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Viewing Collada Models and transformation matrices - Tough

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I have been writing Collada model viewer using a managed library from mogware. The library handles all the parsing of xml nodes and transformation matrices.
Almost every model loads just fine but only certain models when loaded have their meshes offset from their original positions. One way to fix this is export the collada model (dae) into obj and then reimport in max and then re export in dae. This positions every meshes axis to origin and breaks down every node out of its group. Upon exporting to obj and then re importing to dae I noticed the actual vertex positions have changed from the original dae.

Is the collada max exporter plugin to blame here?

I am looking for a programmatic solution rather than simply manipulating model formats.

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I don't know much about Max, I use Maya, but this sounds similar to a problem I once experienced. I'd export a model and it would have little problems, incorrect offsets and sometimes problems with UV coordinates and materials. I discovered that before I exported to FBX or DAE, I had to delete all construction history for each mesh. Sometimes it also helps to "freeze"/reset transformations of objects/components in the editor before exporting too. But just try clearing construction history if you can and see if that solves your problem as it did for me.

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