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I have downloaded Bioblender V0.6 and the pdb file of this molecule. The molecule contains two chains 'A' and 'B'.

If I check the "hydrogen" check box and import the pdb I get the following image: enter image description here

However, I cannot see the hydrogens of this molecule. I would like that my molecule looks more like the picture that one can find on the homepage from Bioblender (see picture below). How can I achieve this? enter image description here

As I already mentioned, my molecule contains two chains 'A' and 'B'. I would like to visualize my molecule such that one can identify each chain, as for example in the following picture (found in this article). How can I achieve this? enter image description here

Edit: Mike Pan noted that I do not have hydrogens in my molecule. Therefore I tried this molecule with hydrogens in the pdb file. When I add it with Bioblender and check hydrogen, the molecule is represented in a very different style then the molecule from the Bioblender homepage - why is that? enter image description here I also tried to check Spacefill and I got the following result. enter image description here However, the hydrogen looks far bigger then in the Bioblender image (second from top). I do not know how I can scale all hydrogens. In the outliner, they are not grouped.

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  • $\begingroup$ I'm not sure this quite belongs here, I left this in the queue because I hoped you could get an answer which you did. As it stands however, it's a rather localized issue as per the scope of this site seeing as you are using a special build of Blender. We are still in beta and aren't sure of what exactly to fit into our scope yet, will post a link to the relevant meta post discussing this soon. $\endgroup$ – iKlsR Nov 11 '14 at 4:00
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Looking at the PDB file of 1AD4 here, it looks like the PDB does not contain hydrogen. So you wouldn't see any Hydrogen atoms in the render.

As for colouring different chains, you can import each chain by itself, and then use a surfacing algorithm (MLP or EP) to generate a surface, once you have the surface, it should be easy to apply the material yourself.

If you want to create something simple without fiddling with Blender as much, take a look at MolecularFlipbook.

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  • $\begingroup$ Thank you for the link to the new tool that looks very promising. I have edited my question with a molecule which contains hydrogen, but I was still not able to reproduce the image from Bioblender. Do you know if I do something wrong? $\endgroup$ – Adam Nov 10 '14 at 10:49

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