Chain selection

PROSS can stabilize only a single chain per query

Stabilizing both interacting parts in a hetero-dimer

Submit a separated job for each chain and use the Interacting chains option to fix residues interacting with the other chain to avoid changes at the binding interface.

Which chain should I choose if there is more than one option?

In some structures, the chain of interest appears more than once. It is not really important which of these to use but for maximum accuracy select the chain containing most structural information
Information includes:

1. Presence of active-site ligands (see the Small-molecule ligands option)
2. More residues (less lack of density regions)

My PDB file does not have a chain identifier or has a numeric one
In models generated by some servers like Phyre2 and others, the output file may come without a chain identifier. In other rare cases, structures deposited in RCSB have a numeric chain identifier.

Open the PDB file on PyMOL and follow these instructions to add/alter the chain identifier:

1. select the chain for which you wish to add/alter the chain id
   *make sure that the selecting state (on the bottom right side) is on chains
2. type the command: alter (sele),chain='A'
   *This will alter the chain id to A, if you want another id change the command accordingly
3. type the command: sort
4. Open the file menu, click on Save Molecule, select the option 'sele' and save (give a new file name)

Now you have a new file with an alphabetical chain identifier. Open the file on PyMOL again or on a text editor to see that this is indeed the case.