ZBrushCentral

The Art & Science of a Virus - Making The Molecular Anatomy of Ebola in ZBrush 4R7b

The following project was originally completed during the summer of 2014, within the course of 2 actual weeks (real-time, not collective hours).

Hardware:
MacBook Pro, late 2008
OS X 10.8.5
2.4Ghz Intel Core Duo
6GB DDR2 RAM
(Painfully underpowered
by today’s standards,
believe me, I know. :confused:)
Wacom Cintiq Companion Hybrid

Software:
VMD 1.9.2
ZBrush 4R7b
Photoshop for editing the HDR Image Map
Video editing: FCP
Music editing: Sound Studio

Once commissioned for this project, I knew I had my work cut out for me, but was also very excited to tackle the challenge.
While the logistics of this project itself felt intimidating, I definitely felt more comfortable dialoguing with experts, and moving forward on the project overall thanks to a predominantly biology/pre-med undergrad (with a short stint of a double major in Fine/Digital Art as well), and several years of experience working in clinical medicine within a hospital setting, -ultimately feeling uniquely qualified for this type of project.

Breakdown of the process

I did research on the virus’ structure and appearance, all of the best electron micrographs, CG renderings, and illustrations of it publicly available, then reached out to some of the world’s leading Ph.Ds on the Ebola Virus at The Scripps Research Institute, in La Jolla, CA. They gave me a crash course on the molecular structure of the virus as well as early access to some fantastic resources on the virus’ composition, which they were preparing to release publicly at a later date (now available here: http://www.rcsb.org/pdb/101/motm.do?momID=178).

For the wide shots of the African Green Monkey Kidney cell, I looked up real electron micrographs, then SubDivided a polysphere, and used a combination of Noise, speckled Alphas texture images, and going back and forth between ZSub and ZAdd with the Standard Brush to make the very dynamic / cavernous surface of the cell, and for the ebola virus covering / emerging from the cell, I used the Insert Mesh Brush: CurveTube to draw out the worm-like structures all over the cell’s surface.

I made the overall virus’ surface shape using ZSpheres and smoothing out the surface via SubDividing, then eventually Decimating it to keep the poly count and in turn, the amount of processing my computer would have to do, to as low a minimum as possible. For the wide shot of the virus alone, I used very customized (see screenshot image) settings in FiberMesh to create a subtle “fuzziness” at a distance to represent the red Glycoprotein Trimers of the virus’ surface.

Once directed to where I could download all the biologically relevant molecule data (the PDB website http://www.rcsb.org/pdb/home/home.do) and was given a list of each of their identifying names, I had to find out how I could convert the .pdb file type into a usable file format ZBrush could import. -This took a bit of time and effort / trial and error before I had a working process down.

Enter VMD (Visual Molecular Dynamics). VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems in 3D. Made available thanks to the Theoretical and Computational Biophysics Group. http://www.ks.uiuc.edu/

Figuring out the best way to export the pdb files from VMD into manageable / ideally-sized (low-but-not-too-low of poly-count) meshes was interesting… i.e. took some experimentation.

Snapshot of my cintiq’s screen when testing out VMD for the first time.

Once i had all the molecular components I needed exported form VMD as usable .OBJ files, I imported them into ZBrush4R7b, cleaned them up; deleted any stray, unused vertices and unneeded polys.

I then proceeded to use NanoMesh to array each of the molecules/proteins over the surface of a very carefully chosen section of the underlying model of the virus’ overall squiggly form.

Attachments

Kidney CellSnaptshot.jpg

Ebola FiberMeshShot Daniel De Leon Lion arts.jpg

NanoMeshArray.jpg

Ebola_All_Parts_Lion-Arts_Daniel_E_De_Leon.jpg

VMDtesting1.jpg

Ebola1_Intro_Lion-Arts_Daniel_E_De_Leon.jpg

Aside from the african green monkey kidney cell, and the overall form of the virus, the only other “manually sculpted/modeled” elements are the Lipid Bilayer -using the new Zmodeler brush (you cans see the base cubes I used to make the final, decimated shape) and the RNA spiral

The background was actually an underwater HDRI Map (as in, from a coral speckled area of the ocean) I edited in Photoshop; mostly blurring it and changing the hues to shades of pinks to simulate the subsurface scattering of light passing through tissue and blood vessels. Once I imported the image as the background, used LightCaps to auto-generate accurate lighting from it to unify the models with the environment. Also making sure to have the background image rotate with the models to keep the illusion of three dimensional movement within a microscopic environment when the “camera” traveled around the models.

underwaterHDRISnapshot2.jpg

A couple renders of the final primary elements

The camera motion was achieved simply using the movie timeline native to ZBrush’s UI and the end result can be seen below! :slight_smile:

The final animation for public viewing:
[youtubehd]dG1RxZOIyYM[/youtubehd]
Thanks for reading, and I hope this breakdown will be helpful to others out there.

great work love the animation and how you created the surface of the virus, I’ve not managed to figure out how to get any obj files out of the PDB website yet, will have to take another look.

Great post Daniel. Thank you for sharing so much with the community.

Impressive work and what an interesting project!

Very good work which helps understanding the structure of the virus!
If my old biological books were informative like that, it would have been easier :slight_smile: