Blender in visualization of molecules
October 17, 2007
Yes, you can use Blender to prepare figures for your next paper and the results for sure will look different than the ones obtained with a standard software (hemoglobin [1HBG] as example below)… But given amount of work and really steep learning curve (at least for somebody who tries that for the very first time), I would not recommend Blender that much… 
UPDATE: if you look for a way to import a PDB file into Blender, some instructions are at the bottom of this page.
Categories: Software, Visualization
blender, hemoglobin, rendering, Visualization
That’s a neat figure. A lot of the figures in my PhD thesis were done in FormZ .. definitely made a difference
Thanks Deepak.
FormZ? I didn’t have a chance to try, but its interface looks way cleaner than Blender’s. Can you share some details (like how to get PDB file inside; I’ve spent more time on importing the structure than on rendering)?
Lights,camera,action ! Once upon a time there lived an hemoglobin in a land called far far way
.
This was a very long time ago … and I didn’t do the images, my wife did.
What I did was open up the structures in a visualizer capable of VRML export. The VRML was then imported into FormZ and material, shadows, shapes, etc were added there. Cool applications – rendering a proton channel, showing off potential ion binding sites, etc.
Thanks Deepak, I did try VRML, however Blender understands only version 1.0… Will look further.
Pedro, if you have a scenario I can start rendering next pictures
. I’m not into animations, but a comic? Why not? 
Hi,
I don’t know if anybody is still interested, but we have developed a tool for importing pdb files in Blender, and also for animating transitions among different conformations, if you have a file NMR that contains more than one.
Want to try?
Just go to our website and download the scripts. There is also a paper on our site, and on the Blender site, you can see a conference in which i describe a little in more details our work.
Will be pleased to know your comments, thanx,
Monica, thank you. Your work is really impressive (ATP had blown me away). I’ll sent address of your page around – there are few people interested.
Unfortunately, I’m blind or not caffeinated enough, because I cannot find any “download” link for your scripts. Can you point me to them?
Monica, could you point us to the URL / Download Link ?
Also a general purpose tutorial (basic to advanced , of how to start with a PDB file , go & create such beautiful images), will be great
along with a consolidated post of all the other such tools (with not so steep learning curve ) will be helpful
Could you provide pointers (or tutorials) to get one started with playing with PDB in Blender?
it will be nice if the importing of pdb, & doing things with it is presented for someone really new to Blender.
akin to starting with Blender by playing with PDB strcutures ?!
someone plz.,
Hi everyone!!,
sorry I never came back to reply. We are restructuring our website, so please email me for blender scripts to do protien work. Although somebasic features are will defined, the major aim of our work is to have proteins moving, as in animation, but based on biological dataset.
This is not fully adjusted yet (it is difficult!), but as soon as we have it all set, we will:
post it everywhere
record a tutorial
be open for further developments
Thanks for your interest, and just mail me if you want the scripts.
Monica