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Opened 3 years ago
Closed 3 years ago
#8470 closed defect (fixed)
KeyError formatting blast results
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.3.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> open /Users/jrutter/Downloads/AF-O75081-F1-model_v4.pdb
AF-O75081-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for protein CBFA2T3 (O75081) [more info...]
Chain information for AF-O75081-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | protein CBFA2T3 | MTG16_HUMAN
> set bgColor white
> lighting soft
> lighting full
> lighting simple
> show cartoons
[Repeated 1 time(s)]
> hide cartoons
> show cartoons
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6
> color #1 #9fc7d7ff
> style nucrib
Expected a keyword
> alias cylinders cartoon style protein modeh tube rad 2 sides 24
> sequence chain #1/A
Alignment identifier is 1/A
> open O75081 fromDatabase uniprot
Summary of feedback from opening O75081 fetched from uniprot
---
notes | Fetching compressed O75081 UniProt info from
https://www.uniprot.org/uniprot/O75081.xml
Alignment identifier is O75081
Associated AF-O75081-F1-model_v4.pdb chain A to O75081 with 0 mismatches
Opened UniProt O75081
> 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
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
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
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
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
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> 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
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 4996 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> 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
> preset "molecular surfaces" "chain id coloring (opaque)"
Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> 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
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> 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
> rainbow
> open /Applications/BBEdit.app/
'/Applications/BBEdit.app/' has no suffix
> mlp
Map values for surface "AF-O75081-F1-model_v4.pdb_A SES surface": minimum
-28.15, mean -5.205, maximum 23.3
To also show corresponding color key, enter the above mlp command and add key
true
> color bypolymer
> color bychain
> color byhetero
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for AF-O75081-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.38, mean -0.23, maximum 13.98
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
Map values for surface "AF-O75081-F1-model_v4.pdb_A SES surface": minimum
-28.15, mean -5.205, maximum 23.3
To also show corresponding color key, enter the above mlp command and add key
true
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style sphere
Changed 4996 atom styles
> mlp
Map values for surface "AF-O75081-F1-model_v4.pdb_A SES surface": minimum
-28.15, mean -5.205, maximum 23.3
To also show corresponding color key, enter the above mlp command and add key
true
> interfaces ~solvent
0 buried areas:
> interfaces ~solvent
0 buried areas:
> interfaces ~solvent
0 buried areas:
> hbonds reveal true
345 hydrogen bonds found
> style stick
Changed 4996 atom styles
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> interfaces ~solvent
0 buried areas:
> 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
> ui tool show AlphaFold
> select add #1
4996 atoms, 5127 bonds, 345 pseudobonds, 653 residues, 2 models selected
> close
> alphafold fetch alphafold fetch p29474
Expected a keyword
> alphafold fetch O95071
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching url https://alphafold.ebi.ac.uk/files/AF-O95071-F1-model_v4.cif
failed: HTTP Error 404: Not Found
> alphafold fetch P10242
Fetching compressed AlphaFold P10242 from
https://alphafold.ebi.ac.uk/files/AF-P10242-F1-model_v4.cif
Chain information for AlphaFold P10242 #1
---
Chain | Description | UniProt
A | Transcriptional activator Myb | MYB_HUMAN
> alphafold pae #1 uniprotId P10242
Fetching compressed AlphaFold PAE P10242 from
https://alphafold.ebi.ac.uk/files/AF-P10242-F1-predicted_aligned_error_v4.json
> trim true
Unknown command: trim true
> ui tool show AlphaFold
> alphafold predict #1
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
> alphafold match #1
1 AlphaFold model found using UniProt identifier: P10242 (chain A)
AlphaFold chains matching AlphaFold P10242
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
A | MYB_HUMAN | P10242 | 0.00 | 640 | 640 | 100
Opened 1 AlphaFold model
> alphafold search #1
Webservices job id: 529A6FQNOAT31LAL
> close #2
> close
> ui tool show AlphaFold
[Repeated 1 time(s)]
> ui tool show ViewDockX
No suitable models found for ViewDockX
No sequence chosen for AlphaFold match
[Repeated 3 time(s)]
> alphafold predict
> MPAIMTMLADHAARQLLDFSQKLDINLLDNVVNCLYHGEGAQQRMAQEVLTHLKEHPDAWTRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPTCVEKEKVYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEVFDFSSGQITQVKSKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPLGYIFETKLISTLIYKFLNVPMFRNVSLKCLTEIAGVSVSQYEEQFVTLFTLTMMQLKQMLPLNTNIRLAYSNGKDDEQNFIQNLSLFLCTFLKEHDQLIEKRLNLRETLMEALHYMLLVSEVEETEIFKICLEYWNHLAAELYRESPFSTSASPLLSGSQHFDVPPRRQLYLPMLFKVRLLMVSRMAKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYVDTERIMTEKLHNQVNGTEWSWKNLNTLCWAIGSISGAMHEEDEKRFLVTVIKDLLGLCEQKRGKDNKAIIASNIMYIVGQYPRFLRAHWKFLKTVVNKLFEFMHETHDGVQDMACDTFIKIAQKCRRHFVQVQVGEVMPFIDEILNNINTIICDLQPQQVHTFYEAVGYMIGAQTDQTVQEHLIEKYMLLPNQVWDSIIQQATKNVDILKDPETVKQLGSILKTNVRACKAVGHPFVIQLGRIYLDMLNVYKCLSENISAAIQANGEMVTKQPLIRSMRTVKRETLKLISGWVSRSNDPQMVAENFVPPLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECTLNMINKDFEEYPEHRTNFFLLLQAVNSHCFPAFLAIPPTQFKLVLDSIIWAFKHTMRNVADTGLQILFTLLQNVAQEEAAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGKISTSLNPGNPVNNQIFLQEYVANLLKSAFPHLQDAQVKLFVTGLFSLNQDIPAFKEHLRDFLVQIKEFAGEDTSDLFLEEREIALRQADEEKHKRQMSVPGIFNPHEIPEEMCD,MSSSMWYIMQSIQSKYSLSERLIRTIAAIRSFPHDNVEDLIRGGADVNCTHGTLKPLHCACMVSDADCVELLLEKGAEVNALDGYNRTALHYAAEKDEACVEVLLEYGANPNALDGNRDTPLHWAAFKNNAECVRALLESGASVNALDYNNDTPLSWAAMKGNLESVSILLDYGAEVRVINLIGQTPISRLVALLVRGLGTEKEDSCFELLHRAVGHFELRKNGTMPREVARDPQLCEKLTVLCSAPGTLKTLARYAVRRSLGLQYLPDAVKGLPLPASLKEYLLLLE
Running AlphaFold prediction
[Repeated 2 time(s)]Traceback (most recent call last):
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 661, in customEvent
func(*args, **kw)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/job.py", line 97, in on_finish
BlastProteinResults.from_job(
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 88, in from_job
return cls(
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 84, in __init__
self._build_ui()
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 216, in _build_ui
param_str = self._format_param_str()
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 191, in _format_param_str
model_formatted = ''.join([str(self.session.models._models[(model_no,)]),
chain])
KeyError: (1,)
KeyError: (1,)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 191, in _format_param_str
model_formatted = ''.join([str(self.session.models._models[(model_no,)]),
chain])
See log for complete Python traceback.
> open 4hat
Summary of feedback from opening 4hat fetched from pdb
---
notes | Fetching compressed mmCIF 4hat from
http://files.rcsb.org/download/4hat.cif
Fetching CCD GNP from http://ligand-expo.rcsb.org/reports/G/GNP/GNP.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD EDO from http://ligand-expo.rcsb.org/reports/E/EDO/EDO.cif
Fetching CCD LMB from http://ligand-expo.rcsb.org/reports/L/LMB/LMB.cif
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif
4hat title:
Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1-Ran-
RanBP1 [more info...]
Chain information for 4hat #1
---
Chain | Description | UniProt
A | GTP-binding nuclear protein Ran | RAN_HUMAN
B | Ran-specific GTPase-activating protein 1 | YRB1_YEAST
C | Exportin-1 | XPO1_YEAST
Non-standard residues in 4hat #1
---
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
GNP — phosphoaminophosphonic acid-guanylate ester
GOL — glycerol (glycerin; propane-1,2,3-triol)
LMB — Leptomycin B, bound form
MG — magnesium ion
> color byelement
> color bychain
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/C
> select
> /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
Destroying pre-existing alignment with identifier 1/C
Alignment identifier is 1/C
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting simple
> set bgColor black
> ui tool show "Side View"
> view orient
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
Hide dust shortcut requires a displayed map surface
[Repeated 1 time(s)]
> volume style surface
No volumes specified
> volume style mesh
No volumes specified
> color sel bychain
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> set bgColor white
> select ligand
96 atoms, 92 bonds, 7 residues, 1 model selected
> view sel
> 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
> show sel atoms
> hide sel atoms
> show sel atoms
> ui windowfill toggle
[Repeated 2 time(s)]
> ui tool show "Selection Inspector"
> hbonds sel reveal true
67 hydrogen bonds found
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> select
> /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> select /C:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:447-450
30 atoms, 29 bonds, 4 residues, 1 model selected
> select /C:443-445,451-453
49 atoms, 47 bonds, 6 residues, 1 model selected
> select
> /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> select /C:447-450
30 atoms, 29 bonds, 4 residues, 1 model selected
> select /C:454
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C:454-458
45 atoms, 45 bonds, 5 residues, 1 model selected
> select /C:443-445,451-453
49 atoms, 47 bonds, 6 residues, 1 model selected
> select /C:454-458
45 atoms, 45 bonds, 5 residues, 1 model selected
> select
> /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> select /C:539
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /C:539
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!1 & sel) yellow
> color (#!1 & sel) #ffd479ff
> color (#!1 & sel) #f8dd74ff
> color (#!1 & sel) #f8de74ff
> color (#!1 & sel) #f8df71ff
> color (#!1 & sel) #f8e06dff
> color (#!1 & sel) #f8df6aff
> color (#!1 & sel) #f8de66ff
> color (#!1 & sel) #f8dc65ff
> color (#!1 & sel) #f8dc63ff
> color (#!1 & sel) #f8de60ff
> color (#!1 & sel) #f8de5dff
> color (#!1 & sel) #f8df5aff
> color (#!1 & sel) #f8df58ff
> color (#!1 & sel) #f8df57ff
[Repeated 1 time(s)]
> color (#!1 & sel) #f8e056ff
[Repeated 2 time(s)]
> color (#!1 & sel) #f8e055ff
[Repeated 1 time(s)]
> color (#!1 & sel) #f8e153ff
> color (#!1 & sel) #f8e152ff
> color (#!1 & sel) #f8e151ff
> color (#!1 & sel) #f8e04fff
> color (#!1 & sel) #f8df4cff
> color (#!1 & sel) #f8e04aff
> color (#!1 & sel) #f8e048ff
> color (#!1 & sel) #f8e047ff
> color (#!1 & sel) #f8df46ff
> color (#!1 & sel) #f8dc43ff
> color (#!1 & sel) #f8d940ff
> color (#!1 & sel) #f8d840ff
> color (#!1 & sel) #f8d73fff
[Repeated 1 time(s)]
> color (#!1 & sel) #f8d63eff
> color (#!1 & sel) #f8d53dff
> color (#!1 & sel) #f8d33cff
> color (#!1 & sel) #f8d039ff
> color (#!1 & sel) #f8cc36ff
> color (#!1 & sel) #f8c732ff
> color (#!1 & sel) #f8c42fff
[Repeated 2 time(s)]
> color (#!1 & sel) #f8c42eff
> color (#!1 & sel) #f8c32aff
> color (#!1 & sel) #f8c124ff
> color (#!1 & sel) #f8bf20ff
> color (#!1 & sel) #f8bd1dff
> color (#!1 & sel) #f8bd1cff
> color (#!1 & sel) #f8bc1cff
> color (#!1 & sel) #f8bd1cff
> color (#!1 & sel) #f8bf19ff
> color (#!1 & sel) #f8c215ff
> color (#!1 & sel) #f8c312ff
> color (#!1 & sel) #f8c411ff
> color (#!1 & sel) #f8c712ff
> color (#!1 & sel) #f8cc14ff
> color (#!1 & sel) #f8cf16ff
> color (#!1 & sel) #f8d218ff
[Repeated 1 time(s)]
> color (#!1 & sel) #f8d318ff
> color (#!1 & sel) #f8d418ff
> color (#!1 & sel) #f8d517ff
[Repeated 1 time(s)]
> color (#!1 & sel) #f8d617ff
> color (#!1 & sel) #f8d716ff
> color (#!1 & sel) #f8d815ff
> color (#!1 & sel) #f8d914ff
[Repeated 1 time(s)]
> color (#!1 & sel) #f8d913ff
> color (#!1 & sel) #f8da12ff
> color (#!1 & sel) #f8db11ff
> color (#!1 & sel) #f8dc0fff
[Repeated 2 time(s)]
> color (#!1 & sel) #f8dd0eff
> color (#!1 & sel) #f8de0dff
> color (#!1 & sel) #f8df0dff
> color (#!1 & sel) #f8df0cff
[Repeated 1 time(s)]
> color (#!1 & sel) #f8e00bff
> color (#!1 & sel) #f8e00aff
> color (#!1 & sel) #f8e109ff
[Repeated 3 time(s)]
> color (#!1 & sel) #f8dd02ff
> color (#!1 & sel) #f8dc01ff
> color (#!1 & sel) #f8d900ff
> color (#!1 & sel) #f8d800ff
> color (#!1 & sel) #f8d600ff
> color (#!1 & sel) #f8d400ff
> color (#!1 & sel) #f8d100ff
> color (#!1 & sel) #f8cf00ff
> color (#!1 & sel) #f8ce00ff
> color (#!1 & sel) #f8d100ff
> color (#!1 & sel) #f8d202ff
[Repeated 2 time(s)]
> color (#!1 & sel) #f8d302ff
> color (#!1 & sel) #f8d301ff
[Repeated 1 time(s)]
> color (#!1 & sel) #f8d400ff
> color (#!1 & sel) #f8d600ff
> color (#!1 & sel) #f8d400ff
> color (#!1 & sel) #f8d600ff
> color (#!1 & sel) #f8d400ff
> select ::name="LMB"
40 atoms, 39 bonds, 1 residue, 1 model selected
> color sel byelement
> view sel
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select
> /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> select /C:-1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /C:-1-1052
8202 atoms, 8359 bonds, 1017 residues, 1 model selected
> mlp sel
Map values for surface "4hat_C SES surface": minimum -30.1, mean -4.745,
maximum 24.83
To also show corresponding color key, enter the above mlp command and add key
true
> select /C:-1-1052
8202 atoms, 8359 bonds, 1017 residues, 1 model selected
> select /C:-1-1052
8202 atoms, 8359 bonds, 1017 residues, 1 model selected
> mlp sel
Map values for surface "4hat_C SES surface": minimum -30.1, mean -4.745,
maximum 24.83
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "4hat_C SES surface": minimum -30.1, mean -4.745,
maximum 24.83
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "4hat_C SES surface": minimum -30.1, mean -4.745,
maximum 24.83
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "4hat_C SES surface": minimum -30.1, mean -4.745,
maximum 24.83
To also show corresponding color key, enter the above mlp command and add key
true
> color sel bychain
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color sel bychain
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 4hat_C SES surface #1.2: minimum, -20.99, mean -2.65,
maximum 11.74
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "4hat_C SES surface": minimum -30.1, mean -4.745,
maximum 24.83
To also show corresponding color key, enter the above mlp command and add key
true
> transparency (#!1 & sel) 30
> transparency (#!1 & sel) 90
> transparency (#!1 & sel) 70
> color sel bychain
> transparency (#!1 & sel) 70
> transparency (#!1 & sel) 50
> select sel :< 3 & sel :> 3
Nothing selected
> select /C:-1-1052
8202 atoms, 8359 bonds, 1017 residues, 1 model selected
> select /C:576
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /C:576-578
23 atoms, 22 bonds, 3 residues, 1 model selected
> select
> /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> select /C:595-596
11 atoms, 10 bonds, 2 residues, 1 model selected
> select /C:595-596
11 atoms, 10 bonds, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Destroying pre-existing alignment with identifier 1/C
Alignment identifier is 1/C
> select
> /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> select /C
9410 atoms, 8415 bonds, 33 pseudobonds, 2170 residues, 2 models selected
> select /C:576
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /C:576-577
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /C:577
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:576-577
15 atoms, 14 bonds, 2 residues, 1 model selected
> open 4hat
4hat title:
Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1-Ran-
RanBP1 [more info...]
Chain information for 4hat #2
---
Chain | Description | UniProt
A | GTP-binding nuclear protein Ran | RAN_HUMAN
B | Ran-specific GTPase-activating protein 1 | YRB1_YEAST
C | Exportin-1 | XPO1_YEAST
Non-standard residues in 4hat #2
---
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
GNP — phosphoaminophosphonic acid-guanylate ester
GOL — glycerol (glycerin; propane-1,2,3-triol)
LMB — Leptomycin B, bound form
MG — magnesium ion
> select ::name="CYS"
240 atoms, 200 bonds, 40 residues, 2 models selected
> select #1/C:596-597
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/C:596-597
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/C:596
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:596
6 atoms, 5 bonds, 1 residue, 1 model selected
> select ::name="CYS"
240 atoms, 200 bonds, 40 residues, 2 models selected
> color (#!1-2 & sel) orange
> 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
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color sel bychain
[Repeated 1 time(s)]
> select
> #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color sel bychain
> select #1/C:-1-1052
8202 atoms, 8359 bonds, 1017 residues, 1 model selected
> color sel bychain
> select #1/C:606
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:606-607
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/C:606
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:606
6 atoms, 5 bonds, 1 residue, 1 model selected
> select
> #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> select #1/C:596
6 atoms, 5 bonds, 1 residue, 1 model selected
> select ::name="CYS"
240 atoms, 200 bonds, 40 residues, 2 models selected
> select #1/C:648
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:648
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:606
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:606
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:710
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:710-711
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/C:710
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:525-710
1507 atoms, 1534 bonds, 186 residues, 1 model selected
> select #1/C:525
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:525
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:255
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:255
6 atoms, 5 bonds, 1 residue, 1 model selected
> select ::name="CYS"
240 atoms, 200 bonds, 40 residues, 2 models selected
> select #1/C:102
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:102
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:255
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:255
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:102
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:102
6 atoms, 5 bonds, 1 residue, 1 model selected
> select ::name="CYS"
240 atoms, 200 bonds, 40 residues, 2 models selected
> select #1/C:1022
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:1022
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:890
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:890
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:840
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:840
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:710
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:710
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show Matchmaker
> select #1/C:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:210-217
58 atoms, 57 bonds, 8 residues, 1 model selected
> select #1/C:239
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:239-251
100 atoms, 101 bonds, 13 residues, 1 model selected
> select #1/C:299
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/C:299-311
96 atoms, 97 bonds, 13 residues, 1 model selected
> select #1/C:361-362
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/C:361-371
94 atoms, 97 bonds, 11 residues, 1 model selected
> select #1/C:89-122
268 atoms, 269 bonds, 34 residues, 1 model selected
> select #1/C:89-131
348 atoms, 352 bonds, 43 residues, 1 model selected
> select #1/C:184-185
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/C:184-193
83 atoms, 83 bonds, 10 residues, 1 model selected
> select #1/C:211-212
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1/C:211-223
113 atoms, 116 bonds, 13 residues, 1 model selected
> select #1/C:244
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:244-284
329 atoms, 332 bonds, 41 residues, 1 model selected
> select #1/C:300
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:300-313
108 atoms, 109 bonds, 14 residues, 1 model selected
> select #1/C:331
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:331-375
389 atoms, 397 bonds, 45 residues, 1 model selected
> select #1/C:364
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:364-373
88 atoms, 91 bonds, 10 residues, 1 model selected
> select #1/C:461
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:461-477
147 atoms, 149 bonds, 17 residues, 1 model selected
> select #1/C:435-436
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/C:435-479
375 atoms, 379 bonds, 45 residues, 1 model selected
> select #1/C:494-535
334 atoms, 341 bonds, 42 residues, 1 model selected
> select #1/C:494-537
350 atoms, 357 bonds, 44 residues, 1 model selected
> select
> #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> select #1/C:539
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:539
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!1 & sel) yellow
> label (#!1 & sel) attribute name
> label (#!1 & sel) attribute label_specifier
> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label (#!1 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> label (#!1 & sel) attribute label_one_letter_code
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label height 1
> label height 0.9
> label (#!1 & sel) atoms text C539
> color (#!1 & sel) yellow
> ~label (#!1 & sel) residues
> label (#!1 & sel) text default
> ~label (#!1 & sel) residues
[Repeated 1 time(s)]
> label (#!1 & sel) attribute label_specifier
> select #1/C#2/C
18820 atoms, 16830 bonds, 33 pseudobonds, 4340 residues, 3 models selected
> ~label (#!1-2 & sel) residues
> ~label (#!1-2 & sel) atoms
> select #1/C:539
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:539
6 atoms, 5 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
No visible Surface models selected
> color sel bychain
> undo
> select #1/C:520
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:520-527
70 atoms, 70 bonds, 8 residues, 1 model selected
> select #1/C:518
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:518-537
162 atoms, 162 bonds, 20 residues, 1 model selected
> select #1/C:540
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:540-604
537 atoms, 549 bonds, 65 residues, 1 model selected
> select #1/C:538
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:538-541
30 atoms, 29 bonds, 4 residues, 1 model selected
> select
> #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> select #1/C:557
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/C:557-575
171 atoms, 178 bonds, 19 residues, 1 model selected
> select #1/C:546
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:546-584
329 atoms, 338 bonds, 39 residues, 1 model selected
> select #1/C:520
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:520-584
539 atoms, 549 bonds, 65 residues, 1 model selected
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
QGestureManager::deliverEvent: could not find the target for gesture
> undo
> cartoon style (#!1 & sel) xsection oval modeHelix default
> select ligand
192 atoms, 184 bonds, 14 residues, 2 models selected
> mlp sel
mlp: no amino acids specified
> ~label sel residues
> select #1/C:520
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:520-584
539 atoms, 549 bonds, 65 residues, 1 model selected
> select #1/C:520-584
539 atoms, 549 bonds, 65 residues, 1 model selected
> select #1/C:520-584
539 atoms, 549 bonds, 65 residues, 1 model selected
> select #1/C:520-584
539 atoms, 549 bonds, 65 residues, 1 model selected
> ~label (#!1 & sel) residues
> select
> #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> select #1/C:582
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:582
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> label (#!1 & sel) attribute label_specifier
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
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
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> ~label (#!1 & sel) residues
> select
> #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> select #1/C:539
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:539
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="CL"
8 atoms, 8 residues, 2 models selected
> hide sel cartoons
> select ::name="EDO"
24 atoms, 18 bonds, 6 residues, 2 models selected
> hide sel cartoons
> select ::name="GNP"
64 atoms, 68 bonds, 2 residues, 2 models selected
> hide sel atoms
> select ::name="GOL"
24 atoms, 20 bonds, 4 residues, 2 models selected
> hide sel atoms
> color bfactor sel
24 atoms, 4 residues, atom bfactor range 36.6 to 71.2
> select #1/C:520
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:520-584
539 atoms, 549 bonds, 65 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> show sel atoms
> hide sel atoms
> undo
[Repeated 1 time(s)]
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> undo
[Repeated 4 time(s)]
> hide sel atoms
> color sel bychain
> select
24862 atoms, 22366 bonds, 79 pseudobonds, 5628 residues, 5 models selected
> color sel bychain
> select ::name="LMB"
80 atoms, 78 bonds, 2 residues, 2 models selected
> color sel byelement
> 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
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> 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
> undo
[Repeated 4 time(s)]
> redo
[Repeated 2 time(s)]
> 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
> select #1/C:520
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:520-584
539 atoms, 549 bonds, 65 residues, 1 model selected
> rainbow sel
> color sel byhetero
[Repeated 1 time(s)]
> color sel bychain
> color sel bynucleotide
> color bfactor sel
539 atoms, 65 residues, 1 surfaces, atom bfactor range 17 to 97.2
> hbonds sel reveal true
390 hydrogen bonds found
> ~hbonds
> select ::name="HOH"
2910 atoms, 2910 residues, 2 models selected
> hide sel atoms
> select #1/C:520
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:520-584
539 atoms, 549 bonds, 65 residues, 1 model selected
> color sel bychain
> show (#!1 & sel-residues & sidechain) target ab
> hide sel atoms
[Repeated 2 time(s)]
> select #1/C:539
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:539
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> color (#!1 & sel) orange
> select ::name="LMB"
80 atoms, 78 bonds, 2 residues, 2 models selected
> color sel byhetero
> color sel byelement
> select
> #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> surface (#!1 & sel)
> select #1/C:-1-1052
8202 atoms, 8359 bonds, 1017 residues, 1 model selected
> surface (#!1 & sel)
> transparency (#!1 & sel) 50
> transparency (#!1 & sel) 80
> open "/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/UCSF
> ChimeraX-YewujI/download.png"
Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF,
I, RGB)
> alphafold fetch
Missing or invalid "uniprotId" argument: Expected a text string
> O14980
Unknown command: O14980
> alphafold fetch O14980
Fetching compressed AlphaFold O14980 from
https://alphafold.ebi.ac.uk/files/AF-O14980-F1-model_v4.cif
Chain information for AlphaFold O14980 #3
---
Chain | Description | UniProt
A | Exportin-1 | XPO1_HUMAN
> ui tool show Matchmaker
> 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 4hat, chain C (#2) with AlphaFold O14980, chain A (#3), sequence
alignment score = 3127.6
RMSD between 763 pruned atom pairs is 1.151 angstroms; (across all 1006 pairs:
3.662)
> surface hidePatches (#!1 & sel)
> color sel bychain
[Repeated 1 time(s)]
> select
33531 atoms, 31217 bonds, 12 pseudobonds, 6699 residues, 7 models selected
> color sel bychain
[Repeated 1 time(s)]
> ui tool show "Model Panel"
> hide #!1 models
> select subtract #1
21100 atoms, 20034 bonds, 6 pseudobonds, 3885 residues, 4 models selected
> color #3 #942193ff
> color #3 #8e668dff
> color #3 #00fdffff
> color #3 #73fdffff
> color #3 #c2f6fdff
> color #3 #c7ebfdff
> color #3 #c9fdc7ff
> color #3 #eddcfdff
> color #3 #dab2fdff
> color #3 #fdaec3ff
> color #3 #fdd4a5ff
> color #3 #d5affdff
> color #3 #c0a4fdff
> color #3 #c7aafdff
> color #3 #c2a5f7ff
> close #1
> ui tool show "Show Sequence Viewer"
> sequence chain #2/C
Alignment identifier is 2/C
> select #2/C:596
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> select
> #2/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051
7083 atoms, 7174 bonds, 877 residues, 1 model selected
> select #2/C:539
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> select ::name="LMB"
40 atoms, 39 bonds, 1 residue, 1 model selected
> color sel byelement
> hbonds sel reveal true
12 hydrogen bonds found
> hide #3 models
> color :sti & C salmon
> color :LMB salmon
> color :sti & LMB salmon
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> select :sti
Nothing selected
> select :LMB
40 atoms, 39 bonds, 1 residue, 1 model selected
> view sel
> hide~ sel
Unknown command: hide~ sel
> hide~sel
Unknown command: hide~sel
> hide ~sel
> hbonds :LMB reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 4hat
3 AlphaFold O14980
12 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
4hat #2/C LYS 525 NZ 4hat #2/C LMB 1101 O5 no hydrogen 3.160 N/A
4hat #2/C LYS 525 NZ 4hat #2/C LMB 1101 O6 no hydrogen 3.505 N/A
4hat #2/C LYS 548 NZ 4hat #2/C LMB 1101 O1 no hydrogen 2.696 N/A
4hat #2/C LMB 1101 O4 4hat #2/C HOH 2126 O no hydrogen 2.648 N/A
4hat #2/C HOH 1892 O 4hat #2/C LMB 1101 O3 no hydrogen 2.793 N/A
4hat #2/C HOH 1892 O 4hat #2/C LMB 1101 O6 no hydrogen 3.091 N/A
4hat #2/C HOH 2126 O 4hat #2/C LMB 1101 O4 no hydrogen 2.648 N/A
4hat #2/C HOH 2300 O 4hat #2/C LMB 1101 O1 no hydrogen 3.399 N/A
4hat #2/C HOH 2300 O 4hat #2/C LMB 1101 O1' no hydrogen 2.950 N/A
4hat #2/C HOH 2307 O 4hat #2/C LMB 1101 O6 no hydrogen 3.304 N/A
4hat #2/C HOH 2308 O 4hat #2/C LMB 1101 O5 no hydrogen 2.503 N/A
AlphaFold O14980 #3/A LYS 537 NZ 4hat #2/C LMB 1101 O1 no hydrogen 2.456 N/A
12 hydrogen bonds found
> save "/Users/jrutter/Dropbox (MIT)/Ebert
> Lab/Ebert_computational/XPO1_LMB.cxs"
Traceback (most recent call last):
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 150, in take_snapshot
, 'table_session': self.table.session_info()
AttributeError: 'BlastProteinResults' object has no attribute 'table'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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 0x106b6db50> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x155ee4760>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
0x106b6db50> -> <chimerax.blastprotein.ui.results.BlastProteinResults object
at 0x155ee4760>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x106b6db50> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x155ee4760>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 150, in take_snapshot
, 'table_session': self.table.session_info()
AttributeError: 'BlastProteinResults' object has no attribute 'table'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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 0x106b6db50> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x155ee4760>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
0x106b6db50> -> <chimerax.blastprotein.ui.results.BlastProteinResults object
at 0x155ee4760>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x106b6db50> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x155ee4760>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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.
> ui tool show Log
> ui tool show "Command Line Interface"
> alphafold predict
> MPAIMTMLADHAARQLLDFSQKLDINLLDNVVNCLYHGEGAQQRMAQEVLTHLKEHPDAWTRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPTCVEKEKVYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEVFDFSSGQITQVKSKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPLGYIFETKLISTLIYKFLNVPMFRNVSLKCLTEIAGVSVSQYEEQFVTLFTLTMMQLKQMLPLNTNIRLAYSNGKDDEQNFIQNLSLFLCTFLKEHDQLIEKRLNLRETLMEALHYMLLVSEVEETEIFKICLEYWNHLAAELYRESPFSTSASPLLSGSQHFDVPPRRQLYLPMLFKVRLLMVSRMAKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYVDTERIMTEKLHNQVNGTEWSWKNLNTLCWAIGSISGAMHEEDEKRFLVTVIKDLLGLCEQKRGKDNKAIIASNIMYIVGQYPRFLRAHWKFLKTVVNKLFEFMHETHDGVQDMACDTFIKIAQKCRRHFVQVQVGEVMPFIDEILNNINTIICDLQPQQVHTFYEAVGYMIGAQTDQTVQEHLIEKYMLLPNQVWDSIIQQATKNVDILKDPETVKQLGSILKTNVRACKAVGHPFVIQLGRIYLDMLNVYKCLSENISAAIQANGEMVTKQPLIRSMRTVKRETLKLISGWVSRSNDPQMVAENFVPPLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECTLNMINKDFEEYPEHRTNFFLLLQAVNSHCFPAFLAIPPTQFKLVLDSIIWAFKHTMRNVADTGLQILFTLLQNVAQEEAAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGKISTSLNPGNPVNNQIFLQEYVANLLKSAFPHLQDAQVKLFVTGLFSLNQDIPAFKEHLRDFLVQIKEFAGEDTSDLFLEEREIALRQADEEKHKRQMSVPGIFNPHEIPEEMCD,MSSSMWYIMQSIQSKYSLSERLIRTIAAIRSFPHDNVEDLIRGGADVNCTHGTLKPLHCACMVSDADCVELLLEKGAEVNALDGYNRTALHYAAEKDEACVEVLLEYGANPNALDGNRDTPLHWAAFKNNAECVRALLESGASVNALDYNNDTPLSWAAMKGNLESVSILLDYGAEVRVINLIGQTPISRLVALLVRGLGTEKEDSCFELLHRAVGHFELRKNGTMPREVARDPQLCEKLTVLCSAPGTLKTLARYAVRRSLGLQYLPDAVKGLPLPASLKEYLLLLE
Running AlphaFold prediction
> save "/Users/jrutter/Dropbox (MIT)/Ebert
> Lab/Ebert_computational/ChimeraX/XPO1.cxs"
Traceback (most recent call last):
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 150, in take_snapshot
, 'table_session': self.table.session_info()
AttributeError: 'BlastProteinResults' object has no attribute 'table'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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 0x106b6db50> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x155ee4760>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
0x106b6db50> -> <chimerax.blastprotein.ui.results.BlastProteinResults object
at 0x155ee4760>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x106b6db50> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x155ee4760>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 150, in take_snapshot
, 'table_session': self.table.session_info()
AttributeError: 'BlastProteinResults' object has no attribute 'table'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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 0x106b6db50> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x155ee4760>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
0x106b6db50> -> <chimerax.blastprotein.ui.results.BlastProteinResults object
at 0x155ee4760>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x106b6db50> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x155ee4760>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 7459.101.3
OS Loader Version: 7459.101.3
Software:
System Software Overview:
System Version: macOS 12.3.1 (21E258)
Kernel Version: Darwin 21.4.0
Time since boot: 9 days 13:50
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → KeyError formatting blast results |
comment:2 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Note:
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Based on the KeyError I think this happens when the BLAST results come back and the user has closed all the models that were open when they submitted the job. We now collect the model name as the job is created instead of after the fact, with some error checking.