier is 1/H
> sequence chain #1/L
Alignment identifier is 1/L
> sequence chain #1/O #1/Q #1/S #2/O #2/Q #2/S
Alignment identifier is 5
> sequence chain #1/P #1/R #1/T #2/P #2/R #2/T
Alignment identifier is 6
> show #!1 models
> hide sel surfaces
> hide sel surfaces
> hide sel surfaces
> hide sel surfaces
> select clear
> show #!5 models
> lighting flat
> lighting full
> lighting shadows false
> lighting soft
> graphics silhouettes false
> select
> ::name="BDP"::name="BMA"::name="FUC"::name="MAN"::name="NAG"::name="XYS"
4640 atoms, 4874 bonds, 365 residues, 5 models selected
> style sel & #!1-2,5 ball
Changed 3528 atom styles
> style sel & #!1-2,5 sphere
Changed 3528 atom styles
> style sel & #!1-2,5 ball
Changed 3528 atom styles
> select clear
> hide #!1 models
> hide #!2 models
> hide #!5 models
> show #!1 models
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> lighting soft
> lighting simple
> graphics silhouettes true
> show #!2 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022_4NAbgroups.cxs"
Drag select of
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_A SES surface,
185899 of 206614 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_a SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_B SES surface,
186612 of 207034 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_b SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_C SES surface,
179441 of 201420 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_c SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_A SES surface,
39602 of 60532 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_a SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_B SES surface,
41468 of 55838 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_b SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_C SES surface,
40934 of 63382 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_c SES surface,
1181 atoms, 1698 residues, 12 pseudobonds, 1248 bonds
Drag select of
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_A SES surface,
173862 of 206614 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_a SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_B SES surface,
178085 of 207034 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_b SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_C SES surface,
162518 of 201420 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_c SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_A SES surface,
36550 of 60532 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_a SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_B SES surface,
40274 of 55838 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_b SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_C SES surface,
34334 of 63382 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_c SES surface,
1128 atoms, 1663 residues, 12 pseudobonds, 1190 bonds
Drag select of
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_A SES surface,
150102 of 206614 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_a SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_B SES surface,
154359 of 207034 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_b SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_C SES surface,
140016 of 201420 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_c SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_A SES surface,
30074 of 60532 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_a SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_B SES surface,
35404 of 55838 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_b SES surface,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_C SES surface,
23869 of 63382 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_c SES surface,
1029 atoms, 1592 residues, 10 pseudobonds, 1083 bonds
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
Drag select of
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_A SES surface,
41668 of 206614 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_B SES surface,
5650 of 207034 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_C SES surface,
32362 of 201420 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_A SES surface,
30872 of 60532 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_C SES surface,
17329 of 63382 triangles, 229 atoms, 181 residues, 239 bonds
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> select #1/C
1814 atoms, 1872 bonds, 2 pseudobonds, 214 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> select clear
Drag select of
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_A SES surface,
6570 of 206614 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_B SES surface,
37147 of 207034 triangles,
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_B SES surface,
17497 of 55838 triangles, 82 atoms, 41 residues, 84 bonds
> hide sel cartoons
> hide sel surfaces
> hide sel atoms
Drag select of
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_B SES surface,
2541 of 55838 triangles, 12 atoms, 12 bonds
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
Drag select of 39 atoms, 41 bonds
> hide sel atoms
> show sel cartoons
> show sel cartoons
> hide sel cartoons
Drag select of 71 atoms, 76 bonds
> show sel surfaces
> show sel cartoons
> select clear
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
Drag select of
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 337 of 206924 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface, 730 of 64992 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 6913 of 67888 triangles, 37 atoms, 37 bonds
Drag select of
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 10045 of 206924 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 10974 of 67888 triangles, 50 atoms, 8 residues, 52 bonds
> hide sel surfaces
> hide sel atoms
Drag select of
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface, 488 of 204572 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface, 8383 of 205288 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 61096 of 206924 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface, 66235 of 178986 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 4827 of 67888 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface, 6891 of 46184 triangles, 47 atoms, 176 residues, 2 pseudobonds, 52
bonds
> show sel surfaces
> select clear
> show #!1 models
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022_4NAbgroups.cxs"
> show #!5 models
> hide #!5 models
> select #2/F:22
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> lighting soft
> graphics silhouettes false
> show #!5 models
> hide #!5 models
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting flat
> lighting full
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting soft
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022_4NAbgroups.cxs"
opened ChimeraX session
> show sel cartoons
> show sel cartoons
> show sel cartoons
> select clear
> hide #!1 models
> show #!1 models
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> graphics silhouettes false
> lighting flat
> lighting full
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> save /Users/haoyangli/Desktop/image1.png supersample 3
> lighting simple
> lighting shadows true
> lighting shadows false
> save /Users/haoyangli/Desktop/image2.png supersample 3
> hide sel cartoons
> hide sel cartoons
> lighting soft
> lighting simple
> lighting full
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting soft
> hide #!1 models
> show #!1 models
> lighting simple
> save /Users/haoyangli/Desktop/image1.png supersample 3
> lighting soft
> save /Users/haoyangli/Desktop/image2.png supersample 3
> hide #!1 models
> show #!1 models
> save /Users/haoyangli/Desktop/image3.png supersample 3
> hide #!1 models
> select #2/F
777 atoms, 805 bonds, 97 residues, 1 model selected
> hide sel cartoons
> select #2/G
813 atoms, 834 bonds, 106 residues, 1 model selected
> hide sel cartoons
> show sel & #!2 cartoons
> show sel & #!2 cartoons
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save /Users/haoyangli/Desktop/image4.png supersample 3
Drag select of
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_C SES surface,
14490 of 63382 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_a SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_b SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_a SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_b SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 57596 of 67888 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface, 1602 atoms, 2344 residues, 1698 bonds, 18 pseudobonds
> select clear
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022_4NAbgroups.cxs"
Drag select of
GP_89F_372D_04282022_067_coot_real_space_refined_069(final).pdb_C SES surface,
14490 of 63382 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_a SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_b SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_a SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_b SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 57596 of 67888 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface, 1602 atoms, 2344 residues, 1698 bonds, 18 pseudobonds
> show sel surfaces
> select clear
> graphics silhouettes false
> graphics silhouettes true
> save /Users/haoyangli/Desktop/image5.png supersample 3
> save /Users/haoyangli/Desktop/image6.png supersample 3
> show #!4 models
> hide #!4 models
> show #!5 models
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022_4NAbgroups.cxs"
> hide #!1 models
> hide #!5 models
> hide sel & #!2 cartoons
> hide sel & #!2 surfaces
> hide sel & #!2 cartoons
> hide sel & #!2 surfaces
> hide sel surfaces
> hide sel cartoons
> hide sel cartoons
> hide sel surfaces
> show #!1 models
> hide sel cartoons
> hide sel surfaces
> hide sel surfaces
> hide sel cartoons
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show sel cartoons
> show sel cartoons
> select clear
> select #5/D
916 atoms, 936 bonds, 117 residues, 1 model selected
> show #!1-2 cartoons
> undo
> select clear
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
Drag select of 219 residues
> hide sel cartoons
Drag select of 220 residues
> hide sel cartoons
> show #!1 models
> show #!2 models
> color (#!5 & sel) #8b8435ff
> color (#!5 & sel) #808003ff
> select clear
> select #2/D
777 atoms, 805 bonds, 97 residues, 1 model selected
> show sel cartoons
> select #2/E
813 atoms, 834 bonds, 106 residues, 1 model selected
> show sel cartoons
> select #2/R
793 atoms, 812 bonds, 104 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #2/Q
972 atoms, 998 bonds, 125 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #2/O
972 atoms, 998 bonds, 125 residues, 1 model selected
> show sel cartoons
> select #2/P
793 atoms, 812 bonds, 104 residues, 1 model selected
> show sel cartoons
> select clear
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022_4NAbgroups.cxs"
> graphics silhouettes false
> lighting soft
> lighting full
> lighting shadows false
> lighting flat
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> graphics silhouettes false
> save /Users/haoyangli/Desktop/image7.png supersample 3
> save /Users/haoyangli/Desktop/image1.png supersample 3
> graphics silhouettes true
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_May29_2022_4NAbgroups.cxs"
opened ChimeraX session
> hide sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel cartoons
> show sel cartoons
> show sel cartoons
> select #2/F
777 atoms, 805 bonds, 97 residues, 1 model selected
> hide sel cartoons
> select #2/G
813 atoms, 834 bonds, 106 residues, 1 model selected
> hide sel cartoons
> graphics silhouettes false
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/Arenavirumab_3.cxs"
opened ChimeraX session
> graphics silhouettes true
> select #5
12664 atoms, 12961 bonds, 36 pseudobonds, 1573 residues, 2 models selected
> hide #!1 models
> graphics silhouettes false
> graphics silhouettes true
Drag select of
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_a SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_b SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_a SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_b SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 57596 of 67888 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface, 1531 atoms, 2101 residues, 18 pseudobonds, 1622 bonds
> hide sel cartoons
> select clear
> show #!1 models
Drag select of
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface, 110161 of 204572 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_a SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface, 100411 of 205288 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_b SES
surface, 178420 of 179524 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 116830 of 206924 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface, 178884 of 178986 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface, 16319 of 65320 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_a SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface, 14588 of 64992 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_b SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 24704 of 67888 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface, 687 residues, 901 atoms, 955 bonds
> hide sel cartoons
> select clear
> save /Users/haoyangli/Desktop/image1.png supersample 3
> graphics silhouettes false
> save /Users/haoyangli/Desktop/image2.png supersample 3
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2/H
777 atoms, 805 bonds, 97 residues, 1 model selected
> show sel cartoons
> select #2/L
813 atoms, 834 bonds, 106 residues, 1 model selected
> show sel cartoons
> show sel cartoons
> save /Users/haoyangli/Desktop/image3.png supersample 3
> select clear
> save /Users/haoyangli/Desktop/image4.png supersample 3
Drag select of
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface, 162069 of 204572 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_a SES
surface, 68701 of 180190 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface, 10273 of 205288 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_b SES
surface, 21713 of 179524 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 70488 of 206924 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface, 19179 of 178986 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface, 65293 of 65320 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_a SES
surface, 23176 of 46682 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface, 915 of 64992 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 20930 of 67888 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface, 9570 of 46184 triangles, 562 atoms, 203 residues, 598 bonds
> hide sel cartoons
> select clear
> select #2/O
972 atoms, 998 bonds, 125 residues, 1 model selected
> show sel cartoons
> select #2/P
793 atoms, 812 bonds, 104 residues, 1 model selected
> show sel cartoons
> select clear
> save /Users/haoyangli/Desktop/image5.png supersample 3
> hide #!2 models
> show #!2 models
Drag select of
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_a SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_b SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_A SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_a SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_B SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_b SES
surface,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_C SES
surface, 57596 of 67888 triangles,
GPFL_121F_372D_04132022_057_coot_new2_real_space_refined_070(final).pdb_c SES
surface, 1531 atoms, 229 residues, 1622 bonds
> hide sel cartoons
> select #5
12664 atoms, 12961 bonds, 36 pseudobonds, 1573 residues, 2 models selected
> ~select #5
9 models selected
> select #5/K
776 atoms, 792 bonds, 102 residues, 1 model selected
> show sel cartoons
> select #5/K
776 atoms, 792 bonds, 102 residues, 1 model selected
> show sel cartoons
> show sel cartoons
> show sel cartoons
> hide sel cartoons
> hide sel cartoons
> show sel cartoons
> select #5/J
916 atoms, 936 bonds, 117 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #5/G
916 atoms, 936 bonds, 117 residues, 1 model selected
> show sel cartoons
> select clear
> save /Users/haoyangli/Desktop/image6.png supersample 3
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/statusbar.py", line 83, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/statusbar.py", line 143, in status
r.draw_background()
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1100, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
Window position QRect(2037,1364 100x30) outside any known screen, using
primary screen
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/statusbar.py", line 83, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/statusbar.py", line 143, in status
r.draw_background()
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1100, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/statusbar.py", line 83, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/statusbar.py", line 143, in status
r.draw_background()
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1100, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/statusbar.py", line 83, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/statusbar.py", line 143, in status
r.draw_background()
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1100, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/statusbar.py", line 83, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/statusbar.py", line 143, in status
r.draw_background()
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1100, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 165, in draw
self._draw_scene(camera, drawings)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 213, in _draw_scene
camera.draw_background(vnum, r)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/camera.py", line 184, in draw_background
render.draw_background()
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1100, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
Window position QRect(2037,1364 100x30) outside any known screen, using
primary screen
OpenGL version: 4.1 ATI-4.7.101
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1715.60.5.0.0 (iBridge: 19.16.10647.0.0,0)
OS Loader Version: 540.60.2~89
Software:
System Software Overview:
System Version: macOS 12.1 (21C52)
Kernel Version: Darwin 21.2.0
Time since boot: 20:48
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-020
Option ROM Version: 113-D32207P1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
ASUS VE278:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: E4LMTF043857
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.55
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.0
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → saving image: glClear: invalid framebuffer operation |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Error drawing status line. Mac laptop with external display connected and laptop closed. AMD graphics.