I automated a PDB download using a Pymol script (below)
python pdb_lists = ['3LZG', '6HJN'] # lots more pdbs for x in pdb_lists: cmd.fetch(x) cmd.select(x) cmd.save(x + '.pdb', x) cmd.delete(x) cmd.quit() python end
When the script is run within Pymol it pulls down a collection of pdbs, however this flopped when I plugged it through a Biopython PDB parser, but was okay when I manually downloaded the same pdb file from RCSB.org
A manual downloaded PDB was perfect, meaning the amino acids which cannot be observed by X-ray crystalography (e.g. they not sufficiently stationary) were recognised as being absent from the parser (resulting in a protein ~390 amino acids), but the Pymol scripted download contained all amino acid residues, i.e. even those which couldn't be observed in the X-ray (resulting in a protein of ~440 amino acid residues). Any ideas why the script resulted in a pdb that flopped and how to correct it?