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JSMol, the molecular modelling software, requires PDB file format to work and render the graphics. Currently, I am writing an annotation software - backend in Perl - that takes in a .faa file (fasta amino acids). Is there any way or tool out there that can easily convert to a PDB file? Many of the tools out there do not seem to give what I need.

My workflow so far:

input.fna -> Bakta -> bakta.faa -> covert tool -> proteins.pdb -> JSMol

Essentially, a tool exists called pdb2fasta that takes a pdb file and converts to a fasta file but can’t seem to find a proper tool that does it the other way around.

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  • $\begingroup$ Or do you just want an unfolded sequence of amino acids (as atoms and bonds)? In any case, you will need something that generates those coordinates, even if just as a linear 'model' of a chain $\endgroup$
    – gilleain
    Mar 8 at 14:05
  • $\begingroup$ Would you happen to have any ideas what I could use to do that? @gilleain $\endgroup$
    – Harish Prabhakar
    Mar 8 at 20:19
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    $\begingroup$ @HarishPrabhakar That is an exceptionally difficult problem for a variety of reasons. there is not an obvious way to translate linear AA sequence into three-dimensional structure. You may have heard of alphafold, which uses neural nets to more or less solve the problem. But you have to understand that this is a stochastic and error-prone prediction! $\endgroup$
    – Maximilian Press
    Mar 8 at 21:32

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