It`s so simply, the tools are:
Chimera : http://www.cgl.ucsf.edu/chimera/
Meshlab : http://meshlab.sourceforge.net
Latex on macOS, windows or Linux.
and Adobe Reader :http://get.adobe.com/es/reader/
First in Chimera open a pdb structure like 1BTL, and simple export the scene as a vrml format, extension .wrl . Then save it. Now you have a 1btl.wrl file.
Open Meshlab, use the import mesh carpet like icon to find the wrl structure and then use in >file>export mesh> and export it as u3d, in this stage the program will create a .tex file and a .u3d file. This step may take some time depending on the machine.
Finally you have a .wrl, .tex and a .u3d file. Use your favorite Latex editor, like TeXnicle in macOs http://www.bobsoft-mac.de/texnicle/texnicle.html. The tex is like this:
\documentclass[a4paper]{article}
\usepackage[3D]{movie15}
\usepackage{hyperref}
\usepackage[UKenglish]{babel}
\begin{document}
\includemovie[
poster,
toolbar, %same as `controls'
label=1btl.u3d,
text=(1btl.u3d),
3Daac=60.000000, 3Droll=0.000000, 3Dc2c=-6.470000 -110.699997 -2.401000, 3Droo=110.914902, 3Dcoo=-6.470039 35.955681 2.401499,
3Dlights=CAD,
]{\linewidth}{\linewidth}{1btl.u3d}
\end{document}
Now you can insert the red lines into a beamer presentations and change the size in {\linewidth}{\linewidth} part to a {5cm}{5cm} for example.
After compilation you only may use Adobe to see and manipulate the 3D pdb structure.
I asume it will work with another kind of 3D informations, like cml, mol etc.
This are the file I obtain after compilation, you can download it here : https://www.dropbox.com/s/k0axmpypts0fspc/1btl.zip
I hoped the information here helped you so
some capture:
Chao.
