1) Polygon Modeling

In this tutorial, we’ll use polygon modeling to

create the gut lumen as well as some cells in the
lumen which have small projections called
microvilli.

When modeling using polygons, we'll start out

making a very rough-looking low polygon model,
and then smooth it afterwards.

Gut Lumen
Create a polygon plane (Create > Polygon
Primitives > Plane) by dragging in the
perspective window on the grid. Smooth shade
the plane (the keyboard shortcut is '6').

Next, open the "polyPlane1" Inputs in the A scanning EM of villi lining the gut.
channel editor. Change the width, height,
subdivisions width and subdivisions height
to 20. You should see that the plane now has a
green grid on it which shows where the
subdivisions have been made. We're going to
create a villi from each of these green squares.

First, however, check out the scanning EM of

villi. Notice that they are rather irregularly
placed and shaped. We need to add some
randomness to our grid for it to look realistic! To
do this we're going to use a Maya plugin called
"polyRandomizer" which was written by Jim
Gaczkowski and downloaded from
Highend3d.com. This handy plugin can
randomize the placement of vertices, faces or
edges in a polygon mesh. We will use it to
create a more random look to our grid.
Changing the plane size and subdivisions through the
To load the plugin, open the Script Editor Inputs node in the Channel box.
(Window > General Editors > Script Editor, or
click on the little icon in the right corner of
Maya). In the Script Editor window, go to File >
Source Script. Find your 'Scripts' folder and
then click on "polyRandomizer.mel." Close
the script editor. Now, in the MEL command line
(under the timeline) type: polyRandomizer. A
little window should pop up. Make sure your
plane is selected, and change the parameters so
that Translate Min = - 0.4 and Translate Max =
0.4. Then press 'Randomize Now!.' You should Using the polyRandomizer plugin to randomize the
see that your plane subdivisions now look quite placement of vertices in the plane.
irregular.

To create the villi, we will extrude each of the

plane faces. First, however, go to the Polygons
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menu, and make sure that "Keep Faces
Together" is turned off (under the Edit Mesh
menu). Next, with your plane selected, go to
Edit Mesh > Extrude.

We want to scale down our extruded faces

uniformly using the manipulator that has
appeared. Click on one of the cubes on any
axis, and a yellow uniform scale cube should
appear in the center of the manipulator. Scale
the faces down just a little tiny bit.
Performing a uniform scale on the extruded faces using
Next, press 'w' to switch to the move tool. We the manipulator.
could also move the faces using the extrude
manipulator, but these would move the faces in
a direction that's normal to the faces, which
would cause our extrusions to collide into each
other (you can try this if you like, then undo).
Using the regular move tool, move the faces up.

With the faces still selected, repeat the extrusion

and moving steps. Repeat one more time, this
time scaling the faces more and moving the
faces in Y less (check out the image on right).

The extrusion tool switched you to component

mode (which is why you were able to select Move the extruded faces straight up in Y using the
faces rather than the entire mesh). To switch to regular move tool (not the extrude manipulator).
object mode, press F8. We'll need to be in
object mode in order to smooth our villi.

With the plane selected (it should be outlined in

green if in object mode), go to Mesh > Smooth.
If you want a more random look to the vertical
height or the direction of the villi, undo the
smoothing step and move around some of the
faces (in component mode - right click on the
plane and select 'Face') and then do the
smoothing operation.

In the texturing tutrorial, we'll apply a bumpy,

ridged texture onto these villi to make them How the plane looks after three sets of extrusions.
appear more like the photo shown on the first
page. Make sure to save your villi model!

The finished villi plane.

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Tube rack with tubes
Polygon modeling can also be used for non-
organic shapes.

Switch your view to the side orthographic

camera (you can either use the Hotbox for this
by using the space bar and right clicking on the
center 'Maya' square, or go to Panels >
Orthographic > Side in the main view panel).

First, create a polygon cylinder (Create >

Polygon Primitives > Cylinder) and open the
options box (the square next to "Cylinder"). We
want to change our cylinder from the default
options to create a cylinder with a rounded top
and bottom. Set radius to 0.8, height to 10,
axis divisions to 20, height divisions to 3, The cylinder and the cylinder creation options box.
cap divisions to 4, and make sure 'Round
cap' is checked off.

Click once in the viewport, and you should see a

cylinder identical to the one shown in the image
to the right. Make sure you're viewing it in wire
mode (shortcut: '4').

With the cylinder selected, press F8 to switch to

component mode. You should see the cylinder
turn light blue and the vertices in magenta.

Select the vertices in the top half of the cylinder

and use the scale tool (shortcut: 'r') and scale
the top half down slightly (using the center cube
in the manipulator). With the vertices still
selected, scale in Y (the green cube in the
manipulator) until the top of the tube is inverted.
Using the move tool (shortcut: 'w') move the Creation of the tube.
vertices down into the tube bottom. Select the
vertices that make the top of the tube, and scale
them so that they are on the same plane, and
move them up to make the tube a little longer.

Set the tube aside for the time being. You can
hide it by pressing Ctrl+h while the tube is
selected (make sure you're in object mode first!
F8 toggles between object and component
modes).

Now we'll start building our tube rack. Create a

polygon cube with the following approximate
dimensions: width = 7, height = 0.5, and depth
= 5. In the channel editor, click on
'polyCube1' under the 'inputs' section.
Change the subdivisions width to 3 and
subdivisions depth to 3. Polygon cube with subdivisions (top) and with
subdivision vertices moved towards corners (bottom).
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Now switch to component mode ('F8'). We want
to move the vertices of the subdivisions so that
they are closer to the corners. This will allow us
to later smooth the edges of the cube while still
maintaining its shape. To move the vertices,
simply select them and move them using the
move tool ('w').

Switch back to object mode ('F8'). Smooth the

cube by going to Mesh > Smooth. Duplicate
the smoothed cube (Ctrl+d) and move the
duplicate down in the Y direction.

Next we need to create stand-in cylinders that'll

be used to make circular cut-outs in our cube.
Create a new polygon cylinder using the same The 6 stand-in cylinders intersecting the two cubes.
settings as we used to make the tube. Go again
to Create > Polygon Primitives > Cylinder.
This time, all you should have to do is click one
in the view panel since your previous settings
should have been saved.

Duplicate the new cylinder (Ctrl+d) and move

them to create a 2x6 array with a little spacing
between each one. Move the top cube so that
the cylinders are completely intersecting it.
Make sure that you don't place the top cube
higher than the height that you made your tube!
Next, place the bottom cube so that the dummy
cylinders are intersecting, but don't pop through
the bottom.

Duplicate all 6 dummy cylinders by selecting all

of them and pressing Ctrl+d. The new
After the Boolean operations, the dummy cylinders
duplicates will be in the same exact spot as the
disappear and leave holes behind.
originals, and that's fine.

To create the cutouts in the cubes, select the top

cube, and then select one of the dummy
cylinders (the order of selection matters!). Go
to: Mesh > Booleans > Difference. Now select
the bottom cube and then the duplicate cylinder
in the same location. Repeat the Boolean
operation with each cylinder for the top and
bottom cubes.

Now we need to connect the top and bottom

halves of the tube rack. With one of the cubes
selected, right click until you see the HotBox,
and select Faces. Select the faces along one
of the short sides, and delete them (using the
backspace key).

In order to create a single mesh out of both

pieces, we need to tell Maya to see them as a
Maya 101 – Modeling Using Polygons, NURBS & Deformers Delete faces from the side of both cubes.
4
single object. Select both top and bottom cubes
and go to Mesh > Combine.

Next, go to Select > Select Border Edge Tool.

Zoom in close to the side where you cut out
faces, and click at the edge of the hole you
created on the top cube. Double click to select
the entire border of the hole (it should turn
orange). Next, select the border edge on the
bottom cube. To create a connecting segment,
go to Edit Mesh > Bridge. You should see that
a rounded, segmented piece connecting the two
halves has now been made.

Now find your hidden tube that you created

The border edges of the holes created by deleting
earlier. Check in the Outliner (Window >
faces are selected and outlined in orange.
Outliner). All hidden items will appear in blue.
Select your tube and press Ctrl+H to un-hide it.
Make some duplicates (Ctrl+d) and move them
in place.

What a sleek and modern-looking tube rack!

Finished tube rack with tubes added.

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2) NURBS Modeling
NURBS modeling is generally used for objects
that have smooth, regular surfaces. We'll use
NURBS to model a few pieces of labware.

Erlenmeyer Flask
To make the Erlenmeyer flask, we will first
create a curve that will define the profile of the
flask.

Switch to the side orthographic camera view

(using the Hotbox or Panels > Orthographic >
side in the main viewport). To create the curve,
go to: Create > CV Curve Tool.

Draw the curve shown to the right, starting at the

origin and creating the outer curve first. It's
important that you have at least three vertices
along the bottom edge so that it'll end up being a
nice straight line (other wise you will have a
divot at the bottom of your flask). To ensure that
your CVs are lined up, use grid snapping by
pressing 'x' before clicking to make CVs. You
should notice that your CV is then placed at the
nearest grid intersection.

Once you've finished drawing your curve, press

Enter to finish your curve. You can move
around CVs if you need to straighten or fix
things by switching to component mode (F8) or
by right-clicking on the curve and selecting
'Control Vertex.' Make sure that the last two CV curve drawn in the side orthographic view
points are on the Y axis, else you'll have a hole
in your flask!

To create the flask surface, we will revolve our

CV curve. Select your curve (making sure
you're in object, not component mode). In the
'Surfaces' menu, and go to Surfaces > Revolve.
By default, Maya will sweep around the Y axis.
Try revolving around the other axes by opening
the Revolve options (select the box next to
Surfaces > Revolve).

The revolve tool can also be useful for creating

cut-away animations. With the flask selected,
open the channel editor and open 'revolve'
under 'Inputs.' You can change the sweep of
the surface, thus creating a cross-section type
effect.
Using the channel box to change the sweep angle.
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Note that you can also go back to the original
curve you created and edit the profile. In the
outliner, select your flask ('revolvedSurface1')
and move it away from the origin. You can now
see your curve again. Move around some of the
CVs in component mode (right click on the curve
and select 'Control Vertex' or press F8).

Also note that if you move the entire curve, your

surface will become warped. So, if you try to
move your surface and accidentally also select
your CV curve, you will get unexpected results!
In practice, you can either delete or hide the
curve so that it's out of your way.
Moving the CVs of the original curve.
Pipette tips
For our next NURBS exercise, we'll make some
pipette tips, as shown in the reference image on
the right.

First we'll make a series of NURBS circles and

adjust some so that they approximately match
the profile of the tip (T-1000 for this exercise).

Switch to the front orthographic view and make Tips!

a circle with 30 sections (Create > NURBS
Primitives > Circle and select the options box).
Change 'Surface degree' to 'Linear' (the default
is 'Cubic.' Also change the axis to 'Active View.'
Click someplace in the viewport to make your
circle. Check out the figure on the right to see
what a difference linear vs. cubic make.

We want to move the CVs around to create the

ridges that we can see at the top of the tip.
Switch to component mode ('F8') and select
every third CV in your circle. Using the scale
tool ('r') scale these out a little bit. I also rotated Two NURBS circles, the left with it's Surface Degree
the other CVs closer together in my example, set to Linear, and on the right, set to Cubic.
but you don't have to if you don't want to. A nice
shortcut to select CVs in this manner, however,
is to use the left and right arrows to select
adjacent CVs. You have to be cautious,
however, since the circle has a seam where
there are two overlapping CVs.

Now duplicate your circle (ctrl+D) and move it to

the side. Make another duplicate and select the
CVs that are sticking out and scale them in a
little. For my tip, I made a series of six circles
that decrease in size and become smoother.

Now switch to the 'Four View' by clicking on the NURBS circles before and after CV pushing.
icon on the left menu or by choosing Window >

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Saved Layouts > Four View. Move your circles
so that they are aligned along the Z axis from
biggest to smallest.

Finally, choose each circle in order from either

biggest to smallest or smallest to biggest (just Series of circles for the tip.
not out of order!) then create the surface by
selecting Surfaces > Loft (in the Surfaces
menu). If you like, you can now adjust the
surface by moving around the curves. The
easiest way to make changes is by moving the
surface aside (called loftedSurface1) and then
moving around the curves.

A couple things to note about this technique: To

loft curves, the curves must have the same
number of vertices. You also need to be careful
about not rotating the circles since your tip
surface will be twisted! Try this out by rotating
one of the circles in the ridged portion of the tip The circles are arranged in descending size along the
Z axis and lofted to create the tip surface.
A last thing to note: you can create a polygon
mesh from a NURBS surface simply by selecting
the surface, then go to Modify > Convert >
NURBS to Polygons.

Rotating one of the circles in the base section of the tip

causes the surface to appear twisted.

Our modeled lab supplies after being textured and rendered!

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3) Modeling Using Deformers

Bacterial flagella
For this example, we are going to use deformer
tools to create helical bacterial flagella. A
number of different nonlinear deformers can be
found under the "animation" submenu - be sure
to play around with them!
A bacteria with shortt cilia and long, wavy
First, we'll build a very simple bacterium out of a flagella.
closed cylinder, and then we'll create several
thin cylinders that will form the flagella.

Create a polygon cylinder (Create > Polygon

Primitives > Cylinder) with the following
options: radius = 1; height = 3; axis = z; axis
divisions = 20; cap divisions = 5; and make sure
"Round Cap" is on. Click once on the grid to
create the cylinder, and move the cylinder to the
origin.
Polygon cylinder and NURBS cylinder.
Now, create a thin long NURBS cylinder for the
flagellum (Create > NURBS Primitives >
Cylinder). Make the length of the cylinder
somewhat longer than the length of the
bacterium, and make sure that there is a high
number of spans - at least 100.

Next, select the flagellum cylinder and go to the

Animation menu, and go to Create Deformers >
Nonlinear > Twist. In your outliner, you should
see that a "twist1Handle" has been created, and
in the channel editor, you now have an input for
your cylinder called "twist1." Click on the input
to look at the twist controls.

Notice that there's a 'Start Angle' and 'End

Angle.' Changing these numbers creates a
helical twist between the start and end points of
Twist options and the resulting twisted cylinder.
the cylinder (where the start and end points are
is controlled by the 'Low Bound' and 'High
Bound' attributes). Change the End Angle to
something high, like 900. Now move the
twist1Handle away from the cylinder. You
should see the twist being created, with the
amplitude of the helical twist controlled by the
distance you move the Handle from the cylinder.
You can also move the Handle in the X direction
to control where the twist starts along the length Moving the TwistHandle in X changes where the
of the cylinder. twist occurs along the length of the cylinder

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Now we want to create duplicates of the
flagellum. Select the flagellum and duplicate it
by pressing Ctrl+d. Notice that the duplicate no
longer has a twist control! We want each
flagellum to have it's own control, so delete it.

This time, select the original flagellum cylinder

and go to Edit > Duplicate Special and open
the options box. Select 'World' for the 'Group
under' options, make 4 copies, and check off
'Duplicate input graph.' Duplicating the input
graph results in all of the input nodes of the
original cylinder to be copied in all of the Duplicate Special options box
duplicates. Press Apply. You should now see
that you have four more cylinders and
twistHandles in the outliner.

Move and rotate the Cylinders with their

individual twistHandles (make sure move/rotate
both together!) and arrange them as shown in
the reference photo. You might want to group
them together and move the pivot point towards The finished bacterium with flagella.
one end (using the 'insert' key) to make this step
easier. Adjust the twist of each flagellum to
make them look slightly different from one
another.

Actin-like filament
In this example, we'll make a long polymer, and
then use a different deformer to create a slight
bend in the filament. We'll use the bacterial
actin-like homologue ParM.

Open the scene file named "filament_scene."

This scene contains a single monomer of ParM.
From electron micrographs of the filament, we
know that each monomer in the filament is
rotated around 166 degrees and is offset by
about a half of a monomer.
Background on the ParM filament.
Using the 'Duplicate Special' command, we can
create many copies of the monomer that each
retain rotational and translational offsets. With
the monomer selected, press ctrl+D (or just 'D'
alone). In the channel box, change the Y
rotation to 166, and move the monomer up in Y
as shown in the figure to the left.

Now comes the magic of the duplicate special

command. Press 'D' repeatedly and watch the
filament grow. Note that it you deselected the
duplicate, this won't work -- the duplicates will be
Moving and rotating the duplicate.
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made, but they won't have the rotations and
transformations set.

Another way to do this is by using the 'Duplicate

Special' options box. Open it (Edit > Duplicate
Special) and make sure that the settings are on
the original settings by selecting Edit > Reset
settings in the options window.

Change the Translate Y to 2.22 (which we

figured out from the previous exercise) and the
Rotate Y to 166, and create 50 copies.

Press apply (make sure your monomer is Duplicating the monomer with translations and
selected first!), and you should see a filament of rotations to create a filament of 50 monomers.
50 monomers.

Now select all of the monomers in the outliner

and group them together.

To bend the filament, with the group selected,

go to Create Defomers > Nonlinear > Bend.
Make the manipulator tool for the BendHandle
visible by selecting the manipulator tool in the
Tool box (the tool with the dark blue box around
it in the figure on the right). You should see that
the BendHandle now has three blue diamonds.
Move these around to change the bend. You
can make the filament form a circle, or have half
the filament form a circle, etc. Play around! You
can also change the bend values in the Channel
box, as we did earlier with the TwistHandle.

The nonlinear deformers are extremely powerful

tools that can be used for a large variety of
effects - try out some others to get a better idea
of how you could use them for modeling as well
as for animation.

Bending the filament using the Manipulator Tool.

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