Opened 5 years ago

Closed 5 years ago

#3453 closed defect (fixed)

Changing id number of model with submodels broken

Reported by: goddard@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 1.1.dev202006250254 (2020-06-25 02:54:05 UTC)
Description
Tried to change the id of a top level model with a submodel.  The two models incorrectly moved as siblings instead of parent/child and raised an error.

Log:
UCSF ChimeraX version: 1.1.dev202006250254 (2020-06-25)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/cov2_rna_twist.cxs

Log from Sat Jun 6 17:27:41 2020UCSF ChimeraX version: 1.1.dev202006052335
(2020-06-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/goddard/Desktop/cov2_rna_twist.cxs format session

Log from Sat Jun 6 17:17:30 2020UCSF ChimeraX version: 1.1.dev202006052335
(2020-06-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> rna path ~/ucsf/presentations/sars-rna-may2020/stems pattern sphere length
> 500 randomLoopTwist 180

RNA sphere radius 47.8  

> rna model ~/ucsf/presentations/sars-rna-may2020/sequence.fasta #1

Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  

Chain information for RNA #2  
---  
Chain | Description  
I | No description available  
  

> style stick

Changed 11096 atom styles  

> hide #1 models

> close

> rna path ~/ucsf/presentations/sars-rna-may2020/stems pattern sphere
> randomLoopTwist 180

RNA sphere radius 340.4  

> rna model ~/ucsf/presentations/sars-rna-may2020/sequence.fasta #1

Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  

Chain information for RNA #2  
---  
Chain | Description  
I | No description available  
  

> hide #1 models

> lighting soft

> lighting simple

> lighting soft

> set bgColor white

> set bgColor black

> save /Users/goddard/Desktop/image1.png supersample 3

> save /Users/goddard/Desktop/cov2_rna_twist.cxs

opened ChimeraX session  

> shape sphere color black

> hide #2 models

> set bgColor white

> close #3

> show #2 models

> shape sphere color black radius 400

> close #3

> shape sphere color black radius 350

> close #3

> shape sphere color black radius 300

> close #3

> shape sphere color black radius 340

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

> lighting full

> lighting soft

> save /Users/goddard/Desktop/cov2_rna_twist.cxs

opened ChimeraX session  

> close #1

> set bgColor black

> rename #3 id #2.1

> set bgColor white

> hide #2 models

> show #2 models

> hide #2.1 models

> show #2.1 models

> rename #2 id #4

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 263, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/rename.py", line 34, in rename  
change_model_id(session, models, id, new_name = nname)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/rename.py", line 54, in change_model_id  
ml.add(models, parent = p)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 647, in add  
self._reparent_model(model, parent, minimum_id = minimum_id)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 736, in _reparent_model  
parent.add_drawing(model)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 281, in add_drawing  
d.parent.remove_drawing(d, delete=False)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 296, in remove_drawing  
self._child_drawings.remove(d)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 296, in remove_drawing  
self._child_drawings.remove(d)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.9.15
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 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: 32 GB
      Boot ROM Version: 1037.120.87.0.0 (iBridge: 17.16.15300.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.5 (19F101)
      Kernel Version: Darwin 19.5.0
      Time since boot: 18:33

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by Tom Goddard, 5 years ago

Component: Unassigned → Core
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Changing id number of model with submodels broken

comment:2 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Changing model id to be child of another model did not add it to the child list.

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