pdb2stl

Conversion of Protein Data Bank (PDB) structures for 3D printing.

pdb2stl is a collection of programs to calculate a representation of molecular surface in the STL file format, given a molecular description in the PDB file format, to be used in 3D printing software. If it is described in PDB, it can be printed!

Basic pipeline is as follows:

PDB (input)

EDTSurf (calculation of Connolly molecular surface)

libigl + Eigen (reduction of number of points, optional)

off2stl (format conversion)

STL (output)

Requirements:

C and C++ compilers
libigl
Eigen
EDTSurf

Installation

The following directories are expected for installing the programs and will be created:

pdb2stl/
pdb2stl/libigl
pdb2stl/eigen
pdb2stl/edtsurf

Commands below will create the directories and download pdb2stl and its requirements:

git clone https://github.com/samuelrsilva/pdb2stl
cd pdb2stl
git clone --recursive https://github.com/libigl/libigl.git
git clone https://github.com/eigenteam/eigen-git-mirror.git
mv eigen-git-mirror eigen
mkdir edtsurf
wget https://zhanglab.ccmb.med.umich.edu/EDTSurf/EDTSurf.zip
unzip EDTSurf.zip -d edtsurf
patch -p0 < edtsurf.patch

Review Makefile

make
make install DESTDIR=/your/directory

/your/directory should be in your $PATH. If omitted, DESTDIR defaults to /usr/local/bin.

Usage

pdb2stl input.pdb [ percentage of faces to keep ]

percentage of faces to keep is an optional argument.

For example, to keep 75% of faces:

pdb2stl input.pdb 75

License

decimate.cc is released under MPL2.

pdb2stl and off2stl.c are under GPLv3 (FAQ).

Please cite

If you use pdb2stl, please acknowledge the appropriate references from libigl, Eigen and EDTSurf, especially:

@misc{libigl,
    title = {{libigl}: A simple {C++} geometry processing library},
    author = {Alec Jacobson and Daniele Panozzo and others},
    note = {http://libigl.github.io/libigl/},
    year = {2017}
}

and

@article{Xu2009,
    author = {Dong Xu and Yang Zhang},
    title = {Generating triangulated macromolecular surfaces by Euclidean Distance Transform},
    journal = {PLoS ONE},
    volume = {4},
    number = {12},
    year = {2009},
    month = {dec.},
    address = {San Francisco}
}

Thanks to laurestk for suggesting the idea for this program.

samuelrsilva / pdb2stl

readme