![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#6330 closed defect (fixed)
KeyError handling Blast results
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19042
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\ouou\Desktop\5531.cxs format session
registering illegal selector name "9H"
Log from Tue Mar 8 17:02:23 2022 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> open C:/Users/admin/Desktop/预测/results/3233.py
ChimeraX cannot open a regular Chimera session.
An exporter from Chimera to ChimeraX is being worked on but is not ready at
this time.
> open C:/Users/admin/Desktop/预测/results/3233.pyc
Python code was compiled for a different version of Python
> open C:/Users/admin/Desktop/预测/5531.pdb
Chain information for 5531.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
> set bgColor white
> select /B
1945 atoms, 1993 bonds, 252 residues, 1 model selected
> color sel cornflower blue
> select /C
2102 atoms, 2153 bonds, 259 residues, 1 model selected
> color sel light sea green
> ui tool show "Color Actions"
> color sel medium aquamarine
> color sel dark cyan
> color sel cornflower blue
> color sel light sea green
> color sel medium turquoise
> color sel turquoise
> color sel dark turquoise
> color sel medium sea green
> color sel forest green
> color sel lime green
> color sel spring green
> color sel lime
> color sel green
> color sel sea green
> color sel medium sea green
> color sel #c0d4ffff
> color sel #c4ecffff
> color sel #aedfffff
> color sel #95daffff
> color sel #7ef9ffff
> color sel #79ffd9ff
> color sel #8bffdeff
> color sel #8bffdcff
> color sel #99ffebff
> color sel #9bffeeff
> color sel #9cffefff
> color sel #b3fffaff
> color sel #79ffe4ff
> color sel #74f1ffff
> color sel #74ecffff
> color sel #60f2ffff
> color sel #4cffe1ff
> color sel #4bffe1ff
> color sel #37f5ffff
> color sel #2bedffff
> color sel #1effe5ff
> color sel #20ffc0ff
> color sel #29ffa6ff
> color sel #31ffa2ff
> color sel #3cffaeff
> color sel #50ffcbff
> color sel #59ffc8ff
> color sel #62ffcbff
> color sel #38ffc7ff
> color sel #39ffc4ff
> color sel #50ffbfff
> color sel #4bff9cff
> color sel #39ff92ff
> color sel #22ff73ff
> color sel #17ff59ff
> color sel #3dff6eff
> color sel #4fff81ff
> color sel #53ff84ff
> color sel #54ff84ff
> color sel #55ff85ff
> color sel #57ff87ff
> color sel #59ff88ff
> color sel #63ff94ff
> color sel #65ff96ff
> color sel #67ff9aff
> color sel #6cff9dff
> color sel #6eff9eff
> color sel #70ffa0ff
> color sel #7effbaff
> color sel #8fffc3ff
> color sel #98ffbaff
> color sel #98ffb9ff
> color sel #86ffacff
> color sel #75ff98ff
> color sel #4effa1ff
> color sel #34ff8fff
> color sel #34fe8fff
> color sel #34fd8eff
> color sel #31ef86ff
> color sel #30ea84ff
> color sel #2fe882ff
> color sel #2fe782ff
> color sel #2fe581ff
> color sel #2ee380ff
> color sel #2ee27fff
> color sel #2ddf7dff
> color sel #2cda7bff
> color sel #2bd578ff
> color sel #2bd477ff
> color sel #2bd175ff
> color sel #28c66fff
> color sel #26b968ff
> color sel #25b666ff
> color sel #25b566ff
> color sel #24b164ff
> color sel #23ac61ff
> color sel #22a65dff
> color sel #22a55dff
> color sel #21a35cff
> color sel #209d58ff
> color sel #1e9152ff
> color sel #1d8f50ff
> color sel #1c8a4eff
> color sel #197a45ff
> color sel #166a3cff
> color sel #15673aff
> color sel #15683aff
> color sel #17703fff
> color sel #187642ff
> color sel #197c46ff
> color sel #1a8149ff
> color sel #1c884cff
> color sel #1d8f50ff
> color sel #1e9353ff
> color sel #1e9554ff
> color sel #209e59ff
> color sel #21a15bff
> color sel #21a35cff
> color sel #22a55dff
> color sel #22a65dff
> color sel #22a85eff
> color sel #24af62ff
> color sel #25b666ff
> color sel #26bc6aff
> color sel #27be6bff
> color sel #27bf6bff
> color sel #28c26dff
> color sel #29c770ff
> color sel #29ca72ff
> color sel #3bca8aff
> color sel #34cac0ff
> color sel #3bc8caff
> color sel #3fca9cff
> color sel #49ca85ff
> color sel #4cca5bff
> color sel #59ca62ff
> color sel #61ca83ff
> color sel #35ca85ff
> color sel #28ca64ff
> color sel #1aca43ff
> color sel #1acb44ff
> color sel #1bcf45ff
> color sel #1bd045ff
> color sel #1bce45ff
> color sel #1ac843ff
> color sel #19c341ff
> color sel #19c140ff
> color sel #19bf40ff
> color sel #18bd3fff
> color sel #19be3fff
> color sel #3bbe59ff
> color sel #2bbe5cff
> color sel #20be74ff
> color sel #19be71ff
> color sel #13be85ff
> color sel #16be81ff
> color sel #18be7eff
> color sel #1fbe6eff
> color sel #1fbe6fff
> color sel #21be45ff
> color sel #23be20ff
> color sel #43be21ff
> color sel #51be22ff
> color sel #82be27ff
> color sel #82be29ff
> color sel #7fbe36ff
> color sel #81be41ff
> color sel #85be48ff
> color sel #89be50ff
> color sel #7bbe22ff
> color sel #99be53ff
> color sel #a2be62ff
> color sel #99be68ff
> color sel #8fbe68ff
> color sel #85be56ff
> color sel #80be4dff
> color sel #7abe43ff
> color sel #71be32ff
> color sel #6ebe24ff
> color sel #6bbe1dff
> color sel #6dc11eff
> color sel #6dc21eff
> color sel #73cc1fff
> color sel #7ad921ff
> color sel #7fe223ff
> color sel #85ec24ff
> color sel #8bf826ff
> color sel #5ef82fff
> color sel #6ef844ff
> color sel #77f850ff
> color sel #71f859ff
> color sel #72f85aff
> color sel #76f85fff
> color sel #77f860ff
> color sel #7af863ff
> color sel #8ff86fff
> color sel #90f870ff
> color sel #93f875ff
> color sel #94f876ff
> color sel #acf86dff
> color sel #b5f876ff
> color sel #acf882ff
> color sel #9af872ff
> color sel #93f86fff
> color sel #8bf863ff
> color sel #80f85eff
> color sel #62f858ff
> color sel #aaaa00ff
> color sel #00ff00ff
> color sel #00aa00ff
> color sel #aaaa00ff
> color sel #00aa00ff
> color sel #05aa05ff
> color sel #0eaa13ff
> color sel #0faa14ff
> color sel #29aa15ff
> color sel #24aa1dff
> color sel #26aa1fff
> color sel #27aa20ff
> color sel #2faa29ff
> color sel #32aa2cff
> color sel #37aa31ff
> color sel #38aa32ff
> color sel #3aaa34ff
> color sel #3caa37ff
> color sel #40aa3aff
> color sel #43aa3dff
> color sel #40aa3eff
> color sel #42aa40ff
> color sel #55aa00ff
> color sel #55ff7fff
> color sel #55ff00ff
> color sel #55ff7fff
> color sel #55aa7fff
> color sel #53a77cff
> color sel #54a87cff
> color sel #56ac7fff
> color sel #59b385ff
> color sel #5ab586ff
> color sel #5dba8aff
> color sel #5fbe8dff
> color sel #5fbf8dff
> color sel #60c18fff
> color sel #61c290ff
> color sel #63c693ff
> color sel #64c894ff
> color sel #65ca96ff
> color sel #65cb96ff
> color sel #66cc97ff
> color sel #67cf99ff
> color sel #68d19bff
> color sel #66d18dff
> color sel #66d18eff
> color sel #67d18eff
> color sel #69d18fff
> color sel #6ad190ff
> color sel #6ad18cff
> color sel #6ad18aff
> color sel #6ad187ff
> color sel #6ad184ff
> color sel #6bd184ff
> color sel #6bd182ff
> color sel #6bd17fff
> color sel #6bd17cff
> color sel #6bd17bff
> color sel #6bd177ff
> color sel #6bd174ff
> color sel #6dd175ff
> color sel #6ed179ff
> color sel #6fd17fff
> color sel #6fd182ff
> color sel #6fd186ff
> color sel #71d18cff
> color sel #71d18fff
> color sel #72d192ff
> select /D
123 atoms, 128 bonds, 15 residues, 1 model selected
> show sel target ab
> cartoon hide sel
> select clear
> select /D
123 atoms, 128 bonds, 15 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 intraMol false intraRes false select true
9 hydrogen bonds found
> show sel target ab
> name frozen 9H sel
registering illegal selector name "9H"
> name frozen 9H sel
registering illegal selector name "9H"
> name frozen 9H sel
registering illegal selector name "9H"
> show (sel-residues & sidechain) target ab
> color sel byhetero
> select clear
[Repeated 1 time(s)]Drag select of 172 atoms, 159 residues, 174 bonds, 9
pseudobonds
> name frozen SHOW sel
Drag select of 172 atoms, 511 residues, 174 bonds, 9 pseudobonds
> select subtract SHOW
2719 atoms, 352 residues, 1 model selected
> cartoon hide sel
> select /D
123 atoms, 128 bonds, 15 residues, 1 model selected
> color sel light gray
> color sel gray
> color sel dark gray
> color sel byhetero
> select clear
> toolshed show
> ui tool show "Command Line Interface"
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
No visible atoms selected
> select /C:69@OH
1 atom, 1 residue, 1 model selected
No visible atoms selected
> select /C:69@CB
1 atom, 1 residue, 1 model selected
> label sel text 37Tyrβ
> select clear
> select /C:89@OD2
1 atom, 1 residue, 1 model selected
> label sel text 57Aspβ
> select /C:93@NE1
1 atom, 1 residue, 1 model selected
> label sel text 61Trpβ
> select /C:46
8 atoms, 7 bonds, 1 residue, 1 model selected
No visible atoms selected
> select clear
> select /B:93@CB
1 atom, 1 residue, 1 model selected
> label sel text 70Asnβ
No visible atoms selected
> select /B:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> label sel text 63Asnβ
> select /C:114
8 atoms, 7 bonds, 1 residue, 1 model selected
> label sel text 82Asnβ
> select add /B:34@CD1
1 atom, 1 bond, 1 residue, 1 model selected
> hide sel target ab
> select add /B:34@CG
1 atom, 2 bonds, 1 residue, 1 model selected
> hide sel target ab
> select add /B:34@CE1
2 atoms, 3 bonds, 1 residue, 1 model selected
> select add /B:34@CE2
3 atoms, 3 bonds, 1 residue, 1 model selected
> select add /B:34@CD2
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel target ab
> select /B:34@CZ
1 atom, 1 residue, 1 model selected
> select add /B:34@OH
2 atoms, 1 residue, 1 model selected
> hide sel target a
> hide sel target ab
> select add /B:34@CB
3 atoms, 1 bond, 1 residue, 1 model selected
> hide sel target a
> select clear
> label sel attribute name
No visible atoms selected
> select /D:12@CA
1 atom, 1 residue, 1 model selected
> select /D:12@CA
1 atom, 1 residue, 1 model selected
> select clear
No visible atoms selected
[Repeated 1 time(s)]
> select /D
123 atoms, 128 bonds, 15 residues, 1 model selected
> hide sel target a
> show sel target ab
> cartoon sel
> cartoon hide sel
> ui tool show "Show Sequence Viewer"
> sequence chain /D
Alignment identifier is 1/D
> select /D:12
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /D:12
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /D:11
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /D:11-12
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /D:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:10-11
19 atoms, 18 bonds, 2 residues, 1 model selected
> select /D:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:10-12
25 atoms, 24 bonds, 3 residues, 1 model selected
> label sel attribute name
No visible atoms selected
[Repeated 1 time(s)]
> select /D:12
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /D:12
6 atoms, 5 bonds, 1 residue, 1 model selected
> label sel text 230Ser
> select /D:11
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /D:11
11 atoms, 10 bonds, 1 residue, 1 model selected
> label sel text 229Arg
> select /D:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:10-11
19 atoms, 18 bonds, 2 residues, 1 model selected
> select /D:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> label sel text 228Leu
> select /D:4
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /D:4-5
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /D:4-5
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /D:4-5
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /D:4
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /D:4
6 atoms, 5 bonds, 1 residue, 1 model selected
> label sel text 222Ser
> select /D:2
14 atoms, 15 bonds, 1 residue, 1 model selected
> label sel text 220Trp
> select clear
> select /B
1945 atoms, 1993 bonds, 252 residues, 1 model selected
> select add /C
4047 atoms, 4146 bonds, 511 residues, 1 model selected
> select add /D
4170 atoms, 4274 bonds, 526 residues, 1 model selected
> ui tool show "Color Actions"
> color sel maroon target l
> color sel dark red target l
> color sel maroon target l
> color sel fire brick target l
> color sel orange red target l
> color sel crimson target l
> color sel dark red target l
> color sel crimson target l
> select clear
> ui tool show Contacts
> select /D
123 atoms, 128 bonds, 15 residues, 1 model selected
> ui tool show Contacts
> contacts sel intraMol false color #ffaa00
230 contacts
> ui tool show "Selection Inspector"
> ui tool show "Command Line Interface"
> toolshed show
> select clear
> save C:/Users/admin/Desktop/预测/results/5531.cxs
——— End of log from Tue Mar 8 17:02:23 2022 ———
opened ChimeraX session
> select /B:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> label sel text "63Asn α"
> ui tool show Distances
> hide #1.3 models
> color #1.1 magenta models transparency 0
> color #1.1 #d7eaf8 models transparency 0
> color #1.1 #cccccc models transparency 0
> color #1.1 red models transparency 0
> color #1.1 #f0f0f0 models transparency 0
> color #1.1 #ff007f models transparency 0
> color #1.1 #aa007f models transparency 0
> color #1.1 #ff557f models transparency 0
> color #1.1 #ff55ff models transparency 0
> color #1.1 magenta models transparency 0
> color #1.1 #5555ff models transparency 0
> color #1.1 #55aa00 models transparency 0
> color #1.1 #00aa7f models transparency 0
> color #1.1 #dce7f0 models transparency 0
> color #1.1 black models transparency 0
> select /B:93
8 atoms, 7 bonds, 1 residue, 1 model selected
> label sel text "70Asn α"
> label height 1
Height must be a number
> select /D:8@N
1 atom, 1 residue, 1 model selected
> select /B
1945 atoms, 1993 bonds, 252 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> select /B:75-76
20 atoms, 20 bonds, 2 residues, 1 model selected
> select /B:75-98
198 atoms, 202 bonds, 24 residues, 1 model selected
> select /B:71-75,80-100,210-249
498 atoms, 501 bonds, 66 residues, 1 model selected
> select /B:68-69
20 atoms, 21 bonds, 2 residues, 1 model selected
> select /B:68-130
497 atoms, 508 bonds, 63 residues, 1 model selected
> select /B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:1-252
1945 atoms, 1993 bonds, 252 residues, 1 model selected
> blastprotein 1/B:1
ChimeraX REST job id:
TTHL84HJJYOAAA39QMTCTWHW7F4KN4DK3TMW2ME75TP0U5U0797GPI9AMB6DGJ2G
BlastProtein finished.
Parsing BLAST results.
Fetching BLAST PDB info failed: <urlopen error [Errno 11001] getaddrinfo
failed>
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 474, in run
self._parse_results(self.database, self.results, self.sequence, self.atomspec)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 529, in _parse_results
blast_results.add_info(self.session, match_chains, sequence_only_hits)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\blastprotein\data_model\databases.py", line 134, in add_info
for k, v in data[chain_id].items():
KeyError: '6PX6_A'
KeyError: '6PX6_A'
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\blastprotein\data_model\databases.py", line 134, in add_info
for k, v in data[chain_id].items():
See log for complete Python traceback.
> select /C
2102 atoms, 2153 bonds, 259 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> blastprotein 1/C:1
ChimeraX REST job id:
FVF6SPPQ7KM46Q5FTASPSMDNKMT2JJQJASMFMT4K8IQOJMCBFXV0NEDDW6NCOXZB
BlastProtein finished.
Parsing BLAST results.
Fetching BLAST PDB info failed: <urlopen error [Errno 11001] getaddrinfo
failed>
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 474, in run
self._parse_results(self.database, self.results, self.sequence, self.atomspec)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 529, in _parse_results
blast_results.add_info(self.session, match_chains, sequence_only_hits)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\blastprotein\data_model\databases.py", line 134, in add_info
for k, v in data[chain_id].items():
KeyError: '6PX6_B'
KeyError: '6PX6_B'
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\blastprotein\data_model\databases.py", line 134, in add_info
for k, v in data[chain_id].items():
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 26.20.100.7926
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel
Manufacturer: HUAWEI
Model: EUL-WX9
OS: Microsoft Windows 10 家庭中文版 (Build 19042)
Memory: 17,003,692,032
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
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
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (6)
comment:1 by , 4 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → KeyError handling Blast results |
comment:2 by , 4 years ago
comment:3 by , 4 years ago
| Cc: | added |
|---|
How does one "pull the results of these jobs from the server", in case there are issues I need to investigate?
comment:5 by , 4 years ago
So I can't really reproduce what happened here, but I have a feeling that
Fetching BLAST PDB info failed: <urlopen error [Errno 11001] getaddrinfo failed>
means the user couldn't contact the site Conrad used to get PDB info. It could be useful to leave urllib3 messages on, in that case, since while we should wrap the traceback code in a try block, it's a red herring.
comment:6 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
I added some defensive code to the blastprotein bundle to handle the case of not being able to contact RCSB to get PDB info, starting with this commit.
Note:
See TracTickets
for help on using tickets.
I'll have to pull the results of these jobs from the server to investigate.