Creative Commons License
The original figures from the book are released here under the Creative Commons Attribution 4.0 International License (CC BY 4.0). When you use a figure for your own work, please, cite the book appropriately, for example, like this:
Luciano, G. (2019). Essential Computer Graphics Techniques for Modeling, Animating, and Rendering Biomolecules and Cells: A Guide for the Scientist and Artist (1st ed.). A K Peters/CRC Press. https://doi.org/10.1201/b21533
FIGURE 3.1 Visualization tools for a specific audience. This figure is based on Figure 2 of Johnson and Hertig. 2014. “A Guide to the Visual Analysis and Communication of Biomolecular Structural Data.” Nature Reviews. Molecular Cell Biology 15 (10). Nature Publishing Group: 690–98. doi:10.1038/nrm3874
FIGURE 3.2 SIV protease crystallized with peptide product pdb:1yti. The colors represent the hydrophobic surface of the molecule; the cylinder represents a scale bar of 10 Ångströms. The image was create using the software Chimera.
FIGURE 3.3 SIV protease crystallized with peptide product pdb:1yti. Double and triple bonds are present in the molecule as seen in this image. This was created using Gabedit.
FIGURE 3.4 Representation of the standard orientation copper crystal shape made using Vesta.
FIGURE 3.5 Examples of different representations of the structure of an NaCl molecule. (a) ball and stick, (b) space fill, (c) polygon style.
FIGURE 3.6 (a) wires representation, (b) ball and stick, (c) Van der Waals representation, (d) Specific DNA representation created to highlight base structure. All models were made in Chimera.
FIGURE 3.7 (a) surface representation. The colors are related to the hydrophobic properties, (b) Surface representation. Colors do not represent any intrinsic properties of the molecule and are used to highlight its morphology in an artistic way, (c) strands representation of the
molecule. It highlights the typical DNA ladder. Each color refers to a base, (d) mixed representations. One strand is made of an atomistic ball and stick representation; for the other a flat ribbon representation is used.All models are made in Chimera.
FIGURE 3.8 (a) molecular surface representation, (b) VDW representation, (c) LSS representation, (d) SAS surface representation. The solvent used for the calculation is water with a probe radius 1.4 Ångström, (e) SES
surface representation. In this case, colors are used to highlight different properties in comparison with SAS, (f) Gaussian Surface, a representation belonging to the Convolution Surface Models family.
FIGURE 3.9 Representation created using Qutemol. All of these are VDW surfaces that use different colors to highlight features of the molecules (a) chains using two different colors, (b) monochrome
representation to highlight the shape of the molecules, (c) “realistic” representation with occlusion surface shows the surface accessi ble to a solvent, (d) cartoon representation helps the viewer
highlight the shape of the molecule, (e) VDW representation; every color refers to CPK convention, (f) a fake electronic microscope for an artistic look.
FIGURE 3.10 Cross-section of a virus. The bar represents 100 Angstroms.
FIGURE 3.11 Cross-section obtained using Qutemol for the PDB entry 1yti.
FIGURE 4.1 Graphic user interface of Avogadro.
FIGURE 4.2 Step-by-step screen capture of the process described.
FIGURE 4.3 Graphic user interface of Vesta.
FIGURE 4.4 Step by step caption of the of the process described
FIGURE 4.5 Graphic user interface of nanoengineer.
FIGURE 4.6 Step-by-step screen capture of the process described.
FIGURE 4.7 Graphic user interface of Chimera.
FIGURE 4.8 Step-by-step screen capture of the process described.
FIGURE 4-9 Step-by-step screen capture of the process described.
FIGURE 4.10 Step-by-step screen capture of the process described
FIGURE 4.11 Cinema4D Interface.
FIGURE 4.12 Modo Interface.
FIGURE 4.13 Houdini Interface.
FIGURE 4.14 How to create a camera a. Cinema4D, b. Modo, c. Houdini
FIGURE 4.15 Effect of using different Focal lengths: 16, 24, 35, 50, 80, 135, and 200 mm. The image used is a render test project that can be found in the Foundry Modo software examples directory
FIGURE 4.16 Effect of using projection: orthographic and perspective camera; notice how the lines on the plane are affected by the chosen camera.
FIGURE 4.17 Effect depth of field (DOF): 0.02, 0.04, 0.08, 0.1, 0.2, 0.5, and 1. It is important to notice how DOF can help us in grabbing the attention of the viewer
FIGURE 4.18 Effect of Film Gate: CCD 1’’, CCD 1/2’’, 1/3’’, 2/3’’, 4/3’’ DSLR, BlackBox Camera, Black Magic 4K and full 35 mm 4K
FIGURE 4.19 Number of Iris Blade: 3, 4, 5, 6, 7, 8, and circle. The effect is only visible while shooting using a very wide aperture
FIGURE 4.20 A primitive with 3D elements highlighted
FIGURE 4.21 Create a primitive in Cinema4D, Modo, and Houdini a. Cinema4D, b. Modo, c. Houdini.
FIGURE 4.22 Different viewport settings in Modo. Starting from the top left: default, flat, wireframe, gooch, reflection and advanced GL full.
FIGURE 4.23 Selection options in Cinema4D, Modo, and Houdini a. Cinema4D, b. Modo, c. Houdini.
FIGURE 4.24 a. Cube, b. add and delete vertex, edge or face, c. subdivide, d. extrude, e. twist, f. bend, g. explode, h. blevel vertex, three edges and single edge.
FIGURE 4.25 Cinema4D Modifiers a. Loft, b. Extrude, c. Lathe
FIGURE 4.26 Menu related to the modeling actions presented in a. Cinema4D, b. Modo, c. Houdini
FIGURE 4.27 NURBS sphere in Maya, the aspect of the donut is changed moving the spline control points.
FIGURE 5.1 Starting from the left, depiction of (a) methane atom, (b) alanine, (c) fullerene C60, (d) carbon nanotube, (e) a collagen filaments, cryo-EM structure of Zika Virus (pdb:5ire) The scale bar represent 10 Å = 10·10–10 m.
FIGURE 5.2 Setting up the scale of your scene in a) Cinema4D b) Modo c) Houdini.
FIGURE 5.3 Wireframe of the scene.
FIGURE 5.4 Example of different kind of shadows a) Shadow/photon size is too small. That is why we do not see any shadow. b) Now the dimension is ok, but we still have problem with the shadow map res
(resolution) c) We increased the shadow maps. Things now are improving; keep in mind that the memory allocated for calculating the shadow increased. d) Raytraced shadows. They look sharper. In
this case it is not necessary to tweak the shadow map res.
FIGURE 5.5 Light Menu. a) Arnold inside Cinema4D b) Modo c) Houdini.
FIGURE 5.6 a) Example of sources of light the source of light is a point light with no dimension. The object near the source of light projects a visible shadow giving a hint of the environment of the scene. b) the dimension of the source of light is bigger than in a) and the shadows look
more diffuse. c) the source of light is even larger; shadows are almost invisible but contribute to the overall atmosphere of the image.
FIGURE 5.7 A fast neutral material applied to the surface of our object. Tweaking the transparency of the shadow gives the image a lighter appearance a) transparency off b) transparency on.
FIGURE 5.8 Example of different kinds of light decay a) Scene setup b) no decay c) inverse decay d) inverse square decay. In order to make the subject visible, the light intensity has been increased 1000x.
FIGURE 5.9 From the top of the image to the bottom. Lighting setup: Inverse Distance Squared, inverse distance, none, volume metrics on, three neutral light setup, red and blue three studio light setup, setting with rim light for subsurface scattering materials.
FIGURE 5.10 Color picker options in Cinema4D.
FIGURE 5.11 Color picker options in Cinema4D for selecting complementary, analogous, split complementary, tetrad colors and equiangular in the color circle.
FIGURE 5.12 The image on the right simulates deuteranopia (top), protanotopia, tritanotopia (bottom).
FIGURE 6.1 Reflection and diffusion of light on a smooth surface (top) and rough surface (bottom)
FIGURE 6.2A AND 6.2B Schematic overview of the most important surface scattering as show by Weidlich and Wilkie in the seminal work “Arbitrarily layered micro-facet surfaces” in: Proceedings of the 5th international conference on Computer graphics and interactive techniques
in Australia and Southeast Asia. ACM, 2007. pp. 171–178 and on the LM Pixar principled shader a) reflection on a smooth surface b) glossy paint c) tinted glazing, d) frosted paint, e) metal foil, f) metallic paint g) frosted metal h) patina i) multi-layer
FIGURE 6.3 From top to bottom we increased the specular amount of the shader leaving all other parameters set as default. In the top image, the aspect of the object (a surface obtained from a DNA sequence) has a plastic aspect
FIGURE 6.4 From top to bottom we increased the transparency amount of the shader leaving all other parameters set as default.
FIGURE 6.5 From top to bottom we increased the subsurface scattering amount of the shader leaving all other parameters set as default.
FIGURE 6.6 Top left. The main focus is the compact structure of NaCl thanks also to the absence of colors. Top right. In this variant, the focus is on the assembly of the different elements. Middle left. Same as the
top right, but in this case the model is a mockup of real molecular model (the plastic model used for teaching in the classroom). Middle right, same as middle left even if leaving out the colors adds focus to the packing of the unit cell. It is still the worst choice for depiction since it overcomplicates the simple message given in
the top left image. Bottom images. Two variations of a photoreal rendering of a plastic model mockup. The message is the same as in a picture of the classroom plastic model.
FIGURE 6.7 Renderings made using lighting scene available at flippednormals.com
FIGURE 6.9 Wireframes of the scene.
FIGURE 6.10 Lights and Camera.
FIGURE 6.11 Shaders.
FIGURE 6.13 Wireframes of the scene.
FIGURE 6.14 Modelling of the scene.
FIGURE 6.15 Clot created filling a metaball with red and white cells.
FIGURE 6.16 Shaders settings.
FIGURE 6.17 Rendering settings
FIGURE 6.18 Wireframes of the scene.
FIGURE 6.19 Lights and Camera.
FIGURE 6.20 Shaders.
FIGURE 6.21 Top original raw image, Bottom contrasted image.
FIGURE 6.22 After importing the model in Chimera, we create a high surface representation of the molecule a) and b) creation of the surface and calculations of the coulombic surface information represented using a red, white and blue gradient. The information is automatically stored in the vertex of the dae file
FIGURES 6.23 AND 6.24 The info present in the vertices of the model is projected on a diffuse texture map created after automatically unwrapping the mode with the tools present in foundry MODO
FIGURE 6.25 Final result.
FIGURE 6.26 Examples of noise used for creating displacement maps.
FIGURES 6.27 AND 6.28 Examples of different settings used for the final rendering in a well-lit and dark “occluded” part of the image
FIGURE 7.1 a) Chimera. b) VMD menus dedicated to animations.
FIGURE 7.2 Importing multiple states of molecules with pdb ID 1r7, rotating it (a and b), and then displaying only model number 0 (#0) (c).
FIGURE 7.3 a) creating a molecular map for model #0 with default grid density of 3. b) creating a molecular map for model #20 with default grid density. c) resampling a molecular map of model 20 with same grid density as model #0. d) deselection of multiple models. e) creation of the final morph
FIGURE 7.4 a) node used for importing the dae sequence in Houdini. b) visualization in the viewport of one of the frames of the animation
FIGURE 7.5 a) Selected objects in the scene. We changed the frame count from 90 to 240 in order to prepare 10 seconds (at 24 frames per second) of animation. b) Autokeying switched on and setting of first reference key. c) After moving the objects, we set another reference key at position 240. d) The parameters are active (they are now marked in orange), so the software took care of creating all of the frames, and our animation is ready to be played.
FIGURE 7.6 Steps of the animation played backward to create the illusion of self-assembly
FIGURE 7.7 Turntable of DNA fragment created using Maxon Cinema4D a) setting up autokeying. b) recording the essential key frames. c) the parameters are recorded by the software. Notice the change in appearance of the radio button on the interface
FIGURE 7.8 Turntable of DNA fragment created using Foundry Modo a) selecting the fragment (the contour is highlighted in orange showing that the software is recording the position of the object; it is set on as default. b) shifting the timeline to the last frame of the animation, we change the Y rotation of the molecule. The position is now recorded as shown by the radio button marked in orange.
FIGURE 7.9 Turntable of DNA fragment created using SideFX Houdini a) selecting the fragment, activating autokeying. b) shifting the timeline to the last frame of the animation and changing the Y rotation of the molecule. The position is now recorded as shown by the text box colored in orange
FIGURE 7.10 Common tools for creating non-linear variations of the animated parameters in a) Cinema4D, b) Foundry Modo, and c) Houdini.
FIGURE 7.11 a) an example of a metaball applied to two spheres. b) a random modifier applied to the position of the small spheres. c) two frames of the animation. d) setup of the scene. One camera, three lights, and a background are present. One light is used to light the background, and two lights are used to light the main cell
FIGURE 7.12 a) settings for the shader of the cell. The main features are due to the reflectance parameters. An old model (phong) confers a wet appearance (the same parameters are generally used for creating wet surfaces). b) camera settings. 50 mm camera with default settings c) Light settings. A blue light for the background, a neutral key, and fill light for the cells; the intensity ratio for the lights is 100:15.
FIGURE 7.13 a) importing of pdb file for the chosen molecule b) emitter settings and project settings. In order to make the particles float, the project gravity was set to 0. c) setting used to export the animation
FIGURE 7.14 a) general setup of the scene. We have two strands of DNA formed by a helix, a spline modifier, a cloner, and an emitter. Cinema4D needs to create clones in order to make them follow a path given by the user. b, c, and d) detailed settings of the emitter, the cloner, and the spline modifier
FIGURE 7.15 a) Setup of the scene. We created an emitter that is used by the matrix object. The matrix object uses a spline to change the trajectory of the particles according to a spline. A sweep modifier is linked to the matrix in order to sweep a circle according to the tracer modifier. b) Several modifiers (wind, rotation, and turbulence) add noise to the trajectories of the particles.
FIGURE 7.15B Four frames of the animation
FIGURE 7.16 a) the cloner modifier attached to the emitter created instances of spheres that flow according to the spline. b) The same setup after activating the metaball modifier for both splines
FIGURE 7.17 Top setup of the scene. On the left, it is possible to see the result of the simulation after more than 100 frames. The six nodes on the top right take care of creating everything. Bottom setup of the scene. Parameters are used for each node in the simulation. You can notice that the only parameter that will change according to time is the total count of the scattered points on the surface of the base primitive ($F parameter). Also, a remesh node is linked to the copy node in order to create a cleaner final model
FIGURE 7.18 Example of different step of the simulation
FIGURE 7.19 Top setup of the scene. On the left, it is possible to see the result of the simulation after more than 400 frames. Again, the six nodes on the top right take care of creating everything. Bottom setup of the scene. Parameters used for each node in the simulation. You can see that we have two parameters that will change according to time (total number of scattered points and dimension of the base sphere). Here we have a vdb mesh remapper, which is similar to the metaball modifier in Cinema4D.
FIGURE 7.20 Example of a different step of the simulation.
FIGURE 8.1 Setup of the membrane scene with all options offered by Arnold Render for creating render passes.
FIGURE 8.2 Images imported in Affinity software photo for final compositing.
Figure 8.3 Imported imported in nuke for final compositing
FIGURE 8.4 All passes rendered. Final Image composed by the following passes a) Z-depth. b) SSS. c) Diffuse_direct, d) Diffuse_indirect e) Specular_indirect f) Specular_direct.
FIGURE 8.5 Same as Figure 8.4, but in order to highlight the individual contribution of each AOV they are presented using increased intensity
FIGURE 8.6 “Raw” composite before performing any adjustment.
FIGURE 8.7 Final composited image after adjusting levels and contrast for all the passes in comparison with beauty pass obtained by means of Affinity designer.
FIGURE 8.8 Final composited image created using nuke.
FIGURE 8.9 Settings for rendering the occlusion pass. Neutral shader applied to all of the objects in the scene. Occlusion pass added to beauty pass. Top beauty pass, middle occlusion pass, bottom, composite. The effect is overdone for the sake of clarity.
FIGURE 8.10 Defocusing added using the software nuke. The same effect can be obtained via the layering technique, but the reader should carefully check if the software is able to perform a depth blur action. In order to better enhance the effect of the zfocus, the beauty pass uses different colors for one selected protein while the other molecules are represented using a neutral shader. For compositing the image in nuke, we used a shuffle node set as seen in a) and a ZDefocus node
using the settings shown in b)
FIGURE 8.11 Image created after applying a glow filter to the specular_indirect aov in Affinity designer.
FIGURE 8.12 Image created after applying a glow filter to the specular_indirect AOV in Foundry nuke.
FIGURE 8.13 Toon material used in order to obtain the silhouette of the molecules that will be finalized via 2D painting software.
FIGURE 8.14 Final NPR after adding highlights manually using pastels.