STL generation tools

From 3D Printables

3D-printers use STL files to represent printable geometries, and a number of programs can generate these files. Most Computer aided design (CAD) programs can save their geometry as STL files. To generate STL files directly from data, you will need some automated processing tool. Some are listed below.

Producing STL Files of from data

• STLGenerator is an open source utility for generating STL files from data. Amongst other options, it can create an STL file directly from a list of points representing sphere clouds, curves, and surfaces. You will generally generate this data using some other program, and the use STLGenerator to convert this data into a printable STL file.
• Most mathematical programs such as MATLAB and Mathematica can produce iso-surfaces of a variety of functions. These surfaces can be converted into STL format.

Producing STL Files of from PDB files

• STLGenerator is an open source utility for generating STL files from data. Amongst other options, it can create an STL file directly from a PDB molecule file. Select Model|Import PDB and browse for your PDB file. A preview will show. Then, select the rendering resolution and the atom enlargement scale (if different than 1.0), and click "Start". The conversion may take a few minutes depending on the resolution selected and the complexity of the molecule. For example, a 54,000 atom molecule will take approximately 20 minutes to render at 0.2 resolution.
• DeepView Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Viewer File open and select a .pdb file. Preferences -> Surfaces: check "ignore selected residues" and set quality to 3 or higher. Then Tools -> Compute Molecular Surface. Then File -> Save -> Surface... This creates a .sfc file which when opened in notepad appears to be a relatively simple binary mesh file containing pretty much what an stl file has, vertices, edges, and faces.
• SRS 3D Go to that link and click on the image of the protein. To open other proteins in it go to the home page and search for them It loads a browser-based java viewer. Right-click -> select -> all, then right-click -> calculate -> surface|surface (reduced)|Accessible Surface. These are three different types of surfaces it can compute. "Surface" is probably the best to start with. "Accessible Surface" (it does more physics by calculating what the molecule looks like to a molecule (water) of a given size bouncing into it), which should be the slowest, took a couple of hours on my laptop, though it should be significantly faster on your desktop. This software is open source and can be downloaded from here.