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Want to know the hundred ways to select stuff in Milkshape? Or what are Vertexes and Normals? This tutorial is for you!
Warnings: Gratious reuse of pictures from my older tutorials, occasional Hungarian words, confusing sentences
After you acquire Milkshape from whatever source (honestly, it’s kind of an abandonware at this point, so no need to feel too guilty about it), open it.
I hate auto smooth!

Untick Auto Smooth! Don’t ask questions, just untick it. It’ll mess up your mesh. Thank you.
The blue mess
If you see a huge blue mess, go to File…/Preferences, and shrink the Joint size on the Misc tab (about 0.010000). The blue mess is actually the joints, and they look like a mess because they’re set to huuuuge by default.

You can also turn off the skeleton on the Joints tab if you don’t need it.
Shortcuts!

That’s right, you can set all kinds of shortcuts to the plugins you add (and the existing features have shortcuts as well). It’s under Tools…/Edit shortcuts.
Viewports
The viewports are the little preview windows where you can view your project!

There are 4 viewports by default, 3 2D ones and a 3D one. You can change these by right clicking on them, and changing some settings. You can change the projection, change if you want it to display the textures or the wireframe, or set more of them to 3D if you want, whatever floats your boat.
You can use the Maximize option to enlarge your selected viewport to fill the whole window.
Important stuff about importing
If you import stuff there are several popups that can appear. Here’s what they mean:

Create blend groups: blend groups are the morph groups. (fatmorph, pregmorph, or other kind of morphs if you’re working with objects) If you want to import them, click yes.

If you import another mesh on top of your existing project, you’ll get this popup. It’s just a warning, you can safely click ok.

Well this is the one that’s always NO. We never want to include more bones, that’ll mess up our project!

Sometimes you also get this one, you can hit yes.
Moving around, zooming
Moving around in viewports: hold Ctrl and drag with left mouse button.
Zooming in: hold Shift and drag with left mouse button.
You can rotate the 3D view by dragging with left mouse button.
If you mess up your view, you can always reset it by right clicking on the panel, and selecting Reset View, or Frame All. You can also only frame your current selection if you choose Frame Selection.
The Groups tab

You can see all groups you imported in the groups tab. The ones start with ~00MORPHMOD are the morph groups under your main group.
You can select / deselect a group by clicking on select, or double clicking on the group name in the list.
You can hide / unhide your group from view by clicking on hide.
You can delete your group by clicking on delete.
You can regroup (merge) your selected groups into one group by clicking on regroup. It only works if you select whole groups before. Don’t forget to rename it after regrouping, because it’ll be named Regroup(number).
You can rename your group by changing the name in the little field, then clicking on rename.
You can edit your group’s comments by clicking on comment. You get a popup window then, which contains the comments that you can edit. Comments are very important when editing meshes, the name should match your group name, and there are other important info here too (I’m not going to go into details right now, just keep it in mind!)
You can move up and down your group in the group list with the up and down buttons.
More basic terms?
Okay, here are some more basic terms, that are good to know.

The dots are the vertexes.
Faces are the triangles between 3 vertexes.
Joints are the blue thingies we fixed earlier. They’re used in animation and can be only rotated.
Selecting!
Go to the Model tab and select Select. You can also hit F1.

You can select what you want to select, Vertex, Face, Group or Joint (we talked about what these mean, above). You can change this selection with the numbers 1,2,3,4 (respectively).
You can use the 2D views for selecting. Just drag with left mouse button.
You can add to your selection by holding down the Shift button, and dragging with left mouse button.
You can remove from your selection by holding down Shift and dragging with right mouse button.
As I mentioned earlier, you can also select whole groups in the Groups tab.

You can also use these shortcuts under the Edit menu to select / deselect the whole thing that’s visible, or to select the inverse of your current selection.

You can also use the 3D view for selecting, although it’s… not very good. I usually just use it as a benchmark, so I can see what vertexes are where.
Turn on the Wireframe Overlay on the 3D view by right clicking and selecting Wireframe Overlay.
Hold Alt and drag with left mouse button to select stuff. It’ll probably select stuff you don’t want to select too, so make sure you check the 2D views to see if you only have the desired stuff selected.
Moving
Select Move on the Model tab. You can also hit F2.

Just like when selecting, there are multiple ways to move what you selected previously.
But… where?
Okay, so, here are the directions in Milkshape: x is left-right, y is up-down, and z is forward-backwards.
You can simply move your selected stuff wherever in the 2D views by dragging with left mouse button. Easy!
If you need to move the stuff by exact values, you can use the values under the move options, then click move.

Useful: if you want to move something by dragging, but only want to move it into a certain direction, you can “turn off” moving to another directions by deselecting the X, Y, or Z buttons. It’ll only allow moving in the direction you have selected (but don’t forget to turn them back on afterwards).
If you want to move something to the center for example, you can choose Absolute from the dropdown menu. It’ll then move your selected stuff to the absolute values you type in.
Rotating
Select Rotate on the Model tab. You can also hit F3.

Works similarly to the moving, you can drag your selected stuff to rotate in the 2D views, or type in the desired values to the little boxes, then hit rotate.
If you rotate joints, you have to select Local to avoid… weird stuff. Also, if you work on joints, you have to turn on the Anim mode. Go to Window…/Show Keyframer, then the Anim button will appear in the right corner.
This was very vague, I’m sorry, this is not a posing tutorial. XD
Scaling
Select Scale on the Model tab. You can also hit F4.

You can use the values to scale. There are two modes (of the three) that are useful for us, the Center of Mass which means it’ll scale from the center of your selection. User point means it’ll scale from the ground. So for example if you want to make something smaller while keeping it on the ground, use the latter (like when you do age conversions for clothes, or resize objects).
Adding textures
You can assign textures to your groups to check how they look with the textures on! Super useful! It’s also useful if you make recolors and don’t want to use bodyshop for previewing.

Go to the Materials tab. Click new, then click on the first <none> button. You can select your texture there to add it to the project. You see it’s now named Material01 in the list.
You can delete the texture by clicking on Delete.
To assign a texture to a group, you have to select the desired group(s) first. If you don’t have a group selected, Milkshape will cry and tell you to do it. If you did, then select the appropriate texture from the list and hit the Assign button. You can assign a texture to as many groups as many you want, but a group can only display one texture.
You can change the way how the texture is displayed in the dropdown menu. The useful ones are Default, which will only show the texture, and not the transparent parts (if you added an image with transparent parts, anyway), or Ignore alpha, which will ignore the transparent parts and transparencies. So if the textures appear kinda see through, or they seem to have weird hollow parts this setting will fix it!
Merging vertexes, what and why?
Basically merging vertexes mean that you select two (or more) vertexes and you mash them together. They still remain two (or more) vertexes, but they will have the exact same position and bone assignments. Easy! You will need the Vertex Data Merge plugin for this.

When merging vertexes from two groups, the vertex that belongs to the group that's higher on the list is used as the reference. You can play with it by changing the order of the groups in the list (the how was explained before in this very tutorial).
Sometimes you want the two (or more) vertexes to meet in the middle, in this case you can use Vertex…/Snap Together. But then you should do a vertex merge anyway, to fix any weird stuff.
Normals
Normals are basically the shading on your mesh. When you merge two mesh parts, sometimes there’s a visible seam, despite the vertexes are merged and everything. That means you need to fix the normals as well!

You can merge the normal values of two (or more) vertexes with the Normal Data Merge plugin. You can also fix the normals with either using Vertex…/Align normals, or Cat’s Normal Smoother plugin, these two work similarly.

There is still some stuff I haven’t covered, but this tutorial is already very long and dry, so I’ll leave it here for now.
I hope it was useful! … at least a little.