Opened 17 months ago

Closed 12 months ago

#15258 closed defect (fixed)

Show missing-structure labels: 'NoneType' object has no attribute 'residues'

Reported by: Greg Couch Owned by: Greg Couch
Priority: normal Milestone:
Component: Depiction Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.5.0-35-generic-x86_64-with-glibc2.38
ChimeraX Version: 1.9.dev202405190643 (2024-05-19 06:43:34 UTC)
Description
Opened model

Log:
UCSF ChimeraX version: 1.9.dev202405190643 (2024-05-19)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/gregc/src/chimerax/I53-50_marshmallow_half_shell_trimer_centered.cif
> format mmcif

Summary of feedback from opening
/home/gregc/src/chimerax/I53-50_marshmallow_half_shell_trimer_centered.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Skipping residue with duplicate label_seq_id 1 in chain  
Skipping residue with duplicate label_seq_id 2 in chain A  
Skipping residue with duplicate label_seq_id 3 in chain A  
Skipping residue with duplicate label_seq_id 4 in chain A  
Skipping residue with duplicate label_seq_id 5 in chain A  
57 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Traceback (most recent call last):  
File "/app/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line
320, in interceptRequest  
self._callback(info)  
File "/app/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line
93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line
353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "/app/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 "/app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 394, in
thread_safe  
func(*args, **kw)  
File "/app/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line
446, in defer  
cxcmd(session, topic)  
File "/app/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line
464, in cxcmd  
run(session, cmd)  
File "/app/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 "/app/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line
3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/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 "/app/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line
3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line
294, in provider_open  
session.models.add(opened_models)  
File "/app/lib/python3.11/site-packages/chimerax/core/models.py", line 780, in
add  
m.added_to_session(session)  
File "/app/lib/python3.11/site-packages/chimerax/atomic/structure.py", line
1263, in added_to_session  
super().added_to_session(session)  
File "/app/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 "/app/lib/python3.11/site-packages/chimerax/atomic/structure.py", line
1420, in apply_auto_styling  
label_missing_cmd(self.session, [self], True)  
File "/app/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 194, in
label_missing_cmd  
gap_size = abs(r1.chain.residues.index(r1) - r2.chain.residues.index(r2)) - 1  
^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'residues'  
  
AttributeError: 'NoneType' object has no attribute 'residues'  
  
File "/app/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 194, in
label_missing_cmd  
gap_size = abs(r1.chain.residues.index(r1) - r2.chain.residues.index(r2)) - 1  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 535.171.04
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:99.0
Manufacturer: Dell Inc.
Model: OptiPlex 7000
OS: Freedesktop SDK 23.08 Flatpak runtime
Architecture: 64bit ELF
Virtual Machine: detection failed
CPU: 24 12th Gen Intel(R) Core(TM) i9-12900
Cache Size: 30720 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       6.6Gi        37Gi        63Mi        19Gi        55Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3070 Lite Hash Rate] [10de:2488] (rev a1)	
	Subsystem: Dell Device [1028:c903]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58
    ChimeraX-AtomicLibrary: 14.0.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.4
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
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File attachment: I53-50_marshmallow_half_shell_trimer_centered.cif

I53-50_marshmallow_half_shell_trimer_centered.cif​

Attachments (1)

I53-50_marshmallow_half_shell_trimer_centered.cif​ (1.9 MB ) - added by Greg Couch 17 months ago.
Added by email2trac

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Change History (24)

by Greg Couch, 17 months ago

Attachment: I53-50_marshmallow_half_shell_trimer_centered.cif​ added

Added by email2trac

comment:1 by Eric Pettersen, 17 months ago

Component: Unassigned → Depiction
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Show missing-structure labels: 'NoneType' object has no attribute 'residues'

comment:2 by Eric Pettersen, 17 months ago

Cc: Eric Pettersen added
Owner: changed from Eric Pettersen to Greg Couch
Status: accepted → assigned

This structure is badly mangled. For instance, in model #1.1 there are missing-structure pseudobonds between residues with different chain IDs (e.g. /A:7 and /F:8), and there are residues missing from the chain object that they _should_ be in (e.g. /A:8 is missing from the chain A object).

The "error" in the missing-structure labeling code is only occurring because the structure data is scrambled nonsense.

comment:3 by Greg Couch, 17 months ago

I can reproduce the error with just the first structure in the file with today's daily build. My April 15 build found the two chains. There were no changes to the mmCIF code in the interim.

comment:4 by Greg Couch, 17 months ago

The error is evoked by the May 13 commit, 607a1d6232c641fc5f1b88dce054e2586a0027ff:
"Make label-missing-structure default True and let the chips fall where they may".
And that commit changes label_missing_attr in Atomic's settings from False to True. Which means the bug is in the 1.8 release, but hidden.

comment:5 by Eric Pettersen, 17 months ago

Yes, setting the default to True means that it tries to label missing-structure pseudobonds, which means that those pseudobonds have to "make sense", i.e. be between two residues in the same chain object.

comment:6 by Greg Couch, 17 months ago

The residue->chain() is null when the missing structure pseudobonds are added.

comment:7 by Greg Couch, 17 months ago

Eric, can the chain making code be fixed to not create inconsistent data structures? Bad data is okay.

comment:8 by Eric Pettersen, 17 months ago

It's my understanding that your code is explicitly telling atomic what the chain information is by calling Structure::set_input_seq_info and is also creating the missing-structure pseudobonds itself. If you simply didn't do these things when you felt you had bad data then things might work.

comment:9 by Greg Couch, 17 months ago

Not in this case. There is no sequence information in the file, so set_input_seq_info is not called.

comment:10 by Eric Pettersen, 17 months ago

How are the missing-structure pseudobonds getting created?

comment:11 by Greg Couch, 17 months ago

The missing structure bonds are created for the missing interresidue bonds after the residues have been created using saved adjacent residue information. No Chain objects exist at that point. After that, if the sequence information is authoritative, then set_input_seq_info is called. A little while later, pdb_connect::find_missing_structure_bonds(mol). Perhaps that creates the Chain objects? And after all of the structures in a file are opened, the chains are used to set the chain descriptions.

FYI, I'm going to fix the symptoms of this bug by improving the entity detection heuristic. But users are good at generating bad data files, so it would be good to not create multiple chains if there is a missing structure bond present, even though there should be multiple chains :-)

comment:12 by Eric Pettersen, 17 months ago

Some of the interresidue bonds you're creating from "adjacent residue information" (whatever that is exactly) must be between residues with different chain IDs. You should have your code not create such bonds.

comment:13 by Greg Couch, 17 months ago

The label_asym_id is " " for all atoms and the auth_asym_id is a letter. So, from a mmCIF perspective, the data says they are all in one chain. And that is how they were connected. The adjacent residue information is just the order in which the residues are in the file.

comment:14 by Eric Pettersen, 17 months ago

When you call new_residue() you provide a chain ID letter, do you not? Do not connect residues where you provided different chain ID letters.

comment:15 by Greg Couch, 17 months ago

Then what other kind of pseudobond should be put there to show the connectivity?

comment:16 by Eric Pettersen, 17 months ago

Look, you have to decide if you want the residues all in a single chain, or in multiple chains. If you want them in one chain, use the same chain ID for all residues. If you want them in multiple chains, do not put any kind of bond between the end of one chain and the start of the next. You're the one that needs to decide what your data means, but a single chain cannot have multiple chain IDs.

comment:17 by Greg Couch, 17 months ago

mmCIF has the same constraint for label_asym_id and entities. But auth_asym_id, that ChimeraX preferably uses, that is not explicit.

I have a related issue with explicitly given bonds in the struct_conn table. If the bond length is not reasonable, the code is creating a missing structure pseudobond instead of a covalent bond. That bond could be between chains. If the atoms happened to be in different chains, the same problem could occur. What is the recommendation in this case?

Last edited 17 months ago by Greg Couch (previous) (diff)

comment:18 by Eric Pettersen, 17 months ago

Upon further consideration, though the structure data did need (a lot of) improvement, it should be allowed to put missing-structure pseudobonds to indicate non-chain missing structure, such as disulphide connectivity where you only have CA atoms.

So I am going to add checks to the pseudobond-labeling code to skip non-chain pseudobonds instead of producing an error, and you could (and probably should) use missing-structure pseudobonds for this structure.

comment:20 by Greg Couch, 17 months ago

Then should pdb_connect::find_missing_pseudobonds() now always replace a long bond with a pseudobond instead of silently deleting some?

comment:21 by Eric Pettersen, 17 months ago

There is no find_missing_pseudobonds() in the pdb_connect namespace. Do you mean find_missing_structure_bonds()? AFAIK, any bonds that routine deletes should automatically be replaced by pseudobonds.

comment:22 by Greg Couch, 17 months ago

Oops, yes, I meant find_missing_structure_bonds(). Should have cut & pasted.

comment:23 by Greg Couch, 12 months ago

Resolution: → fixed
Status: assigned → closed

Fixed by Eric's changes.

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