pdb2blend conversion tool

by Malte Reimold 2006

Version 1.2 is released!

Pdb2blend is a python script for the open source 3d modeling software blender.
Pdb2blend converts 3d structural molecular data in pdb file format to typical models such as Overlapping Spheres, Sticks or Sticks and Balls in the blender environment.
The tool contains some basic functionalities for DNA visualisation.
pdb2blend is still an experimental tool with known and unknown bugs. It might be improved in the future.
It was my first try in both - writing scripts for blender as well as programming in python. Therefore the source code doesn't look nice and could easily be shortened to the half of it.

examples

different views of a DNA-Stick model (left side: isometric along the strand)>

left: C60 as stick model; right: morphine as stick and ball model

left: dodecahedrane - overlapping spheres with changed materials; right: a combined view.

features

The user interface gives acces to all features of pdb2blend.

modes:

1. Balls

creates a ball model with overlapping spheres when using the standard parameters the ball sizes can be adjusted by choosing a constant scaling factor (atom scale) as well as a constant summand (atom sum) that is added to the ball size. With atom scale = 1 and atom sum = 0 one will get the covalent radius for any atom defined. With atom scale = 0 and atom sum > 0 the model will have uniform ball sizes.

2. Sticks

creates a stick model. The stick diameter can be chosen here (Stick Thickness). Until now the regular stick mode (as well as stick and ball) does only work for less than 10000 atoms.

3. Sticks and Balls

A combination of ball and stick mode. When using standard parameters the atoms are scaled down a little bit.

4. DNA Backbone Follow

When turning on this option a stick model will be formed connecting the phosphorous atoms of oligonucleotide backbones. This works even for systems with more than 10000 atoms.

Model refinement:

The refinement of spheres and sticks can be chosen. With higher values the model becomes more detailed.

files

New Version pdb2blend v1.2 is now available!

Download pdb2blend12 as zip file.
It contains a blender file with the script included. It works fine with blender2.41 and python 2.4 installed. Functionality on other systems was not tested yet.
Still available: pdb2blend10 as zip file.
Please report bugs or problems to blendermalte.reimold.de.
For testing purposes I make some pdb-files available too.
dna.pdb
morphine.pdb
c60.pdb