Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-08T14:05:59.417Z
Comments.Text: 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
Comments.UserDisplayName: gilleain
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-08T20:19:16.403Z
Comments.Text: Would you happen to have any ideas what I could use to do that? @gilleain
Comments.UserDisplayName: Harish Prabhakar
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-08T21:32:44.247Z
Comments.Text: @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!
Comments.UserDisplayName: Maximilian Press
Tags: <fasta><protein-structure><sequence-annotation><pdb><perl>
Title: What tool(s) can I use to use a .faa file to feed into JSMol?
ThreadText: # 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? @username_1  
  > **username_2**: @username_0 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
  
  