It's not something that RDKit can do - RDKit is focused more on small organic molecules, rather than biomacromolecules.
For DNA, if all you want is an idealized B-form double helix, there's a number of programs out there which can take in a sequence and make an ideal (or almost-ideal) structure from it. From what I can tell 3DNA ( http://x3dna.org/) is one of the more popular ones. There's also webservers like 3D-DART (http://haddock.science.uu.nl/dna/DARTusage.html) which can do similar things. The big caveat here is that unless you explicitly specify how the DNA is non-standard, these programs will spit out perfectly regular, rod-straight DNA double helixes. They're not going to be able to adequately model sequence-specific subtle irregularities and curvature on their own. Frankly speaking, unless you're looking for a starting model for subsequent modeling steps (e.g. for input into an MD simulation) these models will probably not be worth much. If you're just looking at it with e.g. PyMol, they'll be utterly uninteresting. Regards, -Rocco P.S. Converting protein fastas to structures are a whole 'nother ball of wax. If you're really interested in that, take a look at the Critical Assessment of protein Structure Prediction competition (CASP: http://predictioncenter.org/) for the latest state-of-the-art. On Sun, Dec 4, 2016 at 9:00 AM, Carl MacGentey <[email protected]> wrote: > Dear RDKit Discussion Group- > > > > Is it possible to convert fasta files (DNA nucleotide sequences) into PDB > files? I am wanting to view strands of DNA and full length genes in three > dimensions. > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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