Hi Avogadro users. I’m a newbie. I have both of avogadro and avogadro2 soft wares. I want to draw 3D structure of some polymers. Which of these soft wares is suitable for this aim? Is there any step by step guidance/manual/tutorial for drawing the 3D structure of polymers?
Any help will appreciated.
It is better to focus on avogadro2, because this one is the sole branch in active development. Either pick one of the releases on the dedicated page, or bookmark the project’s landing page with nightly updates; both offer executables suitable for either Linux, Mac, or Windows.
May you extend your question and detail out what kind of polymers you would like to visualize (proteins, sugars; oil based PP, PE, PET)? I’m aware that previous versions of Avogadro contained a peptide builder (see, e.g., Avogadro + ORCA Tutorial: 7. Building Bio-polymers in Avogadro), and the version available to me (1.97.0) contains one (Build → Insert → DNA/RNA) to type/select the letter code corresponding for this specialty, I just don’t see the other one to concatenate Ala, Gly, etc.
Thanks Thomas for your answer. My polymers are not biopolymer such as proteins or nucleic acids.
2D structure of one of my polymers is as follows:
Is Avogadro appropriate for drawing this polymer?
Sure. I drafted a polymer builder for Avogadro 1.x that was exceedingly buggy and wasn’t released. I’ve been working with a few people on how a polymer builder would work for Avo2.
The main thing to remember is that copy / paste is your friend. Also, if you have versions of the polymer in a 2D drawing app (e.g., ChemDraw, ChemDoodle, etc.) you can either save as SDF and import to Avogadro to create 3D coordinates, or copy / paste as SMILES.