Opened 4 years ago

Closed 4 years ago

#6601 closed defect (can't reproduce)

Needleman-Wunsch failure

Reported by: chimerax-bug-report@… Owned by: pett
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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00000003183d6000 (most recent call first):
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x0000000204b8c600 (most recent call first):
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 2008 in add_modified
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seqalign/alignment.py", line 736 in _set_residue_attributes
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seqalign/alignment.py", line 565 in prematched_assoc_structure
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seqalign/alignment.py", line 222 in do_assoc
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seqalign/alignment.py", line 303 in associate
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seqalign/cmd.py", line 238 in seqalign_chain
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36 in run
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/show_sequences/tool.py", line 64 in show_seqs
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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{
  "uptime" : 61000,
  "procLaunch" : "2022-04-13 09:35:54.2945 +0200",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,2",
  "procStartAbsTime" : 1458991143894,
  "coalitionID" : 27257,
  "osVersion" : {
    "train" : "macOS 12.3.1",
    "build" : "21E258",
    "releaseType" : "User"
  },
  "captureTime" : "2022-04-13 09:44:14.3170 +0200",
  "incident" : "21677E76-3D54-4C91-8B73-B09D91B977FB",
  "bug_type" : "309",
  "pid" : 79506,
  "procExitAbsTime" : 1470991455538,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.3.0","CFBundleVersion":"1.3.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"E7585361-00CA-53AB-89DD-F327B7C07C7B","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "5B7A031A-56B5-B567-60F5-AA9B5A419D85",
  "wakeTime" : 1502,
  "sleepWakeUUID" : "15E227EB-8424-45DD-9BD6-7998ED810DE6",
  "sip" : "enabled",
  "vmRegionInfo" : "0x195e66 is not in any region.  Bytes before following region: 4368331162\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10478d000-10478e000    [    4K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x0000000000195e66","rawCodes":[1,1662566],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000195e66"},
  "vmregioninfo" : "0x195e66 is not in any region.  Bytes before following region: 4368331162\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10478d000-10478e000    [    4K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/P2VsPyocin.cxs
> format session

opened ChimeraX session  

> lighting simple

> close #1,3#2

> close #8

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A #5/B #5/C

Alignment identifier is 1  

> sequence chain #6/B #6/C #6/D

Alignment identifier is 2  

> select #6/B-D:245

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select #6/B-D:245-251

174 atoms, 171 bonds, 21 residues, 1 model selected  

> select #5/A-C:45

51 atoms, 48 bonds, 3 residues, 1 model selected  

> select #5/A-C:1-45

1986 atoms, 1992 bonds, 135 residues, 1 model selected  

> select #5/A-C:42

66 atoms, 63 bonds, 3 residues, 1 model selected  

> select #5/A-C:1-42

1845 atoms, 1851 bonds, 126 residues, 1 model selected  

> select #5/A-C:44

48 atoms, 45 bonds, 3 residues, 1 model selected  

> select #5/A-C:1-44

1935 atoms, 1941 bonds, 132 residues, 1 model selected  

> delete sel

> select #6/B-D:245

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select #6/B-D:245-251

174 atoms, 171 bonds, 21 residues, 1 model selected  

> delete sel

> select #6

5415 atoms, 5496 bonds, 732 residues, 1 model selected  

> select #5

6738 atoms, 6777 bonds, 468 residues, 1 model selected  

> select #6

5415 atoms, 5496 bonds, 732 residues, 1 model selected  

> ui mousemode right select

> select #5

6738 atoms, 6777 bonds, 468 residues, 1 model selected  

> select #6/C:241

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #5/C:46

19 atoms, 17 bonds, 2 residues, 2 models selected  

> select up

95 atoms, 94 bonds, 10 residues, 2 models selected  

> select up

4051 atoms, 4091 bonds, 400 residues, 2 models selected  

> select up

12153 atoms, 12273 bonds, 1200 residues, 2 models selected  

> combine sel

Remapping chain ID 'B' in gpH1_250trimer.pdb #6 to 'E'  
Remapping chain ID 'C' in gpH1_250trimer.pdb #6 to 'F'  

> ~select #6

6738 atoms, 6777 bonds, 468 residues, 1 model selected  

> ~select #5

Nothing selected  

> close #5-6

> select #1

12153 atoms, 12273 bonds, 1200 residues, 1 model selected  

> bond sel

Created 6 bonds  

> select clear

> save "/Users/shj152/Desktop/full tailfibre P2.cxs"

FYI: command is replacing existing command: "build modify"  
FYI: command is replacing existing command: "build start"  
FYI: command is replacing existing command: "bond"  
FYI: command is replacing existing command: "~bond"  
FYI: command is replacing existing command: "bond length"  

> select clear

> ui mousemode right translate

> hide #4 models

> show #4 models

> hide #4 models

> hide #7 models

> show #7 models

> close #4

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/P2/gpH_trimer/301-669/gpH301_699trimer.pdb

Chain information for gpH301_699trimer.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> mmaker #2 to #7

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 gpH_gpG_complex.pdb, chain B (#7) with gpH301_699trimer.pdb, chain
B (#2), sequence alignment score = 352.4  
RMSD between 63 pruned atom pairs is 0.797 angstroms; (across all 70 pairs:
1.534)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A #2/B #2/C

Alignment identifier is 1  

> sequence chain #7/B #7/C #7/D

Alignment identifier is 2  

> sequence chain #7/E #7/F #7/G

Alignment identifier is 3  

> ui mousemode right select

> ui mousemode right translate

> ui mousemode right select

> select #7/B:4

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #7/B-D:1

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select #7/B-D:1-4

102 atoms, 105 bonds, 12 residues, 1 model selected  

> delete sel

> select #2/B:305

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #2/A-C:304-305

96 atoms, 96 bonds, 6 residues, 1 model selected  

> select #2/A-C:304-369

3183 atoms, 3210 bonds, 198 residues, 1 model selected  

> delete sel

> select #2/B:302

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select up

4513 atoms, 4556 bonds, 303 residues, 1 model selected  

> select up

13539 atoms, 13668 bonds, 909 residues, 1 model selected  

> select add #7/B:6

13547 atoms, 13675 bonds, 910 residues, 2 models selected  

> select up

13558 atoms, 13687 bonds, 911 residues, 2 models selected  

> select up

14069 atoms, 14207 bonds, 975 residues, 2 models selected  

> select up

19416 atoms, 19662 bonds, 1632 residues, 2 models selected  

> combine sel

Remapping chain ID 'B' in gpH_gpG_complex.pdb #7 to 'H'  
Remapping chain ID 'C' in gpH_gpG_complex.pdb #7 to 'I'  

> bond sel

Created 36 bonds  

> undo

> close #2-3,7

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Desktop/PhD/Bioinformatics/AlphaFold/Bacteriophages/P2/gpH_trimer/301-669/gpH301_699trimer.pdb

Chain information for gpH301_699trimer.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> mmaker #2 to #1

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 360, in match  
score, s1, s2 = align(session, rseq, mseq,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 67, in align  
score, seqs = NeedlemanWunsch.nw(ref, match,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in nw  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in
  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in ss_type  
r = self.residue_at(loc)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1117, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
IndexError: vector  
  
IndexError: vector  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1117, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
  
See log for complete Python traceback.  
  

> mmaker #2 to #1

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 360, in match  
score, s1, s2 = align(session, rseq, mseq,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 67, in align  
score, seqs = NeedlemanWunsch.nw(ref, match,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in nw  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in
  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in ss_type  
r = self.residue_at(loc)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1117, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
IndexError: vector  
  
IndexError: vector  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1117, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
  
See log for complete Python traceback.  
  

> ui mousemode right translate

> ui tool show "Show Sequence Viewer"

> sequence chain #1/E #1/F #1/D

Alignment identifier is 1  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Processor Name: Unknown
      Processor Speed: 2,4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 32 GB

Software:

    System Software Overview:

      System Version: macOS 12.3.1 (21E258)
      Kernel Version: Darwin 21.4.0
      Time since boot: 4 days 17:57

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      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: Yes
          Connection Type: Internal
        P27q-20:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    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
    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: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    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
    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

Change History (2)

comment:1 by pett, 4 years ago

Component: Unassigned → Sequence
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Needleman-Wunsch failure

comment:2 by pett, 4 years ago

Resolution: → can't reproduce
Status: accepted → closed
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