Missing structure labels make opening PDB 8jnb not focus view on full model

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9.dev202407240247 (2024-07-24 02:47:28 UTC)
Description
opening 8jnb in the daily build does not show the full model and seems to focus on the ligand.  If I turn off Label missing-structure segments in preferences then it does show the full model.  Also ChimeraX 1.8 shows the full model.

Log:
UCSF ChimeraX version: 1.9.dev202407240247 (2024-07-24)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1www

1www title:  
NGF In complex with domain 5 of the TRKA receptor [more info...]  
  
Chain information for 1www #1  
---  
Chain | Description | UniProt  
V W | PROTEIN (NERVE GROWTH FACTOR) | NGF_HUMAN 1-120  
X Y | PROTEIN (TRKA RECEPTOR) | NTRK1_HUMAN 282-382  
  

> close

> open 8jnb format pdb fromDatabase pdb

8jnb title:  
Craf ras-binding domain chimera, ligand complex [more info...]  
  
Chain information for 8jnb #1  
---  
Chain | Description | UniProt  
B | raf proto-oncogene serine/threonine-protein kinase, craf | RAF1_HUMAN 50-101 114-141, BRAF_HUMAN 102-113  
  
Non-standard residues in 8jnb #1  
---  
USX — 2-[4-[[(2S)-1-ethanoyl-3-oxidanylidene-2H-indol-2-yl]methyl]-2-methoxy-
phenoxy]ethanamide  
  
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.0, Qt 6.7.1
Qt runtime version: 6.7.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 37 days, 18 hours, 39 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


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[Eric Pettersen]

It's beginning to look like something in the internals of the drawing/viewing code, so reassigning to you. If I comment out "parent.add([lm])" on line 296 of label3d.py (in the labels_model() function) then no problem. Not surprising since commenting that out results in the label model not being added to the session. Nonetheless, still seems more likely to be a graphics thing than not. Perhaps some edge case of handling pseudobond labels.

[goddard@…]

Could be related to how the code detects that the first model is being opened.  I'm guessing because of the label being added the code decides this isn't the first model and does not do the view all.  I'll look into it.

[Tom Goddard]

The stack trace where the intial camera view is set shows something pretty twisted happening. The open structure is half way through being added to the session with models.add(structure) and is calling the structure.add_to_session() method which is then adding the missing segment label which calls models.add() so now we are recursively calling models.add() adding the labels model before its parent model has completed being added to the session. The label model gets added and triggers the initial camera view before returning, and then the structure finishes getting added to the session.

It is actually pretty fortunate this doesn't wipe out with an error because the label model is being added to the session while its parent hasn't yet completed being added to the session.

I'm tempted to say that adding a child model to a session in the added_to_session() handler of the parent is not allowed.

Is there some other sensible place you can add that label, for example, after the structure has completed being added to the open models?

File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1200, in <module>
exit_code = init(sys.argv)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1037, in init
sess.ui.event_loop()
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 329, in event_loop
self.exec()
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 353, in intercept
chimerax_intercept(*args, view=view, session=session)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 455, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 437, in thread_safe
func(*args, **kw)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 446, in defer
cxcmd(session, topic)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 464, in cxcmd
run(session, cmd)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0]
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 294, in provider_open
session.models.add(opened_models)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py", line 782, in add
m.added_to_session(session)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1263, in added_to_session
super().added_to_session(session)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 192, in added_to_session
self.apply_auto_styling(set_lighting = self._is_only_model())
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1420, in apply_auto_styling
label_missing_cmd(self.session, [self], True)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 200, in label_missing_cmd
label(session, Objects(pseudobonds=Pseudobonds([pb])),
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/label/label3d.py", line 148, in label
lm = labels_model(m, create = True)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/label/label3d.py", line 296, in labels_model
parent.add([lm])
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py", line 314, in add
om.add(models, parent = self)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py", line 796, in add
v.initial_camera_view()
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 696, in initial_camera_view
traceback.print_stack()

[Tom Goddard]

Digging a little more into where things go wrong, the labels are being added in the Structure.apply_auto_styling() routine called from Structure.added_to_session() and it is only later in Structure.added_to_session() that the structure is added to the graphics updater that monitors changes in display style. Specifically when the label causes the intial view no ribbon has been created yet because the structure was not registered with the structure graphics updater to detect that the ribbon style was set in the apply_auto_styling().

So basically the label is being added which sets the initial view before Structure.added_to_session() has setup the ribbon generation for the structure.

The label should probably be created either earlier, before the structure is added to the open models, or later, after models.add(structure) has finished. Probably it would work if it were moved to the end of Structure.added_to_session() after the graphics updating has been registered, but that seem precarious to me. I still am inclined to say models should not be added during an added_to_session() call because that is still in the middle of adding some other models.

[Eric Pettersen]

Maybe the labels should be added wherever the missing-structure pseudobond group itself is being created -- since there seems to be no problem creating that model.

[Eric Pettersen]

Adding the labels as the pseudobond group is created seems to solve the problem.

Fix: ​https://github.com/RBVI/ChimeraX/commit/61c2760c719949dda37c86638a09a79c4b7357b0