pdb file conversion

Question

[eleroxx]

I'm trying to convert PDB file, but i'm not really sure, what's important from pdb, how to transfer coordinates to start and end.

Could you give me any hint?

Thanks a lot!

[GouthamAtla]

If you mean Protein Data Bank file, why would you need to convert it to GFF ?

[Devon Ryan]

Do you mean PDB as in the format used to describe crystal structures or something else entirely? I hope the latter, since there's no obvious way to convert a crystal structure into a GFF file.

[eleroxx]

Yes, crystal structure. You say there's no obvious way, is there any way?

[Devon Ryan]

No, there's not any way, the two formats (at least as commonly used) have absolutely nothing to do with each other and describe completely unrelated things. What are you actually trying to do (i.e., what's the biological goal)?

Answer 1

[GouthamAtla]

There is no way to represent PDB file in a GFF Format. The PDB file is complex file format ( in the sense that it holds lot of information). If you want, you can extract the protein/DNA/RNA sequence from it in a fasta format and get the coordinates from the genome (by alignment or databases) and make it in to a GFF file. Other than sequence, it holds the 3D coordinates, which can not be represented in GFF format.