Shape command allows creating submodel without a parent model

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005242323 (2020-05-24 23:23:37 UTC)
Description
shape icos
clip
-> error

Log:
Startup Messages  
---  
warnings | QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already
registered  
QWebEngineUrlScheme::registerScheme: Scheme "help" already registered  
QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered  
QWebEngineUrlScheme::registerScheme: Scheme "help" already registered  
QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered  
8 messages similar to the above omitted  
Replacing file-saver for 'DCD coordinates' from MD-crds bundle with that from
MDcrds bundle  
Replacing opener for 'Gromacs full-precision coordinates' from MD-crds bundle
with that from MDcrds bundle  
Replacing opener for 'Gromacs compressed coordinates' from MD-crds bundle with
that from MDcrds bundle  
Replacing opener for 'DCD coordinates' from MD-crds bundle with that from
MDcrds bundle  
notes | Replacing data format 'Gromacs full-precision coordinates' as defined
by ChimeraX-MD-crds bundle with definition from ChimeraX-MDcrds bundle  
Replacing data format 'Gromacs compressed coordinates' as defined by ChimeraX-
MD-crds bundle with definition from ChimeraX-MDcrds bundle  
Replacing data format 'DCD coordinates' as defined by ChimeraX-MD-crds bundle
with definition from ChimeraX-MDcrds bundle  
  
UCSF ChimeraX version: 1.0rc202005220158 (2020-05-24)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> shape icosahedron modelId #1.1

> clip

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 165, in <lambda>  
lambda *args, ft=self._fill_tree, ar=always_rebuild: ft(always_rebuild=ar))  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 214, in _fill_tree  
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]  
IndexError: list index out of range  
  
Error processing trigger "new frame":  
IndexError: list index out of range  
  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 214, in _fill_tree  
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.8.24
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: 1037.100.362.0.0 (iBridge: 17.16.14281.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E287)
      Kernel Version: Darwin 19.4.0
      Time since boot: 17 days 14:50

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

[goddard@…]

Corrections "shape icos model #1.1 ; clip".

[Tom Goddard]

We have seen this error before on session restore.

The problem is that the Models.add() method does not catch that a model is being added with an id that has no immediate parent.

[Tom Goddard]

All commands that take a model_id argument probably have this same problem.

[Tom Goddard]

These commands take a model_id argument (ModelIdArg).
shape, marker, volume subcommands that make volumes, struts, measure center, measure inertia, rename

[Tom Goddard]

Fixed in ChimeraX 1.1

Rewrote Models.add() and added extensive error checking to assure model hierarchy is not corrupted.
Also made shape command create parent models if they do not exist.

[Eric Pettersen]

So this is committed on the develop branch I'm guessing?

[goddard@…]

Yep, on develop branch, ChimeraX 1.1