Hi soumi -
A command-line version of what David said is the following:
save new_complex.pdb, protein_selection or dna_selection
where `protein_selection` and `dna_selection` include all the atoms you want to
have in the final PDB. They could be object names if you have each protein and
the D
Select the protein you want and the dna, then save the selection as a PDB.
There are many ways to make a selection; visually, the easiest might be:
You said you’ve removed the DNA from the protein-dna complex, so now you should
have:
(1) an object that has just your protein that you want in the
