<p>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.</p>
<p>My workflow so far:</p>
<p>input.fna -&gt; Bakta -&gt; bakta.faa -&gt; <strong>covert tool</strong> -&gt; proteins.pdb -&gt; JSMol</p>
<p>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.</p>

CC BY-SA 4.0
2023-03-08T14:05:59.417Z
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
gilleain
CC BY-SA 4.0
2023-03-08T20:19:16.403Z
Would you happen to have any ideas what I could use to do that? @gilleain
Harish Prabhakar
CC BY-SA 4.0
2023-03-08T21:32:44.247Z
@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](https://www.nature.com/articles/s41586-021-03819-2), 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!
Maximilian Press
<fasta><protein-structure><sequence-annotation><pdb><perl>
What tool(s) can I use to use a .faa file to feed into JSMol?
# What tool(s) can I use to use a .faa file to feed into JSMol?

(Asked by: username_0 on 2023-03-08)

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.

**Tags:** fasta, protein-structure, sequence-annotation, pdb, perl
> **Comments:**
> **username_1**: 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  
> **username_0**: Would you happen to have any ideas what I could use to do that? @gilleain  
> **username_2**: @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](https://www.nature.com/articles/s41586-021-03819-2), 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!  

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## 0 answers

