Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#4782 closed defect (fixed)

Modeller: 'target_name' referenced before assignment

Reported by: blemire@… 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: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Since installing version 1.2.5,  I have  been unable to successfully invoke modeller.

Open an accession from UniProt.
Run blast. 
Load top hit and show alignment.
Invoke modeller using alignment with query aligned to top hit:

Log file:


open A0A1D8PU02 format uniprot fromDatabase uniprot
Summary of feedback from opening A0A1D8PU02 fetched from uniprot
note	Alignment identifier is A0A1D8PU02
Opened UniProt A0A1D8PU02
blastprotein A0A1D8PU02:1Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr or pdb for sequences similar to the given protein sequence
Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service
Opal job id: appBlastProtein2Service1623944771347941833351
Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1623944771347941833351
stdout.txt = standard output
stderr.txt = standard error
BlastProtein finished.
open pdb:3JCM3jcm title:
Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP [more info...]

Chain information for 3jcm #1
Chain	Description
A	Pre-mRNA-splicing factor 8
B	U4/U6 small nuclear ribonucleoprotein PRP4
C	pre-mRNA
D	SNR6 snRNA
E	SNR14 snRNA
F	SNR7-L snRNA
G	Pre-mRNA-splicing factor 6
H	Pre-mRNA-splicing factor SNU114
I	Pre-mRNA-processing factor 31
J R	Small nuclear ribonucleoprotein Sm D3
K	U4/U6 small nuclear ribonucleoprotein PRP3
L	Spliceosomal protein DIB1
M	13 kDa ribonucleoprotein-associated protein
N	Pre-mRNA-splicing helicase BRR2
O S	Small nuclear ribonucleoprotein-associated protein B
P T	Small nuclear ribonucleoprotein Sm D1
Q U	Small nuclear ribonucleoprotein Sm D2
V Y	Small nuclear ribonucleoprotein E
W Z	Small nuclear ribonucleoprotein F
X a	Small nuclear ribonucleoprotein G
b	U6 snRNA-associated Sm-like protein LSm8
c	U6 snRNA-associated Sm-like protein LSm2
d	U6 snRNA-associated Sm-like protein LSm3
e	U6 snRNA-associated Sm-like protein LSm6
f	U6 snRNA-associated Sm-like protein LSm5
g	U6 snRNA-associated Sm-like protein LSm7
h	U6 snRNA-associated Sm-like protein LSm4
Non-standard residues in 3jcm #1
GTP — guanosine-5'-triphosphate
M7M — N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate)

select clearAlignment identifier is bp1 [1]
Associated 3jcm chain B to 3JCM_B with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for alignment bp1 [1]

ui tool show "Modeller Comparative"<QNSWindow: 0x7f945e788800; contentView=<QNSView: 0x7f945e7891f0; QCocoaWindow(0x600002797700, window=QWidgetWindow(0x6000034eac40, name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)! These will stop working now that the window is recreated, and will result in exceptions when the observers are removed. Break in QCocoaWindow::recreateWindowIfNeeded to debug.
<QNSWindow: 0x7f94ae47d310; contentView=<QNSView: 0x7f945ff20d20; QCocoaWindow(0x600002797700, window=QWidgetWindow(0x6000034eaee0, name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)! These will stop working now that the window is recreated, and will result in exceptions when the observers are removed. Break in QCocoaWindow::recreateWindowIfNeeded to debug.

modeller comparative "bp1 [1]:2" multichain false numModels 5 fast false hetPreserve false hydrogens false tempPath /Users/blemire/Desktop/untitled_folder waterPreserve falseTraceback (most recent call last):
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/modeller/tool.py", line 140, in launch_modeller
    run(self.session, "modeller comparative %s multichain %s numModels %d fast %s hetPreserve %s"
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/run.py", line 36, in run
    results = command.run(text, log=log, return_json=return_json)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run
    result = ci.function(session, **kw_args)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/modeller/cmd.py", line 34, in sequence_model
    comparative.model(session, targets, block=block, multichain=multichain,
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/modeller/comparative.py", line 215, in model
    pir_target = Sequence(name=opal_safe_file_name(target_name))
UnboundLocalError: local variable 'target_name' referenced before assignment

UnboundLocalError: local variable 'target_name' referenced before assignment

File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/modeller/comparative.py", line 215, in model
pir_target = Sequence(name=opal_safe_file_name(target_name))

See log for complete Python traceback.


Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open A0A1D8PU02 format uniprot fromDatabase uniprot

Summary of feedback from opening A0A1D8PU02 fetched from uniprot  
---  
note | Alignment identifier is A0A1D8PU02  
  
Opened UniProt A0A1D8PU02  

> blastprotein A0A1D8PU02:1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service1623944771347941833351  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1623944771347941833351  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  

> open pdb:3JCM

3jcm title:  
Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP [more info...]  
  
Chain information for 3jcm #1  
---  
Chain | Description  
A | Pre-mRNA-splicing factor 8  
B | U4/U6 small nuclear ribonucleoprotein PRP4  
C | pre-mRNA  
D | SNR6 snRNA  
E | SNR14 snRNA  
F | SNR7-L snRNA  
G | Pre-mRNA-splicing factor 6  
H | Pre-mRNA-splicing factor SNU114  
I | Pre-mRNA-processing factor 31  
J R | Small nuclear ribonucleoprotein Sm D3  
K | U4/U6 small nuclear ribonucleoprotein PRP3  
L | Spliceosomal protein DIB1  
M | 13 kDa ribonucleoprotein-associated protein  
N | Pre-mRNA-splicing helicase BRR2  
O S | Small nuclear ribonucleoprotein-associated protein B  
P T | Small nuclear ribonucleoprotein Sm D1  
Q U | Small nuclear ribonucleoprotein Sm D2  
V Y | Small nuclear ribonucleoprotein E  
W Z | Small nuclear ribonucleoprotein F  
X a | Small nuclear ribonucleoprotein G  
b | U6 snRNA-associated Sm-like protein LSm8  
c | U6 snRNA-associated Sm-like protein LSm2  
d | U6 snRNA-associated Sm-like protein LSm3  
e | U6 snRNA-associated Sm-like protein LSm6  
f | U6 snRNA-associated Sm-like protein LSm5  
g | U6 snRNA-associated Sm-like protein LSm7  
h | U6 snRNA-associated Sm-like protein LSm4  
  
Non-standard residues in 3jcm #1  
---  
GTP — guanosine-5'-triphosphate  
M7M — N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate)  
  

> select clear

Alignment identifier is bp1 [1]  
Associated 3jcm chain B to 3JCM_B with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [1]  

> ui tool show "Modeller Comparative"

<QNSWindow: 0x7f945e788800; contentView=<QNSView: 0x7f945e7891f0;
QCocoaWindow(0x600002797700, window=QWidgetWindow(0x6000034eac40,
name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)!
These will stop working now that the window is recreated, and will result in
exceptions when the observers are removed. Break in
QCocoaWindow::recreateWindowIfNeeded to debug.  
<QNSWindow: 0x7f94ae47d310; contentView=<QNSView: 0x7f945ff20d20;
QCocoaWindow(0x600002797700, window=QWidgetWindow(0x6000034eaee0,
name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)!
These will stop working now that the window is recreated, and will result in
exceptions when the observers are removed. Break in
QCocoaWindow::recreateWindowIfNeeded to debug.  

> modeller comparative "bp1 [1]:2" multichain false numModels 5 fast false
> hetPreserve false hydrogens false tempPath
> /Users/blemire/Desktop/untitled_folder waterPreserve false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/modeller/tool.py", line 140, in launch_modeller  
run(self.session, "modeller comparative %s multichain %s numModels %d fast %s
hetPreserve %s"  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/modeller/cmd.py", line 34, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/modeller/comparative.py", line 215, in model  
pir_target = Sequence(name=opal_safe_file_name(target_name))  
UnboundLocalError: local variable 'target_name' referenced before assignment  
  
UnboundLocalError: local variable 'target_name' referenced before assignment  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/modeller/comparative.py", line 215, in model  
pir_target = Sequence(name=opal_safe_file_name(target_name))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.5.14
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 64 GB
      System Firmware Version: 1554.120.15.0.0
      SMC Version (system): 2.46f12

Software:

    System Software Overview:

      System Version: macOS 11.4 (20F71)
      Kernel Version: Darwin 20.5.0
      Time since boot: 4 days 18:53

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      EFI Driver Version: 01.B1.042
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        Thunderbolt Display:
          Display Type: LCD
          Resolution: 2048 x 1152
          UI Looks like: 2048 x 1152
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: C02MC33KF2GC
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort

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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (4)

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 → Modeller: 'target_name' referenced before assignment

Reported by Bernard Lemire

comment:2 by pett, 4 years ago

Resolution: → fixed
Status: accepted → closed

Hi Bernard,

Thanks for reporting this problem. There's one additional thing required for it to happen: "Make multichain model from multichain template" has to be turned off -- which is probably why it hasn't been reported until now. I have committed a fix and it will be in the next daily build. You could either wait for that or turn the multichain thing on, depending on what you need.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by blemire@…, 4 years ago 

Hi Eric,

I'm not sure I fully understand this. But, I have run modeller and it has
generated 5 models. I checked the box for making multichain models. Yet
this is not a multichain model (one chain of a multichain template).

Anyways, thank you for your quick response and fix. I will get the next
build when it comes out.

Bernard

On Thu, Jun 17, 2021 at 11:38 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:4 by pett, 4 years ago

If the template only has one chain associated, it doesn't really matter whether or not you have that button checked (except for the fact that the code for the unchecked button is buggy). But let's say you have both chains of a homodimer associated. The button then controls whether the modeling result is a dimer or only a single chain.

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