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1- ok, but make a backup before you edit with notepad
2- after editing, exit notepad and just save when it asks you
4- edit re-converted mdx in mdlvis, as you typed
and it should be alright, but how they'll behave after that 'multi-attaching' is just your bit of trial and error
as for other questions, helpers are also nodes, that probably serve some purpose in regular game models, but really do havoc with our editing tools, especially those who merge geosets and rig mesh, causing them to either crash or have model parts flying around and attach to other models ingame... yeah, weird stuff
that's why it is always helpful to convert all the helper objects to bones, you just don't have to worry about crashing while you work. ALTHOUGH.. mdlvis makes helper objects as well, so you're always encouraged to re-convert and replace, whenever you see those lill 'speech bubbles' with letter 'i' in the model editor's node manager
as for milkshape file.. i'm not sure.. i had to re-install my system and don't have milkshape atm
yes you can assign a vertex to more than one bone, and in mdlvis. you open the model and go to the rigging bit (F3, then bones tab) then selct the vertices and the bone you with to have them follow the most, then press the little 'reattach vertices' button. then after that, select the second bone and press 'attach vertices to bone' button. then save and test, it should work. (also you need to get mdlx converter and edit the mdl files in notepad to replace every 'Helper' word with 'Bone' (exit and save on prompt so you don't ruin the mdl), and then re-convert back to mdx, so that Mdlvis doesn't crash later in the middle of work
I don't think you just use rotation. Is there anything marked as you rotate the bones that makes those vertices seem closing to each other?
Actually, vertex weight is how strong mesh/vertex is attached to the bone but this is not very much concerned with warcraft model. As to my experience, only in gmax and 3ds max you can use vertex weights.
I do not bear the whole understanding of models as of currently, but I believe they hit each other in an absurd way is because of how the rendering of the mesh is not right? but I just have to be honest, I really do not know much yet about models, maybe you should ask the problem to our model moderators such as Misha, MiniMage, or BlinkBoy.
You mean vertex bone weights? AFAIK, only NeoDex supports this. It should theoretically be possible in notepad, but you'd have to ask someone for a model that uses bone weights, convert it to .mdl, and inspect it yourself. Also, it would still be brutally time-consuming considering some models have over 2000 triangles.
animation transfer. There's a tool somewhere when you make a model with the same bone names export the mdl without animations and just transfer all animations. You could also import the model and animations to 3dsmax and build your model around it or adapt the imported bones to your model structure.