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Opened 2 years ago
Closed 2 years ago
#9458 closed defect (fixed)
Table session save: selectionModel is None
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.17763
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Updating list of available bundles failed: [SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: certificate has expired (_ssl.c:1129)
> open C:\Users\guenter\Desktop\Kristallstrukturen\1n9l.pdb format pdb
1n9l.pdb title:
Crystal structure of the phot-LOV1 domain from chlamydomonas reinhardtii In
the dark state. [more info...]
Chain information for 1n9l.pdb #1
---
Chain | Description | UniProt
A | PHOT-LOV1 | Q8LPE0_CHLRE 17-125
Non-standard residues in 1n9l.pdb #1
---
FMN — flavin mononucleotide (riboflavin monophosphate)
SO4 — sulfate ion
> hide surfaces
> select /A:33
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /A:36
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select solvent
108 atoms, 108 residues, 1 model selected
> hide sel atoms
> select ::name="SO4"
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select ::name="GLN"
27 atoms, 24 bonds, 3 residues, 1 model selected
> select clear
> ui mousemode right select
> select clear
> select /A:55@NE2
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 5 time(s)]
> hide target a
> show target ab
> hide target a
> hide #* target a
> show target ab
> hide target a
> select ::name="FMN"
31 atoms, 33 bonds, 1 residue, 1 model selected
> select ::name="FMN"
31 atoms, 33 bonds, 1 residue, 1 model selected
> show target m
> show sel cartoons
> show sel atoms
> select clear
Alignment identifier is 1/A
> show atoms
> hide atoms
> select ::name="FMN"
31 atoms, 33 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /A:38-46,48-53,56-61,66-80
282 atoms, 283 bonds, 36 residues, 1 model selected
> select /A:21-26,34-37,83-90,96-107,113-122
319 atoms, 323 bonds, 40 residues, 1 model selected
> select /A:38-46,48-53,56-61,66-80
282 atoms, 283 bonds, 36 residues, 1 model selected
> select /A:21-26,34-37,83-90,96-107,113-122
319 atoms, 323 bonds, 40 residues, 1 model selected
> select /A:38-46,48-53,56-61,66-80
282 atoms, 283 bonds, 36 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select /A:38-46,48-53,56-61,66-80
282 atoms, 283 bonds, 36 residues, 1 model selected
> ui dockable false "Sequence Viewer"
> ui dockable true "Sequence Viewer"
> select clear
> select ::name="CYS"
18 atoms, 15 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> select /A:83@SG
1 atom, 1 residue, 1 model selected
> hide sel atoms
[Repeated 8 time(s)]
> hide sel cartoons
[Repeated 2 time(s)]
> hide sel atoms
[Repeated 2 time(s)]
> select clear
> hide sel atoms
> select clear
> select /A:21-26,34-37,83-90,96-107,113-122
319 atoms, 323 bonds, 40 residues, 1 model selected
> select clear
> select ::name="CYS"
18 atoms, 15 bonds, 3 residues, 1 model selected
> hide sel atoms
> select clear
> select ::name="CYS"
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A:83
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:83
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select ::name="CYS"
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A:57
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
Drag select of 3 residues
> select clear
> save C:/Users/guenter/Desktop/LOV1_dunkel.cxs
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting full
[Repeated 3 time(s)]
> lighting soft
> lighting simple
> hide cartoons
> show cartoons
> hide cartoons
[Repeated 1 time(s)]
> show cartoons
> select /A:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> ui tool show AlphaFold
> select clear
> select /A:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /A
986 atoms, 898 bonds, 219 residues, 1 model selected
Drag select of 2 residues
> select clear
[Repeated 3 time(s)]
> select protein
842 atoms, 861 bonds, 109 residues, 1 model selected
> select clear
Drag select of 1 residues
> select clear
> select ::name="CYS"
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A:57
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> color byhetero
> color bypolymer
> coulombic
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/A SER 125 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1n9l.pdb_A SES surface #1.1: minimum, -11.89, mean -0.07,
maximum 9.98
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic
Coulombic values for 1n9l.pdb_A SES surface #1.1: minimum, -11.89, mean -0.07,
maximum 9.98
To also show corresponding color key, enter the above coulombic command and
add key true
> color byhetero
[Repeated 1 time(s)]
> style ball
Changed 986 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style stick
Changed 986 atom styles
> undo
[Repeated 9 time(s)]Drag select of 1n9l.pdb_A SES surface, 25152 of 108070
triangles, 14 atoms, 41 residues, 17 bonds
> select clear
> show cartoons
> hide surfaces
> select clear
[Repeated 1 time(s)]Drag select of 5 residues
> select clear
> select /A:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /A:38-46,48-53,56-61,66-80
282 atoms, 283 bonds, 36 residues, 1 model selected
> select clear
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
Drag select of 1 residues
> select clear
> graphics silhouettes false
> set bgColor white
> lighting full
> lighting soft
> lighting full
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
Drag select of 3 residues
> select clear
> ui tool show "Selection Inspector"
> save C:\Users\guenter\Desktop\image1.png supersample 3
> view orient
> ui tool show "Side View"
> alphafold match #1
1 UniProt id does not have an AlphaFold database model: Q8LPE0 (chain A)
Fetching compressed AlphaFold Q8LPD9 from
https://alphafold.ebi.ac.uk/files/AF-Q8LPD9-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: Q8LPD9 (chain A)
AlphaFold prediction matching 1n9l.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | Q8LPD9 | PHOT_CHLRE | 2.35 | 109 | 109 | 100
Opened 1 AlphaFold model
> alphafold search #1
Webservices job id: S1IXQ628CVUQQ558
Drag select of 13 residues
Drag select of 6 residues
> select clear
> alphafold match #1
1 UniProt id does not have an AlphaFold database model: Q8LPE0 (chain A)
1 AlphaFold model found using sequence similarity searches: Q8LPD9 (chain A)
AlphaFold prediction matching 1n9l.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | Q8LPD9 | PHOT_CHLRE | 2.35 | 109 | 109 | 100
Opened 1 AlphaFold model
Drag select of 19 residues
> select clear
> view
> color #3.1 #55ff00ff
> hide #!3 models
> hide #3.1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #2.1 models
> show #!1 models
> select sequence C
54 atoms, 45 bonds, 9 residues, 3 models selected
> select clear
Drag select of 1 residues
> select clear
Drag select of 3 residues, 1 bonds
> select clear
> lighting shadows false
> select #1/A:98
14 atoms, 15 bonds, 1 residue, 1 model selected
Drag select of 6 atoms, 11 residues, 7 bonds
> select #1/A:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
Drag select of 23 residues
Drag select of 34 atoms, 109 residues, 35 bonds
Drag select of 1 residues
Drag select of 34 atoms, 105 residues, 35 bonds
> select clear
[Repeated 6 time(s)]
> lighting soft
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> mlp #!1
Map values for surface "1n9l.pdb_A SES surface": minimum -24.6, mean -3.764,
maximum 21.65
To also show corresponding color key, enter the above mlp command and add key
true
> mlp #!1
Map values for surface "1n9l.pdb_A SES surface": minimum -24.6, mean -3.764,
maximum 21.65
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!1 surfaces
> color #1 lime
> select ligand
36 atoms, 37 bonds, 2 residues, 1 model selected
Drag select of 3 residues
> select clear
> select ligand
36 atoms, 37 bonds, 2 residues, 1 model selected
> color sel red
> color sel byelement
> select clear
> select ::name="CYS"
54 atoms, 45 bonds, 9 residues, 3 models selected
> select #1/A:57
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select clear
> select backbone
1308 atoms, 1305 bonds, 327 residues, 3 models selected
> color (#!1 & sel) cornflower blue
> select clear
> cartoon style #1 modeHelix tube sides 20
> cartoon style (#1 & coil) xsection oval
> cartoon style #1 xsection barbell modeHelix default
> select sidechain
1545 atoms, 1257 bonds, 327 residues, 3 models selected
> select clear
> select strand
943 atoms, 955 bonds, 118 residues, 3 models selected
> color (#!1 & sel) purple
> select clear
> select strand
943 atoms, 955 bonds, 118 residues, 3 models selected
> color (#!1 & sel) #aaaa7fff
> color (#!1 & sel) #aaaa00ff
> color (#!1 & sel) #aa5500ff
> color (#!1 & sel) #ce6700ff
> color (#!1 & sel) #ad5700ff
> color (#!1 & sel) #9c4e00ff
> color (#!1 & sel) #aaaa7fff
> color (#!1 & sel) #b9b98aff
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #ff55ffff
> color (#!1 & sel) #5555ffff
> color (#!1 & sel) #ff8560ff
> color (#!1 & sel) #ff8a66ff
> color (#!1 & sel) #ff8567ff
> color (#!1 & sel) #ff8c78ff
> color (#!1 & sel) #ff8d79ff
> color (#!1 & sel) #4d2b25ff
> color (#!1 & sel) #62362fff
> color (#!1 & sel) #734037ff
> color (#!1 & sel) #84493fff
> color (#!1 & sel) #9f584bff
> color (#!1 & sel) #b16254ff
> color (#!1 & sel) #b13f2bff
> color (#!1 & sel) #aaaa7fff
> color (#!1 & sel) #aaaa00ff
> color (#!1 & sel) #aaaa7fff
> color (#!1 & sel) #00ffffff
> color (#!1 & sel) #ffff7fff
> color (#!1 & sel) #aaffffff
> color (#!1 & sel) #aaff7fff
> color (#!1 & sel) #aaaa7fff
> color (#!1 & sel) #aaaa00ff
> color (#!1 & sel) #aaaaffff
> color (#!1 & sel) #aaaa7fff
> color (#!1 & sel) #aaaa00ff
> color (#!1 & sel) #aaaa7fff
> color (#!1 & sel) #d7eaf8ff
> color (#!1 & sel) #ccccccff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #b9c89eff
> color (#!1 & sel) #b8c89bff
> color (#!1 & sel) #a2c897ff
> color (#!1 & sel) #a4c897ff
> color (#!1 & sel) #afc895ff
> color (#!1 & sel) #adc894ff
> color (#!1 & sel) #aec895ff
> color (#!1 & sel) #abc897ff
> color (#!1 & sel) #a2c8acff
> color (#!1 & sel) #a5c8baff
> color (#!1 & sel) #a6c8c1ff
> color (#!1 & sel) #a6c8c7ff
> color (#!1 & sel) #a5aec8ff
> color (#!1 & sel) #b0a2c8ff
> color (#!1 & sel) #b09fc8ff
> color (#!1 & sel) #b19ec8ff
> color (#!1 & sel) #b59ac8ff
> color (#!1 & sel) #b597c8ff
> color (#!1 & sel) #b697c8ff
> color (#!1 & sel) #bc7bc8ff
> color (#!1 & sel) #c177c8ff
> color (#!1 & sel) #b568c8ff
> color (#!1 & sel) #9e5ac8ff
> color (#!1 & sel) #7852c8ff
> color (#!1 & sel) #664ec8ff
> color (#!1 & sel) #4653c8ff
> color (#!1 & sel) #426cc8ff
> color (#!1 & sel) #4074c8ff
> color (#!1 & sel) #3d87c8ff
> color (#!1 & sel) #3c9cc8ff
> color (#!1 & sel) #39c1c8ff
> color (#!1 & sel) #37c8a4ff
> color (#!1 & sel) #37c893ff
> color (#!1 & sel) #36c873ff
> color (#!1 & sel) #36c858ff
> color (#!1 & sel) #36c847ff
> color (#!1 & sel) #39c836ff
> color (#!1 & sel) #4ac872ff
> color (#!1 & sel) #6c80c8ff
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #ccccccff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #c8b4b6ff
> color (#!1 & sel) #1d1a1aff
> color (#!1 & sel) #e1e1e1ff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #efefefff
> color (#!1 & sel) #e4e4e4ff
> color (#!1 & sel) #d3d3d3ff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #0b0b0bff
> color (#!1 & sel) #080808ff
> color (#!1 & sel) #090909ff
> color (#!1 & sel) #080808ff
> color (#!1 & sel) #090909ff
> color (#!1 & sel) #0f0f0fff
> color (#!1 & sel) #161616ff
> color (#!1 & sel) #1e1e1eff
> color (#!1 & sel) #262626ff
> color (#!1 & sel) #2f2f2fff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #6f6f6fff
> color (#!1 & sel) #737373ff
> color (#!1 & sel) #797979ff
> color (#!1 & sel) #7f7f7fff
> color (#!1 & sel) #c85e56ff
> color (#!1 & sel) #c87b54ff
> color (#!1 & sel) #c87b55ff
> color (#!1 & sel) #c87a56ff
> color (#!1 & sel) #c87b57ff
> color (#!1 & sel) #c8795eff
> color (#!1 & sel) #c87a60ff
> color (#!1 & sel) #c8806aff
> color (#!1 & sel) #c87f6dff
> color (#!1 & sel) #c88574ff
> color (#!1 & sel) #c89081ff
> color (#!1 & sel) #c89389ff
> color (#!1 & sel) #c8918cff
> color (#!1 & sel) #c8928dff
> color (#!1 & sel) #c8938eff
> color (#!1 & sel) #c8948dff
> color (#!1 & sel) #c8968cff
> color (#!1 & sel) #c8978dff
> color (#!1 & sel) #c89c97ff
> color (#!1 & sel) #c8a79eff
> color (#!1 & sel) #c8aba2ff
> color (#!1 & sel) #c8aea5ff
> color (#!1 & sel) #c8b0a7ff
> color (#!1 & sel) #c8b6acff
> color (#!1 & sel) #c8baaeff
> color (#!1 & sel) #c8beb3ff
> color (#!1 & sel) #c8bfb4ff
> color (#!1 & sel) #c8bbb0ff
> color (#!1 & sel) #c8bcb1ff
> color (#!1 & sel) #c8bdb1ff
> color (#!1 & sel) #c8beb3ff
> color (#!1 & sel) #c8c2b4ff
> color (#!1 & sel) #c8c5b7ff
> color (#!1 & sel) #c8bdadff
> color (#!1 & sel) #c8b59eff
> color (#!1 & sel) #c8b49bff
> color (#!1 & sel) #c8ae8dff
> color (#!1 & sel) #c89673ff
> color (#!1 & sel) #c87e65ff
> color (#!1 & sel) #c87255ff
> color (#!1 & sel) #c87154ff
> color (#!1 & sel) #c87554ff
> color (#!1 & sel) #c87c51ff
> color (#!1 & sel) #c87c50ff
> color (#!1 & sel) #c88a4cff
> color (#!1 & sel) #c88f49ff
> color (#!1 & sel) #c89645ff
> color (#!1 & sel) #c89743ff
> color (#!1 & sel) #c89742ff
> color (#!1 & sel) #c8a13dff
> color (#!1 & sel) #c8a439ff
> color (#!1 & sel) #c8a335ff
> color (#!1 & sel) #c89d30ff
> color (#!1 & sel) #c8942dff
> color (#!1 & sel) #c8942cff
> color (#!1 & sel) #c8942bff
> color (#!1 & sel) #c89329ff
> color (#!1 & sel) #c88e29ff
> color (#!1 & sel) #c8a12dff
> color (#!1 & sel) #c8b232ff
> color (#!1 & sel) #c8be37ff
> color (#!1 & sel) #c8c83dff
> color (#!1 & sel) #c1c83fff
> color (#!1 & sel) #c1c845ff
> color (#!1 & sel) #c6c848ff
> color (#!1 & sel) #c8be4dff
> color (#!1 & sel) #c8b153ff
> color (#!1 & sel) #c8a05aff
> color (#!1 & sel) #c89460ff
> color (#!1 & sel) #c89062ff
> color (#!1 & sel) #c88863ff
> color (#!1 & sel) #c88464ff
> color (#!1 & sel) #c87e65ff
> color (#!1 & sel) #c87c65ff
> color (#!1 & sel) #c87a67ff
> color (#!1 & sel) #c87b68ff
> color (#!1 & sel) #c8ac69ff
> color (#!1 & sel) #6779c8ff
> color (#!1 & sel) #c8679eff
> color (#!1 & sel) #c8679bff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #a0a0a0ff
> color (#!1 & sel) #c86c80ff
> color (#!1 & sel) #c86b80ff
> color (#!1 & sel) #c86b7cff
> color (#!1 & sel) #c86b79ff
> color (#!1 & sel) #c86b75ff
> color (#!1 & sel) #c86f75ff
> color (#!1 & sel) #c87a84ff
> color (#!1 & sel) #c87e88ff
> color (#!1 & sel) #c88891ff
> color (#!1 & sel) #c89396ff
> color (#!1 & sel) #c89a9cff
> color (#!1 & sel) #c89c9dff
> color (#!1 & sel) #c8a5a5ff
> color (#!1 & sel) #c8aaaaff
> color (#!1 & sel) #c8b0b0ff
> color (#!1 & sel) #a0a0a0ff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #a0a0a0ff
> color (#!1 & sel) #c89fa5ff
> color (#!1 & sel) #c89baaff
> color (#!1 & sel) #c897adff
> color (#!1 & sel) #c883b3ff
> color (#!1 & sel) #c87cc0ff
> color (#!1 & sel) #c87ac4ff
> color (#!1 & sel) #c37ac8ff
> color (#!1 & sel) #bf7ac8ff
> color (#!1 & sel) #bb7ac8ff
> color (#!1 & sel) #b983c8ff
> color (#!1 & sel) #b48cc8ff
> color (#!1 & sel) #a693c8ff
> color (#!1 & sel) #9b93c8ff
> color (#!1 & sel) #9b97c8ff
> color (#!1 & sel) #9a9ac8ff
> color (#!1 & sel) #a2a7c8ff
> color (#!1 & sel) #a9aec8ff
> color (#!1 & sel) #b0b2c8ff
> color (#!1 & sel) #b5b6c8ff
> color (#!1 & sel) #b8b8c8ff
> color (#!1 & sel) #bdbcc8ff
> color (#!1 & sel) #c4c3c8ff
> color (#!1 & sel) #c7c6c8ff
> color (#!1 & sel) #c8c8c8ff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #c8c6c8ff
> color (#!1 & sel) #c7c3c8ff
> color (#!1 & sel) #c7c8c6ff
> color (#!1 & sel) #c7c8c5ff
> color (#!1 & sel) #c8c7c2ff
> color (#!1 & sel) #c8c2b5ff
> color (#!1 & sel) #c8bea9ff
> color (#!1 & sel) #c8b9a1ff
> color (#!1 & sel) #c8ad82ff
> color (#!1 & sel) #c8aa7aff
> color (#!1 & sel) #c8ac66ff
> color (#!1 & sel) #c8b463ff
> color (#!1 & sel) #c8b963ff
> color (#!1 & sel) #c8b860ff
> color (#!1 & sel) #c8bc5dff
> color (#!1 & sel) #c8bb5bff
> color (#!1 & sel) #c8bb58ff
> color (#!1 & sel) #c8b156ff
> color (#!1 & sel) #c8b153ff
> color (#!1 & sel) #c8b050ff
> color (#!1 & sel) #c8af4aff
> color (#!1 & sel) #c8a641ff
> color (#!1 & sel) #c89e3bff
> color (#!1 & sel) #c89031ff
> color (#!1 & sel) #c88526ff
> color (#!1 & sel) #c87d22ff
> color (#!1 & sel) #c8791fff
> color (#!1 & sel) #c86c1bff
> color (#!1 & sel) #c86a18ff
> color (#!1 & sel) #c86f16ff
> color (#!1 & sel) #c87517ff
> color (#!1 & sel) #c8811eff
> color (#!1 & sel) #c88923ff
> color (#!1 & sel) #c89530ff
> color (#!1 & sel) #c89a3fff
> color (#!1 & sel) #c8af52ff
> color (#!1 & sel) #c8b65bff
> color (#!1 & sel) #c8b65eff
> color (#!1 & sel) #c8af64ff
> color (#!1 & sel) #c8b067ff
> color (#!1 & sel) #c8ad69ff
> color (#!1 & sel) #c8ae6cff
> color (#!1 & sel) #c8ae6dff
> color (#!1 & sel) #c8af71ff
> color (#!1 & sel) #c8b176ff
> color (#!1 & sel) #c8b07aff
> color (#!1 & sel) #c8b17bff
> color (#!1 & sel) #c8af7cff
> color (#!1 & sel) #c8a37eff
> color (#!1 & sel) #c89b81ff
> color (#!1 & sel) #c89881ff
> color (#!1 & sel) #c88e83ff
> color (#!1 & sel) #c89085ff
> color (#!1 & sel) #c89186ff
> color (#!1 & sel) #c89386ff
> color (#!1 & sel) #c89586ff
> color (#!1 & sel) #c89986ff
> color (#!1 & sel) #c89c86ff
> color (#!1 & sel) #c8a786ff
> color (#!1 & sel) #c8b286ff
> color (#!1 & sel) #c8b886ff
> color (#!1 & sel) #c8ba86ff
> color (#!1 & sel) #c8b886ff
> color (#!1 & sel) #c8af85ff
> color (#!1 & sel) #c8a982ff
> color (#!1 & sel) #c8997dff
> color (#!1 & sel) #c8987cff
> color (#!1 & sel) #c8957cff
> color (#!1 & sel) #c87f71ff
> color (#!1 & sel) #c87e71ff
> color (#!1 & sel) #c87d70ff
> color (#!1 & sel) #c88473ff
> color (#!1 & sel) #c88673ff
> color (#!1 & sel) #c8a7a1ff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #828790ff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #bfbfbfff
> color (#!1 & sel) #ccccccff
> color (#!1 & sel) #87a3beff
> color (#!1 & sel) #bea387ff
> color (#!1 & sel) #ccccccff
> color (#!1 & sel) #ccb195ff
> color (#!1 & sel) #ccccb1ff
> color (#!1 & sel) #ccccccff
> color (#!1 & sel) #a38778ff
> color (#!1 & sel) #ccccccff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #aa557fff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #828790ff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #aa5500ff
> color (#!1 & sel) #828790ff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #ccccccff
> color (#!1 & sel) #787878ff
> color (#!1 & sel) #ccccccff
> color (#!1 & sel) #bfc810ff
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #636363ff
> color (#!1 & sel) #dadadaff
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #ccccccff
> color (#!1 & sel) #ffaaffff
> color (#!1 & sel) #ff55ffff
> color (#!1 & sel) #ff0000ff
> color (#!1 & sel) #555500ff
> color (#!1 & sel) #550000ff
> color (#!1 & sel) #005500ff
> color (#!1 & sel) #00007fff
> color (#!1 & sel) #ffaa7fff
> mlp sel & #!1
Map values for surface "1n9l.pdb_A SES surface": minimum -24.6, mean -3.764,
maximum 21.65
To also show corresponding color key, enter the above mlp command and add key
true
Drag select of 1n9l.pdb_A SES surface, 206 of 108070 triangles, 8 residues
> hide sel surfaces
[Repeated 1 time(s)]
> select clear
> hide #!1 surfaces
> select strand
943 atoms, 955 bonds, 118 residues, 3 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #ffaa00ff
> color (#!1 & sel) #ffaa7fff
> color (#!1 & sel) #ffaa00ff
> color (#!1 & sel) #555500ff
> color (#!1 & sel) #ff5500ff
> color (#!1 & sel) #ffaa00ff
> color (#!1 & sel) #ffaa7fff
> color (#!1 & sel) #ffaa00ff
> color (#!1 & sel) #ffff7fff
> color (#!1 & sel) #ffff00ff
> color (#!1 & sel) #ffaa00ff
> color (#!1 & sel) #ffbc14ff
> color (#!1 & sel) #ffa220ff
> color (#!1 & sel) #ffaa42ff
> color (#!1 & sel) #ffe770ff
> color (#!1 & sel) #ffd88aff
> color (#!1 & sel) #ffeea9ff
> color (#!1 & sel) #fff1c6ff
> color (#!1 & sel) #fff8e6ff
> color (#!1 & sel) #fffcf7ff
> color (#!1 & sel) #fff3eaff
> color (#!1 & sel) #ffe0d2ff
> color (#!1 & sel) #ffdccbff
> color (#!1 & sel) #ffcf0fff
> color (#!1 & sel) #ffaa00ff
> color (#!1 & sel) #aaaa7fff
> color (#!1 & sel) #ffaa00ff
> color (#!1 & sel) #aaff7fff
> color (#!1 & sel) #00ff7fff
> color (#!1 & sel) #ffaa00ff
> color (#!1 & sel) #ffaa7fff
> color (#!1 & sel) #aaaa7fff
> color (#!1 & sel) #ffaa7fff
> color (#!1 & sel) #ffff7fff
> color (#!1 & sel) #ffff00ff
> color (#!1 & sel) #ffaa00ff
> color (#!1 & sel) #ffaa7fff
> color (#!1 & sel) #aa0000ff
> color (#!1 & sel) #aa5500ff
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:21-26,34-37,83-90,96-107,113-122
319 atoms, 323 bonds, 40 residues, 1 model selected
> select #1/A:38-46,48-53,56-61,66-80
282 atoms, 283 bonds, 36 residues, 1 model selected
Drag select of 3 residues
> select clear
> select #1/A:38-46,48-53,56-61,66-80
282 atoms, 283 bonds, 36 residues, 1 model selected
> select clear
> select #1/A:17
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Blast Protein"
> select #1/A:21-26,34-37,83-90,96-107,113-122
319 atoms, 323 bonds, 40 residues, 1 model selected
> select clear
> select #1/A:38-46,48-53,56-61,66-80
282 atoms, 283 bonds, 36 residues, 1 model selected
> select #1/A:21-26,34-37,83-90,96-107,113-122
319 atoms, 323 bonds, 40 residues, 1 model selected
> select clear
> select #1/A:38-46,48-53,56-61,66-80
282 atoms, 283 bonds, 36 residues, 1 model selected
> select clear
> select helix
770 atoms, 771 bonds, 96 residues, 3 models selected
> select #1/A:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:38-46,48-53,56-61,66-80
282 atoms, 283 bonds, 36 residues, 1 model selected
> select #1/A:68
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 6 residues
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> blastprotein #1/A database nr cutoff 1e-3 matrix IDENTITY maxSeqs 100
> version 1 name bp2
Webservices job id: YM0IST9DE5SY25ZK
BlastProtein failed: failed
BlastProtein failed: 'bytes' object has no attribute 'items'
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'
> select #1/A:21-26,34-37,83-90,96-107,113-122
319 atoms, 323 bonds, 40 residues, 1 model selected
> select clear
> select #1/A:21-26,34-37,83-90,96-107,113-122
319 atoms, 323 bonds, 40 residues, 1 model selected
> select clear
Drag select of 1 atoms, 2 residues, 1 bonds
> select clear
> select #1/A:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:80
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:80
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #1/A:79
13 atoms, 11 bonds, 2 residues, 2 models selected
Drag select of 1 residues
> select add #1/A:78
29 atoms, 19 bonds, 4 residues, 2 models selected
> select add #1/A:77
37 atoms, 26 bonds, 5 residues, 2 models selected
> select add #1/A:76
42 atoms, 30 bonds, 6 residues, 2 models selected
> select add #1/A:75
50 atoms, 37 bonds, 7 residues, 2 models selected
> select add #1/A:74
61 atoms, 47 bonds, 8 residues, 2 models selected
> select add #1/A:72
70 atoms, 55 bonds, 9 residues, 2 models selected
> select add #1/A:73
78 atoms, 62 bonds, 10 residues, 2 models selected
> select add #1/A:71
87 atoms, 70 bonds, 11 residues, 2 models selected
> select add #1/A:70
94 atoms, 76 bonds, 12 residues, 2 models selected
> select add #1/A:69
103 atoms, 84 bonds, 13 residues, 2 models selected
> select add #1/A:68
112 atoms, 92 bonds, 14 residues, 2 models selected
> select add #1/A:67
119 atoms, 99 bonds, 15 residues, 2 models selected
> select add #1/A:66
127 atoms, 106 bonds, 16 residues, 2 models selected
> color (#!1 & sel) light sea green
> select clear
> select ::name="FMN"
31 atoms, 33 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:39
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:38
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/A:39
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add #1/A:20
25 atoms, 23 bonds, 3 residues, 2 models selected
> select add #1/A:19
36 atoms, 33 bonds, 4 residues, 2 models selected
> select add #1/A:18
44 atoms, 40 bonds, 5 residues, 2 models selected
> select add #1/A:17
48 atoms, 43 bonds, 6 residues, 2 models selected
> select add #1/A:41
59 atoms, 54 bonds, 7 residues, 2 models selected
> select add #1/A:40
63 atoms, 57 bonds, 8 residues, 2 models selected
> select add #1/A:42
75 atoms, 69 bonds, 9 residues, 2 models selected
> select add #1/A:43
80 atoms, 73 bonds, 10 residues, 2 models selected
> select add #1/A:45
87 atoms, 79 bonds, 11 residues, 2 models selected
> select add #1/A:44
95 atoms, 86 bonds, 12 residues, 2 models selected
> select add #1/A:46
99 atoms, 89 bonds, 13 residues, 2 models selected
> select add #1/A:47
111 atoms, 101 bonds, 14 residues, 2 models selected
> select add #1/A:48
115 atoms, 104 bonds, 15 residues, 2 models selected
> select add #1/A:49
122 atoms, 111 bonds, 16 residues, 2 models selected
> select add #1/A:50
130 atoms, 118 bonds, 17 residues, 2 models selected
> select add #1/A:52
137 atoms, 124 bonds, 18 residues, 2 models selected
> select add #1/A:51
146 atoms, 132 bonds, 19 residues, 2 models selected
> select add #1/A:53
154 atoms, 139 bonds, 20 residues, 2 models selected
> select add #1/A:54
158 atoms, 142 bonds, 21 residues, 2 models selected
> select add #1/A:55
168 atoms, 152 bonds, 22 residues, 2 models selected
> select add #1/A:33
175 atoms, 159 bonds, 23 residues, 2 models selected
> select add #1/A:32
181 atoms, 164 bonds, 24 residues, 2 models selected
> select add #1/A:31
189 atoms, 171 bonds, 25 residues, 2 models selected
> select add #1/A:30
196 atoms, 178 bonds, 26 residues, 2 models selected
> select add #1/A:29
204 atoms, 185 bonds, 27 residues, 2 models selected
> select add #1/A:28
211 atoms, 191 bonds, 28 residues, 2 models selected
> select add #1/A:27
216 atoms, 195 bonds, 29 residues, 2 models selected
> select add #1/A:92
225 atoms, 203 bonds, 30 residues, 2 models selected
> select add #1/A:93
233 atoms, 210 bonds, 31 residues, 2 models selected
> select add #1/A:95
240 atoms, 216 bonds, 32 residues, 2 models selected
> select add #1/A:94
244 atoms, 219 bonds, 33 residues, 2 models selected
> select subtract #1/A:92
235 atoms, 211 bonds, 32 residues, 2 models selected
> select add #1/A:92
244 atoms, 219 bonds, 33 residues, 2 models selected
> select add #1/A:62
248 atoms, 222 bonds, 34 residues, 2 models selected
> select add #1/A:63
257 atoms, 230 bonds, 35 residues, 2 models selected
> select add #1/A:64
261 atoms, 233 bonds, 36 residues, 2 models selected
> select add #1/A:65
268 atoms, 239 bonds, 37 residues, 2 models selected
> select add #1/A:59
279 atoms, 250 bonds, 38 residues, 2 models selected
> select add #1/A:58
290 atoms, 260 bonds, 39 residues, 2 models selected
> select add #1/A:57
296 atoms, 265 bonds, 40 residues, 2 models selected
> select subtract #1/A:57
290 atoms, 260 bonds, 39 residues, 2 models selected
> color (#!1 & sel) light gray
> select clear
> select add #1/A:91
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1/A:60
19 atoms, 17 bonds, 2 residues, 2 models selected
> select add #1/A:61
28 atoms, 25 bonds, 3 residues, 2 models selected
> select add #1/A:125
34 atoms, 30 bonds, 4 residues, 2 models selected
> select add #1/A:124
41 atoms, 36 bonds, 5 residues, 2 models selected
> select add #1/A:123
48 atoms, 42 bonds, 6 residues, 2 models selected
> select add #1/A:108
55 atoms, 48 bonds, 7 residues, 2 models selected
> select add #1/A:109
62 atoms, 55 bonds, 8 residues, 2 models selected
> select add #1/A:110
70 atoms, 62 bonds, 9 residues, 2 models selected
> select add #1/A:111
74 atoms, 65 bonds, 10 residues, 2 models selected
> select add #1/A:112
85 atoms, 75 bonds, 11 residues, 2 models selected
> select add #1/A:57
91 atoms, 80 bonds, 12 residues, 2 models selected
> select add #1/A:56
99 atoms, 87 bonds, 13 residues, 2 models selected
> color (#!1 & sel) light gray
> select clear
> select #1/A:82
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:81
14 atoms, 12 bonds, 2 residues, 2 models selected
> color (#!1 & sel) light gray
> select clear
> select add #1/A:57
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> color (#!1 & sel) byelement
> select clear
> select ::name="FMN"
31 atoms, 33 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Alignment identifier is 1
Alignment identifier is 1/A
Alignment identifier is 1
> select #1/A:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> view sel
> undo
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
Drag select of 1n9l.pdb_A SES surface, 327 of 108070 triangles, 4 residues
> select clear
> hide #!1 surfaces
> select #1/A:59
11 atoms, 11 bonds, 1 residue, 1 model selected
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select clear
> select #1/A:39
9 atoms, 8 bonds, 1 residue, 1 model selected
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> lighting full
Drag select of 1 residues
> select clear
> set bgColor black
> set bgColor transparent
> set bgColor gray
> set bgColor #80808000
> set bgColor white
> set bgColor #ffffff00
> save C:/Users/guenter/Desktop/chimera_sessions/LOV1_dark.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 157, in take_snapshot
, 'table_session': self.table.session_info()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\item_table.py", line 590, in session_info
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])
AttributeError: 'NoneType' object has no attribute 'selectedRows'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000014E4BDC0F70> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x0000014E548C4A60>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000014E4BDC0F70> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x0000014E548C4A60>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000014E4BDC0F70> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x0000014E548C4A60>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 157, in take_snapshot
, 'table_session': self.table.session_info()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\item_table.py", line 590, in session_info
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])
AttributeError: 'NoneType' object has no attribute 'selectedRows'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000014E4BDC0F70> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x0000014E548C4A60>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000014E4BDC0F70> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x0000014E548C4A60>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000014E4BDC0F70> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x0000014E548C4A60>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save C:/Users/guenter/Desktop/chimera_sessions/LOV1.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 157, in take_snapshot
, 'table_session': self.table.session_info()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\item_table.py", line 590, in session_info
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])
AttributeError: 'NoneType' object has no attribute 'selectedRows'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000014E4BDC0F70> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x0000014E548C4A60>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000014E4BDC0F70> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x0000014E548C4A60>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000014E4BDC0F70> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x0000014E548C4A60>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 157, in take_snapshot
, 'table_session': self.table.session_info()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\item_table.py", line 590, in session_info
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])
AttributeError: 'NoneType' object has no attribute 'selectedRows'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000014E4BDC0F70> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x0000014E548C4A60>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000014E4BDC0F70> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x0000014E548C4A60>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000014E4BDC0F70> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x0000014E548C4A60>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 432.00
OpenGL renderer: GeForce GT 640/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: de_DE.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: FUJITSU
Model: ESPRIMO P920
OS: Microsoft Windows 10 Enterprise LTSC (Build 17763)
Memory: 8,503,078,912
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-4590 CPU @ 3.30GHz
OSLanguage: de-DE
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
Change History (7)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → General Controls |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Table session save: selectionModel is None |
comment:2 by , 2 years ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
| Status: | accepted → assigned |
comment:3 by , 2 years ago
Does the results window even come up if a blast job fails ? I guess 'yes' since some session is trying to save it, but it shouldn't!
comment:4 by , 2 years ago
If you follow the recipe in #9429 to get a blast failure, no tool window will appear but the BlastProteinResults tool will appear in session.tools[:] and in the list of running tools at the end of the Tools menu.
comment:5 by , 2 years ago
Turns out that tool is not protected by "if self.exited_normally()" -- will be fixed in tomorrow's daily build. I added the guard, launched an NR job, watched it fail, and saved a session successfully.
comment:7 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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This is due to the earlier failure of blast on NR, which created a partially constructed Blast Tool which failed to save into the session. Would be good if a blast failure didn't do this, so reassigning to Zach.