Cannot setattr on surfaces

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-35-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Using ChimeraX instead of Chimera to do some 3D printing. Hence I try to reduce the radius, but here gets an error

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/karl/Bureau/1s3r.pdb1.gz

Summary of feedback from opening /home/karl/Bureau/1s3r.pdb1.gz  
---  
warnings | Start residue of secondary structure not found: HELIX 14 14 ASN B
56 GLY B 70 1 15  
Start residue of secondary structure not found: HELIX 15 15 ASP B 74 LEU B 79
1 6  
Start residue of secondary structure not found: HELIX 16 16 ASP B 137 GLU B
142 1 6  
Start residue of secondary structure not found: HELIX 17 17 SER B 177 SER B
197 1 21  
Start residue of secondary structure not found: HELIX 18 18 SER B 215 GLY B
224 1 10  
36 messages similar to the above omitted  
  
1s3r.pdb1.gz title:  
Crystal structure of the human-specific toxin intermedilysin [more info...]  
  
Chain information for 1s3r.pdb1.gz #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 1s3r.pdb1.gz #1  
---  
SO4 — sulfate ion  
  

> hide atoms

> hide cartoons

> style sphere

Changed 3893 atom styles  

> style sphere

Changed 3893 atom styles  

> style sphere

Changed 3893 atom styles  

> style sphere

Changed 3893 atom styles  

> show cartoons

[Repeated 1 time(s)]

> hide cartoons

> show atoms

> style ball

Changed 3893 atom styles  

> style sphere

Changed 3893 atom styles  

> show surfaces

> hide atoms

> setattr s density 10

Must provide enough attribute-target characters to distinguish 'structures'
from 'surfaces'  

> setattr s density 10.0

Must provide enough attribute-target characters to distinguish 'structures'
from 'surfaces'  

> setattr s density 10.0

Must provide enough attribute-target characters to distinguish 'structures'
from 'surfaces'  

> setattr /a density 10.0

Missing or invalid "attrValue" argument: Expected a text string  

> setattr sel /a density 10.0

Unknown attribute target: '/a'  

> select /A:84@CG

1 atom, 1 residue, 1 model selected  

> select /A:84@CD

1 atom, 1 residue, 1 model selected  

> setattr sel density 10.0

Missing or invalid "attrValue" argument: Expected a text string  

> select

3893 atoms, 3763 bonds, 680 residues, 1 model selected  

> setattr s density 10.0

Must provide enough attribute-target characters to distinguish 'structures'
from 'surfaces'  

> setattr surface density 10.0

Assigning density attribute to 1 item  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/std_commands/setattr.py", line 148, in set_attr  
if attr_name not in type_attrs(class_):  
^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: type object 'MolecularSurface' has no attribute
'_attr_registration'  
  
AttributeError: type object 'MolecularSurface' has no attribute
'_attr_registration'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> setattr surface density

Missing or invalid "attrValue" argument: Expected a text string  

> setattr surface density 1

Assigning density attribute to 1 item  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/std_commands/setattr.py", line 148, in set_attr  
if attr_name not in type_attrs(class_):  
^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: type object 'MolecularSurface' has no attribute
'_attr_registration'  
  
AttributeError: type object 'MolecularSurface' has no attribute
'_attr_registration'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> setattr surface density 1.0

Assigning density attribute to 1 item  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/std_commands/setattr.py", line 148, in set_attr  
if attr_name not in type_attrs(class_):  
^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: type object 'MolecularSurface' has no attribute
'_attr_registration'  
  
AttributeError: type object 'MolecularSurface' has no attribute
'_attr_registration'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> setattr surface radius 0.4

Assigning radius attribute to 1 item  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/std_commands/setattr.py", line 148, in set_attr  
if attr_name not in type_attrs(class_):  
^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: type object 'MolecularSurface' has no attribute
'_attr_registration'  
  
AttributeError: type object 'MolecularSurface' has no attribute
'_attr_registration'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> setattr surfaces radius 0.4

Assigning radius attribute to 1 item  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/std_commands/setattr.py", line 148, in set_attr  
if attr_name not in type_attrs(class_):  
^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: type object 'MolecularSurface' has no attribute
'_attr_registration'  
  
AttributeError: type object 'MolecularSurface' has no attribute
'_attr_registration'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> setattr sel surfaces radius 0.5

Assigning radius attribute to 1 item  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/std_commands/setattr.py", line 148, in set_attr  
if attr_name not in type_attrs(class_):  
^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: type object 'MolecularSurface' has no attribute
'_attr_registration'  
  
AttributeError: type object 'MolecularSurface' has no attribute
'_attr_registration'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: AMD Radeon Vega 8 Graphics (raven, LLVM 15.0.7, DRM 3.54, 6.5.0-35-generic)
OpenGL vendor: AMD

Python: 3.11.2
Locale: fr_FR.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: HUAWEI
Model: NBLK-WAX9X
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 AMD Ryzen 5 3500U with Radeon Vega Mobile Gfx
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           6.7Gi       5.2Gi       477Mi       137Mi       1.1Gi       1.1Gi
	Swap:          2.0Gi       2.0Gi       0.0Ki

Graphics:
	03:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Picasso/Raven 2 [Radeon Vega Series / Radeon Vega Mobile Series] [1002:15d8] (rev c2)	
	Subsystem: Huawei Technologies Co., Ltd. Picasso [19e5:3e19]	
	Kernel driver in use: amdgpu

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
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    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
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    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
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    ChimeraX-ColorActions: 1.0.3
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    ChimeraX-Contacts: 1.0.1
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    ChimeraX-Dssp: 2.0
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    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
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    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
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    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
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    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Eric Pettersen]

ChimeraX surfaces don't have the same attributes as Chimera surfaces, so what the user was doing would never work, but nonetheless it shouldn't produce a traceback.

Fix: ​https://github.com/RBVI/ChimeraX/commit/9a11ebec6c847ed482ba6c02a986d177dee21591