RNA residues have in_chain false

[Tom Goddard]

Most or all RNA residues have in_chain false. For example

open 1h4s
surf

doesn't surface the RNA chain T because it decides it is not part of a chain (hence considered ligand, solvent, ions). Similar with 1jj2 chain 0 (zero), but in this case a few residues seem to have in_chain True but most are false.

RNA used to be identified correctly, in_chain = True.

[Tom Goddard]

Mysteriously, opening pdb format 1jj2 has this problem, but opening mmCIF format 1jj2 does not show this problem.

[Eric Pettersen]

When res names were switched to fixed strings, pdbio::canonicalize_res_name() should have used a reference and didn't, so the "canonicalized" nucleic acid residue names still had their spaces in them, which caused them not to be recognized as polymeric.