combining fixed PDBs

[michelsanner]

Hello
I am wondering is there is an easy way to "combine" 2 fixed moelcules.
Basically I am creating a fixer for a first PDB file

fixer1 = PDBFixer(filename=pdb1)
fixer1.findMissingResidues()
fixer1.findMissingAtoms()
fixer1.findNonstandardResidues()
fixer1.addMissingAtoms()
fixer1.addMissingHydrogens(7.4)
fixer1.removeHeterogens(False)

then create fixer2 for the second molecule and I would like to write you the PDB (or prmtop, and coordinate file) for the complex of the 2

It seems that fixer2.positions.extend(fixer1.positions) does what I expect.
I tried
for n, chain in enumerate(fixer1.topology.chains()):
chain.id = n+1
chain.index = n+1
fixer2.topology.addChain(chain)

but when I writ to write out the PDB for the complex I get
ValueError: The number of positions must match the number of atoms

Would it be reasonable/possible to add an add operator to PDBfixer to perform this ?

thanks for any advise

-M

[michelsanner]

Apologies. I should have dug a little more before asking

I realize now Modeller provides support for this
modeller = Modeller(fixer2.topology, fixer2.positions)
modeller.add(fixer1.topology, fixer1.positions)

did the trick
-M

[peastman]

Glad you figured it out!