World Index of BioMolecular Visualization Resources

Physical Molecular Models and Molecular Sculpture

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  3-D Molecular Designs:
3D Molecular Designs (3dMolecularDesigns.Com), LLC produces accurate, three-dimensional physical models of proteins and other molecular structures using rapid prototyping technology. Models are based on x,y,z coordinates obtained from pdb files of known structures. Five different rapid prototyping technologies are used to produce models in a variety of different formats. The facility is located at the Milwaukee School of Engineering in the Center for BioMolecular Modeling. Shown is a model of an ATPase molecular motor.
        

  Balloon Molecules:   (English, German )
Instructions are given for "knotting" balloons in order to sculpt inexpensive and fun molecular models. Detailed steps for particular molecules are not given, however. Finished models are pictured for tetrahedron, octahedron, Buckminster-Fullerene, diamond, graphite, faujasite, cuban cluster, and a DNA double helix. If you work out details for a specific molecule, please contact emartz@microbio.umass.edu so they can be included here!

  Beevers Miniature Models:
There is a strong tradition of model making in the Chemistry Department of Edinburgh University. Alexander Crum Brown, Professor of Chemistry from 1869-1908, was a pioneer in this field. In the Year the Crum Brown retired, Cecil Arnold Beevers was born in Manchester. In 1929, he became involved, under the influence of Lawrence Bragg in Manchester, in research in crystallography. With Henry Lipson, he made major contribution in the Beevers-Lipson Strips. This method of computing Fourier synthesis was a great aid in the solution of crystal structures from diffraction data, and was later incorporated as the basis of many computer programs. His solution of many important crystal structures added greatly to our understanding of matter.

Beevers devised machines capable of drilling very small balls with great precision, and in the early 1960's he made his first models with 7mm acrylic balls to a scale of 1cm = 1Å. This method was used to make models of myoglobin, the first protein structure solved, by Kendrew et al. Twenty-nine of these were sold in the 1960's at about $US 600 each (see Barker's Myoglobin. By the time he retired from the university in 1977, he had trained seven people at the Simon Square Day Centre (for the disabled) who were making models sent all over the world. In 1980, Beevers Miniature Models was established as a self-financing unit within the Department of Chemistry.

The range of models made is always growing and now numbers over 500 crystal structure models. These include all standard chemical structures as well as a range of complex minerals and many of the materials of modern solid state physics. In addition, many models of molecules, including those of the novel "metal cluster" compounds with their highly individual arrays of atoms, have been made.

Beevers Protein Models are constructed with one ball per residue, with the residues coded with eight colors, representing functional categories. The main chain is picked out with white sleeving, and the other rods show hydrogen bonding and S-S bridges. Included metal atoms, haem groups, etc., can be shown when required. The models may be inspected from any angle and are not mounted on a base. The scale for these models is 1cm = 2Å. The models can be made from standard data, or your own data sets. The price is approximately £1.60 per residue. At right: azurin, a 129 residue blue copper-containing electron transfer protein.

 
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  Crystal Proteins:
Sculptor Bathsheba Grossman makes geometric sculptures of mathematically inspired objects from originally designed computer datasets, using rapid prototyping technologies or laser cutting of sheet metal. She also makes glass blocks containing laser-etched models of macromolecules, which she calls "Crystal Proteins" (crystalprotein.com). These can be designed to customer specifications. The example on the right is short segment of DNA double helix based upon the crystallographic result in PDB entry 1AU7. Here is a description of her methods.
 

  Darling Models:
Although these models are mostly for small organic molecules, an inexpensive kit is available to construct an 11 amino acid alpha helix (7 backbone hydrogen bonds)about one meter long and one third meter in diameter. Alternatively, it can make a three-strand beta sheet. I have also used a single peptide bond model to teach planarity of the peptide bond, phi/psi angles, and the Ramachandran principle. To find the protein kit: click on Specialized Kits, then Protein Alpha Helix. Note that US customers get shipping included in the price when ordering from darlingmodels.com, while customers outside the USA should order from molecularvisions.com (to pay additional shipping costs).     

  Haseltine, Mara G.: Sculpture:
Mara G. Haseltine is a sculptor whose work includes stylized representations of cell structures (mitochondrion) and molecules. One large completed work, "Waltz of the polypeptides", depicts mRNA with ribosomes translating B-lymphocyte stimulator hormone (shown, © 2003 Mara G. Haseltine).

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  History of Visualization of Biological Macromolecules: Physical Representations:
This site traces the history of physical models of macromolecules beginning with the wireframe models of Kendrew et al. (1958), through Fred's Folly used to facilitate construction of such models in the 1960's, ball and stick models of myoglobin (29 of which were purchased in the 1960's), Byron's Bender for constructing wire backbone models and the prize-winning sculpture of rubredoxin executed in Midas Muffler that it inspired, the first recognition of the immunoglobulin domain superfamily based on comparisons of wire backbone models, and more.     

  Luminorum Ltd | Molecular Models Etched in Glass:
Luminorum Ltd specializes in the creation of stunningly beautiful molecular models inside blocks of glass. Accurate 3D images are generated directly from .pdb files, and proteins, DNA, RNA – as well as small organic molecules, ions and other het groups - can all be rendered in a variety of formats. And because Luminorum uses the best commercial laser engraving technology, even complex molecular structures can be recreated in glass at extremely high resolution.

While most of Luminorum’s models are custom-made according to individual specifications, a range of standard models (the DNA double helix, haemoglobin and bacteriorhodopsin, for example) are also available "off the peg". Sample photos and videos of some of these can be viewed on the company website.

Whatever the structure, a Luminorum model makes an ideal memento of a research project/discovery, a gift - or a teaching tool for students of the life sciences.

 

  Made with Molecules:
Made with Molecules offers silver jewelry, keychains, pewter and glass, molecule clothing, and holiday cards that illustrate molecular structures. Custom amino acid charm bracelets are available with an amino acid sequence that spells a word of your choice in the one-letter amino acid code, e.g. PEACE. Or what about earrings with one of the bioactive ingredients of chocolate, theobromine? Or a necklace with three creativity boosters (acetylcholine, dopamine, serotonin)? Items offered are designed by Raven Hanna, a Yale-educated scientist turned artist residing in San Francisco CA USA.

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  Meyer, Edgar - Macromolecular Sculptures in Wood:
Edgar Meyer uses computer-controlled milling to sculpt macromolecules, typically in wood.
  

  Origami, Molecular:
Instructions for making "origamis" that reflect molecular structures, and a gallery of such origamis.

This website describes a method for producing precision scale molecular models from paper. Models are marked with interatomic distances in picometers and bond angles in degrees. Data are from experimental measurements involving x-ray, neutron, and electron diffraction and ultraviolet, infrared, Raman, microwave, and NMR spectroscopy. Data based on calculation in the form of MOL or XYZ files may also be used as a basis for generating models. The online database includes a searchable library of nearly 1000 experimentally determined structures.
   

  Rubin, Byron: Sculpture:
Byron Rubin is an accomplished crystallographer (1CRL, 1MNC, 1LPS, 1LPM) and the inventor of the Byron's Bender, used for constructing wire backbone models of proteins. Such models were particularly important in the 1970's, before computers became widely able to render protein structures. His first large-scale sculpture (rubredoxin) won a sculpture prize, and a smaller one of human neutrophil collagenase is in the Smithsonian (see history). In the early 2000's, he has made scientifically accurate large-scale stainless steel sculptures of human growth hormone (shown at right, © 2003 Byron H. Rubin), follicle stimulating hormone, and interferon beta (for Serono), and HIV protease with inhibitor (for Pfizer). Although there is no website for Rubin's sculpture, he can be contacted at bhrxray@aol.com.   
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  Tele-Manufacturing Facility:
The Tele-Manufacturing Facility (TMF)is creating an automated rapid prototyping (RP) capability on the Internet. It is undertaking the necessary research and development to ensure that it is viable for engineers and scientists to use over long distances. One portion of the effort is the connection itself and how to allow users to easily submit jobs and have the system automatically maintain a queue. Another effort is to reduce the need for human-checking of RP part files. TMF creates physical models for a wide variety of disciplines, including macromolecules, mechanical engineering, earth science, and mathematical surfaces. Shown is a model of light harvesting complex II.
  

  Voss-Andreae, Julian: Sculpture:

Sculptor Julian Voss-Andreae's current body of work plays on the sensuality and beauty which underlies sense and being itself. His work takes a literal look at the foundation of our physical existence. Voss-Andreae creates sculptures of proteins, the universal building blocks of life. More important for him than accurately copying a molecule in all its details is finding a guiding principle and following it to see whether it yields artistically interesting results. The main idea underlying all his protein sculptures is the analogy between the technique of mitered cuts and protein folding. His work resembles nature in its algorithmic quality. The former physicist calculates the cutting angles from scientific protein data using computer software he developed for that purpose. Beside the deterministic side of his work, there is an equally strong intuitive and irrational side, where his pieces stop working as scientific models and become pure art objects. Voss-Andreae's sculptures offer an emotional experience of a world that is usually accessible only through our intellect.

The image on the right shows Voss-Andreae's "Alpha Helix for Linus Pauling" (2004, © Julian Voss-Andreae, used with permission). The 10-foot (3 m) sculpture was created to honor the memory of Linus Pauling, who discovered the alpha helix in 1951. In order to emphasize the tension between the natural environment and man's image of nature's building block, the piece was powder coated in primary red, complementary in color to the green foliage embracing it. The sculpture is located in front of Linus Pauling's boyhood home 3945 SE Hawthorne Boulevard in Portland, Oregon, now home of the Linus Paulinling Center for Science, Peace, and Health, which commissioned the piece.

For more information, see Voss-Andreae's Artist's Statement on his website JulianVossAndreae.com. His site also contains a downloadable instruction to build your own protein sculpture.

    

  Z Corp Color 3D Models:
Full Color Models: The Z Corp. 3D Printer is the only technology that can create full color models from digital data, representing electrical charge or atomic composition in full color.

Rubberized Parts: The system can create parts that can be infiltrated with resin to simulate the qualities of rubber. This makes it possible to produce molecular models that can wrap around each other and accurately represent the interaction in physical space.

Real Space Interaction: The 3D Printer quickly and inexpensively produces dozens of iterations of molecules that can then be physically manipulated to help understand their interaction. The high speed and cost-effectiveness of the System makes it possible to have 3D physical space be a routine working medium.

Hybridized Models for Process Visualization and Training: The Z Corp. parts can be combined with other elements and inserts to provide a complete picture of the behavior of the molecule being studied. For example, a DNA strand can be printed with magnets inserted to demonstrate the unzipping and replication sequence in very clear physical detail. This hands-on understanding is critical to a fast and complete learning process.

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15 total titles.
Visitor-Maintained Index programming by Trevor D. Kramer.