Opened 4 years ago

Closed 4 years ago

#6039 closed defect (duplicate)

Modeller: 'target_name' referenced before assignment

Reported by: isha.raj@… Owned by: pett
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc: Tom Goddard
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: 1.2.4 (2021-05-14 07:23:00 UTC)
Description
(I feed the alignment file to modeller and assign target sequence. from selection. but modeller complains of :  "UnboundLocalError: local variable 'target_name' referenced before assignment"

Log:
UCSF ChimeraX version: 1.2.4 (2021-05-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/rgk680/Desktop/ABCC4.pdb format pdb

Chain information for ABCC4.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Modeller Comparative"

> open /Users/rgk680/Desktop/c4_c5_BBed.aln

Summary of feedback from opening /Users/rgk680/Desktop/c4_c5_BBed.aln  
---  
error | <QNSWindow: 0x7f8456704590; contentView=<QNSView: 0x7f84567042d0;
QCocoaWindow(0x60000333e310, window=QWidgetWindow(0x6000020da6a0,
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.  
notes | Alignment identifier is c4_c5_BBed.aln  
Associated ABCC4.pdb chain A to ABCC4 with 3 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment c4_c5_BBed.aln  
  
Opened 2 sequences from c4_c5_BBed.aln  
No target sequence chosen for alignment c4_c5_BBed.aln  

> modeller comparative c4_c5_BBed.aln:1 multichain false numModels 5 fast
> false hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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.  
  

> open /Users/rgk680/Desktop/c4_c5_BBed.aln

Summary of feedback from opening /Users/rgk680/Desktop/c4_c5_BBed.aln  
---  
error | <QNSWindow: 0x7f843c871320; contentView=<QNSView: 0x7f843c871060;
QCocoaWindow(0x600003386730, window=QWidgetWindow(0x600002109ec0,
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.  
notes | Alignment identifier is c4_c5_BBed.aln  
Associated ABCC4.pdb chain A to ABCC4 with 3 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment c4_c5_BBed.aln  
  
Opened 2 sequences from c4_c5_BBed.aln  

> modeller comparative c4_c5_BBed.aln:1 multichain false numModels 5 fast
> false hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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.  
  

> dssp #1

> modeller comparative c4_c5_BBed.aln:1 multichain false numModels 5 fast
> false hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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.  
  

> modeller comparative c4_c5_BBed.aln:2 multichain false numModels 5 fast
> false hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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.  
  

> modeller comparative c4_c5_BBed.aln:2 multichain false numModels 5 fast
> false hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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-1.2.4.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 INTEL-18.2.10
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 3,1 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 447.40.12.0.0
      OS Loader Version: 540.40.4~45
      SMC Version (system): 2.44f6

Software:

    System Software Overview:

      System Version: macOS 12.0.1 (21A559)
      Kernel Version: Darwin 21.1.0
      Time since boot: 9 days 1:59

Graphics/Displays:

    Intel Iris Plus Graphics 650:

      Chipset Model: Intel Iris Plus Graphics 650
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5927
      Revision ID: 0x0006
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2719D:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 6XF45R2     
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7,55

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: 1.4.1
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    ChimeraX-AddCharge: 1.0
    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: 1.13.3
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    ChimeraX-CoreFormats: 1.0
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    ChimeraX-Crystal: 1.0
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    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
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    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
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    ChimeraX-gltf: 1.0
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    ChimeraX-HKCage: 1.3
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    ChimeraX-IO: 1.0.1
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    ChimeraX-ModelSeries: 1.0
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    ChimeraX-ShowSequences: 1.0
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    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
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    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
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    numexpr: 2.7.3
    numpy: 1.19.2
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    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
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    pip: 21.0.1
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    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    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 (2)

comment:1 by Tom Goddard, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Structure Prediction
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Modeller: 'target_name' referenced before assignment

It looks like this was fixed 8 months ago (bug #4782) so it should work correctly in the current ChimeraX 1.3 version.

If it does not work in ChimeraX 1.3 then report it again from ChimeraX 1.3.

comment:2 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: assigned → closed
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