EMDB SFF segmentation file: AttributeError: 'SFFMesh' object has no attribute 'num_vertices'

[martin.schorb@…]

From: Paul Korir 
Subject: Re: SFF conversion
Date: January 20, 2023 at 3:24:17 AM PST
To: Tom Goddard 
Cc: Martin Schorb 

Hi Tom,

Happy new year!

Martin (cc'ed) has tried to view an EMDB-SFF file with meshes and is getting an error which I think is an integration issue with reading meshes. Could you please take a look? We have verified that the file is OK (we can view it on our local viewer). 

This is for ChimeraX version 1.5.

The traceback is here: https://pastebin.com/FnVVyNxa

I'm am on on hand to help where you need my help.

Thanks so much.


Paul K. Korir, PhD
3D Visualisation Lead
CS3DB
EMBL-EBI

On 20/01/2023 10:03, Martin Schorb wrote:
Dear Paul, 

we are working on an EMPIAR submission and like to add our segmentations to the volume. 

These are in Amira format and I found out that converting the surfaces (surf files) seems to work. 
However, I am left with two issues: 

- How to deal with scaling compared to the original volumes as the segmentations were created using binned data? I get a warning when converting with sfftk but do not have the original volume available in a supported format (tif slices only). Can the scaling be done afterwards? 

- I like to check whether the conversion worked, and the only software to visualize SFF I found was ChimeraX. NOw when trying to load one of the converted files, I end up getting errors: "Attribute Error: 'SFFMEsh object has no attribute 'num_vertices'" 

thanks for looking into this, 
Martin 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Opening EMDB segmentation file fails.

Log:
Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/data/sff/nucleus1.sff

Traceback (most recent call last):  
File
"/Users/goddard/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Users/goddard/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Users/goddard/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/Users/goddard/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/Users/goddard/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/emdb_sff/__init__.py", line 25, in open  
return sff.read_sff(session, path,  
File
"/Users/goddard/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/emdb_sff/sff.py", line 31, in read_sff  
mmodels = mesh_models(session, seg)  
File
"/Users/goddard/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/emdb_sff/sff.py", line 188, in mesh_models  
geoms = [mesh_geometry(mesh, seg) for mesh in segment.mesh_list]  
File
"/Users/goddard/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/emdb_sff/sff.py", line 188, in <listcomp>  
geoms = [mesh_geometry(mesh, seg) for mesh in segment.mesh_list]  
File
"/Users/goddard/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/emdb_sff/sff.py", line 205, in mesh_geometry  
nv = mesh.num_vertices // 2  
AttributeError: 'SFFMesh' object has no attribute 'num_vertices'  
  
AttributeError: 'SFFMesh' object has no attribute 'num_vertices'  
  
File
"/Users/goddard/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/emdb_sff/sff.py", line 205, in mesh_geometry  
nv = mesh.num_vertices // 2  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.9.51
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
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Qt platform: cocoa
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[Tom Goddard]

Fixed.

The ChimeraX EMDB SFF file reader was based on the sfftkrw API from 2019 and it has changed since then. I updated the ChimeraX code to use the improved SFFMesh class API and it now reads and displays nucleus1.sff.

Also updated sfftk-rw from version 0.7.0 to 0.7.2.