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#4983 closed defect (fixed)
drag and drop has file: prepended
| Reported by: | Tristan Croll | Owned by: | pett |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Command Line | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: 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
Attachments (2)
Change History (20)
comment:1 by , 4 years ago
| Component: | Unassigned → Command Line |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → drag and drop has file: prepended |
comment:2 by , 4 years ago
| Status: | accepted → feedback |
|---|
follow-up: 3 comment:3 by , 4 years ago
Added:
self.session.logger.info('Logged drop event')
self.session.logger.info(text)
to the beginning of CmdText.dropEvent() /usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/cmd_line/tool.py. Never gets called. This might be relevant: https://www.qtcentre.org/threads/7163-Drag-and-Drop-dropEvent-not-being-called
Drag and Drop, dropEvent not being called?<https://www.qtcentre.org/threads/7163-Drag-and-Drop-dropEvent-not-being-called>
Hi, I have a tree widget which allows items to be dragged. I have a derived tableview which accepts drops, I have reimplemented the dragEnterEvent and dropEvent in here, the dragEnterEvent gets called but the dropEvent doesn't. At the moment I am just accepting any types of drops. Code in the tableview : void DATableView::dropEvent(QDropEvent *e) { QString strText = e->mimeData()->text();
www.qtcentre.org
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 02 August 2021 18:42
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4983: drag and drop has file: prepended
#4983: drag and drop has file: prepended
------------------------------------+----------------------------
Reporter: Tristan Croll | Owner: Eric Pettersen
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Command Line | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
------------------------------------+----------------------------
Changes (by Eric Pettersen):
* status: accepted => feedback
Comment:
Hi Tristan,
The command line strips 'file://' from drops, so AFAIK the only
way you could get this is if the Nautilus browser is sending
'file://file://' as the text at the start of the drop. Can you go into
chimerax.cmd_line.tool and at the start of the dropEvent embedded method
print out what event.mimeData().text() is. Let me know what it says.
--Eric
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4983#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:4 by , 4 years ago
That thread is 14 years old. The lines you added are incorrect. 'self' has no attribute 'session'. The lines would need to be:
self.tool.session.logger.info('Logged drop event')
self.tool.session.logger.info(text)
I would instead suggest:
import sys
print("drop", text, file=sys.stderr)
follow-up: 5 comment:5 by , 4 years ago
Well, I did try a straightforward print statement first - when that didn't show up in the log, I tried the session.logger approach (sorry - didn't notice the nested class). Just tried your suggestion - still nothing, either to the log or to the terminal window.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 02 August 2021 19:17
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4983: drag and drop has file: prepended
#4983: drag and drop has file: prepended
------------------------------------+----------------------------
Reporter: Tristan Croll | Owner: Eric Pettersen
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Command Line | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
------------------------------------+----------------------------
Comment (by Eric Pettersen):
That thread is 14 years old. The lines you added are incorrect. 'self'
has no attribute 'session'. The lines would need to be:
self.tool.session.logger.info('Logged drop event')
self.tool.session.logger.info(text)
I would instead suggest:
import sys
print("drop", text, file=sys.__stderr__)
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4983#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:6 by , 4 years ago
| Status: | feedback → accepted |
|---|
It would not seem possible for that text to get inserted without going through the dropEvent method. It is possibly this nebulously reported Qt issue: https://bugreports.qt.io/browse/QTBUG-73462. I will be in the office today to do tape-related stuff and will install Nautilus on our Ubuntu test system and see what I can find out.
follow-up: 7 comment:7 by , 4 years ago
Did some really ugly hacking to the `CmdText.__init__` method to make sure my edits were actually having an effect (they are, and I get "Drop: test" printed to the terminal window) - see below. But it still doesn't fire when I drag-and-drop onto it.
class CmdText(QComboBox):
def __init__(self, parent, tool):
self.tool = tool
QComboBox.__init__(self, parent)
self._processing_key = False
from Qt.QtCore import Qt
# defer context menu to parent
self.setContextMenuPolicy(Qt.NoContextMenu)
self.setAcceptDrops(True)
self._out_selection = None
class TestText:
class _TestText:
def text(self):
return 'test'
def mimeData(self):
return self._TestText()
def acceptProposedAction(self):
pass
self.setEditable(True)
self.dropEvent(TestText())
self.setEditable(False)
def dragEnterEvent(self, event):
if event.mimeData().text():
event.acceptProposedAction()
def dropEvent(self, event):
text = event.mimeData().text()
import sys
print(f'Drop: {text}', file=sys.__stderr__)
if text.startswith("file://"):
text = text[7:]
import sys
if sys.platform.startswith("win") and text.startswith('/'):
# Windows seems to provide /C:/...
text = text[1:]
from chimerax.core.commands import StringArg
self.lineEdit().insert(StringArg.unparse(text))
event.acceptProposedAction()
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 02 August 2021 19:21
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4983: drag and drop has file: prepended
#4983: drag and drop has file: prepended
------------------------------------+----------------------------
Reporter: Tristan Croll | Owner: Eric Pettersen
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Command Line | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
------------------------------------+----------------------------
Comment (by Tristan Croll):
{{{
Well, I did try a straightforward print statement first - when that didn't
show up in the log, I tried the session.logger approach (sorry - didn't
notice the nested class). Just tried your suggestion - still nothing,
either to the log or to the terminal window.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 02 August 2021 19:17
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4983: drag and drop has file: prepended
#4983: drag and drop has file: prepended
------------------------------------+----------------------------
Reporter: Tristan Croll | Owner: Eric Pettersen
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Command Line | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
------------------------------------+----------------------------
Comment (by Eric Pettersen):
That thread is 14 years old. The lines you added are incorrect. 'self'
has no attribute 'session'. The lines would need to be:
self.tool.session.logger.info('Logged drop event')
self.tool.session.logger.info(text)
I would instead suggest:
import sys
print("drop", text, file=sys.__stderr__)
--
Ticket URL:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4983#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4983#comment:5>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 8 comment:8 by , 4 years ago
Also doesn't fire when I drag random text from the log onto the command line.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 02 August 2021 19:30
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4983: drag and drop has file: prepended
#4983: drag and drop has file: prepended
------------------------------------+----------------------------
Reporter: Tristan Croll | Owner: Eric Pettersen
Type: defect | Status: accepted
Priority: normal | Milestone:
Component: Command Line | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
------------------------------------+----------------------------
Changes (by Eric Pettersen):
* status: feedback => accepted
Comment:
It would not seem possible for that text to get inserted without going
through the dropEvent method. It is possibly this nebulously reported Qt
issue: https://bugreports.qt.io/browse/QTBUG-73462. I will be in the
office today to do tape-related stuff and will install Nautilus on our
Ubuntu test system and see what I can find out.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4983#comment:6>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:9 by , 4 years ago
The ComboBox simply never receives dropEvent on Linux. It does on Windows and Mac. Don't know if that's a Qt or PyQt bug, but I'm going to have to work up some simple test case -- ugh. In the interim I'm going to have to put in some nasty hack that looks at the currentTextChanged signal when there's a possible drop, and fix the resulting text -- again, ugh.
comment:10 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Have committed a horrible hack to work around this problem. Hoping you can test it out tomorrow Tristan...
Still need to create a simple test case to submit to PyQt/Qt.
follow-up: 11 comment:11 by , 4 years ago
Will do my best, but the next few days will be challenging. Two very different talks to finalise - a general ISOLDE workshop for Thu, and one on electron crystallography for Fri. A bit hesitant to update my ChimeraX until I’m certain I’m done recording examples.
follow-up: 12 comment:12 by , 4 years ago
comment:13 by , 4 years ago
All right - will try that tomorrow morning.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 10 August 2021 20:48
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4983: drag and drop has file: prepended
#4983: drag and drop has file: prepended
------------------------------------+----------------------------
Reporter: Tristan Croll | Owner: Eric Pettersen
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Command Line | Version:
Resolution: fixed | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
------------------------------------+----------------------------
Comment (by Eric Pettersen):
{{{
You could move cmd_line/tool.py aside, drop the attached file in, run a
test, then move the old one back...
--Eric
}}}
[attachment:"tool.py"]
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4983#comment:12>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 13 comment:14 by , 4 years ago
You're going to hate this... turns out that dragLeaveEvent() gets fired *before* the text is received, so _drop_hack_cb() is disconnected before it ever gets a chance to do anything. Simply commenting out the definition of dragLeaveEvent() works, and should be harmless - if the user decides not to drop after all, _drop_hack_cb() will disable itself as soon as they type a character.
... but wait, it gets worse. Occasionally (not sure what the trigger is, but seems to happen more reliably immediately after I move the ChimeraX window from one screen to the other) there is a very long (multi-second) delay between me dragging onto the command line and dragEnterEvent() firing. In this window I can drag-and-drop text and have it appear without dragEnterEvent(), dragLeaveEvent() or dropEvent() ever firing. Yuck. Something to just hand off to the PyQt people, I guess.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 10 August 2021 21:11
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4983: drag and drop has file: prepended
#4983: drag and drop has file: prepended
------------------------------------+----------------------------
Reporter: Tristan Croll | Owner: Eric Pettersen
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Command Line | Version:
Resolution: fixed | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
------------------------------------+----------------------------
Comment (by Tristan Croll):
{{{
All right - will try that tomorrow morning.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 10 August 2021 20:48
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4983: drag and drop has file: prepended
#4983: drag and drop has file: prepended
------------------------------------+----------------------------
Reporter: Tristan Croll | Owner: Eric Pettersen
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Command Line | Version:
Resolution: fixed | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
------------------------------------+----------------------------
Comment (by Eric Pettersen):
{{{
You could move cmd_line/tool.py aside, drop the attached file in, run a
test, then move the old one back...
--Eric
}}}
[attachment:"tool.py"]
--
Ticket URL:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4983#comment:12>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4983#comment:13>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 14 comment:15 by , 4 years ago
That all sounds wonderful -- not. On my Mac, the leave event fired after the text change, which is why the code is the way it is. I may just remove the dragLeaveEvent() definition like you did, but I'm going to wait until the next time I'm at work (possibly not until early September) and mess around with the code on a Linux system there.
comment:16 by , 4 years ago
We are going to Qt 6.2 after the ChimeraX 1.3 release, so I'm going to wait and see if this drop-event bug goes away in 6.2 before I put more effort into this.
comment:17 by , 3 years ago
The horrible hack continues to be necessary as of Qt 6.4.3. Still need to work up a test case to submit.
comment:18 by , 2 years ago
| Description: | modified (diff) |
|---|
Worked up a simple PyQt6 test case and submitted a bug report (https://bugreports.qt.io/browse/QTBUG-117520). Turns out the bug is only for editable comboboxes on Linux, so pretty narrow.
Note:
See TracTickets
for help on using tickets.
Hi Tristan,
--Eric