Convert to PDB Format from Secondary Strucutre

Question

[virpatel3]

I have a sequence of secondary structures in the following format:

CCCCCCCCHHHHHHCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHH

I also have the amino acids underneath these structures. Is there any way I can convert this information to the PDB format?

[GouthamAtla]

See what are the mandatory fields in PDB file format. Check whether you have necessary information. A small script to make the required format and add dummy values in case of missing information.

I think the 3-D coordinates are only the mandatory feature in PDB file.

[Neilfws]

Q. Does the format contain the 3D coordinates? A. Yes - then you can. No - then you cannot.

Answer 1

[Ram]

Elaborating and generalizing Neilfws's response,

"Converting" secondary structure to 3D structure would be possible only if you knew the 3d coordinates of each atom because there are way too many quirks in protein structure for any piece of software to reliable predict possible 3D structure without homology modeling or extensive simulation. Each residue would need for a dozen assumptions to be made and that increases the number of possible structures exponentially with increasing length.

Generalizing Neil's response, "converting" is only possible when you're stepping to a format that has either the same or lesser information content than the source format. The other way is possible if the additional information is not important, in which case you can substitute dummy values (as with FASTA to FASTQ conversion).