Question: pdb file conversion
0
gravatar for eleroxx
3.0 years ago by
eleroxx0
eleroxx0 wrote:

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!

pdb • 1.4k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by eleroxx0
1

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

ADD REPLYlink written 3.0 years ago by geek_y8.1k

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.

ADD REPLYlink written 3.0 years ago by Devon Ryan73k

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

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by eleroxx0

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)?

ADD REPLYlink written 3.0 years ago by Devon Ryan73k
3
gravatar for geek_y
3.0 years ago by
geek_y8.1k
Barcelona/London
geek_y8.1k wrote:

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.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by geek_y8.1k
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