Christian Stern 1, Heinz Stucki 1, Peter Stucki 1, Pekka Jäckli 2
1 Department of Computer Science, University of Zurich, Winterthurerstr. 190, 8057 Zurich
2 Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich
Stereolithography technology allows one to build physical 3D hardcopies of computer-generated representations of objects. Until now, stereolithography has mainly been used for reproducing industrial (CAD) objects, or medical data derived from Computer Tomography (CT) and Magnetic Resonance Imaging (MRI). In this communication, a new application for stereolithography is presented: the straight-forward production of solid and accurate molecular models directly from Protein Databank Brookhaven (PDB) files.
Molecular models have been used in chemical teaching and research ever since knowledge about the geometric structure of molecules was available. Such models help people to get an idea of molecular structure and thereby help to derive information about chemical reactivity. They are also suited for imparting structural information to blind students [1]. The most widely used, commercially available molecular models were developed by Dreiding (wireframe models), and Corey, Pauling and Kultun (CPK, i.e space-filling models).
When the computer-aided handling of digital 3D-objects became possible, first attempts were also made towards the automated production of real objects from digitized datasets. These processes can either be subtractive (fabrication with milling machines) or additive (objects are built slice-by-slice); the latter commonly being called Rapid Prototyping (RP). Stereolithography, the first rapid prototyping method to become commercially available, cures photo-sensitive resins by a highly focused laser beam, which is guided by a set of dynamic mirrors (Figure 1).
Figure 1: Schematic design of a stereolithography apparatus
Stereolithographic parts achieve a high precision that equals the accuracy of NC-milling [2].
The PDB file-format has been designed for describing molecular structures in a platform independent manner. In contrast to Sims [1], we have created our 3D-models directly from PDB files without taking the roundabout way of manual CAD reconstruction. The conversion of PDB files into stereolithography format (STL) was done in three steps:
a) Conversion of the chemical information provided by the PDB-file into a geometrical representation.
b) Conversion of the graphical elements of the geometric representation (e.g. spheres and cylinders), into a polygonal (triangular) description of the shape of the molecule.
c) Generation of an STL-file for further processing by the stereolithography apparatus.
For details concerning the conversion process please contact the authors.
Figure 2 shows the molecule pyridoxal-5'-phosphate, cofactor of the enzyme aspartate aminotransferase, covalently linked to lysine 258 of the protein, visualized with PERMEX [3]. Figure 3 shows its physical representation as stereolithography model.
Figure 2: Pyridoxal-5'-phosphate covalently linked to lysine258 of aspartate aminotransferase
Figure 3: Stereolithographic models of pyridoxal-5'-phosphate covalently linked to lysine 258 of aspartate aminotransferase. The model on the left was coloured by hand.
Stereolithography is a very powerful and valuable tool for generating hardcopies of molecular structures. Especially for large molecular systems, the assembly of Dreiding- or CPK-models is a very time consuming task; furthermore, the geometric accuracy and physical stability of those models is limited, and finally they are restricted to wireframe, spacefilling and ball & stick representations. Our procedure allows one to generate highly accurate models within comparatively small amounts of time at reasonably low cost. It is also possible to make hardcopies of molecular surfaces that have been calculated with molecular graphics packages like InsightII [4].
Novel stereolithography resins have shown the ability to mark selected areas of a model with color [5]. It might therefore soon even become possible to build coloured molecular models automatically.
[1] D.Sims, ăMolecules at your fingertips", IEEE Computer Graphics and Applications,11/95
[2] P.Jacobs, ăEpoxy Resins, Improved Accuracy and Investment Casting", 3D Systems, 1993
[3] P.Jäckli, C.Stern, ăPerformer-Based Molecular Explorer PERMEX", Univ. of Zurich 1995
[4] Biosym/MSI San Diego, CA
[5] K.T.McAloon, M.R.Edwards, A.H.Popat, S.H.Ewart, J.R.Lawson, ăStereolithogra-phy resins for medical applications", Proceedings of the 3rd international workshop on ăRapid prototyping in medicine and computer-assisted surgery", Erlangen, Germany, 1995