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Modelling
From Quake Wiki
To keep it short: Make models in w/e 3d modeling software, like Blender, 3ds MAX etc. Export to FBX (it supports animations).
Then use Noesis to convert to MDL or other format supported by quake engines, like IQM
Blender
Blender is a free and open-source modeling suite that includes tools for modeling, texturing, rigging, and animating. Using plugins Blender can export directly into many of the formats supported by various quake engines
.mdl : classic vertex animated format.
.md3 : A more precise mdl used in quake3.
- Parli's mdl-md2-md3 addon for Blender based on Khreathor's
- Katsbits (old)import and export scripts, tools, and utillities
.md5 : Used in doom3 & Quake Rerelease.
- MD5 Importer/Exporter for Blender 2.80 thru Blender 3.1.2
- Katsbits (old)import and export scripts, tools, and utillities
.iqm : opensource skeletal format.