[chimerax-users] EMDB-SFF segmentation file: application of transform 0 for image-to-physical projection

[Paul Korir]

Hi Tom/ChimeraX admin,

Just to clarify: what are the units of physical space in ChimeraX: Å or nm? 

Kind regards,

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

On 30/01/2023 08:51, Paul Korir wrote:
> Hi Tom,
> 
> To the best of my understanding, ChimeraX displays images and associated segmentations in physical space not image space. However, segmentations are performed in image space. EMDB-SFF uses the first transform in the transforms_list field (with id=0) as the image-to-physical transform. (https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html#segmentation_transform_list <https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html#segmentation_transform_list>)
> 
> I've tested with two files having the same segmentation but different values for transform 0 and they render the same.
> 
> Could you please implement this feature in ChimeraX?
> 
> Kind regards,
> 
> -- 
> Paul K. Korir, PhD
> 3D Visualisation Lead
> CS3DB
> EMBL-EBI
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