Better error handling for binary STL?

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Out of vague interest, I tried opening the STL files for a map of Drosophila sensory neurons from https://zenodo.org/record/3879033#.XxlUl6bTVmM (from https://www.cell.com/current-biology/pdf/S0960-9822(20)30844-7.pdf and https://twitter.com/MRC_LMB/status/1286225160157233153?s=20). ChimeraX throws a somewhat misleading error - looks like the actual reason is that these are in the STL ASCII format, where ChimeraX expects *binary*.

 

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /run/media/tic20/storage/Downloads/fly_brain/VP_SI/neuropil_meshes/MB_LAC_R_VP32.stl

STL file is truncated. Header says it contains 825634869 triangles, but only
1256 were in file.  

> open
> /run/media/tic20/storage/Downloads/fly_brain/VP_SI/neuropil_meshes/MB_LAC_L_VP32.stl

STL file is truncated. Header says it contains 926496053 triangles, but only
1256 were in file.  

> open
> /run/media/tic20/storage/Downloads/fly_brain/VP_SI/glomeruli_meshes/VP3.stl

STL file is truncated. Header says it contains 538970736 triangles, but only
1513 were in file.  

> usage open

open fileNames restOfLine  
— Open/fetch data files  
fileNames: file names to open  
restOfLine: the rest of line

open formats  
— report formats that can be opened  

> open
> /run/media/tic20/storage/Downloads/fly_brain/VP_SI/glomeruli_meshes/VP1l.stl

STL file is truncated. Header says it contains 538970736 triangles, but only
20544 were in file.  




OpenGL version: 3.3.0 NVIDIA 450.51.05
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        5.1G         47G        254M        9.6G         56G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Tristan Croll]

In case it's useful, the (very short) Ruby script at 
https://github.com/cmpolis/convertSTL.git is successful in converting 
these to a binary format that ChimeraX reads. After all that, though, it 
turns out the STL files are just giving the overall brain volume - the 
actual neurons are described in the SWC format 
(http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html). 
Never mind...

On 2020-07-23 10:28, ChimeraX wrote:

[Tom Goddard]

Fixed.

Added reading of ASCII STL files. Also ported Chimera SWC neuron trace file reader to ChimeraX.