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Opened 4 years ago
Last modified 2 years ago
#4983 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Tristan Croll | Owned by: | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Command Line | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3.dev202107240347 (2021-07-24 03:47:26 UTC)
Description
Drag-and-drop from the Linux Nautilus browser to the ChimeraX command line adds "file://" to the beginning of the path, causing the open command to fail.
Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available
> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color bychain; color byhet
cs clipper set contourSensitivity {arguments}
UCSF ChimeraX version: 1.3.dev202107240347 (2021-07-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7o4f
7o4f title:
The DYW domain of A. thaliana OTP86 in its active state [more info...]
Chain information for 7o4f #1
---
Chain | Description | UniProt
A B D G | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
| PP296_ARATH
Non-standard residues in 7o4f #1
---
ZN — zinc ion
7o4f mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
notes | Fetching compressed AlphaFold Q9M1V3 from
https://alphafold.ebi.ac.uk/files/AF-Q9M1V3-F1-model_v1.cif
7522 atoms, 960 residues, atom bfactor range 24.7 to 98.2
Matchmaker 7o4f, chain A (#1) with AlphaFold Q9M1V3, chain A (#), sequence
alignment score = 654.4
RMSD between 102 pruned atom pairs is 0.619 angstroms; (across all 135 pairs:
4.767)
7522 atoms, 960 residues, atom bfactor range 24.7 to 98.2
Matchmaker 7o4f, chain B (#1) with AlphaFold Q9M1V3, chain B (#), sequence
alignment score = 646.3
RMSD between 103 pruned atom pairs is 0.590 angstroms; (across all 135 pairs:
4.891)
7522 atoms, 960 residues, atom bfactor range 24.7 to 98.2
Matchmaker 7o4f, chain D (#1) with AlphaFold Q9M1V3, chain D (#), sequence
alignment score = 654.4
RMSD between 103 pruned atom pairs is 0.611 angstroms; (across all 135 pairs:
4.759)
7522 atoms, 960 residues, atom bfactor range 24.7 to 98.2
Matchmaker 7o4f, chain G (#1) with AlphaFold Q9M1V3, chain G (#), sequence
alignment score = 647.2
RMSD between 103 pruned atom pairs is 0.592 angstroms; (across all 135 pairs:
4.901)
Chain information for UniProt Q9M1V3 chain A #2.1
---
Chain | Description | UniProt
A | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic |
PP296_ARATH
Chain information for UniProt Q9M1V3 chain B #2.2
---
Chain | Description
B | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
Chain information for UniProt Q9M1V3 chain D #2.3
---
Chain | Description
D | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
Chain information for UniProt Q9M1V3 chain G #2.4
---
Chain | Description
G | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
Opened 4 AlphaFold chain models
> ui tool show Shell
> save 7o4f.pdb #1
Fetching compressed Alphafold Q9M1V3 PAE from
https://alphafold.ebi.ac.uk/files/AF-Q9M1V3-F1-predicted_aligned_error_v1.json
> color byattribute r:isolde_domain #2.4 target ra palette rainbow
[Repeated 1 time(s)]1101 atoms, 135 residues, atom isolde_domain range -1 to 4
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> color byattribute r:isolde_domain #2.4 target ra palette rainbow
1101 atoms, 135 residues, atom isolde_domain range -1 to 13
> color byattribute r:isolde_domain #2.4 target ra palette rainbow
1101 atoms, 135 residues, atom isolde_domain range -1 to 23
> color byattribute r:isolde_domain #2.4 target ra palette rainbow
1101 atoms, 135 residues, atom isolde_domain range -1 to 0
> color byattribute r:isolde_domain #2.4 target ra palette rainbow
1101 atoms, 135 residues, atom isolde_domain range -1 to 87
> close #1-2
> open 7cfd
7cfd title:
Drosophila melanogaster Krimper eTud2-AubR15me2 complex [more info...]
Chain information for 7cfd #1
---
Chain | Description | UniProt
A B C D E F G H | FI20010p1 | A1ZAC4_DROME
I J K L M N O Z | Protein aubergine | AUB_DROME
7cfd mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
5| author_defined_assembly
6| author_defined_assembly
7| author_defined_assembly
8| author_defined_assembly
> cartoon
> hide
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
error | Fewer than 3 residues aligned; cannot match 7cfd, chain O with
AlphaFold O76922, chain O
notes | 5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8
Matchmaker 7cfd, chain B (#1) with AlphaFold A1ZAC4, chain B (#), sequence
alignment score = 929
RMSD between 125 pruned atom pairs is 0.984 angstroms; (across all 178 pairs:
2.118)
Fetching compressed AlphaFold O76922 from
https://alphafold.ebi.ac.uk/files/AF-O76922-F1-model_v1.cif
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8
Matchmaker 7cfd, chain I (#1) with AlphaFold O76922, chain I (#), sequence
alignment score = 48.2
RMSD between 4 pruned atom pairs is 0.867 angstroms; (across all 4 pairs:
0.867)
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8
Matchmaker 7cfd, chain C (#1) with AlphaFold A1ZAC4, chain C (#), sequence
alignment score = 935
RMSD between 141 pruned atom pairs is 1.018 angstroms; (across all 179 pairs:
1.674)
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8
Matchmaker 7cfd, chain J (#1) with AlphaFold O76922, chain J (#), sequence
alignment score = 51.8
RMSD between 6 pruned atom pairs is 1.261 angstroms; (across all 7 pairs:
1.648)
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8
Matchmaker 7cfd, chain K (#1) with AlphaFold O76922, chain K (#), sequence
alignment score = 53
RMSD between 8 pruned atom pairs is 1.551 angstroms; (across all 8 pairs:
1.551)
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8
Matchmaker 7cfd, chain D (#1) with AlphaFold A1ZAC4, chain D (#), sequence
alignment score = 925.4
RMSD between 136 pruned atom pairs is 0.934 angstroms; (across all 178 pairs:
1.734)
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8
Matchmaker 7cfd, chain E (#1) with AlphaFold A1ZAC4, chain E (#), sequence
alignment score = 905.6
RMSD between 155 pruned atom pairs is 1.177 angstroms; (across all 180 pairs:
1.888)
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8
Matchmaker 7cfd, chain L (#1) with AlphaFold O76922, chain L (#), sequence
alignment score = 48.2
RMSD between 4 pruned atom pairs is 1.100 angstroms; (across all 4 pairs:
1.100)
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8
Matchmaker 7cfd, chain F (#1) with AlphaFold A1ZAC4, chain F (#), sequence
alignment score = 936.2
RMSD between 143 pruned atom pairs is 1.059 angstroms; (across all 182 pairs:
1.673)
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8
Matchmaker 7cfd, chain A (#1) with AlphaFold A1ZAC4, chain A (#), sequence
alignment score = 931.4
RMSD between 131 pruned atom pairs is 1.015 angstroms; (across all 176 pairs:
1.780)
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8
Matchmaker 7cfd, chain G (#1) with AlphaFold A1ZAC4, chain G (#), sequence
alignment score = 933.8
RMSD between 147 pruned atom pairs is 1.263 angstroms; (across all 181 pairs:
1.573)
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8
Matchmaker 7cfd, chain N (#1) with AlphaFold O76922, chain N (#), sequence
alignment score = 50.6
RMSD between 5 pruned atom pairs is 1.368 angstroms; (across all 6 pairs:
1.962)
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8
Matchmaker 7cfd, chain H (#1) with AlphaFold A1ZAC4, chain H (#), sequence
alignment score = 870.2
RMSD between 151 pruned atom pairs is 1.283 angstroms; (across all 181 pairs:
1.594)
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8
Matchmaker 7cfd, chain M (#1) with AlphaFold O76922, chain M (#), sequence
alignment score = 50.6
RMSD between 5 pruned atom pairs is 0.710 angstroms; (across all 6 pairs:
1.685)
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8
Matchmaker 7cfd, chain Z (#1) with AlphaFold O76922, chain Z (#), sequence
alignment score = 47
RMSD between 3 pruned atom pairs is 0.729 angstroms; (across all 3 pairs:
0.729)
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8
Matchmaker 7cfd, chain O (#1) with AlphaFold O76922, chain O (#), sequence
alignment score = 44.6
Chain information for UniProt A1ZAC4 chain B #2.1
---
Chain | Description
B | FI20010p1
Chain information for UniProt O76922 chain I #2.2
---
Chain | Description
I | Protein aubergine
Chain information for UniProt A1ZAC4 chain C #2.3
---
Chain | Description
C | FI20010p1
Chain information for UniProt O76922 chain J #2.4
---
Chain | Description
J | Protein aubergine
Chain information for UniProt O76922 chain K #2.5
---
Chain | Description
K | Protein aubergine
Chain information for UniProt A1ZAC4 chain D #2.6
---
Chain | Description
D | FI20010p1
Chain information for UniProt A1ZAC4 chain E #2.7
---
Chain | Description
E | FI20010p1
Chain information for UniProt O76922 chain L #2.8
---
Chain | Description
L | Protein aubergine
Chain information for UniProt A1ZAC4 chain F #2.9
---
Chain | Description
F | FI20010p1
Chain information for UniProt A1ZAC4 chain A #2.10
---
Chain | Description | UniProt
A | FI20010p1 | A1ZAC4_DROME
Chain information for UniProt A1ZAC4 chain G #2.11
---
Chain | Description
G | FI20010p1
Chain information for UniProt O76922 chain N #2.12
---
Chain | Description
N | Protein aubergine
Chain information for UniProt A1ZAC4 chain H #2.13
---
Chain | Description
H | FI20010p1
Chain information for UniProt O76922 chain M #2.14
---
Chain | Description
M | Protein aubergine
Chain information for UniProt O76922 chain Z #2.15
---
Chain | Description
Z | Protein aubergine
Chain information for UniProt O76922 chain O #2.16
---
Chain | Description
O | Protein aubergine
Opened 16 AlphaFold chain models
> hide #2.16 models
> show #2.16 models
> select #2.1
1521 atoms, 1562 bonds, 185 residues, 1 model selected
Fetching compressed Alphafold A1ZAC4 PAE from
https://alphafold.ebi.ac.uk/files/AF-A1ZAC4-F1-predicted_aligned_error_v1.json
> color byattribute r:isolde_domain #2.1 target ra palette rainbow
1521 atoms, 185 residues, atom isolde_domain range -1 to 110
> color byattribute r:isolde_domain #2.1 target ra palette rainbow
1521 atoms, 185 residues, atom isolde_domain range -1 to 9
> hide ~sel models
> show #!2 models
> select clear
> color byattribute r:isolde_domain #2.1 target ra palette rainbow
1521 atoms, 185 residues, atom isolde_domain range -1 to 16
> color byattribute r:isolde_domain #2.1 target ra palette rainbow
1521 atoms, 185 residues, atom isolde_domain range -1 to 17
> save 7cfd.pdb #1
> save AF_A1ZAC4_cluster_0.pdb #2.1 selectedOnly true
> save AF_A1ZAC4_cluster_1.pdb #2.1 selectedOnly true
> select clear
> open 7cfb
7cfb title:
Drosophila melanogaster Krimper eTud1 apo structure [more info...]
Chain information for 7cfb #3
---
Chain | Description | UniProt
A B | FI20010p1 | A1ZAC4_DROME
Non-standard residues in 7cfb #3
---
SO4 — sulfate ion
7cfb mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> matchmaker #3 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 7cfd, chain H (#1) with 7cfb, chain B (#3), sequence alignment
score = 114.8
RMSD between 83 pruned atom pairs is 1.228 angstroms; (across all 143 pairs:
5.190)
> matchmaker #3 to #2.1
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 UniProt A1ZAC4 chain B, chain B (#2.1) with 7cfb, chain B (#3),
sequence alignment score = 99.8
RMSD between 76 pruned atom pairs is 1.068 angstroms; (across all 143 pairs:
5.602)
> save 7cfb.pdb #3
> close #1-2#3
> open 7ciw
7ciw title:
Crystal Structure of Agmatine N-Acetyltransferase mutant S171A in complex with
Ac-Agm and CoA [more info...]
Chain information for 7ciw #1
---
Chain | Description | UniProt
A | Agmatine N-acetyltransferase | Q9W469_DROME
Non-standard residues in 7ciw #1
---
COA — coenzyme A
G0R — N-(4-carbamimidamidobutyl)ethanamide
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
notes | Fetching compressed AlphaFold Q9W469 from
https://alphafold.ebi.ac.uk/files/AF-Q9W469-F1-model_v1.cif
1673 atoms, 216 residues, atom bfactor range 40.4 to 98.9
Matchmaker 7ciw, chain A (#1) with AlphaFold Q9W469, chain A (#), sequence
alignment score = 1100.6
RMSD between 208 pruned atom pairs is 0.547 angstroms; (across all 216 pairs:
3.620)
Chain information for UniProt Q9W469 chain A
---
Chain | Description | UniProt
2.1/A | Agmatine N-acetyltransferase | Q9W469_DROME
Opened 1 AlphaFold chain models
> close #1#2
> open 7ck3
7ck3 title:
Crystal structure of Arabidopsis CESA3 catalytic domain [more info...]
Chain information for 7ck3 #1
---
Chain | Description | UniProt
A B | Cellulose synthase A catalytic subunit 3 [UDP-forming],Cellulose
synthase A catalytic subunit 3 [UDP-forming] | CESA3_ARATH
7ck3 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
notes | 8430 atoms, 1065 residues, atom bfactor range 23 to 97.8
Matchmaker 7ck3, chain A (#1) with AlphaFold Q941L0, chain A (#), sequence
alignment score = 1592
RMSD between 50 pruned atom pairs is 0.916 angstroms; (across all 98 pairs:
9.484)
8430 atoms, 1065 residues, atom bfactor range 23 to 97.8
Matchmaker 7ck3, chain B (#1) with AlphaFold Q941L0, chain B (#), sequence
alignment score = 1598.3
RMSD between 51 pruned atom pairs is 0.926 angstroms; (across all 98 pairs:
9.558)
Chain information for UniProt Q941L0 chain A #2.1
---
Chain | Description | UniProt
A | Cellulose synthase A catalytic subunit 3 [UDP-forming] | CESA3_ARATH
Chain information for UniProt Q941L0 chain B #2.2
---
Chain | Description
B | Cellulose synthase A catalytic subunit 3 [UDP-forming]
Opened 2 AlphaFold chain models
> open #1 fromDatabase AlphaFold trim false
Summary of feedback from opening #1 fetched from AlphaFold
---
notes | 8430 atoms, 1065 residues, atom bfactor range 23 to 97.8
Matchmaker 7ck3, chain A (#1) with AlphaFold Q941L0, chain A (#), sequence
alignment score = 1890.2
RMSD between 268 pruned atom pairs is 0.836 angstroms; (across all 369 pairs:
5.904)
8430 atoms, 1065 residues, atom bfactor range 23 to 97.8
Matchmaker 7ck3, chain B (#1) with AlphaFold Q941L0, chain B (#), sequence
alignment score = 1903.7
RMSD between 270 pruned atom pairs is 0.856 angstroms; (across all 369 pairs:
5.907)
Chain information for UniProt Q941L0 chain A #3.1
---
Chain | Description | UniProt
A | Cellulose synthase A catalytic subunit 3 [UDP-forming] | CESA3_ARATH
Chain information for UniProt Q941L0 chain B #3.2
---
Chain | Description
B | Cellulose synthase A catalytic subunit 3 [UDP-forming]
Opened 2 AlphaFold chain models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #2
> hide #2
> show #!3 models
> color bfactor #3
16860 atoms, 2130 residues, atom bfactor range 23 to 97.8
> select #3&@@bfactor>50
13038 atoms, 13380 bonds, 1632 residues, 2 models selected
> select #3&@@bfactor>70
12158 atoms, 12492 bonds, 1518 residues, 2 models selected
> select clear
> hide #!3 models
> show #!3 models
> hide #!2 models
> ~cartoon #3
> show #3@CA
> close #2#1,3
> open 7dl9
7dl9 title:
Crystal structure of nucleoside transporter NupG [more info...]
Chain information for 7dl9 #1
---
Chain | Description | UniProt
A B | Nucleoside permease NupG | NUPG_ECOLI
Non-standard residues in 7dl9 #1
---
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
7dl9 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
notes | Fetching compressed AlphaFold P0AFF4 from
https://alphafold.ebi.ac.uk/files/AF-P0AFF4-F1-model_v1.cif
3268 atoms, 418 residues, atom bfactor range 31 to 98.7
Matchmaker 7dl9, chain A (#1) with AlphaFold P0AFF4, chain A (#), sequence
alignment score = 2122.9
RMSD between 329 pruned atom pairs is 0.770 angstroms; (across all 405 pairs:
2.344)
3268 atoms, 418 residues, atom bfactor range 31 to 98.7
Matchmaker 7dl9, chain B (#1) with AlphaFold P0AFF4, chain B (#), sequence
alignment score = 2116.3
RMSD between 330 pruned atom pairs is 0.795 angstroms; (across all 405 pairs:
2.369)
Chain information for UniProt P0AFF4 chain A #2.1
---
Chain | Description | UniProt
A | Nucleoside permease NupG | NUPG_ECOLI
Chain information for UniProt P0AFF4 chain B #2.2
---
Chain | Description
B | Nucleoside permease NupG
Opened 2 AlphaFold chain models
Fetching compressed Alphafold P0AFF4 PAE from
https://alphafold.ebi.ac.uk/files/AF-P0AFF4-F1-predicted_aligned_error_v1.json
> color byattribute r:isolde_domain #2.2 target ra palette rainbow
3268 atoms, 418 residues, atom isolde_domain range -1 to 61
> hide #1 models
> show #1 models
> select clear
[Repeated 2 time(s)]
> select #1/B:275
8 atoms, 7 bonds, 1 residue, 1 model selected
> color byattribute r:isolde_domain #2.2
3268 atoms, 418 residues, atom isolde_domain range -1 to 61
> hide #1 models
> select clear
> color byattribute r:isolde_domain #2.2 target ra palette rainbow
3268 atoms, 418 residues, atom isolde_domain range -1 to 5
> show #1 models
> color byattribute r:isolde_domain #2.2 target ra palette rainbow
3268 atoms, 418 residues, atom isolde_domain range -1 to 19
> color byattribute r:isolde_domain #2.2 target ra palette rainbow
3268 atoms, 418 residues, atom isolde_domain range -1 to 5
> close #1#2
> open 7e0w
7e0w title:
Crystal Structure of BCH domain from S. pombe [more info...]
Chain information for 7e0w #1
---
Chain | Description | UniProt
A B C D | Putative ρ GTPase-activating protein C1565.02c | YIL2_SCHPO
Non-standard residues in 7e0w #1
---
PG4 — tetraethylene glycol
7e0w mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> mpen #1 from alphafold
Unknown command: mpen #1 from alphafold
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
notes | Fetching compressed AlphaFold Q9P3B1 from
https://alphafold.ebi.ac.uk/files/AF-Q9P3B1-F1-model_v1.cif
3039 atoms, 374 residues, atom bfactor range 31.4 to 98.7
Matchmaker 7e0w, chain A (#1) with AlphaFold Q9P3B1, chain A (#), sequence
alignment score = 736.3
RMSD between 71 pruned atom pairs is 0.880 angstroms; (across all 147 pairs:
19.860)
3039 atoms, 374 residues, atom bfactor range 31.4 to 98.7
Matchmaker 7e0w, chain B (#1) with AlphaFold Q9P3B1, chain B (#), sequence
alignment score = 698.5
RMSD between 72 pruned atom pairs is 0.982 angstroms; (across all 147 pairs:
19.957)
3039 atoms, 374 residues, atom bfactor range 31.4 to 98.7
Matchmaker 7e0w, chain C (#1) with AlphaFold Q9P3B1, chain C (#), sequence
alignment score = 697.9
RMSD between 79 pruned atom pairs is 1.007 angstroms; (across all 147 pairs:
19.904)
3039 atoms, 374 residues, atom bfactor range 31.4 to 98.7
Matchmaker 7e0w, chain D (#1) with AlphaFold Q9P3B1, chain D (#), sequence
alignment score = 676.3
RMSD between 78 pruned atom pairs is 0.977 angstroms; (across all 147 pairs:
19.898)
Chain information for UniProt Q9P3B1 chain A #2.1
---
Chain | Description | UniProt
A | Putative ρ GTPase-activating protein C1565.02c | YIL2_SCHPO
Chain information for UniProt Q9P3B1 chain B #2.2
---
Chain | Description
B | Putative ρ GTPase-activating protein C1565.02c
Chain information for UniProt Q9P3B1 chain C #2.3
---
Chain | Description
C | Putative ρ GTPase-activating protein C1565.02c
Chain information for UniProt Q9P3B1 chain D #2.4
---
Chain | Description
D | Putative ρ GTPase-activating protein C1565.02c
Opened 4 AlphaFold chain models
> color #1 bychain
> ~cartoon #1&~/A
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> hide #1
Fetching compressed Alphafold Q9P3B1 PAE from
https://alphafold.ebi.ac.uk/files/AF-Q9P3B1-F1-predicted_aligned_error_v1.json
> select #2.1
1293 atoms, 1327 bonds, 155 residues, 1 model selected
> color byattribute r:isolde_domain #2.1 target ra palette rainbow
1293 atoms, 155 residues, atom isolde_domain range 1 to 7
> select clear
> color byattribute r:isolde_domain #2.1 target ra palette rainbow
1293 atoms, 155 residues, atom isolde_domain range 0 to 2
> color byattribute r:isolde_domain #2.1 target ra palette rainbow
1293 atoms, 155 residues, atom isolde_domain range 0 to 48
> select clear
> usage color
color [objects] [color [what]] [target characters from 'abcfmprs']
[transparency a number] [halfbond true or false]
— color objects
objects: an objects specifier or nothing
color: a color or one of byatom, bychain, byelement, byhetero, byidentity,
bymodel, bynucleotide, bypolymer, fromatoms, or random
what: a collection of one of All, atoms, bonds, cartoons, labels, models,
pseudobonds, ribbons, rings, or surfaces
Subcommands are:
* color bfactor
* color byattribute
* color cylindrical
* color delete
* color electrostatic
* color gradient
* color height
* color image
* color list
* color modify
* color name
* color radial
* color sample
* color sequential
* color show
* color single
* color zone
> usage color sequential
color sequential [objects] [level] [target characters from 'abcfmprs'] [what
what] [palette a colormap] [transparency a number]
— color a sequence of atomic objects using a palette
objects: an objects specifier or nothing
level: one of chains, polymers, residues, or structures
what: a collection of one of All, atoms, bonds, cartoons, labels, models,
pseudobonds, ribbons, rings, or surfaces
> usage color list
color list [which]
— list colors
which: one of all, builtin, or custom
> help help:user
> palette list
No custom palettes.
310 builtin palettes: Accent, Accent-3, Accent-4, Accent-5, Accent-6,
Accent-7, Accent-8, blue-white-red, bluered, Blues, Blues-3, Blues-4, Blues-5,
Blues-6, Blues-7, Blues-8, Blues-9, BrBG, BrBG-10, BrBG-11, BrBG-3, BrBG-4,
BrBG-5, BrBG-6, BrBG-7, BrBG-8, BrBG-9, BuGn, BuGn-3, BuGn-4, BuGn-5, BuGn-6,
BuGn-7, BuGn-8, BuGn-9, BuPu, BuPu-3, BuPu-4, BuPu-5, BuPu-6, BuPu-7, BuPu-8,
BuPu-9, cyan-gray-maroon, cyan-white-maroon, cyanmaroon, Dark2, Dark2-3,
Dark2-4, Dark2-5, Dark2-6, Dark2-7, Dark2-8, GnBu, GnBu-3, GnBu-4, GnBu-5,
GnBu-6, GnBu-7, GnBu-8, GnBu-9, gray, grayscale, Greens, Greens-3, Greens-4,
Greens-5, Greens-6, Greens-7, Greens-8, Greens-9, Greys, Greys-3, Greys-4,
Greys-5, Greys-6, Greys-7, Greys-8, Greys-9, lipophilicity, Oranges,
Oranges-3, Oranges-4, Oranges-5, Oranges-6, Oranges-7, Oranges-8, Oranges-9,
OrRd, OrRd-3, OrRd-4, OrRd-5, OrRd-6, OrRd-7, OrRd-8, OrRd-9, Paired,
Paired-10, Paired-11, Paired-12, Paired-3, Paired-4, Paired-5, Paired-6,
Paired-7, Paired-8, Paired-9, Pastel1, Pastel1-3, Pastel1-4, Pastel1-5,
Pastel1-6, Pastel1-7, Pastel1-8, Pastel1-9, Pastel2, Pastel2-3, Pastel2-4,
Pastel2-5, Pastel2-6, Pastel2-7, Pastel2-8, PiYG, PiYG-10, PiYG-11, PiYG-3,
PiYG-4, PiYG-5, PiYG-6, PiYG-7, PiYG-8, PiYG-9, PRGn, PRGn-10, PRGn-11,
PRGn-3, PRGn-4, PRGn-5, PRGn-6, PRGn-7, PRGn-8, PRGn-9, PuBu, PuBu-3, PuBu-4,
PuBu-5, PuBu-6, PuBu-7, PuBu-8, PuBu-9, PuBuGn, PuBuGn-3, PuBuGn-4, PuBuGn-5,
PuBuGn-6, PuBuGn-7, PuBuGn-8, PuBuGn-9, PuOr, PuOr-10, PuOr-11, PuOr-3,
PuOr-4, PuOr-5, PuOr-6, PuOr-7, PuOr-8, PuOr-9, PuRd, PuRd-3, PuRd-4, PuRd-5,
PuRd-6, PuRd-7, PuRd-8, PuRd-9, Purples, Purples-3, Purples-4, Purples-5,
Purples-6, Purples-7, Purples-8, Purples-9, rainbow, RdBu, RdBu-10, RdBu-11,
RdBu-3, RdBu-4, RdBu-5, RdBu-6, RdBu-7, RdBu-8, RdBu-9, RdGy, RdGy-10,
RdGy-11, RdGy-3, RdGy-4, RdGy-5, RdGy-6, RdGy-7, RdGy-8, RdGy-9, RdPu, RdPu-3,
RdPu-4, RdPu-5, RdPu-6, RdPu-7, RdPu-8, RdPu-9, RdYlBu, RdYlBu-10, RdYlBu-11,
RdYlBu-3, RdYlBu-4, RdYlBu-5, RdYlBu-6, RdYlBu-7, RdYlBu-8, RdYlBu-9, RdYlGn,
RdYlGn-10, RdYlGn-11, RdYlGn-3, RdYlGn-4, RdYlGn-5, RdYlGn-6, RdYlGn-7,
RdYlGn-8, RdYlGn-9, red-white-blue, redblue, Reds, Reds-3, Reds-4, Reds-5,
Reds-6, Reds-7, Reds-8, Reds-9, Set1, Set1-3, Set1-4, Set1-5, Set1-6, Set1-7,
Set1-8, Set1-9, Set2, Set2-3, Set2-4, Set2-5, Set2-6, Set2-7, Set2-8, Set3,
Set3-10, Set3-11, Set3-12, Set3-3, Set3-4, Set3-5, Set3-6, Set3-7, Set3-8,
Set3-9, Spectral, Spectral-10, Spectral-11, Spectral-3, Spectral-4,
Spectral-5, Spectral-6, Spectral-7, Spectral-8, Spectral-9, YlGn, YlGn-3,
YlGn-4, YlGn-5, YlGn-6, YlGn-7, YlGn-8, YlGn-9, YlGnBu, YlGnBu-3, YlGnBu-4,
YlGnBu-5, YlGnBu-6, YlGnBu-7, YlGnBu-8, YlGnBu-9, YlOrBr, YlOrBr-3, YlOrBr-4,
YlOrBr-5, YlOrBr-6, YlOrBr-7, YlOrBr-8, YlOrBr-9, YlOrRd, YlOrRd-3, YlOrRd-4,
YlOrRd-5, YlOrRd-6, YlOrRd-7, and YlOrRd-8.
> color byattribute r:isolde_domain #2.1 palette paired-12
1293 atoms, 155 residues, atom isolde_domain range 0 to 48
> color byattribute r:isolde_domain #2.1 palette rdgy-5
1293 atoms, 155 residues, atom isolde_domain range 0 to 48
> select #2.1/A:74
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #2.1/A:30
13 atoms, 11 bonds, 2 residues, 1 model selected
> usage color byattr
color byattribute attrName [atoms] [what] [target characters from 'abcfmprs']
[average average] [palette a colormap] [range range] [noValueColor a color]
[transparency a number] [key true or false]
— color atoms by bfactor
attrName: a text string
atoms: an atoms specifier or nothing
what: a collection of one of atoms, cartoons, ribbons, or surfaces
average: residues
range: some numbers or full
> color byattribute r:isolde_domain #2.1 palette paired-12 range 0,11
1293 atoms, 155 residues, atom isolde_domain range 0 to 48
> color byattribute r:isolde_domain #2.1 target ra palette paired-12 range
> 0,11
1293 atoms, 155 residues, atom isolde_domain range 1 to 7
> color byattribute r:isolde_domain #2.1 target ra palette paired-12 range
> 0,11
1293 atoms, 155 residues, atom isolde_domain range 0 to 11
> color byattribute r:isolde_domain #2.1 target ra palette paired-12 range
> 0,11
1293 atoms, 155 residues, atom isolde_domain range 0 to 2
> color byattribute r:isolde_domain #2.1 target ra palette paired-12 range
> 0,11
1293 atoms, 155 residues, atom isolde_domain range 0 to 40
> close #1#2
> open 7dog
7dog title:
Crystal structure of a nuclease and capping domain of SbcD from Staphylococcus
aureus [more info...]
Chain information for 7dog #1
---
Chain | Description | UniProt
A B | Nuclease SbcCD subunit D | SBCD_STAAM
Non-standard residues in 7dog #1
---
MN — manganese (II) ion
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
warning | AlphaFold database does not have models for 1 UniProt ids Q99UD1
(chains A,B)
Opened 0 AlphaFold chain models
> open Q2FYT4 fromDatabase AlphaFold
Summary of feedback from opening Q2FYT4 fetched from AlphaFold
---
notes | Fetching compressed AlphaFold Q2FYT4 from
https://alphafold.ebi.ac.uk/files/AF-Q2FYT4-F1-model_v1.cif
3023 atoms, 373 residues, atom bfactor range 44.1 to 98.9
Chain information for AlphaFold Q2FYT4 #2
---
Chain | Description | UniProt
A | Nuclease SbcCD subunit D | SBCD_STAA8
> 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 7dog, chain A (#1) with AlphaFold Q2FYT4, chain A (#2), sequence
alignment score = 1584.1
RMSD between 305 pruned atom pairs is 0.780 angstroms; (across all 318 pairs:
1.013)
> close #2#1
> open 7e0w
7e0w title:
Crystal Structure of BCH domain from S. pombe [more info...]
Chain information for 7e0w #1
---
Chain | Description | UniProt
A B C D | Putative ρ GTPase-activating protein C1565.02c | YIL2_SCHPO
Non-standard residues in 7e0w #1
---
PG4 — tetraethylene glycol
7e0w mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
notes | 3039 atoms, 374 residues, atom bfactor range 31.4 to 98.7
Matchmaker 7e0w, chain A (#1) with AlphaFold Q9P3B1, chain A (#), sequence
alignment score = 736.3
RMSD between 71 pruned atom pairs is 0.880 angstroms; (across all 147 pairs:
19.860)
3039 atoms, 374 residues, atom bfactor range 31.4 to 98.7
Matchmaker 7e0w, chain B (#1) with AlphaFold Q9P3B1, chain B (#), sequence
alignment score = 698.5
RMSD between 72 pruned atom pairs is 0.982 angstroms; (across all 147 pairs:
19.957)
3039 atoms, 374 residues, atom bfactor range 31.4 to 98.7
Matchmaker 7e0w, chain C (#1) with AlphaFold Q9P3B1, chain C (#), sequence
alignment score = 697.9
RMSD between 79 pruned atom pairs is 1.007 angstroms; (across all 147 pairs:
19.904)
3039 atoms, 374 residues, atom bfactor range 31.4 to 98.7
Matchmaker 7e0w, chain D (#1) with AlphaFold Q9P3B1, chain D (#), sequence
alignment score = 676.3
RMSD between 78 pruned atom pairs is 0.977 angstroms; (across all 147 pairs:
19.898)
Chain information for UniProt Q9P3B1 chain A #2.1
---
Chain | Description | UniProt
A | Putative ρ GTPase-activating protein C1565.02c | YIL2_SCHPO
Chain information for UniProt Q9P3B1 chain B #2.2
---
Chain | Description
B | Putative ρ GTPase-activating protein C1565.02c
Chain information for UniProt Q9P3B1 chain C #2.3
---
Chain | Description
C | Putative ρ GTPase-activating protein C1565.02c
Chain information for UniProt Q9P3B1 chain D #2.4
---
Chain | Description
D | Putative ρ GTPase-activating protein C1565.02c
Opened 4 AlphaFold chain models
> select #2.1
1293 atoms, 1327 bonds, 155 residues, 1 model selected
> color byattribute r:isolde_domain #2.1 target ra palette paired-12 range
> 0,11
1293 atoms, 155 residues, atom isolde_domain range 0 to 2
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> ~cartoon #1&~/A
> hide #1
> select clear
> color byattribute r:isolde_domain #2.1 target ra palette paired-12 range
> 0,11
1293 atoms, 155 residues, atom isolde_domain range 0 to 40
> color byattribute r:isolde_domain #2.1 target ra palette paired-12 range
> 0,11
1293 atoms, 155 residues, atom isolde_domain range 1 to 7
> color byattribute r:isolde_domain #2.1 target ra palette paired-12 range
> 0,11
1293 atoms, 155 residues, atom isolde_domain range 0 to 11
> select clear
> color byattribute r:isolde_domain #2.1 target ra palette paired-12 range
> 0,11
1293 atoms, 155 residues, atom isolde_domain range 0 to 2
> close #1#2
> open 7dus
7dus title:
Crystal structure of Mei2-RRM3 domain in S.pombe [more info...]
Chain information for 7dus #1
---
Chain | Description | UniProt
A | Meiosis protein mei2 | MEI2_SCHPO
Non-standard residues in 7dus #1
---
CIT — citric acid
7dus mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
notes | Fetching compressed AlphaFold P08965 from
https://alphafold.ebi.ac.uk/files/AF-P08965-F1-model_v1.cif
5808 atoms, 750 residues, atom bfactor range 25.3 to 98.5
Matchmaker 7dus, chain A (#1) with AlphaFold P08965, chain A (#), sequence
alignment score = 730.4
RMSD between 108 pruned atom pairs is 0.525 angstroms; (across all 133 pairs:
11.733)
Chain information for UniProt P08965 chain A
---
Chain | Description | UniProt
2.1/A | Meiosis protein mei2 | MEI2_SCHPO
Opened 1 AlphaFold chain models
> close #1#2
> open 7e9k
Summary of feedback from opening 7e9k fetched from pdb
---
warnings | Unknown polymer entity '5' near line 19436
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
7e9k title:
Crystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide
(379Man long peptide) [more info...]
Chain information for 7e9k #1
---
Chain | Description | UniProt
A B D E | Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
| PMGT2_BOVIN
C F | mono-mannosyl peptide (379Man long peptide) |
Non-standard residues in 7e9k #1
---
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
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)
NH2 — amino group
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)
7e9k mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> cartoon
> hide
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
warnings | UniProt sequence identifier not specified in file for chains /C,/F
AlphaFold database does not have models for 1 UniProt ids Q5NDF2 (chains
A,B,D,E)
Opened 0 AlphaFold chain models
> open Q8NAT1 fromDatabase AlphaFold
Summary of feedback from opening Q8NAT1 fetched from AlphaFold
---
notes | Fetching compressed AlphaFold Q8NAT1 from
https://alphafold.ebi.ac.uk/files/AF-Q8NAT1-F1-model_v1.cif
4703 atoms, 580 residues, atom bfactor range 36.2 to 98.9
Chain information for AlphaFold Q8NAT1 #2
---
Chain | Description | UniProt
A | Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 |
PMGT2_HUMAN
> 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 7e9k, chain B (#1) with AlphaFold Q8NAT1, chain A (#2), sequence
alignment score = 2608.1
RMSD between 414 pruned atom pairs is 0.627 angstroms; (across all 521 pairs:
2.663)
> open 6xfi
Summary of feedback from opening 6xfi fetched from pdb
---
warnings | Unknown polymer entity '2' near line 5814
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
6xfi title:
Crystal Structures of beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2):
Structural Basis for Inherited Muscular Dystrophies [more info...]
Chain information for 6xfi #3
---
Chain | Description | UniProt
A | Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 |
PMGT2_HUMAN
Non-standard residues in 6xfi #3
---
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)
PO4 — phosphate ion
6xfi mmCIF Assemblies
---
1| author_and_software_defined_assembly
> matchmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AlphaFold Q8NAT1, chain A (#2) with 6xfi, chain A (#3), sequence
alignment score = 2663.6
RMSD between 386 pruned atom pairs is 0.622 angstroms; (across all 511 pairs:
2.022)
> close #2#1,3
> open 7ec4
Summary of feedback from opening 7ec4 fetched from pdb
---
warnings | Unknown polymer entity '3' near line 10023
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
7ec4 title:
Crystal structure of SdgB (complexed with UDP and peptides) [more info...]
Chain information for 7ec4 #1
---
Chain | Description | UniProt
A C | Glycosyl transferase, group 1 family protein | A0A0H2XGN0_STAA3
E G | ser-asp-ser-asp |
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
warnings | UniProt sequence identifier not specified in file for chains /E,/G
UniProt identifiers must be 6 characters long
AlphaFold database does not have models for 1 UniProt ids A0A0H2XGN0 (chains
A,C)
Opened 0 AlphaFold chain models
> open Q2FZM6 fromDatabase AlphaFold
Summary of feedback from opening Q2FZM6 fetched from AlphaFold
---
notes | Fetching compressed AlphaFold Q2FZM6 from
https://alphafold.ebi.ac.uk/files/AF-Q2FZM6-F1-model_v1.cif
2099 atoms, 260 residues, atom bfactor range 58.6 to 98.9
Chain information for AlphaFold Q2FZM6 #2
---
Chain | Description | UniProt
A | Glycosyl transferase, group 1 | Q2FZM6_STAA8
> 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 7ec4, chain C (#1) with AlphaFold Q2FZM6, chain A (#2), sequence
alignment score = 501.4
RMSD between 180 pruned atom pairs is 1.201 angstroms; (across all 259 pairs:
2.534)
> color #1 bychain
> close #2
> open Q2FZM6 fromDatabase AlphaFold trim false
Summary of feedback from opening Q2FZM6 fetched from AlphaFold
---
note | 2099 atoms, 260 residues, atom bfactor range 58.6 to 98.9
Chain information for AlphaFold Q2FZM6 #2
---
Chain | Description | UniProt
A | Glycosyl transferase, group 1 | Q2FZM6_STAA8
> 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 7ec4, chain C (#1) with AlphaFold Q2FZM6, chain A (#2), sequence
alignment score = 501.4
RMSD between 180 pruned atom pairs is 1.201 angstroms; (across all 259 pairs:
2.534)
> select #2
2099 atoms, 2136 bonds, 260 residues, 1 model selected
> select clear
> select #1/A
4198 atoms, 4293 bonds, 1 pseudobond, 513 residues, 2 models selected
> select clear
> close #2
> open Q2G0L2 fromDatabase AlphaFold
Summary of feedback from opening Q2G0L2 fetched from AlphaFold
---
notes | Fetching compressed AlphaFold Q2G0L2 from
https://alphafold.ebi.ac.uk/files/AF-Q2G0L2-F1-model_v1.cif
4136 atoms, 496 residues, atom bfactor range 49.2 to 98.8
Chain information for AlphaFold Q2G0L2 #2
---
Chain | Description | UniProt
A | Glycos_transf_1 domain-containing protein | Q2G0L2_STAA8
> 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 7ec4, chain A (#1) with AlphaFold Q2G0L2, chain A (#2), sequence
alignment score = 2504.3
RMSD between 339 pruned atom pairs is 0.848 angstroms; (across all 493 pairs:
3.152)
Fetching compressed Alphafold Q2G0L2 PAE from
https://alphafold.ebi.ac.uk/files/AF-Q2G0L2-F1-predicted_aligned_error_v1.json
> select #2
4136 atoms, 4241 bonds, 496 residues, 1 model selected
> color byattribute r:isolde_domain #2 target ra palette paired-12 range 0,11
4136 atoms, 496 residues, atom isolde_domain range -1 to 3
> select clear
> hide #!1 models
> show #!1 models
ERROR:tornado.general:Uncaught exception in ZMQStream callback
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 434, in _run_callback
callback(*args, **kwargs)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 118, in _handle_event
event_f()
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 212, in <lambda>
self.schedule(lambda : self._really_send(*args, **kwargs))
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 220, in _really_send
self.socket.send_multipart(msg, *args, **kwargs)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/inprocess/socket.py", line 58, in send_multipart
self.message_sent += 1
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 604, in __set__
self.set(obj, value)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 593, in set
obj._notify_trait(self.name, old_value, new_value)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1217, in _notify_trait
self.notify_change(Bunch(
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1227, in notify_change
return self._notify_observers(change)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1264, in _notify_observers
c(event)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/inprocess/ipkernel.py", line 130, in _io_dispatch
ident, msg = self.session.recv(self.iopub_socket, copy=False)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/jupyter_client/session.py", line 809, in recv
msg_list = socket.recv_multipart(mode, copy=copy)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 244, in __getattr__
warnings.warn("Accessing zmq Socket attribute %s on BackgroundSocket" % attr,
DeprecationWarning: Accessing zmq Socket attribute recv_multipart on
BackgroundSocket
ERROR:tornado.general:Uncaught exception in zmqstream callback
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 451, in _handle_events
self._handle_recv()
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 434, in _run_callback
callback(*args, **kwargs)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 118, in _handle_event
event_f()
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 212, in <lambda>
self.schedule(lambda : self._really_send(*args, **kwargs))
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 220, in _really_send
self.socket.send_multipart(msg, *args, **kwargs)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/inprocess/socket.py", line 58, in send_multipart
self.message_sent += 1
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 604, in __set__
self.set(obj, value)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 593, in set
obj._notify_trait(self.name, old_value, new_value)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1217, in _notify_trait
self.notify_change(Bunch(
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1227, in notify_change
return self._notify_observers(change)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1264, in _notify_observers
c(event)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/inprocess/ipkernel.py", line 130, in _io_dispatch
ident, msg = self.session.recv(self.iopub_socket, copy=False)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/jupyter_client/session.py", line 809, in recv
msg_list = socket.recv_multipart(mode, copy=copy)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 244, in __getattr__
warnings.warn("Accessing zmq Socket attribute %s on BackgroundSocket" % attr,
DeprecationWarning: Accessing zmq Socket attribute recv_multipart on
BackgroundSocket
ERROR:asyncio:Exception in callback BaseAsyncIOLoop._handle_events(135, 1)
handle: <Handle BaseAsyncIOLoop._handle_events(135, 1)>
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/asyncio/events.py", line
80, in _run
self._context.run(self._callback, *self._args)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/tornado/platform/asyncio.py", line 189, in _handle_events
handler_func(fileobj, events)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 451, in _handle_events
self._handle_recv()
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 434, in _run_callback
callback(*args, **kwargs)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 118, in _handle_event
event_f()
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 212, in <lambda>
self.schedule(lambda : self._really_send(*args, **kwargs))
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 220, in _really_send
self.socket.send_multipart(msg, *args, **kwargs)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/inprocess/socket.py", line 58, in send_multipart
self.message_sent += 1
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 604, in __set__
self.set(obj, value)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 593, in set
obj._notify_trait(self.name, old_value, new_value)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1217, in _notify_trait
self.notify_change(Bunch(
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1227, in notify_change
return self._notify_observers(change)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1264, in _notify_observers
c(event)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/inprocess/ipkernel.py", line 130, in _io_dispatch
ident, msg = self.session.recv(self.iopub_socket, copy=False)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/jupyter_client/session.py", line 809, in recv
msg_list = socket.recv_multipart(mode, copy=copy)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 244, in __getattr__
warnings.warn("Accessing zmq Socket attribute %s on BackgroundSocket" % attr,
DeprecationWarning: Accessing zmq Socket attribute recv_multipart on
BackgroundSocket
> ui tool show Shell
ERROR:tornado.general:Uncaught exception in ZMQStream callback
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 434, in _run_callback
callback(*args, **kwargs)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 118, in _handle_event
event_f()
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 212, in <lambda>
self.schedule(lambda : self._really_send(*args, **kwargs))
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 220, in _really_send
self.socket.send_multipart(msg, *args, **kwargs)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/inprocess/socket.py", line 58, in send_multipart
self.message_sent += 1
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 604, in __set__
self.set(obj, value)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 593, in set
obj._notify_trait(self.name, old_value, new_value)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1217, in _notify_trait
self.notify_change(Bunch(
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1227, in notify_change
return self._notify_observers(change)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1264, in _notify_observers
c(event)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/inprocess/ipkernel.py", line 130, in _io_dispatch
ident, msg = self.session.recv(self.iopub_socket, copy=False)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/jupyter_client/session.py", line 809, in recv
msg_list = socket.recv_multipart(mode, copy=copy)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 244, in __getattr__
warnings.warn("Accessing zmq Socket attribute %s on BackgroundSocket" % attr,
DeprecationWarning: Accessing zmq Socket attribute recv_multipart on
BackgroundSocket
ERROR:tornado.general:Uncaught exception in zmqstream callback
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 451, in _handle_events
self._handle_recv()
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 434, in _run_callback
callback(*args, **kwargs)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 118, in _handle_event
event_f()
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 212, in <lambda>
self.schedule(lambda : self._really_send(*args, **kwargs))
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 220, in _really_send
self.socket.send_multipart(msg, *args, **kwargs)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/inprocess/socket.py", line 58, in send_multipart
self.message_sent += 1
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 604, in __set__
self.set(obj, value)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 593, in set
obj._notify_trait(self.name, old_value, new_value)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1217, in _notify_trait
self.notify_change(Bunch(
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1227, in notify_change
return self._notify_observers(change)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1264, in _notify_observers
c(event)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/inprocess/ipkernel.py", line 130, in _io_dispatch
ident, msg = self.session.recv(self.iopub_socket, copy=False)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/jupyter_client/session.py", line 809, in recv
msg_list = socket.recv_multipart(mode, copy=copy)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 244, in __getattr__
warnings.warn("Accessing zmq Socket attribute %s on BackgroundSocket" % attr,
DeprecationWarning: Accessing zmq Socket attribute recv_multipart on
BackgroundSocket
ERROR:asyncio:Exception in callback BaseAsyncIOLoop._handle_events(157, 1)
handle: <Handle BaseAsyncIOLoop._handle_events(157, 1)>
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/asyncio/events.py", line
80, in _run
self._context.run(self._callback, *self._args)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/tornado/platform/asyncio.py", line 189, in _handle_events
handler_func(fileobj, events)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 451, in _handle_events
self._handle_recv()
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/zmq/eventloop/zmqstream.py", line 434, in _run_callback
callback(*args, **kwargs)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 118, in _handle_event
event_f()
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 212, in <lambda>
self.schedule(lambda : self._really_send(*args, **kwargs))
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 220, in _really_send
self.socket.send_multipart(msg, *args, **kwargs)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/inprocess/socket.py", line 58, in send_multipart
self.message_sent += 1
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 604, in __set__
self.set(obj, value)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 593, in set
obj._notify_trait(self.name, old_value, new_value)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1217, in _notify_trait
self.notify_change(Bunch(
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1227, in notify_change
return self._notify_observers(change)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/traitlets/traitlets.py", line 1264, in _notify_observers
c(event)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/inprocess/ipkernel.py", line 130, in _io_dispatch
ident, msg = self.session.recv(self.iopub_socket, copy=False)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/jupyter_client/session.py", line 809, in recv
msg_list = socket.recv_multipart(mode, copy=copy)
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/ipykernel/iostream.py", line 244, in __getattr__
warnings.warn("Accessing zmq Socket attribute %s on BackgroundSocket" % attr,
DeprecationWarning: Accessing zmq Socket attribute recv_multipart on
BackgroundSocket
> ui tool show Shell
> pwd
Current working directory is:
/run/media/tic20/storage/structure_dump/alphafold2/mr_multidomain_examples/7ec4
> save AF_Q2G0L2_cluster_0.pdb #2 selectedOnly true
> save AF_Q2G0L2_cluster_1.pdb #2 selectedOnly true
> save AF_Q2G0L2_cluster_2.pdb #2 selectedOnly true
> save 7ec4.pdb #1
> open 7ec1
7ec1 title:
Crystal structure of SdgB (ligand-free form) [more info...]
Chain information for 7ec1 #3
---
Chain | Description | UniProt
A B | Glycosyl transferase, group 1 family protein | A0A0H2XGN0_STAA3
Non-standard residues in 7ec1 #3
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
PGE — triethylene glycol
> save 7ec1.pdb #3
> close #2#1,3
> open 7d0e
7d0e title:
Crystal structure of FIP200 Claw/p-CCPG1 FIR2 [more info...]
Chain information for 7d0e #1
---
Chain | Description | UniProt
A | RB1-inducible coiled-coil protein 1 | RBCC1_HUMAN
B | Cell cycle progression protein 1 FIR2 | CCPG1_HUMAN
Non-standard residues in 7d0e #1
---
GO9 —
3-(2-hydroxyethyloxy)-2-[2-(2-hydroxyethyloxy)ethoxymethyl]-2-(2-hydroxyethyloxymethyl)propan-1-ol
PEG — di(hydroxyethyl)ether
7d0e mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
notes | Fetching compressed AlphaFold Q8TDY2 from
https://alphafold.ebi.ac.uk/files/AF-Q8TDY2-F1-model_v1.cif
12816 atoms, 1594 residues, atom bfactor range 24.4 to 97.3
Matchmaker 7d0e, chain A (#1) with AlphaFold Q8TDY2, chain A (#), sequence
alignment score = 517.3
RMSD between 88 pruned atom pairs is 0.492 angstroms; (across all 96 pairs:
2.621)
Fetching compressed AlphaFold Q9ULG6 from
https://alphafold.ebi.ac.uk/files/AF-Q9ULG6-F1-model_v1.cif
6135 atoms, 757 residues, atom bfactor range 28.2 to 97.8
Matchmaker 7d0e, chain B (#1) with AlphaFold Q9ULG6, chain B (#), sequence
alignment score = 45.1
RMSD between 4 pruned atom pairs is 1.078 angstroms; (across all 11 pairs:
4.557)
Chain information for UniProt Q8TDY2 chain A #2.1
---
Chain | Description | UniProt
A | RB1-inducible coiled-coil protein 1 | RBCC1_HUMAN
Chain information for UniProt Q9ULG6 chain B #2.2
---
Chain | Description
B | Cell cycle progression protein 1
Opened 2 AlphaFold chain models
> close #1-2
> open 7cq4
7cq4 title:
Crystal structure of Slx1-Slx4 in complex with 5'flap DNA [more info...]
Chain information for 7cq4 #1
---
Chain | Description | UniProt
A | Structure-specific endonuclease subunit SLX1 | SLX1_YEAS7
B | SLX4 isoform 1 | A0A6A5PU22_YEASX
H | DNA (5'-D(*GP*GP*ap*TP*TP*ap*CP*ap*ap*CP*ap*GP*ap*T)-3') |
K | DNA (5'-D(*ap*GP*GP*ap*CP*ap*TP*CP*TP*TP*TP*GP*CP*C)-3') |
L | DNA (27-mer) |
Non-standard residues in 7cq4 #1
---
ZN — zinc ion
> cartoon
> hide
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
warnings | UniProt sequence identifier not specified in file for chains
/H,/K,/L
UniProt identifiers must be 6 characters long
AlphaFold database does not have models for 2 UniProt ids A6ZLG6 (chains A),
A0A6A5PU22 (chains B)
Opened 0 AlphaFold chain models
> close #1
> open 7crv
7crv title:
Crystal structure of rNLRP1-FIIND [more info...]
Chain information for 7crv #1
---
Chain | Description | UniProt
A C | NLR family protein 1 | D9I2G3_RAT
B D | NLR family protein 1 | D9I2G3_RAT
> open #1 fromDatabase AlphaFold
Summary of feedback from opening #1 fetched from AlphaFold
---
warning | AlphaFold database does not have models for 1 UniProt ids D9I2G3
(chains A,D,C,B)
Opened 0 AlphaFold chain models
> open file:///home/tic20/Downloads/AF-A0A0G2QC28-F1-model_v1.pdb
No such database 'file'
OpenGL version: 3.3.0 NVIDIA 465.19.01
OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
total used free shared buff/cache available
Mem: 62G 13G 35G 501M 14G 48G
Swap: 4.9G 0B 4.9G
Graphics:
03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:11df]
Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.0
chardet: 4.0.0
ChimeraX-AddCharge: 1.1.4
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.27.1
ChimeraX-AtomicLibrary: 4.0
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.17.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.3.2
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3.dev202107240347
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.4
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: 1.1
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.3.dev32
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.4
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.2
ChimeraX-ModelPanel: 1.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.6.2
ChimeraX-PDB: 2.4.4
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-Phenix: 0.3
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-Sample: 0.1
ChimeraX-SaveCommand: 1.4.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.1
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.10.1
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-Voyager: 0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.23
decorator: 4.4.2
distlib: 0.3.1
distro: 1.5.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.3.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.20
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 2.11.3
jupyter-client: 6.1.12
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 1.1.1
matplotlib: 3.4.2
matplotlib-inline: 0.1.2
msgpack: 1.0.2
netCDF4: 1.5.6
networkx: 2.6.2
numexpr: 2.7.3
numpy: 1.21.0
numpydoc: 1.1.0
OpenMM: 7.6.0
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.2.0
pip: 21.1.1
pkginfo: 1.7.0
prompt-toolkit: 3.0.19
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.9.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.1.0
qtconsole: 5.1.0
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.25.1
scipy: 1.6.3
setuptools: 57.0.0
sfftk-rw: 0.7.0.post1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.0.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.26.6
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.2
wheel-filename: 1.3.0
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