This question is one that I'm wondering whether it belongs here or on Graphic Design SE. All I want is some software that can export a PDB structure of a protein (displayed in ribbons style) or DNA double helix, or a combination of the two, to a high-quality SVG file. I know that several pieces of software for 3D molecular modelling can create raster images of PDB files quite easily (e.g., Accelrys DS Visualizer, Jmol, PyMOL, etc.). But SVG files have several advantages over PNGs, now I don't mind if the colours are all bland (i.e., each shape having one colour that is not subject to any shading or other gradients; I am saying this is OK as I realize that vector images often have problems with intricate colour gradients) just so long as the end result is a decent-looking SVG file. I have tried using Avogadro for this purpose but the resulting SVG was 264 MB in size -- a little too big for my taste. If you'd like an acceptable size range it'd be <5 MB.

  • 2
    $\begingroup$ You could try some cartoon settings in Pymol that replace the gradients with solid colors (I don't remember how they are called exactly), and trace the image with Inkscape or similar programs to get an SVG. $\endgroup$ – Mad Scientist Dec 28 '14 at 8:59
  • $\begingroup$ The Avogadro form attempts to generate an SVG from the spherical mesh - not necessarily what you want. I feel like I saw something using JavaScript, so I'll flag this and come back later. $\endgroup$ – Geoff Hutchison Jan 5 '15 at 18:36
  • $\begingroup$ Another way is to save VMD files as postscript (.ps), also a vector format, and then convert to SVG. PyMol does not have the ability to save as vector graphic yet. $\endgroup$ – sridharn Mar 24 at 23:45
  • $\begingroup$ @BH2017 Not about exporting to yield a .svg, however taking into account your other profiles close to computing: there are bridges to enter .pdb into blender, e.g. bioblender (bioblender.org), BlendMol (durrantlab.pitt.edu/blendmol, doi.org/10.1093/bioinformatics/bty968), proteins-blender (dmnfarrell.github.io/bioinformatics/proteins-blender) of varying comfort to interact with, too. $\endgroup$ – Buttonwood Mar 25 at 8:20

If you haven't found answer till now, you can use VESTA (Visualization for Electronic and STructural Analysis) package. It is a freeware and can be downloaded from http://jp-minerals.org/vesta/en/

It is available for both Windows and Linux. It can be used to import any many structural files (pdb included) and get an output in any supported format(which includes SVG). From their website:

VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.

However, if you do not strictly require SVG format them my personal favorite is "QuteMol". It gives way too many options to adjust visual representation It is an open source (citeware, i.e. you have to cite their paper for any academic publishing) molecular rendering software available from:


It can generate PNG, JPEG anf GIF(animated) images of maximum dimensions up to 8192x8192 pixels so you can use them for high resolution printing/posters etc. too. One small flaw is that it is rather ill maintained and considerable amount of bugs are there.For e.g. using default options is fine but in case you want to use customized colour scheme then their example ART(atomic rendering table, just a table of atomic symbols, their radii, and colour in RGB codes) file gives following example:

X 0 0.853 204 0 0

H 1 0.930 199 199 199

He 2 1.085 107 115 140

Li 3 3.100 0 128 128

However in reality you will require 2 colums of radii for programme to recognize it (core and vander waal radii). Similarly atomic symbols with single alphabet are not rendered properly!!! But all these problems have work around and results are worth it (specially for large protein molecules). sample this: nano motor
(source: sourceforge.net)

| improve this answer | |
  • 1
    $\begingroup$ Updated as per suggested. I have tried to restrict answer to free/ open source software only as i believe thats what the user wanted to ask. As in case of paid softwares lot many options creep up $\endgroup$ – ipcamit Mar 14 '15 at 13:37

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.