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Opened 11 months ago
Closed 11 months ago
#16434 closed defect (fixed)
Similar Structures BLAST search with no matches: list index out of range
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.9rc202411260222 (2024-11-26 02:22:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411260222 (2024-11-26)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/lakatoslorant/Desktop/p14.pdb
Chain information for p14.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show "Similar Structures"
> foldseek /A
Found 15 similar structures to p14.pdb #1/A in pdb database using foldseek,
name fs1
> open 7pwf
Summary of feedback from opening 7pwf fetched from pdb
---
notes | Fetching compressed mmCIF 7pwf from http://files.rcsb.org/download/7pwf.cif
Fetching CCD 4AC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/4AC/4AC.cif
Fetching CCD 4OC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/4OC/4OC.cif
Fetching CCD 7MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/7MG/7MG.cif
Fetching CCD A2M from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/A2M/A2M.cif
Fetching CCD C4J from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/J/C4J/C4J.cif
Fetching CCD K from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/K/K.cif
Fetching CCD M7A from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/M7A/M7A.cif
Fetching CCD MA6 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/MA6/MA6.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Fetching CCD OMC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/OMC/OMC.cif
Fetching CCD OMG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/OMG/OMG.cif
Fetching CCD OMU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/OMU/OMU.cif
7pwf title:
Cryo-EM structure of small subunit of Giardia lamblia ribosome at 2.9 A
resolution [more info...]
Chain information for 7pwf #2
---
Chain | Description | UniProt
2 | rRNA 18S |
A | 40S ribosomal protein SA | RSSA_GIAIC 1-245
B | 40S ribosomal protein S3a | RS3A_GIAIC 1-248
C | Ribosomal protein S2 | A8BMZ1_GIAIC 1-242
D | Ribosomal protein S3 | A8B8Z2_GIAIC 1-217
E | 40S ribosomal protein S4 | A8BFE3_GIAIC 1-268
F | Ribosomal protein S5 | A8BZD3_GIAIC 1-190
G | 40S ribosomal protein S6 | A8B6L8_GIAIC 1-248
H | Ribosomal protein eS7 |
I | 40S ribosomal protein S8 | A8B252_GIAIC 1-175
J | Ribosomal protein S9 | A8BKS8_GIAIC 1-189
K | Ribosomal protein S10B | A8BRX3_GIAIC 1-134
L | SSU ribosomal protein S17P | V6TVJ7_GIAIN 2-200
N | Ribosomal protein S13 | A8BE02_GIAIC 1-154
O | Ribosomal protein S14 | E2RU83_GIAIC 1-145
P | Ribosomal protein S15 | A8BBP3_GIAIC 1-145
Q | Ribosomal protein S16 | A8BKC6_GIAIC 1-158
R | Ribosomal protein S17 | A8BRG5_GIAIC 1-137
S | Ribosomal protein S18 | A8BZ58_GIAIC 2-155
T | Ribosomal protein S19e | A0A644F964_GIAIC 1-139
U | Ribosomal protein S20 | A8B4G0_GIAIC 3-128
V | 40S ribosomal protein S21 | A8B484_GIAIC 2-90
W | Ribosomal protein S15A | E2RU77_GIAIC 1-130
X | Ribosomal protein S23 | A8BS96_GIAIC 1-143
Y | Ribosomal protein S24 | A8B593_GIAIC 1-132
Z | 40S ribosomal protein S25 | A8B8H7_GIAIC 1-88
a | 40S ribosomal protein S26 | A8BQZ7_GIAIC 1-109
b | Ribosomal protein S27 | A8BJL1_GIAIC 1-124
c | Ribosomal protein S28 | A8B4F3_GIAIC 1-64
d | Ribosomal protein S29A | A8B7H6_GIAIC 1-137
e | 40S ribosomal protein S30 | A0A644F843_GIAIC 1-69
n | Ribosomal protein eL41 |
Non-standard residues in 7pwf #2
---
C4J —
(5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-
L-arabinitol
K — potassium ion
MG — magnesium ion
Deleted 31 extra chains, 4 C-terminal residues, 2 N-terminal residues, 303
non-polymer residues more than 3.0 Angstroms away.
Alignment of 7pwf chain Y to query has RMSD 1.17 using 23 of 81 paired
residues within cutoff distance 2.0
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 p14.pdb, chain A (#1) with 7pwf_Y, chain Y (#2), sequence alignment
score = 9.5
RMSD between 3 pruned atom pairs is 0.004 angstroms; (across all 3 pairs:
0.004)
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 p14.pdb, chain A (#1) with 7pwf_Y, chain Y (#2), sequence alignment
score = 9.5
RMSD between 3 pruned atom pairs is 0.004 angstroms; (across all 3 pairs:
0.004)
> hide #1 models
> hide #!2 models
> show #1 models
> select add #2
661 atoms, 672 bonds, 1 pseudobond, 84 residues, 2 models selected
> open 6th6
Summary of feedback from opening 6th6 fetched from pdb
---
notes | Fetching compressed mmCIF 6th6 from http://files.rcsb.org/download/6th6.cif
Fetching CCD 4SU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/4SU/4SU.cif
Fetching CCD 5MC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/5MC/5MC.cif
Fetching CCD 5MU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/5MU/5MU.cif
Fetching CCD 6MZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/6MZ/6MZ.cif
Fetching CCD LHH from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/LHH/LHH.cif
Fetching CCD LV2 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/LV2/LV2.cif
6th6 title:
Cryo-EM Structure of T. kodakarensis 70S ribosome [more info...]
Chain information for 6th6 #3
---
Chain | Description | UniProt
Aa | 16S ribosomal RNA |
Ab | 30S ribosomal protein S2 | RS2_THEKO 1-201
Ac | 30S ribosomal protein S3 | RS3_THEKO 1-209
Ad | 30S ribosomal protein S3Ae | RS3A_THEKO 1-200
Ae | 30S ribosomal protein S4 | RS4_THEKO 1-180
Af | 30S ribosomal protein S4e | RS4E_THEKO 1-243
Ag | 30S ribosomal protein S5 | RS5_THEKO 1-235
Ah | 30S ribosomal protein S6e | RS6E_THEKO 1-125
Ai | 30S ribosomal protein S7 | RS7_THEKO 1-215
Aj | 30S ribosomal protein S8 | RS8_THEKO 1-130
Ak | 30S ribosomal protein S8e | RS8E_THEKO 1-130
Al | 30S ribosomal protein S9 | RS9_THEKO 1-135
Am | 30S ribosomal protein S10 | RS10_THEKO 1-102
An | 30S ribosomal protein S11 | RS11_THEKO 1-140
Ao | 30S ribosomal protein S12 | RS12_THEKO 1-147
Ap | 30S ribosomal protein S13 | RS13_THEKO 1-149
Aq | 30S ribosomal protein S15 | RS15_THEKO 1-151
Ar | 30S ribosomal protein S14 type Z | RS14Z_THEKO 1-56
As | 30S ribosomal protein S17 | RS17_THEKO 1-114
At | 30S ribosomal protein S17e | RS17E_THEKO 1-67
Au | 30S ribosomal protein S19 | RS19_THEKO 1-133
Av | 30S ribosomal protein S19e | Q5JGN5_THEKO 1-150
Aw | 30S ribosomal protein S24e | RS24_THEKO 1-98
Ax | 30S ribosomal protein S27e | RS27_THEKO 1-65
Ay | 30S ribosomal protein S28e | RS28_THEKO 1-70
Az | Predicted zinc-ribbon RNA-binding protein involved in translation | Q5JFE2_THEKO 1-62
BA | 23S ribosomal RNA |
BB | 5S ribosomal RNA |
BC | 50S ribosomal protein L2 | RL2_THEKO 1-239
BD | 50S ribosomal protein L3 | RL3_THEKO 1-346
BE | 50S ribosomal protein L4 | RL4_THEKO 1-255
BF | 50S ribosomal protein L5 | RL5_THEKO 1-183
BG | 50S ribosomal protein L6 | RL6_THEKO 1-184
BH BI | 50S ribosomal protein L7Ae | RL7A_THEKO 1-123
BJ | 50S ribosomal protein L10e | RL10E_THEKO 1-182
BK | 50S ribosomal protein L13 | RL13_THEKO 1-142
BL | 50S ribosomal protein L14 | RL14_THEKO 1-141
BM BN | 50S ribosomal protein L14e | RL14E_THEKO 1-83
BO | 50S ribosomal protein L15 | RL15_THEKO 1-148
BP | 50S ribosomal protein L15e | RL15E_THEKO 1-194
BQ | 50S ribosomal protein L18 | RL18_THEKO 1-201
BR | 50S ribosomal protein L18e | RL18E_THEKO 1-121
BS | 50S ribosomal protein L19e | Q5JJG6_THEKO 1-150
BT | 50S ribosomal protein L18Ae | RL18A_THEKO 1-77
BU | 50S ribosomal protein L21e | RL21_THEKO 1-98
BV | 50S ribosomal protein L22 | RL22_THEKO 1-156
BW | 50S ribosomal protein L23 | RL23_THEKO 1-86
BX | 50S ribosomal protein L24 | RL24_THEKO 1-121
BY | 50S ribosomal protein L24e | RL24E_THEKO 1-67
BZ | 50S ribosomal protein L29 | RL29_THEKO 1-66
Ba | 50S ribosomal protein L30 | RL30_THEKO 1-155
Bb | 50S ribosomal protein L30e | RL30E_THEKO 1-102
Bc | 50S ribosomal protein L31e | RL31_THEKO 1-90
Bd | 50S ribosomal protein L32e | RL32_THEKO 1-125
Be | 50S ribosomal protein L34e | RL34_THEKO 1-90
Bg | 50S ribosomal protein L37Ae | RL37A_THEKO 1-86
Bh | 50S ribosomal protein L37e | RL37_THEKO 1-63
Bi | 50S ribosomal protein L39e | RL39_THEKO 1-51
Bj | 50S ribosomal protein L40e | RL40_THEKO 1-51
Bk | LSU ribosomal protein L41E | Q5JEV0_THEKO 1-37
Bl | 50S ribosomal protein L44e | Q5JE51_THEKO 1-94
Non-standard residues in 6th6 #3
---
ZN — zinc ion
Deleted 62 extra chains, 15 C-terminal residues, 2141 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 6th6 chain Aw to query has RMSD 1.05 using 22 of 73 paired
residues within cutoff distance 2.0
> ui tool show Matchmaker
> matchmaker #!3 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 p14.pdb, chain A (#1) with 6th6_Aw, chain Aw (#3), sequence
alignment score = 7
RMSD between 6 pruned atom pairs is 1.215 angstroms; (across all 37 pairs:
17.154)
> select subtract #2
Nothing selected
> hide #!3 models
> foldseek #1/A database afdb50
Found 70 similar structures to p14.pdb #1/A in afdb database using foldseek,
name fs2
> open A0A5J5DM89 fromDatabase alphafold
Summary of feedback from opening A0A5J5DM89 fetched from alphafold
---
notes | Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold A0A5J5DM89 from
https://alphafold.ebi.ac.uk/files/AF-A0A5J5DM89-F1-model_v4.cif
Chain information for AlphaFold A0A5J5DM89 #4
---
Chain | Description | UniProt
A | PIPK domain-containing protein | A0A5J5DM89_9PERO 1-397
Color AlphaFold A0A5J5DM89 by residue attribute pLDDT_score
Deleted 243 C-terminal residues, 69 N-terminal residues.
Alignment of A0A5J5DM89 to query has RMSD 0.764 using 20 of 83 paired residues
within cutoff distance 2.0
> hide #4 models
> open A0A356APH9 fromDatabase alphafold
Summary of feedback from opening A0A356APH9 fetched from alphafold
---
note | Fetching compressed AlphaFold A0A356APH9 from https://alphafold.ebi.ac.uk/files/AF-A0A356APH9-F1-model_v4.cif
Chain information for AlphaFold A0A356APH9 #5
---
Chain | Description | UniProt
A | Uncharacterized protein | A0A356APH9_9FIRM 1-163
Color AlphaFold A0A356APH9 by residue attribute pLDDT_score
Deleted 21 C-terminal residues, 93 N-terminal residues.
Alignment of A0A356APH9 to query has RMSD 0.841 using 13 of 48 paired residues
within cutoff distance 2.0
> hide #5 models
> open A0A543CED6 fromDatabase alphafold
Summary of feedback from opening A0A543CED6 fetched from alphafold
---
note | Fetching compressed AlphaFold A0A543CED6 from https://alphafold.ebi.ac.uk/files/AF-A0A543CED6-F1-model_v4.cif
Chain information for AlphaFold A0A543CED6 #6
---
Chain | Description | UniProt
A | Transcriptional regulator with XRE-family HTH domain | A0A543CED6_9ACTN 1-258
Color AlphaFold A0A543CED6 by residue attribute pLDDT_score
Deleted 16 C-terminal residues, 200 N-terminal residues.
Alignment of A0A543CED6 to query has RMSD 0.819 using 14 of 42 paired residues
within cutoff distance 2.0
> hide #6 models
> sequence search #1/A database afdb
RCSB sequence search failed:
> sequence search #1/A
RCSB sequence search failed:
> sequence search #1/A database afdb
RCSB sequence search failed:
> sequence search #1/A
RCSB sequence search failed:
> similarstructures sequences
> sequence search #1/A
RCSB sequence search failed:
> similarstructures blast #1/A
Webservices job id: FTZFVIQHE3C050MP
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9-rc2024.11.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 836, in customEvent
func(*args, **kw)
File
"/Applications/ChimeraX-1.9-rc2024.11.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/blast_search.py", line 40, in show_results
results = SimilarStructures(hits, chain, program = 'blast', database =
database)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/simstruct.py", line 51, in __init__
self._alignment_indexing = 'coordinates' if hits[0].get('coordinate_indexing')
else 'sequence'
~~~~^^^
IndexError: list index out of range
IndexError: list index out of range
File
"/Applications/ChimeraX-1.9-rc2024.11.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/simstruct.py", line 51, in __init__
self._alignment_indexing = 'coordinates' if hits[0].get('coordinate_indexing')
else 'sequence'
~~~~^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: MK1E3MG/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.41.5
OS Loader Version: 11881.41.5
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B91)
Kernel Version: Darwin 24.1.0
Time since boot: 16 days, 4 hours, 21 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.7
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9rc202411260222
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.11
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.3.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.0
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 11 months ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Similar Structures: list index out of range |
comment:2 by , 11 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
| Summary: | Similar Structures: list index out of range → Similar Structures BLAST search with no matches: list index out of range |
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Fixed in 1.9 and 1.10 daily builds.
Made similarstructures blast and mmseqs searches give clear error message when no matches found and not give a traceback.