SEQRES writer about mdanalysis HOT 7 OPEN

That's an interesting idea @smallfishabc - indeed I do remember other folks asking for a similar thing before.

Could you elaborate on exactly what you would like to see here? How would one fetch the sequence if the input PDB was missing portions of it, etc..?

from mdanalysis.

Hi,
Technically SEQRES provides a reference point, full sequence of the protein construct, for PDBs with missing residues due to the limit of XRD. However, most Python libraries will omit the SEQRES when save PDB to the file after processing. Thus, they loss an important reference point. I want to add SEQRES back so that we can use Pymol, Modeller, pdbfixer to model the loop.

I have already successfully did it by copying SEQRES from original PDBs downloaded at RCSB of corresponding protein chain with missing residues. I did that use BioPandas. But I may need more tools to manipulate and generate SEQRES from input sequences.

I am not sure whether this is clear enough.

from mdanalysis.