enable writing PDB files with original serial number

[orbeckst]

Expected behaviour

For some applications, namely rmsd calculation in PLUMED2, one needs to provide a PDB file with the original ATOM serial numbers. The MDAnalysis PDBWriter should have a kwarg keep_serials (or similar) to keep the ATOM serial numbers from the topology when a subselection is written.

For instance if I want to fit on the CA only (but compute the RMSD for all heavy atoms I would like to do:

u = mda.Universe(topol, structure)
u.add_TopologyAttr("tempfactors")
u.add_TopologyAttr("occupancies")

# calculate RMSD for all heavy atoms
protein_heavy = u.select_atoms("protein and not name H*")
protein_heavy.tempfactors = 1.0

# RMSD fit on C-alphas
ca = protein_heavy.select_atoms("name CA")
ca.occupancies = 1.0

# write file ONLY with atoms of interest (instead of everything with lots
# of zeros in the tempfactors and occupancies)
protein_heavy.write("reference.pdb", keep_serials=True)

The output file will only contain the protein heavy atoms but not the hydrogens (and the rest of the system). The heavy atoms should have the same serial number as in the topology.

Actual behaviour

The serial number in the sub selection always starts at 1 and is incremented sequentially.

Currently version of MDAnalysis:

0.18.1-dev

[orbeckst]

Btw, our PDBWriter does not consider bfactors equivalent to tempfactors; when using bfactors it complains that it does not have tempfactors.

[richardjgowers]

@orbeckst duplicate of #1072?

[orbeckst]

Yes, duplicates #1072